Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_position End_position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_file Sequencer Genome_Change Annotation_Transcript Transcript_Strand Transcript_Exon Transcript_Position cDNA_Change Codon_Change Protein_Change Other_Transcripts Refseq_mRNA_Id Refseq_prot_Id SwissProt_acc_Id SwissProt_entry_Id Description UniProt_AApos UniProt_Region UniProt_Site UniProt_Natural_Variations UniProt_Experimental_Info GO_Biological_Process GO_Cellular_Component GO_Molecular_Function COSMIC_overlapping_mutations COSMIC_fusion_genes COSMIC_tissue_types_affected COSMIC_total_alterations_in_gene Tumorscape_Amplification_Peaks Tumorscape_Deletion_Peaks TCGAscape_Amplification_Peaks TCGAscape_Deletion_Peaks DrugBank i_ACHILLES_Top_Genes CCLE_ONCOMAP_overlapping_mutations CCLE_ONCOMAP_total_mutations_in_gene i_CCLE_SEQ_overlapping_mutations i_CCLE_SEQ_total_mutations_in_gene CGC_Mutation_Type CGC_Translocation_Partner CGC_Tumor_Types_Somatic CGC_Tumor_Types_Germline CGC_Other_Diseases DNARepairGenes_Role FamilialCancerDatabase_Syndromes MUTSIG_Published_Results OREGANNO_ID OREGANNO_Values i_tumor_f i_init_t_lod i_t_lod_fstar i_t_alt_count i_t_ref_count i_judgement validation_status validation_method validation_tumor_sample validation_alt_allele DVL1 1855 broad.mit.edu 37 1 1277873 1277873 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:1277873G>A uc001aer.3 - DVL1_uc002quu.2_5'Flank|DVL1_uc009vka.2_5'Flank|DVL1_uc001aeu.1_5'Flank NM_004421 NP_004412 dishevelled 1 canonical Wnt receptor signaling pathway|dendrite morphogenesis|intracellular signal transduction|negative regulation of protein binding|negative regulation of protein kinase activity|neural tube development|neuromuscular junction development|neurotransmitter secretion|positive regulation of transcription, DNA-dependent|positive regulation of Wnt receptor signaling pathway|protein localization to nucleus|receptor clustering|transcription from RNA polymerase II promoter|Wnt receptor signaling pathway, planar cell polarity pathway cytoplasmic membrane-bounded vesicle|cytosol|plasma membrane|synapse|synaptosome frizzled binding|identical protein binding|protein kinase binding|signal transducer activity 0 all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128) Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145) 137 0.588235 33.953896 34.069947 10 7 KEEP --- --- --- --- ATAD3B 83858 broad.mit.edu 37 1 1423276 1423276 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:1423276C>T uc001afv.2 + 12 1349 c.1248C>T c.(1246-1248)TTC>TTT p.F416F ATAD3B_uc001afx.2_Silent_p.F370F|ATAD3B_uc001afy.2_5'Flank NM_031921 NP_114127 Q5T9A4 ATD3B_HUMAN AAA-ATPase TOB3 416 ATP binding|nucleoside-triphosphatase activity 0 all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217) Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145) 0.5 102.915079 102.915079 32 32 KEEP --- --- --- --- KIAA1751 85452 broad.mit.edu 37 1 1902095 1902095 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:1902095C>T uc001aim.1 - KIAA1751_uc009vkz.1_Intron NM_001080484 NP_001073953 hypothetical protein LOC85452 pancreas(1) 1 all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217) Epithelial(90;8.79e-39)|OV - Ovarian serous cystadenocarcinoma(86;9.61e-25)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;4.84e-05)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205) 0.733333 36.930933 37.668082 11 4 KEEP --- --- --- --- ACTRT2 140625 broad.mit.edu 37 1 2939133 2939133 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:2939133C>T uc001ajz.2 + 1 1088 c.883C>T c.(883-885)CTC>TTC p.L295F NM_080431 NP_536356 Q8TDY3 ACTT2_HUMAN actin-related protein M2 295 cytoplasm|cytoskeleton 0 all_cancers(77;0.00205)|all_epithelial(69;0.0011)|Ovarian(185;0.0634)|Lung NSC(156;0.0893)|all_lung(157;0.0909) all_epithelial(116;2.66e-20)|all_lung(118;1.56e-08)|Lung NSC(185;2.54e-06)|Breast(487;0.00156)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123) Epithelial(90;7.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.15e-22)|GBM - Glioblastoma multiforme(42;1.1e-12)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.000329)|BRCA - Breast invasive adenocarcinoma(365;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.125) 0.5 212.624393 212.624393 63 63 KEEP --- --- --- --- PRDM16 63976 broad.mit.edu 37 1 3319489 3319489 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:3319489G>A uc001akf.2 + 6 891 c.811G>A c.(811-813)GAG>AAG p.E271K PRDM16_uc001akc.2_Missense_Mutation_p.E271K|PRDM16_uc001akd.2_Missense_Mutation_p.E271K|PRDM16_uc001ake.2_Missense_Mutation_p.E271K|PRDM16_uc009vlh.2_5'UTR NM_022114 NP_071397 Q9HAZ2 PRD16_HUMAN PR domain containing 16 isoform 1 271 brown fat cell differentiation|negative regulation of granulocyte differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of cellular respiration|transcription, DNA-dependent transcriptional repressor complex protein binding|sequence-specific DNA binding|transcription coactivator activity|zinc ion binding lung(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1) 7 all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111) all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134) Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137) 1161 T EVI1 MDS|AML 0.55 72.756235 72.843846 22 18 KEEP --- --- --- --- CHD5 26038 broad.mit.edu 37 1 6228309 6228309 + Silent SNP G A A rs146996909 byFrequency MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:6228309G>A uc001amb.1 - 2 208 c.108C>T c.(106-108)TTC>TTT p.F36F NM_015557 NP_056372 Q8TDI0 CHD5_HUMAN chromodomain helicase DNA binding protein 5 36 chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus ATP binding|ATP-dependent helicase activity|DNA binding|zinc ion binding central_nervous_system(3)|breast(3)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1) 12 Ovarian(185;0.0634) all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15) Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193) p.F36F(HDLM2-Tumor) 2304 0.481132 338.040611 338.106296 102 110 KEEP --- --- --- --- NOL9 79707 broad.mit.edu 37 1 6592487 6592487 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:6592487G>A uc001ans.2 - NOL9_uc010nzs.1_Intron NM_024654 NP_078930 nucleolar protein 9 maturation of 5.8S rRNA nucleolus ATP binding|polynucleotide 5'-hydroxyl-kinase activity|RNA binding skin(1) 1 Ovarian(185;0.0212)|all_lung(157;0.154) all_cancers(23;2.46e-35)|all_epithelial(116;1.41e-22)|all_lung(118;7.59e-07)|Lung NSC(185;4.28e-06)|Colorectal(325;4.52e-05)|Breast(487;0.000353)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443) Colorectal(212;1.47e-07)|COAD - Colon adenocarcinoma(227;1.47e-05)|Kidney(185;5.27e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|BRCA - Breast invasive adenocarcinoma(365;0.00113)|STAD - Stomach adenocarcinoma(132;0.0017)|READ - Rectum adenocarcinoma(331;0.0649) 0.472222 49.565354 49.589957 17 19 KEEP --- --- --- --- ZBTB48 3104 broad.mit.edu 37 1 6642430 6642430 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:6642430C>T uc009vmc.1 + ZBTB48_uc001anx.2_Intron|ZBTB48_uc009vmd.1_Intron|ZBTB48_uc001any.1_5'Flank NM_005341 NP_005332 zinc finger and BTB domain containing 48 cytoplasm|nucleus DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding 0 Ovarian(185;0.0212)|all_lung(157;0.154) all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156) Colorectal(212;1.35e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00109)|STAD - Stomach adenocarcinoma(132;0.017)|READ - Rectum adenocarcinoma(331;0.0642) Esophageal Squamous(125;1449 1657 4031 29866 49542) 0.526316 98.050845 98.085038 30 27 KEEP --- --- --- --- SLC45A1 50651 broad.mit.edu 37 1 8384470 8384470 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:8384470G>A uc001apb.2 + 1 81 c.81G>A c.(79-81)CAG>CAA p.Q27Q NM_001080397 NP_001073866 Q9Y2W3 S45A1_HUMAN DNB5 27 carbohydrate transport integral to membrane symporter activity central_nervous_system(2)|pancreas(1)|skin(1) 4 Ovarian(185;0.0661)|all_lung(157;0.127) all_epithelial(116;1.22e-15)|all_lung(118;0.000147)|Lung NSC(185;0.000251)|Renal(390;0.000469)|Colorectal(325;0.00578)|Breast(348;0.00686)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11) UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;3.95e-66)|GBM - Glioblastoma multiforme(8;5.93e-33)|Colorectal(212;2.86e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00199)|READ - Rectum adenocarcinoma(331;0.0649) 0.467391 137.289417 137.376364 43 49 KEEP --- --- --- --- RERE 473 broad.mit.edu 37 1 8684204 8684204 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:8684204G>A uc001ape.2 - RERE_uc001apf.2_Intron|RERE_uc001aph.1_Intron NM_012102 NP_036234 atrophin-1 like protein isoform a multicellular organismal development|NLS-bearing substrate import into nucleus mitochondrion poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(1)|central_nervous_system(1) 2 Ovarian(185;0.0661) all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195) 0.578947 36.727932 36.831248 11 8 KEEP --- --- --- --- ENO1 2023 broad.mit.edu 37 1 8927999 8927999 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:8927999G>A uc001apj.1 - ENO1_uc001api.1_Intron|ENO1_uc001apk.1_Intron|ENO1_uc001apl.1_Intron|ENO1_uc009vmi.1_Intron|ENO1_uc009vmj.1_Intron|ENO1_uc009vmk.1_Intron|ENO1_uc009vml.1_Intron NM_001428 NP_001419 enolase 1 gluconeogenesis|glycolysis|negative regulation of cell growth|negative regulation of transcription from RNA polymerase II promoter|response to virus phosphopyruvate hydratase complex|plasma membrane|sarcomere DNA binding|magnesium ion binding|phosphopyruvate hydratase activity|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity ovary(2)|kidney(1)|central_nervous_system(1) 4 Ovarian(185;0.0661)|all_lung(157;0.127) all_epithelial(116;2.54e-20)|all_lung(118;2.99e-06)|Lung NSC(185;6.25e-06)|Renal(390;0.000147)|Breast(348;0.00086)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;2.42e-07)|COAD - Colon adenocarcinoma(227;2.78e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00177)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|READ - Rectum adenocarcinoma(331;0.0642) Esophageal Squamous(21;302 608 19946 22210 33560) 0.443532 687.030732 688.383482 216 271 KEEP --- --- --- --- SLC25A33 84275 broad.mit.edu 37 1 9613595 9613595 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:9613595C>T uc001apw.2 + SLC25A33_uc001apx.2_Intron NM_032315 NP_115691 mitochondrial carrier protein MGC4399 transport integral to membrane|mitochondrial inner membrane 0 all_lung(157;0.246) all_epithelial(116;1.16e-18)|all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Breast(348;0.00191)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.01e-08)|COAD - Colon adenocarcinoma(227;1.44e-05)|Kidney(185;0.000262)|KIRC - Kidney renal clear cell carcinoma(229;0.000957)|BRCA - Breast invasive adenocarcinoma(304;0.0019)|STAD - Stomach adenocarcinoma(132;0.00355)|READ - Rectum adenocarcinoma(331;0.0419) 0.351351 39.76411 40.485202 13 24 KEEP --- --- --- --- PTCHD2 57540 broad.mit.edu 37 1 11595402 11595403 + Intron DNP CC TT TT MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:11595402_11595403CC>TT uc001ash.3 + NM_020780 NP_065831 patched domain containing 2 cholesterol homeostasis|regulation of lipid transport|smoothened signaling pathway endoplasmic reticulum|integral to membrane|nuclear membrane hedgehog receptor activity skin(3)|ovary(2)|pancreas(1)|breast(1) 7 Ovarian(185;0.249) Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549) 0.526316 33.851182 33.862628 10 9 KEEP --- --- --- --- CLCN6 1185 broad.mit.edu 37 1 11888571 11888571 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:11888571C>T uc001ate.3 + 12 1124 c.1011C>T c.(1009-1011)TTC>TTT p.F337F CLCN6_uc009vnh.1_Intron|CLCN6_uc010oat.1_Silent_p.F53F|CLCN6_uc010oau.1_Silent_p.F315F NM_001286 NP_001277 P51797 CLCN6_HUMAN chloride channel 6 isoform ClC-6a 337 Helical; (By similarity). cell volume homeostasis|signal transduction endosome membrane|integral to membrane antiporter activity|ATP binding|voltage-gated chloride channel activity 0 Ovarian(185;0.249) Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649) 0.474708 393.795117 393.940227 122 135 KEEP --- --- --- --- VPS13D 55187 broad.mit.edu 37 1 12348200 12348200 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:12348200C>T uc001atv.2 + VPS13D_uc001atw.2_Intron|VPS13D_uc001atx.2_Intron NM_015378 NP_056193 vacuolar protein sorting 13D isoform 1 protein localization ovary(4)|pancreas(1) 5 Ovarian(185;0.249) Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209) 0.62963 62.282374 62.680989 17 10 KEEP --- --- --- --- DHRS3 9249 broad.mit.edu 37 1 12639494 12639494 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:12639494G>A uc001auc.2 - DHRS3_uc001aub.2_Intron|DHRS3_uc009vnm.2_Intron NM_004753 NP_004744 dehydrogenase/reductase (SDR family) member 3 retinol metabolic process|visual perception integral to membrane electron carrier activity|NADP-retinol dehydrogenase activity|nucleotide binding skin(1) 1 Ovarian(185;0.249) Lung NSC(185;4.11e-05)|all_lung(284;4.58e-05)|Renal(390;0.000147)|Colorectal(325;0.000585)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|Colorectal(212;9.25e-07)|COAD - Colon adenocarcinoma(227;0.000326)|BRCA - Breast invasive adenocarcinoma(304;0.000344)|Kidney(185;0.00235)|KIRC - Kidney renal clear cell carcinoma(229;0.00656)|STAD - Stomach adenocarcinoma(313;0.00798)|READ - Rectum adenocarcinoma(331;0.0419) Vitamin A(DB00162) 0.4 49.591257 49.941349 16 24 KEEP --- --- --- --- PRAMEF11 440560 broad.mit.edu 37 1 12887322 12887322 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:12887322G>A uc001auk.2 - 3 731 c.535C>T c.(535-537)CCC>TCC p.P179S NM_001146344 NP_001139816 O60813 PRA11_HUMAN PRAME family member 11 179 0 0.464396 459.354494 459.705857 150 173 KEEP --- --- --- --- HNRNPCL1 343069 broad.mit.edu 37 1 12908291 12908291 + 5'UTR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:12908291C>T uc010obf.1 - 2 LOC649330_uc009vno.2_5'Flank NM_001013631 NP_001013653 heterogeneous nuclear ribonucleoprotein C-like ribonucleoprotein complex nucleotide binding 0 0.25 13.267182 14.402166 5 15 KEEP --- --- --- --- Unknown broad.mit.edu 37 1 12987918 12987918 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:12987918C>T PRAMEF8 (7352 upstream) : PRAMEF5 (10384 downstream) 0.333333 139.735989 143.054083 45 90 KEEP --- --- --- --- CLCNKB 1188 broad.mit.edu 37 1 16377898 16377898 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:16377898C>T uc001axw.3 + FAM131C_uc010obz.1_Intron|CLCNKB_uc001axx.3_Intron|CLCNKB_uc001axy.3_Intron NM_000085 NP_000076 chloride channel Kb isoform 1 excretion chloride channel complex|integral to plasma membrane voltage-gated chloride channel activity skin(1) 1 Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649) 0.596154 109.234554 109.654544 31 21 KEEP --- --- --- --- EPHA2 1969 broad.mit.edu 37 1 16460959 16460959 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:16460959G>A uc001aya.1 - NM_004431 NP_004422 ephrin receptor EphA2 precursor activation of Rac GTPase activity|angiogenesis|apoptosis|cell chemotaxis|negative regulation of protein kinase B signaling cascade|positive regulation of establishment of protein localization in plasma membrane|protein kinase B signaling cascade|regulation of blood vessel endothelial cell migration|regulation of cell adhesion mediated by integrin|regulation of lamellipodium assembly|response to growth factor stimulus focal adhesion|integral to plasma membrane|lamellipodium membrane|ruffle membrane ATP binding|ephrin receptor activity|protein binding lung(3)|central_nervous_system(3)|stomach(2)|ovary(2) 10 Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649) Dasatinib(DB01254) 485 0.361111 40.368684 40.978424 13 23 KEEP --- --- --- --- ARHGEF10L 55160 broad.mit.edu 37 1 17914199 17914199 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:17914199G>A uc001ban.2 + ARHGEF10L_uc009vpe.1_Intron|ARHGEF10L_uc001bao.2_Intron|ARHGEF10L_uc001bap.2_Intron|ARHGEF10L_uc010ocr.1_5'Flank NM_018125 NP_060595 Rho guanine nucleotide exchange factor (GEF) regulation of Rho protein signal transduction cytoplasm Rho guanyl-nucleotide exchange factor activity large_intestine(1)|ovary(1)|pancreas(1) 3 Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204) 0.628571 156.417638 157.433811 44 26 KEEP --- --- --- --- ARHGEF10L 55160 broad.mit.edu 37 1 17961541 17961541 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:17961541C>T uc001ban.2 + ARHGEF10L_uc009vpe.1_Intron|ARHGEF10L_uc001bao.2_Intron|ARHGEF10L_uc001bap.2_Intron|ARHGEF10L_uc010ocr.1_Intron|ARHGEF10L_uc001baq.2_Intron|ARHGEF10L_uc010ocs.1_Intron|ARHGEF10L_uc001bar.2_Intron|ARHGEF10L_uc009vpf.2_Intron NM_018125 NP_060595 Rho guanine nucleotide exchange factor (GEF) regulation of Rho protein signal transduction cytoplasm Rho guanyl-nucleotide exchange factor activity large_intestine(1)|ovary(1)|pancreas(1) 3 Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204) 0.5 22.727239 22.727239 7 7 KEEP --- --- --- --- PLA2G2A 5320 broad.mit.edu 37 1 20304824 20304824 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:20304824C>T uc001bcu.2 - PLA2G2A_uc001bcv.2_Intron|PLA2G2A_uc010oda.1_Intron|PLA2G2A_uc010odb.1_Intron NM_001161729 NP_001155201 phospholipase A2, group IIA precursor defense response to Gram-positive bacterium|lipid catabolic process|low-density lipoprotein particle remodeling|phosphatidic acid metabolic process|positive regulation of inflammatory response|positive regulation of macrophage derived foam cell differentiation endoplasmic reticulum|extracellular space|membrane calcium ion binding|calcium-dependent phospholipase A2 activity|phospholipid binding 0 Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00459)|Lung NSC(340;0.00475)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427) UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000138)|Kidney(64;0.000171)|GBM - Glioblastoma multiforme(114;0.00032)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649) 0.55 38.588923 38.645109 11 9 KEEP --- --- --- --- CDA 978 broad.mit.edu 37 1 20915778 20915778 + Splice_Site SNP T G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:20915778T>G uc001bdk.2 + 1 333 c.154_splice c.e1+2 p.G52_splice CDA_uc001bdl.2_Splice_Site|CDA_uc009vpv.2_Splice_Site NM_001785 NP_001776 cytidine deaminase cell surface receptor linked signaling pathway|cytosine metabolic process|negative regulation of cell growth|negative regulation of nucleotide metabolic process|protein homotetramerization|pyrimidine nucleoside salvage cytosol|extracellular region cytidine deaminase activity|nucleoside binding|protein homodimerization activity|zinc ion binding ovary(1) 1 Lung NSC(340;1.75e-08)|all_lung(284;5.99e-08)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|GBM - Glioblastoma multiforme(114;1.06e-08)|COAD - Colon adenocarcinoma(152;1.22e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000148)|Kidney(64;0.000184)|KIRC - Kidney renal clear cell carcinoma(64;0.0027)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0652)|Lung(427;0.199) Azacitidine(DB00928)|Capecitabine(DB01101)|Cytarabine(DB00987)|Gemcitabine(DB00441) Pancreas(74;49 1356 2772 27818 40529) 0.388889 70.265955 70.848972 21 33 KEEP --- --- --- --- ECE1 1889 broad.mit.edu 37 1 21563130 21563130 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:21563130G>A uc001bek.2 - ECE1_uc001bem.2_Intron|ECE1_uc001bej.2_Intron|ECE1_uc001bei.2_Intron|ECE1_uc010odl.1_Intron|ECE1_uc009vqa.1_Intron NM_001397 NP_001388 endothelin converting enzyme 1 isoform 1 bradykinin catabolic process|calcitonin catabolic process|ear development|embryonic digit morphogenesis|endothelin maturation|heart development|positive regulation of receptor recycling|substance P catabolic process early endosome|external side of plasma membrane|integral to membrane|intrinsic to endosome membrane|membrane fraction|perinuclear region of cytoplasm|plasma membrane|Weibel-Palade body metal ion binding|metalloendopeptidase activity|protein homodimerization activity ovary(2)|skin(1) 3 Lung NSC(340;1.14e-05)|all_lung(284;1.23e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00147)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0183)|OV - Ovarian serous cystadenocarcinoma(117;4.83e-27)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;1.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000162)|STAD - Stomach adenocarcinoma(196;0.00326)|KIRC - Kidney renal clear cell carcinoma(1967;0.00755)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.206) 0.466667 21.82383 21.838322 7 8 KEEP --- --- --- --- NBPF3 84224 broad.mit.edu 37 1 21800198 21800198 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:21800198G>A uc001ber.2 + NBPF3_uc001bes.2_Intron|NBPF3_uc009vqb.2_Intron|NBPF3_uc010odm.1_Intron NM_032264 NP_115640 neuroblastoma breakpoint family, member 3 cytoplasm upper_aerodigestive_tract(1)|ovary(1) 2 all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199) 0.333333 18.179677 18.715868 7 14 KEEP --- --- --- --- EPHA8 2046 broad.mit.edu 37 1 22921781 22921781 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:22921781G>A uc001bfx.1 + 8 1787 c.1662G>A c.(1660-1662)CTG>CTA p.L554L NM_020526 NP_065387 P29322 EPHA8_HUMAN ephrin receptor EphA8 isoform 1 precursor 554 Helical; (Potential). integral to plasma membrane ATP binding|ephrin receptor activity central_nervous_system(5)|breast(3)|lung(2)|large_intestine(1)|stomach(1)|skin(1) 13 Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199) 520 0.62069 65.157614 65.52835 18 11 KEEP --- --- --- --- TCEA3 6920 broad.mit.edu 37 1 23720378 23720378 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:23720378C>T uc001bgx.1 - 8 948 c.813G>A c.(811-813)ACG>ACA p.T271T TCEA3_uc009vqm.1_Silent_p.T40T NM_003196 NP_003187 O75764 TCEA3_HUMAN transcription elongation factor A (SII), 3 271 TFIIS central. regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription elongation, DNA-dependent nucleus DNA binding|translation elongation factor activity|zinc ion binding 0 Colorectal(325;3.46e-05)|Lung NSC(340;4.16e-05)|all_lung(284;6.68e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.0054)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.6e-25)|Colorectal(126;8.32e-08)|COAD - Colon adenocarcinoma(152;4.29e-06)|GBM - Glioblastoma multiforme(114;9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00424)|STAD - Stomach adenocarcinoma(196;0.0145)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0963)|LUSC - Lung squamous cell carcinoma(448;0.198) 0.444444 39.493246 39.566257 12 15 KEEP --- --- --- --- SRRM1 10250 broad.mit.edu 37 1 24973349 24973349 + Intron SNP T G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:24973349T>G uc001bjm.2 + SRRM1_uc010oel.1_Intron|SRRM1_uc009vrh.1_Intron|SRRM1_uc009vri.1_5'Flank|SRRM1_uc010oem.1_5'Flank NM_005839 NP_005830 serine/arginine repetitive matrix 1 mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription catalytic step 2 spliceosome|cytosol|nuclear matrix|nuclear speck DNA binding|protein binding|RNA binding ovary(2)|haematopoietic_and_lymphoid_tissue(1) 3 Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19) UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138) Ovarian(68;897 1494 3282 17478) 0.482759 99.799347 99.814286 28 30 KEEP --- --- --- --- SRRM1 10250 broad.mit.edu 37 1 24975269 24975269 + Intron SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:24975269A>G uc001bjm.2 + SRRM1_uc010oel.1_Intron|SRRM1_uc009vrh.1_Intron|SRRM1_uc009vri.1_5'UTR|SRRM1_uc010oem.1_5'Flank NM_005839 NP_005830 serine/arginine repetitive matrix 1 mRNA 3'-end processing|mRNA export from nucleus|termination of RNA polymerase II transcription catalytic step 2 spliceosome|cytosol|nuclear matrix|nuclear speck DNA binding|protein binding|RNA binding ovary(2)|haematopoietic_and_lymphoid_tissue(1) 3 Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19) UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138) Ovarian(68;897 1494 3282 17478) 0.5 45.200996 45.200996 12 12 KEEP --- --- --- --- ARID1A 8289 broad.mit.edu 37 1 27101388 27101388 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:27101388C>T uc001bmv.1 + 18 5043 c.4670C>T c.(4669-4671)CCC>CTC p.P1557L ARID1A_uc001bmt.1_Missense_Mutation_p.P1556L|ARID1A_uc001bmu.1_Intron|ARID1A_uc001bmw.1_Missense_Mutation_p.P1174L|ARID1A_uc001bmx.1_Missense_Mutation_p.P403L|ARID1A_uc009vsm.1_Intron|ARID1A_uc009vsn.1_5'UTR NM_006015 NP_006006 O14497 ARI1A_HUMAN AT rich interactive domain 1A isoform a 1557 androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent nBAF complex|npBAF complex|SWI/SNF complex DNA binding|protein binding ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1) 142 all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242) 478 Mis|N|F|S|D clear cell ovarian carcinoma|RCC 0.521739 36.797526 36.806815 12 11 KEEP --- --- --- --- PPP1R8 5511 broad.mit.edu 37 1 28169807 28169807 + Silent SNP G T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:28169807G>T uc001bov.1 + 5 657 c.603G>T c.(601-603)GTG>GTT p.V201V PPP1R8_uc001bow.1_Silent_p.V59V|PPP1R8_uc001box.1_5'UTR|PPP1R8_uc009vtc.1_RNA|PPP1R8_uc009vtd.1_RNA NM_014110 NP_054829 Q12972 PP1R8_HUMAN protein phosphatase 1 regulatory inhibitor 201 Involved in PP-1 binding.|Interaction with EED.|Nuclear localization signal 1. V->A: Reduces PP-1 binding, no effect on subcellular location or repressor activity and prevents retargeting of PPP1CA and PPP1CC to nuclear speckles; when associated with A-203. mRNA processing|regulation of transcription, DNA-dependent|RNA catabolic process|RNA splicing|transcription, DNA-dependent cytoplasm|nuclear speck|spliceosomal complex DNA binding|endonuclease activity|protein binding|protein serine/threonine phosphatase inhibitor activity|ribonuclease E activity|RNA binding 0 Colorectal(325;3.46e-05)|all_lung(284;0.000129)|Lung NSC(340;0.000259)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;2.76e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00248)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0649) 0.381579 87.154629 88.090223 29 47 KEEP --- --- --- --- TXLNA 200081 broad.mit.edu 37 1 32657807 32657807 + Intron SNP G T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:32657807G>T uc001bui.2 + TXLNA_uc001buj.2_Intron NM_175852 NP_787048 taxilin cell proliferation|exocytosis cytoplasm|extracellular region cytokine activity|high molecular weight B cell growth factor receptor binding ovary(2) 2 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174) 0.075758 -0.380676 11.79843 5 61 KEEP --- --- --- --- ZBTB8OS 339487 broad.mit.edu 37 1 33115948 33115948 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:33115948G>A uc001bvp.2 - ZBTB8OS_uc001bvo.1_Intron|ZBTB8OS_uc001bvq.2_Intron|RBBP4_uc001bvr.2_5'Flank|RBBP4_uc001bvs.2_5'Flank|RBBP4_uc010ohj.1_5'Flank|RBBP4_uc010ohk.1_5'Flank NM_178547 NP_848642 zinc finger and BTB domain containing 8 opposite 0 Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186) 0.555556 68.402846 68.499343 20 16 KEEP --- --- --- --- ZBTB8OS 339487 broad.mit.edu 37 1 33115951 33115951 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:33115951G>A uc001bvp.2 - ZBTB8OS_uc001bvo.1_Intron|ZBTB8OS_uc001bvq.2_Intron|RBBP4_uc001bvr.2_5'Flank|RBBP4_uc001bvs.2_5'Flank|RBBP4_uc010ohj.1_5'Flank|RBBP4_uc010ohk.1_5'Flank NM_178547 NP_848642 zinc finger and BTB domain containing 8 opposite 0 Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186) 0.527778 66.225772 66.249821 19 17 KEEP --- --- --- --- CSMD2 114784 broad.mit.edu 37 1 34052121 34052121 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:34052121G>A uc001bxn.1 - 47 7069 c.7040C>T c.(7039-7041)CCA>CTA p.P2347L CSMD2_uc001bxm.1_Missense_Mutation_p.P2345L NM_052896 NP_443128 Q7Z408 CSMD2_HUMAN CUB and Sushi multiple domains 2 2347 Sushi 13.|Extracellular (Potential). integral to membrane|plasma membrane protein binding ovary(6)|skin(5)|pancreas(1) 12 Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249) 0.464789 95.369184 95.444792 33 38 KEEP --- --- --- --- CSMD2 114784 broad.mit.edu 37 1 34180438 34180439 + Intron DNP GG AA AA MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:34180438_34180439GG>AA uc001bxn.1 - CSMD2_uc001bxm.1_Intron NM_052896 NP_443128 CUB and Sushi multiple domains 2 integral to membrane|plasma membrane protein binding ovary(6)|skin(5)|pancreas(1) 12 Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249) 0.4 18.746744 18.878033 6 9 KEEP --- --- --- --- GJB3 2707 broad.mit.edu 37 1 35250313 35250313 + Intron SNP G T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:35250313G>T uc001bxx.2 + GJB3_uc001bxy.2_Intron|GJB3_uc001bxz.3_5'UTR NM_024009 NP_076872 connexin 31 cell communication connexon complex|integral to membrane gap junction channel activity 0 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234) 0.153846 5.441977 6.930654 2 11 KEEP --- --- --- --- EPHA10 284656 broad.mit.edu 37 1 38188975 38188975 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:38188975C>T uc009vvi.2 - EPHA10_uc001cbt.2_5'Flank|EPHA10_uc009vvh.1_Intron|EPHA10_uc001cbu.2_Intron|EPHA10_uc001cbv.1_Intron NM_001099439 NP_001092909 EPH receptor A10 isofom 3 extracellular region|integral to membrane|integral to plasma membrane ATP binding|ephrin receptor activity|protein binding|transmembrane-ephrin receptor activity breast(4)|stomach(3)|lung(1) 8 Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197) Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164) 328 0.441176 47.620277 47.722843 15 19 KEEP --- --- --- --- SMAP2 64744 broad.mit.edu 37 1 40872555 40872555 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:40872555G>A uc001cfj.2 + SMAP2_uc010ojh.1_Intron|SMAP2_uc001cfk.2_Intron|SMAP2_uc010oji.1_Intron NM_022733 NP_073570 small ArfGAP2 regulation of ARF GTPase activity cytoplasm|nucleus ARF GTPase activator activity|zinc ion binding 0 Lung NSC(20;1.56e-05)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074) Myeloproliferative disorder(586;0.0393) OV - Ovarian serous cystadenocarcinoma(33;1.04e-17) 0.402985 87.111933 87.66336 27 40 KEEP --- --- --- --- KCNQ4 9132 broad.mit.edu 37 1 41288006 41288006 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:41288006C>T uc001cgh.1 + 8 1144 c.1062C>T c.(1060-1062)TCC>TCT p.S354S KCNQ4_uc001cgi.1_Silent_p.S354S NM_004700 NP_004691 P56696 KCNQ4_HUMAN potassium voltage-gated channel KQT-like protein 354 Cytoplasmic. sensory perception of sound basal plasma membrane|voltage-gated potassium channel complex central_nervous_system(1) 1 Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0255) OV - Ovarian serous cystadenocarcinoma(33;1.38e-17) 0.346939 52.164298 53.175802 17 32 KEEP --- --- --- --- KIAA0467 23334 broad.mit.edu 37 1 43904887 43904887 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:43904887C>T uc001cjk.1 + NM_015284 NP_056099 hypothetical protein LOC23334 peroxisome 0 all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0505) 0.322581 29.350308 30.211003 10 21 KEEP --- --- --- --- MKNK1 8569 broad.mit.edu 37 1 47030864 47030864 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:47030864G>A uc001cqb.2 - MKNK1_uc010omd.1_Intron|MKNK1_uc001cqc.2_Intron|MKNK1_uc009vyi.2_Intron|MKNK1_uc010ome.1_Intron|MKNK1_uc009vyj.2_Intron NM_003684 NP_003675 MAP kinase-interacting serine/threonine kinase 1 intracellular protein kinase cascade|peptidyl-serine phosphorylation|regulation of translation cytoplasm|nucleus ATP binding|protein binding|protein serine/threonine kinase activity lung(2) 2 Acute lymphoblastic leukemia(166;0.155) 255 0.538462 160.178665 160.295533 49 42 KEEP --- --- --- --- CYP4X1 260293 broad.mit.edu 37 1 47504941 47504941 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:47504941C>T uc001cqt.2 + CYP4X1_uc001cqr.2_Intron|CYP4X1_uc001cqs.2_Intron NM_178033 NP_828847 cytochrome P450, family 4, subfamily X, endoplasmic reticulum membrane|microsome aromatase activity|electron carrier activity|heme binding ovary(1)|skin(1) 2 0.263158 13.966163 14.930107 5 14 KEEP --- --- --- --- TTC39A 22996 broad.mit.edu 37 1 51778608 51778608 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:51778608C>T uc001csl.2 - 3 262 c.157G>A c.(157-159)GAA>AAA p.E53K TTC39A_uc001csk.2_Missense_Mutation_p.E53K|TTC39A_uc010ond.1_Missense_Mutation_p.E25K|TTC39A_uc010one.1_Missense_Mutation_p.E52K|TTC39A_uc010onf.1_Missense_Mutation_p.E56K|TTC39A_uc001csn.2_Missense_Mutation_p.E52K|TTC39A_uc001cso.1_Missense_Mutation_p.E49K|TTC39A_uc009vyy.1_Missense_Mutation_p.E25K NM_001080494 NP_001073963 Q5SRH9 TT39A_HUMAN tetratricopeptide repeat domain 39A isoform 2 53 binding skin(1) 1 0.465686 303.739447 303.944078 95 109 KEEP --- --- --- --- ZYG11B 79699 broad.mit.edu 37 1 53236578 53236578 + Intron SNP T A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:53236578T>A uc001cuj.2 + ZYG11B_uc009vzg.2_Intron|ZYG11B_uc010onj.1_Intron NM_024646 NP_078922 zyg-11 homolog B protein binding upper_aerodigestive_tract(2)|ovary(1)|pancreas(1) 4 0.509804 92.752384 92.756669 26 25 KEEP --- --- --- --- PODN 127435 broad.mit.edu 37 1 53543293 53543293 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:53543293C>T uc001cuv.2 + PODN_uc001cuw.2_Intron|PODN_uc010onr.1_Intron|PODN_uc010ons.1_Intron NM_153703 NP_714914 podocan negative regulation of cell migration|negative regulation of cell proliferation cytoplasm|extracellular space|proteinaceous extracellular matrix collagen binding ovary(1)|pancreas(1) 2 0.397059 88.211425 88.841875 27 41 KEEP --- --- --- --- C1orf175 374977 broad.mit.edu 37 1 55175957 55175957 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:55175957C>T uc001cxq.2 + Homo sapiens brain my044 protein mRNA, complete cds. integral to membrane binding 0 0.388889 19.918856 20.114174 7 11 KEEP --- --- --- --- TTC4 7268 broad.mit.edu 37 1 55186844 55186844 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:55186844C>T uc001cxx.3 + 4 453 c.400C>T c.(400-402)CGT>TGT p.R134C C1orf175_uc001cxq.2_RNA|TTC4_uc001cxw.3_Missense_Mutation_p.R134C|TTC4_uc001cxv.2_Missense_Mutation_p.R145C NM_004623 NP_004614 O95801 TTC4_HUMAN tetratricopeptide repeat domain 4 134 TPR 2. binding 0 0.378378 44.74107 45.221356 14 23 KEEP --- --- --- --- C1orf177 163747 broad.mit.edu 37 1 55277935 55277935 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:55277935G>A uc001cyb.3 + C1orf177_uc001cya.3_Intron NM_001110533 NP_001104003 hypothetical protein LOC163747 isoform 2 0 0.5 19.750114 19.750114 6 6 KEEP --- --- --- --- PRKAA2 5563 broad.mit.edu 37 1 57159344 57159344 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:57159344G>A uc001cyk.3 + NM_006252 NP_006243 AMP-activated protein kinase alpha 2 catalytic carnitine shuttle|cell cycle arrest|cholesterol biosynthetic process|energy reserve metabolic process|fatty acid biosynthetic process|insulin receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation cytosol|nucleoplasm ATP binding|metal ion binding breast(4)|ovary(1)|stomach(1) 6 168 0.266667 10.693039 11.430876 4 11 KEEP --- --- --- --- PRKAA2 5563 broad.mit.edu 37 1 57161902 57161902 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:57161902C>T uc001cyk.3 + NM_006252 NP_006243 AMP-activated protein kinase alpha 2 catalytic carnitine shuttle|cell cycle arrest|cholesterol biosynthetic process|energy reserve metabolic process|fatty acid biosynthetic process|insulin receptor signaling pathway|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation cytosol|nucleoplasm ATP binding|metal ion binding breast(4)|ovary(1)|stomach(1) 6 168 0.37037 29.441894 29.841014 10 17 KEEP --- --- --- --- DAB1 1600 broad.mit.edu 37 1 57610975 57610975 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:57610975C>T uc001cys.1 - 5 869 c.195G>A c.(193-195)ATG>ATA p.M65I DAB1_uc001cyt.1_Missense_Mutation_p.M65I|DAB1_uc001cyq.1_Missense_Mutation_p.M65I|DAB1_uc001cyr.1_Missense_Mutation_p.M65I|DAB1_uc009vzw.1_Missense_Mutation_p.M65I|DAB1_uc009vzx.1_Missense_Mutation_p.M65I NM_021080 NP_066566 O75553 DAB1_HUMAN disabled homolog 1 65 PID. cell differentiation|nervous system development skin(2)|ovary(1) 3 395 0.470588 104.497122 104.548133 32 36 KEEP --- --- --- --- INADL 10207 broad.mit.edu 37 1 62288701 62288701 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:62288701G>A uc001dab.2 + 15 1882 c.1768G>A c.(1768-1770)GGT>AGT p.G590S INADL_uc009waf.1_Missense_Mutation_p.G590S|INADL_uc001daa.2_Missense_Mutation_p.G590S|INADL_uc001dad.3_Missense_Mutation_p.G287S|INADL_uc001dac.2_RNA NM_176877 NP_795352 Q8NI35 INADL_HUMAN InaD-like 590 PDZ 4. intracellular signal transduction|tight junction assembly apical plasma membrane|perinuclear region of cytoplasm|tight junction protein binding ovary(3)|skin(1) 4 0.507576 222.220841 222.227303 67 65 KEEP --- --- --- --- SGIP1 84251 broad.mit.edu 37 1 67101792 67101792 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:67101792C>T uc001dcr.2 + NM_032291 NP_115667 SH3-domain GRB2-like (endophilin) interacting positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess AP-2 adaptor complex microtubule binding|phospholipid binding|SH3 domain binding ovary(3) 3 0.545455 18.150008 18.169672 6 5 KEEP --- --- --- --- IL23R 149233 broad.mit.edu 37 1 67666689 67666689 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:67666689G>A uc001ddo.2 + IL23R_uc009waz.2_Intron|IL23R_uc001ddp.2_Intron|IL23R_uc010opi.1_Intron|IL23R_uc010opj.1_Intron|IL23R_uc010opk.1_Intron|IL23R_uc010opl.1_Intron|IL23R_uc010opm.1_Intron|IL23R_uc001ddq.2_Intron|IL23R_uc010opn.1_Intron|IL23R_uc001ddr.2_Intron|IL23R_uc010opo.1_Intron|IL23R_uc010opp.1_Intron|IL23R_uc010opq.1_Intron|IL23R_uc010opr.1_Intron|IL23R_uc010ops.1_Intron|IL23R_uc010opt.1_Intron|IL23R_uc010opu.1_Intron|IL23R_uc010opv.1_Intron|IL23R_uc010opw.1_Intron|IL23R_uc010opx.1_Intron|IL23R_uc010opy.1_Intron|IL23R_uc010opz.1_Intron|IL23R_uc010oqa.1_Intron|IL23R_uc010oqb.1_Intron|IL23R_uc010oqc.1_Intron|IL23R_uc010oqd.1_Intron|IL23R_uc010oqe.1_Intron|IL23R_uc010oqf.1_Intron|IL23R_uc010oqg.1_Intron|IL23R_uc010oqh.1_Intron NM_144701 NP_653302 interleukin 23 receptor precursor inflammatory response|negative regulation of interleukin-10 production|positive regulation of defense response to virus by host|positive regulation of interferon-gamma production|positive regulation of interleukin-12 production|positive regulation of memory T cell differentiation|positive regulation of T cell mediated cytotoxicity|positive regulation of T-helper 1 type immune response|positive regulation of T-helper 17 cell lineage commitment|positive regulation of T-helper 17 type immune response|response to interferon-gamma|response to lipopolysaccharide interleukin-23 receptor complex receptor activity 0 0.8 28.205457 29.042332 8 2 KEEP --- --- --- --- Unknown broad.mit.edu 37 1 68841268 68841268 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:68841268C>T WLS (143015 upstream) : RPE65 (53239 downstream) 0.375 15.92215 16.149777 6 10 KEEP --- --- --- --- C1orf173 127254 broad.mit.edu 37 1 75102016 75102016 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:75102016C>T uc001dgg.2 - 6 770 c.551G>A c.(550-552)AGG>AAG p.R184K C1orf173_uc001dgi.3_5'Flank NM_001002912 NP_001002912 Q5RHP9 CA173_HUMAN hypothetical protein LOC127254 184 ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1) 5 0.482412 337.010299 337.06277 96 103 KEEP --- --- --- --- LHX8 431707 broad.mit.edu 37 1 75622725 75622725 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:75622725G>A uc001dgo.2 + 9 1622 c.958G>A c.(958-960)GGA>AGA p.G320R LHX8_uc001dgq.2_Missense_Mutation_p.G259R NM_001001933 NP_001001933 Q68G74 LHX8_HUMAN LIM homeobox 8 320 nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(3) 3 0.566038 209.013308 209.415889 60 46 KEEP --- --- --- --- SLC44A5 204962 broad.mit.edu 37 1 75684255 75684255 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:75684255G>A uc001dgu.2 - 17 1593 c.1449C>T c.(1447-1449)TTC>TTT p.F483F SLC44A5_uc001dgt.2_Silent_p.F483F|SLC44A5_uc001dgs.2_Silent_p.F441F|SLC44A5_uc001dgr.2_Silent_p.F441F|SLC44A5_uc010oqz.1_Silent_p.F522F|SLC44A5_uc010ora.1_Silent_p.F477F|SLC44A5_uc010orb.1_Silent_p.F353F NM_152697 NP_689910 Q8NCS7 CTL5_HUMAN solute carrier family 44, member 5 isoform A 483 Extracellular (Potential). integral to membrane|plasma membrane choline transmembrane transporter activity ovary(2)|skin(2) 4 0.5 212.11834 212.11834 64 64 KEEP --- --- --- --- SLC44A5 204962 broad.mit.edu 37 1 75717052 75717052 + Intron SNP T G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:75717052T>G uc001dgu.2 - SLC44A5_uc001dgt.2_Intron|SLC44A5_uc001dgs.2_Intron|SLC44A5_uc001dgr.2_Intron|SLC44A5_uc010oqz.1_Intron|SLC44A5_uc010ora.1_Intron|SLC44A5_uc010orb.1_Intron NM_152697 NP_689910 solute carrier family 44, member 5 isoform A integral to membrane|plasma membrane choline transmembrane transporter activity ovary(2)|skin(2) 4 0.5 10.725176 10.725176 3 3 KEEP --- --- --- --- RABGGTB 5876 broad.mit.edu 37 1 76251961 76251961 + Splice_Site SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:76251961T>C uc001dgy.1 + 1 74 c.3_splice c.e1+2 p.M1_splice RABGGTB_uc009wbt.1_Splice_Site|SNORD45C_uc001dgz.2_5'Flank|RABGGTB_uc001dha.1_5'Flank|SNORD45A_uc009wbu.1_5'Flank NM_004582 NP_004573 RAB geranylgeranyltransferase, beta subunit protein modification process|visual perception metal ion binding|protein binding|Rab geranylgeranyltransferase activity ovary(1) 1 0.419355 95.54381 95.894793 26 36 KEEP --- --- --- --- Unknown broad.mit.edu 37 1 79520660 79520660 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:79520660C>T ELTD1 (48165 upstream) : None (None downstream) 0.54717 95.678375 95.780944 29 24 KEEP --- --- --- --- DDAH1 23576 broad.mit.edu 37 1 85817086 85817086 + Intron SNP C A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:85817086C>A uc001dlb.2 - DDAH1_uc001dlc.2_Intron|uc001dla.1_Intron|DDAH1_uc010osb.1_Intron|DDAH1_uc009wco.2_Intron NM_012137 NP_036269 dimethylarginine dimethylaminohydrolase 1 arginine catabolic process|citrulline metabolic process|nitric oxide mediated signal transduction dimethylargininase activity|metal ion binding 0 all cancers(265;0.0318)|Epithelial(280;0.0657) L-Citrulline(DB00155) 0.166667 6.213332 8.109732 3 15 KEEP --- --- --- --- CLCA3P 9629 broad.mit.edu 37 1 87101144 87101144 + Intron SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:87101144A>G uc010osh.1 + NR_024604 Synthetic construct DNA, clone: pF1KB7225, Homo sapiens CLCA3 gene for chloride channel, calcium activated, family member 3, without stop codon, in Flexi system. 0 0.222222 5.745224 6.383937 2 7 KEEP --- --- --- --- SH3GLB1 51100 broad.mit.edu 37 1 87200788 87200788 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:87200788C>T uc001dlw.2 + 7 1013 c.687C>T c.(685-687)GAC>GAT p.D229D SH3GLB1_uc001dlx.2_Silent_p.D250D|SH3GLB1_uc001dly.2_Silent_p.D258D|SH3GLB1_uc001dlz.2_Silent_p.D129D NM_016009 NP_057093 Q9Y371 SHLB1_HUMAN SH3-containing protein SH3GLB1 229 BAR. anti-apoptosis|filopodium assembly|signal transduction Golgi membrane|mitochondrial outer membrane cytoskeletal adaptor activity|protein homodimerization activity|SH3 domain binding 0 Lung NSC(277;0.209) all cancers(265;0.0136)|Epithelial(280;0.0414) 0.516129 214.202262 214.230186 64 60 KEEP --- --- --- --- GTF2B 2959 broad.mit.edu 37 1 89322791 89322792 + Intron DNP GG AA AA MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:89322791_89322792GG>AA uc001dmo.3 - NM_001514 NP_001505 general transcription factor IIB interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction nucleoplasm thyroid hormone receptor binding|translation initiation factor activity|zinc ion binding large_intestine(1)|ovary(1) 2 Lung NSC(277;0.123) all cancers(265;0.0131)|Epithelial(280;0.0255) 0.428571 29.872168 29.965556 9 12 KEEP --- --- --- --- Unknown broad.mit.edu 37 1 89570242 89570242 + IGR SNP T G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:89570242T>G GBP1 (39199 upstream) : GBP2 (1601 downstream) 0.418182 82.717602 83.038594 23 32 KEEP --- --- --- --- DPYD 1806 broad.mit.edu 37 1 97915816 97915816 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:97915816C>T uc001drv.2 - NM_000110 NP_000101 dihydropyrimidine dehydrogenase isoform 1 'de novo' pyrimidine base biosynthetic process|purine base catabolic process|thymidine catabolic process|thymine catabolic process|UMP biosynthetic process|uracil catabolic process cytosol 4 iron, 4 sulfur cluster binding|dihydroorotate oxidase activity|dihydropyrimidine dehydrogenase (NADP+) activity|electron carrier activity|flavin adenine dinucleotide binding|metal ion binding|NADP binding|protein homodimerization activity ovary(3)|skin(3)|breast(2) 8 all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994) Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216) Capecitabine(DB01101)|Enfuvirtide(DB00109) 533 0.5 61.997785 61.997785 20 20 KEEP --- --- --- --- COL11A1 1301 broad.mit.edu 37 1 103352497 103352497 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:103352497C>T uc001dul.2 - 63 5042 c.4724G>A c.(4723-4725)GGA>GAA p.G1575E COL11A1_uc001duk.2_Missense_Mutation_p.G771E|COL11A1_uc001dum.2_Missense_Mutation_p.G1587E|COL11A1_uc001dun.2_Missense_Mutation_p.G1536E|COL11A1_uc009weh.2_Missense_Mutation_p.G1459E NM_001854 NP_001845 P12107 COBA1_HUMAN alpha 1 type XI collagen isoform A 1575 collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception collagen type XI extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1) 12 all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181) Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248) 0.4375 222.024226 222.569599 70 90 KEEP --- --- --- --- C1orf59 113802 broad.mit.edu 37 1 109197454 109197454 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:109197454G>A uc001dvt.3 - 5 520 c.282C>T c.(280-282)TTC>TTT p.F94F C1orf59_uc001dvu.3_Silent_p.F94F|C1orf59_uc009wer.2_Silent_p.F94F NM_001102592 NP_001096062 Q5T8I9 HENMT_HUMAN hypothetical protein LOC113802 94 gene silencing by RNA|piRNA metabolic process P granule metal ion binding|O-methyltransferase activity|RNA binding|RNA methyltransferase activity 0 all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508) Colorectal(144;0.0152)|Lung(183;0.0895)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.163) 0.588235 104.558787 104.905258 30 21 KEEP --- --- --- --- WDR47 22911 broad.mit.edu 37 1 109525172 109525172 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:109525172G>A uc001dwj.2 - WDR47_uc001dwl.2_Intron|WDR47_uc001dwi.2_Intron|WDR47_uc010ovf.1_Intron NM_001142551 NP_001136023 WD repeat domain 47 isoform 3 ovary(1) 1 all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822) Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244) 0.460317 94.178895 94.263864 29 34 KEEP --- --- --- --- WDR47 22911 broad.mit.edu 37 1 109547221 109547221 + Missense_Mutation SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:109547221T>C uc001dwj.2 - 6 1623 c.1247A>G c.(1246-1248)AAA>AGA p.K416R WDR47_uc001dwl.2_Missense_Mutation_p.K424R|WDR47_uc001dwi.2_Missense_Mutation_p.K417R|WDR47_uc001dwk.2_Missense_Mutation_p.K388R|WDR47_uc010ovf.1_Missense_Mutation_p.K343R NM_001142551 NP_001136023 O94967 WDR47_HUMAN WD repeat domain 47 isoform 3 416 ovary(1) 1 all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822) Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244) 0.052174 -10.04673 14.337604 6 109 KEEP --- --- --- --- CELSR2 1952 broad.mit.edu 37 1 109810434 109810434 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:109810434C>T uc001dxa.3 + NM_001408 NP_001399 cadherin EGF LAG seven-pass G-type receptor 2 dendrite morphogenesis|homophilic cell adhesion|neural plate anterior/posterior regionalization|neuropeptide signaling pathway|regulation of cell-cell adhesion|regulation of transcription, DNA-dependent|Wnt receptor signaling pathway cytoplasm|integral to membrane|plasma membrane calcium ion binding|G-protein coupled receptor activity|protein binding ovary(4)|lung(3)|skin(1) 8 all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244) Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219) NSCLC(158;1285 2011 34800 34852 42084) 0.571429 53.703254 53.827585 16 12 KEEP --- --- --- --- AMIGO1 57463 broad.mit.edu 37 1 110050178 110050178 + Nonsense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:110050178G>A uc001dxx.3 - 2 1739 c.1357C>T c.(1357-1359)CAA>TAA p.Q453* NM_020703 NP_065754 Q86WK6 AMGO1_HUMAN AMIGO protein precursor 453 Cytoplasmic (Potential). axonal fasciculation|heterophilic cell-cell adhesion|homophilic cell adhesion|myelination|positive regulation of axonogenesis axon|integral to membrane ovary(1)|breast(1) 2 all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244) Colorectal(144;0.0129)|Lung(183;0.0182)|Epithelial(280;0.046)|all cancers(265;0.0492)|READ - Rectum adenocarcinoma(129;0.0689)|LUSC - Lung squamous cell carcinoma(189;0.227) 0.487179 116.35694 116.367452 38 40 KEEP --- --- --- --- GNAI3 2773 broad.mit.edu 37 1 110125272 110125272 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:110125272C>T uc001dxz.2 + NM_006496 NP_006487 guanine nucleotide binding protein (G protein), cell cycle|cell division|inhibition of adenylate cyclase activity by G-protein signaling pathway|platelet activation|synaptic transmission centrosome|heterotrimeric G-protein complex|midbody G-protein beta/gamma-subunit complex binding|GTP binding|GTPase activity|metabotropic serotonin receptor binding|signal transducer activity ovary(1) 1 all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244) Lung(183;0.046)|Colorectal(144;0.119)|Epithelial(280;0.139)|all cancers(265;0.147)|LUSC - Lung squamous cell carcinoma(189;0.237) 0.512195 73.17584 73.181113 21 20 KEEP --- --- --- --- PROK1 84432 broad.mit.edu 37 1 110996634 110996634 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:110996634C>T uc001dzs.2 + 2 175 c.124C>T c.(124-126)CTG>TTG p.L42L NM_032414 NP_115790 P58294 PROK1_HUMAN prokineticin 1 precursor 42 angiogenesis|positive regulation of cell division extracellular region growth factor activity 0 all_cancers(81;6.23e-06)|all_epithelial(167;2.12e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301) Lung(183;0.0239)|all cancers(265;0.0699)|Epithelial(280;0.0753)|Colorectal(144;0.105)|LUSC - Lung squamous cell carcinoma(189;0.135) 0.568627 100.480161 100.689103 29 22 KEEP --- --- --- --- WDR3 10885 broad.mit.edu 37 1 118494726 118494726 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:118494726C>T uc010oxe.1 + WDR3_uc001ehi.2_Intron NM_006784 NP_006775 WD repeat-containing protein 3 nuclear membrane|nucleolus upper_aerodigestive_tract(1) 1 Esophageal squamous(2;0.162) all_cancers(81;2.72e-05)|Acute lymphoblastic leukemia(138;1e-08)|all_epithelial(167;4.4e-07)|all_lung(203;1.7e-06)|Lung NSC(69;1.98e-05)|Prostate(1639;0.00955)|Breast(1374;0.244) OV - Ovarian serous cystadenocarcinoma(397;1.39e-08)|Epithelial(280;1.82e-07)|all cancers(265;2.04e-05)|Lung(183;0.0525)|BRCA - Breast invasive adenocarcinoma(282;0.0695)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.185) 0.527397 258.781377 258.876443 77 69 KEEP --- --- --- --- SPAG17 200162 broad.mit.edu 37 1 118571159 118571159 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:118571159C>T uc001ehk.2 - NM_206996 NP_996879 sperm associated antigen 17 cilium|flagellar axoneme|microtubule upper_aerodigestive_tract(2)|ovary(2)|large_intestine(1)|skin(1) 6 Esophageal squamous(2;0.0106) all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01) Lung(183;0.0858) 0.444444 40.706566 40.77726 12 15 KEEP --- --- --- --- HSD3B1 3283 broad.mit.edu 37 1 120054130 120054130 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:120054130C>T uc001ehv.1 + 3 295 c.150C>T c.(148-150)CTC>CTT p.L50L HSD3B1_uc001ehw.2_Silent_p.L52L NM_000862 NP_000853 P14060 3BHS1_HUMAN 3 beta-hydroxysteroid dehydrogenase 1 50 androgen biosynthetic process|estrogen biosynthetic process|glucocorticoid biosynthetic process|mineralocorticoid biosynthetic process integral to membrane|microsome|mitochondrial inner membrane|mitochondrial intermembrane space|smooth endoplasmic reticulum membrane 3-beta-hydroxy-delta5-steroid dehydrogenase activity|binding|steroid delta-isomerase activity ovary(2) 2 all_neural(166;0.219) all_lung(203;3.16e-06)|Lung NSC(69;2.19e-05)|all_epithelial(167;0.000624) Lung(183;0.0106)|LUSC - Lung squamous cell carcinoma(189;0.0554) NADH(DB00157)|Trilostane(DB01108) 0.326087 45.911415 47.144524 15 31 KEEP --- --- --- --- broad.mit.edu 37 1 120077111 120077111 + 5'Flank SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:120077111C>T uc001ehx.1 - full-length cDNA clone CS0DK008YI13 of HeLa cells Cot 25-normalized of Homo sapiens (human). 0.272727 7.9194 8.432045 3 8 KEEP --- --- --- --- Unknown broad.mit.edu 37 1 121244361 121244361 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:121244361G>A FCGR1B (308417 upstream) : LOC647121 (16549 downstream) 0.666667 6.351094 6.424459 2 1 KEEP --- --- --- --- NBPF9 400818 broad.mit.edu 37 1 144824877 144824877 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:144824877C>T uc009wig.1 + NBPF9_uc010oxn.1_Intron|NBPF9_uc010oxo.1_Intron|NBPF9_uc010oxr.1_Intron|NBPF9_uc010oxt.1_Intron|NBPF9_uc001ekg.1_Intron|NBPF9_uc001ekk.1_Intron|NBPF10_uc009wir.2_Intron|NBPF9_uc010oyd.1_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc001eli.3_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|NBPF9_uc001elp.2_Intron NM_001037675 NP_001032764 hypothetical protein LOC400818 cytoplasm 0 20 0.463415 60.521363 60.56915 19 22 KEEP --- --- --- --- NBPF10 100132406 broad.mit.edu 37 1 145355611 145355611 + Intron SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:145355611T>C uc001end.3 + NBPF9_uc010oye.1_Intron|NBPF10_uc001emp.3_Intron|NBPF10_uc010oyi.1_Intron|NBPF10_uc010oyk.1_Intron|NBPF10_uc010oyl.1_Intron|NBPF10_uc001enc.2_Intron|NBPF10_uc010oyq.1_Intron|NBPF10_uc010oyr.1_Intron NM_001039703 NP_001034792 hypothetical protein LOC100132406 0 all_hematologic(923;0.032) Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258) 0.333333 6.648057 6.795632 2 4 KEEP --- --- --- --- ITGA10 8515 broad.mit.edu 37 1 145536229 145536229 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:145536229G>A uc001eoa.2 + NBPF10_uc001emp.3_Intron|ITGA10_uc010oyv.1_Intron|ITGA10_uc009wiw.2_Intron|ITGA10_uc010oyw.1_Intron NM_003637 NP_003628 integrin, alpha 10 precursor cell-matrix adhesion|integrin-mediated signaling pathway integrin complex collagen binding|receptor activity lung(2)|ovary(2)|kidney(2)|large_intestine(1)|skin(1) 8 all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786) 450 0.6875 39.530848 40.031368 11 5 KEEP --- --- --- --- RNF115 27246 broad.mit.edu 37 1 145663168 145663168 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:145663168C>T uc001eoj.2 + 4 433 c.229C>T c.(229-231)CAT>TAT p.H77Y NBPF10_uc001emp.3_Intron|RNF115_uc001eok.2_Missense_Mutation_p.H44Y|RNF115_uc009wiy.2_5'UTR NM_014455 NP_055270 Q9Y4L5 RN115_HUMAN Rabring 7 77 protein autoubiquitination cytosol protein binding|ubiquitin-protein ligase activity|zinc ion binding ovary(1) 1 0.279412 58.594922 61.570714 19 49 KEEP --- --- --- --- ACP6 51205 broad.mit.edu 37 1 147131118 147131118 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:147131118G>A uc001epr.2 - 4 980 c.516C>T c.(514-516)TCC>TCT p.S172S ACP6_uc009wjj.1_Silent_p.S129S NM_016361 NP_057445 Q9NPH0 PPA6_HUMAN acid phosphatase 6, lysophosphatidic precursor 172 lipid metabolic process extracellular region|mitochondrion acid phosphatase activity|protein binding ovary(4) 4 all_hematologic(923;0.0276) 0.453704 167.368866 167.569729 49 59 KEEP --- --- --- --- Unknown broad.mit.edu 37 1 149036648 149036648 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:149036648G>A LOC645166 (83594 upstream) : LOC388692 (242828 downstream) 0.4 13.59844 13.685781 4 6 KEEP --- --- --- --- Unknown broad.mit.edu 37 1 149045560 149045560 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:149045560C>T LOC645166 (92506 upstream) : LOC388692 (233916 downstream) 0.5 12.99961 12.99961 4 4 KEEP --- --- --- --- Unknown broad.mit.edu 37 1 149096535 149096535 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:149096535G>A LOC645166 (143481 upstream) : LOC388692 (182941 downstream) 0.455621 240.622864 240.916247 77 92 KEEP --- --- --- --- Unknown broad.mit.edu 37 1 149106180 149106180 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:149106180G>A LOC645166 (153126 upstream) : LOC388692 (173296 downstream) 0.526316 34.550835 34.562241 10 9 KEEP --- --- --- --- Unknown broad.mit.edu 37 1 149261455 149261455 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:149261455G>A LOC645166 (308401 upstream) : LOC388692 (18021 downstream) 0.571429 53.504164 53.628913 16 12 KEEP --- --- --- --- C1orf51 148523 broad.mit.edu 37 1 150255506 150255506 + Intron SNP T A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:150255506T>A uc001euh.2 + C1orf51_uc001eui.2_Intron|C1orf51_uc001euj.2_5'UTR NM_144697 NP_653298 hypothetical protein LOC148523 0 Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171) LUSC - Lung squamous cell carcinoma(543;0.171) 0.619048 44.281791 44.543988 13 8 KEEP --- --- --- --- FAM63A 55793 broad.mit.edu 37 1 150972441 150972441 + Splice_Site SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:150972441C>T uc001ewf.2 - 7 2420 c.736_splice c.e7-1 p.S246_splice FAM63A_uc001ewc.2_Splice_Site_p.S104_splice|FAM63A_uc010pcm.1_Splice_Site_p.S151_splice|FAM63A_uc001ewd.2_Splice_Site_p.S104_splice|FAM63A_uc001ewe.2_Splice_Site_p.S80_splice|FAM63A_uc010pcn.1_Splice_Site_p.S294_splice|FAM63A_uc001ewg.2_Splice_Site_p.S246_splice NM_018379 NP_001156731 hypothetical protein LOC55793 isoform 1 protein binding ovary(1) 1 all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185) UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211) 0.5 71.00063 71.00063 20 20 KEEP --- --- --- --- TDRKH 11022 broad.mit.edu 37 1 151742858 151742858 + 3'UTR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:151742858C>T uc001eyy.2 - 14 SubName: Full=cDNA FLJ54003, highly similar to Tudor and KH domain-containing protein; RNA binding ovary(1)|pancreas(1) 2 Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14) LUSC - Lung squamous cell carcinoma(543;0.181) 0.375 36.690999 37.130372 12 20 KEEP --- --- --- --- CRNN 49860 broad.mit.edu 37 1 152382658 152382658 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:152382658C>T uc001ezx.2 - 3 974 c.900G>A c.(898-900)CAG>CAA p.Q300Q NM_016190 NP_057274 Q9UBG3 CRNN_HUMAN cornulin 300 Gln-rich. cell-cell adhesion|response to heat cytoplasm|membrane calcium ion binding ovary(2)|skin(1) 3 Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242) LUSC - Lung squamous cell carcinoma(543;0.206) 0.42446 370.320579 371.673708 118 160 KEEP --- --- --- --- IVL 3713 broad.mit.edu 37 1 152884094 152884094 + 3'UTR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:152884094C>T uc001fau.2 + 2 NM_005547 NP_005538 involucrin isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine|keratinization|response to UV-B cornified envelope|cytoplasm protein binding, bridging|structural molecule activity ovary(3) 3 Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242) LUSC - Lung squamous cell carcinoma(543;0.171) 0.357143 44.813691 45.568521 15 27 KEEP --- --- --- --- SPRR1A 6698 broad.mit.edu 37 1 152957897 152957897 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:152957897C>T uc009wnu.1 + 2 269 c.191C>T c.(190-192)CCC>CTC p.P64L SPRR1A_uc001faw.2_Missense_Mutation_p.P64L NM_005987 NP_005978 P35321 SPR1A_HUMAN small proline-rich protein 1A 64 5.|6 X 8 AA approximate tandem repeats. keratinization|peptide cross-linking cornified envelope|cytoplasm protein binding, bridging|structural molecule activity 0 Lung NSC(65;1.46e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242) LUSC - Lung squamous cell carcinoma(543;0.171) 0.512195 135.127749 135.137814 42 40 KEEP --- --- --- --- SPRR3 6707 broad.mit.edu 37 1 152975600 152975600 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:152975600C>T uc001fax.3 + 3 254 c.104C>T c.(103-105)CCC>CTC p.P35L SPRR3_uc001faz.3_Missense_Mutation_p.P35L|SPRR3_uc001fay.2_Missense_Mutation_p.P35L NM_005416 NP_005407 Q9UBC9 SPRR3_HUMAN small proline-rich protein 3 35 keratinization|peptide cross-linking|wound healing cytoplasm protein binding|structural molecule activity skin(1) 1 Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242) LUSC - Lung squamous cell carcinoma(543;0.171) 0.485714 54.978486 54.984405 17 18 KEEP --- --- --- --- SPRR2E 6704 broad.mit.edu 37 1 153066298 153066298 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:153066298G>A uc001fbh.2 - SPRR2D_uc009wnz.2_Intron|SPRR2A_uc001fbf.2_Intron|SPRR2A_uc009woa.2_Intron NM_001024209 NP_001019380 small proline-rich protein 2E keratinization cornified envelope|cytoplasm protein binding|structural molecule activity ovary(1) 1 Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242) LUSC - Lung squamous cell carcinoma(543;0.171) 0.2375 51.291597 56.323097 19 61 KEEP --- --- --- --- ILF2 3608 broad.mit.edu 37 1 153634977 153634977 + Missense_Mutation SNP C G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:153634977C>G uc001fcr.2 - 14 1149 c.1068G>C c.(1066-1068)AAG>AAC p.K356N ILF2_uc010pdy.1_Missense_Mutation_p.K318N|ILF2_uc009wok.2_Missense_Mutation_p.K334N NM_004515 NP_004506 Q12905 ILF2_HUMAN interleukin enhancer binding factor 2 356 immune response|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleolus|ribonucleoprotein complex ATP binding|DNA binding|double-stranded RNA binding|protein binding|transferase activity 0 all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199) LUSC - Lung squamous cell carcinoma(543;0.171) 0.04878 -9.169747 8.572302 4 78 KEEP --- --- --- --- NPR1 4881 broad.mit.edu 37 1 153661891 153661891 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:153661891C>T uc001fcs.3 + NPR1_uc010pdz.1_Intron|NPR1_uc010pea.1_Intron NM_000906 NP_000897 natriuretic peptide receptor 1 precursor body fluid secretion|intracellular signal transduction|negative regulation of angiogenesis|negative regulation of cell growth|positive regulation of renal sodium excretion|positive regulation of urine volume|receptor guanylyl cyclase signaling pathway|regulation of blood pressure|regulation of blood vessel size|regulation of vascular permeability|regulation of vasodilation ATP binding|GTP binding|guanylate cyclase activity|natriuretic peptide receptor activity|peptide receptor activity, G-protein coupled|protein kinase activity ovary(3)|lung(2)|stomach(1)|breast(1) 7 all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199) LUSC - Lung squamous cell carcinoma(543;0.151) Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Nesiritide(DB04899)|Nitric Oxide(DB00435)|Nitroglycerin(DB00727)|Nitroprusside(DB00325) Pancreas(141;1349 1870 15144 15830 40702) 382 0.482456 185.823059 185.853447 55 59 KEEP --- --- --- --- NUP210L 91181 broad.mit.edu 37 1 154027154 154027154 + Intron SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:154027154A>G uc001fdw.2 - NUP210L_uc009woq.2_Intron|NUP210L_uc010peh.1_Intron NM_207308 NP_997191 nucleoporin 210kDa-like isoform 1 integral to membrane skin(5)|ovary(4)|large_intestine(1)|central_nervous_system(1) 11 all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128) LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198) 0.538462 27.326445 27.343184 7 6 KEEP --- --- --- --- ATP8B2 57198 broad.mit.edu 37 1 154303909 154303909 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:154303909C>T uc001fey.1 + ATP8B2_uc001few.2_Intron|ATP8B2_uc001fex.2_Intron NM_001005855 NP_001005855 ATPase, class I, type 8B, member 2 isoform b ATP biosynthetic process plasma membrane ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity ovary(1)|skin(1) 2 all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877) LUSC - Lung squamous cell carcinoma(543;0.185) 0.531915 84.378232 84.41985 25 22 KEEP --- --- --- --- GON4L 54856 broad.mit.edu 37 1 155727220 155727220 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:155727220G>A uc001flz.2 - GON4L_uc009wrg.1_Intron|GON4L_uc001fly.1_Intron|GON4L_uc009wrh.1_Intron|GON4L_uc001fma.1_Intron|GON4L_uc001fmb.3_Intron NM_001037533 NP_001032622 gon-4-like isoform a regulation of transcription, DNA-dependent cytoplasm|nucleus DNA binding ovary(3) 3 Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195) 0.375 19.045928 19.265485 6 10 KEEP --- --- --- --- KIAA0907 22889 broad.mit.edu 37 1 155895500 155895500 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:155895500G>A uc001fmi.1 - 7 840 c.816C>T c.(814-816)TTC>TTT p.F272F KIAA0907_uc001fmj.1_Silent_p.F272F|KIAA0907_uc009wrk.1_Intron|KIAA0907_uc009wrl.1_RNA|KIAA0907_uc001fml.1_Silent_p.F272F|KIAA0907_uc001fmm.2_3'UTR NM_014949 NP_055764 Q7Z7F0 K0907_HUMAN hypothetical protein LOC22889 272 0 Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195) OV - Ovarian serous cystadenocarcinoma(3;8.82e-06) 0.534653 179.549458 179.654569 54 47 KEEP --- --- --- --- SMG5 23381 broad.mit.edu 37 1 156223307 156223307 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:156223307G>A uc001foc.3 - SMG5_uc009wrv.2_Intron NM_015327 NP_056142 SMG5 homolog nonsense mediated mRNA decay mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation cytoplasm|nucleus protein phosphatase 2A binding ovary(2)|skin(2)|pancreas(1) 5 Hepatocellular(266;0.158) 0.342105 42.063874 42.900773 13 25 KEEP --- --- --- --- INSRR 3645 broad.mit.edu 37 1 156828491 156828491 + 5'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:156828491G>A uc010pht.1 - 1 NTRK1_uc001fqf.1_Intron|NTRK1_uc009wsi.1_Intron|INSRR_uc009wsj.1_5'UTR|NTRK1_uc001fqh.1_5'Flank|NTRK1_uc001fqi.1_5'Flank|NTRK1_uc009wsk.1_5'Flank NM_014215 NP_055030 insulin receptor-related receptor precursor protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|insulin receptor substrate binding|metal ion binding|phosphatidylinositol 3-kinase binding|transmembrane receptor protein tyrosine kinase activity lung(11)|ovary(5)|skin(2)|kidney(1)|central_nervous_system(1) 20 all_hematologic(923;0.0839)|Hepatocellular(266;0.158) 299 0.478261 38.324436 38.333866 11 12 KEEP --- --- --- --- ARHGEF11 9826 broad.mit.edu 37 1 156911692 156911692 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:156911692G>A uc001fqo.2 - 33 4336 c.3296C>T c.(3295-3297)CCC>CTC p.P1099L ARHGEF11_uc010phu.1_Missense_Mutation_p.P515L|ARHGEF11_uc001fqn.2_Missense_Mutation_p.P1139L NM_014784 NP_055599 O15085 ARHGB_HUMAN Rho guanine nucleotide exchange factor (GEF) 11 1099 Poly-Pro. actin cytoskeleton organization|apoptosis|axon guidance|cellular component movement|cytokinesis|establishment of cell polarity|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of cell growth|regulation of Rho protein signal transduction|Rho protein signal transduction|striated muscle contraction cytosol|Golgi apparatus|plasma membrane G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity|signal transducer activity ovary(3)|skin(2)|pleura(1)|lung(1)|kidney(1)|pancreas(1) 9 all_hematologic(923;0.0839)|Hepatocellular(266;0.158) 0.421053 76.690384 76.999681 24 33 KEEP --- --- --- --- FCRL5 83416 broad.mit.edu 37 1 157512449 157512449 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:157512449G>A uc001fqu.2 - FCRL5_uc009wsm.2_Intron|FCRL5_uc010phv.1_Intron|FCRL5_uc010phw.1_Intron|FCRL5_uc001fqv.1_Intron|FCRL5_uc010phx.1_Intron NM_031281 NP_112571 Fc receptor-like 5 integral to membrane|plasma membrane receptor activity ovary(3)|breast(2)|central_nervous_system(1) 6 all_hematologic(112;0.0378)|Hepatocellular(266;0.178) Prostate(1639;0.231) 0.7 22.327314 22.684239 7 3 KEEP --- --- --- --- FCRL2 79368 broad.mit.edu 37 1 157746768 157746769 + Intron DNP CC TT TT MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:157746768_157746769CC>TT uc001fre.2 - FCRL2_uc010phz.1_Intron|FCRL2_uc009wsp.2_Intron|FCRL2_uc010pia.1_Intron NM_030764 NP_110391 Fc receptor-like 2 precursor cell-cell signaling integral to membrane|plasma membrane|soluble fraction receptor activity|SH3/SH2 adaptor activity ovary(1)|pancreas(1) 2 all_hematologic(112;0.0378) LUSC - Lung squamous cell carcinoma(543;0.24) 0.565217 86.855185 87.025515 26 20 KEEP --- --- --- --- CD1C 911 broad.mit.edu 37 1 158261900 158261900 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:158261900G>A uc001fru.2 + 3 647 c.355G>A c.(355-357)GGC>AGC p.G119S CD1C_uc001frv.2_5'UTR NM_001765 NP_001756 P29017 CD1C_HUMAN CD1C antigen precursor 119 Extracellular (Potential). antigen processing and presentation|T cell activation involved in immune response endosome membrane|integral to plasma membrane endogenous lipid antigen binding|exogenous lipid antigen binding|glycolipid binding|lipopeptide binding ovary(2)|skin(1)|pancreas(1) 4 all_hematologic(112;0.0378) 0.466102 178.826058 178.942485 55 63 KEEP --- --- --- --- OR10X1 128367 broad.mit.edu 37 1 158549711 158549711 + 5'Flank SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:158549711G>A uc010pin.1 - NM_001004477 NP_001004477 olfactory receptor, family 10, subfamily X, sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity ovary(1) 1 all_hematologic(112;0.0378) 0.518072 143.627065 143.650532 43 40 KEEP --- --- --- --- PYHIN1 149628 broad.mit.edu 37 1 158914814 158914814 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:158914814C>T uc001ftb.2 + 7 1586 c.1341C>T c.(1339-1341)TCC>TCT p.S447S PYHIN1_uc001ftc.2_Silent_p.S438S|PYHIN1_uc001ftd.2_Silent_p.S447S|PYHIN1_uc001fte.2_Silent_p.S438S NM_152501 NP_689714 Q6K0P9 IFIX_HUMAN pyrin and HIN domain family, member 1 alpha 1 447 cell cycle nuclear speck ovary(3)|pancreas(1) 4 all_hematologic(112;0.0378) 0.396552 143.831781 144.915905 46 70 KEEP --- --- --- --- IFI16 3428 broad.mit.edu 37 1 159021961 159021961 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:159021961G>A uc001ftg.2 + IFI16_uc010pis.1_Intron|IFI16_uc001fth.2_Intron|IFI16_uc010pit.1_Intron NM_005531 NP_005522 interferon, gamma-inducible protein 16 cell proliferation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|monocyte differentiation|negative regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent cytoplasm|nuclear speck|nucleolus double-stranded DNA binding|protein binding ovary(1) 1 all_hematologic(112;0.0429) 0.5 34.550064 34.550064 10 10 KEEP --- --- --- --- CADM3 57863 broad.mit.edu 37 1 159163404 159163404 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:159163404G>A uc001ftl.2 + CADM3_uc009wsx.1_Missense_Mutation_p.E226K|CADM3_uc009wsy.1_Intron|CADM3_uc001ftk.2_Intron NM_001127173 NP_001120645 cell adhesion molecule 3 isoform 2 adherens junction organization|cell junction assembly|heterophilic cell-cell adhesion|homophilic cell adhesion cell-cell junction|integral to membrane protein homodimerization activity ovary(2) 2 all_hematologic(112;0.0429) 0.76 68.237975 69.780274 19 6 KEEP --- --- --- --- CADM3 57863 broad.mit.edu 37 1 159170626 159170626 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:159170626G>A uc001ftl.2 + 9 1253 c.1111G>A c.(1111-1113)GAC>AAC p.D371N CADM3_uc001ftk.2_Missense_Mutation_p.D405N|uc001ftm.1_RNA NM_001127173 NP_001120645 Q8N126 CADM3_HUMAN cell adhesion molecule 3 isoform 2 371 Cytoplasmic (Potential). adherens junction organization|cell junction assembly|heterophilic cell-cell adhesion|homophilic cell adhesion cell-cell junction|integral to membrane protein homodimerization activity ovary(2) 2 all_hematologic(112;0.0429) 0.457447 138.71667 138.864712 43 51 KEEP --- --- --- --- FCER1A 2205 broad.mit.edu 37 1 159274082 159274082 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:159274082G>A uc001ftq.2 + NM_002001 NP_001992 Fc fragment of IgE, high affinity I, receptor integral to plasma membrane lung(2)|skin(2)|prostate(1) 5 all_hematologic(112;0.0429) Benzylpenicilloyl Polylysine(DB00895)|Omalizumab(DB00043) 0.4 19.747135 19.878305 6 9 KEEP --- --- --- --- Unknown broad.mit.edu 37 1 159283452 159283452 + IGR SNP A T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:159283452A>T FCER1A (5439 upstream) : OR10J3 (10 downstream) 0.408451 96.964711 97.483862 29 42 KEEP --- --- --- --- Unknown broad.mit.edu 37 1 159283454 159283454 + IGR SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:159283454T>C FCER1A (5441 upstream) : OR10J3 (8 downstream) 0.459459 125.547111 125.65254 34 40 KEEP --- --- --- --- CCDC19 25790 broad.mit.edu 37 1 159842969 159842969 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:159842969G>A uc001fui.2 - CCDC19_uc009wtb.2_Intron|CCDC19_uc001fuj.2_Intron|CCDC19_uc001fuk.2_Intron|CCDC19_uc001ful.2_Intron NM_012337 NP_036469 nasopharyngeal epithelium specific protein 1 mitochondrion|soluble fraction ovary(1) 1 all_hematologic(112;0.0597) BRCA - Breast invasive adenocarcinoma(70;0.151) 0.407407 32.415667 32.61894 11 16 KEEP --- --- --- --- broad.mit.edu 37 1 159943808 159943808 + Intron SNP A C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:159943808A>C uc001fuu.2 + Homo sapiens full length insert cDNA clone ZE01A04. 0.5 67.229409 67.229409 19 19 KEEP --- --- --- --- ATP1A2 477 broad.mit.edu 37 1 160105889 160105889 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:160105889G>A uc001fvc.2 + ATP1A2_uc001fvb.2_Intron|ATP1A2_uc001fvd.2_Intron NM_000702 NP_000693 Na+/K+ -ATPase alpha 2 subunit proprotein ATP biosynthetic process ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity central_nervous_system(3)|ovary(2)|skin(2) 7 all_cancers(52;1.11e-16)|all_hematologic(112;0.093) BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246) 0.441176 48.520992 48.623454 15 19 KEEP --- --- --- --- ITLN1 55600 broad.mit.edu 37 1 160853293 160853293 + Missense_Mutation SNP C T T rs148429593 MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:160853293C>T uc001fxc.2 - 3 198 c.82G>A c.(82-84)GAA>AAA p.E28K NM_017625 NP_060095 Q8WWA0 ITLN1_HUMAN intelectin precursor 28 positive regulation of glucose import|positive regulation of protein phosphorylation|response to nematode|signal transduction anchored to membrane|brush border membrane|extracellular region|membrane raft receptor binding|sugar binding p.E28K(1) ovary(2)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)|central_nervous_system(1) 7 all_cancers(52;2.99e-17)|all_hematologic(112;0.093) BRCA - Breast invasive adenocarcinoma(70;0.00737) 0.428571 134.012954 134.45279 42 56 KEEP --- --- --- --- ADAMTS4 9507 broad.mit.edu 37 1 161161001 161161001 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:161161001G>A uc001fyt.3 - 9 2869 c.2441C>T c.(2440-2442)CCC>CTC p.P814L NM_005099 NP_005090 O75173 ATS4_HUMAN ADAM metallopeptidase with thrombospondin type 1 814 Spacer. proteolysis|skeletal system development extracellular space|proteinaceous extracellular matrix metalloendopeptidase activity|protease binding|zinc ion binding ovary(4)|central_nervous_system(1) 5 all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093) BRCA - Breast invasive adenocarcinoma(70;0.00275) 0.575758 64.128239 64.29305 19 14 KEEP --- --- --- --- DUSP27 92235 broad.mit.edu 37 1 167097851 167097851 + 3'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:167097851G>A uc001geb.1 + 5 NM_001080426 NP_001073895 dual specificity phosphatase 27 protein dephosphorylation protein tyrosine/serine/threonine phosphatase activity ovary(3) 3 0.433333 42.370681 42.486937 13 17 KEEP --- --- --- --- Unknown broad.mit.edu 37 1 168420381 168420381 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:168420381G>A MIR557 (75522 upstream) : XCL2 (89624 downstream) 0.533333 83.002838 83.046228 24 21 KEEP --- --- --- --- C1orf156 92342 broad.mit.edu 37 1 169762681 169762681 + Missense_Mutation SNP T A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:169762681T>A uc001ggn.2 - 2 434 c.156A>T c.(154-156)CAA>CAT p.Q52H C1orf112_uc001ggj.2_Intron|C1orf112_uc001ggo.2_5'Flank|uc010plt.1_5'Flank|C1orf112_uc001ggp.2_5'Flank|C1orf112_uc001ggq.2_5'Flank|C1orf112_uc009wvt.2_5'Flank NM_033418 NP_219486 O95568 MET18_HUMAN hypothetical protein MGC9084 52 cytoplasm protein methyltransferase activity 0 all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181) 0.466667 165.968834 166.070245 49 56 KEEP --- --- --- --- Unknown broad.mit.edu 37 1 173111355 173111355 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:173111355C>T TNFSF18 (91252 upstream) : TNFSF4 (41516 downstream) 0.444444 12.998964 13.023159 4 5 KEEP --- --- --- --- SLC9A11 284525 broad.mit.edu 37 1 173526360 173526360 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:173526360G>A uc001giz.2 - SLC9A11_uc009wwe.2_Intron|SLC9A11_uc010pmq.1_Intron NM_178527 NP_848622 solute carrier family 9, member 11 sodium ion transport integral to membrane ion channel activity|solute:hydrogen antiporter activity ovary(2) 2 0.25 14.364843 15.501321 5 15 KEEP --- --- --- --- RC3H1 149041 broad.mit.edu 37 1 173952108 173952108 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:173952108G>A uc001gju.3 - RC3H1_uc010pms.1_Intron|RC3H1_uc001gjv.2_Intron|RC3H1_uc010pmt.1_Intron NM_172071 NP_742068 roquin cytoplasmic mRNA processing body assembly|negative regulation of activated T cell proliferation|negative regulation of B cell proliferation|negative regulation of germinal center formation|negative regulation of T-helper cell differentiation|nuclear-transcribed mRNA catabolic process|regulation of mRNA stability|regulation of T cell receptor signaling pathway cytoplasmic mRNA processing body|stress granule mRNA 3'-UTR binding|ubiquitin-protein ligase activity|zinc ion binding ovary(2) 2 0.542857 66.02747 66.083276 19 16 KEEP --- --- --- --- RABGAP1L 9910 broad.mit.edu 37 1 174726135 174726135 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:174726135C>T uc001gjx.2 + RABGAP1L_uc001gkb.3_Intron|RABGAP1L_uc001gkc.3_Intron|RABGAP1L_uc001gkd.3_Intron NM_014857 NP_055672 RAB GTPase activating protein 1-like isoform A regulation of protein localization early endosome|Golgi apparatus|nucleus Rab GTPase activator activity ovary(2)|lung(1)|kidney(1) 4 0.727273 29.105043 29.617011 8 3 KEEP --- --- --- --- TNR 7143 broad.mit.edu 37 1 175325665 175325665 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:175325665C>T uc001gkp.1 - TNR_uc009wwu.1_Intron NM_003285 NP_003276 tenascin R precursor axon guidance|cell adhesion|signal transduction proteinaceous extracellular matrix pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1) 11 Renal(580;0.146) 0.5 39.49995 39.49995 12 12 KEEP --- --- --- --- RFWD2 64326 broad.mit.edu 37 1 176054986 176054986 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:176054986C>T uc001gku.1 - 10 1323 c.1067G>A c.(1066-1068)AGA>AAA p.R356K RFWD2_uc001gkv.1_Missense_Mutation_p.R332K|RFWD2_uc001gkw.1_Missense_Mutation_p.R116K|RFWD2_uc009wwv.2_Missense_Mutation_p.R155K|RFWD2_uc001gkt.1_Missense_Mutation_p.R195K NM_022457 NP_071902 Q8NHY2 RFWD2_HUMAN ring finger and WD repeat domain 2 isoform a 356 DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest centrosome|cytosol|focal adhesion|nuclear speck protein binding|ubiquitin-protein ligase activity|zinc ion binding 0 Ovarian(134;1413 1765 5706 35534 51541) 0.52 179.800213 179.834733 52 48 KEEP --- --- --- --- PAPPA2 60676 broad.mit.edu 37 1 176564619 176564619 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:176564619C>T uc001gkz.2 + 3 3043 c.1879C>T c.(1879-1881)CTC>TTC p.L627F PAPPA2_uc001gky.1_Missense_Mutation_p.L627F|PAPPA2_uc009www.2_RNA NM_020318 NP_064714 Q9BXP8 PAPP2_HUMAN pappalysin 2 isoform 1 627 Metalloprotease. cell differentiation|proteolysis|regulation of cell growth extracellular region|intracellular|membrane metalloendopeptidase activity|zinc ion binding ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1) 16 0.45614 84.244561 84.339325 26 31 KEEP --- --- --- --- RASAL2 9462 broad.mit.edu 37 1 178425849 178425849 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:178425849C>T uc001glr.2 + 11 1907 c.1782C>T c.(1780-1782)TTC>TTT p.F594F RASAL2_uc001glq.2_Intron|RASAL2_uc009wxc.2_Silent_p.F108F NM_004841 NP_004832 Q9UJF2 NGAP_HUMAN RAS protein activator like 2 isoform 1 594 negative regulation of Ras protein signal transduction|signal transduction cytoplasm|intrinsic to internal side of plasma membrane Ras GTPase activator activity ovary(2)|breast(2)|large_intestine(1) 5 0.505837 429.027425 429.034692 130 127 KEEP --- --- --- --- C1orf125 126859 broad.mit.edu 37 1 179520656 179520656 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:179520656G>A uc001gmo.2 + C1orf125_uc009wxg.2_Intron|C1orf125_uc001gmp.2_Intron|C1orf125_uc009wxh.2_Intron|NPHS2_uc001gmq.3_Intron|NPHS2_uc009wxi.2_Intron|C1orf125_uc001gmr.2_RNA NM_144696 NP_653297 hypothetical protein LOC126859 isoform 1 0 0.409091 28.57079 28.729707 9 13 KEEP --- --- --- --- broad.mit.edu 37 1 179556529 179556529 + RNA SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:179556529C>T uc001gmt.2 - 1 c.26G>A DQ571986 0.395349 54.867572 55.279221 17 26 KEEP --- --- --- --- ZNF648 127665 broad.mit.edu 37 1 182027128 182027128 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:182027128G>A uc001goz.2 - 2 226 c.18C>T c.(16-18)TCC>TCT p.S6S NM_001009992 NP_001009992 Q5T619 ZN648_HUMAN zinc finger protein 648 6 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding ovary(1) 1 NSCLC(71;908 1374 5429 20458 35642) 0.425287 119.699501 120.11304 37 50 KEEP --- --- --- --- RGS16 6004 broad.mit.edu 37 1 182569340 182569340 + 3'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:182569340G>A uc001gpl.3 - 5 NM_002928 NP_002919 regulator of G-protein signalling 16 negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway|visual perception cytoplasm|plasma membrane calmodulin binding|GTPase activator activity|signal transducer activity ovary(1) 1 0.464286 43.773103 43.804169 13 15 KEEP --- --- --- --- LAMC2 3918 broad.mit.edu 37 1 183195969 183195969 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:183195969G>A uc001gqa.2 + 9 1517 c.1203G>A c.(1201-1203)AAG>AAA p.K401K LAMC2_uc001gpz.3_Silent_p.K401K|LAMC2_uc010poa.1_Silent_p.K101K NM_005562 NP_005553 Q13753 LAMC2_HUMAN laminin, gamma 2 isoform a precursor 401 Laminin EGF-like 4; second part. cell adhesion|epidermis development|hemidesmosome assembly heparin binding skin(2)|ovary(1) 3 0.435897 339.420219 340.258087 102 132 KEEP --- --- --- --- LAMC2 3918 broad.mit.edu 37 1 183209442 183209442 + Nonsense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:183209442C>T uc001gqa.2 + 22 3558 c.3244C>T c.(3244-3246)CAG>TAG p.Q1082* LAMC2_uc001gpz.3_Nonsense_Mutation_p.Q1082*|LAMC2_uc010poa.1_Nonsense_Mutation_p.Q782* NM_005562 NP_005553 Q13753 LAMC2_HUMAN laminin, gamma 2 isoform a precursor 1082 Domain II and I. cell adhesion|epidermis development|hemidesmosome assembly heparin binding skin(2)|ovary(1) 3 0.418605 57.859363 58.103407 18 25 KEEP --- --- --- --- HMCN1 83872 broad.mit.edu 37 1 185891647 185891647 + Intron SNP T A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:185891647T>A uc001grq.1 + NM_031935 NP_114141 hemicentin 1 precursor response to stimulus|visual perception basement membrane calcium ion binding ovary(22)|skin(1) 23 0.44 35.022058 35.100425 11 14 KEEP --- --- --- --- Unknown broad.mit.edu 37 1 187533064 187533064 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:187533064G>A PLA2G4A (574959 upstream) : None (None downstream) 0.25 13.566166 14.701797 5 15 KEEP --- --- --- --- RGS21 431704 broad.mit.edu 37 1 192321314 192321314 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:192321314G>A uc001gsh.2 + 4 400 c.226G>A c.(226-228)GAA>AAA p.E76K NM_001039152 NP_001034241 Q2M5E4 RGS21_HUMAN regulator of G-protein signaling 21 76 RGS. negative regulation of signal transduction cytoplasm|plasma membrane GTPase activator activity|signal transducer activity ovary(1)|skin(1) 2 0.333333 33.313403 34.125522 11 22 KEEP --- --- --- --- TROVE2 6738 broad.mit.edu 37 1 193045658 193045658 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:193045658C>T uc001gss.2 + 4 1004 c.829C>T c.(829-831)CCG>TCG p.P277S TROVE2_uc001gst.1_Missense_Mutation_p.P2S|TROVE2_uc001gsu.1_Missense_Mutation_p.P2S|TROVE2_uc001gsv.1_Missense_Mutation_p.P277S|TROVE2_uc001gsw.2_Missense_Mutation_p.P277S|TROVE2_uc009wyp.2_Missense_Mutation_p.P277S|TROVE2_uc009wyq.2_Missense_Mutation_p.P277S|TROVE2_uc001gsx.1_Missense_Mutation_p.P277S NM_004600 NP_004591 P10155 RO60_HUMAN TROVE domain family, member 2 isoform 2 277 TROVE. transcription from RNA polymerase III promoter cytoplasm|nucleus|ribonucleoprotein complex protein binding|RNA binding 0 0.032787 -20.995445 8.069473 4 118 KEEP --- --- --- --- CFHR3 10878 broad.mit.edu 37 1 196757587 196757587 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:196757587G>A uc001gtl.2 + CFHR3_uc001gtk.2_Intron|CFHR3_uc010poy.1_Intron|CFHR1_uc001gtm.2_Intron NM_021023 NP_066303 complement factor H-related 3 precursor extracellular space 0 0.528302 95.802521 95.839349 28 25 KEEP --- --- --- --- CFHR3 10878 broad.mit.edu 37 1 196758804 196758804 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:196758804G>A uc001gtl.2 + CFHR3_uc001gtk.2_3'UTR|CFHR3_uc010poy.1_Intron|CFHR1_uc001gtm.2_Intron NM_021023 NP_066303 complement factor H-related 3 precursor extracellular space 0 0.617647 72.98306 73.395773 21 13 KEEP --- --- --- --- CFHR4 10877 broad.mit.edu 37 1 196887516 196887516 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:196887516G>A uc001gto.2 + 6 1045 c.976G>A c.(976-978)GAA>AAA p.E326K CFHR4_uc009wyy.2_Missense_Mutation_p.E572K|CFHR4_uc001gtp.2_Missense_Mutation_p.E573K NM_006684 NP_006675 Q92496 FHR4_HUMAN complement factor H-related 4 precursor 326 Sushi 5. extracellular region lipid transporter activity ovary(1)|pancreas(1)|skin(1) 3 0.355372 137.892186 140.121862 43 78 KEEP --- --- --- --- F13B 2165 broad.mit.edu 37 1 197029723 197029723 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:197029723C>T uc001gtt.1 - NM_001994 NP_001985 coagulation factor XIII B subunit precursor blood coagulation extracellular region upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1) 3 0.357143 15.87077 16.122592 5 9 KEEP --- --- --- --- ASPM 259266 broad.mit.edu 37 1 197102412 197102413 + Intron DNP GG AA AA MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:197102412_197102413GG>AA uc001gtu.2 - ASPM_uc001gtv.2_Intron|ASPM_uc001gtw.3_Intron NM_018136 NP_060606 asp (abnormal spindle)-like, microcephaly mitosis cytoplasm|nucleus calmodulin binding ovary(4)|central_nervous_system(2) 6 0.619048 43.779419 44.040192 13 8 KEEP --- --- --- --- CRB1 23418 broad.mit.edu 37 1 197237641 197237641 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:197237641C>T uc001gtz.2 + CRB1_uc010poz.1_Intron|CRB1_uc001gty.1_Intron|CRB1_uc010ppa.1_Intron|CRB1_uc009wza.2_Intron|CRB1_uc010ppb.1_Intron NM_201253 NP_957705 crumbs homolog 1 precursor cell-cell signaling|establishment or maintenance of cell polarity apical plasma membrane|extracellular region|integral to membrane calcium ion binding|protein binding ovary(5)|skin(3)|large_intestine(1) 9 0.53 177.2734 177.351235 53 47 KEEP --- --- --- --- CRB1 23418 broad.mit.edu 37 1 197390195 197390195 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:197390195G>A uc001gtz.2 + 6 1372 c.1237G>A c.(1237-1239)GAG>AAG p.E413K CRB1_uc010poz.1_Missense_Mutation_p.E344K|CRB1_uc010ppa.1_RNA|CRB1_uc009wza.2_Missense_Mutation_p.E301K|CRB1_uc010ppb.1_Missense_Mutation_p.E413K|CRB1_uc010ppc.1_RNA|CRB1_uc010ppd.1_5'UTR|CRB1_uc001gub.1_Missense_Mutation_p.E62K NM_201253 NP_957705 P82279 CRUM1_HUMAN crumbs homolog 1 precursor 413 Extracellular (Potential).|EGF-like 10; calcium-binding (Potential). cell-cell signaling|establishment or maintenance of cell polarity apical plasma membrane|extracellular region|integral to membrane calcium ion binding|protein binding ovary(5)|skin(3)|large_intestine(1) 9 0.49635 215.492088 215.493737 68 69 KEEP --- --- --- --- PTPRC 5788 broad.mit.edu 37 1 198701498 198701498 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:198701498C>T uc001gur.1 + 19 2218 c.2038C>T c.(2038-2040)CGT>TGT p.R680C PTPRC_uc001gus.1_Missense_Mutation_p.R632C|PTPRC_uc001gut.1_Missense_Mutation_p.R519C|PTPRC_uc009wzf.1_Missense_Mutation_p.R568C|PTPRC_uc010ppg.1_Missense_Mutation_p.R616C NM_002838 NP_002829 P08575 PTPRC_HUMAN protein tyrosine phosphatase, receptor type, C 680 Cytoplasmic (Potential).|Tyrosine-protein phosphatase 1. axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway focal adhesion|integral to plasma membrane|membrane raft protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity breast(4)|skin(3)|ovary(2)|lung(1)|kidney(1)|pancreas(1) 12 815 0.40625 86.847529 87.336202 26 38 KEEP --- --- --- --- PTPRC 5788 broad.mit.edu 37 1 198725203 198725203 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:198725203C>T uc001gur.1 + 33 3988 c.3808C>T c.(3808-3810)CCT>TCT p.P1270S PTPRC_uc001gus.1_Missense_Mutation_p.P1222S|PTPRC_uc001gut.1_Missense_Mutation_p.P1109S NM_002838 NP_002829 P08575 PTPRC_HUMAN protein tyrosine phosphatase, receptor type, C 1270 Cytoplasmic (Potential). axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway focal adhesion|integral to plasma membrane|membrane raft protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity breast(4)|skin(3)|ovary(2)|lung(1)|kidney(1)|pancreas(1) 12 815 0.478261 150.369102 150.401094 44 48 KEEP --- --- --- --- C1orf106 55765 broad.mit.edu 37 1 200878498 200878498 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:200878498G>A uc001gvo.2 + 8 1217 c.1187G>A c.(1186-1188)GGG>GAG p.G396E C1orf106_uc010ppm.1_Missense_Mutation_p.G311E NM_018265 NP_060735 Q3KP66 CA106_HUMAN hypothetical protein LOC55765 isoform 1 396 skin(2)|ovary(1) 3 0.368421 22.654603 22.929712 7 12 KEEP --- --- --- --- NAV1 89796 broad.mit.edu 37 1 201758799 201758799 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:201758799G>A uc001gwu.2 + NAV1_uc001gwv.1_Intron|NAV1_uc001gww.1_Intron|NAV1_uc001gwx.2_Intron|NAV1_uc001gwy.1_Intron NM_020443 NP_065176 neuron navigator 1 cell differentiation|nervous system development cytoplasm|microtubule nucleoside-triphosphatase activity|nucleotide binding central_nervous_system(3)|ovary(1) 4 0.567568 68.873836 69.020237 21 16 KEEP --- --- --- --- ZC3H11A 9877 broad.mit.edu 37 1 203803029 203803029 + Intron SNP T A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:203803029T>A uc001hac.2 + ZC3H11A_uc001had.2_Intron|ZC3H11A_uc001hae.2_Intron|ZC3H11A_uc001haf.2_Intron|ZC3H11A_uc010pqm.1_Intron|ZC3H11A_uc001hag.1_Intron NM_014827 NP_055642 zinc finger CCCH-type containing 11A nucleic acid binding|protein binding|zinc ion binding lung(1)|central_nervous_system(1) 2 all_cancers(21;0.0904)|all_epithelial(62;0.234) BRCA - Breast invasive adenocarcinoma(75;0.109) 0.628571 148.517207 149.533654 44 26 KEEP --- --- --- --- REN 5972 broad.mit.edu 37 1 204135543 204135543 + 5'Flank SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:204135543C>T uc001haq.2 - NM_000537 NP_000528 renin preproprotein angiotensin maturation|regulation of MAPKKK cascade extracellular space|membrane aspartic-type endopeptidase activity skin(3)|central_nervous_system(1) 4 all_cancers(21;0.00965)|Breast(84;0.116)|all_epithelial(62;0.157) KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109) Aliskiren(DB01258)|Remikiren(DB00212) 0.333333 8.922137 9.143474 3 6 KEEP --- --- --- --- NFASC 23114 broad.mit.edu 37 1 204955296 204955296 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:204955296C>T uc001hbj.2 + NFASC_uc010pra.1_Intron|NFASC_uc001hbi.2_Intron|NFASC_uc010prb.1_Intron|NFASC_uc010prc.1_Intron|NFASC_uc001hbk.1_Intron|NFASC_uc001hbl.1_Intron|NFASC_uc001hbm.1_5'Flank|NFASC_uc001hbn.1_5'Flank NM_001005388 NP_001005388 neurofascin isoform 1 precursor axon guidance|cell adhesion|myelination|peripheral nervous system development integral to membrane|node of Ranvier|plasma membrane protein binding ovary(3)|breast(1)|central_nervous_system(1)|skin(1) 6 all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19) KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158) 0.9 32.276464 33.186431 9 1 KEEP --- --- --- --- PM20D1 148811 broad.mit.edu 37 1 205797716 205797716 + 3'UTR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:205797716C>T uc001hdj.2 - 13 PM20D1_uc009xbr.2_RNA NM_152491 NP_689704 peptidase M20 domain containing 1 precursor extracellular region metal ion binding|peptidase activity skin(1) 1 Breast(84;0.201) BRCA - Breast invasive adenocarcinoma(75;0.0252) 0.428571 63.257387 63.477162 21 28 KEEP --- --- --- --- LGTN 1939 broad.mit.edu 37 1 206775715 206775716 + Missense_Mutation DNP GG AA AA MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:206775715_206775716GG>AA uc001heh.2 - 7 1085_1086 c.876_877CC>TT c.(874-879)TTCCTT>TTTTTT p.L293F LGTN_uc009xbw.2_Intron NM_006893 NP_008824 P41214 EIF2D_HUMAN ligatin 293 intracellular protein transport cytoplasm protein binding|receptor activity|translation initiation factor activity 0 Breast(84;0.183) BRCA - Breast invasive adenocarcinoma(75;0.166) 0.5 57.974925 57.974925 17 17 KEEP --- --- --- --- IL10 3586 broad.mit.edu 37 1 206944368 206944368 + Nonsense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:206944368G>A uc001hen.1 - 3 321 c.262C>T c.(262-264)CAG>TAG p.Q88* NM_000572 NP_000563 P22301 IL10_HUMAN interleukin 10 precursor 88 anti-apoptosis|B cell differentiation|B cell proliferation|cytoplasmic sequestering of NF-kappaB|inflammatory response|leukocyte chemotaxis|negative regulation of B cell proliferation|negative regulation of cytokine secretion involved in immune response|negative regulation of interferon-alpha biosynthetic process|negative regulation of interleukin-6 production|negative regulation of membrane protein ectodomain proteolysis|negative regulation of MHC class II biosynthetic process|negative regulation of T cell proliferation|positive regulation of B cell apoptosis|positive regulation of cytokine secretion|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|receptor biosynthetic process|regulation of isotype switching|response to glucocorticoid stimulus|type 2 immune response extracellular space cytokine activity|growth factor activity|interleukin-10 receptor binding 0 Breast(84;0.183) BRCA - Breast invasive adenocarcinoma(75;0.211) 0.441441 159.36696 159.697376 49 62 KEEP --- --- --- --- PIGR 5284 broad.mit.edu 37 1 207104830 207104830 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:207104830C>T uc001hez.2 - PIGR_uc009xbz.2_Intron NM_002644 NP_002635 polymeric immunoglobulin receptor precursor extracellular region|integral to plasma membrane protein binding ovary(1)|central_nervous_system(1)|skin(1) 3 0.449153 175.573202 175.83692 53 65 KEEP --- --- --- --- PLXNA2 5362 broad.mit.edu 37 1 208206866 208206866 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:208206866G>A uc001hgz.2 - NM_025179 NP_079455 plexin A2 precursor axon guidance integral to membrane|intracellular|plasma membrane ovary(2)|central_nervous_system(1) 3 OV - Ovarian serous cystadenocarcinoma(81;0.199) 0.428571 18.847926 18.910202 6 8 KEEP --- --- --- --- CAMK1G 57172 broad.mit.edu 37 1 209778886 209778886 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:209778886C>T uc001hhd.2 + 5 404 c.302C>T c.(301-303)TCT>TTT p.S101F CAMK1G_uc001hhf.3_Missense_Mutation_p.S101F|CAMK1G_uc001hhe.2_Missense_Mutation_p.S101F NM_020439 NP_065172 Q96NX5 KCC1G_HUMAN calcium/calmodulin-dependent protein kinase IG 101 Protein kinase. Golgi membrane|plasma membrane ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity breast(1) 1 OV - Ovarian serous cystadenocarcinoma(81;0.0475) Ovarian(163;530 1939 9680 28669 48710) 224 0.434483 208.905986 209.448359 63 82 KEEP --- --- --- --- CAMK1G 57172 broad.mit.edu 37 1 209779712 209779712 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:209779712G>A uc001hhd.2 + 6 585 c.483G>A c.(481-483)ATG>ATA p.M161I CAMK1G_uc001hhf.3_Missense_Mutation_p.M161I|CAMK1G_uc001hhe.2_Missense_Mutation_p.M161I NM_020439 NP_065172 Q96NX5 KCC1G_HUMAN calcium/calmodulin-dependent protein kinase IG 161 Protein kinase. Golgi membrane|plasma membrane ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity breast(1) 1 OV - Ovarian serous cystadenocarcinoma(81;0.0475) Ovarian(163;530 1939 9680 28669 48710) 224 0.460227 258.12083 258.366677 81 95 KEEP --- --- --- --- TRAF3IP3 80342 broad.mit.edu 37 1 209948705 209948705 + Silent SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:209948705T>C uc001hho.2 + 10 1076 c.786T>C c.(784-786)CCT>CCC p.P262P TRAF3IP3_uc001hhl.2_Silent_p.P242P|TRAF3IP3_uc001hhm.1_Silent_p.P262P|TRAF3IP3_uc001hhn.2_Silent_p.P242P|TRAF3IP3_uc009xcr.2_Silent_p.P262P NM_025228 NP_079504 Q9Y228 T3JAM_HUMAN TRAF3-interacting JNK-activating modulator 262 Cytoplasmic (Potential).|Potential. integral to membrane protein binding large_intestine(1)|ovary(1) 2 OV - Ovarian serous cystadenocarcinoma(81;0.045) 0.269231 22.613656 23.862845 7 19 KEEP --- --- --- --- PROX1 5629 broad.mit.edu 37 1 214209261 214209261 + 3'UTR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:214209261C>T uc001hkh.2 + 5 NM_002763 NP_002754 prospero homeobox 1 aorta smooth muscle tissue morphogenesis|atrial cardiac muscle tissue morphogenesis|brain development|dorsal spinal cord development|embryonic retina morphogenesis in camera-type eye|endocardium formation|hepatocyte differentiation|kidney development|lens fiber cell morphogenesis|lung development|lymphangiogenesis|negative regulation of bile acid biosynthetic process|negative regulation of cell proliferation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of viral genome replication|neural tube development|olfactory placode formation|optic placode formation involved in camera-type eye formation|otic placode formation|pancreas development|positive regulation of cyclin-dependent protein kinase activity|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of heart growth|positive regulation of S phase of mitotic cell cycle|positive regulation of sarcomere organization|positive regulation of transcription, DNA-dependent|regulation of transcription involved in lymphatic endothelial cell fate commitment|skeletal muscle thin filament assembly|venous blood vessel morphogenesis|ventricular cardiac muscle tissue morphogenesis|ventricular cardiac myofibril development|ventricular septum morphogenesis cytoplasm|nucleus DBD domain binding|LBD domain binding|ligand-dependent nuclear receptor binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription corepressor activity|transcription regulatory region DNA binding ovary(3)|lung(1)|central_nervous_system(1)|skin(1) 6 OV - Ovarian serous cystadenocarcinoma(81;0.0179)|all cancers(67;0.0488)|GBM - Glioblastoma multiforme(131;0.188)|Epithelial(68;0.219) 0.411765 21.32178 21.437423 7 10 KEEP --- --- --- --- CENPF 1063 broad.mit.edu 37 1 214821736 214821736 + Intron SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:214821736A>G uc001hkm.2 + NM_016343 NP_057427 centromere protein F cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding ovary(6)|central_nervous_system(4)|large_intestine(2)|skin(1) 13 all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833) Colon(80;575 1284 11000 14801 43496) 0.481481 49.975439 49.983421 13 14 KEEP --- --- --- --- USH2A 7399 broad.mit.edu 37 1 215916657 215916657 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:215916657G>A uc001hku.1 - 59 11797 c.11410C>T c.(11410-11412)CCT>TCT p.P3804S NM_206933 NP_996816 O75445 USH2A_HUMAN usherin isoform B 3804 Fibronectin type-III 23.|Extracellular (Potential). maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound basement membrane|cytoplasm|integral to membrane|stereocilium membrane collagen binding ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1) 26 OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875) HNSCC(13;0.011) 0.471264 132.168416 132.231018 41 46 KEEP --- --- --- --- USH2A 7399 broad.mit.edu 37 1 216465498 216465498 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:216465498G>A uc001hku.1 - USH2A_uc001hkv.2_Intron NM_206933 NP_996816 usherin isoform B maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound basement membrane|cytoplasm|integral to membrane|stereocilium membrane collagen binding ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1) 26 OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875) HNSCC(13;0.011) 0.446809 134.751412 134.980709 42 52 KEEP --- --- --- --- USH2A 7399 broad.mit.edu 37 1 216595526 216595526 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:216595526G>A uc001hku.1 - 2 540 c.153C>T c.(151-153)ATC>ATT p.I51I USH2A_uc001hkv.2_Silent_p.I51I NM_206933 NP_996816 O75445 USH2A_HUMAN usherin isoform B 51 Extracellular (Potential). maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound basement membrane|cytoplasm|integral to membrane|stereocilium membrane collagen binding ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1) 26 OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875) HNSCC(13;0.011) 0.489362 75.323272 75.327883 23 24 KEEP --- --- --- --- Unknown broad.mit.edu 37 1 226626315 226626315 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:226626315G>A PARP1 (30514 upstream) : C1orf95 (110186 downstream) 0.578947 38.22773 38.330917 11 8 KEEP --- --- --- --- ACTA1 58 broad.mit.edu 37 1 229567655 229567655 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:229567655G>A uc001htm.2 - NM_001100 NP_001091 actin, alpha 1, skeletal muscle muscle filament sliding|skeletal muscle fiber development|skeletal muscle thin filament assembly actin filament|cytosol|stress fiber|striated muscle thin filament ADP binding|ATP binding|myosin binding|structural constituent of cytoskeleton 0 Breast(184;0.0858)|Ovarian(103;0.103) Prostate(94;0.167) Dornase Alfa(DB00003) 0.375 43.415243 43.963832 15 25 KEEP --- --- --- --- Unknown broad.mit.edu 37 1 233972023 233972023 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:233972023C>T KCNK1 (163765 upstream) : SLC35F3 (68656 downstream) 0.4375 66.571326 66.73413 21 27 KEEP --- --- --- --- TARBP1 6894 broad.mit.edu 37 1 234603169 234603169 + Intron SNP T A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:234603169T>A uc001hwd.2 - NM_005646 NP_005637 TAR RNA binding protein 1 regulation of transcription from RNA polymerase II promoter|RNA processing nucleus RNA binding|RNA methyltransferase activity ovary(2)|skin(1) 3 Ovarian(103;0.0339) all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172) OV - Ovarian serous cystadenocarcinoma(106;0.000263) 0.571429 51.302841 51.427191 16 12 KEEP --- --- --- --- EDARADD 128178 broad.mit.edu 37 1 236572564 236572564 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:236572564C>T uc001hxu.1 + 2 175 c.110C>T c.(109-111)TCC>TTC p.S37F EDARADD_uc001hxv.1_Missense_Mutation_p.S27F NM_145861 NP_665860 Q8WWZ3 EDAD_HUMAN EDAR-associated death domain isoform A 37 cell differentiation|signal transduction cytoplasm 0 Ovarian(103;0.0634)|Breast(184;0.247) all_cancers(173;0.0232)|Prostate(94;0.174) OV - Ovarian serous cystadenocarcinoma(106;0.00117) 0.516484 155.824942 155.846382 47 44 KEEP --- --- --- --- RYR2 6262 broad.mit.edu 37 1 237969517 237969517 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:237969517C>T uc001hyl.1 + 99 14352 c.14232C>T c.(14230-14232)CTC>CTT p.L4744L RYR2_uc010pyb.1_Silent_p.L177L NM_001035 NP_001026 Q92736 RYR2_HUMAN cardiac muscle ryanodine receptor 4744 cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1) 33 Ovarian(103;0.103) all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225) OV - Ovarian serous cystadenocarcinoma(106;0.00606) 0.423077 69.039674 69.308463 22 30 KEEP --- --- --- --- ZP4 57829 broad.mit.edu 37 1 238051740 238051740 + Silent SNP T G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:238051740T>G uc001hym.2 - 4 471 c.471A>C c.(469-471)TCA>TCC p.S157S LOC100130331_uc010pyc.1_Intron NM_021186 NP_067009 Q12836 ZP4_HUMAN zona pellucida glycoprotein 4 preproprotein 157 P-type.|Extracellular (Potential). acrosomal vesicle exocytosis|negative regulation of binding of sperm to zona pellucida|positive regulation of acrosome reaction|positive regulation of humoral immune response|positive regulation of protein kinase activity|positive regulation of T cell proliferation|protein kinase A signaling cascade|protein kinase C signaling cascade integral to membrane|intracellular|plasma membrane|proteinaceous extracellular matrix acrosin binding|receptor activity ovary(2)|skin(1) 3 Ovarian(103;0.103) all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214) OV - Ovarian serous cystadenocarcinoma(106;0.00989) NSCLC(166;160 2029 11600 18754 19936) 0.552381 206.760268 207.011392 58 47 KEEP --- --- --- --- Unknown broad.mit.edu 37 1 247400787 247400787 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:247400787C>T ZNF124 (65469 upstream) : VN1R5 (18587 downstream) 0.5 9.724838 9.724838 3 3 KEEP --- --- --- --- OR2B11 127623 broad.mit.edu 37 1 247614793 247614793 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:247614793C>T uc010pyx.1 - 1 492 c.492G>A c.(490-492)GTG>GTA p.V164V NM_001004492 NP_001004492 Q5JQS5 OR2BB_HUMAN olfactory receptor, family 2, subfamily B, 164 Extracellular (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity upper_aerodigestive_tract(1) 1 all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724) all_cancers(173;0.241) OV - Ovarian serous cystadenocarcinoma(106;0.0188) 0.5 55.536088 55.536088 17 17 KEEP --- --- --- --- Unknown broad.mit.edu 37 1 247902444 247902444 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:247902444C>T OR6F1 (26387 upstream) : OR1C1 (18322 downstream) 0.453271 324.153413 324.560424 97 117 KEEP --- --- --- --- OR2T8 343172 broad.mit.edu 37 1 248084521 248084521 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:248084521G>A uc010pzc.1 + 1 202 c.202G>A c.(202-204)GAC>AAC p.D68N NM_001005522 NP_001005522 A6NH00 OR2T8_HUMAN olfactory receptor, family 2, subfamily T, 68 Helical; Name=2; (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity 0 all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) all_cancers(173;0.0211) OV - Ovarian serous cystadenocarcinoma(106;0.0319) 0.414815 172.468546 173.32551 56 79 KEEP --- --- --- --- OR2L2 26246 broad.mit.edu 37 1 248201573 248201573 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:248201573G>A uc001idw.2 + 1 100 c.4G>A c.(4-6)GAA>AAA p.E2K OR2L13_uc001ids.2_Intron NM_001004686 NP_001004686 Q8NH16 OR2L2_HUMAN olfactory receptor, family 2, subfamily L, 2 Extracellular (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity ovary(1)|central_nervous_system(1)|skin(1) 3 all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) OV - Ovarian serous cystadenocarcinoma(106;0.0278) 0.403509 148.138866 149.06341 46 68 KEEP --- --- --- --- OR2T12 127064 broad.mit.edu 37 1 248458245 248458245 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:248458245G>A uc010pzj.1 - 1 636 c.636C>T c.(634-636)ATC>ATT p.I212I NM_001004692 NP_001004692 Q8NG77 O2T12_HUMAN olfactory receptor, family 2, subfamily T, 212 Helical; Name=5; (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity skin(2)|ovary(1) 3 all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) OV - Ovarian serous cystadenocarcinoma(106;0.0201) 0.478873 112.207411 112.230343 34 37 KEEP --- --- --- --- OR2T4 127074 broad.mit.edu 37 1 248525228 248525228 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:248525228G>A uc001ieh.1 + 1 346 c.346G>A c.(346-348)GAC>AAC p.D116N NM_001004696 NP_001004696 Q8NH00 OR2T4_HUMAN olfactory receptor, family 2, subfamily T, 116 Extracellular (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity central_nervous_system(1) 1 all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) OV - Ovarian serous cystadenocarcinoma(106;0.0265) 0.136 87.357102 135.486632 51 324 KEEP --- --- --- --- OR2T6 254879 broad.mit.edu 37 1 248551360 248551360 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:248551360G>A uc001iei.1 + 1 451 c.451G>A c.(451-453)GGT>AGT p.G151S NM_001005471 NP_001005471 Q8NHC8 OR2T6_HUMAN olfactory receptor, family 2, subfamily T, 151 Helical; Name=4; (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity ovary(2)|skin(1) 3 all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) OV - Ovarian serous cystadenocarcinoma(106;0.0265) 0.489362 74.515242 74.520068 23 24 KEEP --- --- --- --- OR2T2 401992 broad.mit.edu 37 1 248616440 248616440 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:248616440C>T uc001iek.1 + 1 342 c.342C>T c.(340-342)TTC>TTT p.F114F NM_001004136 NP_001004136 Q6IF00 OR2T2_HUMAN olfactory receptor, family 2, subfamily T, 114 Helical; Name=3; (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity skin(1) 1 all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) OV - Ovarian serous cystadenocarcinoma(106;0.0265) 0.319277 157.515658 162.333841 53 113 KEEP --- --- --- --- OR2G6 391211 broad.mit.edu 37 1 248685793 248685793 + Silent SNP C T T rs144767509 byFrequency MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:248685793C>T uc001ien.1 + 1 846 c.846C>T c.(844-846)ACC>ACT p.T282T NM_001013355 NP_001013373 Q5TZ20 OR2G6_HUMAN olfactory receptor, family 2, subfamily G, 282 Helical; Name=7; (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity ovary(2)|skin(1) 3 all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) all_cancers(173;0.0156) OV - Ovarian serous cystadenocarcinoma(106;0.0265) 0.460526 112.711849 112.81547 35 41 KEEP --- --- --- --- OR2T11 127077 broad.mit.edu 37 1 248790161 248790161 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr1:248790161G>A uc001ier.1 - 1 269 c.269C>T c.(268-270)TCC>TTC p.S90F NM_001001964 NP_001001964 Q8NH01 O2T11_HUMAN olfactory receptor, family 2, subfamily T, 90 Extracellular (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity lung(1) 1 all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) OV - Ovarian serous cystadenocarcinoma(106;0.0265) 0.916667 37.252041 38.848839 11 1 KEEP --- --- --- --- RBM17 84991 broad.mit.edu 37 10 6147121 6147121 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:6147121G>A uc001ijb.2 + RBM17_uc010qav.1_Intron NM_032905 NP_116294 RNA binding motif protein 17 mRNA processing|RNA splicing spliceosomal complex nucleotide binding|protein binding|RNA binding 0 1 76.03665 76.036649 20 0 KEEP --- --- --- --- UPF2 26019 broad.mit.edu 37 10 11973786 11973786 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:11973786G>A uc001ila.2 - UPF2_uc001ilb.2_Intron|UPF2_uc001ilc.2_Intron NM_080599 NP_542166 UPF2 regulator of nonsense transcripts homolog mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay exon-exon junction complex|perinuclear region of cytoplasm identical protein binding|RNA binding central_nervous_system(2)|ovary(1) 3 Renal(717;0.228) 0.982143 211.851035 214.050604 55 1 KEEP --- --- --- --- DHTKD1 55526 broad.mit.edu 37 10 12162067 12162067 + Intron SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:12162067A>G uc001ild.3 + NM_018706 NP_061176 dehydrogenase E1 and transketolase domain glycolysis mitochondrion oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding ovary(1)|central_nervous_system(1) 2 Renal(717;0.228) BRCA - Breast invasive adenocarcinoma(52;0.188) 0.066667 0.725146 6.563405 2 28 KEEP --- --- --- --- CDNF 441549 broad.mit.edu 37 10 14867415 14867416 + Intron DNP CC TT TT MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:14867415_14867416CC>TT uc001inb.1 - CDNF_uc010qbv.1_Intron|CDNF_uc001inc.1_Intron NM_001029954 NP_001025125 arginine-rich, mutated in early stage extracellular region growth factor activity 0 1 264.629321 264.629321 64 0 KEEP --- --- --- --- FAM171A1 221061 broad.mit.edu 37 10 15296725 15296725 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:15296725C>T uc001iob.2 - 4 579 c.572G>A c.(571-573)GGA>GAA p.G191E NM_001010924 NP_001010924 Q5VUB5 F1711_HUMAN hypothetical protein LOC221061 precursor 191 Extracellular (Potential). integral to membrane ovary(2)|breast(1)|skin(1) 4 1 94.146898 94.146898 24 0 KEEP --- --- --- --- NEBL 10529 broad.mit.edu 37 10 21148810 21148810 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:21148810G>A uc001iqi.2 - NEBL_uc001iqj.2_Intron|NEBL_uc001iqk.2_Intron NM_006393 NP_006384 nebulette sarcomeric isoform regulation of actin filament length actin binding|structural constituent of muscle ovary(2) 2 1 38.668773 38.667795 10 0 KEEP --- --- --- --- Unknown broad.mit.edu 37 10 22514528 22514528 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:22514528C>T DNAJC1 (221878 upstream) : COMMD3 (90771 downstream) 1 39.370536 39.369559 10 0 KEEP --- --- --- --- BMI1 648 broad.mit.edu 37 10 22618434 22618434 + Missense_Mutation SNP C T T rs140326477 MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:22618434C>T uc001irh.2 + 10 1583 c.944C>T c.(943-945)TCA>TTA p.S315L BMI1_uc009xkg.2_Missense_Mutation_p.S458L NM_005180 NP_005171 P35226 BMI1_HUMAN BMI1 polycomb ring finger oncogene 315 Pro/Ser-rich. hemopoiesis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of fibroblast proliferation|positive regulation of ubiquitin-protein ligase activity|segment specification|transcription, DNA-dependent cytoplasm|nucleolus|PcG protein complex|ubiquitin ligase complex RING-like zinc finger domain binding|zinc ion binding p.S315L(1) ovary(1)|skin(1) 2 116 0.990654 394.766518 396.883278 106 1 KEEP --- --- --- --- APBB1IP 54518 broad.mit.edu 37 10 26789849 26789849 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:26789849G>A uc001iss.2 + 5 583 c.262G>A c.(262-264)GAG>AAG p.E88K APBB1IP_uc001isr.2_Missense_Mutation_p.E88K|APBB1IP_uc009xks.1_Missense_Mutation_p.E88K NM_019043 NP_061916 Q7Z5R6 AB1IP_HUMAN amyloid beta (A4) precursor protein-binding, 88 blood coagulation|signal transduction cytoskeleton|cytosol|focal adhesion|lamellipodium lung(4)|skin(2)|central_nervous_system(1) 7 307 1 314.366615 314.366615 79 0 KEEP --- --- --- --- APBB1IP 54518 broad.mit.edu 37 10 26792149 26792149 + Silent SNP G A A rs61758872 MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:26792149G>A uc001iss.2 + 6 798 c.477G>A c.(475-477)AAG>AAA p.K159K APBB1IP_uc009xks.1_Silent_p.K159K NM_019043 NP_061916 Q7Z5R6 AB1IP_HUMAN amyloid beta (A4) precursor protein-binding, 159 blood coagulation|signal transduction cytoskeleton|cytosol|focal adhesion|lamellipodium lung(4)|skin(2)|central_nervous_system(1) 7 p.K159K(KMS28BM-Tumor)|p.K159K(KYSE180-Tumor) 307 1 238.364012 238.364012 58 0 KEEP --- --- --- --- PTCHD3 374308 broad.mit.edu 37 10 27702119 27702119 + Missense_Mutation SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:27702119T>C uc001itu.2 - 1 1179 c.1061A>G c.(1060-1062)AAG>AGG p.K354R NM_001034842 NP_001030014 Q3KNS1 PTHD3_HUMAN patched domain containing 3 354 spermatid development integral to membrane hedgehog receptor activity ovary(2)|pancreas(1)|skin(1) 4 0.989873 1659.682451 1666.894447 391 4 KEEP --- --- --- --- ZNF248 57209 broad.mit.edu 37 10 38121172 38121172 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:38121172G>A uc001izd.1 - 6 1610 c.1111C>T c.(1111-1113)CGG>TGG p.R371W ZNF248_uc009xmc.2_Intron|ZNF248_uc001izb.2_Intron|ZNF248_uc001izc.2_Intron|ZNF248_uc010qeu.1_Missense_Mutation_p.R371W NM_021045 NP_066383 Q8NDW4 ZN248_HUMAN zinc finger protein 248 371 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding ovary(1) 1 0.986111 554.371762 557.755796 142 2 KEEP --- --- --- --- ZNF37A 7587 broad.mit.edu 37 10 38403975 38403975 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:38403975C>T uc001izk.2 + ZNF37A_uc001izl.2_Intron|ZNF37A_uc001izm.2_Intron NM_001007094 NP_001007095 zinc finger protein 37a nucleus DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding breast(1) 1 1 23.777331 23.761816 6 0 KEEP --- --- --- --- LOC100133308 100133308 broad.mit.edu 37 10 45637154 45637154 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:45637154G>A uc001jbz.2 - LOC100133308_uc009xmq.1_Intron Homo sapiens cDNA FLJ32851 fis, clone TESTI2003432. 0 1 151.748899 151.748899 37 0 KEEP --- --- --- --- ZNF488 118738 broad.mit.edu 37 10 48370524 48370524 + 5'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:48370524G>A uc001jex.2 + 2 ZNF488_uc001jey.2_5'UTR NM_153034 NP_694579 zinc finger protein 488 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding ovary(1) 1 1 237.03181 237.03181 59 0 KEEP --- --- --- --- FRMPD2 143162 broad.mit.edu 37 10 49379331 49379331 + Intron SNP C G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:49379331C>G uc001jgi.2 - FRMPD2_uc001jgh.2_Intron|FRMPD2_uc001jgj.2_Intron|FRMPD2L1_uc001jgf.2_Intron|FRMPD2_uc001jgg.2_Intron|FRMPD2_uc001jgk.2_Intron NM_001018071 NP_001018081 FERM and PDZ domain containing 2 isoform 3 tight junction assembly basolateral plasma membrane|cytoplasm|cytoskeleton|tight junction 1-phosphatidylinositol binding|protein binding large_intestine(1) 1 Kidney(211;0.201) 0.981651 446.651656 451.573873 107 2 KEEP --- --- --- --- FRMPD2 143162 broad.mit.edu 37 10 49431339 49431339 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:49431339G>A uc001jgi.2 - FRMPD2_uc001jgh.2_Intron|FRMPD2_uc001jgj.2_Intron NM_001018071 NP_001018081 FERM and PDZ domain containing 2 isoform 3 tight junction assembly basolateral plasma membrane|cytoplasm|cytoskeleton|tight junction 1-phosphatidylinositol binding|protein binding large_intestine(1) 1 Kidney(211;0.201) 1 157.370307 157.370307 40 0 KEEP --- --- --- --- C10orf71 118461 broad.mit.edu 37 10 50531535 50531535 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:50531535C>T uc010qgp.1 + 3 1284 c.945C>T c.(943-945)CCC>CCT p.P315P NM_199459 NP_955629 Q711Q0 CJ071_HUMAN hypothetical protein LOC118461 isoform 2 315 0 0.980392 196.567176 197.815283 50 1 KEEP --- --- --- --- DRGX 644168 broad.mit.edu 37 10 50574266 50574266 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:50574266G>A uc010qgq.1 - 6 702 c.702C>T c.(700-702)TCC>TCT p.S234S NM_001080520 NP_001073989 A6NNA5 DRGX_HUMAN dorsal root ganglia homeobox 234 multicellular organismal development nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 1 165.1041 165.1041 43 0 KEEP --- --- --- --- BICC1 80114 broad.mit.edu 37 10 60475432 60475433 + Intron DNP CC TT TT MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:60475432_60475433CC>TT uc001jki.1 + LOC728640_uc010qic.1_RNA NM_001080512 NP_001073981 bicaudal C homolog 1 multicellular organismal development RNA binding ovary(2)|lung(1)|skin(1) 4 0.933333 109.810805 113.569144 28 2 KEEP --- --- --- --- CTNNA3 29119 broad.mit.edu 37 10 68381468 68381468 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:68381468C>T uc009xpn.1 - 10 1479 c.1356G>A c.(1354-1356)TTG>TTA p.L452L CTNNA3_uc001jmw.2_Silent_p.L452L|CTNNA3_uc001jmx.3_Silent_p.L452L NM_001127384 NP_001120856 Q9UI47 CTNA3_HUMAN catenin, alpha 3 452 cell-cell adhesion actin cytoskeleton|cytoplasm|fascia adherens cadherin binding|structural molecule activity skin(3)|ovary(2)|pancreas(1)|lung(1)|central_nervous_system(1) 8 1 167.280849 167.280849 40 0 KEEP --- --- --- --- LRRTM3 347731 broad.mit.edu 37 10 68688290 68688290 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:68688290G>A uc001jmz.1 + CTNNA3_uc009xpn.1_Intron|CTNNA3_uc001jmw.2_Intron|CTNNA3_uc001jmx.3_Intron|CTNNA3_uc009xpo.1_Intron|LRRTM3_uc001jmy.2_3'UTR NM_178011 NP_821079 leucine rich repeat transmembrane neuronal 3 integral to membrane upper_aerodigestive_tract(1)|ovary(1)|skin(1) 3 1 50.899838 50.899716 13 0 KEEP --- --- --- --- OIT3 170392 broad.mit.edu 37 10 74666263 74666263 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:74666263G>A uc001jte.1 + OIT3_uc009xqs.1_Intron NM_152635 NP_689848 oncoprotein-induced transcript 3 precursor nuclear envelope calcium ion binding ovary(2) 2 Prostate(51;0.0198) Colon(7;19 345 13446 17537) 1 109.52734 109.52734 29 0 KEEP --- --- --- --- KCNMA1 3778 broad.mit.edu 37 10 78729674 78729674 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:78729674G>A uc001jxn.2 - KCNMA1_uc001jxj.2_Intron|KCNMA1_uc001jxk.1_Intron|KCNMA1_uc009xrt.1_Intron|KCNMA1_uc001jxl.1_Intron|KCNMA1_uc001jxo.2_Intron|KCNMA1_uc001jxm.2_Intron|KCNMA1_uc001jxq.2_Intron NM_001161352 NP_001154824 large conductance calcium-activated potassium cellular potassium ion homeostasis|negative regulation of cell volume|platelet activation|positive regulation of apoptosis|regulation of membrane potential|response to calcium ion|response to carbon monoxide|response to hypoxia|response to osmotic stress|smooth muscle contraction involved in micturition apical plasma membrane|caveola|integral to membrane|voltage-gated potassium channel complex actin binding|calcium-activated potassium channel activity|large conductance calcium-activated potassium channel activity|metal ion binding|voltage-gated potassium channel activity pancreas(2)|ovary(1) 3 all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198) OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183) Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Chlorzoxazone(DB00356)|Cromoglicate(DB01003)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Enflurane(DB00228)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021) 1 65.780137 65.780133 18 0 KEEP --- --- --- --- FAM190B 54462 broad.mit.edu 37 10 86198276 86198276 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:86198276C>T uc001kdh.1 + 6 2071 c.1877C>T c.(1876-1878)CCC>CTC p.P626L FAM190B_uc010qmd.1_Missense_Mutation_p.P626L|FAM190B_uc001kdi.1_Intron|FAM190B_uc010qme.1_Missense_Mutation_p.P53L NM_018999 NP_061872 Q9H7U1 F190B_HUMAN granule cell antiserum positive 14 626 ovary(3)|skin(1) 4 1 335.934991 335.934991 81 0 KEEP --- --- --- --- IFIT1B 439996 broad.mit.edu 37 10 91143777 91143777 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:91143777G>A uc001kgh.2 + 2 787 c.707G>A c.(706-708)GGA>GAA p.G236E LIPA_uc001kgb.3_Intron|LIPA_uc001kgc.3_Intron NM_001010987 NP_001010987 Q5T764 IFT1B_HUMAN interferon-induced protein with 236 binding 0 1 902.841459 902.841459 232 0 KEEP --- --- --- --- MYOF 26509 broad.mit.edu 37 10 95093732 95093732 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:95093732G>A uc001kin.2 - MYOF_uc001kio.2_Intron|MYOF_uc009xue.2_Intron NM_013451 NP_038479 myoferlin isoform a blood circulation|muscle contraction|plasma membrane repair caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane phospholipid binding|protein binding ovary(3)|breast(1) 4 1 33.489107 33.487145 9 0 KEEP --- --- --- --- CEP55 55165 broad.mit.edu 37 10 95279676 95279676 + Intron SNP C A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:95279676C>A uc009xug.2 + CEP55_uc001kiq.3_Intron NM_001127182 NP_001120654 centrosomal protein 55kDa cell division|mitosis centriole|cleavage furrow|midbody 0 Colorectal(252;0.207) 0.133333 4.439356 6.396517 2 13 KEEP --- --- --- --- PIPSL 266971 broad.mit.edu 37 10 95718530 95718530 + 3'UTR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:95718530C>T uc009xuj.2 - 1 NR_002319 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 1 105.59915 105.59915 26 0 KEEP --- --- --- --- PIPSL 266971 broad.mit.edu 37 10 95719922 95719922 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:95719922C>T uc009xuj.2 - 1 1751 c.1232G>A c.(1231-1233)CGG>CAG p.R411Q NR_002319 RecName: Full=Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha; Short=PtdIns(4)P-5-kinase alpha; Short=PIP5KIalpha; EC=2.7.1.68; AltName: Full=Phosphatidylinositol-4-phosphate 5-kinase type I alpha; AltName: Full=68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alpha; 0 1 203.248795 203.248795 50 0 KEEP --- --- --- --- CYP2C18 1562 broad.mit.edu 37 10 96466825 96466825 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:96466825C>T uc001kjv.3 + CYP2C18_uc001kjw.3_Intron|CYP2C19_uc009xus.1_Intron|CYP2C19_uc010qny.1_Intron NM_000772 NP_000763 cytochrome P450 family 2 subfamily C polypeptide xenobiotic metabolic process endoplasmic reticulum membrane|microsome aromatase activity|electron carrier activity|heme binding|oxygen binding ovary(3)|lung(1)|skin(1) 5 Colorectal(252;0.09) all cancers(201;2.8e-06)|KIRC - Kidney renal clear cell carcinoma(50;0.0646)|Kidney(138;0.0805) 1 91.345708 91.345708 24 0 KEEP --- --- --- --- Unknown broad.mit.edu 37 10 96769571 96769571 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:96769571G>A CYP2C9 (20424 upstream) : CYP2C8 (26959 downstream) 1 125.08581 125.08581 31 0 KEEP --- --- --- --- DNMBP 23268 broad.mit.edu 37 10 101717036 101717036 + Intron SNP C G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:101717036C>G uc001kqj.2 - NCRNA00093_uc001kqk.1_RNA NM_015221 NP_056036 dynamin binding protein intracellular signal transduction|regulation of Rho protein signal transduction cell junction|cytoskeleton|Golgi stack|synapse protein binding|Rho guanyl-nucleotide exchange factor activity ovary(5)|skin(1) 6 Colorectal(252;0.234) Epithelial(162;2.94e-10)|all cancers(201;3.15e-08) 1 25.177575 25.162063 6 0 KEEP --- --- --- --- PPRC1 23082 broad.mit.edu 37 10 103897635 103897635 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:103897635C>T uc001kum.2 + 2 221 c.182C>T c.(181-183)TCT>TTT p.S61F PPRC1_uc001kun.2_5'UTR|PPRC1_uc010qqj.1_Missense_Mutation_p.S61F|PPRC1_uc009xxa.2_5'Flank NM_015062 NP_055877 Q5VV67 PPRC1_HUMAN peroxisome proliferator-activated receptor 61 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus nucleotide binding|RNA binding ovary(1)|central_nervous_system(1)|skin(1) 3 Colorectal(252;0.122) Epithelial(162;4.97e-08)|all cancers(201;8.99e-07) 1 143.944842 143.944842 37 0 KEEP --- --- --- --- ACSL5 51703 broad.mit.edu 37 10 114158819 114158820 + Intron DNP CC TT TT MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:114158819_114158820CC>TT uc001kzs.2 + ACSL5_uc001kzt.2_Intron|ACSL5_uc001kzu.2_Intron|ACSL5_uc009xxz.2_Intron NM_203379 NP_976313 acyl-CoA synthetase long-chain family member 5 fatty acid metabolic process|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process endoplasmic reticulum membrane|integral to membrane|mitochondrial outer membrane ATP binding|long-chain fatty acid-CoA ligase activity large_intestine(2)|skin(1) 3 Colorectal(252;0.117)|Breast(234;0.222) Epithelial(162;0.0343)|all cancers(201;0.137) 1 81.239949 81.239948 20 0 KEEP --- --- --- --- TDRD1 56165 broad.mit.edu 37 10 115973971 115973971 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:115973971C>T uc001lbg.1 + TDRD1_uc001lbf.2_Intron|TDRD1_uc001lbh.1_Intron|TDRD1_uc001lbi.1_Intron|TDRD1_uc010qsc.1_Intron|TDRD1_uc001lbj.2_Intron NM_198795 NP_942090 tudor domain containing 1 DNA methylation involved in gamete generation|gene silencing by RNA|germ cell development|meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis pi-body nucleic acid binding|protein binding|zinc ion binding 0 Colorectal(252;0.172)|Breast(234;0.188) Epithelial(162;0.0343)|all cancers(201;0.0754) 1 106.252422 106.252422 28 0 KEEP --- --- --- --- ABLIM1 3983 broad.mit.edu 37 10 116418033 116418033 + 5'UTR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:116418033C>T uc010qsg.1 - 1 ABLIM1_uc010qsh.1_Intron|ABLIM1_uc010qsi.1_Intron|ABLIM1_uc009xyp.2_Intron|ABLIM1_uc001lbz.1_Intron NM_002313 NP_002304 actin-binding LIM protein 1 isoform a axon guidance|cytoskeleton organization|organ morphogenesis|visual perception actin cytoskeleton|cytoplasm actin binding|zinc ion binding breast(1) 1 Colorectal(252;0.0373)|Breast(234;0.231) Epithelial(162;0.0132)|all cancers(201;0.0383) 1 178.286791 178.286791 45 0 KEEP --- --- --- --- BAG3 9531 broad.mit.edu 37 10 121429292 121429292 + Intron SNP G T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:121429292G>T uc001lem.2 + BAG3_uc001lel.2_Intron NM_004281 NP_004272 BCL2-associated athanogene 3 anti-apoptosis|apoptosis|protein folding cytosol ovary(2) 2 Lung NSC(174;0.109)|all_lung(145;0.142) all cancers(201;0.00187)|BRCA - Breast invasive adenocarcinoma(275;0.148) 0.096774 3.00038 8.051998 3 28 KEEP --- --- --- --- BTBD16 118663 broad.mit.edu 37 10 124045759 124045759 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:124045759G>A uc001lgc.1 + 5 632 c.381G>A c.(379-381)CTG>CTA p.L127L BTBD16_uc001lgd.1_Silent_p.L126L NM_144587 NP_653188 Q32M84 BTBDG_HUMAN BTB (POZ) domain containing 16 127 skin(1) 1 all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238) 1 352.895482 352.895482 95 0 KEEP --- --- --- --- broad.mit.edu 37 10 134648167 134648167 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:134648167G>A uc010qux.1 - 40 6035 c.6035C>T c.(6034-6036)TCC>TTC p.S2012F NM_017609 NP_060079 Homo sapiens cDNA, FLJ17989. 1 77.138222 77.138221 20 0 KEEP --- --- --- --- SYCE1 93426 broad.mit.edu 37 10 135371692 135371692 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr10:135371692C>T uc001lno.2 - 5 403 c.298G>A c.(298-300)GAG>AAG p.E100K CYP2E1_uc001lnl.1_3'UTR|SYCE1_uc001lnm.2_5'UTR|SYCE1_uc009ybn.2_Missense_Mutation_p.E100K|SYCE1_uc001lnn.2_Missense_Mutation_p.E64K NM_001143764 NP_001137236 Q8N0S2 SYCE1_HUMAN synaptonemal complex central element protein 1 100 Potential. cell division central element ovary(1) 1 all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175) OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06) 1 132.414611 132.414611 34 0 KEEP --- --- --- --- C11orf35 256329 broad.mit.edu 37 11 558082 558082 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:558082C>T uc001lpx.2 - uc001lpy.2_RNA|uc001lpz.2_5'Flank|RASSF7_uc001lqa.2_5'Flank|RASSF7_uc001lqb.2_5'Flank NM_173573 NP_775844 hypothetical protein LOC256329 pancreas(1) 1 all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762) all cancers(45;7.18e-28)|Epithelial(43;6.93e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.97e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703) 0.515152 56.875419 56.881968 17 16 KEEP --- --- --- --- CHID1 66005 broad.mit.edu 37 11 883196 883196 + Missense_Mutation SNP A C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:883196A>C uc001lsl.2 - 10 1072 c.911T>G c.(910-912)ATG>AGG p.M304R CHID1_uc010qwu.1_Missense_Mutation_p.M334R|CHID1_uc010qwv.1_Missense_Mutation_p.M365R|CHID1_uc001lsn.2_Missense_Mutation_p.M329R|CHID1_uc001lsm.2_Missense_Mutation_p.M304R|CHID1_uc001lso.2_Missense_Mutation_p.M304R|CHID1_uc001lsp.2_Missense_Mutation_p.M273R|CHID1_uc010qww.1_Missense_Mutation_p.M304R|uc001lsq.1_5'Flank|uc001lsr.1_5'Flank NM_023947 NP_076436 Q9BWS9 CHID1_HUMAN chitinase domain containing 1 isoform a 304 chitin catabolic process|innate immune response extracellular region|lysosome cation binding|chitinase activity 0 all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762) all cancers(45;5.48e-25)|Epithelial(43;3.75e-24)|BRCA - Breast invasive adenocarcinoma(625;4.65e-05)|Lung(200;0.0624)|LUSC - Lung squamous cell carcinoma(625;0.0735) Pancreas(117;992 2327 5172 41921) 0.406061 229.903426 231.172854 67 98 KEEP --- --- --- --- MUC2 4583 broad.mit.edu 37 11 1084452 1084452 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:1084452G>A uc001lsx.1 + NM_002457 NP_002448 mucin 2 precursor inner mucus layer|outer mucus layer protein binding lung(1)|breast(1) 2 all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191) BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703) Pranlukast(DB01411) 0.666667 6.451232 6.524528 2 1 KEEP --- --- --- --- MUC5B 727897 broad.mit.edu 37 11 1269645 1269645 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:1269645G>A uc009ycr.1 + 50 13245 c.13119G>A c.(13117-13119)AGG>AGA p.R4373R MUC5B_uc001ltb.2_Silent_p.R3848R NM_017511 NP_059981 Q9HC84 MUC5B_HUMAN SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming; 3845 7 X Cys-rich subdomain repeats.|11 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich. R -> G (in Ref. 4; CAA96577). cell adhesion extracellular region extracellular matrix structural constituent|protein binding 0 all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229) BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1) 0.338462 65.335864 66.832858 22 43 KEEP --- --- --- --- OR51G2 81282 broad.mit.edu 37 11 4936853 4936853 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:4936853G>A uc001lzr.1 - 1 41 c.41C>T c.(40-42)TCT>TTT p.S14F NM_001005238 NP_001005238 Q8NGK0 O51G2_HUMAN olfactory receptor, family 51, subfamily G, 14 Extracellular (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity skin(2) 2 Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086) Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19) 0.5 72.748787 72.748787 22 22 KEEP --- --- --- --- OR51A4 401666 broad.mit.edu 37 11 4968203 4968204 + Missense_Mutation DNP CC AA AA MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:4968203_4968204CC>AA uc010qys.1 - 1 127_128 c.127_128GG>TT c.(127-129)GGA>TTA p.G43L NM_001005329 NP_001005329 Q8NGJ6 O51A4_HUMAN olfactory receptor, family 51, subfamily A, 43 Helical; Name=1; (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity ovary(2)|skin(1) 3 Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086) Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19) 0.069444 -5.781508 8.024719 5 67 KEEP --- --- --- --- MMP26 56547 broad.mit.edu 37 11 5009524 5009524 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:5009524G>A uc001lzv.2 + 1 101 c.83G>A c.(82-84)GGA>GAA p.G28E NM_021801 NP_068573 Q9NRE1 MMP26_HUMAN matrix metalloproteinase 26 preproprotein 28 collagen catabolic process|proteolysis proteinaceous extracellular matrix metalloendopeptidase activity|zinc ion binding 0 Medulloblastoma(188;0.0025)|Breast(177;0.0204)|all_neural(188;0.0227) Epithelial(150;1.33e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0287)|LUSC - Lung squamous cell carcinoma(625;0.191) 0.439655 166.709561 167.077768 51 65 KEEP --- --- --- --- TRIM5 85363 broad.mit.edu 37 11 5863220 5863220 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:5863220C>T uc001mbq.1 - OR52E6_uc010qzq.1_5'Flank NM_033093 NP_149084 tripartite motif protein TRIM5 isoform delta interspecies interaction between organisms|protein trimerization|response to virus cytoplasm|cytoplasmic mRNA processing body ligase activity|protein binding|protein homodimerization activity|zinc ion binding ovary(1) 1 Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)|Lung NSC(207;0.138)|all_lung(207;0.221) Epithelial(150;7.21e-09)|BRCA - Breast invasive adenocarcinoma(625;0.139) 0.727273 29.004895 29.516819 8 3 KEEP --- --- --- --- ST5 6764 broad.mit.edu 37 11 8752043 8752043 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:8752043G>A uc001mgt.2 - 3 980 c.794C>T c.(793-795)CCC>CTC p.P265L ST5_uc009yfr.2_Intron|ST5_uc001mgu.2_Intron|ST5_uc001mgv.2_Missense_Mutation_p.P265L|ST5_uc010rbq.1_Intron|ST5_uc001mgw.1_Missense_Mutation_p.P265L NM_213618 NP_998783 P78524 ST5_HUMAN suppression of tumorigenicity 5 isoform 1 265 positive regulation of ERK1 and ERK2 cascade protein binding upper_aerodigestive_tract(1) 1 Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352) 0.40678 73.507386 73.949537 24 35 KEEP --- --- --- --- SCUBE2 57758 broad.mit.edu 37 11 9051374 9051374 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:9051374G>A uc001mhh.1 - SCUBE2_uc001mhi.1_Intron|SCUBE2_uc001mhj.1_Intron NM_020974 NP_066025 CEGP1 protein precursor extracellular region calcium ion binding ovary(1)|skin(1) 2 all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116) 0.451852 192.35701 192.62949 61 74 KEEP --- --- --- --- ZNF143 7702 broad.mit.edu 37 11 9530068 9530068 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:9530068C>T uc001mhr.2 + ZNF143_uc009yfu.2_Intron|ZNF143_uc010rby.1_Intron NM_003442 NP_003433 zinc finger protein 143 regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase III promoter|transcription from RNA polymerase II promoter|transcription from RNA polymerase III promoter nucleoplasm DNA binding|zinc ion binding 0 all cancers(16;4.12e-09)|Epithelial(150;2.29e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0212) 0.666667 20.352742 20.573987 6 3 KEEP --- --- --- --- Unknown broad.mit.edu 37 11 11158748 11158748 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:11158748G>A ZBED5 (279128 upstream) : GALNTL4 (133673 downstream) 0.297297 31.209345 32.569285 11 26 KEEP --- --- --- --- BTBD10 84280 broad.mit.edu 37 11 13435010 13435010 + Intron SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:13435010T>C uc001mkz.2 - BTBD10_uc010rcl.1_Intron|BTBD10_uc001mla.2_Intron|BTBD10_uc009ygn.2_Intron|BTBD10_uc010rcm.1_Intron|BTBD10_uc010rcn.1_Intron|BTBD10_uc009ygo.2_Intron NM_032320 NP_115696 K+ channel tetramerization protein nucleus 0 Epithelial(150;0.0214) 0.452381 68.92232 69.005053 19 23 KEEP --- --- --- --- PSMA1 5682 broad.mit.edu 37 11 14529089 14529089 + Intron SNP G T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:14529089G>T uc001mlk.2 - PSMA1_uc001mll.2_Intron|PSMA1_uc010rcp.1_Intron|PSMA1_uc001mlj.2_Intron NM_002786 NP_002777 proteasome alpha 1 subunit isoform 2 anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|mRNA metabolic process|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction cytoplasm|nucleus|polysome|proteasome core complex, alpha-subunit complex protein binding|RNA binding|threonine-type endopeptidase activity upper_aerodigestive_tract(1)|skin(1) 2 0.454545 15.071998 15.091966 5 6 KEEP --- --- --- --- INSC 387755 broad.mit.edu 37 11 15267494 15267495 + Missense_Mutation DNP GG AA AA MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:15267494_15267495GG>AA uc001mly.2 + 13 1694_1695 c.1648_1649GG>AA c.(1648-1650)GGC>AAC p.G550N INSC_uc001mlz.2_Missense_Mutation_p.G503N|INSC_uc001mma.2_3'UTR|INSC_uc010rcs.1_Missense_Mutation_p.G538N|INSC_uc001mmb.2_Missense_Mutation_p.G503N|INSC_uc001mmc.2_Missense_Mutation_p.G461N NM_001031853 NP_001027024 Q1MX18 INSC_HUMAN inscuteable isoform a 550 cell differentiation|nervous system development cytoplasm binding upper_aerodigestive_tract(2)|ovary(2)|central_nervous_system(1) 5 0.4125 100.575708 101.105885 33 47 KEEP --- --- --- --- PLEKHA7 144100 broad.mit.edu 37 11 16847516 16847516 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:16847516C>T uc001mmo.2 - PLEKHA7_uc010rcu.1_Intron|PLEKHA7_uc001mmn.2_Intron NM_175058 NP_778228 pleckstrin homology domain containing, family A epithelial cell-cell adhesion|zonula adherens maintenance centrosome|zonula adherens delta-catenin binding skin(2)|central_nervous_system(1) 3 0.448276 46.472328 46.539855 13 16 KEEP --- --- --- --- Unknown broad.mit.edu 37 11 17074376 17074376 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:17074376G>A PLEKHA7 (38413 upstream) : RPS13 (21564 downstream) 0.6 21.251941 21.33933 6 4 KEEP --- --- --- --- ABCC8 6833 broad.mit.edu 37 11 17449382 17449382 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:17449382G>A uc001mnc.2 - NM_000352 NP_000343 ATP-binding cassette, sub-family C, member 8 carbohydrate metabolic process|energy reserve metabolic process integral to membrane ATP binding|ATPase activity, coupled to transmembrane movement of substances|potassium ion transmembrane transporter activity|sulfonylurea receptor activity ovary(1) 1 READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1) Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)|Gliclazide(DB01120)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912) 0.518519 48.05932 48.068027 14 13 KEEP --- --- --- --- MYOD1 4654 broad.mit.edu 37 11 17742412 17742412 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:17742412C>T uc001mni.2 + NM_002478 NP_002469 myogenic differentiation 1 muscle cell fate commitment|positive regulation of muscle cell differentiation|positive regulation of transcription from RNA polymerase II promoter|protein phosphorylation|skeletal muscle tissue development nuclear chromatin|transcription factor complex E-box binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription coactivator activity breast(2)|ovary(1) 3 0.466667 20.323419 20.337843 7 8 KEEP --- --- --- --- LDHAL6A 160287 broad.mit.edu 37 11 18500304 18500304 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:18500304G>A uc001mop.1 + 8 1147 c.886G>A c.(886-888)GGA>AGA p.G296R LDHAL6A_uc001moq.2_Missense_Mutation_p.G296R NM_001144071 NP_001137543 Q6ZMR3 LDH6A_HUMAN lactate dehydrogenase A-like 6A 296 glycolysis cytoplasm binding|L-lactate dehydrogenase activity 0 NADH(DB00157) 0.507853 326.068541 326.078581 97 94 KEEP --- --- --- --- SPTY2D1 144108 broad.mit.edu 37 11 18637373 18637373 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:18637373G>A uc001moy.2 - 3 664 c.448C>T c.(448-450)CCC>TCC p.P150S SPTY2D1_uc010rdi.1_Missense_Mutation_p.P150S NM_194285 NP_919261 Q68D10 SPT2_HUMAN SPT2, Suppressor of Ty, domain containing 1 150 breast(1) 1 0.463636 164.914939 165.041632 51 59 KEEP --- --- --- --- Unknown broad.mit.edu 37 11 18885445 18885445 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:18885445G>A PTPN5 (72056 upstream) : MRGPRX1 (69916 downstream) 0.681818 51.23476 51.883556 15 7 KEEP --- --- --- --- Unknown broad.mit.edu 37 11 18977633 18977633 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:18977633C>T MRGPRX1 (21084 upstream) : MRGPRX2 (98372 downstream) 0.586207 54.378679 54.566783 17 12 KEEP --- --- --- --- Unknown broad.mit.edu 37 11 27912113 27912113 + IGR SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:27912113A>G BDNF (168508 upstream) : KIF18A (130050 downstream) 0.36 53.735198 54.598393 18 32 KEEP --- --- --- --- broad.mit.edu 37 11 31085954 31085954 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:31085954G>A uc009yjk.1 - uc009yjl.1_Intron|DCDC1_uc001msu.1_Intron RecName: Full=Doublecortin domain-containing protein 5; 0.428571 139.156257 139.62409 45 60 KEEP --- --- --- --- ABTB2 25841 broad.mit.edu 37 11 34192579 34192579 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:34192579G>A uc001mvl.1 - 5 1109 c.879C>T c.(877-879)GCC>GCT p.A293A NM_145804 NP_665803 Q8N961 ABTB2_HUMAN ankyrin repeat and BTB (POZ) domain containing 293 DNA binding central_nervous_system(1)|skin(1) 2 Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691) 0.410714 71.514505 71.904509 23 33 KEEP --- --- --- --- CAT 847 broad.mit.edu 37 11 34474774 34474774 + Intron SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:34474774A>G uc001mvm.2 + CAT_uc009ykc.1_Intron NM_001752 NP_001743 catalase hydrogen peroxide catabolic process|negative regulation of apoptosis|positive regulation of cell division|protein tetramerization|purine base metabolic process|purine nucleotide catabolic process|UV protection peroxisomal matrix|peroxisomal membrane catalase activity|heme binding|NADP binding|protein homodimerization activity ovary(2)|pancreas(1) 3 Lung NSC(402;2.76e-08)|Acute lymphoblastic leukemia(5;0.00143)|all_hematologic(20;0.0116)|Melanoma(852;0.027) BRCA - Breast invasive adenocarcinoma(625;0.000995) Fomepizole(DB01213) 0.387097 114.392249 115.426252 36 57 KEEP --- --- --- --- SLC1A2 6506 broad.mit.edu 37 11 35313696 35313696 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:35313696C>T uc001mwd.2 - SLC1A2_uc001mwe.2_Intron|SLC1A2_uc010rev.1_Intron NM_004171 NP_004162 excitatory amino acid transporter 2 D-aspartate import|L-glutamate import|synaptic transmission integral to membrane|membrane fraction high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity ovary(2)|central_nervous_system(1) 3 all_lung(20;0.211)|all_epithelial(35;0.234) all_hematologic(20;0.109) STAD - Stomach adenocarcinoma(6;0.00731) L-Glutamic Acid(DB00142) NSCLC(100;1273 1575 12993 16869 47409)|Ovarian(164;45 1946 8965 30452 48454) 0.65 45.281196 45.678343 13 7 KEEP --- --- --- --- HSD17B12 51144 broad.mit.edu 37 11 43775517 43775517 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:43775517C>T uc001mxq.3 + HSD17B12_uc001mxp.2_Intron NM_016142 NP_057226 hydroxysteroid (17-beta) dehydrogenase 12 long-chain fatty-acyl-CoA biosynthetic process|steroid biosynthetic process|triglyceride biosynthetic process endoplasmic reticulum membrane|integral to membrane estradiol 17-beta-dehydrogenase activity|long-chain-3-hydroxyacyl-CoA dehydrogenase activity 0 Ovarian(58;548 1143 13948 16572 34258) 0.54386 104.129282 104.224555 31 26 KEEP --- --- --- --- CRY2 1408 broad.mit.edu 37 11 45868922 45868922 + 5'Flank SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:45868922G>A uc010rgn.1 + CRY2_uc009ykw.2_Intron NM_021117 NP_066940 cryptochrome 2 (photolyase-like) isoform 1 DNA repair|protein-chromophore linkage|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus blue light photoreceptor activity|damaged DNA binding|DNA photolyase activity|nucleotide binding|protein binding|single-stranded DNA binding central_nervous_system(1) 1 Esophageal Squamous(106;91 1499 8126 12599 39610) 0.625 28.658276 28.882908 10 6 KEEP --- --- --- --- PHF21A 51317 broad.mit.edu 37 11 45967499 45967499 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:45967499G>A uc001ncc.3 - 14 1965 c.1341C>T c.(1339-1341)TCC>TCT p.S447S PHF21A_uc001ncb.3_Intron|PHF21A_uc009ykx.2_Intron|PHF21A_uc001nce.2_Silent_p.S448S|PHF21A_uc001nca.1_Silent_p.S183S NM_001101802 NP_001095272 Q96BD5 PF21A_HUMAN BRAF35/HDAC2 complex isoform a 447 S -> P (in Ref. 3; BAB13839). blood coagulation|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription, DNA-dependent|transcription, DNA-dependent histone deacetylase complex DNA binding|zinc ion binding central_nervous_system(1)|skin(1) 2 0.401869 133.272707 134.181662 43 64 KEEP --- --- --- --- CHRM4 1132 broad.mit.edu 37 11 46407748 46407748 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:46407748G>A uc001nct.1 - 1 360 c.360C>T c.(358-360)GTC>GTT p.V120V NM_000741 NP_000732 P08173 ACM4_HUMAN cholinergic receptor, muscarinic 4 120 Helical; Name=3; (By similarity). cell proliferation cell junction|integral to plasma membrane|postsynaptic membrane muscarinic acetylcholine receptor activity 0 GBM - Glioblastoma multiforme(35;0.0254)|Lung(87;0.14) Atropine(DB00572)|Benzquinamide(DB00767)|Cryptenamine(DB00785)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Thiethylperazine(DB00372)|Tropicamide(DB00809) Esophageal Squamous(171;1020 1936 4566 30205 42542) 0.516129 49.298888 49.305814 16 15 KEEP --- --- --- --- AMBRA1 55626 broad.mit.edu 37 11 46563720 46563720 + Missense_Mutation SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:46563720A>G uc010rgu.1 - 7 2207 c.1847T>C c.(1846-1848)TTG>TCG p.L616S AMBRA1_uc010rgt.1_Missense_Mutation_p.L182S|AMBRA1_uc009ylc.1_Missense_Mutation_p.L616S|AMBRA1_uc001ncu.1_Missense_Mutation_p.L526S|AMBRA1_uc001ncv.2_Missense_Mutation_p.L526S|AMBRA1_uc001ncw.2_Missense_Mutation_p.L526S|AMBRA1_uc001ncx.2_Missense_Mutation_p.L616S NM_017749 NP_060219 Q9C0C7 AMRA1_HUMAN activating molecule in beclin-1-regulated 616 Ser-rich. autophagy|cell differentiation|nervous system development autophagic vacuole|cytoplasmic vesicle large_intestine(1)|ovary(1)|central_nervous_system(1) 3 GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182) 0.266667 11.098431 11.83277 4 11 KEEP --- --- --- --- LRP4 4038 broad.mit.edu 37 11 46920567 46920567 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:46920567C>T uc001ndn.3 - 6 710 c.564G>A c.(562-564)GCG>GCA p.A188A LRP4_uc009ylh.1_Silent_p.A139A NM_002334 NP_002325 O75096 LRP4_HUMAN low density lipoprotein receptor-related protein 188 Extracellular (Potential). endocytosis|negative regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway integral to membrane calcium ion binding|receptor activity skin(2)|upper_aerodigestive_tract(1)|ovary(1) 4 Lung(87;0.159) 0.5 40.472165 40.472165 13 13 KEEP --- --- --- --- Unknown broad.mit.edu 37 11 48249760 48249760 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:48249760C>T OR4B1 (10470 upstream) : OR4X2 (16896 downstream) 0.75 10.327557 10.554041 3 1 KEEP --- --- --- --- Unknown broad.mit.edu 37 11 48969970 48969970 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:48969970G>A OR4A47 (458698 upstream) : FOLH1 (198218 downstream) 0.586207 56.879208 57.067097 17 12 KEEP --- --- --- --- Unknown broad.mit.edu 37 11 48973132 48973132 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:48973132G>A OR4A47 (461860 upstream) : FOLH1 (195056 downstream) 0.488095 137.425692 137.433632 41 43 KEEP --- --- --- --- FOLH1 2346 broad.mit.edu 37 11 49208461 49208461 + Intron SNP G T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:49208461G>T uc001ngy.2 - FOLH1_uc001ngz.2_Intron|FOLH1_uc009yly.2_Intron|FOLH1_uc009ylz.2_Intron|FOLH1_uc009yma.2_Intron NM_004476 NP_004467 folate hydrolase 1 isoform 1 proteolysis cytoplasm|integral to plasma membrane|membrane fraction|nucleus carboxypeptidase activity|dipeptidase activity|metal ion binding|metallopeptidase activity large_intestine(1)|ovary(1)|skin(1) 3 Capromab(DB00089)|L-Glutamic Acid(DB00142) 0.454545 29.446225 29.485972 10 12 KEEP --- --- --- --- Unknown broad.mit.edu 37 11 49920189 49920189 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:49920189C>T LOC440040 (88222 upstream) : OR4C13 (53786 downstream) 0.8 29.006152 29.843534 8 2 KEEP --- --- --- --- Unknown broad.mit.edu 37 11 50227645 50227645 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:50227645C>T OR4C12 (223608 upstream) : LOC441601 (11355 downstream) 0.495652 183.07201 183.073898 57 58 KEEP --- --- --- --- LOC646813 646813 broad.mit.edu 37 11 50379382 50379382 + RNA SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:50379382G>A uc001nhe.2 + 6 c.865G>A LOC646813_uc001nhf.1_RNA|LOC646813_uc001nhg.1_RNA|LOC646813_uc001nhh.1_RNA|LOC646813_uc010rib.1_RNA NR_024504 Homo sapiens mRNA for hypothetical protein, partial sequence, clone:Hsa11-digit09-11-09-R. 0 0.355556 48.05796 48.897426 16 29 KEEP --- --- --- --- Unknown broad.mit.edu 37 11 55234715 55234715 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:55234715C>T OR4A15 (98322 upstream) : OR4C15 (87068 downstream) 0.357143 29.841584 30.345193 10 18 KEEP --- --- --- --- OR4C15 81309 broad.mit.edu 37 11 55322872 55322872 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:55322872G>A uc010rig.1 + 1 1090 c.1090G>A c.(1090-1092)GAG>AAG p.E364K NM_001001920 NP_001001920 Q8NGM1 OR4CF_HUMAN olfactory receptor, family 4, subfamily C, 310 Cytoplasmic (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity ovary(1)|skin(1) 2 HNSCC(20;0.049) 0.404255 61.015998 61.392678 19 28 KEEP --- --- --- --- OR4C16 219428 broad.mit.edu 37 11 55339783 55339783 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:55339783C>T uc010rih.1 + 1 180 c.180C>T c.(178-180)TTC>TTT p.F60F NM_001004701 NP_001004701 Q8NGL9 OR4CG_HUMAN olfactory receptor, family 4, subfamily C, 60 Helical; Name=2; (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity ovary(1)|skin(1) 2 all_epithelial(135;0.0748) 0.550239 383.436362 383.894573 115 94 KEEP --- --- --- --- OR5L2 26338 broad.mit.edu 37 11 55594756 55594756 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:55594756C>T uc001nhy.1 + 1 62 c.62C>T c.(61-63)CCT>CTT p.P21L NM_001004739 NP_001004739 Q8NGL0 OR5L2_HUMAN olfactory receptor, family 5, subfamily L, 21 Extracellular (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity ovary(1) 1 all_epithelial(135;0.208) HNSCC(27;0.073) 0.449219 386.116557 386.700503 115 141 KEEP --- --- --- --- OR10AG1 282770 broad.mit.edu 37 11 55735754 55735754 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:55735754G>A uc010rit.1 - 1 186 c.186C>T c.(184-186)ATC>ATT p.I62I NM_001005491 NP_001005491 Q8NH19 O10AG_HUMAN olfactory receptor, family 10, subfamily AG, 62 Helical; Name=2; (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity skin(2) 2 Esophageal squamous(21;0.0137) 0.253165 57.060679 61.431199 20 59 KEEP --- --- --- --- OR8H2 390151 broad.mit.edu 37 11 55872882 55872882 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:55872882C>T uc010riy.1 + 1 364 c.364C>T c.(364-366)CGC>TGC p.R122C NM_001005200 NP_001005200 Q8N162 OR8H2_HUMAN olfactory receptor, family 8, subfamily H, 122 Cytoplasmic (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity ovary(1)|skin(1) 2 Esophageal squamous(21;0.00693) HNSCC(53;0.14) 0.458084 502.551413 503.061174 153 181 KEEP --- --- --- --- OR8H2 390151 broad.mit.edu 37 11 55873409 55873409 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:55873409G>A uc010riy.1 + 1 891 c.891G>A c.(889-891)GTG>GTA p.V297V NM_001005200 NP_001005200 Q8N162 OR8H2_HUMAN olfactory receptor, family 8, subfamily H, 297 Cytoplasmic (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity ovary(1)|skin(1) 2 Esophageal squamous(21;0.00693) HNSCC(53;0.14) 0.453901 205.583845 205.845024 64 77 KEEP --- --- --- --- OR8K3 219473 broad.mit.edu 37 11 56085746 56085746 + 5'Flank SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:56085746G>A uc010rjf.1 + NM_001005202 NP_001005202 olfactory receptor, family 8, subfamily K, sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity ovary(2)|large_intestine(1)|central_nervous_system(1) 4 Esophageal squamous(21;0.00448) 0.596774 126.988093 127.496759 37 25 KEEP --- --- --- --- PRG2 5553 broad.mit.edu 37 11 57154771 57154771 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:57154771G>A uc001njw.1 - PRG2_uc001njx.1_Intron|PRG2_uc001njy.1_Intron NM_002728 proteoglycan 2 preproprotein defense response to bacterium|immune response extracellular region|transport vesicle heparin binding|sugar binding central_nervous_system(1) 1 UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18) Sargramostim(DB00020) 0.375 8.322552 8.432468 3 5 KEEP --- --- --- --- CLP1 10978 broad.mit.edu 37 11 57428788 57428788 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:57428788C>T uc001nkw.2 + 3 1297 c.1158C>T c.(1156-1158)TTC>TTT p.F386F CLP1_uc010rjw.1_Silent_p.F322F|CLP1_uc009yml.2_Silent_p.F386F NM_006831 NP_006822 Q92989 CLP1_HUMAN ATP/GTP-binding protein isoform 1 386 mRNA 3'-end processing|nuclear mRNA splicing, via spliceosome|siRNA loading onto RISC involved in RNA interference|targeting of mRNA for destruction involved in RNA interference|termination of RNA polymerase II transcription|tRNA splicing, via endonucleolytic cleavage and ligation nucleoplasm|tRNA-intron endonuclease complex ATP binding|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity|ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity ovary(1) 1 78 0.463636 163.21362 163.340455 51 59 KEEP --- --- --- --- Unknown broad.mit.edu 37 11 58059520 58059520 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:58059520G>A OR10W1 (23788 upstream) : OR5B17 (66080 downstream) 0.4375 23.322988 23.377455 7 9 KEEP --- --- --- --- GLYAT 10249 broad.mit.edu 37 11 58480160 58480160 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:58480160G>A uc001nnb.2 - GLYAT_uc001nnc.2_Intron NM_201648 NP_964011 glycine-N-acyltransferase isoform a acyl-CoA metabolic process|response to toxin|xenobiotic metabolic process mitochondrial matrix glycine N-acyltransferase activity|glycine N-benzoyltransferase activity 0 Breast(21;0.0044)|all_epithelial(135;0.0157) Glycine(DB00145) 191 0.490909 82.982803 82.987554 27 28 KEEP --- --- --- --- GLYATL2 219970 broad.mit.edu 37 11 58604933 58604933 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:58604933G>A uc001nnd.3 - GLYATL2_uc009ymq.2_Intron NM_145016 NP_659453 glycine-N-acyltransferase-like 2 mitochondrion glycine N-acyltransferase activity ovary(1)|skin(1) 2 Breast(21;0.0044)|all_epithelial(135;0.0216) Glycine(DB00145) 196 0.465116 71.097526 71.143028 20 23 KEEP --- --- --- --- Unknown broad.mit.edu 37 11 58645850 58645850 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:58645850C>T GLYATL2 (33853 upstream) : GLYATL1 (49288 downstream) 0.5 24.799193 24.799193 8 8 KEEP --- --- --- --- MS4A2 2206 broad.mit.edu 37 11 59860382 59860382 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:59860382G>A uc001nop.2 + MS4A2_uc009ymu.2_Intron NM_000139 NP_000130 membrane-spanning 4-domains, subfamily A, member cell proliferation|humoral immune response integral to plasma membrane calcium channel activity ovary(1) 1 all_epithelial(135;0.245) Omalizumab(DB00043) 0.585366 83.307266 83.568106 24 17 KEEP --- --- --- --- MS4A4A 51338 broad.mit.edu 37 11 60075462 60075462 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:60075462G>A uc001noz.2 + MS4A4A_uc001npa.2_Intron|MS4A4A_uc001npb.2_Intron|MS4A4A_uc001npc.2_Intron NM_148975 NP_683876 membrane-spanning 4-domains, subfamily A, member integral to membrane receptor activity 0 0.380952 22.893871 23.155323 8 13 KEEP --- --- --- --- ZP1 22917 broad.mit.edu 37 11 60638372 60638372 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:60638372C>T uc001nqd.2 + ZP1_uc001nqe.2_5'UTR NM_207341 NP_997224 zona pellucida glycoprotein 1 precursor single fertilization integral to membrane|plasma membrane|proteinaceous extracellular matrix 0 0.462687 197.32194 197.485714 62 72 KEEP --- --- --- --- CPSF7 79869 broad.mit.edu 37 11 61196818 61196818 + Intron SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:61196818A>G uc001nrq.2 - SDHAF2_uc001nrt.2_5'Flank|CPSF7_uc001nro.2_5'Flank|CPSF7_uc001nrp.2_Intron|CPSF7_uc001nrr.2_Intron|CPSF7_uc001nrs.1_5'Flank|CPSF7_uc009ynp.2_Intron NM_001136040 NP_001129512 pre-mRNA cleavage factor I, 59 kDa subunit mRNA 3'-end processing|nuclear mRNA splicing, via spliceosome|protein tetramerization|termination of RNA polymerase II transcription mRNA cleavage factor complex nucleotide binding|protein binding|RNA binding central_nervous_system(1) 1 0.448276 44.672101 44.739625 13 16 KEEP --- --- --- --- DAGLA 747 broad.mit.edu 37 11 61508757 61508758 + Missense_Mutation DNP CC TT TT MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:61508757_61508758CC>TT uc001nsa.2 + 19 2218_2219 c.2107_2108CC>TT c.(2107-2109)CCG>TTG p.P703L NM_006133 NP_006124 Q9Y4D2 DGLA_HUMAN neural stem cell-derived dendrite regulator 703 Cytoplasmic (Potential). cell death|lipid catabolic process|platelet activation integral to membrane|plasma membrane acylglycerol lipase activity|metal ion binding|triglyceride lipase activity ovary(2)|central_nervous_system(1) 3 READ - Rectum adenocarcinoma(4;0.219) 0.513514 57.922877 57.928849 19 18 KEEP --- --- --- --- B3GAT3 26229 broad.mit.edu 37 11 62384143 62384144 + Missense_Mutation DNP GG AA AA MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:62384143_62384144GG>AA uc001ntw.2 - 4 772_773 c.743_744CC>TT c.(742-744)CCC>CTT p.P248L B3GAT3_uc009ynz.2_Missense_Mutation_p.P241L|B3GAT3_uc001ntx.2_RNA|B3GAT3_uc010rlz.1_Missense_Mutation_p.P248L NM_012200 NP_036332 O94766 B3GA3_HUMAN beta-1,3-glucuronyltransferase 3 248 Lumenal (Potential). glycosaminoglycan biosynthetic process Golgi membrane|integral to membrane galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity|manganese ion binding 0 0.454545 31.748013 31.787539 10 12 KEEP --- --- --- --- TAF6L 10629 broad.mit.edu 37 11 62543789 62543789 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:62543789C>T uc001nvc.2 + TAF6L_uc010rmg.1_Intron|TAF6L_uc009yof.2_Intron NM_006473 NP_006464 TAF6-like RNA polymerase II chromatin remodeling|histone H3 acetylation|regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent histone deacetylase complex|STAGA complex DNA binding|protein binding|transcription coactivator activity ovary(3) 3 0.4 19.648515 19.779233 6 9 KEEP --- --- --- --- SLC22A9 114571 broad.mit.edu 37 11 63149441 63149441 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:63149441G>A uc001nww.2 + SLC22A9_uc001nwx.2_Intron NM_080866 NP_543142 solute carrier family 22 (organic anion/cation transmembrane transport integral to membrane breast(2)|large_intestine(1) 3 0.5 48.725714 48.725714 15 15 KEEP --- --- --- --- MARK2 2011 broad.mit.edu 37 11 63670286 63670286 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:63670286C>T uc001nxw.2 + MARK2_uc001nxx.2_Intron|MARK2_uc001nxy.2_Intron|MARK2_uc001nxv.3_Intron|MARK2_uc001nxz.3_Intron|MARK2_uc009yoy.2_Intron NM_001039469 NP_001034558 MAP/microtubule affinity-regulating kinase 2 cell differentiation|establishment or maintenance of epithelial cell apical/basal polarity|intracellular protein kinase cascade|multicellular organismal development|response to oxidative stress plasma membrane ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity stomach(1)|ovary(1)|lung(1) 3 218 0.384615 14.969888 15.122252 5 8 KEEP --- --- --- --- MEN1 4221 broad.mit.edu 37 11 64575161 64575161 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:64575161G>A uc001obj.2 - MEN1_uc001obk.2_Intron|MEN1_uc001obl.2_Intron|MEN1_uc001obm.2_Intron|MEN1_uc001obn.2_Intron|MEN1_uc001obo.2_Intron|MEN1_uc001obp.2_Intron|MEN1_uc001obq.2_Intron|MEN1_uc001obr.2_Intron NM_130800 NP_570712 menin isoform 1 DNA repair|histone lysine methylation|MAPKKK cascade|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|negative regulation of JNK cascade|negative regulation of osteoblast differentiation|negative regulation of protein phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of telomerase activity|negative regulation of transcription from RNA polymerase II promoter|osteoblast development|positive regulation of protein binding|positive regulation of transforming growth factor beta receptor signaling pathway|response to gamma radiation|response to UV|transcription, DNA-dependent chromatin|cleavage furrow|cytosol|histone methyltransferase complex|nuclear matrix|soluble fraction double-stranded DNA binding|four-way junction DNA binding|protein binding, bridging|protein N-terminus binding|R-SMAD binding|transcription regulatory region DNA binding|Y-form DNA binding parathyroid(105)|pancreas(64)|gastrointestinal_tract_(site_indeterminate)(15)|small_intestine(13)|lung(9)|pituitary(7)|NS(7)|adrenal_gland(5)|soft_tissue(4)|central_nervous_system(4)|thymus(2)|stomach(1)|retroperitoneum(1)|skin(1) 238 Esophageal Squamous(1;83 158 15500 18603 18803 29295) 75 D|Mis|N|F|S parathyroid tumors|Pancreatic neuroendocrine tumors parathyroid adenoma|pituitary adenoma|pancreatic islet cell|carcinoid Hyperparathyroidism_Familial_Isolated|Multiple_Endocrine_Neoplasia_type_1 0.47541 98.371621 98.403716 29 32 KEEP --- --- --- --- SCYL1 57410 broad.mit.edu 37 11 65293902 65293903 + Intron DNP AC TT TT MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:65293902_65293903AC>TT uc001oea.1 + SCYL1_uc009yqk.2_Intron|SCYL1_uc001oeb.1_Intron|SCYL1_uc001oec.1_Intron|SCYL1_uc001oed.1_Intron NM_020680 NP_065731 SCY1-like 1 isoform A regulation of transcription, DNA-dependent|retrograde vesicle-mediated transport, Golgi to ER|transcription, DNA-dependent cis-Golgi network|COPI vesicle coat|ER-Golgi intermediate compartment|microtubule organizing center|nucleus ATP binding|DNA binding|protein tyrosine kinase activity skin(1) 1 387 0.75 21.35479 21.810621 6 2 KEEP --- --- --- --- CATSPER1 117144 broad.mit.edu 37 11 65793144 65793144 + Missense_Mutation SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:65793144T>C uc001ogt.2 - 1 845 c.707A>G c.(706-708)CAG>CGG p.Q236R NM_053054 NP_444282 Q8NEC5 CTSR1_HUMAN sperm-associated cation channel 1 236 His-rich.|Cytoplasmic (Potential). cell differentiation|multicellular organismal development|spermatogenesis cilium|flagellar membrane|integral to membrane protein binding ovary(2) 2 0.5 82.025951 82.025951 23 23 KEEP --- --- --- --- CATSPER1 117144 broad.mit.edu 37 11 65793370 65793370 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:65793370G>A uc001ogt.2 - 1 619 c.481C>T c.(481-483)CAC>TAC p.H161Y NM_053054 NP_444282 Q8NEC5 CTSR1_HUMAN sperm-associated cation channel 1 161 His-rich.|Cytoplasmic (Potential). cell differentiation|multicellular organismal development|spermatogenesis cilium|flagellar membrane|integral to membrane protein binding ovary(2) 2 0.523077 115.651314 115.681272 34 31 KEEP --- --- --- --- SYT12 91683 broad.mit.edu 37 11 66807333 66807333 + Missense_Mutation SNP C G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:66807333C>G uc009yrl.2 + 4 510 c.280C>G c.(280-282)CGC>GGC p.R94G SYT12_uc001oju.2_Missense_Mutation_p.R94G NM_177963 NP_808878 Q8IV01 SYT12_HUMAN synaptotagmin XII 94 Cytoplasmic (Potential). cell junction|integral to membrane|synaptic vesicle membrane ovary(1) 1 Ovarian(65;2862 3307) 0.537037 204.160059 204.289187 58 50 KEEP --- --- --- --- SSH3 54961 broad.mit.edu 37 11 67079302 67079302 + Missense_Mutation SNP C T T rs143186320 MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:67079302C>T uc001okj.2 + 14 2102 c.1924C>T c.(1924-1926)CGG>TGG p.R642W SSH3_uc001okk.2_RNA|SSH3_uc001okl.2_Missense_Mutation_p.R496W NM_017857 NP_060327 Q8TE77 SSH3_HUMAN slingshot homolog 3 642 regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly cytoplasm|cytoskeleton|nucleus actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity ovary(1) 1 BRCA - Breast invasive adenocarcinoma(15;2.26e-06) 0.415385 86.019469 86.423275 27 38 KEEP --- --- --- --- CABP2 51475 broad.mit.edu 37 11 67289396 67289396 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:67289396G>A uc001omc.1 - CABP2_uc001omd.1_Intron|CABP2_uc001ome.1_Intron NM_016366 NP_057450 calcium binding protein 2 isoform 1 signal transduction Golgi apparatus|perinuclear region of cytoplasm|plasma membrane calcium ion binding skin(1) 1 0.545455 39.60182 39.641346 12 10 KEEP --- --- --- --- SUV420H1 51111 broad.mit.edu 37 11 67938931 67938931 + Intron SNP G T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:67938931G>T uc001onm.1 - SUV420H1_uc009yse.1_Intron|SUV420H1_uc001onn.1_Intron|SUV420H1_uc009ysf.2_Intron|SUV420H1_uc001ono.1_Intron|SUV420H1_uc001onp.2_Intron|SUV420H1_uc010rqa.1_Intron|SUV420H1_uc001onq.2_Intron NM_017635 NP_060105 suppressor of variegation 4-20 homolog 1 isoform regulation of transcription, DNA-dependent|transcription, DNA-dependent protein binding ovary(2)|kidney(1) 3 0.333333 20.217151 20.734189 7 14 KEEP --- --- --- --- FGF19 9965 broad.mit.edu 37 11 69513982 69513982 + 3'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:69513982G>A uc001opf.2 - 3 NM_005117 NP_005108 fibroblast growth factor 19 precursor fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|negative regulation of bile acid biosynthetic process|nervous system development|positive regulation of cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of glucose import|positive regulation of JNK cascade extracellular region fibroblast growth factor receptor binding|growth factor activity skin(1) 1 all_cancers(3;5.53e-114)|all_epithelial(3;1.34e-121)|Breast(3;9.28e-34)|all_lung(4;1.99e-21)|Lung NSC(4;4.65e-21)|Hepatocellular(3;6.15e-15)|Melanoma(5;1.89e-05)|Ovarian(3;0.0348) Epithelial(3;3.05e-56)|all cancers(3;2.69e-50)|Lung(3;1.13e-16)|LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)|LUAD - Lung adenocarcinoma(13;0.0537) 15 0.333333 11.295173 11.590794 4 8 KEEP --- --- --- --- P4HA3 283208 broad.mit.edu 37 11 74009321 74009321 + Nonsense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:74009321C>T uc001ouz.2 - 4 696 c.653G>A c.(652-654)TGG>TAG p.W218* P4HA3_uc001ouy.3_RNA|P4HA3_uc010rrj.1_Nonsense_Mutation_p.W218* NM_182904 NP_878907 Q7Z4N8 P4HA3_HUMAN prolyl 4-hydroxylase, alpha III subunit 218 endoplasmic reticulum lumen iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 4-dioxygenase activity skin(1) 1 Breast(11;2.31e-05) 0.421053 156.503578 157.117645 48 66 KEEP --- --- --- --- CAPN5 726 broad.mit.edu 37 11 76834693 76834693 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:76834693G>A uc001oxx.2 + CAPN5_uc009yup.2_Intron|CAPN5_uc009yuq.2_Intron|CAPN5_uc001oxy.2_Intron|CAPN5_uc001oya.2_Intron NM_004055 NP_004046 calpain 5 proteolysis|signal transduction intracellular calcium-dependent cysteine-type endopeptidase activity 0 0.488095 133.375985 133.386185 41 43 KEEP --- --- --- --- GDPD4 220032 broad.mit.edu 37 11 76969353 76969353 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:76969353G>A uc001oyf.2 - NM_182833 NP_878253 glycerophosphodiester phosphodiesterase domain glycerol metabolic process|lipid metabolic process integral to membrane glycerophosphodiester phosphodiesterase activity|metal ion binding skin(1) 1 0.6 39.704114 39.879269 12 8 KEEP --- --- --- --- ODZ4 26011 broad.mit.edu 37 11 78489711 78489711 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:78489711C>T uc001ozl.3 - NM_001098816 NP_001092286 odz, odd Oz/ten-m homolog 4 signal transduction integral to membrane ovary(2)|pancreas(2) 4 0.5 27.103225 27.103225 8 8 KEEP --- --- --- --- DLG2 1740 broad.mit.edu 37 11 84732111 84732111 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:84732111C>T uc001pak.2 - NM_001142699 NP_001136171 chapsyn-110 isoform 1 cell junction|postsynaptic density|postsynaptic membrane guanylate kinase activity|protein binding|protein binding ovary(3)|pancreas(2)|skin(1) 6 all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036) 0.314815 48.231423 49.893221 17 37 KEEP --- --- --- --- FOLH1B 219595 broad.mit.edu 37 11 89403714 89403714 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:89403714G>A uc001pda.2 + NM_153696 NP_710163 folate hydrolase 1B proteolysis cytoplasm dipeptidase activity|metal ion binding|metallopeptidase activity ovary(3)|skin(2)|central_nervous_system(1) 6 0.666667 43.606046 44.048658 12 6 KEEP --- --- --- --- Unknown broad.mit.edu 37 11 89808176 89808176 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:89808176G>A TRIM64 (100938 upstream) : UBTFL1 (10942 downstream) 0.404762 54.671112 55.002829 17 25 KEEP --- --- --- --- Unknown broad.mit.edu 37 11 90016604 90016604 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:90016604C>T CHORDC1 (60072 upstream) : MIR1261 (585685 downstream) 0.454545 101.475918 101.618563 35 42 KEEP --- --- --- --- HEPHL1 341208 broad.mit.edu 37 11 93800871 93800871 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:93800871C>T uc001pep.2 + 5 1175 c.1018C>T c.(1018-1020)CCT>TCT p.P340S uc001pen.1_RNA NM_001098672 NP_001092142 Q6MZM0 HPHL1_HUMAN hephaestin-like 1 precursor 340 Plastocyanin-like 2.|Extracellular (Potential). copper ion transport integral to membrane copper ion binding|oxidoreductase activity ovary(3) 3 Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824) 0.527027 122.225836 122.272705 39 35 KEEP --- --- --- --- KDM4D 55693 broad.mit.edu 37 11 94730481 94730481 + 5'UTR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:94730481C>T uc001pfe.2 + 3 NM_018039 NP_060509 jumonji domain containing 2D chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen 0 0.44 77.052154 77.207285 22 28 KEEP --- --- --- --- CNTN5 53942 broad.mit.edu 37 11 99942436 99942436 + Splice_Site SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:99942436G>A uc001pga.2 + 12 1639 c.1300_splice c.e12-1 p.S434_splice CNTN5_uc009ywv.1_Splice_Site_p.S434_splice|CNTN5_uc001pfz.2_Splice_Site_p.S434_splice|CNTN5_uc001pgb.2_Splice_Site_p.S360_splice NM_014361 NP_055176 contactin 5 isoform long cell adhesion anchored to membrane|plasma membrane protein binding skin(3)|ovary(2)|pancreas(2)|breast(1) 8 all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219) BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196) 1117 0.4 13.198017 13.285495 4 6 KEEP --- --- --- --- Unknown broad.mit.edu 37 11 101079840 101079840 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:101079840G>A PGR (79296 upstream) : TRPC6 (242456 downstream) 0.5 59.395786 59.395786 19 19 KEEP --- --- --- --- MMP12 4321 broad.mit.edu 37 11 102742436 102742436 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:102742436G>A uc001phk.2 - 4 558 c.513C>T c.(511-513)TTC>TTT p.F171F NM_002426 NP_002417 P39900 MMP12_HUMAN matrix metalloproteinase 12 preproprotein 171 positive regulation of epithelial cell proliferation involved in wound healing|proteolysis|wound healing, spreading of epidermal cells proteinaceous extracellular matrix calcium ion binding|metalloendopeptidase activity|zinc ion binding 0 all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967) BRCA - Breast invasive adenocarcinoma(274;0.014) Acetohydroxamic Acid(DB00551) 0.45 28.384601 28.425994 9 11 KEEP --- --- --- --- DDI1 414301 broad.mit.edu 37 11 103908634 103908634 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:103908634C>T uc001phr.2 + 1 1327 c.1084C>T c.(1084-1086)CCT>TCT p.P362S PDGFD_uc001php.2_Intron|PDGFD_uc001phq.2_Intron NM_001001711 NP_001001711 Q8WTU0 DDI1_HUMAN DDI1, DNA-damage inducible 1, homolog 1 362 proteolysis aspartic-type endopeptidase activity large_intestine(3)|upper_aerodigestive_tract(1)|pancreas(1) 5 Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00648)|Melanoma(852;0.055)|all_neural(303;0.164) BRCA - Breast invasive adenocarcinoma(274;0.00128)|Epithelial(105;0.0631)|all cancers(92;0.169) 0.565789 147.360917 147.65503 43 33 KEEP --- --- --- --- CASP5 838 broad.mit.edu 37 11 104868100 104868100 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:104868100G>A uc010rva.1 - CASP5_uc010ruz.1_Intron|CASP5_uc010rvb.1_Intron|CASP5_uc010rvc.1_Intron|CASP5_uc009yxh.2_Intron|CASP5_uc010rvd.1_Intron NM_004347 NP_004338 caspase 5 isoform a precursor apoptosis|cellular response to mechanical stimulus|proteolysis|regulation of apoptosis intracellular cysteine-type endopeptidase activity|protein binding ovary(2)|lung(1) 3 Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047) BRCA - Breast invasive adenocarcinoma(274;0.000943)|Epithelial(105;0.0104)|all cancers(92;0.042) 0.55102 88.52696 88.637612 27 22 KEEP --- --- --- --- ATM 472 broad.mit.edu 37 11 108159688 108159688 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:108159688C>T uc001pkb.1 + ATM_uc009yxr.1_Intron|ATM_uc001pkd.3_Intron|ATM_uc001pke.1_Intron|ATM_uc010rvw.1_Intron|ATM_uc001pkf.2_Intron NM_000051 NP_000042 ataxia telangiectasia mutated isoform 1 cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence cytoplasmic membrane-bounded vesicle|nucleoplasm 1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1) 240 all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147) 1073 D|Mis|N|F|S T-PLL leukemia|lymphoma|medulloblastoma|glioma Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents Ataxia_Telangiectasia TSP Lung(14;0.12) 0.34 104.059817 106.30357 34 66 KEEP --- --- --- --- ATM 472 broad.mit.edu 37 11 108236032 108236032 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:108236032C>T uc001pkb.1 + ATM_uc009yxr.1_Intron|C11orf65_uc010rvx.1_Intron|C11orf65_uc009yxu.1_Intron|ATM_uc001pke.1_Intron NM_000051 NP_000042 ataxia telangiectasia mutated isoform 1 cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence cytoplasmic membrane-bounded vesicle|nucleoplasm 1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding haematopoietic_and_lymphoid_tissue(174)|lung(25)|breast(15)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1) 240 all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072) Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147) 1073 D|Mis|N|F|S T-PLL leukemia|lymphoma|medulloblastoma|glioma Genes_defective_in_diseases_associated_with_sensitivity_to_DNA_damaging_agents Ataxia_Telangiectasia TSP Lung(14;0.12) 0.422535 95.987154 96.36864 30 41 KEEP --- --- --- --- C11orf53 341032 broad.mit.edu 37 11 111154678 111154678 + Intron SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:111154678T>C uc001plc.2 + NM_198498 NP_940900 hypothetical protein LOC341032 0 all_cancers(61;2.05e-09)|Melanoma(852;4.04e-05)|all_epithelial(67;6.15e-05)|all_hematologic(158;0.000826)|Acute lymphoblastic leukemia(157;0.000966)|all_neural(223;0.0332)|Medulloblastoma(222;0.0425)|Breast(348;0.147) Epithelial(105;1.7e-06)|BRCA - Breast invasive adenocarcinoma(274;3.16e-06)|all cancers(92;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0507) OREG0021325 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0.488372 75.975446 75.980464 21 22 KEEP --- --- --- --- FDXACB1 91893 broad.mit.edu 37 11 111746103 111746103 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:111746103G>A uc001pmc.3 - 5 1715 c.1418C>T c.(1417-1419)TCT>TTT p.S473F ALG9_uc010rwo.1_Intron|FDXACB1_uc009yyi.2_Missense_Mutation_p.S324F NM_138378 NP_612387 Q9BRP7 FDXA1_HUMAN ferredoxin-fold anticodon binding domain 473 phenylalanyl-tRNA aminoacylation|tRNA processing ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding 0 0.571429 113.408022 113.656937 32 24 KEEP --- --- --- --- PTS 5805 broad.mit.edu 37 11 112104219 112104219 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:112104219C>T uc001pnj.3 + 6 458 c.379C>T c.(379-381)CTT>TTT p.L127F PTS_uc009yyo.2_Intron NM_000317 NP_000308 Q03393 PTPS_HUMAN 6-pyruvoyltetrahydropterin synthase 127 cellular amino acid metabolic process|central nervous system development|tetrahydrobiopterin biosynthetic process mitochondrion 6-pyruvoyltetrahydropterin synthase activity|metal ion binding 0 all_cancers(61;2.51e-14)|all_epithelial(67;1.64e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425) Epithelial(105;1.27e-06)|BRCA - Breast invasive adenocarcinoma(274;1.43e-06)|all cancers(92;2.1e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0519) 0.490909 89.92312 89.927101 27 28 KEEP --- --- --- --- Unknown broad.mit.edu 37 11 114383955 114383955 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:114383955C>T REXO2 (62957 upstream) : FAM55A (8483 downstream) 0.566667 61.679419 61.795586 17 13 KEEP --- --- --- --- TMPRSS13 84000 broad.mit.edu 37 11 117780677 117780677 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:117780677C>T uc001prs.1 - 8 1046 c.953G>A c.(952-954)GGA>GAA p.G318E TMPRSS13_uc009yzr.1_5'UTR|TMPRSS13_uc001prt.1_5'UTR|TMPRSS13_uc001pru.1_Missense_Mutation_p.G318E NM_001077263 NP_001070731 Q9BYE2 TMPSD_HUMAN transmembrane protease, serine 13 313 Extracellular (Potential).|SRCR. proteolysis integral to membrane scavenger receptor activity|serine-type endopeptidase activity pancreas(1) 1 all_hematologic(175;0.0487) Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234) BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106) 0.493333 114.14318 114.14649 37 38 KEEP --- --- --- --- TMPRSS4 56649 broad.mit.edu 37 11 117975472 117975472 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:117975472C>T uc010rxo.1 + 5 668 c.377C>T c.(376-378)GCC>GTC p.A126V TMPRSS4_uc010rxp.1_Missense_Mutation_p.A126V|TMPRSS4_uc010rxq.1_5'UTR|TMPRSS4_uc010rxr.1_Missense_Mutation_p.A101V|TMPRSS4_uc010rxs.1_Missense_Mutation_p.A86V|TMPRSS4_uc009yzu.2_RNA|TMPRSS4_uc010rxt.1_Missense_Mutation_p.A101V NM_019894 NP_063947 Q9NRS4 TMPS4_HUMAN transmembrane protease, serine 4 isoform 1 126 Extracellular (Potential).|SRCR. proteolysis integral to membrane scavenger receptor activity|serine-type endopeptidase activity large_intestine(1)|central_nervous_system(1) 2 all_hematologic(175;0.0487) Medulloblastoma(222;0.0431)|all_hematologic(192;0.164)|Breast(348;0.183)|all_neural(223;0.238) BRCA - Breast invasive adenocarcinoma(274;4.16e-05)|Epithelial(105;0.00204) 0.546875 113.13422 113.257537 35 29 KEEP --- --- --- --- IFT46 56912 broad.mit.edu 37 11 118430374 118430374 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:118430374G>A uc001ptp.1 - IFT46_uc001pto.1_Intron|IFT46_uc009zaf.1_Intron NM_020153 NP_064538 IFT46 flagellum assembly|intraflagellar transport|protein stabilization microtubule basal body|microtubule-based flagellum|nucleus protein C-terminus binding 0 1 29.218426 29.21452 8 0 KEEP --- --- --- --- CBL 867 broad.mit.edu 37 11 119158606 119158606 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:119158606C>T uc001pwe.2 + 12 2124 c.1986C>T c.(1984-1986)CCC>CCT p.P662P NM_005188 NP_005179 P22681 CBL_HUMAN Cas-Br-M (murine) ecotropic retroviral 662 Interaction with CD2AP.|Pro-rich. epidermal growth factor receptor signaling pathway|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of receptor-mediated endocytosis cytosol|nucleus calcium ion binding|sequence-specific DNA binding transcription factor activity|SH3 domain binding|signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding haematopoietic_and_lymphoid_tissue(135)|lung(10)|central_nervous_system(2)|ovary(1)|breast(1) 149 Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784) 309 CBL_gene-associated_Juvenile_Myelomonocytic_Leukemia_and_Developmental_Anomalies|Noonan_syndrome 0.26087 31.677192 34.06036 12 34 KEEP --- --- --- --- MFRP 83552 broad.mit.edu 37 11 119216905 119216905 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:119216905C>T uc001pwj.2 - MFRP_uc010rzf.1_Intron|MFRP_uc010rzg.1_Intron NM_031433 NP_113621 membrane frizzled-related protein collagen 0 Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224) BRCA - Breast invasive adenocarcinoma(274;3.84e-05) 0.7 23.727953 24.084978 7 3 KEEP --- --- --- --- SORL1 6653 broad.mit.edu 37 11 121445085 121445085 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:121445085C>T uc001pxx.2 + SORL1_uc010rzp.1_5'Flank NM_003105 NP_003096 sortilin-related receptor containing LDLR class cholesterol metabolic process|lipid transport|receptor-mediated endocytosis integral to plasma membrane|low-density lipoprotein particle low-density lipoprotein particle binding|transmembrane receptor activity ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)|pancreas(1) 15 Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113) BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108) 937 0.025862 -22.385891 6.488839 3 113 KEEP --- --- --- --- SORL1 6653 broad.mit.edu 37 11 121492872 121492872 + Silent SNP T A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:121492872T>A uc001pxx.2 + 45 6146 c.6066T>A c.(6064-6066)GTT>GTA p.V2022V SORL1_uc010rzp.1_Silent_p.V868V|SORL1_uc010rzq.1_Silent_p.V637V NM_003105 NP_003096 Q92673 SORL_HUMAN sortilin-related receptor containing LDLR class 2022 Extracellular (Potential).|Fibronectin type-III 5. cholesterol metabolic process|lipid transport|receptor-mediated endocytosis integral to plasma membrane|low-density lipoprotein particle low-density lipoprotein particle binding|transmembrane receptor activity ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)|pancreas(1) 15 Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113) BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108) 937 0.490909 84.020764 84.02477 27 28 KEEP --- --- --- --- GRAMD1B 57476 broad.mit.edu 37 11 123464753 123464753 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:123464753G>A uc001pyx.2 + GRAMD1B_uc001pyw.2_Intron|GRAMD1B_uc010rzw.1_Intron|GRAMD1B_uc010rzx.1_Intron|GRAMD1B_uc009zbe.1_Intron NM_020716 NP_065767 GRAM domain containing 1B integral to membrane ovary(1) 1 Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394) 1503 0.3 17.943123 18.657308 6 14 KEEP --- --- --- --- Unknown broad.mit.edu 37 11 123676006 123676006 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:123676006C>T OR6X1 (50780 upstream) : OR6M1 (111 downstream) 0.5 14.873916 14.873916 5 5 KEEP --- --- --- --- CCDC15 80071 broad.mit.edu 37 11 124857042 124857042 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:124857042C>T uc001qbm.3 + 8 1179 c.920C>T c.(919-921)CCA>CTA p.P307L NM_025004 NP_079280 Q0P6D6 CCD15_HUMAN coiled-coil domain containing 15 307 centrosome ovary(1)|central_nervous_system(1) 2 all_hematologic(175;0.215) Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;1.68e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0413) 0.413793 40.695314 40.883456 12 17 KEEP --- --- --- --- ACRV1 56 broad.mit.edu 37 11 125546335 125546335 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:125546335C>T uc001qcs.2 - 3 859 c.592G>A c.(592-594)GAT>AAT p.D198N ACRV1_uc001qck.2_Missense_Mutation_p.D109N|ACRV1_uc001qcl.2_Missense_Mutation_p.D128N|ACRV1_uc001qcm.2_Missense_Mutation_p.D54N|ACRV1_uc001qcn.2_Missense_Mutation_p.D143N|ACRV1_uc001qco.2_Missense_Mutation_p.D103N|ACRV1_uc001qcp.2_Intron|ACRV1_uc001qcq.2_Intron|ACRV1_uc001qcr.2_Missense_Mutation_p.D179N NM_001612 NP_001603 P26436 ASPX_HUMAN acrosomal vesicle protein 1 isoform a precursor 198 multicellular organismal development acrosomal vesicle 0 all_hematologic(175;0.177) Breast(109;0.0021)|all_lung(97;0.0179)|Lung NSC(97;0.0185)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0713) 0.485507 214.715183 214.740622 67 71 KEEP --- --- --- --- GLB1L2 89944 broad.mit.edu 37 11 134244224 134244224 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr11:134244224G>A uc001qhp.2 + GLB1L2_uc009zdg.1_Intron NM_138342 NP_612351 galactosidase, beta 1-like 2 precursor carbohydrate metabolic process extracellular region cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds ovary(1)|pancreas(1)|skin(1) 3 all_hematologic(175;0.127) all_cancers(12;2.85e-18)|all_epithelial(12;1.21e-12)|all_lung(97;0.000276)|Lung NSC(97;0.000518)|Breast(109;0.00122)|Medulloblastoma(222;0.0399)|all_neural(223;0.0412)|Esophageal squamous(93;0.0844) Epithelial(10;1.37e-11)|all cancers(11;2.2e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000885)|Lung(977;0.223) 1 100.699649 100.699649 26 0 KEEP --- --- --- --- WNK1 65125 broad.mit.edu 37 12 1009546 1009546 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:1009546C>T uc001qio.3 + WNK1_uc001qip.3_Intron|WNK1_uc001qir.3_Intron|WNK1_uc009zdm.1_5'Flank|WNK1_uc009zdn.1_5'Flank|uc009zdo.1_5'Flank NM_018979 NP_061852 WNK lysine deficient protein kinase 1 intracellular protein kinase cascade|ion transport|neuron development cytoplasm ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1) 23 all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632) Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197) Colon(19;451 567 6672 12618 28860) 913 0.541667 43.176503 43.212665 13 11 KEEP --- --- --- --- ITFG2 55846 broad.mit.edu 37 12 2921788 2921788 + 5'Flank SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:2921788G>A uc001qlb.1 + ITFG2_uc001qla.1_5'Flank|ITFG2_uc010seb.1_5'Flank|ITFG2_uc010sec.1_5'Flank NM_018463 NP_060933 integrin alpha FG-GAP repeat containing 2 0 OV - Ovarian serous cystadenocarcinoma(31;0.000818) 0.666667 19.652564 19.87391 6 3 KEEP --- --- --- --- TULP3 7289 broad.mit.edu 37 12 3046877 3046877 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:3046877C>T uc010seh.1 + 9 1086 c.1005C>T c.(1003-1005)ATC>ATT p.I335I TULP3_uc010sef.1_RNA|TULP3_uc009zec.1_Silent_p.I62I|TULP3_uc010seg.1_RNA|TULP3_uc001qlj.2_Silent_p.I335I|TULP3_uc010sei.1_Intron NM_003324 NP_003315 O75386 TULP3_HUMAN tubby like protein 3 isoform 1 335 G-protein coupled receptor protein signaling pathway|regulation of transcription, DNA-dependent cytoplasm|extracellular region|nucleus|plasma membrane phosphatidylinositol-4,5-bisphosphate binding 0 OV - Ovarian serous cystadenocarcinoma(31;0.000818) 0.444444 23.895734 23.944353 8 10 KEEP --- --- --- --- PRMT8 56341 broad.mit.edu 37 12 3702376 3702376 + 3'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:3702376G>A uc001qmf.2 + 10 PRMT8_uc009zed.2_3'UTR|PRMT8_uc001qmg.2_3'UTR|PRMT8_uc001qmh.2_RNA NM_019854 NP_062828 HMT1 hnRNP methyltransferase-like 4 regulation of protein binding cytoplasm|plasma membrane histone-arginine N-methyltransferase activity|protein heterodimerization activity|protein homodimerization activity|protein-arginine omega-N asymmetric methyltransferase activity|protein-arginine omega-N monomethyltransferase activity ovary(3)|central_nervous_system(1)|skin(1) 5 OV - Ovarian serous cystadenocarcinoma(31;0.0109)|COAD - Colon adenocarcinoma(12;0.0264) 0.571429 27.10198 27.16427 8 6 KEEP --- --- --- --- EFCAB4B 84766 broad.mit.edu 37 12 3782807 3782808 + Intron DNP GG AA AA MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:3782807_3782808GG>AA uc001qmj.2 - EFCAB4B_uc010sen.1_Intron|EFCAB4B_uc010seo.1_Intron|EFCAB4B_uc001qmi.1_5'Flank NM_032680 NP_116069 EF-hand calcium binding domain 4B isoform c activation of store-operated calcium channel activity|store-operated calcium entry cytoplasm calcium ion binding|protein binding ovary(1)|pancreas(1) 2 OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264) 0.363636 24.993923 25.353919 8 14 KEEP --- --- --- --- PARP11 57097 broad.mit.edu 37 12 3951834 3951834 + Intron SNP G C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:3951834G>C uc001qml.2 - PARP11_uc009zef.2_Intron|PARP11_uc001qmm.2_Intron|PARP11_uc001qmn.2_Intron NM_020367 NP_065100 poly (ADP-ribose) polymerase family, member 11 NAD+ ADP-ribosyltransferase activity ovary(1)|central_nervous_system(1) 2 all cancers(3;1.58e-07)|OV - Ovarian serous cystadenocarcinoma(31;0.00287)|GBM - Glioblastoma multiforme(3;0.0141)|COAD - Colon adenocarcinoma(12;0.0264) 0.375 8.922895 9.032691 3 5 KEEP --- --- --- --- VWF 7450 broad.mit.edu 37 12 6080927 6080928 + Intron DNP GG AA AA MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:6080927_6080928GG>AA uc001qnn.1 - VWF_uc010set.1_Intron NM_000552 NP_000543 von Willebrand factor preproprotein blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1) 12 Antihemophilic Factor(DB00025) 0.448276 40.771996 40.83949 13 16 KEEP --- --- --- --- LRRC23 10233 broad.mit.edu 37 12 7019120 7019120 + Nonsense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:7019120C>T uc001qrt.3 + 6 1080 c.688C>T c.(688-690)CGA>TGA p.R230* LRRC23_uc001qrp.2_Nonsense_Mutation_p.R230*|LRRC23_uc001qrq.2_Nonsense_Mutation_p.R230*|LRRC23_uc001qrr.2_Nonsense_Mutation_p.R179*|LRRC23_uc001qrs.2_Nonsense_Mutation_p.R179*|LRRC23_uc009zfh.2_Intron NM_001135217 NP_001128689 Q53EV4 LRC23_HUMAN leucine rich repeat containing 23 isoform a 230 LRR 7. ovary(1) 1 0.512195 211.727942 211.743833 63 60 KEEP --- --- --- --- CLSTN3 9746 broad.mit.edu 37 12 7295638 7295638 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:7295638C>T uc001qsr.2 + CLSTN3_uc001qss.2_Intron NM_014718 NP_055533 calsyntenin 3 precursor homophilic cell adhesion endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane calcium ion binding large_intestine(1) 1 0.423077 70.940137 71.208919 22 30 KEEP --- --- --- --- PEX5 5830 broad.mit.edu 37 12 7362862 7362862 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:7362862C>T uc009zfu.1 + PEX5_uc001qsw.2_3'UTR|PEX5_uc010sgc.1_3'UTR|PEX5_uc001qsu.2_3'UTR|PEX5_uc010sgd.1_3'UTR|PEX5_uc001qsv.2_3'UTR NM_001131026 NP_001124498 peroxisomal biogenesis factor 5 isoform d protein import into peroxisome matrix, translocation|protein targeting to peroxisome|protein tetramerization|protein transport cytosol|peroxisomal matrix|peroxisomal membrane peroxisome matrix targeting signal-1 binding|protein C-terminus binding|protein N-terminus binding ovary(1) 1 0.533333 78.404778 78.448545 24 21 KEEP --- --- --- --- ACSM4 341392 broad.mit.edu 37 12 7474890 7474890 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:7474890G>A uc001qsx.1 + NM_001080454 NP_001073923 acyl-CoA synthetase medium-chain family member 4 fatty acid metabolic process mitochondrial matrix ATP binding|butyrate-CoA ligase activity|metal ion binding 0 0.333333 17.743903 18.186763 6 12 KEEP --- --- --- --- CD163 9332 broad.mit.edu 37 12 7634991 7634991 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:7634991G>A uc001qsz.3 - CD163_uc001qta.3_Intron|CD163_uc009zfw.2_Intron NM_004244 NP_004235 CD163 antigen isoform a acute-phase response extracellular region|integral to plasma membrane protein binding|scavenger receptor activity ovary(6)|pancreas(1)|skin(1) 8 0.375 9.322876 9.432687 3 5 KEEP --- --- --- --- CD163 9332 broad.mit.edu 37 12 7640471 7640471 + Missense_Mutation SNP A C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:7640471A>C uc001qsz.3 - 7 1761 c.1633T>G c.(1633-1635)TTC>GTC p.F545V CD163_uc001qta.3_Missense_Mutation_p.F545V|CD163_uc009zfw.2_Missense_Mutation_p.F545V NM_004244 NP_004235 Q86VB7 C163A_HUMAN CD163 antigen isoform a 545 SRCR 5.|Extracellular (Potential). acute-phase response extracellular region|integral to plasma membrane protein binding|scavenger receptor activity ovary(6)|pancreas(1)|skin(1) 8 0.493827 147.999769 148.00244 40 41 KEEP --- --- --- --- CD163 9332 broad.mit.edu 37 12 7651606 7651606 + Silent SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:7651606A>G uc001qsz.3 - 4 764 c.636T>C c.(634-636)TCT>TCC p.S212S CD163_uc001qta.3_Silent_p.S212S|CD163_uc009zfw.2_Silent_p.S212S NM_004244 NP_004235 Q86VB7 C163A_HUMAN CD163 antigen isoform a 212 SRCR 2.|Extracellular (Potential). acute-phase response extracellular region|integral to plasma membrane protein binding|scavenger receptor activity ovary(6)|pancreas(1)|skin(1) 8 0.481781 441.826186 441.8964 119 128 KEEP --- --- --- --- Unknown broad.mit.edu 37 12 8787742 8787742 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:8787742G>A AICDA (22300 upstream) : MFAP5 (10798 downstream) 0.408163 66.190899 66.552076 20 29 KEEP --- --- --- --- A2ML1 144568 broad.mit.edu 37 12 8976141 8976141 + Intron SNP T A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:8976141T>A uc001quz.3 + NM_144670 NP_653271 alpha-2-macroglobulin-like 1 precursor extracellular space endopeptidase inhibitor activity ovary(2)|skin(1) 3 0.461538 20.448591 20.465343 6 7 KEEP --- --- --- --- A2ML1 144568 broad.mit.edu 37 12 8988948 8988948 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:8988948G>A uc001quz.3 + NM_144670 NP_653271 alpha-2-macroglobulin-like 1 precursor extracellular space endopeptidase inhibitor activity ovary(2)|skin(1) 3 0.470588 49.596772 49.622437 16 18 KEEP --- --- --- --- A2ML1 144568 broad.mit.edu 37 12 8994182 8994182 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:8994182G>A uc001quz.3 + A2ML1_uc001qva.1_5'Flank NM_144670 NP_653271 alpha-2-macroglobulin-like 1 precursor extracellular space endopeptidase inhibitor activity ovary(2)|skin(1) 3 0.392857 36.118801 36.400325 11 17 KEEP --- --- --- --- PRB3 5544 broad.mit.edu 37 12 11420548 11420548 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:11420548C>T uc001qzs.2 - 3 673 c.635G>A c.(634-636)GGA>GAA p.G212E PRB4_uc001qzf.1_Intron NM_006249 NP_006240 Q04118 PRB3_HUMAN proline-rich protein BstNI subfamily 3 212 10 X 21 AA tandem repeats of [RH]-P-G-K- P-[EQ]-G-[PQS]-P-[PS]-Q-[GE]-G-N-[QK]- [SP]-[QR]-[GR]-P-P-P.|8.|Pro-rich. Missing (in allele S). extracellular region Gram-negative bacterial cell surface binding skin(1) 1 OV - Ovarian serous cystadenocarcinoma(49;0.201) 0.041667 -58.174959 28.541179 16 368 KEEP --- --- --- --- PRB3 5544 broad.mit.edu 37 12 11420611 11420611 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:11420611C>T uc001qzs.2 - 3 610 c.572G>A c.(571-573)GGA>GAA p.G191E PRB4_uc001qzf.1_Intron NM_006249 NP_006240 Q04118 PRB3_HUMAN proline-rich protein BstNI subfamily 3 191 10 X 21 AA tandem repeats of [RH]-P-G-K- P-[EQ]-G-[PQS]-P-[PS]-Q-[GE]-G-N-[QK]- [SP]-[QR]-[GR]-P-P-P.|7.|Pro-rich. Missing (in allele S). extracellular region Gram-negative bacterial cell surface binding skin(1) 1 OV - Ovarian serous cystadenocarcinoma(49;0.201) 0.687831 402.89649 408.712053 130 59 KEEP --- --- --- --- KIAA1467 57613 broad.mit.edu 37 12 13208704 13208704 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:13208704C>T uc001rbi.2 + 2 280 c.257C>T c.(256-258)CCC>CTC p.P86L KIAA1467_uc009zhx.1_RNA NM_020853 NP_065904 A2RU67 K1467_HUMAN hypothetical protein LOC57613 86 integral to membrane central_nervous_system(2)|skin(1) 3 Prostate(47;0.184) BRCA - Breast invasive adenocarcinoma(232;0.157) 0.359223 117.674137 119.459516 37 66 KEEP --- --- --- --- GSG1 83445 broad.mit.edu 37 12 13243455 13243455 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:13243455C>T uc001rbn.2 - 2 519 c.346G>A c.(346-348)GAA>AAA p.E116K GSG1_uc001rbj.2_Missense_Mutation_p.E103K|GSG1_uc001rbk.2_Missense_Mutation_p.E103K|GSG1_uc001rbl.2_Missense_Mutation_p.E103K|GSG1_uc001rbm.2_Missense_Mutation_p.E103K|GSG1_uc001rbo.2_Missense_Mutation_p.E116K|GSG1_uc001rbp.2_Missense_Mutation_p.E116K|GSG1_uc001rbq.1_Missense_Mutation_p.E116K NM_001080555 NP_001074024 Q2KHT4 GSG1_HUMAN germ cell associated 1 isoform 4 103 endoplasmic reticulum membrane|integral to membrane 0 Prostate(47;0.183) BRCA - Breast invasive adenocarcinoma(232;0.15) 0.45 114.411038 114.581637 36 44 KEEP --- --- --- --- PTPRO 5800 broad.mit.edu 37 12 15704439 15704439 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:15704439C>T uc001rcv.1 + PTPRO_uc001rcw.1_Intron|PTPRO_uc001rcx.1_Intron|PTPRO_uc001rcy.1_Intron|PTPRO_uc001rcz.1_Intron|PTPRO_uc001rda.1_Intron NM_030667 NP_109592 receptor-type protein tyrosine phosphatase O integral to plasma membrane protein binding|transmembrane receptor protein tyrosine phosphatase activity skin(5)|ovary(2)|upper_aerodigestive_tract(1)|lung(1) 9 Hepatocellular(102;0.244) 0.977778 171.310077 173.605346 44 1 KEEP --- --- --- --- PDE3A 5139 broad.mit.edu 37 12 20709514 20709514 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:20709514G>A uc001reh.1 + NM_000921 NP_000912 phosphodiesterase 3A lipid metabolic process|platelet activation|signal transduction cytosol|integral to membrane 3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity|metal ion binding ovary(3)|upper_aerodigestive_tract(1) 4 Esophageal squamous(101;0.125) Breast(259;0.134) Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Cilostazol(DB01166)|Enoximone(DB04880)|Milrinone(DB00235)|Theophylline(DB00277) 0.357143 14.970681 15.222537 5 9 KEEP --- --- --- --- SLCO1B3 28234 broad.mit.edu 37 12 21007938 21007938 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:21007938C>T uc001rek.2 + SLCO1B3_uc001rel.2_Intron|SLCO1B3_uc010sil.1_Intron|LST-3TM12_uc010sim.1_Intron NM_019844 NP_062818 solute carrier organic anion transporter family, bile acid metabolic process|sodium-independent organic anion transport basolateral plasma membrane|cytoplasm|integral to plasma membrane bile acid transmembrane transporter activity|organic anion transmembrane transporter activity large_intestine(2)|ovary(1)|skin(1) 4 Esophageal squamous(101;0.149) 0.27027 28.232569 29.994601 10 27 KEEP --- --- --- --- SLCO1B3 28234 broad.mit.edu 37 12 21013935 21013935 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:21013935C>T uc001rek.2 + SLCO1B3_uc001rel.2_Intron|SLCO1B3_uc010sil.1_Intron|LST-3TM12_uc010sim.1_Intron|SLCO1B3_uc001reo.2_5'Flank NM_019844 NP_062818 solute carrier organic anion transporter family, bile acid metabolic process|sodium-independent organic anion transport basolateral plasma membrane|cytoplasm|integral to plasma membrane bile acid transmembrane transporter activity|organic anion transmembrane transporter activity large_intestine(2)|ovary(1)|skin(1) 4 Esophageal squamous(101;0.149) 0.612245 103.460062 104.000455 30 19 KEEP --- --- --- --- MED21 9412 broad.mit.edu 37 12 27180320 27180320 + Silent SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:27180320A>G uc001rhp.1 + 3 228 c.198A>G c.(196-198)GCA>GCG p.A66A MED21_uc009zjh.1_RNA NM_004264 NP_004255 Q13503 MED21_HUMAN mediator complex subunit 21 66 positive regulation of transcription from RNA polymerase II promoter mediator complex DNA-directed RNA polymerase activity|transcription coactivator activity 0 Colorectal(261;0.0847) 0.434109 186.083033 186.571092 56 73 KEEP --- --- --- --- CCDC91 55297 broad.mit.edu 37 12 28412215 28412215 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:28412215C>T uc001riq.2 + CCDC91_uc001rio.2_Intron|CCDC91_uc009zjk.2_Intron|CCDC91_uc001rip.1_Intron NM_018318 NP_060788 GGA binding partner protein transport Golgi apparatus|membrane central_nervous_system(1) 1 Acute lymphoblastic leukemia(23;0.00718)|all_hematologic(23;0.0113)|Lung SC(9;0.184) 0.565217 47.57839 47.663607 13 10 KEEP --- --- --- --- TMTC1 83857 broad.mit.edu 37 12 29725149 29725149 + Missense_Mutation SNP G C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:29725149G>C uc001rjb.2 - 9 1571 c.1097C>G c.(1096-1098)TCT>TGT p.S366C TMTC1_uc001riz.2_Missense_Mutation_p.S123C|TMTC1_uc001rja.2_Missense_Mutation_p.S210C|TMTC1_uc001rjc.1_Missense_Mutation_p.S428C NM_175861 NP_787057 Q8IUR5 TMTC1_HUMAN transmembrane and tetratricopeptide repeat 474 integral to membrane binding 0 Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032) 0.5 119.502586 119.502586 32 32 KEEP --- --- --- --- DENND5B 160518 broad.mit.edu 37 12 31600582 31600582 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:31600582G>A uc001rki.1 - 6 1937 c.1751C>T c.(1750-1752)CCT>CTT p.P584L DENND5B_uc001rkh.1_Missense_Mutation_p.P619L|DENND5B_uc009zjq.1_Intron|DENND5B_uc001rkj.2_Missense_Mutation_p.P606L NM_144973 NP_659410 Q6ZUT9 DEN5B_HUMAN DENN/MADD domain containing 5B 584 integral to membrane ovary(1)|central_nervous_system(1) 2 0.545455 41.601933 41.641439 12 10 KEEP --- --- --- --- H3F3C 440093 broad.mit.edu 37 12 31944955 31944955 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:31944955C>T uc001rkr.2 - 1 221 c.146G>A c.(145-147)CGA>CAA p.R49Q NM_001013699 NP_001013721 Q6NXT2 H3C_HUMAN histone H3-like 49 nucleosome assembly nucleosome|nucleus DNA binding 0 HNSCC(67;0.2) 0.530303 117.232799 117.285975 35 31 KEEP --- --- --- --- FGD4 121512 broad.mit.edu 37 12 32729368 32729368 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:32729368G>A uc001rkz.2 + 3 554 c.77G>A c.(76-78)CGC>CAC p.R26H FGD4_uc001rlc.2_Missense_Mutation_p.R111H|FGD4_uc001rky.2_5'UTR|FGD4_uc001rla.2_5'UTR|FGD4_uc010ske.1_Missense_Mutation_p.R138H|FGD4_uc001rkx.3_Missense_Mutation_p.R26H NM_139241 NP_640334 Q96M96 FGD4_HUMAN FYVE, RhoGEF and PH domain containing 4 26 Actin filament-binding (By similarity). actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction cytoskeleton|cytosol|filopodium|Golgi apparatus|lamellipodium|ruffle metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding ovary(2)|central_nervous_system(1) 3 Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204) 0.461538 78.499641 78.565969 24 28 KEEP --- --- --- --- FGD4 121512 broad.mit.edu 37 12 32778579 32778579 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:32778579C>T uc001rkz.2 + FGD4_uc001rlc.2_Intron|FGD4_uc001rky.2_Intron|FGD4_uc001rla.2_Intron|FGD4_uc010ske.1_Intron|FGD4_uc001rlb.1_Intron NM_139241 NP_640334 FYVE, RhoGEF and PH domain containing 4 actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction cytoskeleton|cytosol|filopodium|Golgi apparatus|lamellipodium|ruffle metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding ovary(2)|central_nervous_system(1) 3 Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204) 0.404255 63.716908 64.093337 19 28 KEEP --- --- --- --- DNM1L 10059 broad.mit.edu 37 12 32890774 32890774 + Intron SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:32890774T>C uc001rld.2 + DNM1L_uc001rle.2_Intron|DNM1L_uc001rlf.2_Intron|DNM1L_uc010skh.1_Intron|DNM1L_uc001rlg.2_Intron|DNM1L_uc001rlh.2_Intron|DNM1L_uc010ski.1_Intron NM_012062 NP_036192 dynamin 1-like isoform 1 cellular component disassembly involved in apoptosis|mitochondrial fragmentation involved in apoptosis|mitochondrial membrane organization|positive regulation of mitochondrial fission cis-Golgi network|cytosol|endomembrane system|endoplasmic reticulum|mitochondrial outer membrane GTP binding|GTPase activity|ubiquitin protein ligase binding ovary(1)|pancreas(1) 2 Lung NSC(5;2.15e-06)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239) 0.035294 -13.151452 6.797475 3 82 KEEP --- --- --- --- SYT10 341359 broad.mit.edu 37 12 33538124 33538124 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:33538124C>T uc001rll.1 - 4 1477 c.1180G>A c.(1180-1182)GAT>AAT p.D394N SYT10_uc009zju.1_Missense_Mutation_p.D204N NM_198992 NP_945343 Q6XYQ8 SYT10_HUMAN synaptotagmin X 394 C2 2.|Cytoplasmic (Potential). cell junction|integral to membrane|synaptic vesicle membrane metal ion binding|transporter activity ovary(1)|skin(1) 2 Lung NSC(5;8.37e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0334) 0.389831 71.423381 72.046503 23 36 KEEP --- --- --- --- Unknown broad.mit.edu 37 12 37935727 37935727 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:37935727G>A None (None upstream) : ALG10B (774830 downstream) 0.375 9.32292 9.432713 3 5 KEEP --- --- --- --- PPHLN1 51535 broad.mit.edu 37 12 42745864 42745864 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:42745864C>T uc001rng.1 + PPHLN1_uc001rmy.2_Intron|PPHLN1_uc001rna.2_Intron|PPHLN1_uc001rne.2_Intron|PPHLN1_uc001rnb.2_Intron|PPHLN1_uc001rnd.2_Intron|PPHLN1_uc001rnc.2_Intron|PPHLN1_uc001rnf.2_Intron|PPHLN1_uc010skq.1_Intron|PPHLN1_uc010skr.1_Intron|PPHLN1_uc010sks.1_Intron|PPHLN1_uc010skt.1_Intron|PPHLN1_uc001rni.1_Intron|PPHLN1_uc001rnh.1_Intron|PPHLN1_uc010sku.1_Intron NM_016488 NP_057572 periphilin 1 isoform 1 keratinization cytoplasm|nucleus ovary(1)|breast(1) 2 all_cancers(12;0.00049)|Breast(8;0.165) Lung NSC(34;0.123) GBM - Glioblastoma multiforme(48;0.0875) 0.434783 62.393262 62.563858 20 26 KEEP --- --- --- --- ADAMTS20 80070 broad.mit.edu 37 12 43777744 43777744 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:43777744C>T uc010skx.1 - 30 4489 c.4489G>A c.(4489-4491)GAT>AAT p.D1497N NM_025003 NP_079279 P59510 ATS20_HUMAN a disintegrin-like and metalloprotease with 1497 TSP type-1 12. proteinaceous extracellular matrix zinc ion binding central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1) 19 all_cancers(12;2.6e-05)|Lung SC(27;0.184) Lung NSC(34;0.0569)|all_lung(34;0.129) GBM - Glioblastoma multiforme(48;0.0473) p.D1497N(MKN1-Tumor) 2149 0.396552 70.821316 71.36155 23 35 KEEP --- --- --- --- Unknown broad.mit.edu 37 12 43965360 43965360 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:43965360C>T ADAMTS20 (19636 upstream) : PUS7L (157054 downstream) 0.444444 26.898137 26.946502 8 10 KEEP --- --- --- --- DBX2 440097 broad.mit.edu 37 12 45417411 45417411 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:45417411C>T uc001rok.1 - NM_001004329 NP_001004329 developing brain homeobox 2 nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 Lung SC(27;0.192) Lung NSC(34;0.142) GBM - Glioblastoma multiforme(48;0.0515) 0.513158 271.054382 271.077339 78 74 KEEP --- --- --- --- LALBA 3906 broad.mit.edu 37 12 48962398 48962398 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:48962398G>A uc001rrt.2 - NM_002289 NP_002280 lactalbumin, alpha- precursor cell-cell signaling|defense response to bacterium|induction of apoptosis|lactose biosynthetic process|signal transduction extracellular space calcium ion binding|lactose synthase activity 0 0.461538 100.245162 100.328797 30 35 KEEP --- --- --- --- ADCY6 112 broad.mit.edu 37 12 49176645 49176645 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:49176645G>A uc001rsh.3 - 1 1233 c.573C>T c.(571-573)TTC>TTT p.F191F ADCY6_uc001rsj.3_Silent_p.F191F|ADCY6_uc001rsi.3_Silent_p.F191F NM_015270 NP_056085 O43306 ADCY6_HUMAN adenylate cyclase 6 isoform a 191 Helical; (Potential). activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport integral to membrane ATP binding|metal ion binding 0 0.444444 38.797473 38.869934 12 15 KEEP --- --- --- --- KCNH3 23416 broad.mit.edu 37 12 49951829 49951829 + 3'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:49951829G>A uc001ruh.1 + 15 KCNH3_uc010smj.1_3'UTR NM_012284 NP_036416 potassium voltage-gated channel, subfamily H regulation of transcription, DNA-dependent integral to membrane two-component sensor activity|voltage-gated potassium channel activity 0 0.538462 22.62527 22.641917 7 6 KEEP --- --- --- --- TFCP2 7024 broad.mit.edu 37 12 51489634 51489634 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:51489634G>A uc001rxw.2 - TFCP2_uc001rxv.1_Intron|TFCP2_uc009zlx.1_Intron|TFCP2_uc001rxx.2_Intron NM_005653 NP_005644 transcription factor CP2 regulation of transcription from RNA polymerase II promoter nucleus DNA binding|protein binding|sequence-specific DNA binding transcription factor activity ovary(1) 1 0.666667 15.002103 15.149638 4 2 KEEP --- --- --- --- SCN8A 6334 broad.mit.edu 37 12 52100453 52100453 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:52100453G>A uc001ryw.2 + 11 1767 c.1589G>A c.(1588-1590)CGG>CAG p.R530Q SCN8A_uc010snl.1_Missense_Mutation_p.R395Q|SCN8A_uc001ryx.1_Missense_Mutation_p.R395Q|SCN8A_uc001ryz.1_Missense_Mutation_p.R395Q|SCN8A_uc001ryy.2_Missense_Mutation_p.R395Q NM_014191 NP_055006 Q9UQD0 SCN8A_HUMAN sodium channel, voltage gated, type VIII, alpha 530 axon guidance|myelination|peripheral nervous system development cytoplasmic membrane-bounded vesicle|node of Ranvier ATP binding|voltage-gated sodium channel activity ovary(7) 7 BRCA - Breast invasive adenocarcinoma(357;0.181) Lamotrigine(DB00555) 0.285714 10.391374 10.970335 4 10 KEEP --- --- --- --- SCN8A 6334 broad.mit.edu 37 12 52188138 52188138 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:52188138C>T uc001ryw.2 + NM_014191 NP_055006 sodium channel, voltage gated, type VIII, alpha axon guidance|myelination|peripheral nervous system development cytoplasmic membrane-bounded vesicle|node of Ranvier ATP binding|voltage-gated sodium channel activity ovary(7) 7 BRCA - Breast invasive adenocarcinoma(357;0.181) Lamotrigine(DB00555) 0.506667 131.651389 131.654284 38 37 KEEP --- --- --- --- KRT77 374454 broad.mit.edu 37 12 53091504 53091504 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:53091504G>A uc001saw.2 - 2 749 c.720C>T c.(718-720)GTC>GTT p.V240V KRT77_uc009zmi.2_5'UTR NM_175078 NP_778253 Q7Z794 K2C1B_HUMAN keratin 77 240 Coil 1B.|Rod. keratin filament structural molecule activity ovary(1) 1 0.491954 672.601041 672.626069 214 221 KEEP --- --- --- --- MAP3K12 7786 broad.mit.edu 37 12 53878772 53878772 + Intron SNP G T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:53878772G>T uc001sdm.1 - MAP3K12_uc001sdn.1_Intron NM_006301 NP_006292 mitogen-activated protein kinase kinase kinase histone phosphorylation|JNK cascade|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation cytosol|membrane fraction|plasma membrane ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein homodimerization activity|protein kinase binding lung(2)|ovary(1)|breast(1)|skin(1) 5 178 0.615385 27.403096 27.554927 8 5 KEEP --- --- --- --- PDE1B 5153 broad.mit.edu 37 12 54966387 54966387 + Silent SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:54966387T>C uc001sgd.1 + 7 763 c.597T>C c.(595-597)ATT>ATC p.I199I PDE1B_uc010soz.1_Silent_p.I62I|PDE1B_uc010spa.1_Silent_p.I158I|PDE1B_uc001sgf.2_Silent_p.I62I|PDE1B_uc001sge.2_Silent_p.I179I|PDE1B_uc009znq.2_5'UTR NM_000924 NP_000915 Q01064 PDE1B_HUMAN phosphodiesterase 1B isoform 1 199 Catalytic (By similarity). activation of phospholipase C activity|apoptosis|nerve growth factor receptor signaling pathway|platelet activation cytosol|nucleus 3',5'-cyclic-AMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding upper_aerodigestive_tract(1)|ovary(1) 2 0.026862 -152.859824 49.662664 22 797 KEEP --- --- --- --- OR6C74 254783 broad.mit.edu 37 12 55641781 55641781 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:55641781C>T uc010spg.1 + 1 710 c.710C>T c.(709-711)TCT>TTT p.S237F NM_001005490 NP_001005490 A6NCV1 O6C74_HUMAN olfactory receptor, family 6, subfamily C, 237 Cytoplasmic (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity central_nervous_system(1) 1 0.391304 113.078269 114.030767 36 56 KEEP --- --- --- --- OR6C65 403282 broad.mit.edu 37 12 55794568 55794568 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:55794568G>A uc010spl.1 + 1 256 c.256G>A c.(256-258)GGA>AGA p.G86R NM_001005518 NP_001005518 A6NJZ3 O6C65_HUMAN olfactory receptor, family 6, subfamily C, 86 Extracellular (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity 0 0.432692 153.16927 153.578042 45 59 KEEP --- --- --- --- SPRYD4 283377 broad.mit.edu 37 12 56862263 56862264 + 5'Flank DNP CC TT TT MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:56862263_56862264CC>TT uc001sli.3 + SPRYD4_uc010sqo.1_5'Flank NM_207344 NP_997227 SPRY domain containing 4 nucleus 0 0.5 34.824515 34.824515 11 11 KEEP --- --- --- --- ATP5B 506 broad.mit.edu 37 12 57033156 57033156 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:57033156G>A uc001slr.2 - BAZ2A_uc001slq.1_5'Flank|BAZ2A_uc010sqr.1_5'Flank NM_001686 NP_001677 mitochondrial ATP synthase beta subunit angiogenesis|ATP hydrolysis coupled proton transport|regulation of intracellular pH|respiratory electron transport chain cell surface|mitochondrial nucleoid|mitochondrial proton-transporting ATP synthase, catalytic core|plasma membrane ATP binding|eukaryotic cell surface binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|hydrogen-exporting ATPase activity, phosphorylative mechanism|MHC class I protein binding|proton-transporting ATPase activity, rotational mechanism ovary(1) 1 0.478261 38.6243 38.633745 11 12 KEEP --- --- --- --- LRP1 4035 broad.mit.edu 37 12 57577299 57577300 + Intron DNP CC TT TT MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:57577299_57577300CC>TT uc001snd.2 + NM_002332 NP_002323 low density lipoprotein-related protein 1 aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity coated pit|integral to plasma membrane|nucleus apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2) 22 BRCA - Breast invasive adenocarcinoma(357;0.0103) Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031) 1456 0.615385 27.502966 27.654673 8 5 KEEP --- --- --- --- GLI1 2735 broad.mit.edu 37 12 57858619 57858619 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:57858619C>T uc001snx.2 + 4 435 c.357C>T c.(355-357)GGC>GGT p.G119G GLI1_uc009zpp.2_RNA|GLI1_uc009zpq.2_5'UTR|GLI1_uc009zpr.1_RNA NM_005269 NP_005260 P08151 GLI1_HUMAN GLI family zinc finger 1 isoform 1 119 epidermal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|osteoblast differentiation|positive regulation of DNA replication|positive regulation of smoothened signaling pathway|positive regulation of transcription from RNA polymerase II promoter cytosol|nucleus transcription regulatory region DNA binding|zinc ion binding skin(4)|ovary(4)|breast(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)|pancreas(1) 15 GBM - Glioblastoma multiforme(3;3.99e-32) Pancreas(157;841 1936 10503 41495 50368) 277 0.489362 147.151592 147.160538 46 48 KEEP --- --- --- --- ARHGAP9 64333 broad.mit.edu 37 12 57870777 57870777 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:57870777G>A uc001sod.2 - ARHGAP9_uc001sny.2_5'Flank|ARHGAP9_uc001snz.2_Intron|ARHGAP9_uc001soa.2_Intron|ARHGAP9_uc001sob.2_Intron|ARHGAP9_uc001soc.2_Intron|ARHGAP9_uc001soe.1_Intron|ARHGAP9_uc010sro.1_3'UTR NM_032496 NP_115885 Rho GTPase activating protein 9 isoform 1 regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction cytosol GTPase activator activity|protein binding lung(1) 1 GBM - Glioblastoma multiforme(3;3.37e-34) 0.652174 54.530745 55.000521 15 8 KEEP --- --- --- --- GEFT 115557 broad.mit.edu 37 12 58006920 58006920 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:58006920C>T uc001spb.2 + 2 765 c.305C>T c.(304-306)CCA>CTA p.P102L GEFT_uc009zpy.2_Missense_Mutation_p.P141L|GEFT_uc001soz.1_Intron|GEFT_uc001spa.2_5'UTR|uc001spc.2_RNA|GEFT_uc001spd.2_5'Flank NM_182947 NP_891992 Q86VW2 ARHGP_HUMAN RhoA/RAC/CDC42 exchange factor isoform 1 102 regulation of Rho protein signal transduction cytosol|plasma membrane|sarcomere Rho guanyl-nucleotide exchange factor activity 0 Melanoma(17;0.122) 0.576923 48.327964 48.461986 15 11 KEEP --- --- --- --- Unknown broad.mit.edu 37 12 59447486 59447486 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:59447486C>T LRIG3 (133224 upstream) : SLC16A7 (542362 downstream) 0.6 83.308717 83.658877 24 16 KEEP --- --- --- --- GRIP1 23426 broad.mit.edu 37 12 66856711 66856711 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:66856711G>A uc001stk.2 - 9 1276 c.1035C>T c.(1033-1035)CCC>CCT p.P345P GRIP1_uc010sta.1_Silent_p.P289P|GRIP1_uc001stj.2_Silent_p.P75P|GRIP1_uc001stl.1_Silent_p.P289P|GRIP1_uc001stm.2_Silent_p.P345P NM_021150 NP_066973 Q9Y3R0 GRIP1_HUMAN glutamate receptor interacting protein 1 345 androgen receptor signaling pathway|intracellular signal transduction|positive regulation of transcription, DNA-dependent|synaptic transmission cell junction|cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|postsynaptic membrane androgen receptor binding|beta-catenin binding|protein C-terminus binding|receptor signaling complex scaffold activity|transcription coactivator activity ovary(2) 2 GBM - Glioblastoma multiforme(2;0.00069) GBM - Glioblastoma multiforme(28;0.0933) 0.409091 28.070963 28.229791 9 13 KEEP --- --- --- --- PTPRB 5787 broad.mit.edu 37 12 70948917 70948917 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:70948917G>A uc001swb.3 - PTPRB_uc010sto.1_Intron|PTPRB_uc010stp.1_Intron|PTPRB_uc001swc.3_Intron|PTPRB_uc001swa.3_Intron NM_002837 NP_002828 protein tyrosine phosphatase, receptor type, B angiogenesis integral to plasma membrane protein binding|transmembrane receptor protein tyrosine phosphatase activity lung(2)|skin(1) 3 Renal(347;0.236) GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149) 0.389831 68.908985 69.537209 23 36 KEEP --- --- --- --- TRHDE 29953 broad.mit.edu 37 12 72867082 72867082 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:72867082G>A uc001sxa.2 + NM_013381 NP_037513 thyrotropin-releasing hormone degrading enzyme cell-cell signaling|proteolysis|signal transduction integral to plasma membrane aminopeptidase activity|metallopeptidase activity|zinc ion binding ovary(2)|skin(1) 3 0.571429 12.499854 12.530816 4 3 KEEP --- --- --- --- TRHDE 29953 broad.mit.edu 37 12 73015380 73015380 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:73015380C>T uc001sxa.2 + NM_013381 NP_037513 thyrotropin-releasing hormone degrading enzyme cell-cell signaling|proteolysis|signal transduction integral to plasma membrane aminopeptidase activity|metallopeptidase activity|zinc ion binding ovary(2)|skin(1) 3 0.6875 36.427412 36.927013 11 5 KEEP --- --- --- --- KCNC2 3747 broad.mit.edu 37 12 75444047 75444047 + Intron SNP C T T rs111701449 MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:75444047C>T uc001sxg.1 - KCNC2_uc009zry.2_Intron|KCNC2_uc001sxe.2_Intron|KCNC2_uc001sxf.2_Intron|KCNC2_uc010stw.1_Intron NM_139137 NP_631875 Shaw-related voltage-gated potassium channel energy reserve metabolic process|regulation of insulin secretion voltage-gated potassium channel complex voltage-gated potassium channel activity breast(2)|pancreas(2)|skin(1)|lung(1) 6 0.357143 15.470927 15.72268 5 9 KEEP --- --- --- --- Unknown broad.mit.edu 37 12 76531505 76531505 + IGR SNP A T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:76531505A>T NAP1L1 (52767 upstream) : BBS10 (206761 downstream) 0.4375 22.723242 22.77764 7 9 KEEP --- --- --- --- broad.mit.edu 37 12 80749578 80749578 + 5'Flank SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:80749578G>A uc009zsg.1 + uc001szd.2_5'Flank RecName: Full=Uncharacterized protein C12orf64; 0.505495 145.347386 145.34972 46 45 KEEP --- --- --- --- LRRIQ1 84125 broad.mit.edu 37 12 85458922 85458922 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:85458922C>T uc001tac.2 + LRRIQ1_uc001tab.1_Intron NM_001079910 NP_001073379 leucine-rich repeats and IQ motif containing 1 ovary(4)|central_nervous_system(1)|skin(1) 6 GBM - Glioblastoma multiforme(134;0.212) 0.529412 29.683207 29.696891 9 8 KEEP --- --- --- --- TMCC3 57458 broad.mit.edu 37 12 94975870 94975870 + Nonsense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:94975870G>A uc001tdj.2 - 2 641 c.523C>T c.(523-525)CGA>TGA p.R175* TMCC3_uc001tdi.2_Nonsense_Mutation_p.R144* NM_020698 NP_065749 Q9ULS5 TMCC3_HUMAN transmembrane and coiled-coil domain family 3 175 integral to membrane ovary(1)|skin(1) 2 0.481203 208.899974 208.940418 64 69 KEEP --- --- --- --- HAL 3034 broad.mit.edu 37 12 96379836 96379836 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:96379836G>A uc001tem.1 - HAL_uc009zti.1_Intron|HAL_uc010suw.1_Intron|HAL_uc010sux.1_Intron NM_002108 NP_002099 histidine ammonia-lyase biosynthetic process|histidine catabolic process cytosol histidine ammonia-lyase activity ovary(2)|skin(1) 3 L-Histidine(DB00117) NSCLC(169;943 2815 23563 30031) 0.509434 88.225278 88.229352 27 26 KEEP --- --- --- --- C12orf63 374467 broad.mit.edu 37 12 97158923 97158923 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:97158923C>T uc001tet.1 + 27 3561 c.3483C>T c.(3481-3483)AAC>AAT p.N1161N NM_198520 NP_940922 Q6ZTY8 CL063_HUMAN hypothetical protein LOC374467 1161 skin(6)|ovary(1) 7 0.384615 93.034259 93.943789 30 48 KEEP --- --- --- --- SLC5A8 160728 broad.mit.edu 37 12 101555615 101555616 + Intron DNP CC TT TT MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:101555615_101555616CC>TT uc001thz.3 - NM_145913 NP_666018 solute carrier family 5 (iodide transporter), apoptosis|sodium ion transport apical plasma membrane|integral to membrane monocarboxylic acid transmembrane transporter activity|passive transmembrane transporter activity|symporter activity 0 GBM(60;420 1056 13605 22380 47675) 0.368421 21.719722 22.009021 7 12 KEEP --- --- --- --- SLC5A8 160728 broad.mit.edu 37 12 101573687 101573687 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:101573687C>T uc001thz.3 - NM_145913 NP_666018 solute carrier family 5 (iodide transporter), apoptosis|sodium ion transport apical plasma membrane|integral to membrane monocarboxylic acid transmembrane transporter activity|passive transmembrane transporter activity|symporter activity 0 GBM(60;420 1056 13605 22380 47675) 0.5 78.224644 78.224644 23 23 KEEP --- --- --- --- UTP20 27340 broad.mit.edu 37 12 101689338 101689338 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:101689338C>T uc001tia.1 + 12 1488 c.1332C>T c.(1330-1332)GCC>GCT p.A444A NM_014503 NP_055318 O75691 UTP20_HUMAN down-regulated in metastasis 444 endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation 90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome protein binding ovary(2)|breast(2) 4 0.47619 65.497304 65.518037 20 22 KEEP --- --- --- --- UTP20 27340 broad.mit.edu 37 12 101700461 101700461 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:101700461C>T uc001tia.1 + NM_014503 NP_055318 down-regulated in metastasis endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation 90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome protein binding ovary(2)|breast(2) 4 0.529412 96.329271 96.367679 27 24 KEEP --- --- --- --- MYBPC1 4604 broad.mit.edu 37 12 102056091 102056091 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:102056091C>T uc001tii.2 + MYBPC1_uc001tig.2_Intron|MYBPC1_uc010svq.1_Intron|MYBPC1_uc001tih.2_Intron|MYBPC1_uc001tij.2_Intron|MYBPC1_uc010svr.1_Intron|MYBPC1_uc010svs.1_Intron|MYBPC1_uc010svt.1_Intron|MYBPC1_uc010svu.1_Intron|MYBPC1_uc001tik.2_Intron NM_206820 NP_996556 myosin binding protein C, slow type isoform 3 cell adhesion|muscle filament sliding cytosol|myofibril|myosin filament actin binding|structural constituent of muscle|titin binding ovary(2)|liver(1)|skin(1) 4 0.388889 21.720637 21.91544 7 11 KEEP --- --- --- --- NT5DC3 51559 broad.mit.edu 37 12 104190534 104190534 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:104190534G>A uc010swe.1 - NM_001031701 NP_001026871 5'-nucleotidase domain containing 3 hydrolase activity|metal ion binding ovary(2)|skin(1) 3 0.625 53.331004 53.660109 15 9 KEEP --- --- --- --- CKAP4 10970 broad.mit.edu 37 12 106633345 106633345 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:106633345G>A uc001tlk.2 - 2 1350 c.1266C>T c.(1264-1266)TCC>TCT p.S422S NM_006825 NP_006816 Q07065 CKAP4_HUMAN cytoskeleton-associated protein 4 422 Potential. ER-Golgi intermediate compartment membrane|integral to membrane|membrane fraction 0 0.46988 122.916858 122.982535 39 44 KEEP --- --- --- --- WSCD2 9671 broad.mit.edu 37 12 108600151 108600151 + Missense_Mutation SNP C G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:108600151C>G uc001tms.2 + 3 1212 c.468C>G c.(466-468)ATC>ATG p.I156M WSCD2_uc001tmt.2_Missense_Mutation_p.I156M NM_014653 NP_055468 Q2TBF2 WSCD2_HUMAN WSC domain containing 2 156 WSC 1. integral to membrane ovary(1)|large_intestine(1)|breast(1) 3 0.4 97.886061 98.498432 28 42 KEEP --- --- --- --- SART3 9733 broad.mit.edu 37 12 108925103 108925103 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:108925103G>A uc001tmz.1 - SART3_uc001tmy.1_Intron|SART3_uc009zux.1_Intron|SART3_uc010swx.1_Intron|SART3_uc010swy.1_Intron|SART3_uc010swz.1_Intron|SART3_uc001tna.1_Intron NM_014706 NP_055521 squamous cell carcinoma antigen recognized by T RNA processing cytoplasm|nuclear speck nucleotide binding|protein binding|RNA binding pancreas(1) 1 Porokeratosis 0.384615 50.219163 50.673234 15 24 KEEP --- --- --- --- UBE3B 89910 broad.mit.edu 37 12 109971401 109971401 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:109971401C>T uc001top.2 + UBE3B_uc001toq.2_Intron|UBE3B_uc001tos.2_Intron|UBE3B_uc001tot.2_Intron|UBE3B_uc010sxp.1_Intron NM_130466 NP_569733 ubiquitin protein ligase E3B protein ubiquitination involved in ubiquitin-dependent protein catabolic process intracellular ubiquitin-protein ligase activity ovary(2)|lung(2) 4 668 0.47619 97.249219 97.280051 30 33 KEEP --- --- --- --- MYL2 4633 broad.mit.edu 37 12 111350910 111350910 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:111350910G>A uc001try.3 - 6 463 c.392C>T c.(391-393)TCC>TTC p.S131F MYL2_uc001trx.3_Missense_Mutation_p.S112F NM_000432 NP_000423 P10916 MLRV_HUMAN slow cardiac myosin regulatory light chain 2 131 EF-hand 3. cardiac myofibril assembly|heart contraction|muscle filament sliding|negative regulation of cell growth|regulation of striated muscle contraction|ventricular cardiac muscle tissue morphogenesis cytosol|myosin complex|sarcomere actin monomer binding|calcium ion binding|myosin heavy chain binding|structural constituent of muscle ovary(1) 1 GBM(14;268 426 18829 21617 25540) 0.470588 152.097696 152.172627 48 54 KEEP --- --- --- --- RBM19 9904 broad.mit.edu 37 12 114395458 114395458 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:114395458G>A uc009zwi.2 - RBM19_uc001tvn.3_Intron|RBM19_uc001tvm.2_Intron NM_001146699 NP_001140171 RNA binding motif protein 19 multicellular organismal development|positive regulation of embryonic development chromosome|cytoplasm|nucleolus|nucleoplasm nucleotide binding|RNA binding skin(3)|ovary(1)|liver(1)|central_nervous_system(1) 6 Medulloblastoma(191;0.163)|all_neural(191;0.178) 0.428571 9.424302 9.45536 3 4 KEEP --- --- --- --- NOS1 4842 broad.mit.edu 37 12 117685191 117685191 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:117685191C>T uc001twm.1 - 18 3471 c.2785G>A c.(2785-2787)GAA>AAA p.E929K NM_000620 NP_000611 P29475 NOS1_HUMAN nitric oxide synthase 1, neuronal 929 Flavodoxin-like. multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding ovary(3)|skin(3)|pancreas(1) 7 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) BRCA - Breast invasive adenocarcinoma(302;0.0561) L-Citrulline(DB00155) Esophageal Squamous(162;1748 2599 51982 52956) 0.43617 133.574042 133.905227 41 53 KEEP --- --- --- --- NOS1 4842 broad.mit.edu 37 12 117696174 117696174 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:117696174G>A uc001twm.1 - NOS1_uc001twn.1_Intron NM_000620 NP_000611 nitric oxide synthase 1, neuronal multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding ovary(3)|skin(3)|pancreas(1) 7 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) BRCA - Breast invasive adenocarcinoma(302;0.0561) L-Citrulline(DB00155) Esophageal Squamous(162;1748 2599 51982 52956) 0.555556 32.751902 32.800275 10 8 KEEP --- --- --- --- NOS1 4842 broad.mit.edu 37 12 117701685 117701685 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:117701685G>A uc001twm.1 - NM_000620 NP_000611 nitric oxide synthase 1, neuronal multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding ovary(3)|skin(3)|pancreas(1) 7 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) BRCA - Breast invasive adenocarcinoma(302;0.0561) L-Citrulline(DB00155) Esophageal Squamous(162;1748 2599 51982 52956) 0.536082 176.371478 176.490566 52 45 KEEP --- --- --- --- GCN1L1 10985 broad.mit.edu 37 12 120601070 120601070 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:120601070G>A uc001txo.2 - NM_006836 NP_006827 GCN1 general control of amino-acid synthesis regulation of translation ribosome protein binding|translation factor activity, nucleic acid binding ovary(4) 4 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) 0.489796 80.698278 80.702741 24 25 KEEP --- --- --- --- CAMKK2 10645 broad.mit.edu 37 12 121712086 121712086 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:121712086G>A uc001tzu.2 - 2 368 c.244C>T c.(244-246)CCC>TCC p.P82S CAMKK2_uc001tzt.2_Missense_Mutation_p.P82S|CAMKK2_uc001tzv.2_Missense_Mutation_p.P82S|CAMKK2_uc001tzw.2_Missense_Mutation_p.P82S|CAMKK2_uc001tzx.2_Missense_Mutation_p.P82S|CAMKK2_uc001tzy.2_Missense_Mutation_p.P82S|CAMKK2_uc001uaa.1_Missense_Mutation_p.P82S|CAMKK2_uc001uab.2_Missense_Mutation_p.P82S|CAMKK2_uc001uac.2_Missense_Mutation_p.P82S|CAMKK2_uc001uad.1_Missense_Mutation_p.P82S NM_006549 NP_006540 Q96RR4 KKCC2_HUMAN calcium/calmodulin-dependent protein kinase 82 calcium-mediated signaling|MAPKKK cascade|positive regulation of transcription, DNA-dependent|protein autophosphorylation|regulation of protein kinase activity cytoplasm ATP binding|calcium ion binding|calmodulin binding|calmodulin-dependent protein kinase activity|protein tyrosine kinase activity lung(1)|large_intestine(1)|stomach(1) 3 all_neural(191;0.0684)|Medulloblastoma(191;0.0922) 369 0.47619 30.948087 30.958479 10 11 KEEP --- --- --- --- HPD 3242 broad.mit.edu 37 12 122295422 122295422 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:122295422C>T uc001ubj.2 - HPD_uc001ubk.2_Intron NM_002150 NP_002141 4-hydroxyphenylpyruvate dioxygenase L-phenylalanine catabolic process|tyrosine catabolic process cytosol 4-hydroxyphenylpyruvate dioxygenase activity|metal ion binding 0 all_neural(191;0.0684)|Medulloblastoma(191;0.0922) OV - Ovarian serous cystadenocarcinoma(86;0.000105)|Epithelial(86;0.000352)|BRCA - Breast invasive adenocarcinoma(302;0.225) Nitisinone(DB00348) 0.5 11.79938 11.79938 4 4 KEEP --- --- --- --- WDR66 144406 broad.mit.edu 37 12 122437640 122437640 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:122437640G>A uc009zxk.2 + 20 3167 c.3025G>A c.(3025-3027)GAA>AAA p.E1009K NM_144668 NP_653269 Q8TBY9 WDR66_HUMAN WD repeat domain 66 1009 calcium ion binding ovary(1)|skin(1) 2 all_neural(191;0.0496)|Medulloblastoma(191;0.0922) OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248) Esophageal Squamous(85;849 1794 49757 52143) 0.465116 64.91747 64.960305 20 23 KEEP --- --- --- --- WDR66 144406 broad.mit.edu 37 12 122441593 122441593 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:122441593G>A uc009zxk.2 + 22 3515 c.3373G>A c.(3373-3375)GAA>AAA p.E1125K NM_144668 NP_653269 Q8TBY9 WDR66_HUMAN WD repeat domain 66 1125 calcium ion binding ovary(1)|skin(1) 2 all_neural(191;0.0496)|Medulloblastoma(191;0.0922) OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248) Esophageal Squamous(85;849 1794 49757 52143) 0.395349 53.368192 53.779601 17 26 KEEP --- --- --- --- MPHOSPH9 10198 broad.mit.edu 37 12 123706290 123706290 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:123706290G>A uc001uel.2 - 1 152 c.45C>T c.(43-45)ATC>ATT p.I15I MPHOSPH9_uc010tal.1_5'UTR|MPHOSPH9_uc010tam.1_RNA|MPHOSPH9_uc001uem.2_5'UTR NM_022782 NP_073619 Q99550 MPP9_HUMAN M-phase phosphoprotein 9 15 M phase of mitotic cell cycle centriole|Golgi membrane 0 all_neural(191;0.101)|Medulloblastoma(191;0.163) OV - Ovarian serous cystadenocarcinoma(86;0.000182)|Epithelial(86;0.00046)|BRCA - Breast invasive adenocarcinoma(302;0.169) 0.434783 129.486263 129.827571 40 52 KEEP --- --- --- --- TMEM132B 114795 broad.mit.edu 37 12 126136997 126136997 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:126136997C>T uc001uhe.1 + 8 1918 c.1910C>T c.(1909-1911)CCG>CTG p.P637L TMEM132B_uc001uhf.1_Missense_Mutation_p.P149L NM_052907 NP_443139 Q14DG7 T132B_HUMAN transmembrane protein 132B 637 Extracellular (Potential). integral to membrane skin(11)|ovary(5)|large_intestine(1)|pancreas(1)|breast(1) 19 all_neural(191;0.101)|Medulloblastoma(191;0.163) OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362) 0.354839 36.016611 36.592124 11 20 KEEP --- --- --- --- GPR133 283383 broad.mit.edu 37 12 131498827 131498827 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:131498827C>T uc001uit.3 + 13 1974 c.1415C>T c.(1414-1416)ACC>ATC p.T472I GPR133_uc010tbm.1_Missense_Mutation_p.T504I NM_198827 NP_942122 Q6QNK2 GP133_HUMAN G protein-coupled receptor 133 precursor 472 Extracellular (Potential). neuropeptide signaling pathway integral to membrane|plasma membrane G-protein coupled receptor activity pancreas(5)|ovary(3)|skin(2) 10 all_neural(191;0.0982)|Medulloblastoma(191;0.163) OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06) 0.487179 118.341672 118.352947 38 40 KEEP --- --- --- --- GPR133 283383 broad.mit.edu 37 12 131593397 131593397 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:131593397C>T uc001uit.3 + 18 2575 c.2016C>T c.(2014-2016)CAC>CAT p.H672H GPR133_uc010tbm.1_Silent_p.H704H|GPR133_uc009zyo.2_Intron|GPR133_uc001uiv.1_Silent_p.H191H|GPR133_uc009zyp.2_RNA NM_198827 NP_942122 Q6QNK2 GP133_HUMAN G protein-coupled receptor 133 precursor 672 Cytoplasmic (Potential). neuropeptide signaling pathway integral to membrane|plasma membrane G-protein coupled receptor activity pancreas(5)|ovary(3)|skin(2) 10 all_neural(191;0.0982)|Medulloblastoma(191;0.163) OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06) 0.522124 189.132215 189.180661 59 54 KEEP --- --- --- --- ULK1 8408 broad.mit.edu 37 12 132399011 132399011 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:132399011C>T uc001uje.2 + 16 1630 c.1362C>T c.(1360-1362)TTC>TTT p.F454F NM_003565 NP_003556 O75385 ULK1_HUMAN Unc-51-like kinase 1 454 autophagy|protein localization|regulation of autophagy autophagic vacuole|cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex ATP binding|protein complex binding|protein serine/threonine kinase activity ovary(1)|lung(1)|central_nervous_system(1)|skin(1) 4 all_neural(191;0.0982)|Medulloblastoma(191;0.163) OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07) 916 0.566667 53.774798 53.890535 17 13 KEEP --- --- --- --- ULK1 8408 broad.mit.edu 37 12 132400681 132400681 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:132400681C>T uc001uje.2 + 19 2123 c.1855C>T c.(1855-1857)CCC>TCC p.P619S NM_003565 NP_003556 O75385 ULK1_HUMAN Unc-51-like kinase 1 619 autophagy|protein localization|regulation of autophagy autophagic vacuole|cytosol|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex ATP binding|protein complex binding|protein serine/threonine kinase activity ovary(1)|lung(1)|central_nervous_system(1)|skin(1) 4 all_neural(191;0.0982)|Medulloblastoma(191;0.163) OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07) 916 0.5 51.434637 51.434637 17 17 KEEP --- --- --- --- EP400 57634 broad.mit.edu 37 12 132515851 132515851 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:132515851C>T uc001ujn.2 + EP400_uc001ujl.2_Intron|EP400_uc001ujm.2_Intron|SNORA49_uc001ujo.2_RNA NM_015409 NP_056224 E1A binding protein p400 histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity central_nervous_system(4)|ovary(3)|breast(3)|skin(2) 12 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) 0.495575 351.365852 351.369983 112 114 KEEP --- --- --- --- POLE 5426 broad.mit.edu 37 12 133218662 133218662 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:133218662G>A uc001uks.1 - POLE_uc001ukq.1_5'Flank|POLE_uc001ukr.1_Intron|POLE_uc010tbq.1_Intron NM_006231 NP_006222 DNA-directed DNA polymerase epsilon base-excision repair, gap-filling|DNA synthesis involved in DNA repair|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair nucleoplasm chromatin binding|DNA binding|DNA-directed DNA polymerase activity|nucleotide binding|protein binding|zinc ion binding ovary(3)|skin(3)|lung(1)|central_nervous_system(1) 8 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.0416) OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05) DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage 0.677419 69.88012 70.745712 21 10 KEEP --- --- --- --- GOLGA3 2802 broad.mit.edu 37 12 133381383 133381383 + Missense_Mutation SNP G T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr12:133381383G>T uc001ukz.1 - 7 2075 c.1516C>A c.(1516-1518)CAG>AAG p.Q506K GOLGA3_uc001ula.1_Missense_Mutation_p.Q506K|GOLGA3_uc001ulb.2_Missense_Mutation_p.Q506K NM_005895 NP_005886 Q08378 GOGA3_HUMAN Golgi autoantigen, golgin subfamily a, 3 506 Potential. intra-Golgi vesicle-mediated transport Golgi cisterna membrane|Golgi transport complex protein binding|transporter activity ovary(3)|central_nervous_system(2)|pancreas(1) 6 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.0176)|Lung NSC(355;0.204) OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06) 0.034884 -13.140002 7.082664 3 83 KEEP --- --- --- --- DKFZp686A1627 266695 broad.mit.edu 37 13 19624336 19624336 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:19624336G>A uc001umb.1 - NR_002801 Homo sapiens mRNA; cDNA DKFZp686A1627 (from clone DKFZp686A1627). 0 0.6 20.152176 20.239755 6 4 KEEP --- --- --- --- Unknown broad.mit.edu 37 13 19705368 19705368 + IGR SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:19705368T>C DKFZp686A1627 (12945 upstream) : TUBA3C (42552 downstream) 0.209677 36.941178 41.776503 13 49 KEEP --- --- --- --- Unknown broad.mit.edu 37 13 19744512 19744512 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:19744512C>T DKFZp686A1627 (52089 upstream) : TUBA3C (3408 downstream) 0.3 8.22524 8.580281 3 7 KEEP --- --- --- --- PSPC1 55269 broad.mit.edu 37 13 20277485 20277485 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:20277485G>A uc001uml.2 - 9 1588 c.1402C>T c.(1402-1404)CCT>TCT p.P468S PSPC1_uc001umj.1_Intron|PSPC1_uc001umk.1_Intron NM_001042414 NP_001035879 Q8WXF1 PSPC1_HUMAN paraspeckle protein 1 468 Gly-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nuclear matrix|nucleolus nucleotide binding|protein binding|RNA binding breast(1) 1 all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162) all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483) 0.096774 2.600135 7.651979 3 28 KEEP --- --- --- --- PSPC1 55269 broad.mit.edu 37 13 20279925 20279925 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:20279925C>T uc001uml.2 - 8 1449 c.1263G>A c.(1261-1263)ATG>ATA p.M421I PSPC1_uc001umj.1_Intron|PSPC1_uc001umk.1_Intron NM_001042414 NP_001035879 Q8WXF1 PSPC1_HUMAN paraspeckle protein 1 421 Gly-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nuclear matrix|nucleolus nucleotide binding|protein binding|RNA binding breast(1) 1 all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162) all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483) 0.256198 80.761999 87.288097 31 90 KEEP --- --- --- --- SACS 26278 broad.mit.edu 37 13 23909126 23909126 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:23909126G>A uc001uon.2 - 10 9478 c.8889C>T c.(8887-8889)TTC>TTT p.F2963F SACS_uc001uoo.2_Silent_p.F2816F|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron NM_014363 NP_055178 Q9NZJ4 SACS_HUMAN sacsin 2963 cell death|negative regulation of inclusion body assembly|protein folding axon|cell body fiber|dendrite|mitochondrion|nucleus ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1) 12 all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128) all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189) 738 0.393939 123.598788 124.574854 39 60 KEEP --- --- --- --- SACS 26278 broad.mit.edu 37 13 23909874 23909874 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:23909874G>A uc001uon.2 - 10 8730 c.8141C>T c.(8140-8142)TCG>TTG p.S2714L SACS_uc001uoo.2_Missense_Mutation_p.S2567L|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron NM_014363 NP_055178 Q9NZJ4 SACS_HUMAN sacsin 2714 cell death|negative regulation of inclusion body assembly|protein folding axon|cell body fiber|dendrite|mitochondrion|nucleus ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1) 12 all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128) all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189) 738 0.314607 85.067877 87.78943 28 61 KEEP --- --- --- --- ATP12A 479 broad.mit.edu 37 13 25262509 25262509 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:25262509C>T uc001upp.2 + 4 468 c.281C>T c.(280-282)TCC>TTC p.S94F ATP12A_uc010aaa.2_Missense_Mutation_p.S94F NM_001676 NP_001667 P54707 AT12A_HUMAN hydrogen/potassium-exchanging ATPase 12A 94 Cytoplasmic (Potential). ATP biosynthetic process hydrogen:potassium-exchanging ATPase complex ATP binding|hydrogen:potassium-exchanging ATPase activity|metal ion binding ovary(2)|central_nervous_system(2)|large_intestine(1)|breast(1) 6 Lung SC(185;0.0225)|Breast(139;0.077) all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228) Esomeprazole(DB00736)|Pantoprazole(DB00213) Pancreas(156;1582 1935 18898 22665 26498) 0.623824 662.344891 666.675778 199 120 KEEP --- --- --- --- RNF17 56163 broad.mit.edu 37 13 25433136 25433136 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:25433136C>T uc001upr.2 + RNF17_uc010tdd.1_Intron|RNF17_uc010aab.2_Intron|RNF17_uc010tde.1_Intron|RNF17_uc001ups.2_Intron|RNF17_uc010aac.2_Intron|RNF17_uc010aad.2_Intron NM_031277 NP_112567 ring finger protein 17 multicellular organismal development cytoplasm|nucleus hydrolase activity, acting on ester bonds|nucleic acid binding|zinc ion binding ovary(1)|skin(1) 2 Lung SC(185;0.0225)|Breast(139;0.077) all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524) 0.666667 21.152939 21.374198 6 3 KEEP --- --- --- --- FLT1 2321 broad.mit.edu 37 13 28886168 28886168 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:28886168C>T uc001usb.3 - 26 3739 c.3454G>A c.(3454-3456)GAA>AAA p.E1152K FLT1_uc010aap.2_Missense_Mutation_p.E157K|FLT1_uc010aaq.2_Missense_Mutation_p.E277K|FLT1_uc001usa.3_Missense_Mutation_p.E370K NM_002019 NP_002010 P17948 VGFR1_HUMAN fms-related tyrosine kinase 1 isoform 1 1152 Cytoplasmic (Potential).|Protein kinase. cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway extracellular space|Golgi apparatus|integral to plasma membrane|nucleus ATP binding|growth factor binding|vascular endothelial growth factor receptor activity lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1) 24 Acute lymphoblastic leukemia(6;0.04) Lung SC(185;0.0262)|Breast(139;0.188) Colorectal(13;0.000674) all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207) Sunitinib(DB01268) 738 0.491228 94.698381 94.702219 28 29 KEEP --- --- --- --- FLT1 2321 broad.mit.edu 37 13 29004112 29004112 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:29004112C>T uc001usb.3 - FLT1_uc010aar.1_Intron|FLT1_uc001usc.3_Intron|FLT1_uc010tdp.1_Intron NM_002019 NP_002010 fms-related tyrosine kinase 1 isoform 1 cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway extracellular space|Golgi apparatus|integral to plasma membrane|nucleus ATP binding|growth factor binding|vascular endothelial growth factor receptor activity lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1) 24 Acute lymphoblastic leukemia(6;0.04) Lung SC(185;0.0262)|Breast(139;0.188) Colorectal(13;0.000674) all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207) Sunitinib(DB01268) 738 0.576087 183.692484 184.157994 53 39 KEEP --- --- --- --- MTUS2 23281 broad.mit.edu 37 13 29881169 29881169 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:29881169C>T uc001usl.3 + NM_001033602 NP_001028774 hypothetical protein LOC23281 isoform a cytoplasm|microtubule microtubule binding|protein homodimerization activity 0 344 0.75 19.653371 20.107535 6 2 KEEP --- --- --- --- RXFP2 122042 broad.mit.edu 37 13 32340262 32340262 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:32340262C>T uc001utt.2 + RXFP2_uc010aba.2_Intron NM_130806 NP_570718 relaxin/insulin-like family peptide receptor 2 integral to membrane|plasma membrane 0 Lung SC(185;0.0262) all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535) 0.4 18.447528 18.57855 6 9 KEEP --- --- --- --- BRCA2 675 broad.mit.edu 37 13 32928981 32928981 + Intron SNP T G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:32928981T>G uc001uub.1 + NM_000059 NP_000050 breast cancer 2, early onset cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1) 64 Lung SC(185;0.0262) all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704) Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332) 677 D|Mis|N|F|S breast|ovarian|pancreatic breast|ovarian|pancreatic|leukemia (FANCB|FANCD1) Direct_reversal_of_damage|Homologous_recombination Fanconi_Anemia_type_D1_bi-allelic_BRCA2_mutations|Fanconi_Anemia|Pancreatic_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_BRCA2_type|Hereditary_Prostate_Cancer|Li-Fraumeni_syndrome TCGA Ovarian(8;0.087) 0.039216 -5.295334 6.390231 2 49 KEEP --- --- --- --- PDS5B 23047 broad.mit.edu 37 13 33274049 33274049 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:33274049C>T uc010abf.2 + PDS5B_uc010abg.2_Intron NM_015032 NP_055847 PDS5, regulator of cohesion maintenance, homolog cell division|cell proliferation|mitotic sister chromatid cohesion|negative regulation of cell proliferation chromatin|nucleus ATP binding|DNA binding|identical protein binding ovary(2)|lung(1)|pancreas(1) 4 Lung SC(185;0.0367) all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204) 0.689655 70.910335 71.839016 20 9 KEEP --- --- --- --- NBEA 26960 broad.mit.edu 37 13 35739195 35739195 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:35739195G>A uc001uvb.2 + NBEA_uc010abi.2_Intron NM_015678 NP_056493 neurobeachin cytosol|endomembrane system|plasma membrane|trans-Golgi network protein binding ovary(9)|large_intestine(2) 11 Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207) all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199) 0.481481 43.073603 43.081656 13 14 KEEP --- --- --- --- NBEA 26960 broad.mit.edu 37 13 36229811 36229811 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:36229811G>A uc001uvb.2 + 54 8430 c.8224G>A c.(8224-8226)GGA>AGA p.G2742R NBEA_uc010abi.2_Missense_Mutation_p.G1398R|NBEA_uc010tef.1_Missense_Mutation_p.G535R|NBEA_uc001uvd.2_Missense_Mutation_p.G320R NM_015678 NP_056493 Q8NFP9 NBEA_HUMAN neurobeachin 2742 WD 2. cytosol|endomembrane system|plasma membrane|trans-Golgi network protein binding ovary(9)|large_intestine(2) 11 Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207) all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199) 0.034884 -13.542117 6.682406 3 83 KEEP --- --- --- --- NBEA 26960 broad.mit.edu 37 13 36242725 36242725 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:36242725G>A uc001uvb.2 + NBEA_uc010abi.2_Intron|NBEA_uc010tef.1_Intron|NBEA_uc001uvd.2_Intron NM_015678 NP_056493 neurobeachin cytosol|endomembrane system|plasma membrane|trans-Golgi network protein binding ovary(9)|large_intestine(2) 11 Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207) all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199) 0.478261 38.924412 38.93385 11 12 KEEP --- --- --- --- CCNA1 8900 broad.mit.edu 37 13 37011655 37011655 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:37011655C>T uc001uvr.3 + CCNA1_uc010teo.1_Intron|CCNA1_uc010abq.2_Intron|CCNA1_uc010abp.2_Intron|CCNA1_uc001uvs.3_Intron|CCNA1_uc010abr.2_Intron NM_003914 NP_003905 cyclin A1 isoform a cell division|G2/M transition of mitotic cell cycle|male meiosis I|mitosis|regulation of cyclin-dependent protein kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|spermatogenesis cytosol|microtubule cytoskeleton|nucleoplasm protein kinase binding lung(2)|skin(2)|ovary(1) 5 Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174) KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169) all cancers(112;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242) 263 0.555556 130.811188 131.005981 40 32 KEEP --- --- --- --- Unknown broad.mit.edu 37 13 37369135 37369135 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:37369135C>T C13orf36 (97162 upstream) : RFXAP (24204 downstream) 0.6 10.325938 10.369624 3 2 KEEP --- --- --- --- ALG5 29880 broad.mit.edu 37 13 37524178 37524178 + Silent SNP T G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:37524178T>G uc001uvy.2 - 10 943 c.876A>C c.(874-876)CCA>CCC p.P292P ALG5_uc010teq.1_Silent_p.P262P|ALG5_uc010ter.1_RNA NM_013338 NP_037470 Q9Y673 ALG5_HUMAN dolichyl-phosphate beta-glucosyltransferase 292 Lumenal (Potential). dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine endoplasmic reticulum membrane|integral to membrane dolichyl-phosphate beta-glucosyltransferase activity|oligosaccharyl transferase activity 0 Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174) all cancers(112;5.79e-07)|Epithelial(112;1.81e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00785)|BRCA - Breast invasive adenocarcinoma(63;0.0127)|GBM - Glioblastoma multiforme(144;0.0472) 0.172414 13.057438 15.996573 5 24 KEEP --- --- --- --- KIAA0564 23078 broad.mit.edu 37 13 42265503 42265503 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:42265503G>A uc001uyj.2 - 32 3889 c.3819C>T c.(3817-3819)TTC>TTT p.F1273F NM_015058 NP_055873 A3KMH1 K0564_HUMAN hypothetical protein LOC23078 isoform a 1273 extracellular region ATP binding|ATPase activity ovary(3)|upper_aerodigestive_tract(1)|kidney(1)|skin(1) 6 Lung NSC(96;4.61e-06)|Prostate(109;0.0167)|Lung SC(185;0.0262)|Breast(139;0.0854)|Hepatocellular(98;0.114) OV - Ovarian serous cystadenocarcinoma(117;0.000368)|GBM - Glioblastoma multiforme(144;0.0033)|BRCA - Breast invasive adenocarcinoma(63;0.0969) 0.306931 89.481334 92.841503 31 70 KEEP --- --- --- --- KIAA0564 23078 broad.mit.edu 37 13 42461377 42461377 + Missense_Mutation SNP G A A rs141866968 MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:42461377G>A uc001uyj.2 - 6 842 c.772C>T c.(772-774)CGT>TGT p.R258C KIAA0564_uc001uyk.2_Missense_Mutation_p.R258C NM_015058 NP_055873 A3KMH1 K0564_HUMAN hypothetical protein LOC23078 isoform a 258 extracellular region ATP binding|ATPase activity ovary(3)|upper_aerodigestive_tract(1)|kidney(1)|skin(1) 6 Lung NSC(96;4.61e-06)|Prostate(109;0.0167)|Lung SC(185;0.0262)|Breast(139;0.0854)|Hepatocellular(98;0.114) OV - Ovarian serous cystadenocarcinoma(117;0.000368)|GBM - Glioblastoma multiforme(144;0.0033)|BRCA - Breast invasive adenocarcinoma(63;0.0969) 0.534884 76.527787 76.573292 23 20 KEEP --- --- --- --- Unknown broad.mit.edu 37 13 44545193 44545193 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:44545193C>T C13orf31 (77126 upstream) : LOC121838 (51278 downstream) 0.555556 17.076281 17.100519 5 4 KEEP --- --- --- --- RCBTB1 55213 broad.mit.edu 37 13 50141393 50141393 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:50141393G>A uc001vde.1 - 3 284 c.23C>T c.(22-24)CCC>CTC p.P8L NM_018191 NP_060661 Q8NDN9 RCBT1_HUMAN regulator of chromosome condensation (RCC1) and 8 cell cycle|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus ovary(1) 1 Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19) KIRC - Kidney renal clear cell carcinoma(9;0.206) GBM - Glioblastoma multiforme(99;4.7e-09) 0.612903 65.032075 65.378479 19 12 KEEP --- --- --- --- RNASEH2B 79621 broad.mit.edu 37 13 51523764 51523764 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:51523764C>T uc001vfa.3 + RNASEH2B_uc001vfb.3_Intron NM_024570 NP_078846 ribonuclease H2, subunit B isoform 1 RNA catabolic process nucleus|ribonuclease H2 complex 0 Acute lymphoblastic leukemia(7;1.03e-07)|Breast(56;0.00122)|Lung NSC(96;0.00143)|Prostate(109;0.0047)|Hepatocellular(98;0.152)|Glioma(44;0.236) GBM - Glioblastoma multiforme(99;9e-08) 0.3 8.021136 8.378505 3 7 KEEP --- --- --- --- UTP14C 9724 broad.mit.edu 37 13 52603826 52603826 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:52603826C>T uc001vgb.2 + 2 1421 c.886C>T c.(886-888)CTT>TTT p.L296F UTP14C_uc001vgc.2_RNA NM_021645 NP_067677 Q5TAP6 UT14C_HUMAN UTP14, U3 small nucleolar ribonucleoprotein, 296 cell differentiation|meiosis|multicellular organismal development|rRNA processing|spermatogenesis nucleolus|small-subunit processome ovary(3)|large_intestine(1)|breast(1) 5 Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236) GBM - Glioblastoma multiforme(99;2.3e-08) 0.344828 65.582556 66.815879 20 38 KEEP --- --- --- --- Unknown broad.mit.edu 37 13 77562562 77562562 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:77562562C>T BTF3L1 (59339 upstream) : CLN5 (3497 downstream) 0.434783 29.339047 29.425435 10 13 KEEP --- --- --- --- Unknown broad.mit.edu 37 13 81258755 81258755 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:81258755C>T SPRY2 (343669 upstream) : None (None downstream) 1 16.068612 16.007964 4 0 KEEP --- --- --- --- HS6ST3 266722 broad.mit.edu 37 13 97485242 97485242 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:97485242C>T uc001vmw.2 + 2 1230 c.1206C>T c.(1204-1206)TTC>TTT p.F402F NM_153456 NP_703157 Q8IZP7 H6ST3_HUMAN heparan sulfate 6-O-sulfotransferase 3 402 Lumenal (Potential). integral to membrane sulfotransferase activity ovary(1)|skin(1) 2 all_neural(89;0.0878)|Medulloblastoma(90;0.163) 0.454545 124.567083 124.727841 40 48 KEEP --- --- --- --- IPO5 3843 broad.mit.edu 37 13 98671991 98671991 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:98671991C>T uc001vne.2 + 27 3227 c.3047C>T c.(3046-3048)TCT>TTT p.S1016F NM_002271 NP_002262 O00410 IPO5_HUMAN importin 5 998 interspecies interaction between organisms|NLS-bearing substrate import into nucleus|ribosomal protein import into nucleus cytoplasm|nuclear pore|nucleolus GTPase inhibitor activity|protein transporter activity|Ran GTPase binding ovary(1)|lung(1)|skin(1) 3 0.411111 119.162155 119.78229 37 53 KEEP --- --- --- --- RNF113B 140432 broad.mit.edu 37 13 98828890 98828890 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:98828890C>T uc001vnk.2 - 1 632 c.601G>A c.(601-603)GAG>AAG p.E201K FARP1_uc001vnh.2_Intron|FARP1_uc001vni.2_Intron|FARP1_uc001vnj.2_Intron NM_178861 NP_849192 Q8IZP6 R113B_HUMAN ring finger protein 113B 201 C3H1-type. nucleic acid binding|zinc ion binding ovary(1)|central_nervous_system(1)|skin(1) 3 all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184) BRCA - Breast invasive adenocarcinoma(86;0.13) 0.439394 91.965955 92.177268 29 37 KEEP --- --- --- --- FARP1 10160 broad.mit.edu 37 13 99061449 99061449 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:99061449C>T uc001vnj.2 + FARP1_uc001vnh.2_Intron NM_005766 NP_005757 FERM, RhoGEF, and pleckstrin domain protein 1 regulation of Rho protein signal transduction cytoplasm|cytoskeleton|extrinsic to membrane cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity breast(2) 2 all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184) BRCA - Breast invasive adenocarcinoma(86;0.233) 0.666667 6.851367 6.924696 2 1 KEEP --- --- --- --- TM9SF2 9375 broad.mit.edu 37 13 100204508 100204508 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:100204508C>T uc001voj.1 + 13 1549 c.1416C>T c.(1414-1416)GCC>GCT p.A472A TM9SF2_uc010afz.1_Silent_p.A307A NM_004800 NP_004791 Q99805 TM9S2_HUMAN transmembrane 9 superfamily member 2 precursor 472 Helical; (Potential). transport endosome membrane|integral to plasma membrane ovary(1) 1 all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218) 0.503401 244.852627 244.854132 74 73 KEEP --- --- --- --- ZIC2 7546 broad.mit.edu 37 13 100637541 100637541 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:100637541C>T uc001von.2 + NM_007129 NP_009060 zinc finger protein of the cerebellum 2 brain development|negative regulation of transcription, DNA-dependent|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|visual perception cytoplasm|nucleus chromatin DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding 0 all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184) Pancreas(97;119 1522 31925 44771 48764) 0.533333 26.101459 26.116026 8 7 KEEP --- --- --- --- TMTC4 84899 broad.mit.edu 37 13 101320963 101320963 + Missense_Mutation SNP A T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:101320963A>T uc001vou.2 - 2 192 c.32T>A c.(31-33)ATT>AAT p.I11N TMTC4_uc001vot.2_Missense_Mutation_p.I30N|TMTC4_uc010tja.1_Missense_Mutation_p.I11N NM_001079669 NP_001073137 Q5T4D3 TMTC4_HUMAN transmembrane and tetratricopeptide repeat 11 integral to membrane binding ovary(2)|breast(1) 3 all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184) 0.594595 71.149348 71.437417 22 15 KEEP --- --- --- --- MCF2L 23263 broad.mit.edu 37 13 113733045 113733045 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:113733045C>T uc001vsu.2 + 15 1993 c.1971C>T c.(1969-1971)ATC>ATT p.I657I MCF2L_uc001vsq.2_Silent_p.I657I|MCF2L_uc010tjr.1_Silent_p.I600I|MCF2L_uc001vsr.2_Silent_p.I604I|MCF2L_uc001vss.3_Silent_p.I598I|MCF2L_uc010tjs.1_Silent_p.I598I|MCF2L_uc001vst.1_Silent_p.I562I NM_001112732 NP_001106203 O15068 MCF2L_HUMAN MCF.2 cell line derived transforming 630 apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol|plasma membrane Rho guanyl-nucleotide exchange factor activity ovary(1)|kidney(1) 2 all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163) all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188) 0.4 13.301501 13.387819 4 6 KEEP --- --- --- --- TFDP1 7027 broad.mit.edu 37 13 114292256 114292256 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr13:114292256C>T uc001vtw.2 + TFDP1_uc010tkd.1_Intron|TFDP1_uc010tke.1_Intron|TFDP1_uc001vty.3_Intron|TFDP1_uc001vtx.2_Intron NM_007111 NP_009042 transcription factor Dp-1 cell proliferation|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|regulation of transcription from RNA polymerase II promoter transcription factor complex DNA binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding lung(4)|ovary(2)|skin(1) 7 Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218) all_cancers(25;0.132)|all_epithelial(44;0.0731)|all_lung(25;0.149)|Breast(118;0.153) all cancers(43;0.0576) 482 TSP Lung(29;0.18) 0.5 78.599607 78.599607 24 24 KEEP --- --- --- --- Unknown broad.mit.edu 37 14 19118034 19118034 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:19118034G>A None (None upstream) : OR11H12 (259560 downstream) 0.25 11.291819 12.201064 4 12 KEEP --- --- --- --- Unknown broad.mit.edu 37 14 19855314 19855314 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:19855314C>T POTEG (270372 upstream) : P704P (128640 downstream) 0.545455 22.15102 22.170769 6 5 KEEP --- --- --- --- OR4K15 81127 broad.mit.edu 37 14 20444099 20444099 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:20444099C>T uc010tkx.1 + 1 422 c.422C>T c.(421-423)TCC>TTC p.S141F NM_001005486 NP_001005486 Q8NH41 OR4KF_HUMAN olfactory receptor, family 4, subfamily K, 141 Helical; Name=3; (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity ovary(1) 1 all_cancers(95;0.00108) Epithelial(56;9.96e-07)|all cancers(55;3.58e-06) GBM - Glioblastoma multiforme(265;0.00327) 0.544379 307.112104 307.401331 92 77 KEEP --- --- --- --- SALL2 6297 broad.mit.edu 37 14 21993589 21993589 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:21993589G>A uc001wbe.2 - 2 555 c.273C>T c.(271-273)GTC>GTT p.V91V SALL2_uc010tly.1_Silent_p.V89V|SALL2_uc010tlz.1_Silent_p.V89V|SALL2_uc001wbf.3_Silent_p.V89V|SALL2_uc010tma.1_Silent_p.V91V|SALL2_uc001wbg.1_Silent_p.V91V NM_005407 NP_005398 Q9Y467 SALL2_HUMAN sal-like 2 91 DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding ovary(2)|large_intestine(1) 3 all_cancers(95;0.000662) GBM - Glioblastoma multiforme(265;0.0151) 0.56338 124.698827 124.945966 40 31 KEEP --- --- --- --- broad.mit.edu 37 14 22471856 22471856 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:22471856G>A uc001wbw.2 + uc010tmh.1_Intron|uc010aiv.1_Intron|uc010tmi.1_Intron|uc010tmj.1_Intron|uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc001wct.3_Silent_p.L93L SubName: Full=Alpha-chain C region; Flags: Fragment; 0.609756 81.460686 81.889476 25 16 KEEP --- --- --- --- broad.mit.edu 37 14 22989438 22989438 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:22989438G>A uc001wbw.2 + uc010aja.1_Intron|uc010tmk.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc001wcx.3_Intron|uc010ajj.1_Missense_Mutation_p.E120K|uc001wde.1_Intron|uc001wdf.2_Intron|uc010ajk.1_Intron|uc001wdg.1_Intron|uc010ajl.1_Intron|uc010ajo.1_Intron|uc010ajp.1_Intron|uc001wdv.3_Intron|uc001wec.2_Intron|uc001wee.3_Intron|uc010tmt.1_Intron|uc010ajv.1_Intron|uc001weg.2_Intron|uc001wei.2_Intron|uc001wej.2_Intron|uc001wek.2_Intron|uc001wel.2_Intron|uc001wem.3_Intron|uc001wen.1_Intron|uc001weo.2_Intron|uc001wep.2_Intron|uc001weq.2_Intron|uc001wer.2_Intron|uc001wet.2_Intron|uc001weu.2_Intron|uc001wev.2_Intron|uc001wew.2_Intron|uc010tmv.1_Intron|uc001wez.2_Intron|uc010ajx.1_Intron|uc001wfb.1_Intron|uc001wfd.1_Intron|uc001wfe.2_Intron|uc001wfg.2_Intron|uc001wfh.1_Intron|uc001wfi.2_Intron|uc001wfk.2_Intron|uc001wfl.2_Intron|uc010ajy.1_Intron|uc001wfn.2_Intron|uc001wfo.2_RNA|uc001wfp.2_Intron|uc001wfq.1_Intron|uc001wfr.1_RNA|uc010ajz.1_RNA|uc001wfs.1_5'Flank SubName: Full=Alpha-chain C region; Flags: Fragment; 0.440476 120.265261 120.524414 37 47 KEEP --- --- --- --- broad.mit.edu 37 14 23019616 23019616 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:23019616G>A uc001wcx.3 + uc001wdv.3_Intron|uc001wec.2_Intron|uc001wee.3_Intron|uc001wei.2_Intron|uc001wej.2_Intron|uc001wek.2_Intron|uc001wel.2_Intron|uc001wem.3_Intron|uc001wep.2_Intron|uc001weq.2_Intron|uc001wer.2_Intron|uc001weu.2_Intron|uc001wev.2_Intron|uc001wew.2_Intron|uc001wfe.2_Intron|uc001wfk.2_Intron|uc010ajy.1_Intron|uc001wfn.2_Intron|uc001wfp.2_Intron|uc001wfx.2_Intron|uc001wgd.2_Intron|uc001wge.3_Intron|uc010tmx.1_Intron|uc001wgh.2_Intron|uc001wgk.2_Intron Homo sapiens mRNA for T cell receptor alpha variable 13, partial cds, clone: SEB 7. 0.5 68.715815 68.715815 23 23 KEEP --- --- --- --- MYH6 4624 broad.mit.edu 37 14 23863565 23863565 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:23863565C>T uc001wjv.2 - NM_002471 NP_002462 myosin heavy chain 6 adult heart development|atrial cardiac muscle tissue morphogenesis|cardiac muscle fiber development|in utero embryonic development|muscle filament sliding|regulation of ATPase activity|regulation of blood pressure|regulation of heart rate|regulation of the force of heart contraction|sarcomere organization|striated muscle contraction|ventricular cardiac muscle tissue morphogenesis|visceral muscle development cytosol|focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|protein kinase binding|structural constituent of muscle pancreas(2)|ovary(1)|skin(1) 4 all_cancers(95;2.54e-05) GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441) 0.517241 51.825895 51.833366 15 14 KEEP --- --- --- --- MYH7 4625 broad.mit.edu 37 14 23901033 23901033 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:23901033G>A uc001wjx.2 - 7 682 c.576C>T c.(574-576)ATC>ATT p.I192I NM_000257 NP_000248 P12883 MYH7_HUMAN myosin, heavy chain 7, cardiac muscle, beta 192 Myosin head-like. adult heart development|muscle filament sliding|regulation of heart rate|ventricular cardiac muscle tissue morphogenesis focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle ovary(3)|skin(1) 4 all_cancers(95;2.54e-05) GBM - Glioblastoma multiforme(265;0.00725) 0.637931 121.276244 122.243815 37 21 KEEP --- --- --- --- RNF31 55072 broad.mit.edu 37 14 24626721 24626721 + Intron SNP C G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:24626721C>G uc001wmn.1 + RNF31_uc001wml.1_Intron|RNF31_uc010alg.1_Intron|RNF31_uc001wmo.1_Intron|RNF31_uc001wmp.2_Intron|RNF31_uc010alh.1_Intron NM_017999 NP_060469 ring finger protein 31 CD40 signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|protein linear polyubiquitination|T cell receptor signaling pathway CD40 receptor complex|internal side of plasma membrane|LUBAC complex ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding large_intestine(1)|ovary(1) 2 GBM - Glioblastoma multiforme(265;0.00861) 0.098901 7.704918 22.348552 9 82 KEEP --- --- --- --- Unknown broad.mit.edu 37 14 25900555 25900555 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:25900555C>T STXBP6 (381384 upstream) : None (None downstream) 0.538462 21.924883 21.941514 7 6 KEEP --- --- --- --- STRN3 29966 broad.mit.edu 37 14 31375983 31375983 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:31375983C>T uc001wqu.2 - STRN3_uc001wqv.2_Intron|STRN3_uc010tpj.1_Intron NM_001083893 NP_001077362 nuclear autoantigen isoform 1 negative regulation of estrogen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|response to estradiol stimulus cytoplasm|dendrite|Golgi apparatus|neuronal cell body|nucleoplasm|nucleus|plasma membrane|protein complex armadillo repeat domain binding|calmodulin binding|protein complex binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity 0 Hepatocellular(127;0.0877)|Breast(36;0.148) LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805) GBM - Glioblastoma multiforme(265;0.0124) 0.6 21.151989 21.239387 6 4 KEEP --- --- --- --- AKAP6 9472 broad.mit.edu 37 14 33068602 33068602 + Intron SNP A T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:33068602A>T uc001wrq.2 + AKAP6_uc010aml.2_Intron NM_004274 NP_004265 A-kinase anchor protein 6 protein targeting calcium channel complex|nuclear membrane|sarcoplasmic reticulum protein kinase A binding|receptor binding breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1) 21 Breast(36;0.0388)|Prostate(35;0.15) LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116) GBM - Glioblastoma multiforme(265;0.019) Melanoma(49;821 1200 7288 13647 42351) 483 0.061224 -3.526453 16.16287 6 92 KEEP --- --- --- --- SNX6 58533 broad.mit.edu 37 14 35038408 35038408 + Intron SNP G T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:35038408G>T uc001wsf.1 - SNX6_uc001wse.1_Intron|SNX6_uc010tpm.1_Intron|SNX6_uc010amm.1_Intron NM_152233 NP_689419 sorting nexin 6 isoform b cell communication|intracellular protein transport|negative regulation of epidermal growth factor receptor activity|negative regulation of transcription, DNA-dependent|negative regulation of transforming growth factor beta receptor signaling pathway|retrograde transport, endosome to Golgi cytoplasmic vesicle membrane|early endosome membrane|nucleus phosphatidylinositol binding|protein homodimerization activity 0 Breast(36;0.0473)|Hepatocellular(127;0.158) LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00199)|Epithelial(34;0.187) GBM - Glioblastoma multiforme(112;0.0245) 0.222222 6.745192 7.383902 2 7 KEEP --- --- --- --- SSTR1 6751 broad.mit.edu 37 14 38678722 38678722 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:38678722G>A uc001wul.1 + 3 745 c.128G>A c.(127-129)CGA>CAA p.R43Q SSTR1_uc010amu.1_RNA NM_001049 NP_001040 P30872 SSR1_HUMAN somatostatin receptor 1 43 Extracellular (Potential). digestion|G-protein signaling, coupled to cyclic nucleotide second messenger|negative regulation of cell proliferation|response to nutrient integral to plasma membrane somatostatin receptor activity central_nervous_system(3)|ovary(1)|lung(1) 5 Hepatocellular(127;0.213)|Esophageal squamous(585;0.22) Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187) GBM - Glioblastoma multiforme(112;0.00444) Octreotide(DB00104) 0.555556 49.428567 49.501284 15 12 KEEP --- --- --- --- NIN 51199 broad.mit.edu 37 14 51192703 51192703 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:51192703G>A uc001wym.2 - 30 6351 c.6160C>T c.(6160-6162)CTT>TTT p.L2054F NIN_uc001wyi.2_Missense_Mutation_p.L2054F|NIN_uc001wyj.2_RNA|NIN_uc001wyk.2_Missense_Mutation_p.L1341F|NIN_uc010tqp.1_Missense_Mutation_p.L2060F NM_182946 NP_891991 Q8N4C6 NIN_HUMAN ninein isoform 5 2054 Potential. centrosome localization centrosome|microtubule calcium ion binding|GTP binding|protein binding skin(3)|ovary(1)|kidney(1)|central_nervous_system(1) 6 all_epithelial(31;0.00244)|Breast(41;0.127) 745 T PDGFRB MPD 0.398148 138.099881 139.080989 43 65 KEEP --- --- --- --- RTN1 6252 broad.mit.edu 37 14 60076767 60076767 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:60076767G>A uc001xen.1 - RTN1_uc001xem.1_Intron|RTN1_uc001xek.1_Intron|RTN1_uc001xel.1_Intron|RTN1_uc010apl.1_Intron NM_021136 NP_066959 reticulon 1 isoform A neuron differentiation integral to endoplasmic reticulum membrane signal transducer activity ovary(2)|central_nervous_system(2) 4 OV - Ovarian serous cystadenocarcinoma(108;0.0968) 0.769231 36.057118 36.920986 10 3 KEEP --- --- --- --- C14orf39 317761 broad.mit.edu 37 14 60933553 60933553 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:60933553G>A uc001xez.3 - C14orf39_uc010apo.2_Intron NM_174978 NP_777638 hypothetical protein LOC317761 ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1) 4 OV - Ovarian serous cystadenocarcinoma(108;0.0448) 0.3 8.020558 8.378253 3 7 KEEP --- --- --- --- Unknown broad.mit.edu 37 14 60960915 60960916 + IGR DNP GG AA AA MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:60960915_60960916GG>AA C14orf39 (8151 upstream) : SIX6 (15022 downstream) 0.5625 30.97925 31.034307 9 7 KEEP --- --- --- --- SIX6 4990 broad.mit.edu 37 14 60978015 60978015 + 3'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:60978015G>A uc001xfa.3 + 2 NM_007374 NP_031400 SIX homeobox 6 organ morphogenesis|visual perception nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity 0 OV - Ovarian serous cystadenocarcinoma(108;0.088) 0.488372 65.170788 65.175925 21 22 KEEP --- --- --- --- SLC38A6 145389 broad.mit.edu 37 14 61512811 61512811 + Missense_Mutation SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:61512811T>C uc001xfg.1 + 12 967 c.851T>C c.(850-852)GTT>GCT p.V284A SLC38A6_uc001xfh.1_Missense_Mutation_p.V284A|SLC38A6_uc001xfi.2_RNA|SLC38A6_uc001xfj.1_RNA|SLC38A6_uc001xfk.2_RNA|SLC38A6_uc010trz.1_Missense_Mutation_p.V261A NM_153811 NP_722518 Q8IZM9 S38A6_HUMAN solute carrier family 38, member 6 284 amino acid transport|sodium ion transport integral to membrane ovary(1)|central_nervous_system(1)|skin(1) 3 OV - Ovarian serous cystadenocarcinoma(108;0.0981) 0.44898 82.947438 83.058136 22 27 KEEP --- --- --- --- SYT16 83851 broad.mit.edu 37 14 62462679 62462679 + 5'UTR SNP C G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:62462679C>G uc001xfu.1 + 1 SYT16_uc010tsd.1_5'UTR NM_031914 NP_114120 synaptotagmin XIV-like central_nervous_system(1) 1 OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118) 0.147059 11.750877 15.820114 5 29 KEEP --- --- --- --- Unknown broad.mit.edu 37 14 64061676 64061676 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:64061676G>A PPP2R5E (51597 upstream) : WDR89 (2082 downstream) 0.485714 58.474163 58.480369 17 18 KEEP --- --- --- --- PLEKHG3 26030 broad.mit.edu 37 14 65209974 65209974 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:65209974C>T uc001xho.1 + 17 3482 c.3213C>T c.(3211-3213)CCC>CCT p.P1071P PLEKHG3_uc001xhn.1_Silent_p.P1015P|PLEKHG3_uc001xhp.2_Silent_p.P1192P|PLEKHG3_uc010aqh.1_Silent_p.P613P|PLEKHG3_uc001xhq.1_Silent_p.P576P NM_015549 NP_056364 A1L390 PKHG3_HUMAN pleckstrin homology domain containing, family G, 1071 regulation of Rho protein signal transduction intracellular Rho guanyl-nucleotide exchange factor activity skin(1) 1 all cancers(60;0.00802)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)|BRCA - Breast invasive adenocarcinoma(234;0.0485) 0.722222 42.288762 43.100309 13 5 KEEP --- --- --- --- SPTB 6710 broad.mit.edu 37 14 65262127 65262127 + Silent SNP G A A rs149192360 byFrequency MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:65262127G>A uc001xht.2 - 11 1626 c.1572C>T c.(1570-1572)CTC>CTT p.L524L SPTB_uc001xhr.2_Silent_p.L524L|SPTB_uc001xhs.2_Silent_p.L524L|SPTB_uc001xhu.2_Silent_p.L524L NM_000347 NP_000338 P11277 SPTB1_HUMAN spectrin beta isoform b 524 Spectrin 3. actin filament capping|axon guidance cell surface|cytosol|intrinsic to internal side of plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton actin filament binding|structural constituent of cytoskeleton ovary(7)|skin(2)|lung(1)|central_nervous_system(1) 11 all_lung(585;4.15e-09) all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628) 0.533333 51.003293 51.032599 16 14 KEEP --- --- --- --- FAM71D 161142 broad.mit.edu 37 14 67671503 67671503 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:67671503G>A uc001xja.1 + 5 863 c.609G>A c.(607-609)ATG>ATA p.M203I FAM71D_uc010aqn.1_RNA NM_173526 NP_775797 Q8N9W8 FA71D_HUMAN hypothetical protein LOC161142 203 ovary(1) 1 all_hematologic(31;0.0116) all cancers(60;0.00107)|BRCA - Breast invasive adenocarcinoma(234;0.00993)|OV - Ovarian serous cystadenocarcinoma(108;0.012) 0.47 146.219493 146.29736 47 53 KEEP --- --- --- --- SLC8A3 6547 broad.mit.edu 37 14 70634857 70634857 + Missense_Mutation SNP C A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:70634857C>A uc001xly.2 - 2 1037 c.283G>T c.(283-285)GCT>TCT p.A95S SLC8A3_uc001xlw.2_Missense_Mutation_p.A95S|SLC8A3_uc001xlx.2_Missense_Mutation_p.A95S|SLC8A3_uc001xlz.2_Missense_Mutation_p.A95S|SLC8A3_uc010ara.2_RNA NM_183002 NP_892114 P57103 NAC3_HUMAN solute carrier family 8 (sodium/calcium 95 Cytoplasmic (Potential). cell communication|platelet activation integral to membrane|plasma membrane calcium:sodium antiporter activity|calmodulin binding skin(3)|ovary(2)|breast(2) 7 BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555) 0.166667 17.067488 22.125541 8 40 KEEP --- --- --- --- ADAM21P1 145241 broad.mit.edu 37 14 70714078 70714078 + 5'UTR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:70714078C>T uc010ttg.1 - 1 NR_003951 SubName: Full=ADAM21-like protein; 0 0.152174 45.078674 61.062919 21 117 KEEP --- --- --- --- ADAM21 8747 broad.mit.edu 37 14 70924516 70924516 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:70924516G>A uc001xmd.2 + 1 300 c.300G>A c.(298-300)GAG>GAA p.E100E NM_003813 NP_003804 Q9UKJ8 ADA21_HUMAN ADAM metallopeptidase domain 21 preproprotein 100 proteolysis|single fertilization integral to membrane metalloendopeptidase activity|zinc ion binding pancreas(1)|skin(1) 2 all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401) 0.454545 225.462869 225.719988 65 78 KEEP --- --- --- --- ACOT6 641372 broad.mit.edu 37 14 74085899 74085899 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:74085899G>A uc001xop.2 + NM_001037162 NP_001032239 acyl-CoA thioesterase 6 cytosol carboxylesterase activity 0 BRCA - Breast invasive adenocarcinoma(234;0.00331) 0.533333 207.803768 207.919273 64 56 KEEP --- --- --- --- PROX2 283571 broad.mit.edu 37 14 75323627 75323627 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:75323627C>T uc001xqr.1 - 3 1485 c.1485G>A c.(1483-1485)ATG>ATA p.M495I uc001xqp.1_5'Flank|PROX2_uc001xqq.1_Missense_Mutation_p.M194I NM_001080408 NP_001073877 Q3B8N5 PROX2_HUMAN prospero homeobox 2 495 Prospero-type homeobox. multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding 0 KIRC - Kidney renal clear cell carcinoma(43;0.238) BRCA - Breast invasive adenocarcinoma(234;0.00652) 0.51634 273.428974 273.464326 79 74 KEEP --- --- --- --- MLH3 27030 broad.mit.edu 37 14 75508457 75508457 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:75508457G>A uc001xrd.1 - MLH3_uc001xre.1_Intron|MLH3_uc010tuy.1_Intron NM_001040108 NP_001035197 mutL homolog 3 isoform 1 mismatch repair|reciprocal meiotic recombination chiasma|MutLbeta complex|synaptonemal complex ATP binding|ATPase activity|mismatched DNA binding|protein binding|satellite DNA binding ovary(1)|skin(1) 2 BRCA - Breast invasive adenocarcinoma(234;0.00688) MMR 0.53125 59.277205 59.304361 17 15 KEEP --- --- --- --- SPTLC2 9517 broad.mit.edu 37 14 78036877 78036877 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:78036877G>A uc001xub.2 - NM_004863 NP_004854 serine palmitoyltransferase, long chain base integral to membrane|serine C-palmitoyltransferase complex pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups upper_aerodigestive_tract(1)|ovary(1) 2 Kidney(204;0.164) BRCA - Breast invasive adenocarcinoma(234;0.0346) L-Serine(DB00133)|Pyridoxal Phosphate(DB00114) 0.606557 124.484612 125.090241 37 24 KEEP --- --- --- --- TSHR 7253 broad.mit.edu 37 14 81554215 81554215 + Intron SNP T A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:81554215T>A uc001xvd.1 + TSHR_uc001xvb.1_Intron|TSHR_uc001xvc.2_Intron|TSHR_uc010tvs.1_Intron NM_000369 NP_000360 thyroid stimulating hormone receptor isoform 1 cell-cell signaling|positive regulation of cell proliferation integral to plasma membrane protein binding|thyroid-stimulating hormone receptor activity thyroid(289)|ovary(5)|lung(3)|kidney(1)|skin(1) 299 BRCA - Breast invasive adenocarcinoma(234;0.0402) Thyrotropin Alfa(DB00024) 868 Mis toxic thyroid adenoma thyroid adenoma Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism 0.354839 33.119766 33.693829 11 20 KEEP --- --- --- --- FLRT2 23768 broad.mit.edu 37 14 86089701 86089701 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:86089701G>A uc001xvr.2 + 2 2610 c.1843G>A c.(1843-1845)GAT>AAT p.D615N FLRT2_uc010atd.2_Missense_Mutation_p.D615N NM_013231 NP_037363 O43155 FLRT2_HUMAN fibronectin leucine rich transmembrane protein 2 615 Cytoplasmic (Potential). cell adhesion integral to plasma membrane|proteinaceous extracellular matrix protein binding, bridging|receptor signaling protein activity ovary(3)|haematopoietic_and_lymphoid_tissue(1) 4 BRCA - Breast invasive adenocarcinoma(234;0.0319) 0.502242 378.636195 378.637473 112 111 KEEP --- --- --- --- EML5 161436 broad.mit.edu 37 14 89110934 89110934 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:89110934G>A uc001xxg.2 - EML5_uc001xxf.2_Intron|EML5_uc001xxh.1_Intron NM_183387 NP_899243 echinoderm microtubule associated protein like cytoplasm|microtubule ovary(3) 3 0.642857 30.578623 30.830101 9 5 KEEP --- --- --- --- CCDC88C 440193 broad.mit.edu 37 14 91774599 91774599 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:91774599G>A uc010aty.2 - NM_001080414 NP_001073883 DVL-binding protein DAPLE microtubule cytoskeleton organization|protein destabilization|protein homooligomerization|regulation of protein phosphorylation|Wnt receptor signaling pathway cytoplasm|insoluble fraction microtubule binding|PDZ domain binding|protein self-association ovary(3) 3 all_cancers(154;0.0468) 0.545455 20.552672 20.572761 6 5 KEEP --- --- --- --- CATSPERB 79820 broad.mit.edu 37 14 92170796 92170796 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:92170796C>T uc001xzs.1 - NM_024764 NP_079040 cation channel, sperm-associated, beta cell differentiation|multicellular organismal development|spermatogenesis integral to membrane breast(2)|skin(2)|ovary(1) 5 all_cancers(154;0.0663)|all_epithelial(191;0.236) 637 0.512821 66.607494 66.613405 20 19 KEEP --- --- --- --- UBR7 55148 broad.mit.edu 37 14 93686792 93686792 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:93686792C>T uc001ybm.3 + UBR7_uc001ybn.3_Intron|UBR7_uc010auq.2_Intron NM_175748 NP_786924 ubiquitin protein ligase E3 component n-recognin ubiquitin-protein ligase activity|zinc ion binding 0 0.333333 55.810064 57.210271 19 38 KEEP --- --- --- --- SERPINA1 5265 broad.mit.edu 37 14 94844744 94844744 + 3'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:94844744G>A uc001ycx.3 - 5 SERPINA1_uc001ycw.3_RNA|SERPINA1_uc010auw.2_3'UTR|SERPINA1_uc010aux.2_3'UTR|SERPINA1_uc001ycy.3_3'UTR|SERPINA1_uc010auy.2_3'UTR|SERPINA1_uc001ycz.3_3'UTR|SERPINA1_uc010auz.2_3'UTR|SERPINA1_uc010ava.2_3'UTR|SERPINA1_uc001ydb.3_3'UTR|SERPINA1_uc010avb.2_3'UTR|SERPINA1_uc001ydc.3_3'UTR NM_000295 NP_000286 serine proteinase inhibitor, clade A, member 1 acute-phase response|platelet activation|platelet degranulation|regulation of proteolysis extracellular space|platelet alpha granule lumen|proteinaceous extracellular matrix protease binding|serine-type endopeptidase inhibitor activity skin(1) 1 all_cancers(154;0.0649)|all_epithelial(191;0.223) Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221) Alpha-1-proteinase inhibitor(DB00058) Alpha-1-Antitrypsin_Deficiency 0.454545 48.168375 48.220281 15 18 KEEP --- --- --- --- SERPINA11 256394 broad.mit.edu 37 14 94909358 94909358 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:94909358G>A uc001ydd.1 - NM_001080451 NP_001073920 serpin peptidase inhibitor, clade A (alpha-1 regulation of proteolysis extracellular region serine-type endopeptidase inhibitor activity kidney(1) 1 COAD - Colon adenocarcinoma(157;0.211) 0.464286 175.690407 175.814846 52 60 KEEP --- --- --- --- SERPINA3 12 broad.mit.edu 37 14 95085903 95085903 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:95085903G>A uc001ydp.2 + SERPINA3_uc001ydo.3_Intron|SERPINA3_uc001ydr.2_Intron|SERPINA3_uc001ydq.2_Intron|SERPINA3_uc001yds.2_Intron|SERPINA3_uc010avg.2_Intron NM_001085 NP_001076 serpin peptidase inhibitor, clade A, member 3 acute-phase response|maintenance of gastrointestinal epithelium|regulation of lipid metabolic process|regulation of proteolysis extracellular region|nucleus DNA binding|protein binding|serine-type endopeptidase inhibitor activity ovary(2)|central_nervous_system(2)|large_intestine(1)|skin(1) 6 all_cancers(154;0.0525)|all_epithelial(191;0.179) COAD - Colon adenocarcinoma(157;0.212)|Epithelial(152;0.228) 0.384615 33.444215 33.747637 10 16 KEEP --- --- --- --- SERPINA3 12 broad.mit.edu 37 14 95090279 95090279 + 3'UTR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:95090279C>T uc001ydp.2 + 5 SERPINA3_uc001ydo.3_3'UTR|SERPINA3_uc001ydr.2_RNA|SERPINA3_uc001ydq.2_3'UTR|SERPINA3_uc001yds.2_3'UTR|SERPINA3_uc010avg.2_3'UTR NM_001085 NP_001076 serpin peptidase inhibitor, clade A, member 3 acute-phase response|maintenance of gastrointestinal epithelium|regulation of lipid metabolic process|regulation of proteolysis extracellular region|nucleus DNA binding|protein binding|serine-type endopeptidase inhibitor activity ovary(2)|central_nervous_system(2)|large_intestine(1)|skin(1) 6 all_cancers(154;0.0525)|all_epithelial(191;0.179) COAD - Colon adenocarcinoma(157;0.212)|Epithelial(152;0.228) 0.375 19.145954 19.365503 6 10 KEEP --- --- --- --- CLMN 79789 broad.mit.edu 37 14 95657845 95657845 + 3'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:95657845G>A uc001yef.2 - 13 NM_024734 NP_079010 calmin integral to membrane actin binding 0 Epithelial(152;0.193) 0.586207 53.377541 53.565257 17 12 KEEP --- --- --- --- CLMN 79789 broad.mit.edu 37 14 95670258 95670258 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:95670258C>T uc001yef.2 - 9 1544 c.1428G>A c.(1426-1428)CAG>CAA p.Q476Q NM_024734 NP_079010 Q96JQ2 CLMN_HUMAN calmin 476 integral to membrane actin binding 0 Epithelial(152;0.193) 0.552632 73.081205 73.17326 21 17 KEEP --- --- --- --- TCL6 27004 broad.mit.edu 37 14 96135793 96135793 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:96135793C>T uc001yeq.2 + TCL6_uc001yep.1_Intron|TCL6_uc001yes.2_3'UTR|TCL6_uc001yet.1_Intron|TCL6_uc001yeu.2_Intron|TCL6_uc001yev.2_3'UTR|TCL1B_uc001yew.2_Intron|TCL1B_uc001yex.2_Intron|TCL1B_uc010avj.2_Intron|TCL6_uc010avk.1_5'Flank NM_020554 NP_065579 SubName: Full=T-cell leukemia/lymphoma 6 ORF163; 0 all_cancers(154;0.103) Epithelial(152;0.0655)|all cancers(159;0.149)|BRCA - Breast invasive adenocarcinoma(234;0.206)|COAD - Colon adenocarcinoma(157;0.207) 187 T TRA@ T-ALL 0.333333 11.422072 11.704445 4 8 KEEP --- --- --- --- BDKRB2 624 broad.mit.edu 37 14 96706694 96706694 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:96706694C>T uc010avm.1 + BDKRB2_uc010avl.1_3'UTR|BDKRB2_uc010twu.1_Intron|BDKRB2_uc001yfg.2_Intron NM_000623 NP_000614 bradykinin receptor B2 arachidonic acid secretion|elevation of cytosolic calcium ion concentration|transmembrane receptor protein tyrosine kinase signaling pathway endosome|integral to plasma membrane bradykinin receptor activity|phosphatidylinositol phospholipase C activity|protease binding|protein heterodimerization activity|type 1 angiotensin receptor binding ovary(3)|breast(1)|kidney(1) 5 all_cancers(154;0.0678)|Melanoma(154;0.155)|all_epithelial(191;0.179) COAD - Colon adenocarcinoma(157;0.226) 0.458621 448.434896 448.867244 133 157 KEEP --- --- --- --- ATG2B 55102 broad.mit.edu 37 14 96761528 96761528 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:96761528G>A uc001yfi.2 - NM_018036 NP_060506 ATG2 autophagy related 2 homolog B ovary(1)|kidney(1)|skin(1) 3 all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155) Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244) 0.382353 40.267569 40.680056 13 21 KEEP --- --- --- --- VRK1 7443 broad.mit.edu 37 14 97319060 97319060 + Intron SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:97319060A>G uc001yft.2 + NM_003384 NP_003375 vaccinia related kinase 1 cytoplasm|nucleolus ATP binding|protein binding|protein serine/threonine kinase activity large_intestine(1)|stomach(1) 2 Melanoma(154;0.155) COAD - Colon adenocarcinoma(157;0.234) 187 0.4 7.249264 7.292924 2 3 KEEP --- --- --- --- Unknown broad.mit.edu 37 14 99439706 99439706 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:99439706G>A C14orf177 (255609 upstream) : BCL11B (195921 downstream) 0.583333 21.323602 21.396096 7 5 KEEP --- --- --- --- DLK1 8788 broad.mit.edu 37 14 101194816 101194816 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:101194816G>A uc001yhs.3 + DLK1_uc001yhu.3_Intron NM_003836 NP_003827 delta-like 1 homolog precursor multicellular organismal development extracellular space|integral to membrane|soluble fraction ovary(2)|breast(1)|skin(1) 4 Melanoma(154;0.155) 0.48 77.095854 77.113351 24 26 KEEP --- --- --- --- MIR656 724026 broad.mit.edu 37 14 101533099 101533099 + RNA SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:101533099G>A hsa-mir-656|MI0003678 + c.39G>A 0 0.47619 94.74499 94.776167 30 33 KEEP --- --- --- --- TRAF3 7187 broad.mit.edu 37 14 103355991 103355992 + Intron DNP CC TT TT MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:103355991_103355992CC>TT uc001ymc.1 + TRAF3_uc001yme.1_Intron|TRAF3_uc001ymd.1_Intron|TRAF3_uc010txy.1_Intron NM_145725 NP_663777 TNF receptor-associated factor 3 isoform 1 apoptosis|induction of apoptosis|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|regulation of defense response to virus|regulation of interferon-beta production|regulation of proteolysis|toll-like receptor signaling pathway|tumor necrosis factor-mediated signaling pathway CD40 receptor complex|cytosol|endosome|internal side of plasma membrane|mitochondrion signal transducer activity|ubiquitin-protein ligase activity|zinc ion binding ovary(1)|lung(1)|breast(1) 3 all_cancers(154;7.87e-06)|all_epithelial(191;0.0024) Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971) 0.49 165.67408 165.682674 49 51 KEEP --- --- --- --- KIAA0284 283638 broad.mit.edu 37 14 105349511 105349511 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:105349511C>T uc010axb.2 + 8 941 c.717C>T c.(715-717)CCC>CCT p.P239P INF2_uc010tyi.1_Intron|KIAA0284_uc001ypr.2_Silent_p.P169P|KIAA0284_uc001yps.2_Silent_p.P145P NM_001112726 NP_001106197 Q9Y4F5 K0284_HUMAN hypothetical protein LOC283638 isoform 1 239 cytoplasm|microtubule breast(1) 1 all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183) all cancers(16;0.000472)|OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0149)|GBM - Glioblastoma multiforme(11;0.116) Epithelial(152;0.178) 0.333333 13.196175 13.491295 4 8 KEEP --- --- --- --- AHNAK2 113146 broad.mit.edu 37 14 105406305 105406305 + Silent SNP T A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:105406305T>A uc010axc.1 - 7 15603 c.15483A>T c.(15481-15483)CCA>CCT p.P5161P AHNAK2_uc001ypx.2_Silent_p.P5061P NM_138420 NP_612429 Q8IVF2 AHNK2_HUMAN AHNAK nucleoprotein 2 5161 nucleus ovary(1) 1 all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183) all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116) 0.567901 318.907505 319.55665 92 70 KEEP --- --- --- --- AHNAK2 113146 broad.mit.edu 37 14 105411255 105411255 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:105411255G>A uc010axc.1 - 7 10653 c.10533C>T c.(10531-10533)TCC>TCT p.S3511S AHNAK2_uc001ypx.2_Silent_p.S3411S NM_138420 NP_612429 Q8IVF2 AHNK2_HUMAN AHNAK nucleoprotein 2 3511 nucleus ovary(1) 1 all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183) all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116) 0.487805 250.1819 250.203487 80 84 KEEP --- --- --- --- ADAM6 8755 broad.mit.edu 37 14 106054600 106054600 + RNA SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:106054600C>T uc010tyt.1 - 3650 c.62886G>A uc001yrs.2_RNA|uc001yrt.2_Missense_Mutation_p.G51R Parts of antibodies, mostly variable regions. 0 30 0.534884 74.825987 74.871401 23 20 KEEP --- --- --- --- ADAM6 8755 broad.mit.edu 37 14 106235702 106235702 + RNA SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:106235702G>A uc010tyt.1 - 3617 c.58145C>T uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_Intron|uc001ysf.2_Intron|uc001ysh.1_RNA|uc001ysi.1_RNA Parts of antibodies, mostly variable regions. 0 30 0.426087 319.046687 320.155318 98 132 KEEP --- --- --- --- ADAM6 8755 broad.mit.edu 37 14 106320377 106320377 + Intron SNP G A A rs139116944 by1000genomes MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:106320377G>A uc010tyt.1 - uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_Intron|uc001yse.2_Intron|uc001ysf.2_Intron|uc001ysj.2_Intron|uc001ysk.1_Intron|uc001ysl.1_Intron|uc001ysm.1_Intron|uc001ysn.1_Intron|uc001yso.1_Intron Parts of antibodies, mostly variable regions. 0 30 0.3125 30.839947 31.840526 10 22 KEEP --- --- --- --- ADAM6 8755 broad.mit.edu 37 14 106631546 106631546 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:106631546C>T uc010tyt.1 - Parts of antibodies, mostly variable regions. 0 30 0.5 25.89843 25.89843 8 8 KEEP --- --- --- --- ADAM6 8755 broad.mit.edu 37 14 107034876 107034876 + RNA SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:107034876C>T uc010tyt.1 - 154 c.7357G>A uc001ysz.2_Silent_p.G68G Parts of antibodies, mostly variable regions. 0 30 0.428571 44.116908 44.27315 15 20 KEEP --- --- --- --- ADAM6 8755 broad.mit.edu 37 14 107035145 107035145 + RNA SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:107035145G>A uc010tyt.1 - 153 c.7169C>T uc001ysz.2_Silent_p.I6I Parts of antibodies, mostly variable regions. 0 30 0.538462 23.725983 23.742693 7 6 KEEP --- --- --- --- ADAM6 8755 broad.mit.edu 37 14 107122114 107122114 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:107122114G>A uc010tyt.1 - Parts of antibodies, mostly variable regions. 0 30 0.604167 193.876917 194.79339 58 38 KEEP --- --- --- --- ADAM6 8755 broad.mit.edu 37 14 107139954 107139954 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr14:107139954C>T uc010tyt.1 - Parts of antibodies, mostly variable regions. 0 30 0.3 9.420809 9.778338 3 7 KEEP --- --- --- --- Unknown broad.mit.edu 37 15 20193108 20193108 + IGR SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:20193108T>C None (None upstream) : GOLGA6L6 (543986 downstream) 0.432432 56.595486 56.742633 16 21 KEEP --- --- --- --- Unknown broad.mit.edu 37 15 20213639 20213639 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:20213639G>A None (None upstream) : GOLGA6L6 (523455 downstream) 0.205882 17.105477 19.832814 7 27 KEEP --- --- --- --- broad.mit.edu 37 15 20496556 20496556 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:20496556G>A uc001ytf.1 + full-length cDNA clone CS0DI026YN18 of Placenta Cot 25-normalized of Homo sapiens (human). 0.454545 14.271699 14.291701 5 6 KEEP --- --- --- --- OR4M2 390538 broad.mit.edu 37 15 22369069 22369069 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:22369069G>A uc010tzu.1 + 1 494 c.494G>A c.(493-495)CGA>CAA p.R165Q LOC727924_uc001yua.2_Intron|LOC727924_uc001yub.1_Intron|OR4N4_uc001yuc.1_Intron NM_001004719 NP_001004719 Q8NGB6 OR4M2_HUMAN olfactory receptor, family 4, subfamily M, 165 Extracellular (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity ovary(1) 1 all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101) GBM - Glioblastoma multiforme(6;0.124) all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963) 0.47343 316.7548 316.879617 98 109 KEEP --- --- --- --- OR4N4 283694 broad.mit.edu 37 15 22382727 22382727 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:22382727C>T uc001yuc.1 + 7 1236 c.255C>T c.(253-255)TTC>TTT p.F85F LOC727924_uc001yub.1_RNA|OR4N4_uc010tzv.1_Silent_p.F85F NM_001005241 NP_001005241 Q8N0Y3 OR4N4_HUMAN olfactory receptor, family 4, subfamily N, 85 Extracellular (Potential). sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity ovary(4)|skin(1) 5 all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101) GBM - Glioblastoma multiforme(6;0.124) all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963) 0.107843 10.245118 25.805409 11 91 KEEP --- --- --- --- OR4N3P 390539 broad.mit.edu 37 15 22413716 22413716 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:22413716C>T uc001yuf.2 + 1 15 c.15C>T c.(13-15)TTC>TTT p.F5F NM_001080841 NP_001074310 RecName: Full=Olfactory receptor 4N2; AltName: Full=Olfactory receptor OR14-8; AltName: Full=Olfactory receptor OR14-13; 0 0.298969 165.181182 172.183812 58 136 KEEP --- --- --- --- NDN 4692 broad.mit.edu 37 15 23931839 23931839 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:23931839G>A uc001ywk.2 - 1 612 c.526C>T c.(526-528)CTG>TTG p.L176L NM_002487 NP_002478 Q99608 NECD_HUMAN necdin 176 MAGE. negative regulation of cell proliferation|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus|perikaryon DNA binding 0 all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14) all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00179)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153) Prader-Willi_syndrome 0.083333 0.594663 6.948844 3 33 KEEP --- --- --- --- C15orf2 23742 broad.mit.edu 37 15 24923412 24923412 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:24923412C>T uc001ywo.2 + 1 2872 c.2398C>T c.(2398-2400)CCT>TCT p.P800S NM_018958 NP_061831 Q9NZP6 CO002_HUMAN hypothetical protein LOC23742 800 cell differentiation|multicellular organismal development|spermatogenesis ovary(2)|large_intestine(2)|skin(2)|kidney(1)|central_nervous_system(1) 8 all_cancers(20;2.14e-21)|all_epithelial(15;4.77e-19)|Lung NSC(15;1.43e-14)|all_lung(15;9.57e-14)|Breast(32;0.00086) all cancers(64;3.19e-24)|Epithelial(43;2.67e-17)|GBM - Glioblastoma multiforme(186;7.36e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000273)|Lung(196;0.229) 443 0.456989 258.906728 259.211087 85 101 KEEP --- --- --- --- broad.mit.edu 37 15 25422062 25422062 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:25422062G>A uc001yys.1 + SNORD115-5_uc001yyv.1_5'Flank Homo sapiens clone Rt-5 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced. 0.535211 370.509365 370.746189 114 99 KEEP --- --- --- --- broad.mit.edu 37 15 25429678 25429678 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:25429678C>T uc001yyy.1 + uc001yza.1_Intron|SNORD115-9_uc001yzc.1_5'Flank Homo sapiens clone Rt-7 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced. 0.5 41.974137 41.974137 13 13 KEEP --- --- --- --- PAR4 347745 broad.mit.edu 37 15 25442683 25442683 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:25442683G>A uc001yzk.1 + PAR4_uc010ayo.1_Intron|SNORD115-16_uc001yzm.1_5'Flank Homo sapiens clone Rt-13I SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced. 0 0.503356 233.999643 234.0009 75 74 KEEP --- --- --- --- SNORD115-20 100033460 broad.mit.edu 37 15 25474241 25474241 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:25474241C>T uc001yzq.1 + SNORD115-26_uc001yzw.1_Intron|SNORD115-33_uc001zab.1_5'Flank NR_003313 Homo sapiens small nucleolar RNA, C/D box 115-15 (SNORD115-15), non-coding RNA. 0 0.45283 149.304477 149.506741 48 58 KEEP --- --- --- --- broad.mit.edu 37 15 25494620 25494620 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:25494620G>A uc001zae.2 + SNORD115-44_uc001zam.1_5'Flank Homo sapiens clone Rt-16 SNURF-SNRPN mRNA, downstream untranslated exons, alternatively spliced. 0.4 12.797886 12.885391 4 6 KEEP --- --- --- --- Unknown broad.mit.edu 37 15 28702811 28702812 + IGR DNP GG AA AA MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:28702811_28702812GG>AA GOLGA8G (65640 upstream) : WHAMML2 (279917 downstream) 0.5 29.432921 29.432921 10 10 KEEP --- --- --- --- ACTC1 70 broad.mit.edu 37 15 35085357 35085357 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:35085357C>T uc001ziu.1 - uc001zit.1_Intron NM_005159 NP_005150 cardiac muscle alpha actin 1 proprotein apoptosis|cardiac muscle tissue morphogenesis|cardiac myofibril assembly|muscle filament sliding|skeletal muscle thin filament assembly actomyosin, actin part|cytosol|I band ATP binding|ATPase activity|myosin binding upper_aerodigestive_tract(1)|ovary(1) 2 all_lung(180;2.3e-08) all cancers(64;5.83e-19)|GBM - Glioblastoma multiforme(113;1.98e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0244) 0.36 27.168089 27.599481 9 16 KEEP --- --- --- --- JMJD7-PLA2G4B 8681 broad.mit.edu 37 15 42127985 42127985 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:42127985C>T uc001zoo.3 + JMJD7-PLA2G4B_uc001zom.2_Intron|JMJD7-PLA2G4B_uc001zon.2_Intron|JMJD7-PLA2G4B_uc010bcn.2_Intron|JMJD7-PLA2G4B_uc001zop.1_Intron|JMJD7-PLA2G4B_uc001zoq.3_5'Flank NM_005090 NP_005081 JMJD7-PLA2G4B protein arachidonic acid metabolic process|calcium-mediated signaling|glycerophospholipid catabolic process|inflammatory response|parturition cytosol|early endosome membrane|extracellular region|mitochondrial membrane calcium ion binding|calcium-dependent phospholipase A2 activity|calcium-dependent phospholipid binding|lysophospholipase activity large_intestine(1) 1 0.307692 9.6904 10.121914 4 9 KEEP --- --- --- --- SPTBN5 51332 broad.mit.edu 37 15 42156230 42156230 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:42156230G>A uc001zos.2 - NM_016642 NP_057726 spectrin, beta, non-erythrocytic 5 actin cytoskeleton organization|actin filament capping|axon guidance cytosol|membrane|spectrin ovary(1)|central_nervous_system(1) 2 all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173) all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908) 0.576471 173.581728 174.014369 49 36 KEEP --- --- --- --- TTBK2 146057 broad.mit.edu 37 15 43038431 43038431 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:43038431C>T uc001zqo.2 - 15 3736 c.3297G>A c.(3295-3297)GGG>GGA p.G1099G TTBK2_uc010bcy.2_Silent_p.G1030G|uc001zqn.2_5'Flank NM_173500 NP_775771 Q6IQ55 TTBK2_HUMAN tau tubulin kinase 2 1099 cell death ATP binding|protein serine/threonine kinase activity ovary(2)|lung(2)|stomach(1)|pancreas(1)|skin(1) 7 all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216) GBM - Glioblastoma multiforme(94;3.23e-07) 253 0.4 48.712454 49.055545 16 24 KEEP --- --- --- --- TTBK2 146057 broad.mit.edu 37 15 43094555 43094555 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:43094555G>A uc001zqo.2 - TTBK2_uc010bcy.2_Intron|TTBK2_uc001zqp.2_Intron|TTBK2_uc010bcz.1_Intron NM_173500 NP_775771 tau tubulin kinase 2 cell death ATP binding|protein serine/threonine kinase activity ovary(2)|lung(2)|stomach(1)|pancreas(1)|skin(1) 7 all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216) GBM - Glioblastoma multiforme(94;3.23e-07) 253 0.607143 59.180946 59.462371 17 11 KEEP --- --- --- --- TGM7 116179 broad.mit.edu 37 15 43577036 43577036 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:43577036G>A uc001zrf.1 - 7 985 c.980C>T c.(979-981)TCA>TTA p.S327L NM_052955 NP_443187 Q96PF1 TGM7_HUMAN transglutaminase 7 327 peptide cross-linking acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity ovary(2) 2 all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215) GBM - Glioblastoma multiforme(94;9.14e-07) L-Glutamine(DB00130) 0.318548 230.033918 237.292959 79 169 KEEP --- --- --- --- MAP1A 4130 broad.mit.edu 37 15 43814383 43814383 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:43814383G>A uc001zrt.2 + 4 1179 c.712G>A c.(712-714)GAG>AAG p.E238K NM_002373 NP_002364 P78559 MAP1A_HUMAN microtubule-associated protein 1A 238 cytoplasm|microtubule|microtubule associated complex protein binding|structural molecule activity ovary(3)|breast(3)|pancreas(2)|skin(1) 9 all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215) GBM - Glioblastoma multiforme(94;3.05e-06) Estramustine(DB01196) 0.657143 228.802994 231.092814 69 36 KEEP --- --- --- --- Unknown broad.mit.edu 37 15 45507825 45507825 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:45507825G>A SHF (14452 upstream) : SLC28A2 (36603 downstream) OREG0011603 type=TRANSCRIPTION FACTOR BINDING SITE|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip); Conservation found by scanning with a motif model 0.722222 45.382398 46.181792 13 5 KEEP --- --- --- --- C15orf33 196951 broad.mit.edu 37 15 49800629 49800629 + Intron SNP T A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:49800629T>A uc001zxl.2 - C15orf33_uc001zxm.2_Intron NM_152647 NP_689860 hypothetical protein LOC196951 ovary(1) 1 all_lung(180;0.00187) all cancers(107;3.45e-08)|GBM - Glioblastoma multiforme(94;0.000124) 0.666667 47.256172 47.772583 14 7 KEEP --- --- --- --- SLC27A2 11001 broad.mit.edu 37 15 50519287 50519287 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:50519287G>A uc001zxw.2 + 7 1601 c.1369G>A c.(1369-1371)GGA>AGA p.G457R SLC27A2_uc010bes.2_Missense_Mutation_p.G404R|SLC27A2_uc001zxx.2_Missense_Mutation_p.G222R NM_003645 NP_003636 O14975 S27A2_HUMAN solute carrier family 27 (fatty acid 457 Cytoplasmic (Potential). bile acid biosynthetic process|fatty acid alpha-oxidation endoplasmic reticulum membrane|integral to membrane|peroxisomal matrix|peroxisomal membrane ATP binding|long-chain fatty acid-CoA ligase activity|phytanate-CoA ligase activity|pristanate-CoA ligase activity ovary(1)|skin(1) 2 all_lung(180;0.00177) all cancers(107;1.16e-06)|GBM - Glioblastoma multiforme(94;0.000113) 0.37234 113.614703 114.954964 35 59 KEEP --- --- --- --- GLDN 342035 broad.mit.edu 37 15 51669650 51669650 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:51669650G>A uc002aba.2 + 2 537 c.368G>A c.(367-369)CGA>CAA p.R123Q GLDN_uc010bez.1_Intron|GLDN_uc002abb.2_5'UTR NM_181789 NP_861454 Q6ZMI3 GLDN_HUMAN gliomedin 123 Extracellular (Potential). cell differentiation|nervous system development collagen|integral to membrane|plasma membrane ovary(2) 2 all cancers(107;0.00194)|GBM - Glioblastoma multiforme(94;0.00942) 0.55102 90.929467 91.040464 27 22 KEEP --- --- --- --- TMOD2 29767 broad.mit.edu 37 15 52100468 52100468 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:52100468C>T uc002abk.2 + TMOD2_uc002abl.3_Intron|TMOD2_uc010bfb.2_Intron NM_014548 NP_055363 neuronal tropomodulin isoform a nervous system development cytoplasm|cytoskeleton actin binding|tropomyosin binding ovary(2) 2 all cancers(107;0.00435) 0.5625 30.176495 30.230839 9 7 KEEP --- --- --- --- MYO5A 4644 broad.mit.edu 37 15 52643802 52643802 + Intron SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:52643802T>C uc002aby.2 - MYO5A_uc002abx.3_Intron|MYO5A_uc010ugd.1_5'Flank|MYO5A_uc002aca.1_5'Flank|MYO5A_uc002acb.1_5'Flank|MYO5A_uc002acc.1_5'Flank NM_000259 NP_000250 myosin VA isoform 1 actin filament-based movement|transport cytoplasm|growth cone|myosin complex|ruffle actin binding|ATP binding|calmodulin binding|microfilament motor activity ovary(3)|central_nervous_system(1) 4 all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196) 0.272727 7.419711 7.932151 3 8 KEEP --- --- --- --- Unknown broad.mit.edu 37 15 53229955 53229955 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:53229955C>T ONECUT1 (147746 upstream) : WDR72 (575983 downstream) 0.631579 40.804543 41.093431 12 7 KEEP --- --- --- --- UNC13C 440279 broad.mit.edu 37 15 54542603 54542603 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:54542603G>A uc002ack.2 + 6 3409 c.3409G>A c.(3409-3411)GAA>AAA p.E1137K NM_001080534 NP_001074003 Q8NB66 UN13C_HUMAN unc-13 homolog C 1137 Phorbol-ester/DAG-type. exocytosis|intracellular signal transduction cell junction|cytoplasm|presynaptic membrane metal ion binding ovary(5)|pancreas(2) 7 GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124) 2691 0.391892 93.658977 94.416391 29 45 KEEP --- --- --- --- UNC13C 440279 broad.mit.edu 37 15 54786846 54786846 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:54786846G>A uc002ack.2 + 18 4974 c.4974G>A c.(4972-4974)ATG>ATA p.M1658I NM_001080534 NP_001074003 Q8NB66 UN13C_HUMAN unc-13 homolog C 1658 MHD1. exocytosis|intracellular signal transduction cell junction|cytoplasm|presynaptic membrane metal ion binding ovary(5)|pancreas(2) 7 GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124) 2691 0.396226 122.132582 123.129182 42 64 KEEP --- --- --- --- Unknown broad.mit.edu 37 15 56615292 56615292 + IGR SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:56615292T>C RFX7 (79809 upstream) : TEX9 (42352 downstream) 0.533333 29.801788 29.816343 8 7 KEEP --- --- --- --- FAM63B 54629 broad.mit.edu 37 15 59063869 59063869 + Missense_Mutation SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:59063869T>C uc002afj.2 + 1 477 c.275T>C c.(274-276)TTG>TCG p.L92S FAM63B_uc002afi.2_Missense_Mutation_p.L92S|FAM63B_uc002afk.2_RNA|FAM63B_uc002afl.2_RNA NM_001040450 NP_001035540 Q8NBR6 FA63B_HUMAN hypothetical protein LOC54629 isoform a 92 central_nervous_system(1) 1 0.789474 53.036192 54.511307 15 4 KEEP --- --- --- --- FAM63B 54629 broad.mit.edu 37 15 59064335 59064335 + Missense_Mutation SNP G C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:59064335G>C uc002afj.2 + 1 943 c.741G>C c.(739-741)TGG>TGC p.W247C FAM63B_uc002afi.2_Missense_Mutation_p.W247C|FAM63B_uc002afk.2_RNA|FAM63B_uc002afl.2_RNA NM_001040450 NP_001035540 Q8NBR6 FA63B_HUMAN hypothetical protein LOC54629 isoform a 247 central_nervous_system(1) 1 0.086957 2.684062 14.662294 6 63 KEEP --- --- --- --- Unknown broad.mit.edu 37 15 63245909 63245909 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:63245909C>T TLN2 (109082 upstream) : TPM1 (88929 downstream) 0.633333 62.831597 63.300059 19 11 KEEP --- --- --- --- HERC1 8925 broad.mit.edu 37 15 63984789 63984789 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:63984789G>A uc002amp.2 - NM_003922 NP_003913 hect domain and RCC1-like domain 1 protein modification process|transport cytosol|Golgi apparatus|membrane acid-amino acid ligase activity|ARF guanyl-nucleotide exchange factor activity ovary(6)|breast(6)|lung(5)|central_nervous_system(2) 19 0.333333 28.83879 29.577414 10 20 KEEP --- --- --- --- CILP 8483 broad.mit.edu 37 15 65496805 65496805 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:65496805C>T uc002aon.2 - 6 901 c.720G>A c.(718-720)GGG>GGA p.G240G NM_003613 NP_003604 O75339 CILP1_HUMAN cartilage intermediate layer protein 240 negative regulation of insulin-like growth factor receptor signaling pathway extracellular matrix part|extracellular space|proteinaceous extracellular matrix ovary(4)|pancreas(2)|skin(1) 7 0.268657 99.148276 105.61623 36 98 KEEP --- --- --- --- MEGF11 84465 broad.mit.edu 37 15 66210270 66210270 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:66210270C>T uc002apm.2 - MEGF11_uc002apl.2_Intron|MEGF11_uc002apn.1_Intron NM_032445 NP_115821 multiple EGF-like-domains 11 precursor basolateral plasma membrane|integral to membrane pancreas(1) 1 0.25 21.383932 23.202271 8 24 KEEP --- --- --- --- LBXCOR1 390598 broad.mit.edu 37 15 68123072 68123072 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:68123072C>T uc002aqy.1 + NM_001031807 NP_001026977 transcriptional corepressor Corl1 negative regulation of BMP signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|transcription, DNA-dependent cytoplasm|dendrite|neuronal cell body|nucleus nucleotide binding|SMAD binding|transcription repressor activity 0 0.520833 244.528727 244.582988 75 69 KEEP --- --- --- --- CORO2B 10391 broad.mit.edu 37 15 68987458 68987458 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:68987458C>T uc002arj.3 + CORO2B_uc010bic.2_Intron NM_006091 NP_006082 coronin, actin binding protein, 2B actin cytoskeleton organization actin cytoskeleton|cytoplasm|membrane actin filament binding ovary(3)|skin(2)|large_intestine(1) 6 0.254545 37.921989 40.93002 14 41 KEEP --- --- --- --- PAQR5 54852 broad.mit.edu 37 15 69692171 69692171 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:69692171C>T uc002arz.2 + PAQR5_uc002asa.2_Intron NM_017705 NP_060175 progestin and adipoQ receptor family member V cell differentiation|multicellular organismal development|oogenesis integral to membrane receptor activity|steroid binding ovary(2) 2 0.375 18.645807 18.865405 6 10 KEEP --- --- --- --- LARP6 55323 broad.mit.edu 37 15 71125181 71125181 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:71125181G>A uc002ass.2 - 3 757 c.686C>T c.(685-687)TCA>TTA p.S229L NM_018357 NP_060827 Q9BRS8 LARP6_HUMAN La ribonucleoprotein domain family, member 6 229 RNA processing Golgi apparatus|nucleus|ribonucleoprotein complex nucleotide binding|RNA binding 0 0.295082 51.924195 54.216874 18 43 KEEP --- --- --- --- LMAN1L 79748 broad.mit.edu 37 15 75108966 75108966 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:75108966C>T uc002ayt.1 + LMAN1L_uc010bkd.2_Intron|LMAN1L_uc010ulo.1_Intron|LMAN1L_uc010bke.1_Intron NM_021819 NP_068591 lectin, mannose-binding, 1 like precursor ER-Golgi intermediate compartment membrane|integral to membrane sugar binding 0 0.342105 40.664081 41.500877 13 25 KEEP --- --- --- --- SIN3A 25942 broad.mit.edu 37 15 75682168 75682168 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:75682168G>A uc002bai.2 - SIN3A_uc002baj.2_Intron|SIN3A_uc010uml.1_Intron NM_015477 NP_056292 transcriptional co-repressor Sin3A blood coagulation|cellular lipid metabolic process|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleolus|Sin3 complex protein binding skin(3)|ovary(1)|lung(1) 5 0.6 223.546502 224.464907 63 42 KEEP --- --- --- --- SIN3A 25942 broad.mit.edu 37 15 75688738 75688738 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:75688738G>A uc002bai.2 - 13 2213 c.1954C>T c.(1954-1956)CGC>TGC p.R652C SIN3A_uc002baj.2_Missense_Mutation_p.R652C|SIN3A_uc010uml.1_Missense_Mutation_p.R652C NM_015477 NP_056292 Q96ST3 SIN3A_HUMAN transcriptional co-repressor Sin3A 652 Interactions with SUDS3 and SAP130.|Interaction with NCOR1 (By similarity). blood coagulation|cellular lipid metabolic process|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleolus|Sin3 complex protein binding skin(3)|ovary(1)|lung(1) 5 0.629139 330.864383 333.077 95 56 KEEP --- --- --- --- broad.mit.edu 37 15 76067767 76067767 + 5'Flank SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:76067767G>A uc010umm.1 + SubName: Full=cDNA FLJ59077, highly similar to Golgin subfamily A member 6; 0.714286 47.426609 48.289984 15 6 KEEP --- --- --- --- RASGRF1 5923 broad.mit.edu 37 15 79324415 79324415 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:79324415C>T uc002beq.2 - RASGRF1_uc002bep.2_Intron|RASGRF1_uc010blm.1_Intron|RASGRF1_uc002ber.3_Intron NM_002891 NP_002882 Ras protein-specific guanine activation of Rac GTPase activity|apoptosis|induction of apoptosis by extracellular signals|long-term memory|nerve growth factor receptor signaling pathway|neuron projection development|regulation of Rac protein signal transduction|small GTPase mediated signal transduction|synaptic transmission cytosol|growth cone|plasma membrane|synaptosome Rho guanyl-nucleotide exchange factor activity skin(4)|ovary(1)|central_nervous_system(1) 6 694 0.4 12.997961 13.085451 4 6 KEEP --- --- --- --- IL16 3603 broad.mit.edu 37 15 81592095 81592095 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:81592095C>T uc002bgh.3 + 14 2804 c.2428C>T c.(2428-2430)CCT>TCT p.P810S IL16_uc010blq.1_Missense_Mutation_p.P764S|IL16_uc002bge.3_RNA|IL16_uc010unp.1_Missense_Mutation_p.P852S|IL16_uc002bgg.2_Missense_Mutation_p.P810S|IL16_uc002bgi.1_Missense_Mutation_p.P200S|IL16_uc002bgj.2_Missense_Mutation_p.P304S|IL16_uc002bgk.2_Missense_Mutation_p.P109S|IL16_uc002bgl.1_Missense_Mutation_p.P109S|IL16_uc010unq.1_Missense_Mutation_p.P109S NM_172217 NP_757366 Q14005 IL16_HUMAN interleukin 16 isoform 2 810 immune response|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|extracellular space|nucleus|plasma membrane cytokine activity ovary(2)|lung(1)|skin(1) 4 0.326087 84.398031 86.877489 30 62 KEEP --- --- --- --- ADAMTSL3 57188 broad.mit.edu 37 15 84372936 84372936 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:84372936C>T uc002bjz.3 + ADAMTSL3_uc002bjy.1_Intron|ADAMTSL3_uc010bmt.1_Intron|ADAMTSL3_uc010bmu.1_Intron NM_207517 NP_997400 ADAMTS-like 3 precursor proteinaceous extracellular matrix metallopeptidase activity|zinc ion binding ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1) 27 BRCA - Breast invasive adenocarcinoma(143;0.211) 580 0.3 8.421376 8.778588 3 7 KEEP --- --- --- --- NTRK3 4916 broad.mit.edu 37 15 88420086 88420086 + 3'UTR SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:88420086A>G uc002bme.1 - 19 NTRK3_uc002bmh.2_3'UTR|NTRK3_uc002bmf.1_3'UTR NM_001012338 NP_001012338 neurotrophic tyrosine kinase, receptor, type 3 transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity ETV6/NTRK3(234) soft_tissue(85)|kidney(66)|breast(56)|salivary_gland(26)|lung(22)|large_intestine(6)|ovary(6)|stomach(5)|central_nervous_system(3)|pancreas(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1) 281 BRCA - Breast invasive adenocarcinoma(143;0.211) 506 T ETV6 congenital fibrosarcoma|Secretory breast TSP Lung(13;0.10) 0.571429 78.106531 78.26237 20 15 KEEP --- --- --- --- NTRK3 4916 broad.mit.edu 37 15 88680758 88680758 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:88680758C>T uc002bme.1 - 6 661 c.499G>A c.(499-501)GAC>AAC p.D167N NTRK3_uc002bmh.2_Missense_Mutation_p.D167N|NTRK3_uc002bmf.1_Missense_Mutation_p.D167N|NTRK3_uc010upl.1_Missense_Mutation_p.D69N|NTRK3_uc010bnh.1_Missense_Mutation_p.D167N|NTRK3_uc002bmg.2_Missense_Mutation_p.D167N NM_001012338 NP_001012338 Q16288 NTRK3_HUMAN neurotrophic tyrosine kinase, receptor, type 3 167 Extracellular (Potential).|LRRCT. transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity ETV6/NTRK3(234) soft_tissue(85)|kidney(66)|breast(56)|salivary_gland(26)|lung(22)|large_intestine(6)|ovary(6)|stomach(5)|central_nervous_system(3)|pancreas(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1) 281 BRCA - Breast invasive adenocarcinoma(143;0.211) 506 T ETV6 congenital fibrosarcoma|Secretory breast TSP Lung(13;0.10) 0.3 36.942709 38.77246 15 35 KEEP --- --- --- --- ACAN 176 broad.mit.edu 37 15 89398313 89398313 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:89398313G>A uc010upo.1 + 12 2871 c.2497G>A c.(2497-2499)GAG>AAG p.E833K ACAN_uc010upp.1_Missense_Mutation_p.E833K|ACAN_uc002bna.2_RNA NM_013227 NP_037359 E7EX88 E7EX88_HUMAN aggrecan isoform 2 precursor 833 cell adhesion hyaluronic acid binding|sugar binding ovary(2)|central_nervous_system(1) 3 Lung NSC(78;0.0392)|all_lung(78;0.077) BRCA - Breast invasive adenocarcinoma(143;0.146) 0.722222 46.882987 47.682545 13 5 KEEP --- --- --- --- ACAN 176 broad.mit.edu 37 15 89400356 89400356 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:89400356G>A uc010upo.1 + 12 4914 c.4540G>A c.(4540-4542)GGT>AGT p.G1514S ACAN_uc010upp.1_Missense_Mutation_p.G1514S|ACAN_uc002bna.2_RNA NM_013227 NP_037359 E7EX88 E7EX88_HUMAN aggrecan isoform 2 precursor 1514 cell adhesion hyaluronic acid binding|sugar binding ovary(2)|central_nervous_system(1) 3 Lung NSC(78;0.0392)|all_lung(78;0.077) BRCA - Breast invasive adenocarcinoma(143;0.146) 0.45679 127.368247 127.499854 37 44 KEEP --- --- --- --- ANPEP 290 broad.mit.edu 37 15 90347477 90347477 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:90347477G>A uc002bop.3 - NM_001150 NP_001141 membrane alanine aminopeptidase precursor angiogenesis|cell differentiation|interspecies interaction between organisms cytosol|ER-Golgi intermediate compartment|integral to plasma membrane aminopeptidase activity|metallopeptidase activity|receptor activity|zinc ion binding ovary(3)|skin(1) 4 Lung NSC(78;0.0221)|all_lung(78;0.0448) BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169) Ezetimibe(DB00973) NSCLC(30;827 977 2459 19669 26125) 0.525926 234.044918 234.1256 71 64 KEEP --- --- --- --- CRTC3 64784 broad.mit.edu 37 15 91150594 91150594 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:91150594C>T uc002bpp.2 + CRTC3_uc002bpo.2_Intron NM_022769 NP_073606 transducer of regulated CREB protein 3 isoform interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus CRTC3/MAML2(26) salivary_gland(26)|ovary(1) 27 Melanoma(11;0.00551)|Lung NSC(78;0.0931)|all_lung(78;0.163) BRCA - Breast invasive adenocarcinoma(143;0.0745) T MAML2 salivary gland mucoepidermoid 0.465116 193.290949 193.427117 60 69 KEEP --- --- --- --- UNC45A 55898 broad.mit.edu 37 15 91492037 91492037 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:91492037C>T uc002bqg.2 + UNC45A_uc002bqd.2_Intron|UNC45A_uc010uqr.1_Intron|UNC45A_uc002bqi.2_5'Flank NM_018671 NP_061141 smooth muscle cell associated protein-1 isoform cell differentiation|muscle organ development nucleus|perinuclear region of cytoplasm protein binding ovary(2) 2 Lung NSC(78;0.0771)|all_lung(78;0.137) Lung(145;0.189) 0.555556 15.381138 15.406921 5 4 KEEP --- --- --- --- SV2B 9899 broad.mit.edu 37 15 91824952 91824952 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:91824952C>T uc002bqv.2 + SV2B_uc010uqv.1_Intron|SV2B_uc002bqu.3_Intron NM_014848 NP_055663 synaptic vesicle protein 2B homolog neurotransmitter transport acrosomal vesicle|cell junction|integral to membrane|synaptic vesicle membrane transmembrane transporter activity ovary(3)|central_nervous_system(2)|skin(2)|upper_aerodigestive_tract(1) 8 Lung NSC(78;0.0987)|all_lung(78;0.172) BRCA - Breast invasive adenocarcinoma(143;0.0895) 0.352459 137.813154 140.144282 43 79 KEEP --- --- --- --- SV2B 9899 broad.mit.edu 37 15 91835647 91835647 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:91835647C>T uc002bqv.2 + 12 2308 c.1917C>T c.(1915-1917)ATC>ATT p.I639I SV2B_uc010uqv.1_Silent_p.I488I|SV2B_uc002bqu.3_RNA NM_014848 NP_055663 Q7L1I2 SV2B_HUMAN synaptic vesicle protein 2B homolog 639 Helical; (Potential). neurotransmitter transport acrosomal vesicle|cell junction|integral to membrane|synaptic vesicle membrane transmembrane transporter activity ovary(3)|central_nervous_system(2)|skin(2)|upper_aerodigestive_tract(1) 8 Lung NSC(78;0.0987)|all_lung(78;0.172) BRCA - Breast invasive adenocarcinoma(143;0.0895) 0.417219 201.597656 202.501478 63 88 KEEP --- --- --- --- SPATA8 145946 broad.mit.edu 37 15 97327384 97327384 + Missense_Mutation SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:97327384A>G uc002bue.2 + 2 301 c.91A>G c.(91-93)ACC>GCC p.T31A uc010urp.1_5'Flank|uc002bud.1_5'Flank NM_173499 NP_775770 Q6RVD6 SPAT8_HUMAN spermatogenesis associated 8 31 ovary(1)|skin(1) 2 Melanoma(26;0.0142)|Lung NSC(78;0.041)|all_lung(78;0.0468) OV - Ovarian serous cystadenocarcinoma(32;0.0718) 0.424242 148.33892 148.83356 42 57 KEEP --- --- --- --- LYSMD4 145748 broad.mit.edu 37 15 100271728 100271728 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:100271728G>A uc002bvk.2 - LYSMD4_uc002bvj.1_Intron|LYSMD4_uc010bou.1_Intron|LYSMD4_uc002bvl.2_Intron|LYSMD4_uc002bvm.2_Intron|LYSMD4_uc010bov.2_Intron SubName: Full=cDNA FLJ77040, highly similar to Homo sapiens LysM, putative peptidoglycan-binding, domain containing 4, mRNA; SubName: Full=LysM, putative peptidoglycan-binding, domain containing 4, isoform CRA_c; cell wall macromolecule catabolic process integral to membrane 0 Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163) OV - Ovarian serous cystadenocarcinoma(32;0.00162)|LUSC - Lung squamous cell carcinoma(107;0.17)|Lung(145;0.208) 0.448276 44.97225 45.039778 13 16 KEEP --- --- --- --- C15orf51 196968 broad.mit.edu 37 15 100332024 100332024 + RNA SNP G A A rs113026694 MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:100332024G>A uc010urx.1 - 5 c.2168C>T C15orf51_uc010ury.1_RNA NR_003260 Homo sapiens cDNA FLJ43799 fis, clone TESTI4000288. 0 Pancreas(153;1369 2628 17791 35146) 0.377778 53.763721 54.353808 17 28 KEEP --- --- --- --- C15orf51 196968 broad.mit.edu 37 15 100332862 100332862 + RNA SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:100332862G>A uc010urx.1 - 5 c.1330C>T C15orf51_uc010ury.1_RNA NR_003260 Homo sapiens cDNA FLJ43799 fis, clone TESTI4000288. 0 Pancreas(153;1369 2628 17791 35146) 0.375 91.827799 92.926191 30 50 KEEP --- --- --- --- broad.mit.edu 37 15 102291678 102291678 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:102291678C>T uc010usj.1 + uc002bxp.3_5'Flank|uc002bxt.2_5'Flank|uc002bxz.3_5'Flank RecName: Full=Uncharacterized protein C15orf51.; Flags: Fragment; 0.409091 30.070887 30.229773 9 13 KEEP --- --- --- --- broad.mit.edu 37 15 102319243 102319243 + 5'Flank SNP G C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr15:102319243G>C uc002cdb.2 + DQ596816 0.625 35.953773 36.173228 10 6 KEEP --- --- --- --- RAB40C 57799 broad.mit.edu 37 16 668273 668273 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:668273C>T uc002chr.2 + RAB40C_uc002chq.2_Intron NM_021168 NP_066991 RAB40C, member RAS oncogene family protein transport|small GTPase mediated signal transduction plasma membrane GTP binding 0 Hepatocellular(780;0.0218) Melanoma(123;1631 1690 28262 44104 44957) 0.416667 65.792042 66.082994 20 28 KEEP --- --- --- --- MSLN 10232 broad.mit.edu 37 16 815554 815554 + Silent SNP G A A rs149515875 MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:815554G>A uc002cjw.1 + 9 783 c.732G>A c.(730-732)ACG>ACA p.T244T MSLN_uc002cjt.1_Silent_p.T244T|MSLN_uc002cju.1_Silent_p.T244T|MSLN_uc010brd.1_Silent_p.T243T|MSLN_uc002cjv.1_Silent_p.T244T|MSLN_uc002cjx.1_Silent_p.T244T|MSLN_uc002cjy.1_5'Flank NM_013404 NP_037536 Q13421 MSLN_HUMAN mesothelin isoform 2 preproprotein 244 cell adhesion anchored to membrane|extracellular region|Golgi apparatus|plasma membrane pancreas(1) 1 Hepatocellular(780;0.00335) 0.586207 56.080817 56.269526 17 12 KEEP --- --- --- --- MSLN 10232 broad.mit.edu 37 16 816053 816053 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:816053C>T uc002cjw.1 + MSLN_uc002cjt.1_Intron|MSLN_uc002cju.1_Intron|MSLN_uc010brd.1_Intron|MSLN_uc002cjv.1_Intron|MSLN_uc002cjx.1_Intron|MSLN_uc002cjy.1_5'Flank NM_013404 NP_037536 mesothelin isoform 2 preproprotein cell adhesion anchored to membrane|extracellular region|Golgi apparatus|plasma membrane pancreas(1) 1 Hepatocellular(780;0.00335) 0.529412 31.276058 31.288851 9 8 KEEP --- --- --- --- LMF1 64788 broad.mit.edu 37 16 904604 904604 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:904604G>A uc002ckj.2 - 11 1636 c.1632C>T c.(1630-1632)TTC>TTT p.F544F LMF1_uc010brg.2_RNA|LMF1_uc010brh.2_Silent_p.F327F|LMF1_uc010bri.2_Silent_p.F307F|LMF1_uc002ckk.2_Silent_p.F327F NM_022773 NP_073610 Q96S06 LMF1_HUMAN lipase maturation factor 1 544 Lumenal (Potential). endoplasmic reticulum membrane|integral to membrane 0 Hepatocellular(780;0.00308) 0.333333 7.820015 8.042415 3 6 KEEP --- --- --- --- CACNA1H 8912 broad.mit.edu 37 16 1250535 1250535 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:1250535C>T uc002cks.2 + 7 1331 c.1083C>T c.(1081-1083)TTC>TTT p.F361F CACNA1H_uc002ckt.2_Silent_p.F361F NM_021098 NP_066921 O95180 CAC1H_HUMAN calcium channel, voltage-dependent, T type, 361 Extracellular (Potential).|I. aldosterone biosynthetic process|axon guidance|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|muscle contraction|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction voltage-gated calcium channel complex low voltage-gated calcium channel activity breast(2) 2 Hepatocellular(780;0.00369) Flunarizine(DB04841)|Mibefradil(DB01388) 0.461538 55.742513 55.792971 18 21 KEEP --- --- --- --- MMP25 64386 broad.mit.edu 37 16 3100376 3100376 + Nonsense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:3100376C>T uc002cth.2 + 4 727 c.490C>T c.(490-492)CAG>TAG p.Q164* MMP25_uc002cti.1_Nonsense_Mutation_p.Q100* NM_022468 NP_071913 Q9NPA2 MMP25_HUMAN matrix metalloproteinase 25 preproprotein 164 inflammatory response|proteolysis anchored to membrane|cell surface|plasma membrane|proteinaceous extracellular matrix calcium ion binding|metalloendopeptidase activity|zinc ion binding 0 NSCLC(147;665 1067 3888 6863 19894 30469 40247 45633 51336) 0.453125 86.963666 87.086455 29 35 KEEP --- --- --- --- ZNF597 146434 broad.mit.edu 37 16 3493220 3493220 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:3493220G>A uc002cvd.2 - NAT15_uc002cvh.3_5'Flank|NAT15_uc010uxb.1_5'Flank NM_152457 NP_689670 zinc finger protein 597 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding 0 0.636364 46.955329 47.314957 14 8 KEEP --- --- --- --- NLRC3 197358 broad.mit.edu 37 16 3614559 3614559 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:3614559G>A uc010btn.2 - 5 790 c.379C>T c.(379-381)CTC>TTC p.L127F NM_178844 NP_849172 Q7RTR2 NLRC3_HUMAN NOD3 protein 127 I-kappaB kinase/NF-kappaB cascade|negative regulation of NF-kappaB transcription factor activity|T cell activation cytoplasm ATP binding ovary(2)|pancreas(2)|central_nervous_system(1)|skin(1) 6 0.407407 32.135286 32.332735 11 16 KEEP --- --- --- --- ADCY9 115 broad.mit.edu 37 16 4029071 4029071 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:4029071G>A uc002cvx.2 - NM_001116 NP_001107 adenylate cyclase 9 activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport integral to plasma membrane adenylate cyclase activity|ATP binding|metal ion binding ovary(4)|large_intestine(1)|central_nervous_system(1) 6 0.419355 83.267317 83.611773 26 36 KEEP --- --- --- --- TFAP4 7023 broad.mit.edu 37 16 4310579 4310579 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:4310579G>A uc010uxg.1 - 5 797 c.543C>T c.(541-543)GCC>GCT p.A181A NM_003223 NP_003214 Q01664 TFAP4_HUMAN transcription factor AP-4 (activating enhancer 181 DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|negative regulation by host of viral transcription|negative regulation of cell cycle arrest|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|negative regulation of DNA binding|negative regulation of transcription, DNA-dependent|positive regulation by host of viral transcription|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein complex assembly|regulation of S phase of mitotic cell cycle transcriptional repressor complex E-box binding|histone deacetylase binding|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity ovary(1) 1 0.347826 24.897181 25.365374 8 15 KEEP --- --- --- --- C16orf68 79091 broad.mit.edu 37 16 8728848 8728848 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:8728848C>T uc002cyz.2 + C16orf68_uc002cza.2_Intron NM_024109 NP_077014 hypothetical protein LOC79091 methyltransferase activity 0 0.54717 98.079397 98.182048 29 24 KEEP --- --- --- --- TEKT5 146279 broad.mit.edu 37 16 10721399 10721399 + 3'UTR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:10721399C>T uc002czz.1 - 7 NM_144674 NP_653275 tektin 5 microtubule cytoskeleton organization cilium axoneme|flagellar axoneme|microtubule ovary(2) 2 0.377358 63.087726 63.787139 20 33 KEEP --- --- --- --- TEKT5 146279 broad.mit.edu 37 16 10787964 10787964 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:10787964G>A uc002czz.1 - NM_144674 NP_653275 tektin 5 microtubule cytoskeleton organization cilium axoneme|flagellar axoneme|microtubule ovary(2) 2 0.785714 37.631945 38.686649 11 3 KEEP --- --- --- --- KIAA0430 9665 broad.mit.edu 37 16 15717034 15717034 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:15717034G>A uc002ddr.2 - KIAA0430_uc002ddq.2_Intron|KIAA0430_uc010uzv.1_Intron|KIAA0430_uc010uzw.1_Intron NM_014647 NP_055462 limkain b1 peroxisome nucleotide binding|RNA binding 0 0.357143 13.970486 14.222408 5 9 KEEP --- --- --- --- ABCC1 4363 broad.mit.edu 37 16 16150173 16150173 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:16150173C>T uc010bvi.2 + ABCC1_uc010bvj.2_Intron|ABCC1_uc010bvk.2_Intron|ABCC1_uc010bvl.2_Intron|ABCC1_uc010bvm.2_Intron|ABCC1_uc002del.3_Intron|ABCC1_uc010bvn.2_Silent_p.F429F NM_004996 NP_004987 ATP-binding cassette, sub-family C, member 1 hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|response to drug Golgi apparatus|integral to plasma membrane|membrane fraction|nucleus ATP binding|ATPase activity, coupled to transmembrane movement of substances ovary(4) 4 Daunorubicin(DB00694)|Glibenclamide(DB01016)|Probenecid(DB01032)|Saquinavir(DB01232)|Sulfinpyrazone(DB01138) 0.465116 65.996375 66.041957 20 23 KEEP --- --- --- --- ITPRIPL2 162073 broad.mit.edu 37 16 19126991 19126991 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:19126991C>T uc002dfu.3 + 1 1738 c.1208C>T c.(1207-1209)TCC>TTC p.S403F ITPRIPL2_uc002dft.2_Missense_Mutation_p.S99F NM_001034841 NP_001030013 Q3MIP1 IPIL2_HUMAN inositol 1,4,5-triphosphate receptor interacting 403 Cytoplasmic (Potential). integral to membrane skin(2) 2 0.516667 199.463247 199.493115 62 58 KEEP --- --- --- --- PDILT 204474 broad.mit.edu 37 16 20387229 20387229 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:20387229C>T uc002dhc.1 - NM_174924 NP_777584 protein disulfide isomerase-like, testis cell differentiation|cell redox homeostasis|multicellular organismal development|spermatogenesis endoplasmic reticulum isomerase activity large_intestine(1) 1 0.666667 7.351303 7.424805 2 1 KEEP --- --- --- --- ACSM2A 123876 broad.mit.edu 37 16 20482305 20482305 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:20482305C>T uc010bwe.2 + ACSM2A_uc010bwd.1_Intron|ACSM2A_uc010vax.1_Intron|ACSM2A_uc002dhf.3_Intron|ACSM2A_uc002dhg.3_Intron|ACSM2A_uc010vay.1_Intron NM_001010845 NP_001010845 acyl-CoA synthetase medium-chain family member fatty acid metabolic process mitochondrial matrix ATP binding|butyrate-CoA ligase activity|metal ion binding skin(2)|breast(1) 3 0.588235 34.453019 34.568562 10 7 KEEP --- --- --- --- ACSM1 116285 broad.mit.edu 37 16 20638782 20638782 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:20638782C>T uc002dhm.1 - ACSM1_uc002dhn.1_Intron|ACSM1_uc010bwg.1_Intron NM_052956 NP_443188 acyl-CoA synthetase medium-chain family member benzoate metabolic process|butyrate metabolic process|energy derivation by oxidation of organic compounds|fatty acid oxidation|xenobiotic metabolic process mitochondrial matrix acyl-CoA ligase activity|ATP binding|butyrate-CoA ligase activity|GTP binding|metal ion binding central_nervous_system(1)|skin(1) 2 0.488889 66.644921 66.649845 22 23 KEEP --- --- --- --- ACSM3 6296 broad.mit.edu 37 16 20788690 20788690 + Intron SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:20788690T>C uc002dhr.2 + ACSM3_uc002dhq.2_Intron|ACSM3_uc010vba.1_Intron NM_005622 NP_005613 SA hypertension-associated homolog isoform 1 regulation of blood pressure mitochondrial matrix ATP binding|butyrate-CoA ligase activity|metal ion binding ovary(1) 1 0.5 116.626603 116.626603 31 31 KEEP --- --- --- --- ZP2 7783 broad.mit.edu 37 16 21221601 21221601 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:21221601G>A uc002dii.2 - ZP2_uc010bwn.1_Intron|ZP2_uc010bwo.2_Intron NM_003460 NP_003451 zona pellucida glycoprotein 2 preproprotein binding of sperm to zona pellucida|intracellular protein transport endoplasmic reticulum|Golgi apparatus|integral to membrane|multivesicular body|plasma membrane|proteinaceous extracellular matrix|stored secretory granule acrosin binding|coreceptor activity central_nervous_system(2)|ovary(1) 3 GBM - Glioblastoma multiforme(48;0.0573) 0.428571 37.794411 37.919255 12 16 KEEP --- --- --- --- ERN2 10595 broad.mit.edu 37 16 23713399 23713399 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:23713399G>A uc002dma.3 - ERN2_uc010bxp.2_Intron|ERN2_uc010bxq.1_Intron NM_033266 NP_150296 endoplasmic reticulum to nucleus signalling 2 apoptosis|induction of apoptosis|mRNA processing|negative regulation of transcription, DNA-dependent|rRNA catabolic process|transcription, DNA-dependent endoplasmic reticulum membrane|integral to membrane ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|magnesium ion binding|protein serine/threonine kinase activity large_intestine(2)|lung(2)|ovary(2) 6 GBM - Glioblastoma multiforme(48;0.0156) 225 0.512821 62.725342 62.732196 20 19 KEEP --- --- --- --- CHP2 63928 broad.mit.edu 37 16 23767656 23767656 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:23767656G>A uc002dmb.1 + NM_022097 NP_071380 hepatocellular carcinoma antigen gene 520 calcium ion binding central_nervous_system(1) 1 GBM - Glioblastoma multiforme(48;0.0144) 0.428571 27.171224 27.264777 9 12 KEEP --- --- --- --- SLC5A11 115584 broad.mit.edu 37 16 24895238 24895238 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:24895238C>T uc002dmu.2 + SLC5A11_uc002dms.2_Intron|SLC5A11_uc010vcd.1_Intron|SLC5A11_uc002dmt.2_Intron|SLC5A11_uc010vce.1_Intron|SLC5A11_uc010bxt.2_Intron NM_052944 NP_443176 solute carrier family 5 (sodium/glucose apoptosis|carbohydrate transport|sodium ion transport integral to membrane|plasma membrane polyol transmembrane transporter activity|symporter activity ovary(2) 2 GBM - Glioblastoma multiforme(48;0.0365) 0.642857 119.613206 120.619171 36 20 KEEP --- --- --- --- AQP8 343 broad.mit.edu 37 16 25228508 25228508 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:25228508C>T uc002doc.2 + NM_001169 NP_001160 aquaporin 8 cellular response to cAMP integral to plasma membrane water channel activity upper_aerodigestive_tract(1)|breast(1)|pancreas(1) 3 GBM - Glioblastoma multiforme(48;0.044) 0.439628 448.089047 449.117155 142 181 KEEP --- --- --- --- IL21R 50615 broad.mit.edu 37 16 27457450 27457450 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:27457450C>T uc002doq.1 + IL21R_uc002dor.1_Intron|IL21R_uc002dos.1_Intron NM_181078 NP_851564 interleukin 21 receptor precursor natural killer cell activation integral to membrane interleukin-21 receptor activity ovary(2)|lung(1)|breast(1) 4 423 T BCL6 NHL 0.428571 9.723835 9.755008 3 4 KEEP --- --- --- --- broad.mit.edu 37 16 29124383 29124383 + Intron SNP A T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:29124383A>T uc010vct.1 - RRN3P2_uc002dsf.3_RNA|RRN3P2_uc002dsg.3_RNA|RRN3P2_uc010vdn.1_RNA RecName: Full=Nuclear pore complex-interacting protein-like 2; Flags: Precursor; 0.416667 47.318938 47.537177 15 21 KEEP --- --- --- --- SEZ6L2 26470 broad.mit.edu 37 16 29910417 29910417 + 5'UTR SNP C A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:29910417C>A uc002duq.3 - 1 uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|SEZ6L2_uc002dup.3_5'UTR|SEZ6L2_uc002dur.3_5'UTR|SEZ6L2_uc002dus.3_5'UTR|SEZ6L2_uc010vec.1_5'UTR|SEZ6L2_uc010ved.1_5'UTR|ASPHD1_uc002dut.2_5'Flank|ASPHD1_uc002duu.3_5'Flank|ASPHD1_uc010bzi.2_5'Flank NM_201575 NP_963869 seizure related 6 homolog (mouse)-like 2 isoform endoplasmic reticulum membrane|integral to membrane|plasma membrane ovary(1)|skin(1) 2 0.666667 19.952626 20.173829 6 3 KEEP --- --- --- --- CD2BP2 10421 broad.mit.edu 37 16 30364517 30364517 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:30364517G>A uc002dxr.2 - 5 1153 c.900C>T c.(898-900)ACC>ACT p.T300T CD2BP2_uc002dxs.2_Silent_p.T300T NM_006110 NP_006101 O95400 CD2B2_HUMAN CD2 antigen (cytoplasmic tail) binding protein 300 GYF. assembly of spliceosomal tri-snRNP cytoplasm|nucleoplasm|U5 snRNP protein binding|ribonucleoprotein binding ovary(1) 1 0.4375 61.670062 61.832825 21 27 KEEP --- --- --- --- ITGAX 3687 broad.mit.edu 37 16 31371840 31371840 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:31371840C>T uc002ebu.1 + ITGAX_uc002ebt.2_Intron|ITGAX_uc010vfk.1_5'Flank NM_000887 NP_000878 integrin alpha X precursor blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration|organ morphogenesis integrin complex protein binding|receptor activity ovary(2)|central_nervous_system(1)|pancreas(1) 4 0.55 72.052954 72.139856 22 18 KEEP --- --- --- --- ITGAX 3687 broad.mit.edu 37 16 31371907 31371907 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:31371907C>T uc002ebu.1 + ITGAX_uc002ebt.2_Intron|ITGAX_uc010vfk.1_5'Flank NM_000887 NP_000878 integrin alpha X precursor blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration|organ morphogenesis integrin complex protein binding|receptor activity ovary(2)|central_nervous_system(1)|pancreas(1) 4 0.636364 25.027588 25.207419 7 4 KEEP --- --- --- --- broad.mit.edu 37 16 32190860 32190860 + RNA SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:32190860G>A uc010vfv.1 - 7 c.964C>T Homo sapiens cDNA FLJ60890 complete cds, moderately similar to HECT domain and RCC1-like domain-containing protein 2. 0.3 17.842655 18.557134 6 14 KEEP --- --- --- --- broad.mit.edu 37 16 32190890 32190890 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:32190890G>A uc010vfv.1 - Homo sapiens cDNA FLJ60890 complete cds, moderately similar to HECT domain and RCC1-like domain-containing protein 2. 0.333333 12.495956 12.791186 4 8 KEEP --- --- --- --- Unknown broad.mit.edu 37 16 32402187 32402187 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:32402187C>T HERC2P4 (238313 upstream) : TP53TG3B (282654 downstream) 0.288136 50.812173 53.151258 17 42 KEEP --- --- --- --- Unknown broad.mit.edu 37 16 32616853 32616853 + IGR SNP A T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:32616853A>T HERC2P4 (452979 upstream) : TP53TG3B (67988 downstream) 0.276923 46.522112 49.433486 18 47 KEEP --- --- --- --- Unknown broad.mit.edu 37 16 33408512 33408512 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:33408512G>A SLC6A10P (512049 upstream) : MIR1826 (556996 downstream) 0.166667 12.431728 16.220541 6 30 KEEP --- --- --- --- Unknown broad.mit.edu 37 16 33546298 33546298 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:33546298C>T SLC6A10P (649835 upstream) : MIR1826 (419210 downstream) 0.727273 29.00501 29.516966 8 3 KEEP --- --- --- --- Unknown broad.mit.edu 37 16 33741198 33741198 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:33741198C>T SLC6A10P (844735 upstream) : MIR1826 (224310 downstream) 0.255814 31.00369 33.329499 11 32 KEEP --- --- --- --- Unknown broad.mit.edu 37 16 34324959 34324959 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:34324959G>A MIR1826 (359367 upstream) : UBE2MP1 (78843 downstream) 0.384615 46.719126 47.173157 15 24 KEEP --- --- --- --- Unknown broad.mit.edu 37 16 34582672 34582672 + IGR SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:34582672A>G UBE2MP1 (177910 upstream) : LOC283914 (15115 downstream) 0.333333 14.796174 15.091295 4 8 KEEP --- --- --- --- MYLK3 91807 broad.mit.edu 37 16 46772027 46772027 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:46772027C>T uc002eei.3 - 3 713 c.597G>A c.(595-597)GGG>GGA p.G199G MYLK3_uc010vge.1_Intron|MYLK3_uc002eej.1_5'UTR NM_182493 NP_872299 Q32MK0 MYLK3_HUMAN myosin light chain kinase 3 199 G -> R (in Ref. 1; CAC42766). cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis cytosol ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity stomach(2)|skin(2)|large_intestine(1)|ovary(1)|central_nervous_system(1) 7 all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116) 207 0.5 12.462506 12.462506 4 4 KEEP --- --- --- --- BRD7 29117 broad.mit.edu 37 16 50388431 50388431 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:50388431G>A uc002egf.1 - BRD7_uc002ege.1_Intron NM_013263 NP_037395 bromodomain containing 7 cell cycle|negative regulation of cell proliferation|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of transcription, DNA-dependent|positive regulation of histone acetylation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|Wnt receptor signaling pathway cytoplasm|nucleus histone acetyl-lysine binding|p53 binding|transcription coactivator activity|transcription corepressor activity|transcription factor binding|transcription regulatory region DNA binding 0 all_cancers(37;0.0127) 0.429577 619.650824 621.494959 183 243 KEEP --- --- --- --- SNX20 124460 broad.mit.edu 37 16 50707442 50707442 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:50707442G>A uc002egk.2 - 4 999 c.826C>T c.(826-828)CTG>TTG p.L276L SNX20_uc010vgp.1_Intron|SNX20_uc002egi.3_Intron NM_182854 NP_878274 Q7Z614 SNX20_HUMAN sorting nexin 20 isoform 1 276 cell communication|protein transport endosome membrane|nucleus|plasma membrane phosphatidylinositol binding|protein binding ovary(1) 1 0.470588 73.3775 73.417049 24 27 KEEP --- --- --- --- Unknown broad.mit.edu 37 16 51098505 51098506 + IGR DNP CC TT TT MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:51098505_51098506CC>TT CYLD (262659 upstream) : SALL1 (71380 downstream) 0.375 347.326332 351.278271 108 180 KEEP --- --- --- --- MT3 4504 broad.mit.edu 37 16 56623765 56623766 + Intron DNP GG AA AA MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:56623765_56623766GG>AA uc002ejf.2 + MT3_uc002ejg.2_3'UTR NM_005954 NP_005945 metallothionein 3 cell proliferation|cellular metal ion homeostasis|removal of superoxide radicals|response to hypoxia synaptic vesicle antioxidant activity|copper ion binding|zinc ion binding 0 0.392857 32.517921 32.799689 11 17 KEEP --- --- --- --- RSPRY1 89970 broad.mit.edu 37 16 57250181 57250181 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:57250181C>T uc002elb.2 + RSPRY1_uc002elc.2_Intron|RSPRY1_uc002eld.2_Intron NM_133368 NP_588609 ring finger and SPRY domain containing 1 extracellular region zinc ion binding ovary(1) 1 0.480769 77.870356 77.887215 25 27 KEEP --- --- --- --- GPR56 9289 broad.mit.edu 37 16 57690120 57690120 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:57690120C>T uc002emb.2 + GPR56_uc002elz.1_Intron|GPR56_uc002ema.1_Intron|GPR56_uc002emc.2_Intron|GPR56_uc002emf.2_Intron|GPR56_uc010vhs.1_Intron|GPR56_uc002emd.2_Intron|GPR56_uc002eme.2_Intron|GPR56_uc010vht.1_Intron|GPR56_uc002emg.3_Intron|GPR56_uc010vhu.1_Intron NM_005682 NP_005673 G protein-coupled receptor 56 isoform a brain development|cell adhesion|cell-cell signaling|neuropeptide signaling pathway integral to plasma membrane G-protein coupled receptor activity 0 0.506849 124.775026 124.777983 37 36 KEEP --- --- --- --- CDH16 1014 broad.mit.edu 37 16 66942409 66942409 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:66942409G>A uc002eql.2 - CDH16_uc010cdy.2_Intron|CDH16_uc002eqm.2_Intron NM_004062 NP_004053 cadherin 16 precursor homophilic cell adhesion integral to membrane|plasma membrane calcium ion binding ovary(2)|upper_aerodigestive_tract(1) 3 Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.0877)|Epithelial(162;0.203) 0.52381 73.942883 73.963135 22 20 KEEP --- --- --- --- HSF4 3299 broad.mit.edu 37 16 67199395 67199395 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:67199395C>T uc002erl.1 + HSF4_uc002erm.1_Intron|HSF4_uc002ern.1_Intron|HSF4_uc010cec.1_Intron NM_001040667 NP_001035757 heat shock transcription factor 4 isoform b response to stress nucleus sequence-specific DNA binding transcription factor activity|transcription corepressor activity 0 Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.0335)|all cancers(182;0.184) 0.407407 33.719555 33.92186 11 16 KEEP --- --- --- --- NOL3 8996 broad.mit.edu 37 16 67209133 67209133 + 3'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:67209133G>A uc010vjd.1 + 4 NOL3_uc010vjc.1_3'UTR|NOL3_uc002erp.2_3'UTR RecName: Full=Nucleolar protein 3; AltName: Full=Apoptosis repressor with CARD; AltName: Full=Muscle-enriched cytoplasmic protein; Short=Myp; AltName: Full=Nucleolar protein of 30 kDa; Short=Nop30; anti-apoptosis|apoptosis|mRNA processing|RNA splicing cytosol|nucleolus identical protein binding|RNA binding 0 Ovarian(137;0.192) OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.0335)|all cancers(182;0.184) 0.407407 34.71938 34.921822 11 16 KEEP --- --- --- --- SLC9A5 6553 broad.mit.edu 37 16 67304697 67304697 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:67304697G>A uc002esm.2 + 16 2338 c.2275G>A c.(2275-2277)GAA>AAA p.E759K SLC9A5_uc010cee.2_Missense_Mutation_p.E464K|SLC9A5_uc010vji.1_Missense_Mutation_p.E263K NM_004594 NP_004585 Q14940 SL9A5_HUMAN solute carrier family 9 (sodium/hydrogen 759 regulation of pH integral to membrane|plasma membrane sodium:hydrogen antiporter activity ovary(1)|pancreas(1) 2 Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116) 0.5 68.299224 68.299224 20 20 KEEP --- --- --- --- KCTD19 146212 broad.mit.edu 37 16 67323610 67323610 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:67323610C>T uc002esu.2 - KCTD19_uc002est.2_Intron|KCTD19_uc010vjj.1_Intron NM_001100915 NP_001094385 potassium channel tetramerisation domain voltage-gated potassium channel complex voltage-gated potassium channel activity skin(1) 1 Ovarian(137;0.192) OV - Ovarian serous cystadenocarcinoma(108;0.0311)|Epithelial(162;0.0906) 0.37037 28.440766 28.840231 10 17 KEEP --- --- --- --- SLC12A4 6560 broad.mit.edu 37 16 67980876 67980876 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:67980876G>A uc002euz.2 - 17 2346 c.2205C>T c.(2203-2205)TTC>TTT p.F735F LCAT_uc002euy.1_5'Flank|SLC12A4_uc010ceu.2_Silent_p.F729F|SLC12A4_uc010vkh.1_Silent_p.F704F|SLC12A4_uc010vki.1_Silent_p.F735F|SLC12A4_uc010vkj.1_Silent_p.F737F|SLC12A4_uc002eva.2_Silent_p.F735F|SLC12A4_uc010cev.1_RNA|SLC12A4_uc002evb.2_RNA NM_005072 NP_005063 Q9UP95 S12A4_HUMAN solute carrier family 12, member 4 isoform a 735 cell volume homeostasis|potassium ion transport|sodium ion transport integral to plasma membrane|membrane fraction potassium:chloride symporter activity ovary(1) 1 Ovarian(137;0.192) OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121) Bumetanide(DB00887)|Potassium Chloride(DB00761) 0.424242 46.448773 46.613009 14 19 KEEP --- --- --- --- DPEP2 64174 broad.mit.edu 37 16 68026370 68026370 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:68026370C>T uc010cey.2 - DPEP2_uc002evd.3_Intron|DPEP2_uc002eve.2_Intron|DPEP2_uc002evf.2_Intron|DPEP2_uc002evg.2_Intron NM_022355 NP_071750 dipeptidase 2 precursor hormone biosynthetic process|leukotriene biosynthetic process|prostanoid metabolic process|proteolysis anchored to membrane|plasma membrane dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metalloexopeptidase activity skin(1) 1 Ovarian(137;0.192) OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0489)|all cancers(182;0.239) 0.465116 134.293632 134.384674 40 46 KEEP --- --- --- --- TERF2 7014 broad.mit.edu 37 16 69390733 69390733 + 3'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:69390733G>A uc002exd.2 - 10 NM_005652 NP_005643 telomeric repeat binding factor 2 age-dependent telomere shortening|cell cycle|cellular senescence|negative regulation of telomere maintenance via semi-conservative replication|protection from non-homologous end joining at telomere|protein localization to chromosome, telomeric region|regulation of transcription, DNA-dependent|telomeric loop formation Golgi apparatus|nuclear telomere cap complex|nucleoplasm double-stranded telomeric DNA binding|protein C-terminus binding|protein homodimerization activity lung(1) 1 Ovarian(137;0.101) Ovarian(13;63 524 30420 31710 34037) 0.469388 76.571929 76.606255 23 26 KEEP --- --- --- --- HYDIN 54768 broad.mit.edu 37 16 70871567 70871567 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:70871567C>T uc002ezr.2 - HYDIN_uc010cfy.2_Intron NM_032821 NP_116210 hydrocephalus inducing isoform a ovary(1)|skin(1) 2 Ovarian(137;0.0654) 0.412698 88.442943 88.861193 26 37 KEEP --- --- --- --- HYDIN 54768 broad.mit.edu 37 16 70902548 70902548 + Nonsense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:70902548C>T uc002ezr.2 - 66 11360 c.11232G>A c.(11230-11232)TGG>TGA p.W3744* HYDIN_uc010cfy.2_5'Flank NM_032821 NP_116210 Q4G0P3 HYDIN_HUMAN hydrocephalus inducing isoform a 3745 ovary(1)|skin(1) 2 Ovarian(137;0.0654) 0.472727 88.349031 88.384403 26 29 KEEP --- --- --- --- HYDIN 54768 broad.mit.edu 37 16 70954628 70954628 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:70954628C>T uc002ezr.2 - 46 7776 c.7648G>A c.(7648-7650)GAA>AAA p.E2550K NM_032821 NP_116210 Q4G0P3 HYDIN_HUMAN hydrocephalus inducing isoform a 2551 ovary(1)|skin(1) 2 Ovarian(137;0.0654) 0.75 19.152634 19.606587 6 2 KEEP --- --- --- --- HYDIN 54768 broad.mit.edu 37 16 70995904 70995904 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:70995904C>T uc002ezr.2 - 38 6051 c.5923G>A c.(5923-5925)GAA>AAA p.E1975K NM_032821 NP_116210 Q4G0P3 HYDIN_HUMAN hydrocephalus inducing isoform a 1976 Poly-Glu. ovary(1)|skin(1) 2 Ovarian(137;0.0654) 0.413333 100.512596 101.004356 31 44 KEEP --- --- --- --- PHLPP2 23035 broad.mit.edu 37 16 71682667 71682667 + 3'UTR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:71682667C>T uc002fax.2 - 18 PHLPP2_uc002fav.2_Intron|PHLPP2_uc010cgf.2_3'UTR NM_015020 NP_055835 PH domain and leucine rich repeat protein cytoplasm|membrane|nucleus metal ion binding|phosphoprotein phosphatase activity ovary(1)|central_nervous_system(1) 2 0.4 19.047012 19.178219 6 9 KEEP --- --- --- --- broad.mit.edu 37 16 72762469 72762469 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:72762469C>T uc002fcj.1 + Homo sapiens cDNA FLJ11501 fis, clone HEMBA1002100. 0.375 34.99187 35.430878 12 20 KEEP --- --- --- --- CLEC18B 497190 broad.mit.edu 37 16 74447089 74447089 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:74447089G>A uc002fct.2 - CLEC18B_uc002fcu.2_Intron|CLEC18B_uc010vmu.1_Intron|CLEC18B_uc010vmv.1_5'Flank NM_001011880 NP_001011880 C-type lectin domain family 18, member B extracellular region sugar binding 0 0.242424 59.655379 65.642611 24 75 KEEP --- --- --- --- RFWD3 55159 broad.mit.edu 37 16 74657784 74657784 + 3'UTR SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:74657784A>G uc002fda.2 - 13 RFWD3_uc010vmx.1_3'UTR|RFWD3_uc010cgq.2_3'UTR NM_018124 NP_060594 ring finger and WD repeat domain 3 DNA repair|mitotic cell cycle G1/S transition DNA damage checkpoint|response to ionizing radiation nucleus MDM2 binding|p53 binding|ubiquitin-protein ligase activity|zinc ion binding lung(2)|breast(1) 3 0.4 74.839243 75.320127 22 33 KEEP --- --- --- --- CHST5 23563 broad.mit.edu 37 16 75563010 75563010 + 3'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:75563010G>A uc002fei.2 - 3 CHST5_uc002fej.1_3'UTR NM_024533 NP_078809 carbohydrate (N-acetylglucosamine 6-O) N-acetylglucosamine metabolic process|protein sulfation integral to membrane|intrinsic to Golgi membrane N-acetylglucosamine 6-O-sulfotransferase activity 0 0.5 19.94984 19.94984 6 6 KEEP --- --- --- --- ADAMTS18 170692 broad.mit.edu 37 16 77353836 77353836 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:77353836G>A uc002ffc.3 - 16 2861 c.2442C>T c.(2440-2442)TTC>TTT p.F814F ADAMTS18_uc010chc.1_Silent_p.F402F|ADAMTS18_uc002ffe.1_Silent_p.F510F NM_199355 NP_955387 Q8TE60 ATS18_HUMAN ADAM metallopeptidase with thrombospondin type 1 814 Spacer. proteolysis proteinaceous extracellular matrix metalloendopeptidase activity|zinc ion binding large_intestine(4)|lung(4)|kidney(4)|skin(3)|breast(1)|ovary(1)|pancreas(1) 18 1451 0.491803 97.249252 97.252794 30 31 KEEP --- --- --- --- CDYL2 124359 broad.mit.edu 37 16 80718765 80718765 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:80718765G>A uc002ffs.2 - 2 391 c.286C>T c.(286-288)CCT>TCT p.P96S NM_152342 NP_689555 Q8N8U2 CDYL2_HUMAN chromodomain protein, Y-like 2 96 nucleus catalytic activity|protein binding central_nervous_system(1) 1 0.552239 123.478916 123.637693 37 30 KEEP --- --- --- --- PKD1L2 114780 broad.mit.edu 37 16 81208534 81208534 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:81208534G>A uc002fgh.1 - PKD1L2_uc002fgg.1_Intron|PKD1L2_uc002fgi.2_Intron|PKD1L2_uc002fgj.2_Intron|PKD1L2_uc002fgk.1_Intron|PKD1L2_uc002fgl.1_Intron NM_052892 NP_443124 polycystin 1-like 2 isoform a neuropeptide signaling pathway integral to membrane calcium ion binding|ion channel activity|sugar binding ovary(1)|central_nervous_system(1)|pancreas(1) 3 0.583333 95.206433 95.497083 28 20 KEEP --- --- --- --- CTU2 348180 broad.mit.edu 37 16 88781462 88781462 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:88781462C>T uc002flm.2 + 14 1474 c.1426C>T c.(1426-1428)CTG>TTG p.L476L CTU2_uc002fln.2_Intron|CTU2_uc010chz.2_Silent_p.L547L|CTU2_uc010cia.2_Silent_p.L389L NM_001012759 NP_001012777 Q2VPK5 CTU2_HUMAN cytoplasmic tRNA 2-thiolation protein 2 isoform 476 tRNA thio-modification|tRNA wobble uridine modification cytoplasm|protein complex|soluble fraction protein binding skin(1) 1 0.75 18.052195 18.506138 6 2 KEEP --- --- --- --- CBFA2T3 863 broad.mit.edu 37 16 88958234 88958234 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:88958234G>A uc002fmm.1 - CBFA2T3_uc002fml.1_Intron|CBFA2T3_uc010cif.1_Intron|CBFA2T3_uc002fmn.1_Intron NM_005187 NP_005178 myeloid translocation gene on chromosome 16 cell proliferation|granulocyte differentiation Golgi membrane|nucleolus|nucleoplasm protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding large_intestine(3)|ovary(1) 4 BRCA - Breast invasive adenocarcinoma(80;0.0275) 305 T RUNX1 AML 0.428571 7.116442 7.148856 3 4 KEEP --- --- --- --- CPNE7 27132 broad.mit.edu 37 16 89651822 89651823 + Intron DNP GG AA AA MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr16:89651822_89651823GG>AA uc002fnp.2 + CPNE7_uc002fnq.2_Intron NM_014427 NP_055242 copine 7 isoform b lipid metabolic process transporter activity 0 all_hematologic(23;0.0748) all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147) 0.642857 30.478967 30.730963 9 5 KEEP --- --- --- --- PITPNA 5306 broad.mit.edu 37 17 1438378 1438378 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:1438378G>A uc002fst.3 - PITPNA_uc010cjt.2_Intron|PITPNA_uc010cju.2_Intron NM_006224 NP_006215 phosphatidylinositol transfer protein, alpha axon guidance|lipid metabolic process|visual perception cytoplasm phosphatidylcholine transmembrane transporter activity|phosphatidylinositol transporter activity|protein binding ovary(1) 1 UCEC - Uterine corpus endometrioid carcinoma (25;0.0845) 0.571429 12.335107 12.377115 4 3 KEEP --- --- --- --- PITPNA 5306 broad.mit.edu 37 17 1438410 1438410 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:1438410G>A uc002fst.3 - PITPNA_uc010cjt.2_Intron|PITPNA_uc010cju.2_Intron NM_006224 NP_006215 phosphatidylinositol transfer protein, alpha axon guidance|lipid metabolic process|visual perception cytoplasm phosphatidylcholine transmembrane transporter activity|phosphatidylinositol transporter activity|protein binding ovary(1) 1 UCEC - Uterine corpus endometrioid carcinoma (25;0.0845) 0.583333 24.326975 24.399666 7 5 KEEP --- --- --- --- RPA1 6117 broad.mit.edu 37 17 1747080 1747080 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:1747080G>A uc002fto.2 + NM_002945 NP_002936 replication protein A1 cell cycle checkpoint|DNA recombinase assembly|DNA strand elongation involved in DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair actin cytoskeleton|cytoplasm|DNA replication factor A complex|PML body metal ion binding|protein binding|single-stranded DNA binding 0 NER 0.444444 12.798842 12.823059 4 5 KEEP --- --- --- --- RAP1GAP2 23108 broad.mit.edu 37 17 2888375 2888375 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:2888375C>T uc010ckd.2 + RAP1GAP2_uc010cke.2_Intron NM_015085 NP_055900 RAP1 GTPase activating protein 2 isoform 1 regulation of small GTPase mediated signal transduction centrosome|cytosol|perinuclear region of cytoplasm GTPase activator activity ovary(1) 1 0.488889 141.694366 141.704119 44 46 KEEP --- --- --- --- TRPV3 162514 broad.mit.edu 37 17 3436054 3436054 + Missense_Mutation SNP T C C rs112265558 MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:3436054T>C uc002fvt.1 - 8 1284 c.962A>G c.(961-963)TAC>TGC p.Y321C TRPV3_uc002fvs.1_RNA|TRPV3_uc010vrh.1_Missense_Mutation_p.Y305C|TRPV3_uc010vri.1_Missense_Mutation_p.Y276C|TRPV3_uc010vrj.1_Missense_Mutation_p.Y305C|TRPV3_uc010vrk.1_RNA|TRPV3_uc010vrl.1_Missense_Mutation_p.Y305C|TRPV3_uc010vrm.1_RNA|TRPV3_uc002fvr.2_Missense_Mutation_p.Y321C|TRPV3_uc002fvu.2_Missense_Mutation_p.Y321C|TRPV3_uc010vrn.1_5'Flank NM_145068 NP_659505 Q8NET8 TRPV3_HUMAN transient receptor potential cation channel, 321 Cytoplasmic (Potential). integral to membrane calcium channel activity ovary(4) 4 Menthol(DB00825) 0.055556 -0.680156 6.800003 2 34 KEEP --- --- --- --- TRPV3 162514 broad.mit.edu 37 17 3445784 3445784 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:3445784C>T uc002fvt.1 - TRPV3_uc010vrh.1_Intron|TRPV3_uc010vri.1_Intron|TRPV3_uc010vrj.1_Intron|TRPV3_uc010vrk.1_Intron|TRPV3_uc010vrl.1_Intron|TRPV3_uc010vrm.1_Intron|TRPV3_uc002fvr.2_Intron|TRPV3_uc002fvu.2_Intron NM_145068 NP_659505 transient receptor potential cation channel, integral to membrane calcium channel activity ovary(4) 4 Menthol(DB00825) 0.727273 29.305152 29.817306 8 3 KEEP --- --- --- --- TRPV3 162514 broad.mit.edu 37 17 3457916 3457916 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:3457916G>A uc002fvt.1 - TRPV3_uc010vrj.1_Intron|TRPV3_uc010vrk.1_Intron|TRPV3_uc002fvr.2_Intron|TRPV3_uc002fvu.2_Intron NM_145068 NP_659505 transient receptor potential cation channel, integral to membrane calcium channel activity ovary(4) 4 Menthol(DB00825) 0.538462 20.219806 20.236093 7 6 KEEP --- --- --- --- ITGAE 3682 broad.mit.edu 37 17 3653554 3653554 + Intron SNP C A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:3653554C>A uc002fwo.3 - NM_002208 NP_002199 integrin, alpha E precursor cell adhesion|integrin-mediated signaling pathway integrin complex receptor activity large_intestine(2)|breast(1)|pancreas(1) 4 UCEC - Uterine corpus endometrioid carcinoma (3;0.0813) NSCLC(182;635 2928 8995 38788) 37 0.153846 7.294529 10.263977 4 22 KEEP --- --- --- --- ZZEF1 23140 broad.mit.edu 37 17 3947524 3947524 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:3947524G>A uc002fxe.2 - 38 6224 c.6160C>T c.(6160-6162)CTT>TTT p.L2054F ZZEF1_uc002fxh.2_Missense_Mutation_p.L368F|ZZEF1_uc002fxi.2_Missense_Mutation_p.L289F|ZZEF1_uc002fxj.1_Missense_Mutation_p.L667F NM_015113 NP_055928 O43149 ZZEF1_HUMAN zinc finger, ZZ type with EF hand domain 1 2054 calcium ion binding|zinc ion binding ovary(2)|central_nervous_system(1)|pancreas(1) 4 0.353659 92.65059 94.199028 29 53 KEEP --- --- --- --- ZZEF1 23140 broad.mit.edu 37 17 4020353 4020353 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:4020353G>A uc002fxe.2 - 3 671 c.607C>T c.(607-609)CCG>TCG p.P203S ZZEF1_uc002fxk.1_Missense_Mutation_p.P203S NM_015113 NP_055928 O43149 ZZEF1_HUMAN zinc finger, ZZ type with EF hand domain 1 203 calcium ion binding|zinc ion binding ovary(2)|central_nervous_system(1)|pancreas(1) 4 0.393939 201.014624 202.613602 65 100 KEEP --- --- --- --- SPNS3 201305 broad.mit.edu 37 17 4390924 4390924 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:4390924G>A uc002fxt.2 + SPNS3_uc002fxu.2_Intron|SPNS3_uc002fxv.2_Intron|uc002fxw.1_5'Flank NM_182538 NP_872344 spinster homolog 3 lipid transport|transmembrane transport integral to membrane large_intestine(1) 1 0.714286 33.953249 34.52939 10 4 KEEP --- --- --- --- MYBBP1A 10514 broad.mit.edu 37 17 4445974 4445974 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:4445974G>A uc002fyb.3 - 21 3017 c.2955C>T c.(2953-2955)TTC>TTT p.F985F MYBBP1A_uc002fxz.3_Silent_p.F985F|MYBBP1A_uc002fya.3_5'Flank|MYBBP1A_uc010vsa.1_Silent_p.F27F NM_014520 NP_055335 Q9BQG0 MBB1A_HUMAN MYB binding protein 1a isoform 2 985 nucleocytoplasmic transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|NLS-dependent protein nuclear import complex|nucleolus DNA binding|DNA-directed DNA polymerase activity|transcription factor binding ovary(1)|skin(1) 2 0.486486 114.195034 114.206853 36 38 KEEP --- --- --- --- USP6 9098 broad.mit.edu 37 17 5039961 5039961 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:5039961G>A uc002gau.1 + 18 2921 c.691G>A c.(691-693)GTC>ATC p.V231I USP6_uc002gav.1_Missense_Mutation_p.V231I|USP6_uc010ckz.1_5'UTR|uc002gbb.2_5'Flank NM_004505 NP_004496 P35125 UBP6_HUMAN ubiquitin specific protease 6 231 Rab-GAP TBC. protein deubiquitination|regulation of vesicle-mediated transport|ubiquitin-dependent protein catabolic process lysosome|plasma membrane|recycling endosome calmodulin binding|cysteine-type endopeptidase activity|nucleic acid binding|protein binding|Rab GTPase activator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity skin(2)|upper_aerodigestive_tract(1)|lung(1)|breast(1) 5 464 T COL1A1|CDH11|ZNF9|OMD aneurysmal bone cysts 0.636364 267.404462 269.382638 77 44 KEEP --- --- --- --- USP6 9098 broad.mit.edu 37 17 5072273 5072273 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:5072273G>A uc002gau.1 + 35 5670 c.3440G>A c.(3439-3441)AGT>AAT p.S1147N USP6_uc002gav.1_Missense_Mutation_p.S1147N|USP6_uc010ckz.1_Missense_Mutation_p.S830N NM_004505 NP_004496 P35125 UBP6_HUMAN ubiquitin specific protease 6 1147 protein deubiquitination|regulation of vesicle-mediated transport|ubiquitin-dependent protein catabolic process lysosome|plasma membrane|recycling endosome calmodulin binding|cysteine-type endopeptidase activity|nucleic acid binding|protein binding|Rab GTPase activator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity skin(2)|upper_aerodigestive_tract(1)|lung(1)|breast(1) 5 464 T COL1A1|CDH11|ZNF9|OMD aneurysmal bone cysts 0.666667 192.729649 194.798529 56 28 KEEP --- --- --- --- RABEP1 9135 broad.mit.edu 37 17 5268650 5268650 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:5268650C>T uc002gbm.3 + RABEP1_uc010clc.1_Intron|RABEP1_uc010cld.1_Intron|RABEP1_uc010vsw.1_Intron|RABEP1_uc002gbl.3_Intron|NUP88_uc002gbn.2_Intron NM_004703 NP_004694 rabaptin, RAB GTPase binding effector protein 1 apoptosis|cellular membrane fusion|endocytosis|protein transport centrosome|early endosome|endocytic vesicle|recycling endosome growth factor activity|GTPase activator activity|protein homodimerization activity large_intestine(1)|ovary(1) 2 903 0.4 10.79212 10.881083 4 6 KEEP --- --- --- --- KIAA0753 9851 broad.mit.edu 37 17 6515500 6515500 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:6515500G>A uc002gde.3 - KIAA0753_uc010vtd.1_Intron|KIAA0753_uc010clo.2_Intron|KIAA0753_uc010vte.1_Intron NM_014804 NP_055619 hypothetical protein LOC9851 centrosome 0 COAD - Colon adenocarcinoma(228;0.157) 0.475 63.022657 63.044435 19 21 KEEP --- --- --- --- SLC2A4 6517 broad.mit.edu 37 17 7188418 7188418 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:7188418G>A uc002gfp.2 + 9 1232 c.1032G>A c.(1030-1032)GTG>GTA p.V344V SLC2A4_uc002gfo.2_Silent_p.V344V|SLC2A4_uc010cmd.2_RNA NM_001042 NP_001033 P14672 GTR4_HUMAN glucose transporter 4 344 Helical; Name=8; (Potential). carbohydrate metabolic process|glucose homeostasis|glucose import external side of plasma membrane|integral to plasma membrane|perinuclear region of cytoplasm D-glucose transmembrane transporter activity|protein binding 0 0.666667 13.80186 13.949364 4 2 KEEP --- --- --- --- NEURL4 84461 broad.mit.edu 37 17 7225088 7225088 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:7225088C>T uc002gga.1 - 18 2897 c.2890G>A c.(2890-2892)GAT>AAT p.D964N NEURL4_uc002gfy.1_5'Flank|GPS2_uc002gfz.1_5'Flank|NEURL4_uc002ggb.1_Missense_Mutation_p.D962N|NEURL4_uc002ggc.1_Missense_Mutation_p.D310N NM_032442 NP_115818 Q96JN8 NEUL4_HUMAN neuralized homolog 4 isoform 1 964 NHR 5. protein binding upper_aerodigestive_tract(1)|ovary(1) 2 0.423077 37.221534 37.355626 11 15 KEEP --- --- --- --- ACAP1 9744 broad.mit.edu 37 17 7251702 7251702 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:7251702G>A uc002ggd.2 + 17 1792 c.1586G>A c.(1585-1587)CGA>CAA p.R529Q NM_014716 NP_055531 Q15027 ACAP1_HUMAN centaurin beta1 529 Required for interaction with GULP1. intracellular signal transduction|lipid metabolic process|protein transport|regulation of ARF GTPase activity ARF GTPase activator activity|phospholipase C activity|protein binding|zinc ion binding breast(2)|large_intestine(1) 3 0.692308 28.172229 28.598551 9 4 KEEP --- --- --- --- SPEM1 374768 broad.mit.edu 37 17 7324578 7324579 + Nonsense_Mutation DNP GG AA AA MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:7324578_7324579GG>AA uc002ggv.2 + 3 609_610 c.584_585GG>AA c.(583-585)TGG>TAA p.W195* FGF11_uc010vtw.1_Intron NM_199339 NP_955371 Q8N4L4 SPEM1_HUMAN spermatid maturation 1 195 cell differentiation|multicellular organismal development|spermatogenesis cytoplasm|integral to membrane 0 Prostate(122;0.173) 0.4 46.788153 47.138981 16 24 KEEP --- --- --- --- TP53 7157 broad.mit.edu 37 17 7577539 7577539 + Missense_Mutation SNP G A A rs121912651 MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:7577539G>A uc002gim.2 - 7 936 c.742C>T c.(742-744)CGG>TGG p.R248W TP53_uc002gig.1_Missense_Mutation_p.R248W|TP53_uc002gih.2_Missense_Mutation_p.R248W|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R116W|TP53_uc010cng.1_Missense_Mutation_p.R116W|TP53_uc002gii.1_Missense_Mutation_p.R116W|TP53_uc010cnh.1_Missense_Mutation_p.R248W|TP53_uc010cni.1_Missense_Mutation_p.R248W|TP53_uc002gij.2_Missense_Mutation_p.R248W|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Missense_Mutation_p.R155W|TP53_uc002gio.2_Missense_Mutation_p.R116W NM_001126112 NP_001119584 P04637 P53_HUMAN tumor protein p53 isoform a 248 |Interaction with HIPK1 (By similarity).|Interacts with the 53BP2 SH3 domain.|Interaction with AXIN1 (By similarity). R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|NR -> IP (in a sporadic cancer; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.R248Q(516)|p.R248W(443)|p.R248L(63)|p.R248P(12)|p.R248G(11)|p.R248R(10)|p.0?(7)|p.N247_R248delNR(2)|p.N247_R248>KW(2)|p.M246_P250delMNRRP(2)|p.R248fs*97(2)|p.R248_P250delRRP(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1) large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1) 22245 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) Pancreas(47;798 1329 9957 10801) R248W(CAS1_CENTRAL_NERVOUS_SYSTEM)|R248W(COLO680N_OESOPHAGUS)|R248W(SW837_LARGE_INTESTINE)|R248W(KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(RD_SOFT_TISSUE)|R248W(VCAP_PROSTATE)|R248W(JIMT1_BREAST)|R248W(GCT_SOFT_TISSUE)|R248W(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(786O_KIDNEY)|R248W(COLO320_LARGE_INTESTINE)|R248W(LXF289_LUNG)|R248W(LUDLU1_LUNG)|R248W(MIAPACA2_PANCREAS)|R248W(HCC2157_BREAST) 111 p.R248W(SW837-Tumor)|p.R248W(786O-Tumor)|p.R248W(LUDLU1-Tumor)|p.R248W(VCAP-Tumor)|p.R248*(DB-Tumor)|p.R248W(MIAPACA2-Tumor)|p.R248W(HCC2157-Tumor)|p.R248W(LXF289-Tumor)|p.R248G(8505C-Tumor)|p.R248A(SF126-Tumor)|p.R248W(SET2-Tumor)|p.R248W(KO52-Tumor)|p.R248W(SNU1040-Tumor)|p.R248W(GCT-Tumor)|p.R248W(JIMT1-Tumor)|p.R248W(COLO320-Tumor)|p.R248W(CAS1-Tumor)|p.R248W(NCIH2106-Tumor)|p.R248W(SNUC5-Tumor)|p.R248W(COLO680N-Tumor)|p.R248W(RD-Tumor) 690 Mis|N|F breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types Other_conserved_DNA_damage_response_genes Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) 0.625 65.001612 65.439311 20 12 KEEP --- --- --- --- C17orf68 80169 broad.mit.edu 37 17 8141802 8141802 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:8141802C>T uc002gkq.3 - 3 402 c.343G>A c.(343-345)GGG>AGG p.G115R C17orf68_uc010cnv.2_RNA NM_025099 NP_079375 Q2NKJ3 CTC1_HUMAN alpha accessory factor 132 115 positive regulation of DNA replication|telomere maintenance Stn1-Ten1 complex protein binding|single-stranded DNA binding 0 0.612403 279.964257 281.398068 79 50 KEEP --- --- --- --- PFAS 5198 broad.mit.edu 37 17 8168540 8168540 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:8168540C>T uc002gkr.2 + PFAS_uc010vuv.1_Intron|PFAS_uc002gks.2_5'Flank NM_012393 NP_036525 phosphoribosylformylglycinamidine synthase 'de novo' IMP biosynthetic process|glutamine metabolic process|purine base metabolic process cytosol ATP binding|phosphoribosylformylglycinamidine synthase activity|protein binding ovary(2)|central_nervous_system(2)|pancreas(1) 5 L-Glutamic Acid(DB00142)|L-Glutamine(DB00130) 0.619048 44.479638 44.7405 13 8 KEEP --- --- --- --- PFAS 5198 broad.mit.edu 37 17 8171835 8171835 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:8171835C>T uc002gkr.2 + PFAS_uc010vuv.1_Intron|PFAS_uc002gks.2_Intron NM_012393 NP_036525 phosphoribosylformylglycinamidine synthase 'de novo' IMP biosynthetic process|glutamine metabolic process|purine base metabolic process cytosol ATP binding|phosphoribosylformylglycinamidine synthase activity|protein binding ovary(2)|central_nervous_system(2)|pancreas(1) 5 L-Glutamic Acid(DB00142)|L-Glutamine(DB00130) 0.297297 32.212885 33.570748 11 26 KEEP --- --- --- --- WDR16 146845 broad.mit.edu 37 17 9531898 9531898 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:9531898C>T uc002gly.2 + WDR16_uc002glz.2_Intron|WDR16_uc010coc.2_Intron NM_145054 NP_659491 WD40-repeat protein upregulated in HCC isoform cytoplasm|intracellular membrane-bounded organelle protein binding skin(2)|ovary(1)|central_nervous_system(1) 4 0.5 16.074704 16.074704 5 5 KEEP --- --- --- --- GLP2R 9340 broad.mit.edu 37 17 9763312 9763312 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:9763312C>T uc002gmd.1 + 7 819 c.819C>T c.(817-819)GCC>GCT p.A273A NM_004246 NP_004237 O95838 GLP2R_HUMAN glucagon-like peptide 2 receptor precursor 273 Helical; Name=3; (Potential). G-protein signaling, coupled to cAMP nucleotide second messenger|positive regulation of cell proliferation integral to membrane|plasma membrane lung(2)|ovary(1) 3 Glucagon recombinant(DB00040) 0.590909 83.241043 83.555929 26 18 KEEP --- --- --- --- MYH13 8735 broad.mit.edu 37 17 10224748 10224748 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:10224748C>T uc002gmk.1 - MYH13_uc010vve.1_Intron NM_003802 NP_003793 myosin, heavy polypeptide 13, skeletal muscle muscle contraction muscle myosin complex|myofibril|myosin filament actin binding|ATP binding|calmodulin binding|microfilament motor activity ovary(4)|skin(2) 6 0.388889 22.320894 22.515633 7 11 KEEP --- --- --- --- MYH4 4622 broad.mit.edu 37 17 10368109 10368109 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:10368109C>T uc002gmn.2 - uc002gml.1_Intron NM_017533 NP_060003 myosin, heavy polypeptide 4, skeletal muscle muscle filament sliding muscle myosin complex|myosin filament|sarcomere actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle ovary(10)|skin(2)|central_nervous_system(1) 13 0.428571 20.748115 20.810387 6 8 KEEP --- --- --- --- MYH1 4619 broad.mit.edu 37 17 10402157 10402157 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:10402157G>A uc002gmo.2 - uc002gml.1_Intron NM_005963 NP_005954 myosin, heavy chain 1, skeletal muscle, adult muscle myosin complex|myofibril|myosin filament actin binding|ATP binding|calmodulin binding|motor activity ovary(10)|skin(6)|breast(3)|upper_aerodigestive_tract(1)|kidney(1) 21 585 0.47541 93.170565 93.202729 29 32 KEEP --- --- --- --- MYH2 4620 broad.mit.edu 37 17 10427737 10427737 + Intron SNP G T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:10427737G>T uc010coi.2 - uc002gml.1_Intron|MYH2_uc002gmp.3_Intron|MYH2_uc010coj.2_Intron NM_001100112 NP_001093582 myosin heavy chain IIa muscle filament sliding muscle myosin complex|myosin filament|sarcomere actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1) 14 0.367347 53.135128 53.893979 18 31 KEEP --- --- --- --- MYH2 4620 broad.mit.edu 37 17 10427991 10427991 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:10427991G>A uc010coi.2 - uc002gml.1_Intron|MYH2_uc002gmp.3_Intron|MYH2_uc010coj.2_Intron NM_001100112 NP_001093582 myosin heavy chain IIa muscle filament sliding muscle myosin complex|myosin filament|sarcomere actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1) 14 0.568966 108.4808 108.720748 33 25 KEEP --- --- --- --- HS3ST3A1 9955 broad.mit.edu 37 17 13400034 13400034 + Missense_Mutation SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:13400034T>C uc002gob.1 - 2 1499 c.701A>G c.(700-702)AAG>AGG p.K234R NM_006042 NP_006033 Q9Y663 HS3SA_HUMAN heparan sulfate D-glucosaminyl 234 Lumenal (Potential). Golgi membrane|integral to membrane [heparan sulfate]-glucosamine 3-sulfotransferase 3 activity ovary(1)|central_nervous_system(1) 2 all_lung(20;0.114) UCEC - Uterine corpus endometrioid carcinoma (92;0.101) 0.31746 67.178403 69.044171 20 43 KEEP --- --- --- --- CDRT15 146822 broad.mit.edu 37 17 14140257 14140257 + 5'Flank SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:14140257C>T uc010vvu.1 - CDRT15_uc010coq.2_5'Flank NM_001007530 NP_001007531 CMT1A duplicated region transcript 15 0 UCEC - Uterine corpus endometrioid carcinoma (92;0.0822) 0.583333 23.426646 23.499279 7 5 KEEP --- --- --- --- Unknown broad.mit.edu 37 17 14683457 14683457 + IGR SNP G T T rs146755663 MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:14683457G>T HS3ST3B1 (433965 upstream) : PMP22 (449640 downstream) 0.074074 -0.84624 9.218433 4 50 KEEP --- --- --- --- FAM18B2 201158 broad.mit.edu 37 17 15410523 15410523 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:15410523C>T uc002goq.2 - CDRT4_uc010vvw.1_Intron|FAM18B2_uc010vvx.1_Intron NM_145301 NP_660344 hypothetical protein LOC201158 isoform 1 integral to membrane 0 UCEC - Uterine corpus endometrioid carcinoma (92;0.0872)|BRCA - Breast invasive adenocarcinoma(8;0.0581)|READ - Rectum adenocarcinoma(1115;0.0967) 0.666667 24.802499 25.09731 8 4 KEEP --- --- --- --- ADORA2B 136 broad.mit.edu 37 17 15878268 15878268 + Missense_Mutation SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:15878268A>G uc002gpd.1 + 2 943 c.611A>G c.(610-612)AAG>AGG p.K204R NM_000676 NP_000667 P29275 AA2BR_HUMAN adenosine A2b receptor 204 Cytoplasmic (By similarity). activation of MAPK activity|cellular defense response|excretion|JNK cascade integral to plasma membrane ovary(2) 2 UCEC - Uterine corpus endometrioid carcinoma (92;0.0855) Defibrotide(DB04932)|Enprofylline(DB00824)|Pegademase bovine(DB00061)|Theophylline(DB00277) 0.393443 80.987802 81.593952 24 37 KEEP --- --- --- --- TRPV2 51393 broad.mit.edu 37 17 16336868 16336868 + Intron SNP G C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:16336868G>C uc002gpy.2 + TRPV2_uc002gpz.2_Intron NM_016113 NP_057197 transient receptor potential cation channel, sensory perception integral to plasma membrane|melanosome calcium channel activity ovary(1) 1 UCEC - Uterine corpus endometrioid carcinoma (92;0.0837) 0.122449 22.526682 36.203915 12 86 KEEP --- --- --- --- RAI1 10743 broad.mit.edu 37 17 17707077 17707077 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:17707077C>T uc002grm.2 + 4 6042 c.5573C>T c.(5572-5574)TCC>TTC p.S1858F NM_030665 NP_109590 Q7Z5J4 RAI1_HUMAN retinoic acid induced 1 1858 PHD-type. cytoplasm|nucleus zinc ion binding central_nervous_system(1)|skin(1) 2 READ - Rectum adenocarcinoma(1115;0.0276) 0.319149 41.800997 43.171275 15 32 KEEP --- --- --- --- FBXW10 10517 broad.mit.edu 37 17 18659367 18659367 + Missense_Mutation SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:18659367A>G uc002guk.2 + 6 1364 c.1132A>G c.(1132-1134)AAC>GAC p.N378D FBXW10_uc002guj.2_Missense_Mutation_p.N378D|FBXW10_uc002gul.2_Missense_Mutation_p.N407D|FBXW10_uc010cqh.1_Missense_Mutation_p.N378D NM_031456 NP_113644 Q5XX13 FBW10_HUMAN F-box and WD-40 domain protein 10 378 ovary(1) 1 0.125 3.607138 6.905816 3 21 KEEP --- --- --- --- PRPSAP2 5636 broad.mit.edu 37 17 18811810 18811810 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:18811810C>T uc002gup.1 + PRPSAP2_uc002guo.1_Intron|PRPSAP2_uc010vyi.1_Intron|PRPSAP2_uc010vyj.1_Intron|PRPSAP2_uc010vyk.1_Intron NM_002767 NP_002758 phosphoribosyl pyrophosphate nucleotide biosynthetic process enzyme inhibitor activity|magnesium ion binding|ribose phosphate diphosphokinase activity skin(1) 1 0.307692 11.895145 12.323695 4 9 KEEP --- --- --- --- PRPSAP2 5636 broad.mit.edu 37 17 18834017 18834017 + 3'UTR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:18834017C>T uc002gup.1 + 12 PRPSAP2_uc002guo.1_3'UTR|PRPSAP2_uc010vyi.1_3'UTR|PRPSAP2_uc010vyj.1_3'UTR|PRPSAP2_uc010vyk.1_3'UTR|PRPSAP2_uc002guq.1_3'UTR NM_002767 NP_002758 phosphoribosyl pyrophosphate nucleotide biosynthetic process enzyme inhibitor activity|magnesium ion binding|ribose phosphate diphosphokinase activity skin(1) 1 0.34375 33.217377 33.906481 11 21 KEEP --- --- --- --- Unknown broad.mit.edu 37 17 25739848 25739848 + IGR SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:25739848A>G WSB1 (99203 upstream) : KSR1 (59188 downstream) 0.727273 59.210109 60.234704 16 6 KEEP --- --- --- --- SUPT6H 6830 broad.mit.edu 37 17 27000492 27000492 + Nonsense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:27000492C>T uc002hby.2 + 2 163 c.73C>T c.(73-75)CGA>TGA p.R25* SUPT6H_uc010crt.2_Nonsense_Mutation_p.R25* NM_003170 NP_003161 Q7KZ85 SPT6H_HUMAN suppressor of Ty 6 homolog 25 Asp/Glu-rich. chromatin remodeling|regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter nucleus hydrolase activity, acting on ester bonds|RNA binding|sequence-specific DNA binding transcription factor activity ovary(2)|skin(1) 3 Lung NSC(42;0.00431) 0.636364 72.984329 73.52505 21 12 KEEP --- --- --- --- SSH2 85464 broad.mit.edu 37 17 27958412 27958412 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:27958412G>A uc002heo.1 - 15 3719 c.3719C>T c.(3718-3720)TCT>TTT p.S1240F SSH2_uc010wbh.1_Missense_Mutation_p.S1267F NM_033389 NP_203747 Q76I76 SSH2_HUMAN slingshot 2 1240 actin cytoskeleton organization|regulation of actin polymerization or depolymerization|regulation of axonogenesis|regulation of lamellipodium assembly cytoplasm|cytoskeleton actin binding|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity skin(2) 2 0.358209 72.479077 73.666358 24 43 KEEP --- --- --- --- NF1 4763 broad.mit.edu 37 17 29687609 29687609 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:29687609C>T uc002hgg.2 + 57 8598 c.8265C>T c.(8263-8265)CTC>CTT p.L2755L NF1_uc002hgh.2_Silent_p.L2734L|NF1_uc010cso.2_Silent_p.L943L|NF1_uc010wbt.1_Silent_p.L233L|NF1_uc010wbu.1_RNA NM_001042492 NP_001035957 P21359 NF1_HUMAN neurofibromin isoform 1 2755 actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus protein binding|Ras GTPase activator activity p.S2751fs*27(1) soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1) 330 all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659) UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146) 847 D|Mis|N|F|S|O neurofibroma|glioma neurofibroma|glioma Neurofibromatosis_type_1 TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088) 0.390909 135.902683 137.048665 43 67 KEEP --- --- --- --- ZNF207 7756 broad.mit.edu 37 17 30692492 30692492 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:30692492C>T uc002hhh.3 + 7 914 c.766C>T c.(766-768)CCC>TCC p.P256S ZNF207_uc002hhj.3_Missense_Mutation_p.P272S|ZNF207_uc002hhi.3_Missense_Mutation_p.P272S|ZNF207_uc010csz.2_Missense_Mutation_p.P275S|ZNF207_uc002hhk.1_Missense_Mutation_p.P272S|ZNF207_uc002hhl.1_RNA NM_003457 NP_003448 O43670 ZN207_HUMAN zinc finger protein 207 isoform a 256 nucleus DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding 0 Breast(31;0.116)|Ovarian(249;0.182) BRCA - Breast invasive adenocarcinoma(9;0.239) 0.333333 38.394697 39.276981 12 24 KEEP --- --- --- --- MYO1D 4642 broad.mit.edu 37 17 31087186 31087186 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:31087186G>A uc002hho.1 - MYO1D_uc002hhp.1_Intron|MYO1D_uc010wcb.1_Intron NM_015194 NP_056009 myosin ID myosin complex actin binding|ATP binding|calmodulin binding large_intestine(1)|ovary(1)|central_nervous_system(1) 3 BRCA - Breast invasive adenocarcinoma(9;0.0362) 0.7 76.487093 77.558849 21 9 KEEP --- --- --- --- CCL7 6354 broad.mit.edu 37 17 32598246 32598246 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:32598246G>A uc002hhz.2 + 2 228 c.158G>A c.(157-159)AGG>AAG p.R53K CCL7_uc010ctf.2_Intron NM_006273 NP_006264 P80098 CCL7_HUMAN chemokine (C-C motif) ligand 7 precursor 53 cell-cell signaling|cellular calcium ion homeostasis|chemotaxis|immune response|inflammatory response|signal transduction extracellular space chemokine activity|heparin binding ovary(1) 1 Breast(3;0.00224) Breast(31;0.151)|Ovarian(249;0.17) BRCA - Breast invasive adenocarcinoma(366;0.155) 0.679245 128.621352 130.136385 36 17 KEEP --- --- --- --- UNC45B 146862 broad.mit.edu 37 17 33496836 33496836 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:33496836C>T uc002hja.2 + UNC45B_uc002hjb.2_Intron|UNC45B_uc002hjc.2_Intron|UNC45B_uc010cto.2_Intron NM_173167 NP_775259 cardiomyopathy associated 4 isoform 1 cell differentiation|muscle organ development cytosol binding ovary(3)|central_nervous_system(2)|breast(1) 6 Ovarian(249;0.17) 0.205882 17.804866 20.53268 7 27 KEEP --- --- --- --- UNC45B 146862 broad.mit.edu 37 17 33496896 33496896 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:33496896G>A uc002hja.2 + 11 1590 c.1493G>A c.(1492-1494)GGT>GAT p.G498D UNC45B_uc002hjb.2_Missense_Mutation_p.G498D|UNC45B_uc002hjc.2_Missense_Mutation_p.G498D|UNC45B_uc010cto.2_Intron NM_173167 NP_775259 Q8IWX7 UN45B_HUMAN cardiomyopathy associated 4 isoform 1 498 cell differentiation|muscle organ development cytosol binding ovary(3)|central_nervous_system(2)|breast(1) 6 Ovarian(249;0.17) 0.307692 32.78432 34.070662 12 27 KEEP --- --- --- --- AMAC1 146861 broad.mit.edu 37 17 33521331 33521331 + 5'UTR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:33521331C>T uc002hjd.2 - 1 NM_152462 NP_689675 acyl-malonyl condensing enzyme 1 integral to membrane 0 BRCA - Breast invasive adenocarcinoma(366;0.0917) 0.631579 40.604534 40.89344 12 7 KEEP --- --- --- --- Unknown broad.mit.edu 37 17 33734533 33734533 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:33734533G>A SLFN11 (33813 upstream) : SLFN12 (3550 downstream) 0.45098 71.513992 71.621063 23 28 KEEP --- --- --- --- AP2B1 163 broad.mit.edu 37 17 34037254 34037254 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:34037254G>A uc002hjr.2 + 19 2688 c.2499G>A c.(2497-2499)GAG>GAA p.E833E AP2B1_uc002hjq.2_Silent_p.E847E|AP2B1_uc010wci.1_Silent_p.E809E|AP2B1_uc002hjs.2_Silent_p.E776E|AP2B1_uc002hjt.2_Silent_p.E847E|AP2B1_uc010ctv.2_Silent_p.E847E|AP2B1_uc010wcj.1_Silent_p.E584E NM_001282 NP_001273 P63010 AP2B1_HUMAN adaptor-related protein complex 2, beta 1 833 axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|vesicle-mediated transport|viral reproduction clathrin adaptor complex|coated pit|cytosol|endocytic vesicle membrane|plasma membrane clathrin binding|protein transporter activity ovary(1) 1 Ovarian(249;0.17) UCEC - Uterine corpus endometrioid carcinoma (308;0.0227) 0.52381 36.611378 36.621022 11 10 KEEP --- --- --- --- ACACA 31 broad.mit.edu 37 17 35454077 35454077 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:35454077G>A uc002hnm.2 - 54 6825 c.6634C>T c.(6634-6636)CGT>TGT p.R2212C ACACA_uc002hnk.2_Missense_Mutation_p.R2134C|ACACA_uc002hnl.2_Missense_Mutation_p.R2154C|ACACA_uc002hnn.2_Missense_Mutation_p.R2212C|ACACA_uc002hno.2_Missense_Mutation_p.R2249C|ACACA_uc010cuy.2_Missense_Mutation_p.R857C|ACACA_uc010wdb.1_Missense_Mutation_p.R250C|ACACA_uc010wdc.1_Missense_Mutation_p.R338C NM_198836 NP_942133 Q13085 ACACA_HUMAN acetyl-Coenzyme A carboxylase alpha isoform 2 2212 acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process cytosol acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding large_intestine(1)|ovary(1) 2 Breast(25;0.00157)|Ovarian(249;0.15) Biotin(DB00121) Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249) p.R2212C(NCIH2106-Tumor) 742 0.6 44.50424 44.679122 12 8 KEEP --- --- --- --- broad.mit.edu 37 17 37187966 37187966 + RNA SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:37187966C>T uc002hrd.1 + 1 c.1808C>T Homo sapiens cDNA FLJ43826 fis, clone TESTI4002703. 0.4 24.897367 25.071838 8 12 KEEP --- --- --- --- broad.mit.edu 37 17 37209276 37209276 + RNA SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:37209276C>T uc002hrd.1 + 5 c.3398C>T Homo sapiens cDNA FLJ43826 fis, clone TESTI4002703. 0.333333 14.169406 14.538712 5 10 KEEP --- --- --- --- IKZF3 22806 broad.mit.edu 37 17 37944681 37944681 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:37944681C>T uc002hsu.2 - IKZF3_uc002htd.2_Intron|IKZF3_uc010cwd.2_Intron|IKZF3_uc002hsv.2_Intron|IKZF3_uc010cwe.2_Intron|IKZF3_uc010cwf.2_Intron|IKZF3_uc010cwg.2_Intron|IKZF3_uc002hsw.2_Intron|IKZF3_uc002hsx.2_Intron|IKZF3_uc002hsy.2_Intron|IKZF3_uc002hsz.2_Intron|IKZF3_uc002hta.2_Intron|IKZF3_uc002htb.2_Intron|IKZF3_uc010cwh.2_Intron|IKZF3_uc002htc.2_Intron NM_012481 NP_036613 aiolos isoform 1 B cell activation|mesoderm development|regulation of transcription from RNA polymerase II promoter cytoplasm|nucleus DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding lung(2)|kidney(2)|skin(2) 6 Breast(7;4.5e-103)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052) UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171) 312 0.632653 99.633727 100.391456 31 18 KEEP --- --- --- --- Unknown broad.mit.edu 37 17 39369239 39369239 + IGR SNP G T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:39369239G>T KRTAP4-1 (6113 upstream) : KRTAP9-2 (13661 downstream) 0.4 6.649068 6.692787 2 3 KEEP --- --- --- --- JUP 3728 broad.mit.edu 37 17 39768297 39768297 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:39768297C>T uc010wfs.1 - KRT16_uc002hxg.3_Intron NM_021991 NP_068831 junction plakoglobin adherens junction organization|atrioventricular valve morphogenesis|cell migration|cell morphogenesis|cellular response to indole-3-methanol|cytoskeletal anchoring at plasma membrane|detection of mechanical stimulus|ectoderm development|endothelial cell-cell adhesion|gastrulation|morphogenesis of embryonic epithelium|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway involved in heart development|nervous system development|oocyte development|positive regulation of protein import into nucleus|positive regulation of sequence-specific DNA binding transcription factor activity|skin development actin cytoskeleton|Axin-APC-beta-catenin-GSK3B complex|basolateral plasma membrane|catenin complex|desmosome|fascia adherens|gamma-catenin-TCF7L2 complex|internal side of plasma membrane|nucleus|protein-DNA complex|Z disc|zonula adherens alpha-catenin binding|cadherin binding|protein homodimerization activity|protein kinase binding|protein phosphatase binding|RPTP-like protein binding|specific RNA polymerase II transcription factor activity|transcription coactivator activity ovary(2)|lung(2)|breast(1) 5 Breast(137;0.000162) BRCA - Breast invasive adenocarcinoma(4;0.233) BRCA - Breast invasive adenocarcinoma(366;0.15) Colon(16;42 520 6044 17852 28530) 0.789474 51.534779 53.006941 15 4 KEEP --- --- --- --- broad.mit.edu 37 17 40180194 40180194 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:40180194G>A uc002hyu.2 - 2 194 c.51C>T c.(49-51)TCC>TCT p.S17S RecName: Full=Zinc finger protein 385C; 0.375 59.251393 60.022893 21 35 KEEP --- --- --- --- RAMP2 10266 broad.mit.edu 37 17 40914570 40914570 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:40914570C>T uc002ibg.2 + LOC100190938_uc002ibd.1_5'Flank|LOC100190938_uc002ibe.3_5'Flank|LOC100190938_uc002ibf.3_5'Flank|RAMP2_uc010cyt.2_Intron|RAMP2_uc002ibh.2_Intron NM_005854 NP_005845 receptor activity modifying protein 2 precursor intracellular protein transport|receptor-mediated endocytosis|regulation of G-protein coupled receptor protein signaling pathway coated pit|integral to plasma membrane|lysosome protein transporter activity 0 Breast(137;0.000143) BRCA - Breast invasive adenocarcinoma(366;0.0741) Pramlintide(DB01278) 0.621622 162.611876 163.599887 46 28 KEEP --- --- --- --- MPP2 4355 broad.mit.edu 37 17 41958279 41958279 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:41958279C>T uc010wip.1 - MPP2_uc002ien.1_Intron|MPP2_uc010wim.1_Intron|MPP2_uc002ieo.1_Intron|MPP2_uc010win.1_Intron|MPP2_uc010wio.1_Intron NM_005374 NP_005365 palmitoylated membrane protein 2 signal transduction cell surface|integral to plasma membrane|membrane fraction guanylate kinase activity 0 Breast(137;0.00314) BRCA - Breast invasive adenocarcinoma(366;0.12) OREG0024443 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0.674419 98.585786 99.748138 29 14 KEEP --- --- --- --- NAGS 162417 broad.mit.edu 37 17 42086122 42086122 + 3'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:42086122G>A uc002ies.2 + 7 NAGS_uc010czn.2_3'UTR|NAGS_uc002iet.2_3'UTR NM_153006 NP_694551 N-acetylglutamate synthase arginine biosynthetic process|urea cycle mitochondrial matrix acetyl-CoA:L-glutamate N-acetyltransferase activity 0 Breast(137;0.00536)|Prostate(33;0.0724) BRCA - Breast invasive adenocarcinoma(366;0.113) L-Glutamic Acid(DB00142) 0.666667 15.802225 15.949831 4 2 KEEP --- --- --- --- ITGA2B 3674 broad.mit.edu 37 17 42457166 42457166 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:42457166C>T uc002igt.1 - 18 1801 c.1769G>A c.(1768-1770)CGG>CAG p.R590Q ITGA2B_uc002igu.1_Missense_Mutation_p.R71Q NM_000419 NP_000410 P08514 ITA2B_HUMAN integrin alpha 2b preproprotein 590 Extracellular (Potential). axon guidance|integrin-mediated signaling pathway|platelet activation|platelet degranulation integrin complex|platelet alpha granule membrane identical protein binding|receptor activity ovary(2)|lung(1) 3 Prostate(33;0.0181) BRCA - Breast invasive adenocarcinoma(366;0.191) Tirofiban(DB00775) 0.561644 137.698889 137.946174 41 32 KEEP --- --- --- --- GPATCH8 23131 broad.mit.edu 37 17 42512491 42512491 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:42512491C>T uc002igw.1 - 5 354 c.290G>A c.(289-291)CGG>CAG p.R97Q GPATCH8_uc002igv.1_Missense_Mutation_p.R19Q|GPATCH8_uc010wiz.1_Missense_Mutation_p.R19Q NM_001002909 NP_001002909 Q9UKJ3 GPTC8_HUMAN G patch domain containing 8 97 Potential. intracellular nucleic acid binding|zinc ion binding ovary(2)|kidney(1)|skin(1) 4 Prostate(33;0.0181) BRCA - Breast invasive adenocarcinoma(366;0.206) 0.307692 31.179873 32.469182 12 27 KEEP --- --- --- --- DBF4B 80174 broad.mit.edu 37 17 42814328 42814328 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:42814328C>T uc002ihf.2 + DBF4B_uc010wjb.1_Intron|DBF4B_uc002ihe.2_Intron|DBF4B_uc010wjc.1_Intron NM_145663 NP_663696 DBF4 homolog B isoform 1 cell cycle nucleus nucleic acid binding|zinc ion binding 0 Prostate(33;0.0322) 0.407407 37.320157 37.522436 11 16 KEEP --- --- --- --- GFAP 2670 broad.mit.edu 37 17 42992801 42992801 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:42992801C>T uc002ihq.2 - 1 114 c.54G>A c.(52-54)GGG>GGA p.G18G GFAP_uc002ihr.2_Silent_p.G18G|GFAP_uc010wjg.1_RNA NM_002055 NP_002046 P14136 GFAP_HUMAN glial fibrillary acidic protein isoform 1 18 Head. cytoplasm|intermediate filament structural constituent of cytoskeleton ovary(1)|pancreas(1) 2 Prostate(33;0.0959) 0.571429 12.900778 12.931881 4 3 KEEP --- --- --- --- NMT1 4836 broad.mit.edu 37 17 43176824 43176824 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:43176824C>T uc002ihz.2 + 8 954 c.936C>T c.(934-936)TCC>TCT p.S312S NMT1_uc002iia.2_RNA NM_021079 NP_066565 P30419 NMT1_HUMAN N-myristoyltransferase 1 312 activation of pro-apoptotic gene products|induction of apoptosis by intracellular signals|N-terminal protein myristoylation|protein lipoylation actin cytoskeleton|cell junction|cytosol glycylpeptide N-tetradecanoyltransferase activity 0 Prostate(33;0.155) OREG0024470 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0.561644 134.085549 134.32859 41 32 KEEP --- --- --- --- ARHGAP27 201176 broad.mit.edu 37 17 43473692 43473692 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:43473692G>A uc002iix.2 - ARHGAP27_uc010dak.2_Intron NM_199282 NP_954976 Rho GTPase activating protein 27 isoform a positive regulation of Cdc42 GTPase activity|receptor-mediated endocytosis|signal transduction cytoplasm|membrane Rac GTPase activator activity|SH3 domain binding 0 Renal(3;0.0405) 0.666667 20.252777 20.474069 6 3 KEEP --- --- --- --- PLEKHM1 9842 broad.mit.edu 37 17 43552723 43552723 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:43552723G>A uc002ija.2 - 4 836 c.666C>T c.(664-666)TCC>TCT p.S222S PLEKHM1_uc010wjm.1_Silent_p.S194S|PLEKHM1_uc002ijb.2_5'UTR|PLEKHM1_uc010wjn.1_Silent_p.S171S NM_014798 NP_055613 Q9Y4G2 PKHM1_HUMAN pleckstrin homology domain containing, family M 222 intracellular signal transduction cytoplasm metal ion binding 0 Renal(3;0.0405) 0.357143 45.725717 46.475223 15 27 KEEP --- --- --- --- Unknown broad.mit.edu 37 17 43675883 43675883 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:43675883G>A LRRC37A4 (80367 upstream) : LOC644172 (1608 downstream) 0.28125 25.861127 27.237373 9 23 KEEP --- --- --- --- NSF 4905 broad.mit.edu 37 17 44788538 44788538 + Intron SNP T A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:44788538T>A uc002iku.2 + NSF_uc010wke.1_Intron|NSF_uc010wkf.1_Intron|NSF_uc010wkg.1_Intron NM_006178 NP_006169 vesicle-fusing ATPase protein transport|synaptic transmission cytosol ATP binding|metal ion binding ovary(1) 1 Melanoma(429;0.203) BRCA - Breast invasive adenocarcinoma(9;0.0257) BRCA - Breast invasive adenocarcinoma(366;0.241) Ovarian(25;472 742 1472 36813 50223) 0.521739 39.600412 39.609823 12 11 KEEP --- --- --- --- MYL4 4635 broad.mit.edu 37 17 45297148 45297148 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:45297148G>A uc002ilg.2 + MYL4_uc002ilh.2_Intron NM_001002841 NP_001002841 atrial/embryonic alkali myosin light chain cardiac muscle contraction|muscle filament sliding|muscle organ development|positive regulation of ATPase activity|regulation of the force of heart contraction A band|cytosol|muscle myosin complex actin filament binding|actin monomer binding|calcium ion binding|myosin II heavy chain binding|structural constituent of muscle ovary(2) 2 0.5 6.450027 6.450026 2 2 KEEP --- --- --- --- C17orf57 124989 broad.mit.edu 37 17 45451810 45451810 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:45451810G>A uc002iln.2 + C17orf57_uc002ilm.2_Intron|C17orf57_uc002ill.1_Intron|C17orf57_uc010daz.1_Intron NM_152347 NP_689560 hypothetical protein LOC124989 calcium ion binding breast(1)|central_nervous_system(1)|skin(1) 3 0.633333 63.431816 63.900284 19 11 KEEP --- --- --- --- KPNB1 3837 broad.mit.edu 37 17 45730179 45730179 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:45730179G>A uc002ilt.1 + 3 555 c.219G>A c.(217-219)AAG>AAA p.K73K KPNB1_uc010wkw.1_5'UTR NM_002265 NP_002256 Q14974 IMB1_HUMAN karyopherin beta 1 73 Importin N-terminal. DNA fragmentation involved in apoptotic nuclear change|NLS-bearing substrate import into nucleus|protein import into nucleus, translocation|ribosomal protein import into nucleus|viral genome transport in host cell|viral infectious cycle cytosol|nuclear pore|nucleoplasm nuclear localization sequence binding|protein domain specific binding|zinc ion binding ovary(1)|pancreas(1)|skin(1) 3 0.271429 56.494231 59.791528 19 51 KEEP --- --- --- --- OSBPL7 114881 broad.mit.edu 37 17 45886847 45886847 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:45886847G>A uc002ilx.1 - OSBPL7_uc002ilw.1_Intron NM_145798 NP_665741 oxysterol-binding protein-like protein 7 lipid transport lipid binding 0 0.547619 73.926259 74.008783 23 19 KEEP --- --- --- --- SKAP1 8631 broad.mit.edu 37 17 46259856 46259856 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:46259856C>T uc002ini.1 - SKAP1_uc002inj.1_Intron|SKAP1_uc010dbd.1_Intron|SKAP1_uc010dbe.1_Intron NM_003726 NP_003717 src kinase associated phosphoprotein 1 isoform positive regulation of transcription from RNA polymerase II promoter|T cell receptor signaling pathway cytoplasm|nucleus|plasma membrane antigen binding|protein kinase binding|SH2 domain binding 0 0.074074 0.283838 15.376697 6 75 KEEP --- --- --- --- GIP 2695 broad.mit.edu 37 17 47041604 47041604 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:47041604G>A uc002iol.1 - NM_004123 NP_004114 gastric inhibitory polypeptide preproprotein energy reserve metabolic process|signal transduction extracellular region|soluble fraction hormone activity skin(1) 1 0.333333 29.212396 30.025019 11 22 KEEP --- --- --- --- SGCA 6442 broad.mit.edu 37 17 48243473 48243473 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:48243473G>A uc002iqi.2 + SGCA_uc010wmh.1_Intron|SGCA_uc002iqj.2_Intron|SGCA_uc010wmi.1_Intron NM_000023 NP_000014 sarcoglycan, alpha isoform 1 precursor muscle contraction|muscle organ development cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma calcium ion binding ovary(2) 2 0.378151 132.140918 133.693126 45 74 KEEP --- --- --- --- CUEDC1 404093 broad.mit.edu 37 17 55950226 55950226 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:55950226G>A uc002ivd.1 - CUEDC1_uc002ive.1_Intron NM_017949 NP_060419 CUE domain-containing 1 skin(2) 2 0.543478 81.67386 81.749044 25 21 KEEP --- --- --- --- LPO 4025 broad.mit.edu 37 17 56329697 56329697 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:56329697C>T uc002ivt.2 + 8 1251 c.935C>T c.(934-936)TCC>TTC p.S312F LPO_uc010wns.1_Missense_Mutation_p.S253F|LPO_uc010dcp.2_Missense_Mutation_p.S229F|LPO_uc010dcq.2_5'UTR|LPO_uc010dcr.2_5'UTR NM_006151 NP_006142 P22079 PERL_HUMAN lactoperoxidase isoform 1 preproprotein 312 hydrogen peroxide catabolic process extracellular space heme binding|peroxidase activity ovary(1)|breast(1) 2 0.416667 28.450032 28.594168 10 14 KEEP --- --- --- --- TEX14 56155 broad.mit.edu 37 17 56679054 56679054 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:56679054C>T uc010dcz.1 - TEX14_uc002iwr.1_Intron|TEX14_uc002iws.1_Intron|TEX14_uc010dda.1_Intron NM_198393 NP_938207 testis expressed sequence 14 isoform a cytoplasm ATP binding|protein kinase activity stomach(4)|lung(3)|breast(3)|ovary(3)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)|pancreas(1) 17 Medulloblastoma(34;0.127)|all_neural(34;0.237) 598 0.538462 46.251106 46.284441 14 12 KEEP --- --- --- --- PRR11 55771 broad.mit.edu 37 17 57252099 57252099 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:57252099C>T uc002ixf.1 + PRR11_uc002ixg.1_Intron NM_018304 NP_060774 proline rich 11 ovary(2) 2 Medulloblastoma(34;0.0922)|all_neural(34;0.101) 0.722222 93.757592 95.354722 26 10 KEEP --- --- --- --- DHX40P1 653645 broad.mit.edu 37 17 58066759 58066759 + Intron SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:58066759T>C uc002iyf.2 - uc002iye.1_Intron NR_002924 Homo sapiens DEAH (Asp-Glu-Ala-His) box polypeptide 40 pseudogene, mRNA (cDNA clone IMAGE:5170263). 0 0.571429 15.601229 15.632372 4 3 KEEP --- --- --- --- DHX40P1 653645 broad.mit.edu 37 17 58086568 58086568 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:58086568G>A uc002iyf.2 - uc010woq.1_5'Flank NR_002924 Homo sapiens DEAH (Asp-Glu-Ala-His) box polypeptide 40 pseudogene, mRNA (cDNA clone IMAGE:5170263). 0 0.272727 8.520403 9.032331 3 8 KEEP --- --- --- --- BCAS3 54828 broad.mit.edu 37 17 59147226 59147226 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:59147226C>T uc002iyv.3 + BCAS3_uc002iyu.3_Intron|BCAS3_uc002iyw.3_Intron|BCAS3_uc002iyy.3_Intron|BCAS3_uc002iyz.3_Intron|BCAS3_uc002iza.3_Intron NM_001099432 NP_001092902 breast carcinoma amplified sequence 3 isoform 1 nucleus ovary(2)|central_nervous_system(2)|skin(1) 5 BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06) 0.6 80.039438 80.415532 27 18 KEEP --- --- --- --- INTS2 57508 broad.mit.edu 37 17 59981916 59981916 + Silent SNP C A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:59981916C>A uc002izn.2 - 9 1312 c.1236G>T c.(1234-1236)CTG>CTT p.L412L INTS2_uc002izm.2_Silent_p.L404L NM_020748 NP_065799 Q9H0H0 INT2_HUMAN integrator complex subunit 2 412 snRNA processing integral to membrane|integrator complex|nuclear membrane protein binding ovary(1)|lung(1)|pancreas(1) 3 0.181818 5.443014 6.489276 2 9 KEEP --- --- --- --- SCN4A 6329 broad.mit.edu 37 17 62019249 62019249 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:62019249C>T uc002jds.1 - 24 4470 c.4393G>A c.(4393-4395)GCC>ACC p.A1465T NM_000334 NP_000325 P35499 SCN4A_HUMAN voltage-gated sodium channel type 4 alpha 1465 Helical; Voltage-sensor; Name=S4 of repeat IV; (Potential).|IV. muscle contraction voltage-gated sodium channel complex voltage-gated sodium channel activity ovary(1)|pancreas(1)|skin(1) 3 Lamotrigine(DB00555) 0.538462 17.197951 17.212625 7 6 KEEP --- --- --- --- MAP2K6 5608 broad.mit.edu 37 17 67501792 67501792 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:67501792G>A uc002jij.2 + MAP2K6_uc002jii.2_Intron|MAP2K6_uc002jik.2_5'UTR NM_002758 NP_002749 mitogen-activated protein kinase kinase 6 activation of MAPK activity|cell cycle arrest|DNA damage induced protein phosphorylation|innate immune response|muscle cell differentiation|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of muscle cell differentiation|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway cytosol|nucleoplasm ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity lung(2)|stomach(1)|ovary(1)|pancreas(1) 5 Breast(10;6.05e-10) 234 0.538462 20.22503 20.241939 7 6 KEEP --- --- --- --- CD300A 11314 broad.mit.edu 37 17 72473647 72473647 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:72473647G>A uc002jkv.2 + 4 927 c.606G>A c.(604-606)AGG>AGA p.R202R CD300A_uc002jkw.2_Silent_p.R89R|CD300A_uc010dfr.2_Silent_p.R89R|CD300A_uc010dfs.2_Intron NM_007261 NP_009192 Q9UGN4 CLM8_HUMAN leukocyte membrane antigen 202 Cytoplasmic (Potential). cell adhesion integral to membrane|plasma membrane receptor activity ovary(1)|skin(1) 2 0.309524 35.656031 37.015781 13 29 KEEP --- --- --- --- EXOC7 23265 broad.mit.edu 37 17 74093881 74093881 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:74093881G>A uc002jqs.2 - 5 731 c.636C>T c.(634-636)AAC>AAT p.N212N EXOC7_uc010dgv.1_Silent_p.N159N|EXOC7_uc002jqq.2_Silent_p.N212N|EXOC7_uc010wsw.1_Silent_p.N212N|EXOC7_uc010wsx.1_Silent_p.N212N|EXOC7_uc002jqr.2_Silent_p.N212N|EXOC7_uc010wsv.1_Silent_p.N171N|EXOC7_uc002jqu.2_Silent_p.N212N NM_001145297 NP_001138769 Q9UPT5 EXOC7_HUMAN exocyst complex component 7 isoform 4 212 exocytosis|protein transport centriolar satellite|cytosol|exocyst|plasma membrane protein binding 0 LUSC - Lung squamous cell carcinoma(166;0.187) 0.605634 142.538556 143.231978 43 28 KEEP --- --- --- --- MGAT5B 146664 broad.mit.edu 37 17 74928870 74928870 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:74928870C>T uc002jti.2 + MGAT5B_uc002jth.2_Intron NM_198955 NP_945193 N-acetylglucosaminyltranferase VB isoform 2 Golgi membrane|integral to membrane alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity|metal ion binding ovary(2)|skin(1) 3 0.4375 40.852939 40.960102 14 18 KEEP --- --- --- --- DNAH17 8632 broad.mit.edu 37 17 76449600 76449600 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:76449600G>A uc010dhp.1 - DNAH17_uc002jvs.2_Intron SubName: Full=DNAH17 variant protein; Flags: Fragment; ovary(6)|breast(2)|skin(1) 9 BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656) 0.176471 7.714965 9.391388 3 14 KEEP --- --- --- --- DNAH17 8632 broad.mit.edu 37 17 76548690 76548690 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:76548690G>A uc002jvv.1 - RecName: Full=Dynein heavy chain 17, axonemal; AltName: Full=Axonemal beta dynein heavy chain 17; AltName: Full=Ciliary dynein heavy chain 17; AltName: Full=Ciliary dynein heavy chain-like protein 1; AltName: Full=Axonemal dynein heavy chain-like protein 1; AltName: Full=Dynein light chain 2, axonemal; ovary(6)|breast(2)|skin(1) 9 BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656) 0.363636 38.390902 38.930894 12 21 KEEP --- --- --- --- DNAH17 8632 broad.mit.edu 37 17 76562760 76562760 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:76562760C>T uc002jvv.1 - 7 717 c.611G>A c.(610-612)AGG>AAG p.R204K RecName: Full=Dynein heavy chain 17, axonemal; AltName: Full=Axonemal beta dynein heavy chain 17; AltName: Full=Ciliary dynein heavy chain 17; AltName: Full=Ciliary dynein heavy chain-like protein 1; AltName: Full=Axonemal dynein heavy chain-like protein 1; AltName: Full=Dynein light chain 2, axonemal; ovary(6)|breast(2)|skin(1) 9 BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656) 0.454545 17.17401 17.193795 5 6 KEEP --- --- --- --- CBX8 57332 broad.mit.edu 37 17 77769682 77769682 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:77769682C>T uc002jxd.1 - NM_020649 NP_065700 chromobox homolog 8 negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear chromatin|PcG protein complex methylated histone residue binding 0 OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224) 0.25 16.837845 18.201646 6 18 KEEP --- --- --- --- CCDC40 55036 broad.mit.edu 37 17 78039258 78039258 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:78039258C>T uc010dht.2 + CCDC40_uc010wub.1_Intron|CCDC40_uc002jxm.3_Intron NM_017950 NP_060420 coiled-coil domain containing 40 axonemal dynein complex assembly|ciliary cell motility|cilium movement involved in determination of left/right asymmetry|flagellar cell motility cilium|cytoplasm ovary(3) 3 all_neural(118;0.167) OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149) 0.632353 144.31585 145.356832 43 25 KEEP --- --- --- --- RNF213 57674 broad.mit.edu 37 17 78320860 78320860 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:78320860G>A uc002jyh.1 + 4 3167 c.2944G>A c.(2944-2946)GAG>AAG p.E982K NM_020914 NP_065965 Q9HCF4 ALO17_HUMAN ring finger protein 213 Error:Variant_position_missing_in_Q9HCF4_after_alignment ovary(8)|lung(6)|breast(3)|large_intestine(2)|central_nervous_system(1)|pancreas(1) 21 all_neural(118;0.0538) BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057) 0.55 36.648326 36.696541 11 9 KEEP --- --- --- --- NPTX1 4884 broad.mit.edu 37 17 78445571 78445571 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:78445571G>A uc002jyp.1 - 4 1196 c.1038C>T c.(1036-1038)CCC>CCT p.P346P NM_002522 NP_002513 Q15818 NPTX1_HUMAN neuronal pentraxin I precursor 346 Pentaxin. central nervous system development|synaptic transmission|transport transport vesicle metal ion binding 0 all_neural(118;0.0538) BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0487) 0.4 50.836566 51.231276 18 27 KEEP --- --- --- --- SLC25A10 1468 broad.mit.edu 37 17 79684824 79684824 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:79684824C>T uc002kbi.2 + 9 724 c.638C>T c.(637-639)GCC>GTC p.A213V SLC25A10_uc010wut.1_Missense_Mutation_p.A368V|SLC25A10_uc010dif.2_Missense_Mutation_p.A222V|SLC25A10_uc010wuu.1_Missense_Mutation_p.A167V NM_012140 NP_036272 Q9UBX3 DIC_HUMAN solute carrier family 25 (mitochondrial carrier; 213 Helical; Name=5; (Potential).|Solcar 3. gluconeogenesis|mitochondrial transport integral to membrane|mitochondrial inner membrane|nucleus protein binding 0 all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.23) BRCA - Breast invasive adenocarcinoma(99;0.0117)|OV - Ovarian serous cystadenocarcinoma(97;0.0955) Succinic acid(DB00139) 0.333333 14.16966 14.538839 5 10 KEEP --- --- --- --- HEXDC 284004 broad.mit.edu 37 17 80394947 80394947 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:80394947C>T uc002kew.2 + HEXDC_uc002kev.3_Intron|HEXDC_uc010diq.2_Intron|HEXDC_uc010wvm.1_Intron|HEXDC_uc010wvn.1_5'Flank SubName: Full=Hexosaminidase (Glycosyl hydrolase family 20, catalytic domain) containing, isoform CRA_c; SubName: Full=Hexosaminidase D; carbohydrate metabolic process cytoplasm|nucleus beta-N-acetylhexosaminidase activity|cation binding ovary(1)|skin(1) 2 Breast(20;0.00106)|all_neural(118;0.0804) OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369) 0.423077 29.056212 29.18052 11 15 KEEP --- --- --- --- TBCD 6904 broad.mit.edu 37 17 80788868 80788869 + Intron DNP GA AC AC MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr17:80788868_80788869GA>AC uc002kfz.2 + TBCD_uc002kfx.1_Intron|TBCD_uc002kfy.1_Intron|ZNF750_uc002kga.2_Intron NM_005993 NP_005984 beta-tubulin cofactor D 'de novo' posttranslational protein folding|adherens junction assembly|negative regulation of cell-substrate adhesion|negative regulation of microtubule polymerization|post-chaperonin tubulin folding pathway|tight junction assembly adherens junction|cytoplasm|lateral plasma membrane|microtubule|tight junction beta-tubulin binding|chaperone binding|GTPase activator activity 0 Breast(20;0.000523)|all_neural(118;0.0779) all_cancers(8;0.0266)|all_epithelial(8;0.0696) OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18) 0.33871 125.71629 128.566452 42 82 KEEP --- --- --- --- COLEC12 81035 broad.mit.edu 37 18 334847 334847 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:334847G>A uc002kkm.2 - 6 1926 c.1711C>T c.(1711-1713)CCA>TCA p.P571S NM_130386 NP_569057 Q5KU26 COL12_HUMAN collectin sub-family member 12 571 Collagen-like 3.|Extracellular (Potential). carbohydrate mediated signaling|innate immune response|phagocytosis, recognition|protein homooligomerization collagen|integral to membrane galactose binding|low-density lipoprotein particle binding|metal ion binding|pattern recognition receptor activity|scavenger receptor activity ovary(1)|pancreas(1) 2 all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426) 0.666667 13.201799 13.349364 4 2 KEEP --- --- --- --- LPIN2 9663 broad.mit.edu 37 18 2924336 2924336 + Intron SNP G T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:2924336G>T uc002klo.2 - NM_014646 NP_055461 lipin 2 fatty acid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|triglyceride biosynthetic process cytosol|endoplasmic reticulum membrane|nucleus phosphatidate phosphatase activity|transcription coactivator activity ovary(1)|skin(1) 2 READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156) 0.214286 15.335035 17.445188 6 22 KEEP --- --- --- --- LPIN2 9663 broad.mit.edu 37 18 2934479 2934479 + Intron SNP T G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:2934479T>G uc002klo.2 - NM_014646 NP_055461 lipin 2 fatty acid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|triglyceride biosynthetic process cytosol|endoplasmic reticulum membrane|nucleus phosphatidate phosphatase activity|transcription coactivator activity ovary(1)|skin(1) 2 READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156) 0.666667 106.015056 107.04824 28 14 KEEP --- --- --- --- DLGAP1 9229 broad.mit.edu 37 18 3977716 3977716 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:3977716G>A uc010wyz.1 - NM_004746 NP_004737 discs large homolog-associated protein 1 isoform synaptic transmission cell junction|postsynaptic density|postsynaptic membrane ovary(2)|pancreas(1)|skin(1) 4 Colorectal(8;0.0257) 0.375 9.523017 9.632775 3 5 KEEP --- --- --- --- ARHGAP28 79822 broad.mit.edu 37 18 6890376 6890376 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:6890376G>A uc010wzi.1 + ARHGAP28_uc002knc.2_Intron|ARHGAP28_uc002knd.2_Intron|ARHGAP28_uc002kne.2_Intron|ARHGAP28_uc002knf.2_Intron SubName: Full=Putative uncharacterized protein ARHGAP28; signal transduction intracellular pancreas(1) 1 Colorectal(10;0.168) 0.428571 8.923599 8.954813 3 4 KEEP --- --- --- --- ANKRD12 23253 broad.mit.edu 37 18 9263804 9263804 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:9263804C>T uc002knv.2 + 10 5938 c.5681C>T c.(5680-5682)TCA>TTA p.S1894L ANKRD12_uc002knw.2_Missense_Mutation_p.S1871L|ANKRD12_uc002knx.2_Missense_Mutation_p.S1871L NM_015208 NP_056023 Q6UB98 ANR12_HUMAN ankyrin repeat domain 12 isoform 1 1894 nucleus ovary(2)|central_nervous_system(1) 3 0.354839 34.216353 34.791969 11 20 KEEP --- --- --- --- PPP4R1 9989 broad.mit.edu 37 18 9583873 9583873 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:9583873G>A uc002koe.1 - PPP4R1_uc010wzo.1_Intron|PPP4R1_uc002kod.1_Intron|PPP4R1_uc010wzp.1_Intron NM_001042388 NP_001035847 protein phosphatase 4, regulatory subunit 1 protein phosphorylation|signal transduction protein phosphatase 4 complex protein binding|protein phosphatase type 4 regulator activity skin(1) 1 Melanoma(188;1232 2082 5061 11948 35994) 0.315789 17.843039 18.416553 6 13 KEEP --- --- --- --- Unknown broad.mit.edu 37 18 11644838 11644838 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:11644838G>A FAM38B (942859 upstream) : GNAL (44298 downstream) 0.375 10.02332 10.132963 3 5 KEEP --- --- --- --- SPIRE1 56907 broad.mit.edu 37 18 12546931 12546932 + Intron DNP GG AA AA MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:12546931_12546932GG>AA uc002kre.2 - SPIRE1_uc002krc.2_Intron|SPIRE1_uc010wzw.1_Intron|SPIRE1_uc010wzx.1_Intron|SPIRE1_uc010wzy.1_Intron NM_001128626 NP_001122098 spire homolog 1 isoform a cytoskeleton|perinuclear region of cytoplasm actin binding 0 0.818182 32.381867 33.427859 9 2 KEEP --- --- --- --- CEP192 55125 broad.mit.edu 37 18 13095596 13095596 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:13095596G>A uc010xac.1 + 35 6429 c.6349G>A c.(6349-6351)GCT>ACT p.A2117T CEP192_uc010dlf.1_RNA|CEP192_uc010xad.1_Missense_Mutation_p.A1642T|CEP192_uc002kru.2_RNA|CEP192_uc002krv.2_Missense_Mutation_p.A539T|CEP192_uc002krw.2_Missense_Mutation_p.A266T|CEP192_uc002krx.2_Missense_Mutation_p.A121T|CEP192_uc002kry.2_RNA NM_032142 NP_115518 E9PF99 E9PF99_HUMAN centrosomal protein 192kDa 2117 ovary(4)|pancreas(1) 5 0.0625 -5.602438 7.12371 4 60 KEEP --- --- --- --- Unknown broad.mit.edu 37 18 14890014 14890014 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:14890014C>T ANKRD30B (37277 upstream) : LOC644669 (423541 downstream) 0.666667 48.85643 49.372625 14 7 KEEP --- --- --- --- CTAGE1 64693 broad.mit.edu 37 18 19995732 19995732 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:19995732G>A uc002ktv.1 - 1 2147 c.2043C>T c.(2041-2043)TTC>TTT p.F681F NM_172241 NP_758441 Q96RT6 CTGE2_HUMAN cutaneous T-cell lymphoma-associated antigen 1 681 Pro-rich. integral to membrane ovary(1) 1 all_cancers(21;0.000361)|all_epithelial(16;9.61e-06)|Colorectal(14;0.0533)|Lung NSC(20;0.0605)|Ovarian(2;0.116)|all_lung(20;0.135) 0.168675 27.084831 35.733969 14 69 KEEP --- --- --- --- C18orf8 29919 broad.mit.edu 37 18 21110155 21110155 + Intron SNP A T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:21110155A>T uc010xax.1 + C18orf8_uc002kul.2_Intron|C18orf8_uc010xay.1_Intron|NPC1_uc010dlu.1_Intron NM_013326 NP_037458 colon cancer-associated protein Mic1 ovary(1) 1 all_cancers(21;0.000122)|all_epithelial(16;8.08e-07)|Lung NSC(20;0.00206)|all_lung(20;0.00659)|Colorectal(14;0.0202)|Ovarian(20;0.127) 0.274194 97.298391 102.992302 34 90 KEEP --- --- --- --- LAMA3 3909 broad.mit.edu 37 18 21487385 21487385 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:21487385C>T uc002kuq.2 + LAMA3_uc002kur.2_Intron|LAMA3_uc002kus.3_Intron|LAMA3_uc002kut.3_Intron NM_198129 NP_937762 laminin alpha 3 subunit isoform 1 cell adhesion|epidermis development|hemidesmosome assembly|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development laminin-1 complex receptor binding|structural molecule activity ovary(8)|skin(2)|central_nervous_system(1) 11 all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17) Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031) 0.75 51.334181 52.469973 15 5 KEEP --- --- --- --- Unknown broad.mit.edu 37 18 21741606 21741606 + IGR SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:21741606A>G CABYR (43 upstream) : OSBPL1A (407 downstream) 0.571429 14.501212 14.532374 4 3 KEEP --- --- --- --- CDH2 1000 broad.mit.edu 37 18 25573281 25573281 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:25573281G>A uc002kwg.2 - CDH2_uc010xbn.1_Intron NM_001792 NP_001783 cadherin 2, type 1 preproprotein adherens junction organization|cell junction assembly|positive regulation of muscle cell differentiation catenin complex|integral to membrane alpha-catenin binding|beta-catenin binding|calcium ion binding|gamma-catenin binding ovary(3)|lung(1) 4 264 0.411765 21.421844 21.537435 7 10 KEEP --- --- --- --- Unknown broad.mit.edu 37 18 26231986 26231986 + IGR SNP T G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:26231986T>G CDH2 (474541 upstream) : None (None downstream) 0.578947 41.32848 41.431836 11 8 KEEP --- --- --- --- DSG1 1828 broad.mit.edu 37 18 28923417 28923417 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:28923417C>T uc002kwp.2 + 12 1904 c.1692C>T c.(1690-1692)GTC>GTT p.V564V DSG1_uc010xbp.1_5'Flank NM_001942 NP_001933 Q02413 DSG1_HUMAN desmoglein 1 preproprotein 564 Helical; (Potential). calcium-dependent cell-cell adhesion|cell-cell junction assembly|cellular component disassembly involved in apoptosis|homophilic cell adhesion|protein stabilization cytosol|desmosome|integral to membrane|internal side of plasma membrane calcium ion binding|gamma-catenin binding|toxin binding skin(3)|ovary(2)|central_nervous_system(2) 7 OV - Ovarian serous cystadenocarcinoma(10;0.00559) 0.319149 133.26887 137.344436 45 96 KEEP --- --- --- --- DSG4 147409 broad.mit.edu 37 18 28968999 28968999 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:28968999C>T uc002kwq.2 + DSG4_uc002kwr.2_Intron NM_177986 NP_817123 desmoglein 4 isoform 2 preproprotein homophilic cell adhesion desmosome|integral to membrane calcium ion binding central_nervous_system(5)|ovary(3) 8 OV - Ovarian serous cystadenocarcinoma(10;0.00504) 0.409836 81.064718 81.497749 25 36 KEEP --- --- --- --- ASXL3 80816 broad.mit.edu 37 18 31324936 31324936 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:31324936G>A uc010dmg.1 + 12 5179 c.5124G>A c.(5122-5124)ATG>ATA p.M1708I ASXL3_uc002kxq.2_Missense_Mutation_p.M1415I NM_030632 NP_085135 Q9C0F0 ASXL3_HUMAN additional sex combs like 3 1708 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus metal ion binding ovary(2)|pancreas(1) 3 0.308824 60.548006 62.763656 21 47 KEEP --- --- --- --- ASXL3 80816 broad.mit.edu 37 18 31326064 31326064 + Silent SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:31326064T>C uc010dmg.1 + 12 6307 c.6252T>C c.(6250-6252)CTT>CTC p.L2084L ASXL3_uc002kxq.2_Silent_p.L1791L NM_030632 NP_085135 Q9C0F0 ASXL3_HUMAN additional sex combs like 3 2084 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus metal ion binding ovary(2)|pancreas(1) 3 0.569892 204.390825 204.787106 53 40 KEEP --- --- --- --- RIT2 6014 broad.mit.edu 37 18 40695492 40695492 + 5'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:40695492G>A uc002lav.2 - 1 RIT2_uc010dnf.2_5'UTR NM_002930 NP_002921 Ras-like without CAAX 2 nerve growth factor receptor signaling pathway|small GTPase mediated signal transduction|synaptic transmission intracellular|plasma membrane calmodulin binding|GTP binding|GTPase activity ovary(1) 1 0.565789 145.234455 145.520913 43 33 KEEP --- --- --- --- SETBP1 26040 broad.mit.edu 37 18 42532215 42532215 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:42532215C>T uc010dni.2 + 4 3206 c.2910C>T c.(2908-2910)TCC>TCT p.S970S NM_015559 NP_056374 Q9Y6X0 SETBP_HUMAN SET binding protein 1 isoform a 970 nucleus DNA binding upper_aerodigestive_tract(2)|large_intestine(1) 3 Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201) Schinzel-Giedion_syndrome 0.5125 137.874095 137.884858 41 39 KEEP --- --- --- --- KATNAL2 83473 broad.mit.edu 37 18 44589334 44589335 + Intron DNP CC TT TT MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:44589334_44589335CC>TT uc002lco.2 + KATNAL2_uc010dnq.1_Intron|KATNAL2_uc002lcp.3_Intron NM_031303 NP_112593 katanin p60 subunit A-like 2 cytoplasm|microtubule ATP binding|microtubule-severing ATPase activity ovary(1)|skin(1)|central_nervous_system(1)|pancreas(1) 4 0.42 68.173959 68.451294 21 29 KEEP --- --- --- --- MYO5B 4645 broad.mit.edu 37 18 47432896 47432896 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:47432896G>A uc002leb.2 - 19 2595 c.2307C>T c.(2305-2307)ATC>ATT p.I769I NM_001080467 NP_001073936 Q9ULV0 MYO5B_HUMAN myosin VB 769 IQ 1. protein transport myosin complex actin binding|ATP binding|calmodulin binding|motor activity ovary(2)|skin(2)|central_nervous_system(1) 5 READ - Rectum adenocarcinoma(32;0.103) 0.671875 145.44381 147.118618 43 21 KEEP --- --- --- --- MYO5B 4645 broad.mit.edu 37 18 47527589 47527589 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:47527589C>T uc002leb.2 - MYO5B_uc002lec.1_Intron NM_001080467 NP_001073936 myosin VB protein transport myosin complex actin binding|ATP binding|calmodulin binding|motor activity ovary(2)|skin(2)|central_nervous_system(1) 5 READ - Rectum adenocarcinoma(32;0.103) 0.333333 49.860264 51.113765 17 34 KEEP --- --- --- --- MAPK4 5596 broad.mit.edu 37 18 48190255 48190255 + 5'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:48190255G>A uc002lev.2 + 2 MAPK4_uc010xdm.1_Intron|MAPK4_uc010doz.2_5'UTR NM_002747 NP_002738 mitogen-activated protein kinase 4 cell cycle ATP binding|MAP kinase activity lung(4)|skin(2) 6 Colorectal(6;0.0297) Colorectal(21;0.156) 110 0.444444 40.400679 40.472529 12 15 KEEP --- --- --- --- DCC 1630 broad.mit.edu 37 18 50912324 50912324 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:50912324G>A uc002lfe.1 + DCC_uc010xdr.1_Intron|DCC_uc010dpf.1_Intron NM_005215 NP_005206 netrin receptor DCC precursor apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development cytosol|integral to membrane skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1) 17 all_cancers(7;0.11)|all_epithelial(6;0.00126) Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942) 0.75 10.327207 10.554006 3 1 KEEP --- --- --- --- ALPK2 115701 broad.mit.edu 37 18 56203708 56203708 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:56203708C>T uc002lhj.3 - 5 3925 c.3711G>A c.(3709-3711)AAG>AAA p.K1237K ALPK2_uc002lhk.1_Silent_p.K568K NM_052947 NP_443179 Q86TB3 ALPK2_HUMAN heart alpha-kinase 1237 ATP binding|protein serine/threonine kinase activity ovary(7)|skin(5)|lung(1)|central_nervous_system(1) 14 343 0.158333 40.643351 53.998758 19 101 KEEP --- --- --- --- ALPK2 115701 broad.mit.edu 37 18 56204265 56204265 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:56204265G>A uc002lhj.3 - 5 3368 c.3154C>T c.(3154-3156)CCT>TCT p.P1052S ALPK2_uc002lhk.1_Missense_Mutation_p.P383S NM_052947 NP_443179 Q86TB3 ALPK2_HUMAN heart alpha-kinase 1052 ATP binding|protein serine/threonine kinase activity ovary(7)|skin(5)|lung(1)|central_nervous_system(1) 14 343 0.534091 154.527498 154.616126 47 41 KEEP --- --- --- --- Unknown broad.mit.edu 37 18 57863688 57863688 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:57863688C>T PMAIP1 (292150 upstream) : MC4R (174876 downstream) 0.363636 12.196896 12.376916 4 7 KEEP --- --- --- --- SERPINB3 6317 broad.mit.edu 37 18 61323115 61323115 + Missense_Mutation SNP T A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:61323115T>A uc002lji.2 - 8 1093 c.949A>T c.(949-951)ATG>TTG p.M317L SERPINB4_uc002ljg.2_Intron|SERPINB3_uc010dqa.2_Missense_Mutation_p.M265L NM_006919 NP_008850 P29508 SPB3_HUMAN serine (or cysteine) proteinase inhibitor, clade 317 regulation of proteolysis cytoplasm|extracellular region protein binding|serine-type endopeptidase inhibitor activity ovary(1)|central_nervous_system(1)|skin(1) 3 0.555556 188.226413 188.491505 55 44 KEEP --- --- --- --- SERPINB2 5055 broad.mit.edu 37 18 61568881 61568881 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:61568881G>A uc010xeu.1 + SERPINB2_uc002ljo.2_Intron|SERPINB2_uc010dqh.2_Intron|SERPINB2_uc002ljp.1_Intron|SERPINB2_uc002ljq.1_Intron NM_001143818 NP_001137290 serine (or cysteine) proteinase inhibitor, clade anti-apoptosis|blood coagulation|fibrinolysis|regulation of proteolysis extracellular space|Golgi apparatus|plasma membrane serine-type endopeptidase inhibitor activity lung(1)|skin(1) 2 Esophageal squamous(42;0.131) Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013) 0.555556 48.526914 48.599267 15 12 KEEP --- --- --- --- SERPINB10 5273 broad.mit.edu 37 18 61585373 61585373 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:61585373G>A uc010xev.1 + SERPINB10_uc010xew.1_Intron NM_005024 NP_005015 serine (or cysteine) proteinase inhibitor, clade cytoplasm|nucleus serine-type endopeptidase inhibitor activity lung(1)|kidney(1)|skin(1) 3 Esophageal squamous(42;0.131) 0.259259 19.411722 20.829416 7 20 KEEP --- --- --- --- NETO1 81832 broad.mit.edu 37 18 70451088 70451088 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr18:70451088C>T uc002lkw.2 - 7 977 c.693G>A c.(691-693)AGG>AGA p.R231R NETO1_uc002lkx.1_Silent_p.R230R|NETO1_uc002lky.1_Silent_p.R231R NM_138966 NP_620416 Q8TDF5 NETO1_HUMAN neuropilin- and tolloid-like protein 1 isoform 3 231 CUB 2.|Extracellular (Potential). memory|regulation of long-term neuronal synaptic plasticity|visual learning cell junction|excitatory synapse|extracellular region|integral to membrane|postsynaptic density|postsynaptic membrane receptor activity ovary(2)|skin(2) 4 Esophageal squamous(42;0.129) READ - Rectum adenocarcinoma(1;0.0487) 0.504673 176.765124 176.767531 54 53 KEEP --- --- --- --- C19orf21 126353 broad.mit.edu 37 19 763453 763453 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:763453G>A uc002lpo.2 + NM_173481 NP_775752 hypothetical protein LOC126353 upper_aerodigestive_tract(1) 1 Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000145)|all_lung(49;0.000236)|Breast(49;0.0014) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18) 0.363636 10.79633 10.976561 4 7 KEEP --- --- --- --- PTBP1 5725 broad.mit.edu 37 19 808716 808716 + Nonsense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:808716C>T uc002lpr.2 + 12 1445 c.1339C>T c.(1339-1341)CAG>TAG p.Q447* PTBP1_uc002lpp.2_Nonsense_Mutation_p.Q473*|PTBP1_uc002lpq.2_Nonsense_Mutation_p.Q466*|PTBP1_uc002lps.2_Nonsense_Mutation_p.Q113*|PTBP1_uc002lpt.2_RNA|PTBP1_uc002lpu.1_Nonsense_Mutation_p.Q443* NM_031991 NP_114368 P26599 PTBP1_HUMAN polypyrimidine tract-binding protein 1 isoform 447 negative regulation of muscle cell differentiation|nuclear mRNA splicing, via spliceosome|regulation of alternative nuclear mRNA splicing, via spliceosome heterogeneous nuclear ribonucleoprotein complex|nucleolus|nucleoplasm mRNA binding|nucleotide binding|poly-pyrimidine tract binding|protein binding kidney(1)|skin(1) 2 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18) 0.384615 16.572117 16.723819 5 8 KEEP --- --- --- --- MUM1 84939 broad.mit.edu 37 19 1360552 1360553 + Missense_Mutation DNP GG TA TA MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:1360552_1360553GG>TA uc010xgm.1 + 4 701_702 c.632_633GG>TA c.(631-633)TGG>TTA p.W211L MUM1_uc010dsi.2_Missense_Mutation_p.W143L|MUM1_uc002lrz.2_Missense_Mutation_p.W212L|MUM1_uc002lsb.2_Missense_Mutation_p.W143L|MUM1_uc002lsc.1_Missense_Mutation_p.W143L Q2TAK8 MUM1_HUMAN SubName: Full=MUM1 protein; 211 chromatin organization|DNA repair nucleus nucleosome binding|protein binding 0 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18) OREG0025088 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0.310345 26.36381 27.293223 9 20 KEEP --- --- --- --- TBXA2R 6915 broad.mit.edu 37 19 3600147 3600147 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:3600147C>T uc002lyg.1 - 2 700 c.486G>A c.(484-486)GCG>GCA p.A162A TBXA2R_uc002lye.1_Intron NM_001060 NP_001051 P21731 TA2R_HUMAN thromboxane A2 receptor isoform alpha 162 Helical; Name=4; (Potential). platelet activation integral to plasma membrane guanyl-nucleotide exchange factor activity|protein binding|thromboxane A2 receptor activity 0 Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18) Ridogrel(DB01207) 0.666667 31.849576 32.217903 10 5 KEEP --- --- --- --- TJP3 27134 broad.mit.edu 37 19 3738770 3738770 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:3738770C>T uc010xhv.1 + TJP3_uc010xhs.1_Intron|TJP3_uc010xht.1_Intron|TJP3_uc010xhu.1_Intron|TJP3_uc010xhw.1_Intron NM_014428 NP_055243 tight junction protein 3 tight junction protein binding ovary(1)|central_nervous_system(1)|skin(1) 3 UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0118)|STAD - Stomach adenocarcinoma(1328;0.18) 0.25 25.929816 28.202946 10 30 KEEP --- --- --- --- ITGB1BP3 27231 broad.mit.edu 37 19 3942015 3942015 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:3942015C>T uc002lyz.3 + ITGB1BP3_uc010xia.1_Intron NM_170678 NP_733778 integrin beta 1 binding protein 3 pyridine nucleotide biosynthetic process ATP binding|metal ion binding|protein binding|ribosylnicotinamide kinase activity skin(2) 2 Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00463)|STAD - Stomach adenocarcinoma(1328;0.18) 0.75 44.407888 45.3167 12 4 KEEP --- --- --- --- FSD1 79187 broad.mit.edu 37 19 4323079 4323079 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:4323079G>A uc002lzy.2 + 11 1289 c.1136G>A c.(1135-1137)GGC>GAC p.G379D FSD1_uc002lzz.2_Missense_Mutation_p.G379D|FSD1_uc002maa.2_Missense_Mutation_p.G192D NM_024333 NP_077309 Q9BTV5 FSD1_HUMAN fibronectin type III and SPRY domain containing 379 B30.2/SPRY. cell division|mitosis cleavage furrow|microtubule|microtubule organizing center|nucleus skin(1) 1 UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.034)|STAD - Stomach adenocarcinoma(1328;0.18) 0.913043 72.413112 76.360554 21 2 KEEP --- --- --- --- FUT3 2525 broad.mit.edu 37 19 5844110 5844110 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:5844110G>A uc002mdk.2 - 2 838 c.741C>T c.(739-741)TTC>TTT p.F247F FUT3_uc002mdm.2_Silent_p.F247F|FUT3_uc002mdj.2_Silent_p.F247F|FUT3_uc002mdl.2_Silent_p.F247F NM_001097641 NP_001091110 P21217 FUT3_HUMAN fucosyltransferase 3 247 Lumenal (Potential). protein glycosylation Golgi cisterna membrane|integral to membrane|membrane fraction 3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity 0 Esophageal Squamous(82;745 1728 24593 44831) 0.294118 111.812307 116.933887 40 96 KEEP --- --- --- --- FUT5 2527 broad.mit.edu 37 19 5896817 5896817 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:5896817G>A uc010duo.2 - NDUFA11_uc002mdp.1_Intron|NDUFA11_uc002mdq.1_Intron|NDUFA11_uc002mdr.1_Intron NM_002034 NP_002025 fucosyltransferase 5 L-fucose catabolic process|protein glycosylation Golgi cisterna membrane|integral to membrane 3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity|alpha(1,3)-fucosyltransferase activity 0 0.466667 42.74595 42.774959 14 16 KEEP --- --- --- --- ACSBG2 81616 broad.mit.edu 37 19 6182928 6182928 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:6182928C>T uc002mef.1 + 9 1300 c.1073C>T c.(1072-1074)TCA>TTA p.S358L ACSBG2_uc002mee.1_Missense_Mutation_p.S171L|ACSBG2_uc002meg.1_Missense_Mutation_p.S358L|ACSBG2_uc002meh.1_Missense_Mutation_p.S358L|ACSBG2_uc002mei.1_Missense_Mutation_p.S308L|ACSBG2_uc010xiz.1_Missense_Mutation_p.S358L NM_030924 NP_112186 Q5FVE4 ACBG2_HUMAN bubblegum-related acyl-CoA synthetase 2 358 cell differentiation|fatty acid metabolic process|multicellular organismal development|spermatogenesis membrane|microsome|mitochondrion acyl-CoA thioesterase activity|ATP binding|long-chain fatty acid-CoA ligase activity ovary(1) 1 0.465116 58.665341 58.713276 20 23 KEEP --- --- --- --- CRB3 92359 broad.mit.edu 37 19 6466512 6466512 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:6466512C>T uc002mey.2 + 4 723 c.192C>T c.(190-192)TTC>TTT p.F64F CRB3_uc002mez.2_Silent_p.F64F|CRB3_uc002mfa.2_Silent_p.F64F NM_139161 NP_631900 Q9BUF7 CRUM3_HUMAN crumbs 3 isoform a precursor 64 Helical; (Potential). protein localization in plasma membrane|tight junction assembly apical plasma membrane|integral to membrane|tight junction SH3 domain binding 0 0.306122 180.621543 187.194628 60 136 KEEP --- --- --- --- C3 718 broad.mit.edu 37 19 6713184 6713184 + Intron SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:6713184T>C uc002mfm.2 - NM_000064 NP_000055 complement component 3 precursor complement activation, alternative pathway|complement activation, classical pathway|G-protein coupled receptor protein signaling pathway|inflammatory response|positive regulation vascular endothelial growth factor production extracellular space endopeptidase inhibitor activity|receptor binding skin(3)|ovary(1)|pancreas(1) 5 GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661) 0.244444 33.904239 36.58031 11 34 KEEP --- --- --- --- GPR108 56927 broad.mit.edu 37 19 6733932 6733932 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:6733932G>A uc002mfp.2 - GPR108_uc010duv.2_5'Flank|GPR108_uc002mfn.2_Intron|GPR108_uc002mfo.3_Intron|GPR108_uc010duw.2_Intron NM_001080452 NP_001073921 G protein-coupled receptor 108 isoform 1 integral to membrane 0 OREG0025092 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0.68 115.065401 116.503709 34 16 KEEP --- --- --- --- ZNF557 79230 broad.mit.edu 37 19 7081963 7081963 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:7081963C>T uc002mgb.2 + ZNF557_uc002mga.2_Intron|ZNF557_uc002mgc.2_Intron NM_001044388 NP_001037853 zinc finger protein 557 isoform b regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding ovary(1)|pancreas(1) 2 Lung(535;0.179) 0.652174 52.031446 52.501215 15 8 KEEP --- --- --- --- CD209 30835 broad.mit.edu 37 19 7806763 7806763 + 3'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:7806763G>A uc002mht.2 - 7 CD209_uc010xju.1_3'UTR|CD209_uc010dvp.2_3'UTR|CD209_uc002mhr.2_3'UTR|CD209_uc002mhs.2_3'UTR|CD209_uc002mhu.2_3'UTR|CD209_uc010dvq.2_3'UTR|CD209_uc002mhq.2_3'UTR|CD209_uc002mhv.2_3'UTR|CD209_uc002mhx.2_3'UTR|CD209_uc002mhw.2_3'UTR|CD209_uc010dvr.2_3'UTR NM_021155 NP_066978 CD209 molecule isoform 1 cell-cell recognition|endocytosis|heterophilic cell-cell adhesion|innate immune response|intracellular signal transduction|intracellular virion transport|leukocyte cell-cell adhesion|peptide antigen transport|viral genome replication|virion attachment to host cell surface receptor cytoplasm|extracellular region|integral to membrane|plasma membrane mannose binding|metal ion binding|peptide antigen binding|receptor activity|virion binding skin(1) 1 0.75 10.727821 10.954169 3 1 KEEP --- --- --- --- CLEC4M 10332 broad.mit.edu 37 19 7832583 7832583 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:7832583C>T uc002mih.2 + CLEC4M_uc002mhy.2_3'UTR|CLEC4M_uc010xjw.1_Intron|CLEC4M_uc010dvt.2_Intron|CLEC4M_uc010dvs.2_Intron|CLEC4M_uc010xjx.1_Intron|CLEC4M_uc002mhz.2_Intron|CLEC4M_uc002mic.2_Intron|CLEC4M_uc002mia.2_Intron NM_001144910 NP_001138382 C-type lectin domain family 4, member M isoform cell-cell recognition|endocytosis|innate immune response|intracellular signal transduction|intracellular virion transport|leukocyte cell-cell adhesion|peptide antigen transport|viral genome replication|virion attachment to host cell surface receptor cytoplasm|extracellular region|integral to plasma membrane ICAM-3 receptor activity|mannose binding|metal ion binding|peptide antigen binding|virion binding pancreas(1) 1 0.272727 8.419954 8.932166 3 8 KEEP --- --- --- --- ANGPTL4 51129 broad.mit.edu 37 19 8434222 8434222 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:8434222G>A uc002mjq.1 + ANGPTL4_uc002mjr.1_Intron|ANGPTL4_uc010xkc.1_Intron NM_139314 NP_647475 angiopoietin-like 4 protein isoform a precursor angiogenesis|cell differentiation|cellular lipid metabolic process|negative regulation of apoptosis|negative regulation of lipoprotein lipase activity|positive regulation of angiogenesis|response to hypoxia|signal transduction|triglyceride homeostasis extracellular space|proteinaceous extracellular matrix enzyme inhibitor activity|receptor binding ovary(1) 1 110 0.5625 30.77713 30.831581 9 7 KEEP --- --- --- --- ADAMTS10 81794 broad.mit.edu 37 19 8661951 8661952 + Missense_Mutation DNP GG AA AA rs150725480 byFrequency MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:8661951_8661952GG>AA uc002mkj.1 - 8 1233_1234 c.959_960CC>TT c.(958-960)TCC>TTT p.S320F ADAMTS10_uc002mkk.1_5'UTR NM_030957 NP_112219 Q9H324 ATS10_HUMAN ADAM metallopeptidase with thrombospondin type 1 320 Peptidase M12B. proteolysis proteinaceous extracellular matrix metalloendopeptidase activity|zinc ion binding pancreas(2)|skin(2) 4 0.564103 130.864857 131.127151 44 34 KEEP --- --- --- --- ACTL9 284382 broad.mit.edu 37 19 8808646 8808646 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:8808646C>T uc002mkl.2 - 1 527 c.406G>A c.(406-408)GAC>AAC p.D136N NM_178525 NP_848620 Q8TC94 ACTL9_HUMAN actin-like 9 136 cytoplasm|cytoskeleton large_intestine(2)|pancreas(1) 3 0.65 40.782669 41.183648 13 7 KEEP --- --- --- --- MUC16 94025 broad.mit.edu 37 19 9008426 9008426 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:9008426G>A uc002mkp.2 - MUC16_uc010dwi.2_5'Flank|MUC16_uc010dwj.2_5'Flank|MUC16_uc010xki.1_Intron NM_024690 NP_078966 mucin 16 cell adhesion extracellular space|extrinsic to membrane|integral to membrane|plasma membrane protein binding lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1) 57 0.333333 21.818171 22.334699 7 14 KEEP --- --- --- --- MUC16 94025 broad.mit.edu 37 19 9014505 9014505 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:9014505G>A uc002mkp.2 - MUC16_uc010xki.1_5'Flank NM_024690 NP_078966 mucin 16 cell adhesion extracellular space|extrinsic to membrane|integral to membrane|plasma membrane protein binding lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1) 57 0.445783 119.884838 120.093554 37 46 KEEP --- --- --- --- MUC16 94025 broad.mit.edu 37 19 9018424 9018424 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:9018424G>A uc002mkp.2 - NM_024690 NP_078966 mucin 16 cell adhesion extracellular space|extrinsic to membrane|integral to membrane|plasma membrane protein binding lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1) 57 0.295918 71.887686 75.517569 29 69 KEEP --- --- --- --- MUC16 94025 broad.mit.edu 37 19 9067330 9067330 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:9067330G>A uc002mkp.2 - 3 20320 c.20116C>T c.(20116-20118)CAT>TAT p.H6706Y NM_024690 NP_078966 Q8WXI7 MUC16_HUMAN mucin 16 6708 Thr-rich.|Extracellular (Potential). cell adhesion extracellular space|extrinsic to membrane|integral to membrane|plasma membrane protein binding lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1) 57 0.346535 197.276815 201.482415 70 132 KEEP --- --- --- --- MUC16 94025 broad.mit.edu 37 19 9074021 9074021 + Silent SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:9074021A>G uc002mkp.2 - 3 13629 c.13425T>C c.(13423-13425)CAT>CAC p.H4475H NM_024690 NP_078966 Q8WXI7 MUC16_HUMAN mucin 16 4477 Thr-rich.|Extracellular (Potential). cell adhesion extracellular space|extrinsic to membrane|integral to membrane|plasma membrane protein binding lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1) 57 0.2875 74.99499 78.232845 23 57 KEEP --- --- --- --- ZNF561 93134 broad.mit.edu 37 19 9727771 9727771 + Missense_Mutation SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:9727771T>C uc002mlu.2 - 4 396 c.191A>G c.(190-192)TAC>TGC p.Y64C ZNF561_uc010dwu.2_Translation_Start_Site|ZNF561_uc010xkr.1_Translation_Start_Site NM_152289 NP_689502 Q8N587 ZN561_HUMAN zinc finger protein 561 64 KRAB. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding ovary(1) 1 0.069767 -2.311082 6.326471 3 40 KEEP --- --- --- --- broad.mit.edu 37 19 9803501 9803501 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:9803501G>A uc010xkx.1 - RecName: Full=Zinc finger protein 562; 0.333333 18.343839 18.78673 6 12 KEEP --- --- --- --- COL5A3 50509 broad.mit.edu 37 19 10089326 10089326 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:10089326G>A uc002mmq.1 - NM_015719 NP_056534 collagen, type V, alpha 3 preproprotein collagen fibril organization|skin development collagen type V collagen binding|extracellular matrix structural constituent ovary(7)|lung(1)|central_nervous_system(1)|skin(1) 10 Epithelial(33;7.11e-05) 0.483871 48.923302 48.93035 15 16 KEEP --- --- --- --- PPAN-P2RY11 692312 broad.mit.edu 37 19 10218628 10218628 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:10218628C>T uc002mna.2 + PPAN-P2RY11_uc010xla.1_Intron|PPAN_uc002mmz.1_Intron|PPAN_uc002mnb.1_Intron|SNORD105B_uc010dwz.1_5'Flank NM_001040664 NP_001035754 PPAN-P2RY11 protein RNA splicing nucleolus protein binding ovary(2) 2 OV - Ovarian serous cystadenocarcinoma(20;2.19e-08)|Epithelial(33;1.76e-05)|all cancers(31;3.54e-05) 0.45 28.874066 28.917386 9 11 KEEP --- --- --- --- TYK2 7297 broad.mit.edu 37 19 10461558 10461558 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:10461558G>A uc002moc.3 - 25 3894 c.3516C>T c.(3514-3516)GTC>GTT p.V1172V TYK2_uc010dxe.2_Silent_p.V987V NM_003331 NP_003322 P29597 TYK2_HUMAN tyrosine kinase 2 1172 Protein kinase 2. intracellular protein kinase cascade|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway cytoskeleton|cytosol|membrane|nucleus ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity lung(5)|large_intestine(2)|ovary(1)|breast(1) 9 OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06) 414 0.716667 149.143261 151.670075 43 17 KEEP --- --- --- --- SMARCA4 6597 broad.mit.edu 37 19 11136987 11136987 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:11136987C>T uc002mqf.3 + 23 3464 c.3180C>T c.(3178-3180)TCC>TCT p.S1060S SMARCA4_uc010dxp.2_Silent_p.S1060S|SMARCA4_uc010dxo.2_Silent_p.S1060S|SMARCA4_uc002mqg.1_Silent_p.S1060S|SMARCA4_uc010dxq.2_Silent_p.S1060S|SMARCA4_uc010dxr.2_Silent_p.S1060S|SMARCA4_uc002mqj.3_Silent_p.S1060S|SMARCA4_uc010dxs.2_Silent_p.S1060S|SMARCA4_uc010dxt.1_Silent_p.S280S|SMARCA4_uc002mqh.3_Silent_p.S183S|SMARCA4_uc002mqi.1_Silent_p.S263S NM_003072 NP_003063 P51532 SMCA4_HUMAN SWI/SNF-related matrix-associated 1060 chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity p.?(1) lung(29)|ovary(8)|pancreas(7)|large_intestine(5)|central_nervous_system(5)|skin(3)|prostate(3)|breast(2)|adrenal_gland(1)|stomach(1)|liver(1)|autonomic_ganglia(1)|kidney(1) 67 all_lung(6;0.0512)|Lung NSC(9;0.0568) 582 F|N|Mis NSCLC Rhabdoid_Predisposition_syndrome 0.612903 65.131045 65.476942 19 12 KEEP --- --- --- --- KANK2 25959 broad.mit.edu 37 19 11304168 11304168 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:11304168C>T uc010dxv.2 - 6 1146 c.588G>A c.(586-588)CTG>CTA p.L196L KANK2_uc002mqm.2_Silent_p.L196L|KANK2_uc002mqo.3_Silent_p.L196L|KANK2_uc002mqp.1_Silent_p.L5L|KANK2_uc002mqq.2_Silent_p.L196L NM_015493 NP_056308 Q63ZY3 KANK2_HUMAN ankyrin repeat domain 25 isoform 1 196 Potential. 0 0.583333 21.025223 21.097659 7 5 KEEP --- --- --- --- PRKCSH 5589 broad.mit.edu 37 19 11556379 11556379 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:11556379C>T uc002mrt.2 + PRKCSH_uc002mru.2_Intron|PRKCSH_uc010xlz.1_Intron|PRKCSH_uc010dya.2_Intron|PRKCSH_uc002mrv.1_Intron|PRKCSH_uc010dyb.2_Intron NM_002743 NP_002734 protein kinase C substrate 80K-H isoform 1 innate immune response|intracellular protein kinase cascade|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine endoplasmic reticulum lumen calcium ion binding|protein kinase C binding 0 0.75 9.729587 9.953288 3 1 KEEP --- --- --- --- ELOF1 84337 broad.mit.edu 37 19 11665062 11665062 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:11665062G>A uc002mse.1 - 2 165 c.101C>T c.(100-102)TCC>TTC p.S34F ELOF1_uc002msd.1_Missense_Mutation_p.S55F NM_032377 NP_115753 P60002 ELOF1_HUMAN elongation factor 1 homolog (ELF1, S. 34 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus metal ion binding 0 0.329897 91.66847 94.155499 32 65 KEEP --- --- --- --- ZNF20 7568 broad.mit.edu 37 19 12244072 12244072 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:12244072G>A uc002mtf.1 - 4 1072 c.929C>T c.(928-930)CCC>CTC p.P310L ZNF20_uc002mte.1_Missense_Mutation_p.P275L|ZNF20_uc002mtg.1_Missense_Mutation_p.P310L NM_021143 NP_066966 P17024 ZNF20_HUMAN zinc finger protein 20 310 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding 0 0.527778 130.955467 131.003884 38 34 KEEP --- --- --- --- ZNF799 90576 broad.mit.edu 37 19 12490670 12490670 + 3'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:12490670G>A uc002mts.3 - 4 Homo sapiens cDNA clone IMAGE:30340957, **** WARNING: chimeric clone ****. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding breast(3)|ovary(2)|skin(1) 6 0.545455 18.85044 18.870166 6 5 KEEP --- --- --- --- MAST1 22983 broad.mit.edu 37 19 12979860 12979860 + Intron SNP C A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:12979860C>A uc002mvm.2 + NM_014975 NP_055790 microtubule associated serine/threonine kinase cytoskeleton organization|intracellular protein kinase cascade cytoplasm|cytoskeleton|plasma membrane ATP binding|magnesium ion binding|protein serine/threonine kinase activity ovary(3)|lung(2)|large_intestine(1)|skin(1) 7 239 0.056604 -4.221594 6.726965 3 50 KEEP --- --- --- --- RAD23A 5886 broad.mit.edu 37 19 13059460 13059460 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:13059460C>T uc002mvw.1 + RAD23A_uc002mvx.1_Intron|RAD23A_uc002mvz.1_Intron|RAD23A_uc002mwa.1_Intron|RAD23A_uc002mvy.1_Intron|RAD23A_uc010xmw.1_Intron NM_005053 NP_005044 UV excision repair protein RAD23 homolog A interspecies interaction between organisms|nucleotide-excision repair|positive regulation of viral genome replication|proteasomal ubiquitin-dependent protein catabolic process|regulation of proteasomal ubiquitin-dependent protein catabolic process nucleus|proteasome complex damaged DNA binding|polyubiquitin binding|single-stranded DNA binding central_nervous_system(1) 1 NER 0.608696 142.575803 143.295961 42 27 KEEP --- --- --- --- CACNA1A 773 broad.mit.edu 37 19 13325167 13325167 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:13325167G>A uc010dze.2 - CACNA1A_uc010xnd.1_Intron|CACNA1A_uc002mwx.3_Intron|CACNA1A_uc010dzc.2_Intron|CACNA1A_uc002mwy.3_Intron|CACNA1A_uc002mwv.3_Intron NM_001127221 NP_001120693 calcium channel, alpha 1A subunit isoform 3 cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion cytoplasm|nucleus syntaxin binding large_intestine(2) 2 OV - Ovarian serous cystadenocarcinoma(19;5.07e-21) Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230) 0.642857 29.87829 30.129749 9 5 KEEP --- --- --- --- IL27RA 9466 broad.mit.edu 37 19 14161518 14161518 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:14161518G>A uc002mxx.2 + NM_004843 NP_004834 class I cytokine receptor precursor cell surface receptor linked signaling pathway|immune response integral to plasma membrane transmembrane receptor activity 0 Colon(164;1849 1896 4443 37792 47834) 0.764706 44.683257 45.772392 13 4 KEEP --- --- --- --- PGLYRP2 114770 broad.mit.edu 37 19 15587426 15587426 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:15587426G>A uc002nbf.3 - PGLYRP2_uc002nbg.3_Intron NM_052890 NP_443122 peptidoglycan recognition protein 2 precursor defense response to Gram-positive bacterium|detection of bacterium|innate immune response|peptide amidation|peptidoglycan catabolic process extracellular region|intracellular|membrane N-acetylmuramoyl-L-alanine amidase activity|peptidoglycan receptor activity|zinc ion binding ovary(3) 3 0.384615 15.677782 15.82736 5 8 KEEP --- --- --- --- CYP4F3 4051 broad.mit.edu 37 19 15769394 15769394 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:15769394C>T uc002nbj.2 + CYP4F3_uc010xok.1_Intron|CYP4F3_uc010xol.1_Intron|CYP4F3_uc010xom.1_Intron|CYP4F3_uc002nbk.2_Intron|CYP4F3_uc010xon.1_Intron NM_000896 NP_000887 cytochrome P450, family 4, subfamily F, leukotriene metabolic process|xenobiotic metabolic process endoplasmic reticulum membrane|integral to membrane|microsome electron carrier activity|heme binding|leukotriene-B4 20-monooxygenase activity|oxygen binding ovary(3) 3 0.4 157.707353 158.89222 54 81 KEEP --- --- --- --- CYP4F12 66002 broad.mit.edu 37 19 15789126 15789126 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:15789126C>T uc002nbl.2 + 3 315 c.254C>T c.(253-255)TCC>TTC p.S85F CYP4F12_uc010xoo.1_Missense_Mutation_p.S85F|CYP4F12_uc010xop.1_Missense_Mutation_p.S85F NM_023944 NP_076433 cytochrome P450, family 4, subfamily F, skin(3)|ovary(2)|central_nervous_system(2) 7 Acute lymphoblastic leukemia(2;0.0367) 0.540984 107.278335 107.367256 33 28 KEEP --- --- --- --- CYP4F2 8529 broad.mit.edu 37 19 16003310 16003310 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:16003310C>T uc002nbs.1 - CYP4F2_uc010xot.1_5'UTR|CYP4F2_uc010xou.1_Intron NM_001082 NP_001073 cytochrome P450, family 4, subfamily F, leukotriene metabolic process|long-chain fatty acid metabolic process|very long-chain fatty acid metabolic process|xenobiotic metabolic process endoplasmic reticulum membrane|microsome alkane 1-monooxygenase activity|electron carrier activity|heme binding|leukotriene-B4 20-monooxygenase activity|oxygen binding|protein binding ovary(1)|skin(1) 2 0.533333 74.767797 74.809308 24 21 KEEP --- --- --- --- CYP4F2 8529 broad.mit.edu 37 19 16004743 16004743 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:16004743G>A uc002nbs.1 - CYP4F2_uc010xot.1_Intron|CYP4F2_uc010xou.1_Intron NM_001082 NP_001073 cytochrome P450, family 4, subfamily F, leukotriene metabolic process|long-chain fatty acid metabolic process|very long-chain fatty acid metabolic process|xenobiotic metabolic process endoplasmic reticulum membrane|microsome alkane 1-monooxygenase activity|electron carrier activity|heme binding|leukotriene-B4 20-monooxygenase activity|oxygen binding|protein binding ovary(1)|skin(1) 2 0.328358 66.342553 68.084913 22 45 KEEP --- --- --- --- CPAMD8 27151 broad.mit.edu 37 19 17086750 17086750 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:17086750G>A uc002nfb.2 - NM_015692 NP_056507 C3 and PZP-like, alpha-2-macroglobulin domain extracellular space|plasma membrane serine-type endopeptidase inhibitor activity ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1) 13 1067 0.285714 16.641106 17.506544 6 15 KEEP --- --- --- --- CPAMD8 27151 broad.mit.edu 37 19 17122433 17122433 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:17122433C>T uc002nfb.2 - 4 575 c.543G>A c.(541-543)ACG>ACA p.T181T NM_015692 NP_056507 Q8IZJ3 CPMD8_HUMAN C3 and PZP-like, alpha-2-macroglobulin domain 134 extracellular space|plasma membrane serine-type endopeptidase inhibitor activity ovary(4)|breast(4)|large_intestine(3)|pancreas(1)|skin(1) 13 1067 0.288889 74.929994 78.515715 26 64 KEEP --- --- --- --- UNC13A 23025 broad.mit.edu 37 19 17735813 17735813 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:17735813G>A uc002nhd.2 - NM_001080421 NP_001073890 unc-13 homolog A exocytosis|intracellular signal transduction cell junction|cytoplasm|presynaptic membrane metal ion binding ovary(3) 3 0.533333 25.298085 25.312375 8 7 KEEP --- --- --- --- JAK3 3718 broad.mit.edu 37 19 17948623 17948623 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:17948623G>A uc002nhn.3 - JAK3_uc010ebh.2_Intron|JAK3_uc002nho.2_Intron NM_000215 NP_000206 Janus kinase 3 B cell differentiation|cytokine-mediated signaling pathway|enzyme linked receptor protein signaling pathway|intracellular protein kinase cascade|negative regulation of dendritic cell cytokine production|negative regulation of FasL biosynthetic process|negative regulation of interleukin-10 production|negative regulation of interleukin-12 production|negative regulation of T-helper 1 cell differentiation|negative regulation of thymocyte apoptosis|peptidyl-tyrosine phosphorylation|positive regulation of anti-apoptosis|response to interleukin-15|response to interleukin-2|response to interleukin-4|response to interleukin-9|T cell homeostasis cytoskeleton|cytosol|endomembrane system|membrane ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding haematopoietic_and_lymphoid_tissue(40)|lung(5)|breast(5)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1) 56 2 364 Mis acute megakaryocytic leukemia| 0.528846 165.419734 165.494215 55 49 KEEP --- --- --- --- SLC5A5 6528 broad.mit.edu 37 19 18004507 18004507 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:18004507C>T uc002nhr.3 + NM_000453 NP_000444 solute carrier family 5 (sodium iodide cellular nitrogen compound metabolic process|cellular response to cAMP|cellular response to gonadotropin stimulus|hormone biosynthetic process integral to membrane|nucleus|plasma membrane iodide transmembrane transporter activity|sodium:iodide symporter activity skin(2)|ovary(1)|central_nervous_system(1) 4 Melanoma(65;1008 1708 7910 46650) 0.269231 18.918345 20.164751 7 19 KEEP --- --- --- --- FKBP8 23770 broad.mit.edu 37 19 18650017 18650017 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:18650017C>T uc002njk.1 - FKBP8_uc002nji.1_Intron|FKBP8_uc010xqi.1_Intron|FKBP8_uc002njj.1_Intron|FKBP8_uc002njl.1_Intron|FKBP8_uc002njm.1_Intron|FKBP8_uc010ebr.1_Intron|FKBP8_uc002njn.2_Intron NM_012181 NP_036313 FK506-binding protein 8 apoptosis|interspecies interaction between organisms|intracellular signal transduction|protein folding integral to endoplasmic reticulum membrane|mitochondrial membrane FK506 binding|peptidyl-prolyl cis-trans isomerase activity|protein binding ovary(1) 1 0.375 8.522502 8.632436 3 5 KEEP --- --- --- --- UBA52 7311 broad.mit.edu 37 19 18685748 18685748 + Nonsense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:18685748C>T uc002njr.2 + 4 373 c.259C>T c.(259-261)CAG>TAG p.Q87* UBA52_uc002njs.2_Nonsense_Mutation_p.Q87*|UBA52_uc002njt.2_Nonsense_Mutation_p.Q87* NM_001033930 NP_001029102 P62987 RL40_HUMAN ubiquitin and ribosomal protein L40 precursor 87 activation of MAPK activity|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|anti-apoptosis|apoptosis|cellular membrane organization|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA repair|endocrine pancreas development|endosome transport|epidermal growth factor receptor signaling pathway|G1/S transition of mitotic cell cycle|I-kappaB kinase/NF-kappaB cascade|induction of apoptosis by extracellular signals|innate immune response|JNK cascade|M/G1 transition of mitotic cell cycle|mRNA metabolic process|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of type I interferon production|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|S phase of mitotic cell cycle|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|translational elongation|translational termination|viral transcription cytosol|endocytic vesicle membrane|endosome membrane|nucleoplasm|plasma membrane|ribosome protein binding|structural constituent of ribosome 0 0.318182 21.917512 22.563776 7 15 KEEP --- --- --- --- COMP 1311 broad.mit.edu 37 19 18898343 18898343 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:18898343C>T uc002nke.2 - 10 1128 c.1092G>A c.(1090-1092)CAG>CAA p.Q364Q COMP_uc002nkd.2_Silent_p.Q331Q|COMP_uc010xqj.1_Silent_p.Q311Q NM_000095 NP_000086 P49747 COMP_HUMAN cartilage oligomeric matrix protein precursor 364 TSP type-3 4. anti-apoptosis|apoptosis|cell adhesion|limb development extracellular space|proteinaceous extracellular matrix calcium ion binding|collagen binding|extracellular matrix structural constituent|heparan sulfate proteoglycan binding|heparin binding 0 0.365217 130.81832 132.655868 42 73 KEEP --- --- --- --- COPE 11316 broad.mit.edu 37 19 19030185 19030185 + 5'UTR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:19030185C>T uc002nkk.2 - 1 COPE_uc002nkl.2_5'UTR|COPE_uc002nkm.2_5'UTR|COPE_uc002nkn.2_5'UTR|HOMER3_uc002nko.1_Intron|HOMER3_uc002nkp.1_Intron|DDX49_uc002nkq.1_5'Flank|DDX49_uc002nkr.1_5'Flank|DDX49_uc002nks.1_5'Flank|DDX49_uc002nkt.1_5'Flank NM_007263 NP_009194 epsilon subunit of coatomer protein complex COPI coating of Golgi vesicle|intra-Golgi vesicle-mediated transport|protein transport|retrograde vesicle-mediated transport, Golgi to ER COPI vesicle coat|cytosol binding|structural molecule activity 0 0.363636 46.192992 46.910638 16 28 KEEP --- --- --- --- SF4 57794 broad.mit.edu 37 19 19414027 19414027 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:19414027G>A uc002nmh.2 - SF4_uc002nmf.2_5'Flank|SF4_uc002nmg.2_Intron|SF4_uc002nmi.2_Intron|SF4_uc002nmj.2_Intron|SF4_uc010xqr.1_Intron|SF4_uc010xqs.1_Intron NM_172231 NP_757386 splicing factor 4 nuclear mRNA splicing, via spliceosome nucleoplasm|spliceosomal complex RNA binding 0 0.4 12.398057 12.485504 4 6 KEEP --- --- --- --- broad.mit.edu 37 19 19862111 19862111 + 5'Flank SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:19862111C>T uc002nnr.1 - uc002nns.2_5'Flank|uc002nnt.1_5'Flank|uc010xrd.1_5'Flank|uc002nnu.2_5'Flank|uc010xre.1_5'Flank|uc002nnw.2_5'Flank DQ584258 0.5 7.050023 7.050023 2 2 KEEP --- --- --- --- Unknown broad.mit.edu 37 19 20067473 20067473 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:20067473G>A ZNF93 (21708 upstream) : ZNF682 (47756 downstream) 0.45 29.477218 29.51998 9 11 KEEP --- --- --- --- ZNF714 148206 broad.mit.edu 37 19 21266831 21266831 + 5'UTR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:21266831C>T uc002npo.3 + 2 ZNF714_uc002npl.2_5'UTR|ZNF714_uc010ecp.1_5'UTR|ZNF714_uc002npn.2_RNA NM_182515 NP_872321 zinc finger protein 714 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding 0 0.5 13.199882 13.199882 4 4 KEEP --- --- --- --- ZNF431 170959 broad.mit.edu 37 19 21366132 21366132 + Silent SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:21366132A>G uc002npp.2 + 5 1173 c.1026A>G c.(1024-1026)AAA>AAG p.K342K ZNF431_uc010ecq.2_Silent_p.K251K|ZNF431_uc010ecr.2_Silent_p.K343K NM_133473 NP_597730 Q8TF32 ZN431_HUMAN zinc finger protein 431 342 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding central_nervous_system(2) 2 0.6 92.209147 92.559282 24 16 KEEP --- --- --- --- ZNF43 7594 broad.mit.edu 37 19 21990389 21990389 + 3'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:21990389G>A uc002nqj.2 - 4 ZNF43_uc010ecv.2_3'UTR|ZNF43_uc002nql.2_3'UTR|ZNF43_uc002nqm.2_3'UTR|ZNF43_uc002nqk.2_3'UTR NM_003423 NP_003414 zinc finger protein 43 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding large_intestine(1)|ovary(1) 2 Renal(1328;0.000219)|Hepatocellular(1079;0.121) GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127) 0.36 30.168162 30.599567 9 16 KEEP --- --- --- --- Unknown broad.mit.edu 37 19 23031172 23031172 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:23031172G>A ZNF99 (78388 upstream) : ZNF91 (490247 downstream) 0.590909 183.516616 184.151857 52 36 KEEP --- --- --- --- broad.mit.edu 37 19 23311278 23311278 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:23311278C>T uc002nrb.1 + Homo sapiens cDNA FLJ16640 fis, clone TESTI4028938, moderately similar to Zinc finger protein 85. 0.5 22.124416 22.124416 7 7 KEEP --- --- --- --- broad.mit.edu 37 19 23318841 23318841 + RNA SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:23318841C>T uc002nrb.1 + 3 c.421C>T Homo sapiens cDNA FLJ16640 fis, clone TESTI4028938, moderately similar to Zinc finger protein 85. p.P74P(1) 0.459459 53.771796 53.824668 17 20 KEEP --- --- --- --- SLC7A9 11136 broad.mit.edu 37 19 33351604 33351604 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:33351604C>T uc002ntv.3 - SLC7A9_uc002ntt.3_Intron|SLC7A9_uc002ntu.3_Intron|SLC7A9_uc002ntw.3_Intron NM_001126335 NP_001119807 solute carrier family 7, member 9 blood coagulation|cellular amino acid metabolic process|ion transport|leukocyte migration|protein complex assembly integral to plasma membrane L-cystine transmembrane transporter activity|neutral amino acid transmembrane transporter activity|peptide antigen binding skin(1) 1 Esophageal squamous(110;0.137) L-Cystine(DB00138) GBM(181;1335 2108 9644 44178 46689) 0.615385 28.416036 28.575367 8 5 KEEP --- --- --- --- WDR88 126248 broad.mit.edu 37 19 33654918 33654918 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:33654918C>T uc002nui.2 + NM_173479 NP_775750 PQQ repeat and WD repeat domain containing ovary(1)|breast(1)|central_nervous_system(1) 3 Esophageal squamous(110;0.137) 0.5 14.20014 14.20014 4 4 KEEP --- --- --- --- KIAA0355 9710 broad.mit.edu 37 19 34843444 34843444 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:34843444G>A uc002nvd.3 + NM_014686 NP_055501 hypothetical protein LOC9710 ovary(1) 1 Esophageal squamous(110;0.162) 0.411765 22.022258 22.137758 7 10 KEEP --- --- --- --- GRAMD1A 57655 broad.mit.edu 37 19 35500952 35500952 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:35500952C>T uc010xse.1 + GRAMD1A_uc002nxi.1_Intron|GRAMD1A_uc002nxk.2_Intron|GRAMD1A_uc002nxl.2_Intron|GRAMD1A_uc010xsf.1_Intron NM_020895 NP_065946 GRAM domain containing 1A isoform 1 integral to membrane 0 all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0849) 0.280702 39.987855 42.444767 16 41 KEEP --- --- --- --- HPN 3249 broad.mit.edu 37 19 35556984 35556984 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:35556984C>T uc002nxq.1 + HPN_uc002nxr.1_Intron|HPN_uc002nxs.1_Intron|HPN_uc010xsh.1_Silent_p.V390V|HPN_uc002nxt.1_Silent_p.V305V|LOC100128675_uc010xsi.1_Intron NM_002151 NP_002142 hepsin cell growth|proteolysis cytoplasm|integral to plasma membrane scavenger receptor activity|serine-type endopeptidase activity ovary(1)|central_nervous_system(1) 2 all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0849) Coagulation factor VIIa(DB00036) 0.449275 104.421832 104.575657 31 38 KEEP --- --- --- --- ATP4A 495 broad.mit.edu 37 19 36053944 36053944 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:36053944C>T uc002oal.1 - NM_000704 NP_000695 hydrogen/potassium-exchanging ATPase 4A ATP biosynthetic process|ATP hydrolysis coupled proton transport integral to plasma membrane ATP binding|hydrogen:potassium-exchanging ATPase activity|magnesium ion binding ovary(1) 1 all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0724) Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)|Trifluoperazine(DB00831) 0.454545 15.673363 15.69321 5 6 KEEP --- --- --- --- ZBTB32 27033 broad.mit.edu 37 19 36206149 36206149 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:36206149G>A uc002oay.2 + 2 831 c.621G>A c.(619-621)GGG>GGA p.G207G ZBTB32_uc002oaz.2_RNA|MLL4_uc010eei.2_5'Flank NM_014383 NP_055198 Q9Y2Y4 ZBT32_HUMAN zinc finger and BTB domain containing 32 207 DNA repair|negative regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter nucleoplasm DNA binding|protein binding|transcription corepressor activity|zinc ion binding ovary(1)|skin(1) 2 all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0515) 0.5 64.488189 64.488189 20 20 KEEP --- --- --- --- NPHS1 4868 broad.mit.edu 37 19 36332601 36332601 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:36332601C>T uc002oby.2 - NPHS1_uc010eem.1_5'Flank NM_004646 NP_004637 nephrin precursor cell adhesion|excretion|muscle organ development integral to plasma membrane ovary(4)|skin(1) 5 all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0515) 0.25 21.485568 23.302787 8 24 KEEP --- --- --- --- APLP1 333 broad.mit.edu 37 19 36362183 36362183 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:36362183C>T uc002oce.2 + 4 607 c.469C>T c.(469-471)CGG>TGG p.R157W APLP1_uc010xsz.1_Missense_Mutation_p.R118W|APLP1_uc002ocf.2_Missense_Mutation_p.R157W|APLP1_uc002ocg.2_Missense_Mutation_p.R60W|APLP1_uc010xta.1_Missense_Mutation_p.R151W NM_005166 NP_005157 P51693 APLP1_HUMAN amyloid precursor-like protein 1 isoform 2 157 Extracellular (Potential). apoptosis|cell adhesion|cellular response to norepinephrine stimulus|endocytosis|negative regulation of cAMP biosynthetic process|nervous system development|organ morphogenesis basement membrane|integral to membrane|perinuclear region of cytoplasm|plasma membrane alpha-2A adrenergic receptor binding|alpha-2B adrenergic receptor binding|alpha-2C adrenergic receptor binding|heparin binding|identical protein binding|metal ion binding ovary(2) 2 all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0515) 0.35 21.419724 21.816422 7 13 KEEP --- --- --- --- APLP1 333 broad.mit.edu 37 19 36364499 36364499 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:36364499C>T uc002oce.2 + APLP1_uc010xsz.1_Intron|APLP1_uc002ocf.2_Intron|APLP1_uc002ocg.2_Intron|APLP1_uc010xta.1_Intron NM_005166 NP_005157 amyloid precursor-like protein 1 isoform 2 apoptosis|cell adhesion|cellular response to norepinephrine stimulus|endocytosis|negative regulation of cAMP biosynthetic process|nervous system development|organ morphogenesis basement membrane|integral to membrane|perinuclear region of cytoplasm|plasma membrane alpha-2A adrenergic receptor binding|alpha-2B adrenergic receptor binding|alpha-2C adrenergic receptor binding|heparin binding|identical protein binding|metal ion binding ovary(2) 2 all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0515) 0.631579 41.104834 41.393996 12 7 KEEP --- --- --- --- THAP8 199745 broad.mit.edu 37 19 36531081 36531081 + Intron SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:36531081A>G uc002oda.1 - uc002ocy.2_Intron|THAP8_uc010xtb.1_Intron|THAP8_uc010xtc.1_Intron NM_152658 NP_689871 THAP domain containing 8 DNA binding|metal ion binding 0 Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.06) 0.181818 5.843832 6.889435 2 9 KEEP --- --- --- --- ZFP30 22835 broad.mit.edu 37 19 38135573 38135573 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:38135573G>A uc002ogv.1 - 4 590 c.74C>T c.(73-75)TCA>TTA p.S25L ZFP30_uc002ogw.1_Missense_Mutation_p.S25L|ZFP30_uc002ogx.1_Missense_Mutation_p.S25L|ZFP30_uc010xtt.1_Missense_Mutation_p.S25L NM_014898 NP_055713 Q9Y2G7 ZFP30_HUMAN zinc finger protein 30 homolog 25 KRAB. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding 0 COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177) 0.528736 150.250855 150.312996 46 41 KEEP --- --- --- --- RYR1 6261 broad.mit.edu 37 19 38945769 38945769 + Intron SNP C A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:38945769C>A uc002oit.2 + RYR1_uc002oiu.2_Intron NM_000540 NP_000531 skeletal muscle ryanodine receptor isoform 1 muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1) 12 all_cancers(60;7.91e-06) Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272) Dantrolene(DB01219) 0.642857 32.279115 32.53078 9 5 KEEP --- --- --- --- RYR1 6261 broad.mit.edu 37 19 38960167 38960168 + Intron DNP CC TT TT MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:38960167_38960168CC>TT uc002oit.2 + RYR1_uc002oiu.2_Intron NM_000540 NP_000531 skeletal muscle ryanodine receptor isoform 1 muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1) 12 all_cancers(60;7.91e-06) Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272) Dantrolene(DB01219) 0.641791 150.161104 151.362072 43 24 KEEP --- --- --- --- RYR1 6261 broad.mit.edu 37 19 38985161 38985161 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:38985161C>T uc002oit.2 + 39 6574 c.6444C>T c.(6442-6444)TCC>TCT p.S2148S RYR1_uc002oiu.2_Silent_p.S2148S|RYR1_uc002oiv.1_5'Flank NM_000540 NP_000531 P21817 RYR1_HUMAN skeletal muscle ryanodine receptor isoform 1 2148 Cytoplasmic.|6 X approximate repeats. muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1) 12 all_cancers(60;7.91e-06) Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272) Dantrolene(DB01219) 0.6 84.208519 84.558594 24 16 KEEP --- --- --- --- RYR1 6261 broad.mit.edu 37 19 39018376 39018376 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:39018376C>T uc002oit.2 + 73 10906 c.10776C>T c.(10774-10776)ATC>ATT p.I3592I RYR1_uc002oiu.2_Silent_p.I3587I|RYR1_uc002oiv.1_Silent_p.I507I|RYR1_uc010xuf.1_Silent_p.I512I NM_000540 NP_000531 P21817 RYR1_HUMAN skeletal muscle ryanodine receptor isoform 1 3592 muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity ovary(7)|pancreas(2)|breast(1)|central_nervous_system(1)|skin(1) 12 all_cancers(60;7.91e-06) Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272) Dantrolene(DB01219) 0.633333 64.635284 65.106045 19 11 KEEP --- --- --- --- PAPL 390928 broad.mit.edu 37 19 39591754 39591754 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:39591754C>T uc002oki.2 + PAPL_uc010egl.2_Intron NM_001004318 NP_001004318 iron/zinc purple acid phosphatase-like protein extracellular region acid phosphatase activity|metal ion binding 0 0.75 85.015215 86.832767 24 8 KEEP --- --- --- --- PAK4 10298 broad.mit.edu 37 19 39667040 39667040 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:39667040G>A uc002okj.1 + PAK4_uc002okl.1_Intron|PAK4_uc002okn.1_Intron|PAK4_uc002okm.1_Intron|PAK4_uc002oko.1_Intron|PAK4_uc002okp.1_Intron NM_001014831 NP_001014831 p21-activated kinase 4 isoform 1 cellular component movement|signal transduction Golgi apparatus ATP binding|protein binding|protein serine/threonine kinase activity lung(3)|ovary(1) 4 all_cancers(60;1.03e-07)|all_epithelial(25;9.66e-08)|all_lung(34;1.58e-07)|Lung NSC(34;1.88e-07)|Ovarian(47;0.0454) Epithelial(26;4.82e-25)|all cancers(26;2.94e-22)|Lung(45;0.000797)|LUSC - Lung squamous cell carcinoma(53;0.00113) 223 0.526316 34.951309 34.962753 10 9 KEEP --- --- --- --- PLEKHG2 64857 broad.mit.edu 37 19 39907432 39907432 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:39907432C>T uc010xuz.1 + PLEKHG2_uc010xuy.1_Intron|PLEKHG2_uc002olj.2_Intron|PLEKHG2_uc010xva.1_Intron NM_022835 NP_073746 common-site lymphoma/leukemia guanine nucleotide apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol Rho guanyl-nucleotide exchange factor activity skin(2)|pancreas(1)|breast(1) 4 all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569) Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657) 0.313131 96.818606 99.879635 31 68 KEEP --- --- --- --- TIMM50 92609 broad.mit.edu 37 19 39979162 39979162 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:39979162C>T uc002olu.1 + TIMM50_uc002olt.1_Intron|TIMM50_uc002olv.1_Intron NM_001001563 NP_001001563 translocase of inner mitochondrial membrane 50 mitochondrial membrane organization|protein transport|release of cytochrome c from mitochondria|transmembrane transport integral to membrane|mitochondrial inner membrane presequence translocase complex|nuclear speck interleukin-2 receptor binding|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|ribonucleoprotein binding|RNA binding ovary(1) 1 all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159) Epithelial(26;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657) 0.243478 73.546375 80.441214 28 87 KEEP --- --- --- --- Unknown broad.mit.edu 37 19 40186773 40186773 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:40186773C>T LOC400696 (9760 upstream) : LGALS14 (8173 downstream) 0.666667 6.851178 6.924648 2 1 KEEP --- --- --- --- FCGBP 8857 broad.mit.edu 37 19 40412073 40412073 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:40412073G>A uc002omp.3 - 7 3563 c.3555C>T c.(3553-3555)CCC>CCT p.P1185P NM_003890 NP_003881 Q9Y6R7 FCGBP_HUMAN Fc fragment of IgG binding protein precursor 1185 Cys-rich.|TIL 2. extracellular region protein binding ovary(4)|skin(4)|central_nervous_system(1) 9 all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06) Epithelial(26;6.25e-23)|all cancers(26;1.13e-20) 0.317073 40.860803 42.080379 13 28 KEEP --- --- --- --- FCGBP 8857 broad.mit.edu 37 19 40434309 40434309 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:40434309C>T uc002omp.3 - NM_003890 NP_003881 Fc fragment of IgG binding protein precursor extracellular region protein binding ovary(4)|skin(4)|central_nervous_system(1) 9 all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06) Epithelial(26;6.25e-23)|all cancers(26;1.13e-20) 0.454545 11.458869 11.479577 5 6 KEEP --- --- --- --- AKT2 208 broad.mit.edu 37 19 40739880 40739880 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:40739880G>A uc002onf.2 - AKT2_uc010egs.2_Intron|AKT2_uc010egt.2_Intron|AKT2_uc010xvj.1_Intron|AKT2_uc002one.2_Intron NM_001626 NP_001617 AKT2 kinase insulin receptor signaling pathway|negative regulation of plasma membrane long-chain fatty acid transport|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process cytosol|nucleus ATP binding|protein binding|protein serine/threonine kinase activity lung(2) 2 Lung(22;0.000499) 232 A ovarian|pancreatic 0.681818 52.73444 53.38265 15 7 KEEP --- --- --- --- CYP2A7 1549 broad.mit.edu 37 19 41447142 41447142 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:41447142C>T uc002opo.2 - CYP2B7P1_uc010ehh.1_Intron|CYP2B7P1_uc002opq.2_Intron NM_000764 NP_000755 cytochrome P450, family 2, subfamily A, endoplasmic reticulum membrane|microsome aromatase activity|electron carrier activity|heme binding|oxygen binding ovary(1)|haematopoietic_and_lymphoid_tissue(1)|skin(1) 3 LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959) 177 0.538462 45.150842 45.184217 14 12 KEEP --- --- --- --- AXL 558 broad.mit.edu 37 19 41754330 41754330 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:41754330C>T uc010ehj.2 + CYP2F1_uc010xvw.1_Intron|AXL_uc010ehk.2_Intron NM_021913 NP_068713 AXL receptor tyrosine kinase isoform 1 integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity lung(4)|stomach(3)|ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1) 13 318 0.791667 65.737116 67.626952 19 5 KEEP --- --- --- --- AXL 558 broad.mit.edu 37 19 41762436 41762436 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:41762436G>A uc010ehj.2 + 18 2306 c.2116G>A c.(2116-2118)GGA>AGA p.G706R CYP2F1_uc010xvw.1_Intron|AXL_uc010ehk.2_Missense_Mutation_p.G697R NM_021913 NP_068713 P30530 UFO_HUMAN AXL receptor tyrosine kinase isoform 1 706 Cytoplasmic (Potential).|Protein kinase. integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity lung(4)|stomach(3)|ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1) 13 318 0.546667 138.380779 138.522834 41 34 KEEP --- --- --- --- TMEM145 284339 broad.mit.edu 37 19 42819334 42819334 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:42819334C>T uc002otk.1 + NM_173633 NP_775904 transmembrane protein 145 integral to membrane 0 Prostate(69;0.00682) 0.792453 147.27929 151.479218 42 11 KEEP --- --- --- --- CEACAM8 1088 broad.mit.edu 37 19 43092871 43092871 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:43092871C>T uc002oud.2 - uc010eif.1_Intron|uc010eig.1_Intron|uc010eih.1_Intron NM_001816 NP_001807 carcinoembryonic antigen-related cell adhesion immune response anchored to membrane|extracellular space|integral to plasma membrane ovary(1) 1 Prostate(69;0.00899) 0.423077 34.220841 34.355055 11 15 KEEP --- --- --- --- PSG1 5669 broad.mit.edu 37 19 43343354 43343354 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:43343354G>A uc010eio.1 - PSG3_uc002ouf.2_Intron|PSG1_uc002oug.1_Intron|PSG11_uc002ouw.2_Intron|PSG7_uc002ous.1_Intron|PSG7_uc002out.1_Intron|PSG10_uc002ouv.1_Intron|PSG8_uc002ouj.3_Intron|PSG8_uc002ouk.3_Intron|PSG8_uc002oul.3_Intron|PSG8_uc002oum.3_Intron|PSG1_uc002oun.2_Intron|PSG8_uc002oup.3_Intron|PSG10_uc010eip.2_Intron|PSG1_uc002our.1_Intron NM_006905 NP_008836 pregnancy specific beta-1-glycoprotein 1 female pregnancy extracellular region ovary(2) 2 Prostate(69;0.00682) 0.666667 19.452305 19.673412 6 3 KEEP --- --- --- --- PSG11 5680 broad.mit.edu 37 19 43519367 43519367 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:43519367G>A uc002ovm.1 - 4 972 c.865C>T c.(865-867)CCT>TCT p.P289S PSG11_uc002ouw.2_Intron|PSG10_uc002ouv.1_Intron|PSG6_uc002ovh.1_Intron|PSG6_uc002ovi.2_Intron|PSG6_uc010xwk.1_Intron|PSG11_uc002ovk.1_Intron|PSG11_uc002ovn.1_Missense_Mutation_p.P295S|PSG11_uc002ovo.1_Missense_Mutation_p.P167S|PSG11_uc002ovp.1_Missense_Mutation_p.P167S NM_002785 NP_002776 Q9UQ72 PSG11_HUMAN pregnancy specific beta-1-glycoprotein 11 289 Ig-like C2-type 2. female pregnancy extracellular region 0 Prostate(69;0.00682) 0.580153 261.618843 262.352359 76 55 KEEP --- --- --- --- PSG6 5675 broad.mit.edu 37 19 43519561 43519561 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:43519561G>A uc002ovh.1 - PSG11_uc002ouw.2_Intron|PSG10_uc002ouv.1_Intron|PSG6_uc002ovi.2_Intron|PSG6_uc010xwk.1_Intron|PSG11_uc002ovk.1_Intron|PSG11_uc002ovm.1_Intron|PSG11_uc002ovn.1_Intron|PSG11_uc002ovo.1_Intron|PSG11_uc002ovp.1_Intron SubName: Full=Putative uncharacterized protein PSG6; female pregnancy extracellular region ovary(1)|skin(1) 2 Prostate(69;0.00899) 0.77551 129.974142 133.391263 38 11 KEEP --- --- --- --- PSG6 5675 broad.mit.edu 37 19 43586642 43586642 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:43586642G>A uc002ovi.2 - PSG6_uc010xwk.1_Intron|PSG2_uc002ovr.2_Intron|PSG2_uc002ovq.3_Intron|PSG2_uc010eiq.1_Intron|PSG2_uc002ovs.3_Intron|PSG2_uc002ovt.3_Intron SubName: Full=Putative uncharacterized protein PSG6; female pregnancy extracellular region ovary(1)|skin(1) 2 Prostate(69;0.00899) 0.710526 270.32522 274.869119 81 33 KEEP --- --- --- --- PSG9 5678 broad.mit.edu 37 19 43763393 43763393 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:43763393C>T uc002owd.3 - PSG9_uc002owe.3_Intron|PSG9_uc010xwm.1_Intron|PSG9_uc002owf.3_Intron|PSG9_uc002owg.2_Intron|PSG9_uc002owh.2_Intron NM_002784 NP_002775 pregnancy specific beta-1-glycoprotein 9 female pregnancy extracellular region ovary(1)|skin(1) 2 Prostate(69;0.00682) 1 61.130612 61.130597 16 0 KEEP --- --- --- --- Unknown broad.mit.edu 37 19 43783132 43783132 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:43783132C>T PSG9 (9450 upstream) : PRG1 (70076 downstream) 1 8.377201 8.154024 2 0 KEEP --- --- --- --- CADM4 199731 broad.mit.edu 37 19 44128184 44128184 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:44128184C>T uc002oxc.1 - NM_145296 NP_660339 cell adhesion molecule 4 precursor cell adhesion integral to membrane 0 Prostate(69;0.0199) 0.444444 24.897454 24.94591 8 10 KEEP --- --- --- --- ZNF283 284349 broad.mit.edu 37 19 44352336 44352336 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:44352336C>T uc002oxr.3 + 7 1851 c.1583C>T c.(1582-1584)TCA>TTA p.S528L ZNF283_uc002oxp.3_Missense_Mutation_p.S389L NM_181845 NP_862828 Q8N7M2 ZN283_HUMAN zinc finger protein 283 528 C2H2-type 12. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding 0 Prostate(69;0.0352) 0.428571 94.14307 94.4536 30 40 KEEP --- --- --- --- ZNF229 7772 broad.mit.edu 37 19 44933334 44933334 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:44933334C>T uc002oze.1 - 6 2056 c.1622G>A c.(1621-1623)GGA>GAA p.G541E ZNF229_uc010ejk.1_Missense_Mutation_p.G195E|ZNF229_uc010ejl.1_Missense_Mutation_p.G535E NM_014518 NP_055333 Q9UJW7 ZN229_HUMAN zinc finger protein 229 541 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding skin(2)|ovary(1)|pancreas(1) 4 Prostate(69;0.0352) 0.333333 78.533551 80.44765 26 52 KEEP --- --- --- --- RELB 5971 broad.mit.edu 37 19 45525272 45525272 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:45525272C>T uc002paj.1 + NM_006509 NP_006500 reticuloendotheliosis viral oncogene homolog B nucleus protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity ovary(1) 1 Ovarian(192;0.0728)|all_neural(266;0.112) OV - Ovarian serous cystadenocarcinoma(262;0.00986) 0.666667 31.149368 31.516786 10 5 KEEP --- --- --- --- EXOC3L2 90332 broad.mit.edu 37 19 45731226 45731227 + Intron DNP CC TT TT MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:45731226_45731227CC>TT uc002pay.1 - NM_138568 NP_612635 exocyst complex component 3-like 2 ovary(1) 1 all_neural(266;0.224)|Ovarian(192;0.231) OV - Ovarian serous cystadenocarcinoma(262;0.00883) 0.392857 34.819048 35.100469 11 17 KEEP --- --- --- --- ERCC2 2068 broad.mit.edu 37 19 45854979 45854979 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:45854979C>T uc002pbj.2 - 23 2238 c.2191G>A c.(2191-2193)GAG>AAG p.E731K ERCC2_uc002pbh.2_Missense_Mutation_p.E294K|ERCC2_uc002pbi.2_Missense_Mutation_p.E424K|ERCC2_uc010ejz.2_Missense_Mutation_p.E653K NM_000400 NP_000391 P18074 ERCC2_HUMAN excision repair cross-complementing rodent 731 cell cycle checkpoint|chromosome segregation|hair cell differentiation|induction of apoptosis|interspecies interaction between organisms|mRNA capping|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA incision|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein phosphorylation|response to oxidative stress|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|UV protection|viral reproduction cytoplasm|holo TFIIH complex|MMXD complex 5'-3' DNA helicase activity|ATP binding|ATP-dependent DNA helicase activity|DNA binding|iron-sulfur cluster binding|metal ion binding|protein C-terminus binding|protein N-terminus binding lung(2)|pancreas(1) 3 Ovarian(192;0.0728)|all_neural(266;0.112) OV - Ovarian serous cystadenocarcinoma(262;0.0226) 447 Mis|N|F|S skin basal cell|skin squamous cell|melanoma Direct_reversal_of_damage|NER Xeroderma_Pigmentosum 0.356164 75.649408 76.970912 26 47 KEEP --- --- --- --- RSPH6A 81492 broad.mit.edu 37 19 46314036 46314036 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:46314036G>A uc002pdm.2 - 2 856 c.713C>T c.(712-714)TCT>TTT p.S238F RSPH6A_uc002pdl.2_5'UTR NM_030785 NP_110412 Q9H0K4 RSH6A_HUMAN radial spokehead-like 1 238 intracellular ovary(1)|central_nervous_system(1) 2 0.384615 31.345281 31.648268 10 16 KEEP --- --- --- --- HIF3A 64344 broad.mit.edu 37 19 46842963 46842963 + 3'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:46842963G>A uc002peh.2 + 15 HIF3A_uc002pek.2_3'UTR|HIF3A_uc010xxy.1_3'UTR|HIF3A_uc002pel.2_3'UTR NM_152795 NP_690008 hypoxia inducible factor 3, alpha subunit regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus DNA binding|signal transducer activity upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1) 3 Ovarian(192;0.00965)|all_neural(266;0.0887) OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136) 0.294118 14.772702 15.414981 5 12 KEEP --- --- --- --- SLC1A5 6510 broad.mit.edu 37 19 47280372 47280372 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:47280372G>A uc002pfs.2 - SLC1A5_uc010xyh.1_Intron|SLC1A5_uc002pfq.2_Intron|SLC1A5_uc002pfr.2_Intron NM_005628 NP_005619 solute carrier family 1 member 5 isoform 1 cellular nitrogen compound metabolic process integral to plasma membrane|melanosome|membrane fraction neutral amino acid transmembrane transporter activity|protein binding|receptor activity|sodium:dicarboxylate symporter activity 0 all_epithelial(76;0.00314)|Ovarian(192;0.0798)|all_neural(266;0.107) OV - Ovarian serous cystadenocarcinoma(262;0.000338)|all cancers(93;0.000882)|Epithelial(262;0.0211)|GBM - Glioblastoma multiforme(486;0.0341) L-Asparagine(DB00174)|L-Glutamine(DB00130) 0.428571 39.595893 39.720457 12 16 KEEP --- --- --- --- ZC3H4 23211 broad.mit.edu 37 19 47585313 47585313 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:47585313G>A uc002pga.3 - ZC3H4_uc002pgb.1_Intron NM_015168 NP_055983 zinc finger CCCH-type containing 4 nucleic acid binding|zinc ion binding skin(4)|ovary(2) 6 all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889) OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372) 0.333333 8.821785 9.043298 3 6 KEEP --- --- --- --- CABP5 56344 broad.mit.edu 37 19 48533793 48533793 + 3'UTR SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:48533793T>C uc002phu.1 - 6 NM_019855 NP_062829 calcium binding protein 5 signal transduction cytoplasm calcium ion binding skin(1) 1 all_cancers(25;1.86e-08)|all_lung(116;1.14e-06)|all_epithelial(76;1.16e-06)|Lung NSC(112;2.54e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203) OV - Ovarian serous cystadenocarcinoma(262;4.09e-05)|all cancers(93;0.000322)|Epithelial(262;0.01)|GBM - Glioblastoma multiforme(486;0.058) 0.507463 119.448039 119.451257 34 33 KEEP --- --- --- --- CGB 1082 broad.mit.edu 37 19 49553756 49553756 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:49553756C>T uc010yad.1 - CGB8_uc002pma.2_5'Flank|CGB8_uc002pmb.3_5'Flank|CGB8_uc002pmc.2_Intron NM_033183 NP_149439 chorionic gonadotropin, beta polypeptide 8 apoptosis|cell-cell signaling|cellular nitrogen compound metabolic process|female gamete generation|hormone biosynthetic process|peptide hormone processing|signal transduction extracellular region|soluble fraction hormone activity 0 all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261) all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427) Choriogonadotropin alfa(DB00097) 0.555556 29.445254 29.492948 10 8 KEEP --- --- --- --- CGB7 94027 broad.mit.edu 37 19 49557595 49557595 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:49557595G>A uc002pmd.2 - 3 816 c.451C>T c.(451-453)CCA>TCA p.P151S CGB_uc010yad.1_Intron|CGB8_uc002pmc.2_Intron|CGB7_uc002pme.2_Missense_Mutation_p.P151S NM_033142 NP_149133 P01233 CGHB_HUMAN chorionic gonadotropin, beta polypeptide 7 151 apoptosis|cell-cell signaling|cellular nitrogen compound metabolic process|female gamete generation|hormone biosynthetic process|peptide hormone processing|signal transduction extracellular region|soluble fraction hormone activity 0 all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261) all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427) Choriogonadotropin alfa(DB00097) 0.351852 56.609675 57.654633 19 35 KEEP --- --- --- --- PPFIA3 8541 broad.mit.edu 37 19 49642991 49642991 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:49642991C>T uc002pmr.2 + 17 2475 c.2143C>T c.(2143-2145)CCA>TCA p.P715S PPFIA3_uc010yai.1_RNA|PPFIA3_uc010yaj.1_RNA|PPFIA3_uc002pms.2_Missense_Mutation_p.P583S NM_003660 NP_003651 O75145 LIPA3_HUMAN PTPRF interacting protein alpha 3 715 cell surface|cytoplasm protein binding lung(1) 1 all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392) all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677) 0.421053 42.349074 42.563886 16 22 KEEP --- --- --- --- ALDH16A1 126133 broad.mit.edu 37 19 49973471 49973471 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:49973471C>T uc002pnt.2 + ALDH16A1_uc010yar.1_Intron|ALDH16A1_uc010yas.1_Intron|ALDH16A1_uc010yat.1_Intron NM_153329 NP_699160 aldehyde dehydrogenase 16 family, member A1 oxidoreductase activity|protein binding skin(1) 1 all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15) OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251) 0.75 58.058525 59.420664 18 6 KEEP --- --- --- --- SCAF1 58506 broad.mit.edu 37 19 50149268 50149268 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:50149268C>T uc002poq.2 + NM_021228 NP_067051 SR-related CTD-associated factor 1 mRNA processing|RNA splicing nucleus RNA binding 0 all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231) OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204) 0.571429 13.901057 13.932199 4 3 KEEP --- --- --- --- Unknown broad.mit.edu 37 19 50223413 50223413 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:50223413C>T CPT1C (6425 upstream) : TSKS (19599 downstream) 0.454545 8.097069 8.124839 5 6 KEEP --- --- --- --- TSKS 60385 broad.mit.edu 37 19 50244997 50244997 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:50244997C>T uc002ppm.2 - NM_021733 NP_068379 testis-specific kinase substrate protein binding large_intestine(1)|skin(1) 2 all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728) OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145) 0.444444 24.797415 24.845877 8 10 KEEP --- --- --- --- MED25 81857 broad.mit.edu 37 19 50333488 50333488 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:50333488C>T uc002ppw.1 + MED25_uc010ybe.1_Intron|MED25_uc002ppx.1_Intron NM_030973 NP_112235 mediator complex subunit 25 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleoplasm ovary(1) 1 all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728) OV - Ovarian serous cystadenocarcinoma(262;0.00822)|GBM - Glioblastoma multiforme(134;0.0122) GBM(51;894 1657 37868) 0.333333 10.12232 10.343565 3 6 KEEP --- --- --- --- MED25 81857 broad.mit.edu 37 19 50339558 50339558 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:50339558C>T uc002ppw.1 + 17 2094 c.2041C>T c.(2041-2043)CCG>TCG p.P681S MED25_uc010ybe.1_Missense_Mutation_p.P468S|MED25_uc002ppx.1_Missense_Mutation_p.P462S NM_030973 NP_112235 Q71SY5 MED25_HUMAN mediator complex subunit 25 681 Interaction with RARA.|Pro-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleoplasm ovary(1) 1 all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728) OV - Ovarian serous cystadenocarcinoma(262;0.00822)|GBM - Glioblastoma multiforme(134;0.0122) GBM(51;894 1657 37868) 0.714286 34.556182 35.133638 10 4 KEEP --- --- --- --- LIM2 3982 broad.mit.edu 37 19 51890508 51890509 + Intron DNP GG AA AA MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:51890508_51890509GG>AA uc002pwm.2 - LIM2_uc002pwl.2_Nonsense_Mutation_p.Q64* NM_001161748 NP_001155220 lens intrinsic membrane protein 2, 19kDa isoform cell-cell junction assembly cell junction|integral to membrane structural constituent of eye lens 0 all_neural(266;0.0529) GBM - Glioblastoma multiforme(134;0.000214)|OV - Ovarian serous cystadenocarcinoma(262;0.00985) 0.322581 51.97391 53.709254 20 42 KEEP --- --- --- --- SIGLEC10 89790 broad.mit.edu 37 19 51918614 51918614 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:51918614C>T uc002pwo.2 - 7 1767 c.1151G>A c.(1150-1152)AGC>AAC p.S384N SIGLEC10_uc002pwp.2_Missense_Mutation_p.S326N|SIGLEC10_uc002pwq.2_Missense_Mutation_p.S326N|SIGLEC10_uc002pwr.2_Missense_Mutation_p.S384N|SIGLEC10_uc010ycy.1_Missense_Mutation_p.S294N|SIGLEC10_uc010ycz.1_Missense_Mutation_p.S336N|SIGLEC10_uc010eow.2_Missense_Mutation_p.S196N|SIGLEC10_uc002pws.1_Missense_Mutation_p.S220N NM_033130 NP_149121 Q96LC7 SIG10_HUMAN sialic acid binding Ig-like lectin 10 precursor 384 Ig-like C2-type 3.|Extracellular (Potential). cell adhesion extracellular region|integral to membrane|plasma membrane sugar binding skin(1) 1 all_neural(266;0.0199) GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101) 0.631579 81.328406 81.920373 24 14 KEEP --- --- --- --- SIGLEC8 27181 broad.mit.edu 37 19 51961256 51961256 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:51961256C>T uc002pwt.2 - 1 453 c.386G>A c.(385-387)GGA>GAA p.G129E SIGLEC8_uc010yda.1_Missense_Mutation_p.G129E|SIGLEC8_uc002pwu.2_RNA|SIGLEC8_uc010eox.2_Missense_Mutation_p.G129E NM_014442 NP_055257 Q9NYZ4 SIGL8_HUMAN sialic acid binding Ig-like lectin 8 precursor 129 Extracellular (Potential). cell adhesion integral to membrane sugar binding|transmembrane receptor activity ovary(2)|kidney(1)|central_nervous_system(1)|skin(1) 5 all_neural(266;0.0199) GBM - Glioblastoma multiforme(134;0.000627)|OV - Ovarian serous cystadenocarcinoma(262;0.00979) 0.699187 288.759418 293.106286 86 37 KEEP --- --- --- --- VN1R4 317703 broad.mit.edu 37 19 53770214 53770214 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:53770214G>A uc010ydu.1 - 1 705 c.705C>T c.(703-705)ATC>ATT p.I235I NM_173857 NP_776256 Q7Z5H5 VN1R4_HUMAN vomeronasal 1 receptor 4 235 Helical; Name=6; (Potential). response to pheromone actin cytoskeleton|cytoplasm|integral to membrane|plasma membrane pheromone receptor activity ovary(2) 2 GBM - Glioblastoma multiforme(134;0.00294) HNSCC(26;0.072) 0.478261 36.223722 36.233195 11 12 KEEP --- --- --- --- ZNF331 55422 broad.mit.edu 37 19 54072529 54072529 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:54072529C>T uc002qbx.1 + ZNF331_uc002qby.1_Intron|ZNF331_uc002qbz.1_Intron|ZNF331_uc002qca.1_Intron|ZNF331_uc010eqr.1_Intron|ZNF331_uc002qcb.1_Intron|ZNF331_uc002qcc.1_Intron|ZNF331_uc002qcd.1_Intron NM_018555 NP_061025 zinc finger protein 331 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding skin(3)|upper_aerodigestive_tract(1)|ovary(1)|lung(1) 6 GBM - Glioblastoma multiforme(134;0.00555) 85 T ? follicular thyroid adenoma 0.395833 58.914914 59.370759 19 29 KEEP --- --- --- --- MYADM 91663 broad.mit.edu 37 19 54377841 54377841 + 3'UTR SNP T A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:54377841T>A uc002qcl.2 + 3 MYADM_uc002qcm.2_3'UTR|MYADM_uc002qcn.2_3'UTR|MYADM_uc002qco.2_3'UTR|MYADM_uc002qcp.2_3'UTR NM_001020820 NP_001018656 myeloid-associated differentiation marker integral to membrane ovary(1) 1 Ovarian(34;0.19) GBM - Glioblastoma multiforme(134;0.0488) 0.333333 14.069888 14.438953 5 10 KEEP --- --- --- --- LAIR1 3903 broad.mit.edu 37 19 54868176 54868176 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:54868176C>T uc002qfk.1 - 6 817 c.507G>A c.(505-507)GGG>GGA p.G169G LAIR1_uc002qfl.1_Silent_p.G152G|LAIR1_uc002qfm.1_Silent_p.G168G|LAIR1_uc002qfn.1_Silent_p.G151G|LAIR1_uc010yex.1_Silent_p.G162G|LAIR1_uc002qfo.2_Silent_p.G151G NM_002287 NP_002278 Q6GTX8 LAIR1_HUMAN leukocyte-associated immunoglobulin-like 169 Helical; (Potential). integral to membrane|plasma membrane protein binding|receptor activity ovary(4) 4 Ovarian(34;0.19) GBM - Glioblastoma multiforme(193;0.0573) 0.522727 78.326668 78.346377 23 21 KEEP --- --- --- --- LILRA1 11024 broad.mit.edu 37 19 55106122 55106122 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:55106122C>T uc002qgh.1 + LILRA2_uc010yfg.1_Intron|LILRA1_uc010yfh.1_Intron NM_006863 NP_006854 leukocyte immunoglobulin-like receptor, cell surface receptor linked signaling pathway|defense response|regulation of immune response integral to membrane|plasma membrane antigen binding|transmembrane receptor activity skin(2)|ovary(1) 3 GBM - Glioblastoma multiforme(193;0.0348) 0.283333 49.048959 51.578928 17 43 KEEP --- --- --- --- LILRB1 10859 broad.mit.edu 37 19 55142469 55142469 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:55142469C>T uc002qgj.2 + LILRB1_uc010erp.1_Intron|LILRB1_uc002qgl.2_Intron|LILRB1_uc002qgk.2_Intron|LILRB1_uc002qgm.2_Intron|LILRB1_uc010erq.2_5'Flank|LILRB1_uc010err.2_5'Flank NM_006669 NP_006660 leukocyte immunoglobulin-like receptor, regulation of immune response|response to virus integral to membrane|plasma membrane protein phosphatase 1 binding|receptor activity large_intestine(1)|ovary(1)|skin(1) 3 GBM - Glioblastoma multiforme(193;0.0188) HNSCC(37;0.09) 0.52 86.851852 86.869213 26 24 KEEP --- --- --- --- LILRB1 10859 broad.mit.edu 37 19 55144870 55144870 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:55144870G>A uc002qgj.2 + LILRB1_uc010erp.1_Intron|LILRB1_uc002qgl.2_Intron|LILRB1_uc002qgk.2_Intron|LILRB1_uc002qgm.2_Intron|LILRB1_uc010erq.2_Intron|LILRB1_uc010err.2_Intron NM_006669 NP_006660 leukocyte immunoglobulin-like receptor, regulation of immune response|response to virus integral to membrane|plasma membrane protein phosphatase 1 binding|receptor activity large_intestine(1)|ovary(1)|skin(1) 3 GBM - Glioblastoma multiforme(193;0.0188) HNSCC(37;0.09) 0.684211 45.482838 46.057402 13 6 KEEP --- --- --- --- LILRB4 11006 broad.mit.edu 37 19 55177825 55177825 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:55177825C>T uc002qgp.2 + LILRB4_uc002qgq.2_Intron|LILRB4_uc002qgr.2_Intron|LILRB4_uc010ert.2_Intron|LILRB4_uc010eru.2_Intron NM_006847 NP_006838 leukocyte immunoglobulin-like receptor, integral to membrane|plasma membrane antigen binding|receptor activity ovary(3) 3 GBM - Glioblastoma multiforme(193;0.035) 0.3 35.884192 37.313747 12 28 KEEP --- --- --- --- KIR2DS4 3809 broad.mit.edu 37 19 55349256 55349256 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:55349256G>A uc002qhm.1 + 3 342 c.296G>A c.(295-297)AGA>AAA p.R99K KIR2DS4_uc010yfj.1_Missense_Mutation_p.R92K|KIR2DS4_uc010yfk.1_RNA|KIR3DL1_uc002qhl.3_Intron|KIR2DS4_uc010esg.1_Missense_Mutation_p.R99K|KIR2DS4_uc002qhn.1_Missense_Mutation_p.R46K NM_012314 NP_036446 P43632 KI2S4_HUMAN killer cell immunoglobulin-like receptor, two 99 Extracellular (Potential).|Ig-like C2-type 1. integral to plasma membrane receptor activity 0 GBM - Glioblastoma multiforme(193;0.0192) 0.990099 792.729811 796.018481 200 2 KEEP --- --- --- --- KIR3DL1 3811 broad.mit.edu 37 19 55378274 55378274 + 3'UTR SNP G A A rs57766694 MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:55378274G>A uc002qhl.3 + 9 KIR3DL2_uc010esh.2_3'UTR|KIR3DL2_uc002qho.3_3'UTR SubName: Full=KIR3DS1; immune response|regulation of immune response integral to plasma membrane HLA-B specific inhibitory MHC class I receptor activity ovary(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|skin(1) 5 GBM - Glioblastoma multiforme(193;0.0192) 0.482759 45.647989 45.655522 14 15 KEEP --- --- --- --- KIR3DL1 3811 broad.mit.edu 37 19 55378295 55378295 + 3'UTR SNP G A A rs58983092 by1000genomes MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:55378295G>A uc002qhl.3 + 9 KIR3DL2_uc010esh.2_3'UTR|KIR3DL2_uc002qho.3_3'UTR SubName: Full=KIR3DS1; immune response|regulation of immune response integral to plasma membrane HLA-B specific inhibitory MHC class I receptor activity ovary(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|skin(1) 5 GBM - Glioblastoma multiforme(193;0.0192) 0.428571 26.972976 27.066057 9 12 KEEP --- --- --- --- NCR1 9437 broad.mit.edu 37 19 55423605 55423605 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:55423605C>T uc002qib.2 + NCR1_uc002qic.2_Intron|NCR1_uc002qie.2_Intron|NCR1_uc002qid.2_Intron|NCR1_uc002qif.2_Intron|NCR1_uc010esj.2_Intron NM_004829 NP_004820 natural cytotoxicity triggering receptor 1 cellular defense response|natural killer cell activation|regulation of natural killer cell mediated cytotoxicity integral to plasma membrane|SWI/SNF complex receptor activity|receptor signaling protein activity large_intestine(1)|ovary(1) 2 GBM - Glioblastoma multiforme(193;0.0449) 0.319588 91.898467 94.699728 31 66 KEEP --- --- --- --- NLRP9 338321 broad.mit.edu 37 19 56223763 56223763 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:56223763G>A uc002qly.2 - NM_176820 NP_789790 NLR family, pyrin domain containing 9 cytoplasm ATP binding skin(4)|ovary(2)|breast(1) 7 Colorectal(82;0.000133)|Ovarian(87;0.133) GBM - Glioblastoma multiforme(193;0.123) 0.673469 114.492655 115.801461 33 16 KEEP --- --- --- --- NLRP13 126204 broad.mit.edu 37 19 56423214 56423214 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:56423214G>A uc010ygg.1 - 5 1994 c.1969C>T c.(1969-1971)CGT>TGT p.R657C NM_176810 NP_789780 Q86W25 NAL13_HUMAN NACHT, leucine rich repeat and PYD containing 657 ATP binding skin(4)|ovary(3)|pancreas(1)|lung(1) 9 Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218) GBM - Glioblastoma multiforme(193;0.0642) 0.65 226.501933 228.486978 65 35 KEEP --- --- --- --- ZSCAN5A 79149 broad.mit.edu 37 19 56736366 56736366 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:56736366C>T uc002qmq.2 - 2 216 c.50G>A c.(49-51)AGA>AAA p.R17K ZSCAN5A_uc010ygi.1_Intron|ZSCAN5A_uc002qmr.2_Missense_Mutation_p.R17K|ZSCAN5A_uc002qms.1_Missense_Mutation_p.R17K NM_024303 NP_077279 Q9BUG6 ZSA5A_HUMAN zinc finger and SCAN domain containing 5A 17 viral reproduction nucleus DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding large_intestine(1)|ovary(1)|skin(1) 3 0.634615 108.683188 109.51071 33 19 KEEP --- --- --- --- ZNF667 63934 broad.mit.edu 37 19 56973638 56973638 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:56973638G>A uc002qnd.2 - ZNF667_uc010etl.2_Intron|ZNF667_uc002qne.2_Intron|ZNF667_uc010etm.2_Intron NM_022103 NP_071386 zinc finger protein 667 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding pancreas(1) 1 Colorectal(82;0.000256)|Ovarian(87;0.243) GBM - Glioblastoma multiforme(193;0.0615) 0.691176 157.033962 159.243864 47 21 KEEP --- --- --- --- ZNF667 63934 broad.mit.edu 37 19 56973687 56973687 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:56973687G>A uc002qnd.2 - ZNF667_uc010etl.2_Intron|ZNF667_uc002qne.2_Intron|ZNF667_uc010etm.2_Intron NM_022103 NP_071386 zinc finger protein 667 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding pancreas(1) 1 Colorectal(82;0.000256)|Ovarian(87;0.243) GBM - Glioblastoma multiforme(193;0.0615) 0.275229 82.599711 87.560891 30 79 KEEP --- --- --- --- ZIM3 114026 broad.mit.edu 37 19 57646883 57646883 + Missense_Mutation SNP A C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:57646883A>C uc002qnz.1 - 5 1208 c.822T>G c.(820-822)AAT>AAG p.N274K NM_052882 NP_443114 Q96PE6 ZIM3_HUMAN zinc finger, imprinted 3 274 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding pancreas(1)|skin(1) 2 Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243) UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026) 0.663462 269.312532 271.772037 69 35 KEEP --- --- --- --- ZNF17 7565 broad.mit.edu 37 19 57931705 57931705 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:57931705C>T uc002qoo.1 + 3 1076 c.845C>T c.(844-846)GCT>GTT p.A282V ZNF547_uc002qpm.3_Intron|ZNF17_uc002qop.1_Missense_Mutation_p.A284V NM_006959 NP_008890 P17021 ZNF17_HUMAN zinc finger protein 17 282 C2H2-type 4. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding central_nervous_system(1) 1 Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157) UCEC - Uterine corpus endometrioid carcinoma (67;0.0234)|GBM - Glioblastoma multiforme(193;0.000426)|Lung(386;0.176) Melanoma(149;1637 1853 29914 42869 44988) 0.627907 90.532704 91.149962 27 16 KEEP --- --- --- --- A1BG 1 broad.mit.edu 37 19 58863703 58863703 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr19:58863703C>T uc002qsd.3 - 4 621 c.559G>A c.(559-561)GAT>AAT p.D187N NCRNA00181_uc002qse.2_Intron|A1BG_uc002qsf.1_RNA|NCRNA00181_uc002qsg.2_RNA NM_130786 NP_570602 P04217 A1BG_HUMAN alpha 1B-glycoprotein precursor 187 Ig-like V-type 2. extracellular region 0 all_cancers(17;3.04e-16)|all_epithelial(17;7.77e-12)|Lung NSC(17;3.25e-05)|Colorectal(82;5.46e-05)|all_lung(17;0.000129)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(17;0.157) UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0269) 0.258065 40.652019 43.959624 16 46 KEEP --- --- --- --- SNTG2 54221 broad.mit.edu 37 2 1241684 1241684 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:1241684C>T uc002qwq.2 + 10 872 c.744C>T c.(742-744)GCC>GCT p.A248A SNTG2_uc010ewi.2_Silent_p.A121A NM_018968 NP_061841 Q9NY99 SNTG2_HUMAN syntrophin, gamma 2 248 central nervous system development cytoplasm|cytoskeleton|sarcolemma|syntrophin complex actin binding|PDZ domain binding ovary(1)|large_intestine(1)|breast(1) 3 Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797) all_cancers(51;0.00469) all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173) 0.666667 7.451318 7.524823 2 1 KEEP --- --- --- --- ALLC 55821 broad.mit.edu 37 2 3727606 3727606 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:3727606C>T uc010ewt.2 + NM_018436 NP_060906 allantoicase isoform a allantoicase activity central_nervous_system(1) 1 Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088) all_cancers(51;0.24) OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206) HNSCC(21;0.051) 0.238095 24.928355 27.56036 10 32 KEEP --- --- --- --- ODC1 4953 broad.mit.edu 37 2 10584103 10584103 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:10584103G>A uc010exg.1 - ODC1_uc002ran.1_5'Flank|ODC1_uc002rao.1_Intron|ODC1_uc010yjd.1_Intron NM_002539 NP_002530 ornithine decarboxylase 1 polyamine biosynthetic process|regulation of cellular amino acid metabolic process|response to virus cytosol ornithine decarboxylase activity|protein binding ovary(1) 1 all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155) Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.161) Pyridoxal Phosphate(DB00114)|Spermine(DB00127) 0.673469 99.117249 100.404969 33 16 KEEP --- --- --- --- ROCK2 9475 broad.mit.edu 37 2 11354553 11354553 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:11354553C>T uc002rbd.1 - 17 2422 c.1973G>A c.(1972-1974)GGC>GAC p.G658D NM_004850 NP_004841 O75116 ROCK2_HUMAN Rho-associated, coiled-coil containing protein 658 Potential.|Interaction with PPP1R12A. axon guidance|cytokinesis|intracellular signal transduction cytosol|plasma membrane ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|structural molecule activity stomach(2)|skin(2) 4 all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155) Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162) p.G658D(NCIH1975-Tumor) 587 0.078947 0.293474 7.174972 3 35 KEEP --- --- --- --- WDR35 57539 broad.mit.edu 37 2 20137920 20137920 + Intron SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:20137920T>C uc002rdi.2 - WDR35_uc002rdj.2_Intron|WDR35_uc010ext.2_Intron|WDR35_uc002rdh.2_Intron|WDR35_uc002rdk.3_Intron NM_001006657 NP_001006658 WD repeat domain 35 isoform 1 ovary(1) 1 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) 0.545455 43.202708 43.242326 12 10 KEEP --- --- --- --- CENPO 79172 broad.mit.edu 37 2 25037528 25037528 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:25037528G>A uc002rfo.1 + CENPO_uc002rfn.2_Intron|CENPO_uc002rfp.1_Intron|CENPO_uc002rfq.1_Intron NM_024322 NP_077298 centromere protein O cell division|CenH3-containing nucleosome assembly at centromere|chromosome segregation|mitotic prometaphase condensed chromosome kinetochore|cytosol|nucleoplasm protein binding ovary(1) 1 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203) 0.75 20.753796 21.208171 6 2 KEEP --- --- --- --- ADCY3 109 broad.mit.edu 37 2 25061508 25061508 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:25061508G>A uc002rfs.3 - ADCY3_uc002rfr.3_Intron|ADCY3_uc010ykm.1_Intron NM_004036 NP_004027 adenylate cyclase 3 activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|sensory perception of smell|synaptic transmission|transmembrane transport|water transport cytoplasm|integral to plasma membrane ATP binding|calmodulin binding|metal ion binding breast(3)|ovary(1) 4 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203) 0.514563 172.976139 172.995083 53 50 KEEP --- --- --- --- DNMT3A 1788 broad.mit.edu 37 2 25471190 25471190 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:25471190G>A uc002rgc.2 - DNMT3A_uc002rgd.2_Intron|DNMT3A_uc010eyi.2_Intron|DNMT3A_uc002rgb.2_Intron NM_022552 NP_072046 DNA cytosine methyltransferase 3 alpha isoform regulation of gene expression by genetic imprinting cytoplasm|euchromatin|nuclear matrix DNA (cytosine-5-)-methyltransferase activity|DNA binding|metal ion binding|protein binding haematopoietic_and_lymphoid_tissue(133)|lung(4)|ovary(3) 140 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) Mis|F|N|S AML 0.416667 16.873058 16.9458 5 7 KEEP --- --- --- --- CENPA 1058 broad.mit.edu 37 2 27016121 27016121 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:27016121C>T uc002rhr.2 + 4 580 c.397C>T c.(397-399)CGG>TGG p.R133W CENPA_uc002rht.2_RNA|CENPA_uc002rhs.2_Missense_Mutation_p.R107W NM_001809 NP_001800 P49450 CENPA_HUMAN centromere protein A isoform a 133 H3-like. CenH3-containing nucleosome assembly at centromere|establishment of mitotic spindle orientation|interspecies interaction between organisms|kinetochore assembly|mitotic prometaphase|protein localization to chromosome, centromeric region condensed nuclear chromosome kinetochore|cytosol|nucleoplasm|nucleosome chromatin binding|DNA binding|protein binding 0 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) Pancreas(28;769 878 30250 30578 41330) 0.516304 321.740637 321.783888 95 89 KEEP --- --- --- --- DPYSL5 56896 broad.mit.edu 37 2 27163108 27163108 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:27163108C>T uc002rhu.3 + DPYSL5_uc002rhv.3_Intron NM_020134 NP_064519 dihydropyrimidinase-like 5 axon guidance|pyrimidine base catabolic process|signal transduction cytosol hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides ovary(2) 2 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) 0.357143 42.411575 43.167264 15 27 KEEP --- --- --- --- PREB 10113 broad.mit.edu 37 2 27355433 27355433 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:27355433G>A uc002rix.1 - PREB_uc002riy.1_Intron|PREB_uc002riz.1_Intron|PREB_uc002rja.1_Intron NM_013388 NP_037520 prolactin regulatory element binding protein COPII vesicle coating|post-translational protein modification|protein N-linked glycosylation via asparagine|protein transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent endoplasmic reticulum membrane|integral to membrane|nucleus DNA binding|guanyl-nucleotide exchange factor activity|protein binding ovary(1) 1 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) 0.590909 41.471229 41.628761 13 9 KEEP --- --- --- --- TRIM54 57159 broad.mit.edu 37 2 27505510 27505510 + 5'Flank SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:27505510G>A uc002rjo.2 + TRIM54_uc002rjn.2_5'Flank NM_187841 NP_912730 ring finger protein 30 isoform 2 cell differentiation|microtubule-based process|multicellular organismal development|negative regulation of microtubule depolymerization microtubule|sarcomere signal transducer activity|zinc ion binding ovary(1) 1 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) 0.542373 105.209777 105.302905 32 27 KEEP --- --- --- --- TRIM54 57159 broad.mit.edu 37 2 27529003 27529003 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:27529003G>A uc002rjo.2 + TRIM54_uc002rjn.2_Intron NM_187841 NP_912730 ring finger protein 30 isoform 2 cell differentiation|microtubule-based process|multicellular organismal development|negative regulation of microtubule depolymerization microtubule|sarcomere signal transducer activity|zinc ion binding ovary(1) 1 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) 0.27907 31.984042 33.870469 12 31 KEEP --- --- --- --- IFT172 26160 broad.mit.edu 37 2 27706915 27706915 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:27706915G>A uc002rku.2 - IFT172_uc002rkw.2_Intron|IFT172_uc010yls.1_Intron|IFT172_uc010ezc.2_Intron|IFT172_uc002rkv.2_Intron|IFT172_uc010ylt.1_3'UTR NM_015662 NP_056477 selective LIM binding factor homolog cilium assembly cilium binding large_intestine(1)|ovary(1) 2 Acute lymphoblastic leukemia(172;0.155) 0.5 15.774352 15.774352 5 5 KEEP --- --- --- --- GCKR 2646 broad.mit.edu 37 2 27728830 27728831 + Intron DNP CC TT TT MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:27728830_27728831CC>TT uc002rky.2 + GCKR_uc010ezd.2_Intron|GCKR_uc010ylu.1_Intron NM_001486 NP_001477 glucokinase regulatory protein carbohydrate metabolic process|glucose transport|negative regulation of glucokinase activity|positive regulation of gene expression|protein import into nucleus, translocation|regulation of glucose transport|response to fructose stimulus|transmembrane transport|triglyceride homeostasis|urate metabolic process cytosol|nucleoplasm fructose-6-phosphate binding|protein binding ovary(2) 2 Acute lymphoblastic leukemia(172;0.155) 0.62963 60.48213 60.880712 17 10 KEEP --- --- --- --- PLB1 151056 broad.mit.edu 37 2 28761986 28761986 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:28761986C>T uc002rmb.1 + 11 639 c.639C>T c.(637-639)AAC>AAT p.N213N PLB1_uc010ezj.1_Silent_p.N224N NM_153021 NP_694566 Q6P1J6 PLB1_HUMAN phospholipase B1 precursor 213 4 X 308-326 AA approximate repeats.|Extracellular (Potential).|1. lipid catabolic process|retinoid metabolic process|steroid metabolic process apical plasma membrane|integral to membrane lysophospholipase activity|phospholipase A2 activity|retinyl-palmitate esterase activity ovary(4)|large_intestine(2)|skin(2)|breast(1) 9 Acute lymphoblastic leukemia(172;0.155) 0.735849 133.047501 135.711827 39 14 KEEP --- --- --- --- GALNT14 79623 broad.mit.edu 37 2 31133883 31133883 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:31133883G>A uc002rnr.2 - 15 2162 c.1543C>T c.(1543-1545)CAC>TAC p.H515Y GALNT14_uc002rnq.2_Missense_Mutation_p.H495Y|GALNT14_uc002rns.2_Missense_Mutation_p.H520Y|GALNT14_uc010ymr.1_Missense_Mutation_p.H480Y NM_024572 NP_078848 Q96FL9 GLT14_HUMAN N-acetylgalactosaminyltransferase 14 515 Lumenal (Potential).|Ricin B-type lectin. Golgi membrane|integral to membrane polypeptide N-acetylgalactosaminyltransferase activity|sugar binding upper_aerodigestive_tract(2)|skin(1) 3 Acute lymphoblastic leukemia(172;0.155) 0.547945 138.306503 138.452326 40 33 KEEP --- --- --- --- XDH 7498 broad.mit.edu 37 2 31624230 31624230 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:31624230C>T uc002rnv.1 - NM_000379 NP_000370 xanthine dehydrogenase purine nucleotide catabolic process|xanthine catabolic process cytosol|extracellular region|peroxisome 2 iron, 2 sulfur cluster binding|electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|molybdopterin cofactor binding|protein homodimerization activity|xanthine dehydrogenase activity|xanthine oxidase activity skin(4)|breast(2)|ovary(1)|central_nervous_system(1) 8 Acute lymphoblastic leukemia(172;0.155) Allopurinol(DB00437)|Carvedilol(DB01136)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Desflurane(DB01189)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|NADH(DB00157)|Nitrofurazone(DB00336)|Papaverine(DB01113)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Rasburicase(DB00049)|Spermine(DB00127)|Trifluoperazine(DB00831)|Vitamin E(DB00163) Colon(66;682 1445 30109 40147) 0.25 11.092193 12.00117 4 12 KEEP --- --- --- --- SLC30A6 55676 broad.mit.edu 37 2 32390904 32390905 + 5'Flank DNP CC TT TT MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:32390904_32390905CC>TT uc002roe.1 + SLC30A6_uc002rof.1_5'Flank|SLC30A6_uc010ymw.1_5'Flank|SLC30A6_uc010ezr.1_5'Flank|SLC30A6_uc002rog.1_5'Flank|SLC30A6_uc010ezs.1_5'Flank|SLC30A6_uc002roh.1_5'Flank NM_017964 NP_060434 solute carrier family 30 (zinc transporter), Golgi membrane|integral to membrane zinc ion transmembrane transporter activity 0 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208) 0.16 8.383194 11.135487 4 21 KEEP --- --- --- --- LTBP1 4052 broad.mit.edu 37 2 33500890 33500890 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:33500890G>A uc002ros.2 + 18 2895 c.2895G>A c.(2893-2895)CCG>CCA p.P965P LTBP1_uc002rot.2_Silent_p.P639P|LTBP1_uc002rou.2_Silent_p.P638P|LTBP1_uc002rov.2_Silent_p.P585P|LTBP1_uc010ymz.1_Silent_p.P638P|LTBP1_uc010yna.1_Silent_p.P585P NM_206943 NP_996826 Q14766 LTBP1_HUMAN latent transforming growth factor beta binding 964 EGF-like 6; calcium-binding (Potential). negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta proteinaceous extracellular matrix calcium ion binding|growth factor binding|transforming growth factor beta receptor activity ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1) 8 all_hematologic(175;0.115) Medulloblastoma(90;0.215) 0.560345 224.490518 224.858639 65 51 KEEP --- --- --- --- RASGRP3 25780 broad.mit.edu 37 2 33787890 33787890 + 3'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:33787890G>A uc002rox.2 + 19 RASGRP3_uc010ync.1_3'UTR|RASGRP3_uc002roy.2_3'UTR NM_170672 NP_733772 RAS guanyl releasing protein 3 (calcium and MAPKKK cascade|small GTPase mediated signal transduction integral to plasma membrane|intracellular calcium ion binding|diacylglycerol binding|guanyl-nucleotide exchange factor activity|protein binding|Rap GTPase activator activity|signal transducer activity lung(3)|ovary(1)|pancreas(1) 5 all_hematologic(175;0.115) 0.5 23.424858 23.424858 7 7 KEEP --- --- --- --- CEBPZ 10153 broad.mit.edu 37 2 37447621 37447621 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:37447621G>A uc002rpz.2 - NM_005760 NP_005751 CCAAT/enhancer binding protein zeta regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter nucleus DNA binding pancreas(1) 1 all_hematologic(82;0.21) 0.35 20.518343 20.91567 7 13 KEEP --- --- --- --- SFRS7 6432 broad.mit.edu 37 2 38974026 38974026 + Intron SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:38974026T>C uc002rqz.2 - SFRS7_uc002rra.2_Intron|SFRS7_uc010ynp.1_Intron NM_001031684 NP_001026854 splicing factor, arginine/serine-rich 7 mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription nucleoplasm nucleotide binding|protein binding|RNA binding|zinc ion binding 0 all_hematologic(82;0.248) 0.8 15.511636 15.921987 4 1 KEEP --- --- --- --- SOS1 6654 broad.mit.edu 37 2 39213205 39213205 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:39213205G>A uc002rrk.3 - 23 3803 c.3762C>T c.(3760-3762)TCC>TCT p.S1254S SOS1_uc002rrj.3_Silent_p.S853S NM_005633 NP_005624 Q07889 SOS1_HUMAN son of sevenless homolog 1 1254 apoptosis|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction cytosol DNA binding|protein binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity ovary(4)|breast(3)|lung(2)|central_nervous_system(1) 10 all_hematologic(82;0.21) 444 Noonan_syndrome 0.352113 79.954168 81.323537 25 46 KEEP --- --- --- --- SLC8A1 6546 broad.mit.edu 37 2 40366898 40366898 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:40366898C>T uc002rrx.2 - uc002rrw.2_Intron|SLC8A1_uc002rry.2_Intron|SLC8A1_uc002rrz.2_Intron|SLC8A1_uc002rsa.2_Intron|SLC8A1_uc002rsd.3_Intron NM_021097 NP_066920 solute carrier family 8 (sodium/calcium cell communication|muscle contraction|platelet activation integral to plasma membrane calcium:sodium antiporter activity|calmodulin binding|heat shock protein binding ovary(1)|kidney(1)|central_nervous_system(1)|skin(1) 4 Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159) 0.644444 93.484343 94.311657 29 16 KEEP --- --- --- --- SLC3A1 6519 broad.mit.edu 37 2 44507825 44507825 + Intron SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:44507825T>C uc002ruc.3 + SLC3A1_uc002rty.2_Intron|SLC3A1_uc002rtz.2_Intron|SLC3A1_uc002rua.2_Intron|SLC3A1_uc002rub.2_Intron NM_000341 NP_000332 solute carrier family 3, member 1 carbohydrate metabolic process|cellular amino acid metabolic process|ion transport integral to plasma membrane|membrane fraction basic amino acid transmembrane transporter activity|catalytic activity|cation binding|L-cystine transmembrane transporter activity 0 all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17) L-Cystine(DB00138) 0.5 22.350511 22.350511 6 6 KEEP --- --- --- --- CRIPT 9419 broad.mit.edu 37 2 46851196 46851196 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:46851196C>T uc002rve.2 + NM_014171 NP_054890 postsynaptic protein CRIPT cell junction|cytoplasm|dendritic spine 0 all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175) LUSC - Lung squamous cell carcinoma(58;0.114) 0.285714 6.347349 6.635614 2 5 KEEP --- --- --- --- NRXN1 9378 broad.mit.edu 37 2 50723209 50723209 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:50723209C>T uc010fbq.2 - 15 4501 c.3024G>A c.(3022-3024)TTG>TTA p.L1008L NRXN1_uc002rxb.3_Silent_p.L640L|NRXN1_uc002rxe.3_Silent_p.L968L|NRXN1_uc002rxc.1_RNA NM_001135659 NP_001129131 P58400 NRX1B_HUMAN neurexin 1 isoform alpha2 precursor Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment angiogenesis|neuron cell-cell adhesion|neuronal signal transduction cell surface|endocytic vesicle|integral to membrane|presynaptic membrane cell adhesion molecule binding|receptor binding ovary(2) 2 all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192) Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116) 0.9 32.248522 33.780928 9 1 KEEP --- --- --- --- NRXN1 9378 broad.mit.edu 37 2 51255081 51255081 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:51255081C>T uc010fbq.2 - 2 1808 c.331G>A c.(331-333)GAC>AAC p.D111N NRXN1_uc002rxe.3_Missense_Mutation_p.D111N|NRXN1_uc002rxd.1_Missense_Mutation_p.D111N NM_001135659 NP_001129131 P58400 NRX1B_HUMAN neurexin 1 isoform alpha2 precursor 174 Extracellular (Potential).|Laminin G-like. angiogenesis|neuron cell-cell adhesion|neuronal signal transduction cell surface|endocytic vesicle|integral to membrane|presynaptic membrane cell adhesion molecule binding|receptor binding ovary(2) 2 all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192) Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116) 0.611111 37.327537 37.52204 11 7 KEEP --- --- --- --- Unknown broad.mit.edu 37 2 54278634 54278634 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:54278634C>T PSME4 (80657 upstream) : ACYP2 (63776 downstream) 0.545455 22.051174 22.070933 6 5 KEEP --- --- --- --- TMEM17 200728 broad.mit.edu 37 2 62728427 62728427 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:62728427G>A uc002sbt.2 - 4 854 c.514C>T c.(514-516)CGT>TGT p.R172C TMEM17_uc002sbu.2_3'UTR|TMEM17_uc002sbv.1_3'UTR NM_198276 NP_938017 Q86X19 TMM17_HUMAN transmembrane protein 17 172 integral to membrane 0 Lung NSC(7;0.0274)|all_lung(7;0.0568) LUSC - Lung squamous cell carcinoma(7;1.31e-05)|Epithelial(17;0.169) 0.54 179.859093 179.998526 54 46 KEEP --- --- --- --- Unknown broad.mit.edu 37 2 62788016 62788016 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:62788016C>T TMEM17 (25236 upstream) : EHBP1 (112997 downstream) 0.363636 12.197136 12.377054 4 7 KEEP --- --- --- --- GKN2 200504 broad.mit.edu 37 2 69177295 69177295 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:69177295C>T uc002sfa.2 - 3 276 c.167G>A c.(166-168)GGA>GAA p.G56E GKN2_uc002sfb.3_Missense_Mutation_p.G56E NM_182536 NP_872342 Q86XP6 GKN2_HUMAN trefoil factor interactions(z) 1 precursor 56 BRICHOS. extracellular region 0 0.454545 99.236794 99.356226 30 36 KEEP --- --- --- --- CD207 50489 broad.mit.edu 37 2 71058118 71058118 + 3'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:71058118G>A uc002shg.2 - 6 NM_015717 NP_056532 CD207 antigen, langerin defense response to virus endocytic vesicle|integral to membrane mannose binding ovary(1)|lung(1) 2 0.529412 29.175132 29.187874 9 8 KEEP --- --- --- --- ATP6V1B1 525 broad.mit.edu 37 2 71187131 71187131 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:71187131C>T uc002shj.2 + 6 595 c.508C>T c.(508-510)CCT>TCT p.P170S ATP6V1B1_uc002shi.1_Missense_Mutation_p.P170S|ATP6V1B1_uc010fdv.2_Missense_Mutation_p.P170S|ATP6V1B1_uc010fdw.2_RNA|ATP6V1B1_uc010fdx.2_Missense_Mutation_p.P128S NM_001692 NP_001683 P15313 VATB1_HUMAN ATPase, H+ transporting, lysosomal 56/58kDa, V1 170 ATP hydrolysis coupled proton transport|calcium ion homeostasis|cellular iron ion homeostasis|excretion|inner ear morphogenesis|insulin receptor signaling pathway|ossification|pH reduction|sensory perception of sound|transferrin transport apical plasma membrane|basolateral plasma membrane|cytosol|endomembrane system|lateral plasma membrane|microvillus|proton-transporting V-type ATPase, V1 domain|vacuolar proton-transporting V-type ATPase complex ATP binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism skin(1) 1 0.391304 80.923368 81.632085 27 42 KEEP --- --- --- --- ATP6V1B1 525 broad.mit.edu 37 2 71191705 71191705 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:71191705C>T uc002shj.2 + ATP6V1B1_uc010fdv.2_Intron|ATP6V1B1_uc010fdw.2_Intron|ATP6V1B1_uc010fdx.2_Intron NM_001692 NP_001683 ATPase, H+ transporting, lysosomal 56/58kDa, V1 ATP hydrolysis coupled proton transport|calcium ion homeostasis|cellular iron ion homeostasis|excretion|inner ear morphogenesis|insulin receptor signaling pathway|ossification|pH reduction|sensory perception of sound|transferrin transport apical plasma membrane|basolateral plasma membrane|cytosol|endomembrane system|lateral plasma membrane|microvillus|proton-transporting V-type ATPase, V1 domain|vacuolar proton-transporting V-type ATPase complex ATP binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism skin(1) 1 OREG0014686 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0.521739 39.801769 39.811286 12 11 KEEP --- --- --- --- DYSF 8291 broad.mit.edu 37 2 71730462 71730462 + Intron SNP C A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:71730462C>A uc002sie.2 + DYSF_uc010feg.2_Intron|DYSF_uc010feh.2_Intron|DYSF_uc002sig.3_Intron|DYSF_uc010yqx.1_Intron|DYSF_uc010fee.2_Intron|DYSF_uc010fef.2_Intron|DYSF_uc010fei.2_Intron|DYSF_uc010fek.2_Intron|DYSF_uc010fej.2_Intron|DYSF_uc010fel.2_Intron|DYSF_uc010feo.2_Intron|DYSF_uc010fem.2_Intron|DYSF_uc010fen.2_Intron|DYSF_uc002sif.2_Intron NM_003494 NP_003485 dysferlin isoform 8 cytoplasmic vesicle membrane|integral to membrane|sarcolemma calcium-dependent phospholipid binding ovary(3)|breast(2)|pancreas(1)|skin(1) 7 0.659574 210.475737 212.589946 62 32 KEEP --- --- --- --- CCT7 10574 broad.mit.edu 37 2 73461393 73461393 + 5'Flank SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:73461393C>T uc002siz.2 + C2orf7_uc002siy.2_5'Flank|CCT7_uc002sja.2_5'Flank|CCT7_uc010yrf.1_5'Flank|CCT7_uc010feu.2_5'Flank|CCT7_uc010yrg.1_5'Flank|CCT7_uc010yrh.1_5'Flank|CCT7_uc010yri.1_5'Flank NM_006429 NP_006420 chaperonin containing TCP1, subunit 7 isoform a 'de novo' posttranslational protein folding ATP binding|unfolded protein binding 0 0.571429 13.200849 13.23195 4 3 KEEP --- --- --- --- MOBKL1B 55233 broad.mit.edu 37 2 74386369 74386369 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:74386369G>A uc002skh.3 - 5 616 c.422C>T c.(421-423)CCC>CTC p.P141L NM_018221 NP_060691 Q9H8S9 MOL1B_HUMAN Mob4B protein 141 hippo signaling cascade metal ion binding|protein binding 0 0.85 63.088016 65.436205 17 3 KEEP --- --- --- --- WDR54 84058 broad.mit.edu 37 2 74650021 74650021 + Nonsense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:74650021C>T uc002slb.2 + 3 307 c.247C>T c.(247-249)CGA>TGA p.R83* NM_032118 NP_115494 Q9H977 WDR54_HUMAN WD repeat domain 54 83 0 0.625 108.763568 109.422706 30 18 KEEP --- --- --- --- Unknown broad.mit.edu 37 2 85329808 85329808 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:85329808C>T KCMF1 (43214 upstream) : TCF7L1 (30926 downstream) 0.928571 91.807064 95.869397 26 2 KEEP --- --- --- --- RPIA 22934 broad.mit.edu 37 2 89036070 89036070 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:89036070C>T uc002ste.2 + 7 656 c.615C>T c.(613-615)CTC>CTT p.L205L NM_144563 NP_653164 P49247 RPIA_HUMAN ribose 5-phosphate isomerase A 205 pentose-phosphate shunt, non-oxidative branch cytosol ribose-5-phosphate isomerase activity ovary(1) 1 Acute lymphoblastic leukemia(2;0.000456)|all_hematologic(2;0.00287) 0.346154 80.901143 82.531278 27 51 KEEP --- --- --- --- broad.mit.edu 37 2 89161295 89161295 + RNA SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:89161295G>A uc010ytr.1 - 208 c.9106C>T uc002sti.1_5'Flank|uc002stj.1_Intron Parts of antibodies, mostly variable regions. 0.645161 70.408358 70.983616 20 11 KEEP --- --- --- --- broad.mit.edu 37 2 89442301 89442301 + RNA SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:89442301G>A uc010ytr.1 - 33 c.4116C>T uc002stl.2_Intron Parts of antibodies, mostly variable regions. 0.514706 113.523489 113.536125 35 33 KEEP --- --- --- --- broad.mit.edu 37 2 90043718 90043718 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:90043718G>A uc010fhm.2 + Parts of antibodies, mostly variable regions. 0.909091 34.43925 36.211945 10 1 KEEP --- --- --- --- Unknown broad.mit.edu 37 2 90458687 90458687 + IGR SNP C G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:90458687C>G None (None upstream) : None (None downstream) 0.029787 -40.087737 16.970006 7 228 KEEP --- --- --- --- Unknown broad.mit.edu 37 2 95619003 95619003 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:95619003C>T TEKT4 (76435 upstream) : MAL (72476 downstream) 0.380952 74.981626 75.765841 24 39 KEEP --- --- --- --- SEMA4C 54910 broad.mit.edu 37 2 97526713 97526713 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:97526713G>A uc002sxh.3 - 15 2312 c.2152C>T c.(2152-2154)CCC>TCC p.P718S ANKRD39_uc002sxd.3_5'Flank|SEMA4C_uc002sxf.3_Missense_Mutation_p.P218S|SEMA4C_uc002sxe.2_Missense_Mutation_p.P259S|SEMA4C_uc002sxg.3_Missense_Mutation_p.P771S NM_017789 NP_060259 Q9C0C4 SEM4C_HUMAN semaphorin 4C precursor 718 Pro-rich.|Cytoplasmic (Potential). muscle cell differentiation|nervous system development|positive regulation of stress-activated MAPK cascade cell junction|integral to membrane|postsynaptic density|postsynaptic membrane|synaptic vesicle membrane receptor activity skin(2) 2 0.761905 104.089737 106.711866 32 10 KEEP --- --- --- --- VWA3B 200403 broad.mit.edu 37 2 98797649 98797649 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:98797649G>A uc002syo.2 + 9 1549 c.1285G>A c.(1285-1287)GAG>AAG p.E429K VWA3B_uc010yvh.1_Missense_Mutation_p.E279K|VWA3B_uc002syj.2_RNA|VWA3B_uc002syk.1_RNA|VWA3B_uc002syl.1_5'UTR|VWA3B_uc002sym.2_Missense_Mutation_p.E429K|VWA3B_uc002syn.1_RNA|VWA3B_uc010yvi.1_Missense_Mutation_p.E86K NM_144992 NP_659429 Q502W6 VWA3B_HUMAN von Willebrand factor A domain containing 3B 429 ovary(3)|large_intestine(2)|skin(1) 6 0.37931 68.83757 69.578192 22 36 KEEP --- --- --- --- REV1 51455 broad.mit.edu 37 2 100052469 100052469 + Intron SNP T G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:100052469T>G uc002tad.2 - REV1_uc002tac.2_Intron NM_016316 NP_057400 REV1-like isoform 1 DNA replication|error-prone translesion synthesis|response to UV nucleoplasm damaged DNA binding|DNA-directed DNA polymerase activity|magnesium ion binding|protein binding ovary(2) 2 DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage 0.541667 47.7777 47.81398 13 11 KEEP --- --- --- --- Unknown broad.mit.edu 37 2 101207643 101207643 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:101207643C>T PDCL3 (14442 upstream) : NPAS2 (228970 downstream) 0.5 19.249622 19.249622 6 6 KEEP --- --- --- --- IL18RAP 8807 broad.mit.edu 37 2 103068339 103068339 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:103068339C>T uc002tbx.2 + 12 1982 c.1498C>T c.(1498-1500)CTT>TTT p.L500F IL18RAP_uc010fiz.2_Missense_Mutation_p.L358F NM_003853 NP_003844 O95256 I18RA_HUMAN interleukin 18 receptor accessory protein 500 TIR.|Cytoplasmic (Potential). cell surface receptor linked signaling pathway|inflammatory response|innate immune response integral to membrane transmembrane receptor activity skin(3)|ovary(2) 5 0.63 221.949233 223.433276 63 37 KEEP --- --- --- --- SLC9A2 6549 broad.mit.edu 37 2 103320951 103320951 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:103320951G>A uc002tca.2 + NM_003048 NP_003039 solute carrier family 9 (sodium/hydrogen integral to membrane|plasma membrane sodium:hydrogen antiporter activity central_nervous_system(3)|skin(3)|breast(2) 8 0.636364 43.853796 44.213051 14 8 KEEP --- --- --- --- MFSD9 84804 broad.mit.edu 37 2 103353121 103353121 + Missense_Mutation SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:103353121T>C uc002tcb.2 - 1 217 c.149A>G c.(148-150)TAC>TGC p.Y50C TMEM182_uc002tcc.3_5'Flank|TMEM182_uc002tcd.3_5'Flank|MFSD9_uc010fja.2_RNA NM_032718 NP_116107 Q8NBP5 MFSD9_HUMAN major facilitator superfamily domain containing 50 Helical; (Potential). transmembrane transport integral to membrane|plasma membrane transporter activity ovary(2)|breast(2) 4 0.095238 4.496551 11.376148 4 38 KEEP --- --- --- --- CCDC138 165055 broad.mit.edu 37 2 109455646 109455646 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:109455646G>A uc002ten.1 + 11 1272 c.1212G>A c.(1210-1212)TTG>TTA p.L404L CCDC138_uc002teo.1_Silent_p.L404L|CCDC138_uc002tep.1_Silent_p.L88L|CCDC138_uc010fjm.1_Silent_p.L88L NM_144978 NP_659415 Q96M89 CC138_HUMAN coiled-coil domain containing 138 404 0 0.558824 60.326726 60.429107 19 15 KEEP --- --- --- --- TTL 150465 broad.mit.edu 37 2 113278041 113278041 + Intron SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:113278041T>C uc002thu.2 + TTL_uc010fkm.1_Intron NM_153712 NP_714923 tubulin tyrosine ligase protein modification process ATP binding|tubulin-tyrosine ligase activity 0 Ovarian(717;0.024) BRCA - Breast invasive adenocarcinoma(221;6.17e-07)|STAD - Stomach adenocarcinoma(1183;0.00644) 130 T ETV6 ALL 0.266667 24.072178 25.559914 8 22 KEEP --- --- --- --- Unknown broad.mit.edu 37 2 113690326 113690326 + IGR SNP C A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:113690326C>A IL1F7 (13870 upstream) : IL1F9 (45280 downstream) 0.333333 17.743513 18.186568 6 12 KEEP --- --- --- --- IL1F10 84639 broad.mit.edu 37 2 113832562 113832562 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:113832562C>T uc002tiu.2 + IL1F10_uc002tiv.2_Intron|IL1F10_uc002tiw.2_Intron NM_173161 NP_775184 interleukin 1 family, member 10 extracellular space cytokine activity|interleukin-1 receptor antagonist activity ovary(1) 1 0.47619 34.248433 34.258827 10 11 KEEP --- --- --- --- PSD4 23550 broad.mit.edu 37 2 113940641 113940641 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:113940641C>T uc002tjc.2 + 2 791 c.608C>T c.(607-609)TCC>TTC p.S203F PSD4_uc002tjd.2_5'UTR|PSD4_uc002tje.2_Missense_Mutation_p.S202F|PSD4_uc002tjf.2_5'Flank NM_012455 NP_036587 Q8NDX1 PSD4_HUMAN pleckstrin and Sec7 domain containing 4 203 regulation of ARF protein signal transduction cytoplasm|plasma membrane ARF guanyl-nucleotide exchange factor activity ovary(2) 2 0.340426 45.58335 46.64228 16 31 KEEP --- --- --- --- MARCO 8685 broad.mit.edu 37 2 119740103 119740103 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:119740103C>T uc002tln.1 + MARCO_uc010yyf.1_Intron NM_006770 NP_006761 macrophage receptor with collagenous structure cell surface receptor linked signaling pathway|innate immune response collagen|integral to plasma membrane pattern recognition receptor activity|scavenger receptor activity ovary(3)|skin(2)|central_nervous_system(1) 6 GBM(8;18 374 7467 11269 32796) 0.565217 41.976798 42.061845 13 10 KEEP --- --- --- --- EPB41L5 57669 broad.mit.edu 37 2 120918702 120918702 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:120918702C>T uc002tmg.2 + EPB41L5_uc010fll.2_Intron|EPB41L5_uc010flm.2_Intron NM_020909 NP_065960 erythrocyte membrane protein band 4.1 like 5 cytoplasm|cytoskeleton|extrinsic to membrane cytoskeletal protein binding ovary(1) 1 0.5 12.69974 12.69974 4 4 KEEP --- --- --- --- CNTNAP5 129684 broad.mit.edu 37 2 125174942 125174942 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:125174942C>T uc002tno.2 + CNTNAP5_uc010flu.2_Intron NM_130773 NP_570129 contactin associated protein-like 5 precursor cell adhesion|signal transduction integral to membrane receptor binding ovary(10) 10 BRCA - Breast invasive adenocarcinoma(221;0.248) 0.5 10.024944 10.024944 3 3 KEEP --- --- --- --- GYPC 2995 broad.mit.edu 37 2 127453616 127453616 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:127453616G>A uc002tnq.2 + 4 441 c.285G>A c.(283-285)GAG>GAA p.E95E GYPC_uc002tnr.2_Silent_p.E76E|GYPC_uc010flv.2_RNA NM_002101 NP_002092 P04921 GLPC_HUMAN glycophorin C isoform 1 95 Cytoplasmic. cortical cytoskeleton|integral to plasma membrane protein binding central_nervous_system(1) 1 Colorectal(110;0.0533) BRCA - Breast invasive adenocarcinoma(221;0.075) Melanoma(110;806 1600 6704 9981 33404) 0.565789 150.532877 150.819024 43 33 KEEP --- --- --- --- CCDC74B 91409 broad.mit.edu 37 2 130897839 130897839 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:130897839G>A uc002tqm.1 - 5 851 c.789C>T c.(787-789)CCC>CCT p.P263P CCDC74B_uc010yzw.1_Silent_p.P365P|CCDC74B_uc002tqn.1_Silent_p.P197P NM_207310 NP_997193 Q96LY2 CC74B_HUMAN coiled-coil domain containing 74B 263 0 Colorectal(110;0.1) 0.304878 71.396938 74.153587 25 57 KEEP --- --- --- --- PLEKHB2 55041 broad.mit.edu 37 2 131960111 131960111 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:131960111C>T uc002tsh.2 + SubName: Full=Putative uncharacterized protein PLEKHB2; membrane protein binding ovary(2) 2 BRCA - Breast invasive adenocarcinoma(221;0.0828) 0.8 27.605424 28.442134 8 2 KEEP --- --- --- --- GPR39 2863 broad.mit.edu 37 2 133403193 133403193 + 3'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:133403193G>A uc002ttl.2 + 2 LYPD1_uc002ttm.3_3'UTR|LYPD1_uc002ttn.2_3'UTR|LYPD1_uc002tto.2_3'UTR NM_001508 NP_001499 G protein-coupled receptor 39 integral to plasma membrane G-protein coupled receptor activity|metal ion binding 0 0.393939 40.567131 40.89238 13 20 KEEP --- --- --- --- MGAT5 4249 broad.mit.edu 37 2 135185842 135185842 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:135185842G>A uc002ttv.1 + NM_002410 NP_002401 N-acetylglucosaminyltransferase V post-translational protein modification|protein N-linked glycosylation via asparagine Golgi membrane|integral to membrane alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase activity ovary(2)|skin(1) 3 BRCA - Breast invasive adenocarcinoma(221;0.0964) 0.461538 36.196187 36.229814 12 14 KEEP --- --- --- --- UBXN4 23190 broad.mit.edu 37 2 136511643 136511643 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:136511643C>T uc002tur.2 + UBXN4_uc002tus.2_5'UTR NM_014607 NP_055422 UBX domain containing 2 response to unfolded protein endoplasmic reticulum membrane|nuclear envelope protein binding skin(2) 2 0.65625 71.683929 72.373558 21 11 KEEP --- --- --- --- LCT 3938 broad.mit.edu 37 2 136570058 136570058 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:136570058G>A uc002tuu.1 - 7 2187 c.2176C>T c.(2176-2178)CGT>TGT p.R726C NM_002299 NP_002290 P09848 LPH_HUMAN lactase-phlorizin hydrolase preproprotein 726 Extracellular (Potential).|4 X approximate repeats.|2. carbohydrate metabolic process|polysaccharide digestion apical plasma membrane|integral to plasma membrane|membrane fraction cation binding|glycosylceramidase activity|lactase activity ovary(7)|central_nervous_system(2)|skin(2)|pancreas(1)|lung(1) 13 BRCA - Breast invasive adenocarcinoma(221;0.169) 0.396825 76.659374 77.24676 25 38 KEEP --- --- --- --- THSD7B 80731 broad.mit.edu 37 2 138030030 138030030 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:138030030C>T uc002tva.1 + THSD7B_uc010zbj.1_Intron|THSD7B_uc002tvb.2_Intron NM_001080427 NP_001073896 thrombospondin, type I, domain containing 7B ovary(4)|central_nervous_system(2)|pancreas(1) 7 BRCA - Breast invasive adenocarcinoma(221;0.19) 0.5 6.449852 6.449852 2 2 KEEP --- --- --- --- LRP1B 53353 broad.mit.edu 37 2 141215150 141215150 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:141215150C>T uc002tvj.1 - 61 10668 c.9696G>A c.(9694-9696)GGG>GGA p.G3232G NM_018557 NP_061027 Q9NZR2 LRP1B_HUMAN low density lipoprotein-related protein 1B 3232 Extracellular (Potential).|LDL-receptor class B 32. protein transport|receptor-mediated endocytosis integral to membrane calcium ion binding lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1) 50 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103) Colon(99;50 2074 2507 20106) 2546 TSP Lung(27;0.18) 0.568807 207.764642 208.214401 62 47 KEEP --- --- --- --- LRP1B 53353 broad.mit.edu 37 2 141250314 141250314 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:141250314C>T uc002tvj.1 - NM_018557 NP_061027 low density lipoprotein-related protein 1B protein transport|receptor-mediated endocytosis integral to membrane calcium ion binding lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1) 50 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103) Colon(99;50 2074 2507 20106) 2546 TSP Lung(27;0.18) 0.636364 70.782284 71.321737 21 12 KEEP --- --- --- --- LRP1B 53353 broad.mit.edu 37 2 141643907 141643907 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:141643907G>A uc002tvj.1 - LRP1B_uc010fnl.1_Intron NM_018557 NP_061027 low density lipoprotein-related protein 1B protein transport|receptor-mediated endocytosis integral to membrane calcium ion binding lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1) 50 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103) Colon(99;50 2074 2507 20106) 2546 TSP Lung(27;0.18) 0.52381 35.825495 35.835805 11 10 KEEP --- --- --- --- MBD5 55777 broad.mit.edu 37 2 149225855 149225855 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:149225855C>T uc002twm.3 + MBD5_uc010zbs.1_Intron|MBD5_uc010fns.2_Intron|MBD5_uc002twn.1_5'Flank NM_018328 NP_060798 methyl-CpG binding domain protein 5 chromosome|nucleus chromatin binding|DNA binding skin(3)|ovary(2) 5 BRCA - Breast invasive adenocarcinoma(221;0.0569) 0.5 10.525129 10.525129 3 3 KEEP --- --- --- --- GALNT5 11227 broad.mit.edu 37 2 158140839 158140839 + Silent SNP C G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:158140839C>G uc002tzg.2 + 2 1755 c.1500C>G c.(1498-1500)GTC>GTG p.V500V GALNT5_uc010zci.1_RNA NM_014568 NP_055383 Q7Z7M9 GALT5_HUMAN N-acetylgalactosaminyltransferase 5 500 Catalytic subdomain A.|Lumenal (Potential). glycosaminoglycan biosynthetic process Golgi membrane|integral to membrane polypeptide N-acetylgalactosaminyltransferase activity|sugar binding breast(3)|skin(1) 4 0.15 27.743875 37.140028 12 68 KEEP --- --- --- --- GRB14 2888 broad.mit.edu 37 2 165378682 165378682 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:165378682C>T uc002ucl.2 - GRB14_uc010zcv.1_Intron|GRB14_uc002ucm.2_Intron NM_004490 NP_004481 growth factor receptor-bound protein 14 blood coagulation|leukocyte migration cytosol|endosome membrane|Golgi membrane|microsome|plasma membrane SH3/SH2 adaptor activity ovary(5)|upper_aerodigestive_tract(1)|lung(1) 7 0.5 31.075015 31.075015 9 9 KEEP --- --- --- --- SCN3A 6328 broad.mit.edu 37 2 165984416 165984416 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:165984416G>A uc002ucx.2 - 18 3610 c.3118C>T c.(3118-3120)CAT>TAT p.H1040Y SCN3A_uc002ucy.2_Missense_Mutation_p.H991Y|SCN3A_uc002ucz.2_Missense_Mutation_p.H991Y|SCN3A_uc002uda.1_Missense_Mutation_p.H860Y|SCN3A_uc002udb.1_Missense_Mutation_p.H860Y NM_006922 NP_008853 Q9NY46 SCN3A_HUMAN sodium channel, voltage-gated, type III, alpha 1040 voltage-gated sodium channel complex voltage-gated sodium channel activity ovary(4)|breast(3)|skin(2)|central_nervous_system(1) 10 Lamotrigine(DB00555) 0.340909 91.421772 93.390926 30 58 KEEP --- --- --- --- SCN7A 6332 broad.mit.edu 37 2 167262723 167262723 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:167262723C>T uc002udu.1 - 25 4543 c.4416G>A c.(4414-4416)GGG>GGA p.G1472G NM_002976 NP_002967 Q01118 SCN7A_HUMAN sodium channel, voltage-gated, type VII, alpha 1472 Helical; Name=S6 of repeat IV; (By similarity). muscle contraction voltage-gated sodium channel complex voltage-gated sodium channel activity large_intestine(1) 1 0.62963 115.663619 116.461021 34 20 KEEP --- --- --- --- SCN7A 6332 broad.mit.edu 37 2 167284379 167284379 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:167284379C>T uc002udu.1 - 17 2899 c.2772G>A c.(2770-2772)AGG>AGA p.R924R SCN7A_uc010fpm.1_RNA NM_002976 NP_002967 Q01118 SCN7A_HUMAN sodium channel, voltage-gated, type VII, alpha 924 muscle contraction voltage-gated sodium channel complex voltage-gated sodium channel activity large_intestine(1) 1 0.6 38.224861 38.385164 12 8 KEEP --- --- --- --- XIRP2 129446 broad.mit.edu 37 2 168100690 168100690 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:168100690G>A uc002udx.2 + 8 2806 c.2788G>A c.(2788-2790)GAG>AAG p.E930K XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.E755K|XIRP2_uc010fpq.2_Missense_Mutation_p.E708K|XIRP2_uc010fpr.2_Intron NM_152381 NP_689594 A4UGR9 XIRP2_HUMAN xin actin-binding repeat containing 2 isoform 1 755 actin cytoskeleton organization cell junction actin binding skin(7)|ovary(6)|pancreas(1) 14 0.5 56.034537 56.034537 18 18 KEEP --- --- --- --- Unknown broad.mit.edu 37 2 168572425 168572425 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:168572425C>T XIRP2 (456166 upstream) : B3GALT1 (102757 downstream) 0.615385 52.50191 52.804405 16 10 KEEP --- --- --- --- ABCB11 8647 broad.mit.edu 37 2 169783583 169783583 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:169783583G>A uc002ueo.1 - ABCB11_uc010zda.1_Intron|ABCB11_uc010zdb.1_Intron NM_003742 NP_003733 ATP-binding cassette, sub-family B (MDR/TAP), bile acid biosynthetic process apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction ATP binding|bile acid-exporting ATPase activity|canalicular bile acid transmembrane transporter activity|sodium-exporting ATPase activity, phosphorylative mechanism ovary(2)|large_intestine(2)|breast(1) 5 Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Glibenclamide(DB01016) 0.392157 61.891303 62.409846 20 31 KEEP --- --- --- --- OLA1 29789 broad.mit.edu 37 2 175111499 175111499 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:175111499G>A uc002uih.2 - 2 231 c.45C>T c.(43-45)ATC>ATT p.I15I OLA1_uc002uii.2_Intron|OLA1_uc010fqq.2_Silent_p.I15I|OLA1_uc002uij.2_Intron|OLA1_uc002uik.2_5'UTR|OLA1_uc010fqr.2_Silent_p.I15I NM_013341 NP_037473 Q9NTK5 OLA1_HUMAN Obg-like ATPase 1 isoform 1 15 ATP catabolic process cytoplasm ATP binding|GTP binding|hydrolase activity|protein binding ovary(1)|breast(1) 2 0.661017 132.139317 133.490375 39 20 KEEP --- --- --- --- Unknown broad.mit.edu 37 2 175165542 175165542 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:175165542G>A OLA1 (52177 upstream) : SP9 (34279 downstream) 0.59375 67.83135 68.077094 19 13 KEEP --- --- --- --- Unknown broad.mit.edu 37 2 176190020 176190020 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:176190020G>A ATP5G3 (143530 upstream) : KIAA1715 (600390 downstream) 0.6 39.203165 39.377833 12 8 KEEP --- --- --- --- TTN 7273 broad.mit.edu 37 2 179458084 179458084 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:179458084C>T uc010zfg.1 - 248 51371 c.51147G>A c.(51145-51147)AAG>AAA p.K17049K uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Silent_p.K10744K|TTN_uc010zfi.1_Silent_p.K10677K|TTN_uc010zfj.1_Silent_p.K10552K NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 17976 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) 8722 0.330097 106.915371 109.550456 34 69 KEEP --- --- --- --- TTN 7273 broad.mit.edu 37 2 179483151 179483151 + Nonsense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:179483151C>T uc010zfg.1 - 201 39554 c.39330G>A c.(39328-39330)TGG>TGA p.W13110* TTN_uc010zfh.1_Nonsense_Mutation_p.W6805*|TTN_uc010zfi.1_Nonsense_Mutation_p.W6738*|TTN_uc010zfj.1_Nonsense_Mutation_p.W6613* NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 14037 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) 8722 0.352941 55.831286 56.805363 18 33 KEEP --- --- --- --- TTN 7273 broad.mit.edu 37 2 179579328 179579328 + Intron SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:179579328T>C uc010zfg.1 - TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron NM_133378 NP_596869 titin isoform N2-A ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) 8722 0.277778 17.067704 17.867087 5 13 KEEP --- --- --- --- TTN 7273 broad.mit.edu 37 2 179584073 179584073 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:179584073G>A uc010zfg.1 - 80 20536 c.20312C>T c.(20311-20313)TCA>TTA p.S6771L TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.S3432L NM_133378 NP_596869 Q8WZ42 TITIN_HUMAN titin isoform N2-A 7698 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) 8722 0.325581 80.568468 82.890732 28 58 KEEP --- --- --- --- TTN 7273 broad.mit.edu 37 2 179616643 179616643 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:179616643G>A uc002unb.2 - 46 10708 c.10484C>T c.(10483-10485)ACA>ATA p.T3495I TTN_uc010zfg.1_Intron|TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Intron NM_133379 NP_596870 Q8WZ42 TITIN_HUMAN titin isoform novex-3 Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) 8722 0.345291 224.50021 229.216909 77 146 KEEP --- --- --- --- TTN 7273 broad.mit.edu 37 2 179635889 179635889 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:179635889G>A uc010zfg.1 - TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002unb.2_Intron NM_133378 NP_596869 titin isoform N2-A ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1) 153 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) 8722 0.25 27.832979 30.103757 10 30 KEEP --- --- --- --- CCDC141 285025 broad.mit.edu 37 2 179714967 179714967 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:179714967C>T uc002unf.1 - NM_173648 NP_775919 coiled-coil domain containing 141 protein binding ovary(7)|pancreas(2)|skin(1) 10 OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147) 0.214286 7.379321 8.390407 3 11 KEEP --- --- --- --- CCDC141 285025 broad.mit.edu 37 2 179721202 179721202 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:179721202G>A uc002unf.1 - NM_173648 NP_775919 coiled-coil domain containing 141 protein binding ovary(7)|pancreas(2)|skin(1) 10 OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147) 0.461538 19.948977 19.965713 6 7 KEEP --- --- --- --- PDE1A 5136 broad.mit.edu 37 2 183050729 183050729 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:183050729G>A uc002uos.2 - 14 1538 c.1454C>T c.(1453-1455)TCC>TTC p.S485F PDE1A_uc010zfp.1_Missense_Mutation_p.S381F|PDE1A_uc002uoq.1_Missense_Mutation_p.S485F|PDE1A_uc010zfq.1_Missense_Mutation_p.S485F|PDE1A_uc002uor.2_Missense_Mutation_p.S469F|PDE1A_uc002uou.2_Missense_Mutation_p.S451F NM_001003683 NP_001003683 P54750 PDE1A_HUMAN phosphodiesterase 1A isoform 2 485 Catalytic (By similarity). activation of phospholipase C activity|nerve growth factor receptor signaling pathway|platelet activation cytosol 3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|calmodulin binding|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity|metal ion binding skin(2)|ovary(1) 3 OV - Ovarian serous cystadenocarcinoma(117;0.061) 0.371795 89.064929 90.187194 29 49 KEEP --- --- --- --- Unknown broad.mit.edu 37 2 187867362 187867362 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:187867362G>A ZSWIM2 (153465 upstream) : CALCRL (340489 downstream) 0.272727 17.140995 18.164757 6 16 KEEP --- --- --- --- COL3A1 1281 broad.mit.edu 37 2 189855822 189855822 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:189855822C>T uc002uqj.1 + COL3A1_uc010frw.1_5'Flank NM_000090 NP_000081 collagen type III alpha 1 preproprotein axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway collagen type III|extracellular space extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding central_nervous_system(7)|ovary(4)|large_intestine(2) 13 OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141) Collagenase(DB00048)|Palifermin(DB00039) 1079 0.125 4.174217 8.577178 4 28 KEEP --- --- --- --- COL3A1 1281 broad.mit.edu 37 2 189866275 189866276 + Missense_Mutation DNP CC TT TT MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:189866275_189866276CC>TT uc002uqj.1 + 34 2468_2469 c.2351_2352CC>TT c.(2350-2352)GCC>GTT p.A784V NM_000090 NP_000081 P02461 CO3A1_HUMAN collagen type III alpha 1 preproprotein 784 Triple-helical region. axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway collagen type III|extracellular space extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding central_nervous_system(7)|ovary(4)|large_intestine(2) 13 OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141) Collagenase(DB00048)|Palifermin(DB00039) 1079 0.6 196.622291 197.550439 60 40 KEEP --- --- --- --- COL3A1 1281 broad.mit.edu 37 2 189868120 189868120 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:189868120C>T uc002uqj.1 + NM_000090 NP_000081 collagen type III alpha 1 preproprotein axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway collagen type III|extracellular space extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding central_nervous_system(7)|ovary(4)|large_intestine(2) 13 OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141) Collagenase(DB00048)|Palifermin(DB00039) (COLO818-Tumor) 1079 0.103448 1.901292 6.44838 3 26 KEEP --- --- --- --- COL3A1 1281 broad.mit.edu 37 2 189868378 189868378 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:189868378C>T uc002uqj.1 + NM_000090 NP_000081 collagen type III alpha 1 preproprotein axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway collagen type III|extracellular space extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding central_nervous_system(7)|ovary(4)|large_intestine(2) 13 OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141) Collagenase(DB00048)|Palifermin(DB00039) 1079 0.363636 37.392809 37.931975 12 21 KEEP --- --- --- --- COL3A1 1281 broad.mit.edu 37 2 189875722 189875722 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:189875722G>A uc002uqj.1 + NM_000090 NP_000081 collagen type III alpha 1 preproprotein axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway collagen type III|extracellular space extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding central_nervous_system(7)|ovary(4)|large_intestine(2) 13 OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141) Collagenase(DB00048)|Palifermin(DB00039) 1079 0.583333 24.027286 24.100109 7 5 KEEP --- --- --- --- COL5A2 1290 broad.mit.edu 37 2 189923252 189923252 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:189923252C>T uc002uqk.2 - 33 2407 c.2132G>A c.(2131-2133)GGA>GAA p.G711E COL5A2_uc010frx.2_Missense_Mutation_p.G287E NM_000393 NP_000384 P05997 CO5A2_HUMAN alpha 2 type V collagen preproprotein 711 axon guidance|collagen fibril organization|eye morphogenesis|skin development collagen type V extracellular matrix structural constituent ovary(2) 2 OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127) 0.448276 41.571681 41.639263 13 16 KEEP --- --- --- --- COL5A2 1290 broad.mit.edu 37 2 189961990 189961990 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:189961990C>T uc002uqk.2 - NM_000393 NP_000384 alpha 2 type V collagen preproprotein axon guidance|collagen fibril organization|eye morphogenesis|skin development collagen type V extracellular matrix structural constituent ovary(2) 2 OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127) 0.414634 55.668572 55.929296 17 24 KEEP --- --- --- --- SLC39A10 57181 broad.mit.edu 37 2 196599852 196599852 + 3'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:196599852G>A uc002utg.3 + 10 SLC39A10_uc002uth.3_3'UTR|SLC39A10_uc010zgp.1_3'UTR NM_001127257 NP_001120729 solute carrier family 39 (zinc transporter), zinc ion transport integral to membrane metal ion transmembrane transporter activity pancreas(1)|skin(1) 2 OV - Ovarian serous cystadenocarcinoma(117;0.221) 0.35 44.237585 45.031856 14 26 KEEP --- --- --- --- DNAH7 56171 broad.mit.edu 37 2 196642599 196642599 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:196642599G>A uc002utj.3 - 59 11090 c.10989C>T c.(10987-10989)TTC>TTT p.F3663F DNAH7_uc002uti.3_Silent_p.F146F NM_018897 NP_061720 Q8WXX0 DYH7_HUMAN dynein, axonemal, heavy chain 7 3663 ciliary or flagellar motility|microtubule-based movement axonemal dynein complex|cilium axoneme|cytoplasm|microtubule ATP binding|microtubule motor activity skin(10)|ovary(2) 12 0.285714 37.927163 39.947857 14 35 KEEP --- --- --- --- Unknown broad.mit.edu 37 2 198245456 198245456 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:198245456C>T ANKRD44 (69961 upstream) : SF3B1 (11244 downstream) 0.666667 42.805283 43.247683 12 6 KEEP --- --- --- --- TRAK2 66008 broad.mit.edu 37 2 202272213 202272213 + Nonsense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:202272213G>A uc002uyb.3 - 3 645 c.199C>T c.(199-201)CAA>TAA p.Q67* TRAK2_uc002uyc.2_Nonsense_Mutation_p.Q67* NM_015049 NP_055864 O60296 TRAK2_HUMAN trafficking protein, kinesin binding 2 67 early endosome|plasma membrane GABA receptor binding 0 0.66 107.486643 108.617518 33 17 KEEP --- --- --- --- NRP2 8828 broad.mit.edu 37 2 206617650 206617650 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:206617650C>T uc002vaw.2 + 12 2786 c.1995C>T c.(1993-1995)CTC>CTT p.L665L NRP2_uc002vau.2_Silent_p.L665L|NRP2_uc002vav.2_Silent_p.L665L|NRP2_uc002vax.2_Silent_p.L665L|NRP2_uc002vay.2_Silent_p.L665L NM_201266 NP_957718 O60462 NRP2_HUMAN neuropilin 2 isoform 1 precursor 665 Extracellular (Potential).|MAM. angiogenesis|axon guidance|cell adhesion integral to membrane|membrane fraction|plasma membrane heparin binding|metal ion binding|semaphorin receptor activity|vascular endothelial growth factor receptor activity skin(2)|ovary(1)|central_nervous_system(1) 4 0.413043 58.115698 58.419728 19 27 KEEP --- --- --- --- DYTN 391475 broad.mit.edu 37 2 207583057 207583057 + 5'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:207583057G>A uc002vbr.1 - 1 NM_001093730 NP_001087199 dystrotelin plasma membrane zinc ion binding ovary(1)|central_nervous_system(1) 2 LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153) 0.6 40.303367 40.478075 12 8 KEEP --- --- --- --- PIKFYVE 200576 broad.mit.edu 37 2 209190425 209190425 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:209190425C>T uc002vcz.2 + 20 3048 c.2890C>T c.(2890-2892)CCG>TCG p.P964S PIKFYVE_uc010fun.1_Missense_Mutation_p.P645S|PIKFYVE_uc002vcy.1_Missense_Mutation_p.P908S NM_015040 NP_055855 Q9Y2I7 FYV1_HUMAN phosphatidylinositol-3-phosphate 5-kinase type 964 cellular protein metabolic process|intracellular signal transduction|protein localization to nucleus|retrograde transport, endosome to Golgi early endosome membrane|membrane raft 1-phosphatidylinositol-3-phosphate 5-kinase activity|1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|metal ion binding|protein binding ovary(5)|kidney(2)|pancreas(1)|central_nervous_system(1)|skin(1) 10 756 0.573529 130.534037 130.85455 39 29 KEEP --- --- --- --- PTH2R 5746 broad.mit.edu 37 2 209302447 209302447 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:209302447G>A uc002vdb.2 + PTH2R_uc010zjb.1_Intron NM_005048 NP_005039 parathyroid hormone 2 receptor precursor integral to plasma membrane parathyroid hormone receptor activity ovary(1)|breast(1)|skin(1) 3 Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836) 0.65625 71.966345 72.651792 21 11 KEEP --- --- --- --- CPS1 1373 broad.mit.edu 37 2 211465259 211465259 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:211465259C>T uc002vee.3 + CPS1_uc010fur.2_Intron|CPS1_uc010fus.2_Intron NM_001875 NP_001866 carbamoyl-phosphate synthetase 1 isoform b carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle mitochondrial nucleoid ATP binding|carbamoyl-phosphate synthase (ammonia) activity ovary(8)|central_nervous_system(3)|breast(1)|skin(1) 13 Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843) 0.290323 52.024331 54.466992 18 44 KEEP --- --- --- --- SPAG16 79582 broad.mit.edu 37 2 215146092 215146092 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:215146092C>T uc002veq.2 + SPAG16_uc002ver.2_Intron|SPAG16_uc010zjk.1_Intron NM_024532 NP_078808 sperm associated antigen 16 isoform 1 cilium assembly cilium axoneme|flagellar axoneme ovary(1)|skin(1) 2 Renal(323;0.00461) UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599) 1 30.819311 30.815408 8 0 KEEP --- --- --- --- ABCA12 26154 broad.mit.edu 37 2 215833605 215833605 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:215833605G>A uc002vew.2 - ABCA12_uc002vev.2_Intron|ABCA12_uc010zjn.1_Intron NM_173076 NP_775099 ATP-binding cassette, sub-family A, member 12 cellular homeostasis|lipid transport integral to membrane ATP binding|ATPase activity ovary(6)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1) 11 Renal(323;0.127) Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011) Ovarian(66;664 1488 5121 34295) 0.391304 25.96833 26.206805 9 14 KEEP --- --- --- --- FN1 2335 broad.mit.edu 37 2 216286754 216286754 + Intron SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:216286754A>G uc002vfa.2 - FN1_uc002vfb.2_Intron|FN1_uc002vfc.2_Intron|FN1_uc002vfd.2_Intron|FN1_uc002vfe.2_Intron|FN1_uc002vff.2_Intron|FN1_uc002vfg.2_Intron|FN1_uc002vfh.2_Intron|FN1_uc002vfi.2_Intron|FN1_uc002vfj.2_Intron|FN1_uc002vfl.2_Intron NM_212482 NP_997647 fibronectin 1 isoform 1 preproprotein acute-phase response|angiogenesis|leukocyte migration|peptide cross-linking|platelet activation|platelet degranulation|regulation of cell shape|substrate adhesion-dependent cell spreading ER-Golgi intermediate compartment|fibrinogen complex|platelet alpha granule lumen|proteinaceous extracellular matrix collagen binding|extracellular matrix structural constituent|heparin binding central_nervous_system(7)|large_intestine(2)|breast(2)|ovary(1)|pancreas(1) 13 Renal(323;0.127) Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948) Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031) 1374 0.421053 59.295588 59.501895 16 22 KEEP --- --- --- --- IGFBP2 3485 broad.mit.edu 37 2 217528721 217528721 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:217528721G>A uc010zjt.1 + 6 1001 c.851G>A c.(850-852)GGG>GAG p.G284E IGFBP2_uc010zju.1_3'UTR NM_000597 NP_000588 P18065 IBP2_HUMAN insulin-like growth factor binding protein 2, 291 Thyroglobulin type-1. positive regulation of activated T cell proliferation|regulation of cell growth|regulation of insulin-like growth factor receptor signaling pathway extracellular space insulin-like growth factor I binding|insulin-like growth factor II binding 0 Renal(323;0.0458) Epithelial(149;2.9e-06)|all cancers(144;0.000223)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00968) 0.48 37.390027 37.399084 12 13 KEEP --- --- --- --- ZNF142 7701 broad.mit.edu 37 2 219505478 219505478 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:219505478G>A uc002vin.2 - 9 4939 c.4503C>T c.(4501-4503)ATC>ATT p.I1501I ZNF142_uc002vil.2_Silent_p.I1462I|ZNF142_uc010fvt.2_Silent_p.I1338I|ZNF142_uc002vim.2_Silent_p.I1338I NM_001105537 NP_001099007 P52746 ZN142_HUMAN zinc finger protein 142 1501 C2H2-type 26. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding breast(2)|ovary(1)|skin(1) 4 Renal(207;0.0474) Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948) Colon(170;867 1942 8995 15834 18053) 0.275862 22.386612 23.698767 8 21 KEEP --- --- --- --- ZNF142 7701 broad.mit.edu 37 2 219508464 219508464 + Missense_Mutation SNP C G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:219508464C>G uc002vin.2 - 8 3211 c.2775G>C c.(2773-2775)AAG>AAC p.K925N ZNF142_uc002vil.2_Missense_Mutation_p.K886N|ZNF142_uc010fvt.2_Missense_Mutation_p.K762N|ZNF142_uc002vim.2_Missense_Mutation_p.K762N NM_001105537 NP_001099007 P52746 ZN142_HUMAN zinc finger protein 142 925 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding breast(2)|ovary(1)|skin(1) 4 Renal(207;0.0474) Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948) Colon(170;867 1942 8995 15834 18053) 0.658031 442.307869 446.570778 127 66 KEEP --- --- --- --- STK36 27148 broad.mit.edu 37 2 219563286 219563286 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:219563286C>T uc002viu.2 + STK36_uc002viv.2_Intron|STK36_uc002viw.2_Intron|STK36_uc002vix.2_Intron NM_015690 NP_056505 serine/threonine kinase 36 cilium assembly|positive regulation of hh target transcription factor activity|positive regulation of smoothened signaling pathway|post-embryonic development aggresome|cytoplasm|focal adhesion|intermediate filament cytoskeleton|nucleus ATP binding|protein serine/threonine kinase activity|transcription factor binding ovary(4)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1) 11 Renal(207;0.0915) Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984) 551 0.257732 66.425174 71.588024 25 72 KEEP --- --- --- --- ATG9A 79065 broad.mit.edu 37 2 220089199 220089199 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:220089199G>A uc002vke.1 - 8 1080 c.894C>T c.(892-894)TTC>TTT p.F298F ATG9A_uc002vkd.1_RNA|ATG9A_uc002vkf.1_Silent_p.F298F NM_001077198 NP_001070666 Q7Z3C6 ATG9A_HUMAN APG9 autophagy 9-like 1 298 Helical; (Potential). autophagic vacuole assembly|protein transport autophagic vacuole membrane|cytoplasmic vesicle|Golgi apparatus|integral to membrane|late endosome membrane skin(1) 1 Renal(207;0.0474) Epithelial(149;1.37e-06)|all cancers(144;0.000222)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942) 0.208333 12.510935 14.365698 5 19 KEEP --- --- --- --- PTPRN 5798 broad.mit.edu 37 2 220156089 220156089 + Intron SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:220156089A>G uc002vkz.2 - PTPRN_uc010zlc.1_Intron|PTPRN_uc002vla.2_Intron NM_002846 NP_002837 protein tyrosine phosphatase, receptor type, N response to reactive oxygen species integral to plasma membrane transmembrane receptor protein tyrosine phosphatase activity ovary(2)|lung(1)|skin(1) 4 Renal(207;0.0474) Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875) 0.222222 6.045288 6.683935 2 7 KEEP --- --- --- --- Unknown broad.mit.edu 37 2 223591348 223591348 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:223591348G>A MOGAT1 (16699 upstream) : ACSL3 (134384 downstream) 0.521739 41.400976 41.410397 12 11 KEEP --- --- --- --- COL4A4 1286 broad.mit.edu 37 2 227912265 227912265 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:227912265C>T uc010zlt.1 - 35 3869 c.3215G>A c.(3214-3216)GGA>GAA p.G1072E NM_000092 NP_000083 P53420 CO4A4_HUMAN alpha 4 type IV collagen precursor 1072 Triple-helical region. axon guidance|glomerular basement membrane development basal lamina|collagen type IV extracellular matrix structural constituent|protein binding ovary(5)|central_nervous_system(3)|pancreas(1)|breast(1)|skin(1) 11 Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242) Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181) 0.384615 46.915677 47.370998 15 24 KEEP --- --- --- --- COL4A4 1286 broad.mit.edu 37 2 227925013 227925013 + Intron SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:227925013A>G uc010zlt.1 - NM_000092 NP_000083 alpha 4 type IV collagen precursor axon guidance|glomerular basement membrane development basal lamina|collagen type IV extracellular matrix structural constituent|protein binding ovary(5)|central_nervous_system(3)|pancreas(1)|breast(1)|skin(1) 11 Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242) Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181) 0.7 105.915928 107.3456 28 12 KEEP --- --- --- --- COL4A3 1285 broad.mit.edu 37 2 228155511 228155511 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:228155511G>A uc002vom.1 + 37 3281 c.3119G>A c.(3118-3120)AGA>AAA p.R1040K COL4A3_uc002von.1_Missense_Mutation_p.R1040K|COL4A3_uc002voo.1_Missense_Mutation_p.R1040K|COL4A3_uc002vop.1_Missense_Mutation_p.R1040K|uc002voq.1_Intron|uc002vor.1_Intron NM_000091 NP_000082 Q01955 CO4A3_HUMAN alpha 3 type IV collagen isoform 1 precursor 1040 Triple-helical region. activation of caspase activity|axon guidance|blood circulation|cell adhesion|cell proliferation|cell surface receptor linked signaling pathway|glomerular basement membrane development|induction of apoptosis|negative regulation of angiogenesis|negative regulation of cell proliferation|sensory perception of sound collagen type IV extracellular matrix structural constituent|integrin binding|metalloendopeptidase inhibitor activity skin(2)|ovary(1) 3 all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247) Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187) 0.380952 25.693962 25.955386 8 13 KEEP --- --- --- --- SPHKAP 80309 broad.mit.edu 37 2 228973696 228973696 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:228973696C>T uc002vpq.2 - SPHKAP_uc002vpp.2_Intron|SPHKAP_uc010zlx.1_Intron NM_001142644 NP_001136116 sphingosine kinase type 1-interacting protein cytoplasm protein binding skin(5)|ovary(4)|lung(1) 10 Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23) Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232) 0.568627 98.078141 98.286852 29 22 KEEP --- --- --- --- Unknown broad.mit.edu 37 2 231438462 231438462 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:231438462C>T SP100 (28145 upstream) : CAB39 (139095 downstream) 0.52381 35.224546 35.234819 11 10 KEEP --- --- --- --- ALPI 248 broad.mit.edu 37 2 233321975 233321975 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:233321975C>T uc002vst.3 + 5 668 c.591C>T c.(589-591)GCC>GCT p.A197A ALPI_uc002vsu.3_Silent_p.A108A NM_001631 NP_001622 P09923 PPBI_HUMAN intestinal alkaline phosphatase precursor 197 phosphorylation anchored to membrane|integral to membrane|plasma membrane alkaline phosphatase activity|metal ion binding|protein binding central_nervous_system(1) 1 all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132) Epithelial(121;1.64e-16)|Kidney(3;9.71e-08)|KIRC - Kidney renal clear cell carcinoma(3;2.74e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000763)|Lung(119;0.00564)|LUSC - Lung squamous cell carcinoma(224;0.00746) 0.336449 113.796042 116.313729 36 71 KEEP --- --- --- --- TRPM8 79054 broad.mit.edu 37 2 234878182 234878182 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:234878182C>T uc002vvh.2 + TRPM8_uc010fyj.2_Intron NM_024080 NP_076985 transient receptor potential cation channel, integral to membrane skin(4) 4 Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224) Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108) Menthol(DB00825) 505 0.75 22.054105 22.508584 6 2 KEEP --- --- --- --- LRRFIP1 9208 broad.mit.edu 37 2 238629337 238629337 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:238629337C>T uc002vxe.2 + LRRFIP1_uc002vxc.2_Intron|LRRFIP1_uc010znm.1_Intron|LRRFIP1_uc002vxd.2_Intron|LRRFIP1_uc002vxf.2_Intron NM_001137552 NP_001131024 leucine rich repeat (in FLII) interacting negative regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent cytoplasm|cytoskeleton|nucleus DNA binding|double-stranded RNA binding|protein binding breast(3) 3 Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182) Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228) 0.36 28.268507 28.69974 9 16 KEEP --- --- --- --- ESPNL 339768 broad.mit.edu 37 2 239038780 239038780 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:239038780G>A uc002vxq.3 + 9 1535 c.1425G>A c.(1423-1425)GGG>GGA p.G475G ESPNL_uc010fyw.2_Silent_p.G171G NM_194312 NP_919288 Q6ZVH7 ESPNL_HUMAN espin-like 475 pancreas(1) 1 Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244) Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253) 0.666667 52.497938 53.086081 16 8 KEEP --- --- --- --- KIF1A 547 broad.mit.edu 37 2 241663402 241663402 + Silent SNP C G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:241663402C>G uc002vzy.2 - 39 4151 c.4005G>C c.(4003-4005)GCG>GCC p.A1335A KIF1A_uc010fzk.2_Silent_p.A1436A|KIF1A_uc002vzz.1_Silent_p.A1444A|KIF1A_uc002vzw.2_5'UTR|KIF1A_uc002vzx.2_Silent_p.A62A NM_004321 NP_004312 Q12756 KIF1A_HUMAN axonal transport of synaptic vesicles 1335 anterograde axon cargo transport cytoplasm|microtubule|nucleus ATP binding|microtubule motor activity lung(1) 1 all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244) Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176) 0.208333 21.517075 25.307011 10 38 KEEP --- --- --- --- SNED1 25992 broad.mit.edu 37 2 241991541 241991541 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:241991541C>T uc002wah.1 + 14 1936 c.1936C>T c.(1936-1938)CCC>TCC p.P646S NM_001080437 NP_001073906 Q8TER0 SNED1_HUMAN 6720455I24Rik homolog precursor 646 EGF-like 9. cell-matrix adhesion extracellular region calcium ion binding breast(1)|central_nervous_system(1) 2 all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238) Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109) 0.375 25.265974 25.596116 9 15 KEEP --- --- --- --- FARP2 9855 broad.mit.edu 37 2 242418052 242418052 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr2:242418052C>T uc002wbi.1 + NM_014808 NP_055623 FERM, RhoGEF and pleckstrin domain protein 2 axon guidance|neuron remodeling|Rac protein signal transduction|regulation of Rho protein signal transduction cytoskeleton|cytosol|extrinsic to membrane cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity upper_aerodigestive_tract(1)|ovary(1)|skin(1) 3 all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238) Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121) 0.470588 27.598991 27.611793 8 9 KEEP --- --- --- --- ANGPT4 51378 broad.mit.edu 37 20 855070 855070 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:855070C>T uc002wei.2 - ANGPT4_uc010zpn.1_Intron NM_015985 NP_057069 angiopoietin 4 precursor anti-apoptosis|blood coagulation|cellular response to hypoxia|leukocyte migration|negative regulation of angiogenesis|negative regulation of blood vessel endothelial cell migration|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of peptidyl-tyrosine phosphorylation|signal transduction extracellular space receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity ovary(2) 2 Pancreas(181;481 2077 3259 31286 49856) 1 151.248452 151.248452 41 0 KEEP --- --- --- --- TMC2 117532 broad.mit.edu 37 20 2605168 2605168 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:2605168G>A uc002wgf.1 + TMC2_uc002wgg.1_Intron NM_080751 NP_542789 transmembrane cochlear-expressed protein 2 integral to membrane ovary(3) 3 1 78.963513 78.963511 19 0 KEEP --- --- --- --- CPXM1 56265 broad.mit.edu 37 20 2779411 2779411 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:2779411G>A uc002wgu.2 - 2 365 c.301C>T c.(301-303)CCA>TCA p.P101S CPXM1_uc010gas.2_Missense_Mutation_p.P101S NM_019609 NP_062555 Q96SM3 CPXM1_HUMAN carboxypeptidase X, member 1 precursor 101 cell adhesion|proteolysis metallocarboxypeptidase activity|zinc ion binding ovary(2)|skin(2) 4 1 159.754432 159.754432 41 0 KEEP --- --- --- --- GNRH2 2797 broad.mit.edu 37 20 3025215 3025215 + Splice_Site SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:3025215G>A uc002whr.1 + 2 205 c.154_splice c.e2+1 p.G52_splice GNRH2_uc002whp.1_Splice_Site_p.A52_splice|GNRH2_uc002whq.1_Splice_Site_p.G52_splice|GNRH2_uc010gau.1_Splice_Site_p.G52_splice|MRPS26_uc002whs.2_5'Flank NM_001501 NP_001492 gonadotropin-releasing hormone 2 isoform a multicellular organismal development|signal transduction extracellular region|soluble fraction hormone activity 0 0.241379 17.716814 19.481901 7 22 KEEP --- --- --- --- SLC4A11 83959 broad.mit.edu 37 20 3215452 3215452 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:3215452G>A uc002wig.2 - 2 273 c.225C>T c.(223-225)ATC>ATT p.I75I SLC4A11_uc010zqe.1_Silent_p.I102I|SLC4A11_uc002wih.2_RNA|SLC4A11_uc010zqf.1_Silent_p.I59I NM_032034 NP_114423 Q8NBS3 S4A11_HUMAN solute carrier family 4 member 11 75 Cytoplasmic (Potential). cellular cation homeostasis|fluid transport|phosphoenolpyruvate-dependent sugar phosphotransferase system basolateral plasma membrane|integral to membrane bicarbonate transmembrane transporter activity|borate transmembrane transporter activity|hydrogen ion channel activity|inorganic anion exchanger activity|sodium channel activity|sugar:hydrogen symporter activity ovary(1) 1 NSCLC(190;922 2139 10266 10292 38692) 1 86.092327 86.092327 22 0 KEEP --- --- --- --- TMX4 56255 broad.mit.edu 37 20 7980274 7980274 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:7980274G>A uc002wmx.1 - NM_021156 NP_066979 thioredoxin-related transmembrane protein 4 cell redox homeostasis|electron transport chain|transport integral to membrane 0 1 17.814168 17.783344 5 0 KEEP --- --- --- --- C20orf103 24141 broad.mit.edu 37 20 9498814 9498814 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:9498814G>A uc002wni.1 + 5 832 c.603G>A c.(601-603)ATG>ATA p.M201I C20orf103_uc010zrc.1_Missense_Mutation_p.M157I NM_012261 NP_036393 Q9UJQ1 CT103_HUMAN chromosome 20 open reading frame 103 precursor 201 Extracellular (Potential). integral to membrane p.M201fs*33(1) upper_aerodigestive_tract(1)|lung(1)|breast(1) 3 COAD - Colon adenocarcinoma(9;0.194) 1 124.447833 124.447833 34 0 KEEP --- --- --- --- MKKS 8195 broad.mit.edu 37 20 10389253 10389253 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:10389253G>A uc002wnt.1 - MKKS_uc002wnu.1_Intron|MKKS_uc010zrd.1_Intron NM_018848 NP_061336 McKusick-Kaufman syndrome protein brain morphogenesis|cerebral cortex development|convergent extension involved in gastrulation|detection of mechanical stimulus involved in sensory perception of sound|fat cell differentiation|flagellum assembly|gonad development|heart looping|hippocampus development|intracellular transport|melanosome transport|photoreceptor cell maintenance|pigment granule aggregation in cell center|protein folding|regulation of cilium beat frequency involved in ciliary motility|sensory perception of smell|social behavior|spermatid development|striatum development cytosol|microtubule organizing center|motile cilium ATP binding|unfolded protein binding 0 Melanoma(79;1979 2212 6640) Bardet-Biedl_syndrome 0.941176 55.699972 58.370489 16 1 KEEP --- --- --- --- JAG1 182 broad.mit.edu 37 20 10626682 10626682 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:10626682C>T uc002wnw.2 - 15 2452 c.1936G>A c.(1936-1938)GAT>AAT p.D646N JAG1_uc010gcd.1_Missense_Mutation_p.D204N NM_000214 NP_000205 P78504 JAG1_HUMAN jagged 1 precursor 646 Extracellular (Potential).|EGF-like 11; calcium-binding (Potential). angiogenesis|cell communication|cell fate determination|endothelial cell differentiation|hemopoiesis|keratinocyte differentiation|myoblast differentiation|Notch receptor processing|Notch signaling pathway|regulation of cell migration|regulation of cell proliferation extracellular region|integral to plasma membrane calcium ion binding|growth factor activity|Notch binding|structural molecule activity lung(3)|ovary(2)|central_nervous_system(2)|breast(1)|pancreas(1) 9 587 Alagille_Syndrome 1 284.36706 284.36706 74 0 KEEP --- --- --- --- CRNKL1 51340 broad.mit.edu 37 20 20020567 20020567 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:20020567G>A uc002wrs.2 - NM_016652 NP_057736 crooked neck-like 1 protein spliceosome assembly catalytic step 2 spliceosome|cytoplasm|nuclear speck RNA binding ovary(2)|large_intestine(1) 3 1 38.495284 38.493331 9 0 KEEP --- --- --- --- NINL 22981 broad.mit.edu 37 20 25484380 25484380 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:25484380G>A uc002wux.1 - NINL_uc010gdn.1_Intron|NINL_uc010gdo.1_Intron|NINL_uc010ztf.1_Intron NM_025176 NP_079452 ninein-like G2/M transition of mitotic cell cycle cytosol|microtubule|microtubule organizing center calcium ion binding ovary(2)|pancreas(1)|central_nervous_system(1)|skin(1) 5 1 56.95319 56.953159 15 0 KEEP --- --- --- --- BPIL3 128859 broad.mit.edu 37 20 31622150 31622150 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:31622150C>T uc010zuc.1 + BPIL3_uc010zud.1_Intron NM_174897 NP_777557 bactericidal/permeability-increasing extracellular region lipid binding ovary(1)|pancreas(1) 2 0.813953 245.788014 253.726609 70 16 KEEP --- --- --- --- C20orf185 359710 broad.mit.edu 37 20 31651597 31651597 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:31651597C>T uc002wym.1 + NM_182658 NP_872599 antimicrobial peptide RYA3 precursor innate immune response cytoplasm|extracellular region lipid binding|protein binding ovary(4) 4 0.807692 71.790477 74.0921 21 5 KEEP --- --- --- --- MYH7B 57644 broad.mit.edu 37 20 33580780 33580780 + Intron SNP G C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:33580780G>C uc002xbi.1 + NM_020884 NP_065935 myosin, heavy polypeptide 7B, cardiac muscle, membrane|myosin filament actin binding|ATP binding|motor activity ovary(1)|breast(1) 2 BRCA - Breast invasive adenocarcinoma(18;0.00691) 0.851064 297.018294 308.121315 80 14 KEEP --- --- --- --- CPNE1 8904 broad.mit.edu 37 20 34215371 34215371 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:34215371G>A uc002xdf.2 - CPNE1_uc002xdc.2_Intron|CPNE1_uc010zvj.1_Intron|CPNE1_uc002xde.2_Intron|CPNE1_uc002xdg.2_Intron|CPNE1_uc010gfi.2_Intron|CPNE1_uc010gfj.2_Intron|CPNE1_uc002xdh.2_Intron|CPNE1_uc002xdi.2_Intron|CPNE1_uc002xdj.2_Intron|CPNE1_uc002xdk.2_Intron|CPNE1_uc002xdl.2_Intron|CPNE1_uc002xdm.2_Intron NM_152931 NP_690908 copine I isoform a lipid metabolic process|vesicle-mediated transport calcium-dependent phospholipid binding|phosphatidylserine binding|transporter activity upper_aerodigestive_tract(1) 1 Lung NSC(9;0.0053)|all_lung(11;0.00785) BRCA - Breast invasive adenocarcinoma(18;0.00953) 0.25 57.534074 62.306347 21 63 KEEP --- --- --- --- CHD6 84181 broad.mit.edu 37 20 40074372 40074372 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:40074372C>T uc002xka.1 - 25 3988 c.3810G>A c.(3808-3810)ATG>ATA p.M1270I CHD6_uc002xkb.1_Missense_Mutation_p.M36I NM_032221 NP_115597 Q8TD26 CHD6_HUMAN chromodomain helicase DNA binding protein 6 1270 chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding ovary(6)|skin(5)|lung(2)|central_nervous_system(1) 14 Myeloproliferative disorder(115;0.00425) 0.16092 26.990632 36.512822 14 73 KEEP --- --- --- --- PTPRT 11122 broad.mit.edu 37 20 40864884 40864884 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:40864884G>A uc002xkg.2 - 15 2511 c.2327C>T c.(2326-2328)TCC>TTC p.S776F PTPRT_uc010ggj.2_Missense_Mutation_p.S795F NM_007050 NP_008981 O14522 PTPRT_HUMAN protein tyrosine phosphatase, receptor type, T 776 Cytoplasmic (Potential). homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway cell surface|integral to membrane|plasma membrane alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity skin(8)|ovary(7)|lung(5) 20 Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783) 646 0.695876 471.210307 477.872833 135 59 KEEP --- --- --- --- PTPRT 11122 broad.mit.edu 37 20 40979340 40979340 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:40979340G>A uc002xkg.2 - 11 1977 c.1793C>T c.(1792-1794)ACC>ATC p.T598I PTPRT_uc010ggj.2_Missense_Mutation_p.T598I NM_007050 NP_008981 O14522 PTPRT_HUMAN protein tyrosine phosphatase, receptor type, T 598 Extracellular (Potential).|Fibronectin type-III 4. homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway cell surface|integral to membrane|plasma membrane alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity skin(8)|ovary(7)|lung(5) 20 Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783) 646 0.790323 677.722809 697.083143 196 52 KEEP --- --- --- --- GDAP1L1 78997 broad.mit.edu 37 20 42885871 42885871 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:42885871C>T uc002xlq.2 + 2 326 c.259C>T c.(259-261)CCC>TCC p.P87S GDAP1L1_uc002xlp.1_Missense_Mutation_p.P87S|GDAP1L1_uc010zwl.1_Missense_Mutation_p.P87S|GDAP1L1_uc010zwm.1_Missense_Mutation_p.P87S|GDAP1L1_uc010zwn.1_Intron NM_024034 NP_076939 Q96MZ0 GD1L1_HUMAN ganglioside-induced differentiation-associated 87 GST N-terminal. large_intestine(1) 1 Myeloproliferative disorder(115;0.0122) COAD - Colon adenocarcinoma(18;0.00189) 0.810345 155.45417 160.675617 47 11 KEEP --- --- --- --- HNF4A 3172 broad.mit.edu 37 20 43048306 43048306 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:43048306G>A uc002xma.2 + HNF4A_uc002xlt.2_Intron|HNF4A_uc002xlu.2_Intron|HNF4A_uc002xlv.2_Intron|HNF4A_uc002xly.2_Intron|HNF4A_uc002xlz.2_Intron|HNF4A_uc010ggq.2_Intron NM_000457 NP_000448 hepatocyte nuclear factor 4 alpha isoform b blood coagulation|endocrine pancreas development|glucose homeostasis|negative regulation of cell growth|negative regulation of cell proliferation|ornithine metabolic process|phospholipid homeostasis|positive regulation of cholesterol homeostasis|regulation of growth hormone receptor signaling pathway|regulation of insulin secretion|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to glucose stimulus|triglyceride homeostasis|xenobiotic metabolic process cytoplasm activating transcription factor binding|protein homodimerization activity|receptor binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|steroid hormone receptor activity|transcription regulatory region DNA binding|zinc ion binding ovary(1)|lung(1)|skin(1) 3 Myeloproliferative disorder(115;0.0122) COAD - Colon adenocarcinoma(18;0.00189) Colon(79;2 1269 8820 14841 52347) 0.1875 67.722616 82.303182 30 130 KEEP --- --- --- --- WISP2 8839 broad.mit.edu 37 20 43353390 43353390 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:43353390G>A uc002xmn.2 + 4 642 c.289G>A c.(289-291)GAC>AAC p.D97N uc002xml.1_Intron|uc002xmm.1_Intron|WISP2_uc002xmp.2_Missense_Mutation_p.D97N|WISP2_uc002xmq.2_Intron NM_003881 NP_003872 O76076 WISP2_HUMAN WNT1 inducible signaling pathway protein 2 97 cell adhesion|cell-cell signaling|signal transduction extracellular region|soluble fraction insulin-like growth factor binding skin(1) 1 Myeloproliferative disorder(115;0.0122) 0.69697 80.03844 81.182259 23 10 KEEP --- --- --- --- PABPC1L 80336 broad.mit.edu 37 20 43559331 43559331 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:43559331G>A uc010ggv.1 + 8 1285 c.1203G>A c.(1201-1203)CAG>CAA p.Q401Q PABPC1L_uc010zwq.1_RNA|PABPC1L_uc002xmv.2_RNA|PABPC1L_uc002xmw.2_5'Flank|PABPC1L_uc002xmx.2_5'Flank NM_001124756 NP_001118228 Q4VXU2 PAP1L_HUMAN poly(A)-binding protein, cytoplasmic 1-like 401 nucleotide binding|RNA binding ovary(1) 1 0.791123 1015.04982 1045.08838 303 80 KEEP --- --- --- --- SEMG2 6407 broad.mit.edu 37 20 43850039 43850039 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:43850039C>T uc010ggz.2 + SEMG2_uc002xnk.2_Silent_p.S3S|SEMG2_uc002xnl.2_Silent_p.S3S NM_003008 NP_002999 semenogelin II precursor sexual reproduction extracellular space|stored secretory granule structural molecule activity skin(1) 1 Myeloproliferative disorder(115;0.0122) 0.782609 258.849698 265.622506 72 20 KEEP --- --- --- --- MATN4 8785 broad.mit.edu 37 20 43922583 43922583 + Missense_Mutation SNP C A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:43922583C>A uc002xnn.2 - 9 1839 c.1652G>T c.(1651-1653)CGC>CTC p.R551L MATN4_uc002xno.2_Missense_Mutation_p.R510L|MATN4_uc002xnp.2_Missense_Mutation_p.R469L|MATN4_uc010zwr.1_Missense_Mutation_p.R499L|MATN4_uc002xnr.1_Missense_Mutation_p.R551L NM_003833 NP_003824 O95460 MATN4_HUMAN matrilin 4 isoform 1 precursor 592 Potential. extracellular region protein binding 0 Myeloproliferative disorder(115;0.0122) 0.021459 -50.612874 9.010398 5 228 KEEP --- --- --- --- RBPJL 11317 broad.mit.edu 37 20 43942835 43942835 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:43942835G>A uc002xns.2 + RBPJL_uc002xnt.2_Intron NM_014276 NP_055091 recombining binding protein L signal transduction nucleus DNA binding|sequence-specific DNA binding transcription factor activity ovary(1) 1 Myeloproliferative disorder(115;0.0122) 0.201299 73.632484 86.40624 31 123 KEEP --- --- --- --- SPINLW1 57119 broad.mit.edu 37 20 44171516 44171516 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:44171516G>A uc002xou.2 - SPINLW1_uc010zxc.1_Intron|SPINLW1_uc002xot.2_Intron|SPINLW1_uc002xov.1_3'UTR NM_020398 NP_065131 serine peptidase inhibitor-like, with Kunitz and extracellular region serine-type endopeptidase inhibitor activity pancreas(1) 1 Myeloproliferative disorder(115;0.0122) 0.169935 56.147736 71.923654 26 127 KEEP --- --- --- --- WFDC8 90199 broad.mit.edu 37 20 44181659 44181659 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:44181659C>T uc002xow.2 - WFDC8_uc002xox.2_Intron NM_181510 NP_852611 WAP four-disulfide core domain 8 precursor extracellular region serine-type endopeptidase inhibitor activity 0 Myeloproliferative disorder(115;0.0122) 0.189781 65.772747 78.09819 26 111 KEEP --- --- --- --- ZSWIM3 140831 broad.mit.edu 37 20 44506490 44506490 + Missense_Mutation SNP G T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:44506490G>T uc002xqd.2 + 2 1496 c.1293G>T c.(1291-1293)TTG>TTT p.L431F ZSWIM3_uc010zxg.1_Missense_Mutation_p.L425F NM_080752 NP_542790 Q96MP5 ZSWM3_HUMAN zinc finger, SWIM domain containing 3 431 zinc ion binding ovary(2) 2 Myeloproliferative disorder(115;0.0122) 0.046358 -17.810229 15.343354 7 144 KEEP --- --- --- --- SLC12A5 57468 broad.mit.edu 37 20 44663446 44663446 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:44663446C>T uc010zxl.1 + SLC12A5_uc002xra.2_Intron|SLC12A5_uc010zxm.1_Intron|SLC12A5_uc002xrb.2_Intron NM_001134771 NP_001128243 solute carrier family 12 (potassium-chloride potassium ion transport|sodium ion transport integral to membrane potassium:chloride symporter activity ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1) 5 Myeloproliferative disorder(115;0.0122) Bumetanide(DB00887)|Potassium Chloride(DB00761) 0.19403 34.634014 40.486853 13 54 KEEP --- --- --- --- SLC12A5 57468 broad.mit.edu 37 20 44664214 44664214 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:44664214G>A uc010zxl.1 + SLC12A5_uc002xra.2_Intron|SLC12A5_uc010zxm.1_Intron|SLC12A5_uc002xrb.2_Intron NM_001134771 NP_001128243 solute carrier family 12 (potassium-chloride potassium ion transport|sodium ion transport integral to membrane potassium:chloride symporter activity ovary(2)|large_intestine(1)|central_nervous_system(1)|skin(1) 5 Myeloproliferative disorder(115;0.0122) Bumetanide(DB00887)|Potassium Chloride(DB00761) 0.864407 180.964477 188.556359 51 8 KEEP --- --- --- --- CDH22 64405 broad.mit.edu 37 20 44815401 44815401 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:44815401G>A uc002xrm.2 - CDH22_uc010ghk.1_Intron NM_021248 NP_067071 cadherin 22 precursor homophilic cell adhesion integral to membrane|plasma membrane calcium ion binding ovary(4)|skin(1) 5 Myeloproliferative disorder(115;0.0122) 0.823944 405.847008 419.892162 117 25 KEEP --- --- --- --- CDH22 64405 broad.mit.edu 37 20 44845571 44845571 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:44845571C>T uc002xrm.2 - 4 1133 c.732G>A c.(730-732)GTG>GTA p.V244V CDH22_uc010ghk.1_Silent_p.V244V|CDH22_uc002xrn.1_5'UTR NM_021248 NP_067071 Q9UJ99 CAD22_HUMAN cadherin 22 precursor 244 Extracellular (Potential).|Cadherin 2. homophilic cell adhesion integral to membrane|plasma membrane calcium ion binding ovary(4)|skin(1) 5 Myeloproliferative disorder(115;0.0122) 0.712963 512.511814 521.288966 154 62 KEEP --- --- --- --- ZNF334 55713 broad.mit.edu 37 20 45130098 45130098 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:45130098G>A uc002xsc.2 - 5 2064 c.1880C>T c.(1879-1881)CCA>CTA p.P627L ZNF334_uc002xsa.2_Missense_Mutation_p.P650L|ZNF334_uc002xsb.2_Missense_Mutation_p.P589L|ZNF334_uc002xsd.2_Missense_Mutation_p.P589L|ZNF334_uc010ghl.2_Missense_Mutation_p.P626L NM_018102 NP_060572 Q9HCZ1 ZN334_HUMAN zinc finger protein 334 isoform a 627 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding ovary(1)|pancreas(1) 2 Myeloproliferative disorder(115;0.0122) 0.156757 108.413255 150.016115 58 312 KEEP --- --- --- --- ZNF334 55713 broad.mit.edu 37 20 45130103 45130103 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:45130103C>T uc002xsc.2 - 5 2059 c.1875G>A c.(1873-1875)GAG>GAA p.E625E ZNF334_uc002xsa.2_Silent_p.E648E|ZNF334_uc002xsb.2_Silent_p.E587E|ZNF334_uc002xsd.2_Silent_p.E587E|ZNF334_uc010ghl.2_Silent_p.E624E NM_018102 NP_060572 Q9HCZ1 ZN334_HUMAN zinc finger protein 334 isoform a 625 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding ovary(1)|pancreas(1) 2 Myeloproliferative disorder(115;0.0122) 0.157895 117.614752 160.089028 60 320 KEEP --- --- --- --- EYA2 2139 broad.mit.edu 37 20 45717880 45717880 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:45717880G>A uc002xsm.2 + 8 1038 c.664G>A c.(664-666)GAA>AAA p.E222K EYA2_uc010ghp.2_Missense_Mutation_p.E222K|EYA2_uc002xsn.2_Missense_Mutation_p.E227K|EYA2_uc002xso.2_Missense_Mutation_p.E222K|EYA2_uc002xsp.2_Missense_Mutation_p.E222K|EYA2_uc002xsq.2_Missense_Mutation_p.E222K NM_005244 NP_005235 O00167 EYA2_HUMAN eyes absent 2 isoform a 222 DNA repair|histone dephosphorylation|mesodermal cell fate specification|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus magnesium ion binding|protein binding|protein tyrosine phosphatase activity ovary(1) 1 Myeloproliferative disorder(115;0.0241) Pancreas(120;56 1725 18501 25218 43520) 0.207048 108.416875 126.457513 47 180 KEEP --- --- --- --- PTGIS 5740 broad.mit.edu 37 20 48130930 48130930 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:48130930C>T uc002xut.2 - 7 912 c.858G>A c.(856-858)GGG>GGA p.G286G PTGIS_uc010zyi.1_Silent_p.G147G NM_000961 NP_000952 Q16647 PTGIS_HUMAN prostaglandin I2 synthase 286 hormone biosynthetic process|prostaglandin biosynthetic process|xenobiotic metabolic process endoplasmic reticulum lumen|endoplasmic reticulum membrane|integral to membrane electron carrier activity|heme binding|monooxygenase activity|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|prostaglandin-I synthase activity skin(2)|ovary(1) 3 BRCA - Breast invasive adenocarcinoma(12;2.37e-05)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166) Phenylbutazone(DB00812) 0.243902 51.557975 56.459996 20 62 KEEP --- --- --- --- MOCS3 27304 broad.mit.edu 37 20 49575256 49575256 + 5'Flank SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:49575256G>A uc002xvy.1 + DPM1_uc002xvw.1_5'Flank|DPM1_uc002xvx.1_5'Flank NM_014484 NP_055299 molybdenum cofactor synthesis 3 enzyme active site formation via L-cysteine persulfide|Mo-molybdopterin cofactor biosynthetic process|tRNA thio-modification|tRNA wobble uridine modification|water-soluble vitamin metabolic process cytosol ATP binding|metal ion binding|nucleotidyltransferase activity|protein binding|thiosulfate sulfurtransferase activity|URM1 activating enzyme activity skin(2)|ovary(1) 3 0.823529 100.420103 103.773029 28 6 KEEP --- --- --- --- NFATC2 4773 broad.mit.edu 37 20 50140296 50140296 + Missense_Mutation SNP G T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:50140296G>T uc002xwd.2 - 2 704 c.484C>A c.(484-486)CGC>AGC p.R162S NFATC2_uc002xwc.2_Missense_Mutation_p.R162S|NFATC2_uc010zyv.1_Intron|NFATC2_uc010zyw.1_Intron|NFATC2_uc010zyx.1_Missense_Mutation_p.R142S|NFATC2_uc010zyy.1_Intron|NFATC2_uc010zyz.1_Intron|NFATC2_uc002xwe.2_Missense_Mutation_p.R142S NM_173091 NP_775114 Q13469 NFAC2_HUMAN nuclear factor of activated T-cells, 162 Required for cytoplasmic retention of the phosphorylated form (By similarity).|Trans-activation domain A (TAD-A). B cell receptor signaling pathway|positive regulation of B cell proliferation|response to DNA damage stimulus|response to drug actin cytoskeleton|nucleus|plasma membrane protein binding|sequence-specific DNA binding transcription factor activity ovary(2) 2 Hepatocellular(150;0.248) 0.28 19.620416 20.704692 7 18 KEEP --- --- --- --- SALL4 57167 broad.mit.edu 37 20 50405646 50405646 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:50405646G>A uc002xwh.3 - 3 2597 c.2496C>T c.(2494-2496)GCC>GCT p.A832A SALL4_uc010gii.2_Silent_p.A395A|SALL4_uc002xwi.3_Silent_p.A55A NM_020436 NP_065169 Q9UJQ4 SALL4_HUMAN sal-like 4 832 transcription, DNA-dependent nucleus DNA binding|zinc ion binding ovary(2) 2 0.738095 217.483414 221.789663 62 22 KEEP --- --- --- --- DOK5 55816 broad.mit.edu 37 20 53171464 53171464 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:53171464C>T uc002xwy.2 + DOK5_uc010gin.2_Intron|DOK5_uc002xwz.2_Intron NM_018431 NP_060901 docking protein 5 insulin receptor binding ovary(1) 1 Colorectal(105;0.202) 0.794118 288.730307 296.909916 81 21 KEEP --- --- --- --- C20orf106 200232 broad.mit.edu 37 20 55101125 55101125 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:55101125G>A uc002xxx.2 + 2 595 c.515G>A c.(514-516)TGA>TAA p.*172* GCNT7_uc010zzg.1_5'Flank|C20orf107_uc010zzh.1_Intron NM_001012971 NP_001012989 Q5JX71 CT106_HUMAN hypothetical protein LOC200232 precursor 172 integral to membrane 0 Colorectal(105;0.202) 0.173913 63.09604 79.256488 28 133 KEEP --- --- --- --- SPO11 23626 broad.mit.edu 37 20 55918295 55918295 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:55918295C>T uc002xye.2 + SPO11_uc002xyf.2_Intron NM_012444 NP_036576 meiotic recombination protein SPO11 isoform a female gamete generation|reciprocal meiotic recombination chromosome|nucleus ATP binding|DNA binding|hydrolase activity breast(2)|skin(1) 3 Lung NSC(12;0.0066)|all_lung(29;0.0188)|Melanoma(10;0.242) BRCA - Breast invasive adenocarcinoma(4;1.73e-14)|Epithelial(14;9.02e-10)|all cancers(14;9.31e-09) Editing_and_processing_nucleases 0.142857 9.750103 14.052523 5 30 KEEP --- --- --- --- ZBP1 81030 broad.mit.edu 37 20 56190115 56190115 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:56190115C>T uc002xyo.2 - 4 611 c.330G>A c.(328-330)GAG>GAA p.E110E ZBP1_uc010gjm.2_Silent_p.E110E|ZBP1_uc002xyp.2_Silent_p.E35E|ZBP1_uc010zzn.1_Silent_p.E110E NM_030776 NP_110403 Q9H171 ZBP1_HUMAN Z-DNA binding protein 1 isoform a 110 DRADA 2. cytoplasm|nucleus double-stranded RNA adenosine deaminase activity|left-handed Z-DNA binding|RNA binding ovary(2) 2 Lung NSC(12;0.000545)|all_lung(29;0.00195)|Melanoma(10;0.242) BRCA - Breast invasive adenocarcinoma(13;7.87e-13)|Epithelial(14;3.26e-09)|all cancers(14;3.62e-08) 0.787952 1186.295694 1218.078364 327 88 KEEP --- --- --- --- ZNF831 128611 broad.mit.edu 37 20 57767635 57767635 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:57767635G>A uc002yan.2 + 1 1561 c.1561G>A c.(1561-1563)GAG>AAG p.E521K NM_178457 NP_848552 Q5JPB2 ZN831_HUMAN zinc finger protein 831 521 intracellular nucleic acid binding|zinc ion binding skin(13)|ovary(1) 14 all_lung(29;0.0085) 0.137931 5.77879 9.45743 4 25 KEEP --- --- --- --- ZNF831 128611 broad.mit.edu 37 20 57770791 57770792 + Intron DNP CC TT TT MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:57770791_57770792CC>TT uc002yan.2 + NM_178457 NP_848552 zinc finger protein 831 intracellular nucleic acid binding|zinc ion binding skin(13)|ovary(1) 14 all_lung(29;0.0085) 0.209877 90.159965 102.777048 34 128 KEEP --- --- --- --- ZNF831 128611 broad.mit.edu 37 20 57781897 57781897 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:57781897C>T uc002yan.2 + NM_178457 NP_848552 zinc finger protein 831 intracellular nucleic acid binding|zinc ion binding skin(13)|ovary(1) 14 all_lung(29;0.0085) 0.186747 229.075907 274.852819 93 405 KEEP --- --- --- --- LSM14B 149986 broad.mit.edu 37 20 60699569 60699569 + Intron SNP C G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:60699569C>G uc010gjy.1 + LSM14B_uc002ybt.2_Intron|LSM14B_uc010gjx.1_Intron|LSM14B_uc002ybv.2_Intron|LSM14B_uc010gjz.1_Intron|LSM14B_uc010zzz.1_5'Flank NM_144703 NP_653304 LSM14 homolog B multicellular organismal development|regulation of translation ribonucleoprotein complex 0 Breast(26;3.97e-09) BRCA - Breast invasive adenocarcinoma(19;1.28e-07) OREG0026104 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0.612903 70.431677 70.777678 19 12 KEEP --- --- --- --- LSM14B 149986 broad.mit.edu 37 20 60699660 60699660 + Intron SNP C G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:60699660C>G uc010gjy.1 + LSM14B_uc002ybt.2_Intron|LSM14B_uc010gjx.1_Intron|LSM14B_uc002ybv.2_Intron|LSM14B_uc010gjz.1_Intron|LSM14B_uc010zzz.1_5'Flank NM_144703 NP_653304 LSM14 homolog B multicellular organismal development|regulation of translation ribonucleoprotein complex 0 Breast(26;3.97e-09) BRCA - Breast invasive adenocarcinoma(19;1.28e-07) OREG0026104 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0.791045 415.323826 425.831749 106 28 KEEP --- --- --- --- LSM14B 149986 broad.mit.edu 37 20 60699885 60699885 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:60699885C>T uc010gjy.1 + LSM14B_uc002ybt.2_Intron|LSM14B_uc010gjx.1_Intron|LSM14B_uc002ybv.2_Intron|LSM14B_uc010gjz.1_Intron|LSM14B_uc010zzz.1_Intron NM_144703 NP_653304 LSM14 homolog B multicellular organismal development|regulation of translation ribonucleoprotein complex 0 Breast(26;3.97e-09) BRCA - Breast invasive adenocarcinoma(19;1.28e-07) 0.795455 128.252023 131.818523 35 9 KEEP --- --- --- --- LAMA5 3911 broad.mit.edu 37 20 60909087 60909087 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:60909087G>A uc002ycq.2 - 23 2815 c.2748C>T c.(2746-2748)ATC>ATT p.I916I NM_005560 NP_005551 O15230 LAMA5_HUMAN laminin alpha 5 precursor 916 Domain IV 1 (domain IV B). angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex integrin binding ovary(1)|pancreas(1)|skin(1) 3 Breast(26;1.57e-08) BRCA - Breast invasive adenocarcinoma(19;4.36e-06) Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031) 0.219512 21.852653 24.824902 9 32 KEEP --- --- --- --- LAMA5 3911 broad.mit.edu 37 20 60913609 60913609 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:60913609C>T uc002ycq.2 - 12 1600 c.1533G>A c.(1531-1533)AGG>AGA p.R511R NM_005560 NP_005551 O15230 LAMA5_HUMAN laminin alpha 5 precursor 511 Laminin EGF-like 4. angiogenesis|cell proliferation|cell recognition|cytoskeleton organization|endothelial cell differentiation|focal adhesion assembly|integrin-mediated signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development|substrate adhesion-dependent cell spreading extracellular space|laminin-1 complex|laminin-10 complex|laminin-11 complex integrin binding ovary(1)|pancreas(1)|skin(1) 3 Breast(26;1.57e-08) BRCA - Breast invasive adenocarcinoma(19;4.36e-06) Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031) 0.121212 6.57697 11.216255 4 29 KEEP --- --- --- --- TCFL5 10732 broad.mit.edu 37 20 61473309 61473309 + 3'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:61473309G>A uc002ydp.2 - 6 TCFL5_uc002ydo.2_3'UTR NM_006602 NP_006593 transcription factor-like 5 protein cell differentiation|multicellular organismal development|regulation of cell differentiation|regulation of cell proliferation|spermatogenesis|transcription from RNA polymerase II promoter DNA binding|sequence-specific DNA binding transcription factor activity large_intestine(1) 1 Breast(26;5.68e-08) 0.186667 30.803424 37.703951 14 61 KEEP --- --- --- --- PRIC285 85441 broad.mit.edu 37 20 62192594 62192594 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr20:62192594G>A uc002yfm.2 - 15 7879 c.6987C>T c.(6985-6987)TTC>TTT p.F2329F PRIC285_uc002yfl.1_Silent_p.F1760F NM_001037335 NP_001032412 Q9BYK8 PR285_HUMAN PPAR-alpha interacting complex protein 285 2329 cellular lipid metabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleoplasm ATP binding|DNA binding|helicase activity|ribonuclease activity|RNA binding|transcription coactivator activity|zinc ion binding central_nervous_system(2) 2 all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13) Epithelial(9;1.27e-08)|all cancers(9;7.32e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06) 0.2 71.347764 84.316203 31 124 KEEP --- --- --- --- Unknown broad.mit.edu 37 21 10862882 10862882 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr21:10862882C>T None (None upstream) : TPTE (43861 downstream) 0.128788 25.696057 43.403236 17 115 KEEP --- --- --- --- Unknown broad.mit.edu 37 21 10885083 10885083 + IGR SNP C A A rs549081 by1000genomes MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr21:10885083C>A None (None upstream) : TPTE (21660 downstream) 0.466667 20.322332 20.336952 7 8 KEEP --- --- --- --- Unknown broad.mit.edu 37 21 11181129 11181129 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr21:11181129C>T BAGE (82192 upstream) : None (None downstream) 0.096573 23.201656 75.547947 31 290 KEEP --- --- --- --- SAMSN1 64092 broad.mit.edu 37 21 15884799 15884799 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr21:15884799G>A uc002yju.1 - 4 457 c.375C>T c.(373-375)TCC>TCT p.S125S SAMSN1_uc010gky.1_Intron|SAMSN1_uc002yjv.1_Silent_p.S193S NM_022136 NP_071419 Q9NSI8 SAMN1_HUMAN SAM domain, SH3 domain and nuclear localization 125 negative regulation of adaptive immune response|negative regulation of B cell activation|negative regulation of peptidyl-tyrosine phosphorylation cytoplasm|nucleus|ruffle phosphotyrosine binding ovary(3)|pancreas(1) 4 Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164) 0.493671 264.051056 264.056498 78 80 KEEP --- --- --- --- Unknown broad.mit.edu 37 21 20618450 20618450 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr21:20618450G>A TMPRSS15 (842480 upstream) : None (None downstream) 0.5 20.150094 20.150094 6 6 KEEP --- --- --- --- TTC3 7267 broad.mit.edu 37 21 38469064 38469064 + Intron SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr21:38469064A>G uc002yvz.2 + TTC3_uc011aee.1_Intron|TTC3_uc002ywa.2_Intron|TTC3_uc002ywb.2_Intron|TTC3_uc010gnf.2_Intron|TTC3_uc011aed.1_Intron|TTC3_uc010gne.1_Intron NM_001001894 NP_001001894 tetratricopeptide repeat domain 3 protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process nucleus protein binding|ubiquitin-protein ligase activity|zinc ion binding skin(3)|ovary(2)|lung(2)|breast(2) 9 Myeloproliferative disorder(46;0.0412) Ovarian(38;194 1649 35661) 0.4 14.198512 14.285835 4 6 KEEP --- --- --- --- TTC3 7267 broad.mit.edu 37 21 38521017 38521017 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr21:38521017C>T uc002yvz.2 + TTC3_uc011aee.1_Intron|TTC3_uc002ywa.2_Intron|TTC3_uc002ywb.2_Intron|TTC3_uc010gnf.2_Intron|TTC3_uc002ywc.2_Intron|TTC3_uc011aed.1_Intron NM_001001894 NP_001001894 tetratricopeptide repeat domain 3 protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process nucleus protein binding|ubiquitin-protein ligase activity|zinc ion binding skin(3)|ovary(2)|lung(2)|breast(2) 9 Myeloproliferative disorder(46;0.0412) Ovarian(38;194 1649 35661) 0.388889 22.020719 22.215515 7 11 KEEP --- --- --- --- TTC3 7267 broad.mit.edu 37 21 38564494 38564495 + Missense_Mutation DNP TC GT GT MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr21:38564494_38564495TC>GT uc002yvz.2 + 41 5302_5303 c.5197_5198TC>GT c.(5197-5199)TCA>GTA p.S1733V TTC3_uc002ywa.2_Missense_Mutation_p.S1733V|TTC3_uc002ywb.2_Missense_Mutation_p.S1733V|TTC3_uc010gnf.2_Missense_Mutation_p.S1498V|TTC3_uc002ywc.2_Missense_Mutation_p.S1423V NM_001001894 NP_001001894 P53804 TTC3_HUMAN tetratricopeptide repeat domain 3 1733 protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process nucleus protein binding|ubiquitin-protein ligase activity|zinc ion binding skin(3)|ovary(2)|lung(2)|breast(2) 9 Myeloproliferative disorder(46;0.0412) Ovarian(38;194 1649 35661) 0.5 34.213348 34.213348 11 11 KEEP --- --- --- --- KCNJ6 3763 broad.mit.edu 37 21 39086795 39086795 + Missense_Mutation SNP A T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr21:39086795A>T uc011aej.1 - 3 718 c.665T>A c.(664-666)TTC>TAC p.F222Y KCNJ6_uc002ywo.2_Missense_Mutation_p.F222Y NM_002240 NP_002231 P48051 IRK6_HUMAN potassium inwardly-rectifying channel J6 222 Cytoplasmic (By similarity). synaptic transmission Golgi apparatus|voltage-gated potassium channel complex G-protein activated inward rectifier potassium channel activity|protein binding skin(1) 1 Halothane(DB01159) Pancreas(48;379 1118 2936 19024 28214) 0.485714 106.346923 106.359343 34 36 KEEP --- --- --- --- IGSF5 150084 broad.mit.edu 37 21 41142996 41142996 + Missense_Mutation SNP C T T rs140750069 MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr21:41142996C>T uc002yyo.2 + 4 675 c.572C>T c.(571-573)CCG>CTG p.P191L NM_001080444 NP_001073913 Q9NSI5 IGSF5_HUMAN immunoglobulin superfamily 5 like 191 Ig-like V-type 2.|Extracellular (Potential). integral to membrane|tight junction 0 Prostate(19;5.35e-06) 0.595238 87.282287 87.615068 25 17 KEEP --- --- --- --- DSCAM 1826 broad.mit.edu 37 21 41561106 41561106 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr21:41561106C>T uc002yyq.1 - 12 2868 c.2416G>A c.(2416-2418)GAG>AAG p.E806K DSCAM_uc002yyr.1_RNA NM_001389 NP_001380 O60469 DSCAM_HUMAN Down syndrome cell adhesion molecule isoform 806 Ig-like C2-type 9.|Extracellular (Potential). cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction protein binding ovary(6)|skin(4)|upper_aerodigestive_tract(1) 11 all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103) Melanoma(134;970 1778 1785 21664 32388) 0.407895 95.545969 96.124105 31 45 KEEP --- --- --- --- CBS 875 broad.mit.edu 37 21 44483172 44483172 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr21:44483172G>A uc002zcu.2 - 10 1090 c.845C>T c.(844-846)CCC>CTC p.P282L CBS_uc002zcs.1_Missense_Mutation_p.P177L|CBS_uc002zct.2_Missense_Mutation_p.P282L|CBS_uc002zcw.3_Missense_Mutation_p.P282L|CBS_uc002zcv.2_Missense_Mutation_p.P282L|CBS_uc002zcx.2_5'Flank NM_000071 NP_000062 P35520 CBS_HUMAN cystathionine-beta-synthase 282 cysteine biosynthetic process from serine|cysteine biosynthetic process via cystathionine|homocysteine catabolic process|hydrogen sulfide biosynthetic process|L-cysteine catabolic process|L-serine catabolic process cytosol|nucleolus cystathionine beta-synthase activity|heme binding|protein homodimerization activity|pyridoxal phosphate binding|ubiquitin protein ligase binding 0 L-Cysteine(DB00151)|L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|S-Adenosylmethionine(DB00118) 0.635135 163.542267 164.729992 47 27 KEEP --- --- --- --- CBS 875 broad.mit.edu 37 21 44485223 44485223 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr21:44485223G>A uc002zcu.2 - CBS_uc002zcs.1_Intron|CBS_uc002zct.2_Intron|CBS_uc002zcw.3_Intron|CBS_uc002zcv.2_Intron NM_000071 NP_000062 cystathionine-beta-synthase cysteine biosynthetic process from serine|cysteine biosynthetic process via cystathionine|homocysteine catabolic process|hydrogen sulfide biosynthetic process|L-cysteine catabolic process|L-serine catabolic process cytosol|nucleolus cystathionine beta-synthase activity|heme binding|protein homodimerization activity|pyridoxal phosphate binding|ubiquitin protein ligase binding 0 L-Cysteine(DB00151)|L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|S-Adenosylmethionine(DB00118) 0.3 15.540385 16.2563 6 14 KEEP --- --- --- --- TRAPPC10 7109 broad.mit.edu 37 21 45523244 45523244 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr21:45523244C>T uc002zea.2 + 23 3781 c.3612C>T c.(3610-3612)CTC>CTT p.L1204L TRAPPC10_uc010gpo.2_Silent_p.L915L|TRAPPC10_uc011afa.1_Silent_p.L582L NM_003274 NP_003265 P48553 TPC10_HUMAN trafficking protein particle complex 10 1204 vesicle-mediated transport Golgi apparatus|integral to membrane binding|sodium ion transmembrane transporter activity ovary(1)|skin(1) 2 0.5 18.84972 18.84972 6 6 KEEP --- --- --- --- PWP2 5822 broad.mit.edu 37 21 45544454 45544454 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr21:45544454C>T uc002zeb.2 + NM_005049 NP_005040 PWP2 periodic tryptophan protein homolog cytoplasm|nucleolus signal transducer activity pancreas(1) 1 STAD - Stomach adenocarcinoma(101;0.172)|Colorectal(79;0.2) 0.466667 68.871037 68.914566 21 24 KEEP --- --- --- --- C21orf33 8209 broad.mit.edu 37 21 45560131 45560131 + Splice_Site SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr21:45560131G>A uc002zec.3 + 5 515 c.429_splice c.e5-1 p.L143_splice C21orf33_uc002zed.3_Intron NM_004649 NP_004640 es1 protein isoform Ia precursor mitochondrion ovary(1) 1 STAD - Stomach adenocarcinoma(101;0.168)|Colorectal(79;0.191) 0.368421 67.759903 68.627501 21 36 KEEP --- --- --- --- AIRE 326 broad.mit.edu 37 21 45706887 45706887 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr21:45706887G>A uc002zei.2 + 3 461 c.334G>A c.(334-336)GGG>AGG p.G112R NM_000383 NP_000374 O43918 AIRE_HUMAN autoimmune regulator isoform 1 112 positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|nucleus chromatin binding|histone binding|transcription regulatory region DNA binding|translation regulator activity|zinc ion binding skin(1) 1 Colorectal(79;0.0806) Autoimmune_PolyEndocrinopathy_Candidiasis_Ectodermal_Dystrophy 0.5 74.523501 74.523501 23 23 KEEP --- --- --- --- TRPM2 7226 broad.mit.edu 37 21 45821539 45821539 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr21:45821539C>T uc002zet.1 + TRPM2_uc002zeu.1_Intron|TRPM2_uc002zew.1_Intron|TRPM2_uc010gpt.1_Intron|TRPM2_uc002zex.1_Intron|TRPM2_uc002zey.1_Intron NM_003307 NP_003298 transient receptor potential cation channel, integral to plasma membrane ADP-ribose diphosphatase activity|calcium channel activity|sodium channel activity ovary(1)|central_nervous_system(1)|pancreas(1) 3 0.636364 70.88251 71.422025 21 12 KEEP --- --- --- --- C21orf29 54084 broad.mit.edu 37 21 45929163 45929163 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr21:45929163G>A uc002zfe.1 - 10 1739 c.1673C>T c.(1672-1674)TCC>TTC p.S558F C21orf29_uc010gpv.1_Missense_Mutation_p.S490F NM_144991 NP_659428 Q8WU66 TSEAR_HUMAN chromosome 21 open reading frame 29 precursor 558 EAR 5. cell adhesion extracellular region structural molecule activity 0 0.172414 10.856023 13.796729 5 24 KEEP --- --- --- --- C21orf29 54084 broad.mit.edu 37 21 45945854 45945854 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr21:45945854G>A uc002zfe.1 - C21orf29_uc010gpv.1_Intron NM_144991 NP_659428 chromosome 21 open reading frame 29 precursor cell adhesion extracellular region structural molecule activity 0 0.666667 13.301825 13.449411 4 2 KEEP --- --- --- --- UBE2G2 7327 broad.mit.edu 37 21 46208117 46208117 + Intron SNP C A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr21:46208117C>A uc002zfy.2 - UBE2G2_uc002zfx.2_Intron NM_003343 NP_003334 ubiquitin-conjugating enzyme E2G 2 isoform 1 protein K48-linked ubiquitination cytosol ATP binding|protein binding|ubiquitin-protein ligase activity breast(3)|central_nervous_system(1) 4 Colorectal(79;0.0638) 0.2 6.043971 6.881091 2 8 KEEP --- --- --- --- MCM3AP 8888 broad.mit.edu 37 21 47693251 47693251 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr21:47693251C>T uc002zir.1 - NM_003906 NP_003897 minichromosome maintenance complex component 3 DNA replication|protein import into nucleus cytosol|nucleus DNA binding|nucleotide binding large_intestine(2)|lung(1)|ovary(1)|skin(1) 5 Breast(49;0.112) 639 0.473684 28.27317 28.284669 9 10 KEEP --- --- --- --- Unknown broad.mit.edu 37 22 16352120 16352120 + IGR SNP G T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:16352120G>T POTEH (64183 upstream) : OR11H1 (96706 downstream) 0.375 35.99101 36.430403 12 20 KEEP --- --- --- --- Unknown broad.mit.edu 37 22 17063302 17063302 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:17063302C>T OR11H1 (613498 upstream) : CCT8L2 (8346 downstream) 0.571429 13.80096 13.832059 4 3 KEEP --- --- --- --- CECR5 27440 broad.mit.edu 37 22 17621931 17621931 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:17621931G>A uc002zmf.2 - CECR5_uc002zmd.2_Intron|CECR5_uc002zme.2_Intron|CECR5_uc002zmg.2_Intron|CECR5_uc002zmh.2_Intron NM_033070 NP_149061 cat eye syndrome chromosome region, candidate 5 hydrolase activity 0 all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132) 0.625 85.787556 86.338019 25 15 KEEP --- --- --- --- MICAL3 57553 broad.mit.edu 37 22 18383716 18383716 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:18383716C>T uc002zng.3 - 6 1092 c.739G>A c.(739-741)GCA>ACA p.A247T MICAL3_uc011agl.1_Missense_Mutation_p.A247T|MICAL3_uc002znh.2_Missense_Mutation_p.A247T|MICAL3_uc002znj.1_5'UTR|MICAL3_uc002znk.1_Missense_Mutation_p.A247T|MICAL3_uc002znl.1_5'UTR|MICAL3_uc010grf.2_Missense_Mutation_p.A247T|MICAL3_uc011agm.1_Missense_Mutation_p.A247T NM_015241 NP_056056 Q7RTP6 MICA3_HUMAN microtubule associated monoxygenase, calponin 247 cytoplasm|cytoskeleton monooxygenase activity|zinc ion binding 0 all_epithelial(15;0.198) Lung(27;0.0427) 0.03125 -16.151822 6.93786 3 93 KEEP --- --- --- --- CLTCL1 8218 broad.mit.edu 37 22 19241407 19241407 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:19241407G>A uc002zpb.2 - CLTCL1_uc011agv.1_Intron|CLTCL1_uc011agw.1_Intron NM_007098 NP_009029 clathrin, heavy polypeptide-like 1 isoform 1 anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network protein binding|signal transducer activity|structural molecule activity ovary(4)|central_nervous_system(1) 5 Colorectal(54;0.0993) 1206 T ? ALCL 0.5 16.174805 16.174805 5 5 KEEP --- --- --- --- C22orf25 128989 broad.mit.edu 37 22 20043439 20043439 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:20043439C>T uc010grw.1 + C22orf25_uc002zrb.1_Intron|C22orf25_uc002zrc.1_Intron|C22orf25_uc002zrd.1_Intron|C22orf25_uc002zre.2_3'UTR|C22orf25_uc010grx.2_Intron|C22orf25_uc011ahe.1_Intron|C22orf25_uc011ahf.1_Intron|C22orf25_uc011ahg.1_Intron|C22orf25_uc002zrg.2_Intron|C22orf25_uc011ahh.1_Intron|C22orf25_uc002zrf.2_Intron|C22orf25_uc011ahi.1_Intron|C22orf25_uc010gry.1_Intron|C22orf25_uc002zrh.1_Intron NM_152906 NP_690870 hypothetical protein LOC128989 0 Colorectal(54;0.0533) 0.470588 25.398917 25.411704 8 9 KEEP --- --- --- --- broad.mit.edu 37 22 20731657 20731657 + 5'Flank SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:20731657G>A uc011ahq.1 - RecName: Full=Putative ubiquitin carboxyl-terminal hydrolase 41; EC=3.1.2.15; AltName: Full=Ubiquitin thioesterase 41; AltName: Full=Ubiquitin-specific-processing protease 41; AltName: Full=Deubiquitinating enzyme 41; 0.5 31.649002 31.649002 10 10 KEEP --- --- --- --- PI4KA 5297 broad.mit.edu 37 22 21064295 21064295 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:21064295G>A uc002zsz.3 - PI4KA_uc010gsp.2_Intron|PI4KA_uc002zsy.3_Intron NM_058004 NP_477352 phosphatidylinositol 4-kinase type 3 alpha phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|synaptic transmission Golgi-associated vesicle 1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding lung(2)|upper_aerodigestive_tract(1)|salivary_gland(1) 4 all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196) GBM(136;1332 1831 3115 23601 50806) 873 0.333333 39.563524 40.522187 13 26 KEEP --- --- --- --- LZTR1 8216 broad.mit.edu 37 22 21349233 21349233 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:21349233C>T uc002zto.2 + 16 1963 c.1860C>T c.(1858-1860)CTC>CTT p.L620L LZTR1_uc002ztn.2_Silent_p.L579L|LZTR1_uc011ahy.1_Silent_p.L601L|LZTR1_uc002ztp.2_5'Flank NM_006767 NP_006758 Q8N653 LZTR1_HUMAN leucine-zipper-like transcription regulator 1 620 anatomical structure morphogenesis sequence-specific DNA binding transcription factor activity ovary(2)|lung(2) 4 all_cancers(11;1.83e-25)|all_epithelial(7;9.19e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195) 1299 0.443299 143.71349 143.985192 43 54 KEEP --- --- --- --- LOC96610 96610 broad.mit.edu 37 22 22730744 22730744 + RNA SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:22730744G>A uc011aim.1 + 44 c.4911G>A Parts of antibodies, mostly variable regions. 0 0.371681 122.132391 123.762044 42 71 KEEP --- --- --- --- LOC96610 96610 broad.mit.edu 37 22 22786849 22786849 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:22786849C>T uc011aim.1 + Parts of antibodies, mostly variable regions. 0 0.466667 89.693343 89.751522 28 32 KEEP --- --- --- --- LOC96610 96610 broad.mit.edu 37 22 23007016 23007016 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:23007016G>A uc011aim.1 + Parts of antibodies, mostly variable regions. 0 0.461538 19.948878 19.965629 6 7 KEEP --- --- --- --- BCR 613 broad.mit.edu 37 22 23631881 23631881 + Intron SNP C T T rs139191913 by1000genomes MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:23631881C>T uc002zww.2 + BCR_uc002zwx.2_Intron|BCR_uc011aiy.1_Intron|BCR_uc002zwy.1_3'UTR NM_004327 NP_004318 breakpoint cluster region isoform 1 regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol ATP binding|GTPase activator activity|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity BCR/JAK2(6) haematopoietic_and_lymphoid_tissue(6)|central_nervous_system(3)|urinary_tract(1)|lung(1)|skin(1) 12 (RAJI-Tumor)|(NCIH23-Tumor)|(ZR7530-Tumor) 1115 T ABL1| FGFR1|JAK2 CML|ALL|AML OREG0026390 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0.6 10.626013 10.669716 3 2 KEEP --- --- --- --- CABIN1 23523 broad.mit.edu 37 22 24445700 24445700 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:24445700C>T uc002zzi.1 + CABIN1_uc002zzj.1_Intron|CABIN1_uc002zzl.1_Intron|CABIN1_uc010guk.1_Intron|CABIN1_uc002zzk.1_Intron NM_012295 NP_036427 calcineurin binding protein 1 cell surface receptor linked signaling pathway|chromatin modification nucleus protein phosphatase inhibitor activity ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1) 5 0.646154 149.87486 151.103213 42 23 KEEP --- --- --- --- CABIN1 23523 broad.mit.edu 37 22 24560249 24560249 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:24560249C>T uc002zzi.1 + CABIN1_uc002zzj.1_Intron|CABIN1_uc002zzl.1_Intron|CABIN1_uc002zzm.1_Intron NM_012295 NP_036427 calcineurin binding protein 1 cell surface receptor linked signaling pathway|chromatin modification nucleus protein phosphatase inhibitor activity ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1) 5 0.375 28.16915 28.498372 9 15 KEEP --- --- --- --- CABIN1 23523 broad.mit.edu 37 22 24562709 24562709 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:24562709C>T uc002zzi.1 + 32 5237 c.5110C>T c.(5110-5112)CCC>TCC p.P1704S CABIN1_uc002zzj.1_Missense_Mutation_p.P1625S|CABIN1_uc002zzl.1_Missense_Mutation_p.P1704S|CABIN1_uc002zzm.1_Missense_Mutation_p.P129S NM_012295 NP_036427 Q9Y6J0 CABIN_HUMAN calcineurin binding protein 1 1704 cell surface receptor linked signaling pathway|chromatin modification nucleus protein phosphatase inhibitor activity ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1) 5 0.522222 133.181696 133.219346 47 43 KEEP --- --- --- --- MYO18B 84700 broad.mit.edu 37 22 26423272 26423272 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:26423272C>T uc003abz.1 + 43 7582 c.7332C>T c.(7330-7332)TTC>TTT p.F2444F MYO18B_uc003aca.1_Silent_p.F2325F|MYO18B_uc010guy.1_Silent_p.F2326F|MYO18B_uc010guz.1_Silent_p.F2324F|MYO18B_uc011aka.1_Silent_p.F1598F|MYO18B_uc011akb.1_Silent_p.F1957F|MYO18B_uc010gva.1_Silent_p.F427F|MYO18B_uc010gvb.1_RNA NM_032608 NP_115997 Q8IUG5 MY18B_HUMAN myosin XVIIIB 2444 nucleus|sarcomere|unconventional myosin complex actin binding|ATP binding|motor activity ovary(5)|central_nervous_system(3)|large_intestine(2)|breast(2) 12 968 0.457831 119.445556 119.573407 38 45 KEEP --- --- --- --- SEZ6L 23544 broad.mit.edu 37 22 26688897 26688897 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:26688897C>T uc003acb.2 + 2 776 c.620C>T c.(619-621)TCG>TTG p.S207L SEZ6L_uc003acc.2_Missense_Mutation_p.S207L|SEZ6L_uc011akc.1_Missense_Mutation_p.S207L|SEZ6L_uc003acd.2_Missense_Mutation_p.S207L|SEZ6L_uc011akd.1_Missense_Mutation_p.S207L|SEZ6L_uc003ace.2_Missense_Mutation_p.S207L|SEZ6L_uc003acf.1_5'UTR|SEZ6L_uc010gvc.1_5'UTR NM_021115 NP_066938 Q9BYH1 SE6L1_HUMAN seizure related 6 homolog (mouse)-like 207 Extracellular (Potential). endoplasmic reticulum membrane|integral to membrane ovary(4)|central_nervous_system(1)|pancreas(1) 6 0.407767 125.540381 126.327705 42 61 KEEP --- --- --- --- HPS4 89781 broad.mit.edu 37 22 26854419 26854419 + Missense_Mutation SNP A C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:26854419A>C uc003acl.2 - 12 2497 c.1838T>G c.(1837-1839)TTG>TGG p.L613W HPS4_uc003aci.2_Missense_Mutation_p.L608W|HPS4_uc003acj.2_Missense_Mutation_p.L477W|HPS4_uc003ack.2_Missense_Mutation_p.L404W|HPS4_uc003acn.2_Missense_Mutation_p.L459W|HPS4_uc003ach.2_Missense_Mutation_p.L348W NM_022081 NP_071364 Q9NQG7 HPS4_HUMAN light ear protein isoform a 613 lysosome organization|positive regulation of eye pigmentation|protein stabilization|protein targeting lysosome|melanosome|membrane fraction|platelet dense granule protein homodimerization activity 0 Hermansky-Pudlak_syndrome 0.44186 70.721302 70.847716 19 24 KEEP --- --- --- --- HORMAD2 150280 broad.mit.edu 37 22 30490021 30490021 + Intron SNP A T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:30490021A>T uc003agy.2 + NM_152510 NP_689723 HORMA domain containing 2 meiosis|mitosis chromosome|nucleus 0 Epithelial(10;0.125) 0.5 14.400235 14.400235 4 4 KEEP --- --- --- --- DEPDC5 9681 broad.mit.edu 37 22 32206743 32206743 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:32206743C>T uc003als.2 + DEPDC5_uc011als.1_Intron|DEPDC5_uc011alu.1_Intron|DEPDC5_uc011alv.1_Intron|DEPDC5_uc003alt.2_Intron|DEPDC5_uc003alr.1_Intron|DEPDC5_uc011alt.1_Intron NM_014662 NP_055477 DEP domain containing 5 isoform 1 intracellular signal transduction ovary(4)|central_nervous_system(3)|pancreas(1) 8 0.551724 54.338311 54.41358 16 13 KEEP --- --- --- --- MCM5 4174 broad.mit.edu 37 22 35802819 35802819 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:35802819C>T uc003anu.3 + MCM5_uc010gwr.2_Intron|MCM5_uc003anv.3_Intron|MCM5_uc010gws.1_5'Flank NM_006739 NP_006730 minichromosome maintenance complex component 5 cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle MCM complex ATP binding|DNA binding|helicase activity|protein binding ovary(1) 1 0.5 14.874024 14.874024 5 5 KEEP --- --- --- --- APOL3 80833 broad.mit.edu 37 22 36545072 36545072 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:36545072G>A uc003aot.2 - APOL3_uc003aoq.2_Intron|APOL3_uc003aor.2_Intron|APOL3_uc003aos.2_Intron|APOL3_uc003aou.2_Intron|APOL3_uc003aov.2_Intron NM_145640 NP_663615 apolipoprotein L3 isoform 1 inflammatory response|lipoprotein metabolic process|positive regulation of I-kappaB kinase/NF-kappaB cascade cytoplasm|extracellular region lipid binding|lipid transporter activity|signal transducer activity 0 0.405405 93.232067 93.811778 30 44 KEEP --- --- --- --- CACNG2 10369 broad.mit.edu 37 22 36983721 36983721 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:36983721G>A uc003aps.1 - NM_006078 NP_006069 voltage-dependent calcium channel gamma-2 membrane depolarization|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane|voltage-gated calcium channel complex protein binding|voltage-gated calcium channel activity 0 0.625 33.353393 33.572675 10 6 KEEP --- --- --- --- SUN2 25777 broad.mit.edu 37 22 39148428 39148428 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:39148428G>A uc003awh.1 - SUN2_uc011anz.1_Intron|SUN2_uc011aoa.1_Intron|SUN2_uc003awi.1_Intron|SUN2_uc010gxq.1_Intron|SUN2_uc010gxr.1_Intron|SUN2_uc010gxs.1_Intron NM_015374 NP_056189 unc-84 homolog B centrosome localization|cytoskeletal anchoring at nuclear membrane|mitotic spindle organization|nuclear envelope organization|nuclear matrix anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration endosome membrane|integral to membrane|nuclear inner membrane|SUN-KASH complex lamin binding|microtubule binding large_intestine(1)|skin(1) 2 0.61194 133.063101 133.794577 41 26 KEEP --- --- --- --- Unknown broad.mit.edu 37 22 39345153 39345153 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:39345153G>A CBX6 (76895 upstream) : APOBEC3A (8374 downstream) 0.442857 106.917137 107.11622 31 39 KEEP --- --- --- --- APOBEC3F 200316 broad.mit.edu 37 22 39441685 39441685 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:39441685C>T uc003aww.2 + APOBEC3F_uc011aog.1_3'UTR NM_145298 NP_660341 apolipoprotein B mRNA editing enzyme, catalytic base conversion or substitution editing|DNA cytosine deamination|innate immune response|interspecies interaction between organisms|negative regulation of retroviral genome replication|negative regulation of transposition|positive regulation of defense response to virus by host|response to virus|viral reproduction apolipoprotein B mRNA editing enzyme complex|cytosol|mitochondrion cytidine deaminase activity|dCTP deaminase activity|protein homodimerization activity|RNA binding|zinc ion binding 0 Melanoma(58;0.04) 0.692308 60.959736 61.817214 18 8 KEEP --- --- --- --- CYP2D6 1565 broad.mit.edu 37 22 42524851 42524851 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:42524851G>A uc003bce.2 - 4 691 c.601C>T c.(601-603)CGC>TGC p.R201C uc003bcd.1_Intron|CYP2D6_uc010gyu.2_5'UTR|CYP2D6_uc003bcf.2_Missense_Mutation_p.R150C NM_000106 NP_000097 Q6NWU0 Q6NWU0_HUMAN cytochrome P450, family 2, subfamily D, 201 electron carrier activity|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen breast(1)|skin(1) 2 0.6 21.352115 21.439574 6 4 KEEP --- --- --- --- A4GALT 53947 broad.mit.edu 37 22 43089118 43089118 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:43089118G>A uc003bdb.2 - 3 1101 c.840C>T c.(838-840)CCC>CCT p.P280P A4GALT_uc010gzd.2_Silent_p.P280P NM_017436 NP_059132 Q9NPC4 A4GAT_HUMAN alpha 1,4-galactosyltransferase 280 Lumenal (Potential). glycosphingolipid biosynthetic process|plasma membrane organization Golgi stack|integral to Golgi membrane|membrane fraction lactosylceramide 4-alpha-galactosyltransferase activity central_nervous_system(2) 2 0.555556 33.95158 33.999861 10 8 KEEP --- --- --- --- ARFGAP3 26286 broad.mit.edu 37 22 43231396 43231396 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:43231396G>A uc003bdd.2 - 4 585 c.365C>T c.(364-366)TCT>TTT p.S122F ARFGAP3_uc010gzf.2_Intron|ARFGAP3_uc011apu.1_Intron NM_014570 NP_055385 Q9NP61 ARFG3_HUMAN ADP-ribosylation factor GTPase activating 122 Arf-GAP. intracellular protein transport|protein secretion|regulation of ARF GTPase activity|vesicle-mediated transport cytosol|Golgi membrane ARF GTPase activator activity|protein transporter activity|zinc ion binding breast(1) 1 GBM(58;544 1030 21460 27159 48838) 0.493333 125.17591 125.178766 37 38 KEEP --- --- --- --- TTLL12 23170 broad.mit.edu 37 22 43579150 43579150 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:43579150G>A uc003bdq.2 - 2 215 c.183C>T c.(181-183)TTC>TTT p.F61F TTLL12_uc003bdr.1_Silent_p.F61F NM_015140 NP_055955 Q14166 TTL12_HUMAN tubulin tyrosine ligase-like family, member 12 61 protein modification process tubulin-tyrosine ligase activity central_nervous_system(1) 1 Ovarian(80;0.221)|Glioma(61;0.222) 0.468468 167.390893 167.48695 52 59 KEEP --- --- --- --- PNPLA3 80339 broad.mit.edu 37 22 44332978 44332978 + Missense_Mutation SNP A T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:44332978A>T uc003bei.1 + 6 978 c.805A>T c.(805-807)ATG>TTG p.M269L PNPLA3_uc010gzm.1_RNA NM_025225 NP_079501 Q9NST1 PLPL3_HUMAN patatin-like phospholipase domain containing 3 269 Lumenal (Potential). triglyceride biosynthetic process|triglyceride catabolic process integral to membrane diolein transacylation activity|mono-olein transacylation activity|phospholipase A2 activity|triglyceride lipase activity 0 Ovarian(80;0.024)|all_neural(38;0.0416) 0.512195 66.975488 66.980793 21 20 KEEP --- --- --- --- TBC1D22A 25771 broad.mit.edu 37 22 47290676 47290676 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:47290676C>T uc003bib.2 + TBC1D22A_uc010haf.2_Intron|TBC1D22A_uc003bic.2_Intron|TBC1D22A_uc003bie.2_Intron|TBC1D22A_uc003bid.2_Intron|TBC1D22A_uc010hag.2_Intron|TBC1D22A_uc003bif.2_Intron NM_014346 NP_055161 TBC1 domain family, member 22A intracellular protein homodimerization activity|Rab GTPase activator activity ovary(1) 1 all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236) UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231) 0.414414 147.030376 147.74047 46 65 KEEP --- --- --- --- TBC1D22A 25771 broad.mit.edu 37 22 47393661 47393661 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:47393661C>T uc003bib.2 + TBC1D22A_uc010haf.2_Intron|TBC1D22A_uc003bic.2_Intron|TBC1D22A_uc003bie.2_Intron|TBC1D22A_uc003bid.2_Intron|TBC1D22A_uc010hag.2_Intron|TBC1D22A_uc003bif.2_Intron NM_014346 NP_055161 TBC1 domain family, member 22A intracellular protein homodimerization activity|Rab GTPase activator activity ovary(1) 1 all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236) UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231) 0.6 18.651436 18.738973 6 4 KEEP --- --- --- --- PLXNB2 23654 broad.mit.edu 37 22 50728599 50728599 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:50728599C>T uc003bkv.3 - 3 521 c.415G>A c.(415-417)GGG>AGG p.G139R NM_012401 NP_036533 O15031 PLXB2_HUMAN plexin B2 precursor 139 Extracellular (Potential).|Sema. regulation of small GTPase mediated signal transduction integral to membrane|intracellular GTPase activator activity|protein binding|receptor activity ovary(4)|central_nervous_system(1)|skin(1) 6 all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113) BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247) 0.586207 58.280053 58.468242 17 12 KEEP --- --- --- --- CPT1B 1375 broad.mit.edu 37 22 51010385 51010385 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:51010385C>T uc003bmk.3 - CPT1B_uc003bml.2_Intron|CPT1B_uc003bmm.2_Intron|CPT1B_uc003bmo.2_Intron|CPT1B_uc011asa.1_Intron|CPT1B_uc003bmn.2_Intron|CPT1B_uc011asb.1_Intron|CHKB-CPT1B_uc003bmp.2_Intron|uc003bmr.1_RNA NM_001145137 NP_001138609 carnitine palmitoyltransferase 1B isoform a carnitine shuttle|fatty acid beta-oxidation|regulation of fatty acid oxidation integral to membrane|mitochondrial outer membrane carnitine O-palmitoyltransferase activity ovary(1)|central_nervous_system(1) 2 all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113) all cancers(3;3.56e-77)|OV - Ovarian serous cystadenocarcinoma(4;5.39e-74)|Epithelial(4;5.58e-70)|GBM - Glioblastoma multiforme(4;5.59e-08)|LUAD - Lung adenocarcinoma(64;0.0016)|Lung(4;0.00942)|BRCA - Breast invasive adenocarcinoma(115;0.207) Esophageal Squamous(170;988 1933 25577 30295 48163) 0.397727 106.805339 107.611095 35 53 KEEP --- --- --- --- ACR 49 broad.mit.edu 37 22 51182306 51182306 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr22:51182306C>T uc003bnh.3 + NM_001097 NP_001088 acrosin precursor acrosome matrix dispersal|activation of adenylate cyclase activity acrosomal matrix|protein complex amidase activity|copper ion binding|DNA binding|drug binding|fucose binding|mannose binding|protein binding|serine-type endopeptidase activity|zinc ion binding 0 all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113) BRCA - Breast invasive adenocarcinoma(115;1.1e-06)|LUAD - Lung adenocarcinoma(64;0.247) 0.538462 23.626077 23.642806 7 6 KEEP --- --- --- --- CHL1 10752 broad.mit.edu 37 3 447193 447193 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:447193G>A uc003bou.2 + 27 3697 c.3426G>A c.(3424-3426)AAG>AAA p.K1142K CHL1_uc003bot.2_Silent_p.K1158K|CHL1_uc011asi.1_Silent_p.K1105K NM_006614 NP_006605 O00533 CHL1_HUMAN cell adhesion molecule with homology to L1CAM 1142 Cytoplasmic (Potential). axon guidance|cell adhesion|signal transduction integral to membrane|plasma membrane|proteinaceous extracellular matrix skin(5)|central_nervous_system(4)|large_intestine(2)|ovary(1) 12 all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201) Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198) 659 0.357143 47.012565 47.767911 15 27 KEEP --- --- --- --- SRGAP3 9901 broad.mit.edu 37 3 9068548 9068548 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:9068548C>T uc003brf.1 - SRGAP3_uc003brg.1_Intron|SRGAP3_uc003bri.1_Intron NM_014850 NP_055665 SLIT-ROBO Rho GTPase activating protein 3 regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction cytosol GTPase activator activity|protein binding SRGAP3/RAF1(4) central_nervous_system(4)|skin(3)|urinary_tract(1)|breast(1) 9 OV - Ovarian serous cystadenocarcinoma(96;0.0563) T RAF1 pilocytic astrocytoma 0.54386 103.026149 103.121276 31 26 KEEP --- --- --- --- TADA3 10474 broad.mit.edu 37 3 9831493 9831493 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:9831493G>A uc003bsx.1 - 3 910 c.362C>T c.(361-363)CCC>CTC p.P121L TADA3_uc010hcn.1_Missense_Mutation_p.P121L|TADA3_uc003bsy.2_Missense_Mutation_p.P121L|ARPC4_uc003bsz.1_5'Flank|ARPC4_uc003bta.1_5'Flank|ARPC4_uc003btb.1_5'Flank|ARPC4_uc003btc.1_5'Flank NM_006354 NP_006345 O75528 TADA3_HUMAN transcriptional adaptor 3 isoform a 121 estrogen receptor signaling pathway|histone H3 acetylation|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter Ada2/Gcn5/Ada3 transcription activator complex|STAGA complex|transcription factor TFTC complex ligand-dependent nuclear receptor binding|protein domain specific binding|sequence-specific DNA binding transcription factor activity 0 0.486842 247.860622 247.882739 74 78 KEEP --- --- --- --- CRELD1 78987 broad.mit.edu 37 3 9982776 9982776 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:9982776C>T uc003bug.2 + CIDEC_uc003bto.2_Intron|CRELD1_uc003buf.2_Intron|CRELD1_uc003buh.2_Intron|CRELD1_uc003bui.2_Intron|CRELD1_uc003buj.2_Intron NM_001077415 NP_001070883 cysteine-rich with EGF-like domains 1 isoform 3 cardiac septum development|endocardial cushion development integral to membrane calcium ion binding ovary(1) 1 0.474359 119.168389 119.213144 37 41 KEEP --- --- --- --- FANCD2 2177 broad.mit.edu 37 3 10074635 10074635 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:10074635G>A uc003buw.2 + 3 262 c.184G>A c.(184-186)GGA>AGA p.G62R FANCD2_uc003bux.1_Missense_Mutation_p.G62R|FANCD2_uc003buy.1_Missense_Mutation_p.G62R|FANCD2_uc003buv.2_Missense_Mutation_p.G62R NM_033084 NP_149075 Q9BXW9 FACD2_HUMAN Fanconi anemia complementation group D2 isoform 62 Interaction with FANCE. DNA repair|response to gamma radiation nucleoplasm protein binding|protein binding central_nervous_system(2)|ovary(1)|skin(1) 4 OV - Ovarian serous cystadenocarcinoma(96;0.148) p.G62R(SKUT1-Tumor) 587 D|Mis|N|F AML|leukemia Involved_in_tolerance_or_repair_of_DNA_crosslinks Fanconi_Anemia 0.418367 140.259635 140.82954 41 57 KEEP --- --- --- --- ATP2B2 491 broad.mit.edu 37 3 10387218 10387218 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:10387218G>A uc003bvt.2 - 18 2992 c.2553C>T c.(2551-2553)ATC>ATT p.I851I ATP2B2_uc003bvv.2_Silent_p.I806I|ATP2B2_uc003bvw.2_Silent_p.I806I|ATP2B2_uc010hdo.2_Silent_p.I556I NM_001001331 NP_001001331 Q01814 AT2B2_HUMAN plasma membrane calcium ATPase 2 isoform 1 851 Cytoplasmic (Potential). ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation cytosol|integral to membrane|plasma membrane ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding ovary(3)|skin(2)|central_nervous_system(1) 6 Ovarian(125;1619 1709 15675 19819 38835) 0.512821 64.5004 64.50595 20 19 KEEP --- --- --- --- SYN2 6854 broad.mit.edu 37 3 12198267 12198267 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:12198267C>T uc003bwm.2 + SYN2_uc003bwl.1_Intron|SYN2_uc003bwn.2_Intron|TIMP4_uc003bwo.2_Intron NM_133625 NP_598328 synapsin II isoform IIa neurotransmitter secretion synaptic vesicle ATP binding|ligase activity ovary(1)|central_nervous_system(1) 2 0.5625 61.555034 61.664177 18 14 KEEP --- --- --- --- CAND2 23066 broad.mit.edu 37 3 12845036 12845036 + Nonsense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:12845036C>T uc003bxk.2 + 2 167 c.118C>T c.(118-120)CAG>TAG p.Q40* CAND2_uc003bxj.2_Nonsense_Mutation_p.Q40* NM_001162499 NP_001155971 O75155 CAND2_HUMAN TBP-interacting protein isoform 1 40 positive regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus protein binding skin(3)|pancreas(1) 4 GBM(43;676 868 1633 6395 37496) 0.341463 39.535932 40.447327 14 27 KEEP --- --- --- --- CAND2 23066 broad.mit.edu 37 3 12861722 12861722 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:12861722C>T uc003bxk.2 + CAND2_uc003bxj.2_Intron NM_001162499 NP_001155971 TBP-interacting protein isoform 1 positive regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus protein binding skin(3)|pancreas(1) 4 GBM(43;676 868 1633 6395 37496) 0.740741 67.611199 69.027884 20 7 KEEP --- --- --- --- NUP210 23225 broad.mit.edu 37 3 13367335 13367335 + Missense_Mutation SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:13367335A>G uc003bxv.1 - 33 4687 c.4604T>C c.(4603-4605)GTT>GCT p.V1535A NM_024923 NP_079199 Q8TEM1 PO210_HUMAN nucleoporin 210 precursor 1535 Lumenal (Probable). carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction endoplasmic reticulum membrane|nuclear membrane|nuclear pore ovary(3)|large_intestine(3)|skin(3)|pancreas(1)|liver(1) 11 all_neural(104;0.187) 587 0.324675 76.550537 78.705336 25 52 KEEP --- --- --- --- NUP210 23225 broad.mit.edu 37 3 13399774 13399774 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:13399774G>A uc003bxv.1 - 16 2359 c.2276C>T c.(2275-2277)ACC>ATC p.T759I NUP210_uc003bxx.2_Missense_Mutation_p.T431I NM_024923 NP_079199 Q8TEM1 PO210_HUMAN nucleoporin 210 precursor 759 Lumenal (Probable). carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction endoplasmic reticulum membrane|nuclear membrane|nuclear pore ovary(3)|large_intestine(3)|skin(3)|pancreas(1)|liver(1) 11 all_neural(104;0.187) 587 0.444444 98.790979 98.984483 32 40 KEEP --- --- --- --- C3orf20 84077 broad.mit.edu 37 3 14755452 14755452 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:14755452G>A uc003byy.2 + C3orf20_uc003byz.2_Intron|C3orf20_uc003bza.2_Intron|C3orf20_uc003bzb.1_5'Flank NM_032137 NP_115513 hypothetical protein LOC84077 cytoplasm|integral to membrane ovary(3)|skin(1) 4 0.6 56.452699 56.71433 18 12 KEEP --- --- --- --- COLQ 8292 broad.mit.edu 37 3 15495316 15495316 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:15495316G>A uc003bzx.2 - COLQ_uc003bzv.2_Intron|COLQ_uc003bzz.2_Intron|COLQ_uc010heo.2_Intron|COLQ_uc003cac.1_Intron|COLQ_uc003cae.1_Intron|COLQ_uc003cad.1_Intron NM_005677 NP_005668 acetylcholinesterase collagen-like tail subunit acetylcholine catabolic process in synaptic cleft|asymmetric protein localization basal lamina|cell junction|collagen|extracellular space|synaptic cleft 0 0.357143 14.770515 15.022436 5 9 KEEP --- --- --- --- GALNTL2 117248 broad.mit.edu 37 3 16216989 16216990 + Missense_Mutation DNP GG AA AA MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:16216989_16216990GG>AA uc003car.3 + 1 806_807 c.331_332GG>AA c.(331-333)GGC>AAC p.G111N GALNTL2_uc003caq.3_Intron NM_054110 NP_473451 Q8N3T1 GLTL2_HUMAN UDP-N-acetyl-alpha-D-galactosamine:polypeptide 111 Lumenal (Potential). Golgi membrane|integral to membrane|transport vesicle polypeptide N-acetylgalactosaminyltransferase activity|sugar binding breast(1) 1 0.5 31.549678 31.549678 10 10 KEEP --- --- --- --- KCNH8 131096 broad.mit.edu 37 3 19432180 19432180 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:19432180C>T uc003cbk.1 + KCNH8_uc011awe.1_Intron|KCNH8_uc010hex.1_Intron|KCNH8_uc011awf.1_Intron NM_144633 NP_653234 potassium voltage-gated channel, subfamily H, integral to membrane two-component sensor activity lung(4)|ovary(1) 5 NSCLC(124;1625 1765 8018 24930 42026) 0.46 74.020768 74.090302 23 27 KEEP --- --- --- --- KCNH8 131096 broad.mit.edu 37 3 19551857 19551857 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:19551857G>A uc003cbk.1 + 12 2238 c.2043G>A c.(2041-2043)GTG>GTA p.V681V KCNH8_uc010hex.1_Silent_p.V142V NM_144633 NP_653234 Q96L42 KCNH8_HUMAN potassium voltage-gated channel, subfamily H, 681 Cytoplasmic (Potential). integral to membrane two-component sensor activity lung(4)|ovary(1) 5 NSCLC(124;1625 1765 8018 24930 42026) 0.390244 49.992625 50.424659 16 25 KEEP --- --- --- --- RAB5A 5868 broad.mit.edu 37 3 20017544 20017544 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:20017544C>T uc003cbn.2 + 4 856 c.321C>T c.(319-321)TCC>TCT p.S107S RAB5A_uc010hey.2_RNA|RAB5A_uc011awg.1_Silent_p.S93S NM_004162 NP_004153 P20339 RAB5A_HUMAN RAB5A, member RAS oncogene family 107 blood coagulation|protein transport|receptor internalization|regulation of filopodium assembly|small GTPase mediated signal transduction early endosome membrane|melanosome|plasma membrane GDP binding|GTP binding|GTPase activity 0 0.439024 59.843929 59.976859 18 23 KEEP --- --- --- --- broad.mit.edu 37 3 22423579 22423580 + 5'Flank DNP GG AA AA MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:22423579_22423580GG>AA uc003ccf.2 + Homo sapiens HMG1 mRNA, 3' untranslated region. 0.444444 117.091091 117.308691 36 45 KEEP --- --- --- --- TOP2B 7155 broad.mit.edu 37 3 25666096 25666096 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:25666096G>A uc011awn.1 - TOP2B_uc003cdj.2_Intron NM_001068 NP_001059 DNA topoisomerase II, beta isozyme DNA topological change|DNA-dependent DNA replication|mitotic cell cycle G2/M transition decatenation checkpoint|mitotic recombination|resolution of meiotic recombination intermediates|sister chromatid segregation cytosol|DNA topoisomerase complex (ATP-hydrolyzing)|nucleolus|nucleoplasm|synaptonemal complex|WINAC complex ATP binding|chromatin binding|DNA topoisomerase (ATP-hydrolyzing) activity|DNA-dependent ATPase activity|histone deacetylase binding|protein C-terminus binding|protein heterodimerization activity|protein kinase C binding|sequence-specific DNA binding transcription factor activity breast(2)|ovary(1)|lung(1)|skin(1) 5 789 0.357143 16.771058 17.022763 5 9 KEEP --- --- --- --- NGLY1 55768 broad.mit.edu 37 3 25791235 25791235 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:25791235G>A uc003cdl.2 - NGLY1_uc010hfg.2_Intron|NGLY1_uc003cdm.2_Intron|NGLY1_uc011awo.1_Intron|NGLY1_uc003cdk.2_Intron NM_018297 NP_060767 N-glycanase 1 isoform 1 glycoprotein catabolic process cytoplasm metal ion binding|peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity|protein binding breast(1) 1 0.532468 132.576696 132.647014 41 36 KEEP --- --- --- --- NEK10 152110 broad.mit.edu 37 3 27352469 27352469 + Missense_Mutation SNP C G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:27352469C>G uc003cdt.1 - 10 881 c.607G>C c.(607-609)GAA>CAA p.E203Q NM_199347 NP_955379 Q6ZWH5 NEK10_HUMAN NIMA-related kinase 10 isoform 3 203 ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity ovary(5)|stomach(2)|central_nervous_system(2)|lung(2)|skin(1)|pancreas(1) 13 332 0.46875 167.371382 167.452788 45 51 KEEP --- --- --- --- RBMS3 27303 broad.mit.edu 37 3 29781394 29781394 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:29781394C>T uc003cel.2 + RBMS3_uc003cek.2_Intron|RBMS3_uc010hfq.2_Intron|RBMS3_uc003cem.2_Intron|RBMS3_uc010hfr.2_Intron NM_001003793 NP_001003793 RNA binding motif, single stranded interacting cytoplasm nucleotide binding|RNA binding central_nervous_system(1) 1 Ovarian(412;0.0956) 0.4 103.293128 103.9899 32 48 KEEP --- --- --- --- Unknown broad.mit.edu 37 3 31494657 31494657 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:31494657G>A GADL1 (558504 upstream) : STT3B (79834 downstream) 0.520833 167.751731 167.78777 50 46 KEEP --- --- --- --- Unknown broad.mit.edu 37 3 31495638 31495638 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:31495638G>A GADL1 (559485 upstream) : STT3B (78853 downstream) 0.387755 58.713911 59.254784 19 30 KEEP --- --- --- --- OSBPL10 114884 broad.mit.edu 37 3 31712483 31712483 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:31712483G>A uc003cev.2 - OSBPL10_uc003ceu.1_Intron|OSBPL10_uc011axf.1_Intron NM_017784 NP_060254 oxysterol-binding protein-like protein 10 lipid transport lipid binding skin(1) 1 STAD - Stomach adenocarcinoma(1;0.00406) 0.485714 55.673792 55.680012 17 18 KEEP --- --- --- --- CMTM7 112616 broad.mit.edu 37 3 32495723 32495723 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:32495723C>T uc003cey.1 + CMTM7_uc003cez.1_Intron NM_138410 NP_612419 CKLF-like MARVEL transmembrane domain containing chemotaxis extracellular space|integral to membrane cytokine activity 0 0.555556 79.372398 79.492517 25 20 KEEP --- --- --- --- CNOT10 25904 broad.mit.edu 37 3 32767045 32767045 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:32767045G>A uc003cfc.1 + 9 1221 c.966G>A c.(964-966)GAG>GAA p.E322E CNOT10_uc011axi.1_Silent_p.E94E|CNOT10_uc003cfd.1_Silent_p.E321E|CNOT10_uc003cfe.1_Silent_p.E322E|CNOT10_uc010hfv.1_RNA|CNOT10_uc011axj.1_Silent_p.E382E|CNOT10_uc010hfw.1_Silent_p.E17E NM_015442 NP_056257 Q9H9A5 CNOTA_HUMAN CCR4-NOT transcription complex, subunit 10 322 nuclear-transcribed mRNA poly(A) tail shortening cytosol protein binding central_nervous_system(1)|skin(1) 2 0.359551 101.775577 103.321344 32 57 KEEP --- --- --- --- ARPP21 10777 broad.mit.edu 37 3 35730713 35730713 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:35730713G>A uc003cgb.2 + ARPP21_uc003cga.2_Intron|ARPP21_uc011axy.1_Intron|ARPP21_uc003cgf.2_5'Flank NM_016300 NP_057384 cyclic AMP-regulated phosphoprotein, 21 kD cytoplasm nucleic acid binding ovary(2)|skin(1) 3 0.666667 47.456338 47.97254 14 7 KEEP --- --- --- --- ARPP21 10777 broad.mit.edu 37 3 35770849 35770849 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:35770849C>T uc003cgb.2 + 15 1544 c.1280C>T c.(1279-1281)CCA>CTA p.P427L ARPP21_uc003cga.2_Missense_Mutation_p.P373L|ARPP21_uc011axy.1_Missense_Mutation_p.P393L|ARPP21_uc003cgf.2_Missense_Mutation_p.P228L|ARPP21_uc003cgg.2_5'UTR NM_016300 NP_057384 Q9UBL0 ARP21_HUMAN cyclic AMP-regulated phosphoprotein, 21 kD 427 cytoplasm nucleic acid binding ovary(2)|skin(1) 3 0.466667 105.307554 105.380951 35 40 KEEP --- --- --- --- ARPP21 10777 broad.mit.edu 37 3 35781012 35781012 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:35781012G>A uc003cgb.2 + 17 2112 c.1848G>A c.(1846-1848)CAG>CAA p.Q616Q ARPP21_uc003cga.2_Silent_p.Q597Q|ARPP21_uc011axy.1_Silent_p.Q617Q|ARPP21_uc003cgf.2_Silent_p.Q452Q|ARPP21_uc003cgg.2_Silent_p.Q139Q NM_016300 NP_057384 Q9UBL0 ARP21_HUMAN cyclic AMP-regulated phosphoprotein, 21 kD 616 Gln-rich. cytoplasm nucleic acid binding ovary(2)|skin(1) 3 0.433962 74.317193 74.518778 23 30 KEEP --- --- --- --- TRANK1 9881 broad.mit.edu 37 3 36896633 36896633 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:36896633C>T uc003cgj.2 - NM_014831 NP_055646 lupus brain antigen 1 DNA repair ATP binding|ATP-dependent DNA helicase activity|DNA binding ovary(1)|central_nervous_system(1) 2 0.454545 33.547893 33.587469 10 12 KEEP --- --- --- --- SCN11A 11280 broad.mit.edu 37 3 38888584 38888584 + Silent SNP G A A rs150087925 byFrequency MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:38888584G>A uc011ays.1 - 26 5176 c.4977C>T c.(4975-4977)GTC>GTT p.V1659V NM_014139 NP_054858 Q9UI33 SCNBA_HUMAN sodium channel, voltage-gated, type XI, alpha 1659 response to drug voltage-gated sodium channel complex voltage-gated sodium channel activity skin(6)|ovary(1)|haematopoietic_and_lymphoid_tissue(1)|pancreas(1) 9 Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226) Cocaine(DB00907) 0.508065 207.326644 207.333692 63 61 KEEP --- --- --- --- XIRP1 165904 broad.mit.edu 37 3 39230587 39230587 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:39230587G>A uc003cjk.1 - 2 571 c.350C>T c.(349-351)CCC>CTC p.P117L XIRP1_uc003cji.2_Missense_Mutation_p.P117L|XIRP1_uc003cjj.2_Intron NM_194293 NP_919269 Q702N8 XIRP1_HUMAN xin actin-binding repeat containing 1 117 actin binding ovary(4)|breast(2)|central_nervous_system(1)|pancreas(1) 8 KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065) 0.465753 109.343937 109.418419 34 39 KEEP --- --- --- --- FAM198A 729085 broad.mit.edu 37 3 43078993 43078993 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:43078993G>A uc003cmp.3 + FAM198A_uc010hii.2_Intron|FAM198A_uc003cmo.3_Intron|FAM198A_uc010hih.2_Intron NM_001129908 NP_001123380 hypothetical protein LOC729085 extracellular region 0 0.294118 14.768862 15.413376 5 12 KEEP --- --- --- --- KIF15 56992 broad.mit.edu 37 3 44869707 44869707 + Missense_Mutation SNP T A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:44869707T>A uc003cnx.3 + 24 3007 c.2858T>A c.(2857-2859)ATG>AAG p.M953K KIF15_uc010hiq.2_Missense_Mutation_p.M856K|KIF15_uc010hir.2_Missense_Mutation_p.M1K NM_020242 NP_064627 Q9NS87 KIF15_HUMAN kinesin family member 15 953 Potential. blood coagulation|cell proliferation|microtubule-based movement|mitosis centrosome|cytosol|microtubule|plus-end kinesin complex|spindle ATP binding|DNA binding|microtubule motor activity ovary(1) 1 BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707) 0.469388 78.02249 78.06239 23 26 KEEP --- --- --- --- LZTFL1 54585 broad.mit.edu 37 3 45867793 45867793 + 3'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:45867793G>A uc003cox.1 - 10 LZTFL1_uc003coy.1_3'UTR|LZTFL1_uc011bak.1_RNA NM_020347 NP_065080 leucine zipper transcription factor-like 1 0 BRCA - Breast invasive adenocarcinoma(193;0.00867)|KIRC - Kidney renal clear cell carcinoma(197;0.0177)|Kidney(197;0.0208) 0.556452 231.97985 232.322709 69 55 KEEP --- --- --- --- CSPG5 10675 broad.mit.edu 37 3 47604368 47604368 + Intron SNP G C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:47604368G>C uc003crp.3 - CSPG5_uc003crm.2_RNA|CSPG5_uc003crn.2_Intron|CSPG5_uc003cro.3_Intron|CSPG5_uc011bbb.1_Intron NM_006574 NP_006565 chondroitin sulfate proteoglycan 5 (neuroglycan cell differentiation|intracellular transport|nervous system development|regulation of growth endoplasmic reticulum membrane|Golgi-associated vesicle membrane|integral to plasma membrane|membrane fraction growth factor activity ovary(1)|central_nervous_system(1) 2 BRCA - Breast invasive adenocarcinoma(193;0.000266)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621) 0.615385 31.803479 31.955219 8 5 KEEP --- --- --- --- COL7A1 1294 broad.mit.edu 37 3 48620938 48620939 + Intron DNP GG AA AA MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:48620938_48620939GG>AA uc003ctz.2 - NM_000094 NP_000085 alpha 1 type VII collagen precursor cell adhesion|epidermis development basement membrane|collagen type VII protein binding|serine-type endopeptidase inhibitor activity ovary(4)|breast(3)|skin(3)|central_nervous_system(1) 11 BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632) 0.566667 58.779284 58.895532 17 13 KEEP --- --- --- --- ARIH2 10425 broad.mit.edu 37 3 49004800 49004800 + Intron SNP T G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:49004800T>G uc003cvb.2 + ARIH2_uc003cvc.2_Intron|ARIH2_uc003cvf.2_Intron|ARIH2_uc010hkl.2_Intron NM_006321 NP_006312 ariadne homolog 2 developmental cell growth|hemopoietic stem cell proliferation|protein K48-linked ubiquitination|protein K63-linked ubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process cytoplasm|nucleus nucleic acid binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding ovary(1) 1 BRCA - Breast invasive adenocarcinoma(193;9.42e-05)|Kidney(197;0.00258)|KIRC - Kidney renal clear cell carcinoma(197;0.00269) 0.565217 47.077776 47.162927 13 10 KEEP --- --- --- --- WDR6 11180 broad.mit.edu 37 3 49050571 49050571 + Missense_Mutation SNP G T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:49050571G>T uc003cvj.2 + 2 1832 c.1694G>T c.(1693-1695)CGG>CTG p.R565L WDR6_uc011bbx.1_Intron|WDR6_uc011bby.1_Intron|WDR6_uc010hkn.2_Missense_Mutation_p.R509L|WDR6_uc011bbz.1_Missense_Mutation_p.R484L NM_018031 NP_060501 Q9NNW5 WDR6_HUMAN WD repeat domain 6 protein 535 cell cycle arrest|negative regulation of cell proliferation cytoplasm central_nervous_system(1) 1 Kidney(197;9.12e-07)|KIRC - Kidney renal clear cell carcinoma(197;1.32e-05)|BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000155) 0.460317 96.779977 96.864833 29 34 KEEP --- --- --- --- NICN1 84276 broad.mit.edu 37 3 49463955 49463955 + Intron SNP A C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:49463955A>C uc003cwz.1 - NICN1_uc003cxa.2_Intron|NICN1_uc011bcr.1_Intron NM_032316 NP_115692 nicolin 1 microtubule|nucleus 0 BRCA - Breast invasive adenocarcinoma(193;4.52e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244) 0.333333 6.419942 6.642379 3 6 KEEP --- --- --- --- BSN 8927 broad.mit.edu 37 3 49689857 49689857 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:49689857G>A uc003cxe.3 + 5 2982 c.2868G>A c.(2866-2868)CTG>CTA p.L956L NM_003458 NP_003449 Q9UPA5 BSN_HUMAN bassoon protein 956 synaptic transmission cell junction|cytoplasm|cytoskeleton|nucleus|synaptosome metal ion binding ovary(5)|pancreas(1)|central_nervous_system(1)|skin(1) 8 BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336) 0.493671 126.824298 126.827023 39 40 KEEP --- --- --- --- SLC38A3 10991 broad.mit.edu 37 3 50254671 50254671 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:50254671G>A uc003cyn.3 + 8 691 c.550G>A c.(550-552)GAC>AAC p.D184N SLC38A3_uc011bdl.1_Missense_Mutation_p.D159N|SLC38A3_uc011bdm.1_Missense_Mutation_p.D115N NM_006841 NP_006832 Q99624 S38A3_HUMAN solute carrier family 38, member 3 184 cellular nitrogen compound metabolic process|sodium ion transport integral to plasma membrane antiporter activity|L-alanine transmembrane transporter activity|L-asparagine transmembrane transporter activity|L-glutamine transmembrane transporter activity|L-histidine transmembrane transporter activity|symporter activity breast(1) 1 BRCA - Breast invasive adenocarcinoma(193;0.000275)|KIRC - Kidney renal clear cell carcinoma(197;0.00548)|Kidney(197;0.00615) L-Asparagine(DB00174)|L-Glutamine(DB00130)|L-Histidine(DB00117) 0.333333 17.243631 17.686627 6 12 KEEP --- --- --- --- DOCK3 1795 broad.mit.edu 37 3 50824121 50824121 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:50824121C>T uc011bds.1 + NM_004947 NP_004938 dedicator of cytokinesis 3 cytoplasm GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding 0 BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518) 1034 0.4375 22.822861 22.877346 7 9 KEEP --- --- --- --- DOCK3 1795 broad.mit.edu 37 3 51312545 51312545 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:51312545C>T uc011bds.1 + 25 2607 c.2584C>T c.(2584-2586)CAC>TAC p.H862Y NM_004947 NP_004938 Q8IZD9 DOCK3_HUMAN dedicator of cytokinesis 3 862 cytoplasm GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding 0 BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518) 1034 0.548077 372.459211 372.876282 114 94 KEEP --- --- --- --- RAD54L2 23132 broad.mit.edu 37 3 51680353 51680353 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:51680353C>T uc011bdt.1 + 18 3007 c.2882C>T c.(2881-2883)ACC>ATC p.T961I RAD54L2_uc003dbh.2_Missense_Mutation_p.T550I|RAD54L2_uc011bdu.1_Missense_Mutation_p.T655I|RAD54L2_uc003dbj.2_Missense_Mutation_p.T287I NM_015106 NP_055921 Q9Y4B4 ARIP4_HUMAN RAD54-like 2 961 nucleus ATP binding|DNA binding|helicase activity ovary(3) 3 BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896) 0.428571 19.147837 19.210153 6 8 KEEP --- --- --- --- IQCF3 401067 broad.mit.edu 37 3 51863803 51863803 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:51863803C>T uc010hlx.1 + IQCF1_uc003dbq.3_Intron|IQCF3_uc010hlw.1_Intron|IQCF3_uc011bdw.1_Intron NM_001085479 NP_001078948 IQ motif containing F3 ovary(1) 1 BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716) 0.8 27.505579 28.342379 8 2 KEEP --- --- --- --- ITIH3 3699 broad.mit.edu 37 3 52830608 52830608 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:52830608G>A uc003dfv.2 + 3 262 c.226G>A c.(226-228)GAG>AAG p.E76K ITIH3_uc011bek.1_Missense_Mutation_p.E76K NM_002217 NP_002208 Q06033 ITIH3_HUMAN inter-alpha (globulin) inhibitor H3 76 VIT. hyaluronan metabolic process extracellular region serine-type endopeptidase inhibitor activity ovary(2)|liver(1) 3 BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496) 0.391304 28.371183 28.608749 9 14 KEEP --- --- --- --- IL17RB 55540 broad.mit.edu 37 3 53886868 53886868 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:53886868G>A uc003dha.2 + NM_018725 NP_061195 interleukin 17B receptor precursor defense response|regulation of cell growth extracellular region|integral to plasma membrane cytokine receptor activity ovary(2)|pancreas(1) 3 BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118) 0.425926 74.412317 74.671543 23 31 KEEP --- --- --- --- CACNA2D3 55799 broad.mit.edu 37 3 54914790 54914790 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:54914790G>A uc003dhf.2 + CACNA2D3_uc011beu.1_Intron|CACNA2D3_uc003dhg.1_Intron|CACNA2D3_uc003dhh.1_Intron|CACNA2D3_uc010hmv.1_Intron|uc003dhk.1_Intron NM_018398 NP_060868 calcium channel, voltage-dependent, alpha integral to membrane calcium channel activity|metal ion binding|voltage-gated ion channel activity large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1) 7 KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327) 0.483333 278.914098 278.957764 87 93 KEEP --- --- --- --- FLNB 2317 broad.mit.edu 37 3 58107165 58107165 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:58107165G>A uc003djj.2 + 20 3226 c.3061G>A c.(3061-3063)GAT>AAT p.D1021N FLNB_uc010hne.2_Missense_Mutation_p.D1021N|FLNB_uc003djk.2_Missense_Mutation_p.D1021N|FLNB_uc010hnf.2_Missense_Mutation_p.D1021N|FLNB_uc003djl.2_Missense_Mutation_p.D852N|FLNB_uc003djm.2_Missense_Mutation_p.D852N NM_001457 NP_001448 O75369 FLNB_HUMAN filamin B isoform 2 1021 Filamin 8. actin cytoskeleton organization|cell differentiation|cytoskeletal anchoring at plasma membrane|signal transduction cell cortex|integral to membrane|nucleus|sarcomere actin binding breast(8)|ovary(5)|lung(3)|skin(2)|central_nervous_system(1) 19 BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898) 676 0.429577 199.622885 200.220925 61 81 KEEP --- --- --- --- FEZF2 55079 broad.mit.edu 37 3 62357358 62357358 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:62357358G>A uc003dlh.2 - FEZF2_uc003dli.2_Intron NM_018008 NP_060478 FEZ family zinc finger 2 transcription, DNA-dependent nucleus zinc ion binding lung(1) 1 Lung SC(41;0.0262) BRCA - Breast invasive adenocarcinoma(55;0.000221)|KIRC - Kidney renal clear cell carcinoma(15;0.00834)|Kidney(15;0.00957) NSCLC(170;1772 2053 12525 15604 23984) 0.409091 56.241383 56.559127 18 26 KEEP --- --- --- --- FAM19A1 407738 broad.mit.edu 37 3 68194242 68194242 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:68194242G>A uc003dnd.2 + FAM19A1_uc003dne.2_Intron|FAM19A1_uc003dng.2_Intron NM_213609 NP_998774 family with sequence similarity 19 (chemokine endoplasmic reticulum|extracellular region ovary(1) 1 Lung NSC(201;0.0117) BRCA - Breast invasive adenocarcinoma(55;7.7e-05)|Epithelial(33;0.000937)|KIRC - Kidney renal clear cell carcinoma(39;0.0579)|Kidney(39;0.0743) 0.461538 72.688247 72.75581 24 28 KEEP --- --- --- --- C3orf64 285203 broad.mit.edu 37 3 69026938 69026938 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:69026938G>A uc003dnl.2 - C3orf64_uc003dnj.2_Intron|C3orf64_uc003dnk.2_Intron|C3orf64_uc011bfw.1_Intron NM_173654 NP_775925 AER61 glycosyltransferase extracellular region transferase activity, transferring glycosyl groups ovary(1) 1 Lung NSC(201;0.126) BRCA - Breast invasive adenocarcinoma(55;4.61e-05)|Epithelial(33;0.000291)|LUSC - Lung squamous cell carcinoma(21;0.0127)|KIRC - Kidney renal clear cell carcinoma(39;0.216) 0.481481 41.073972 41.082001 13 14 KEEP --- --- --- --- TMF1 7110 broad.mit.edu 37 3 69079081 69079081 + Nonsense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:69079081G>A uc003dnn.2 - 11 2726 c.2479C>T c.(2479-2481)CAG>TAG p.Q827* TMF1_uc011bfx.1_Nonsense_Mutation_p.Q830* NM_007114 NP_009045 P82094 TMF1_HUMAN TATA element modulatory factor 1 827 Potential. regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter Golgi membrane|nucleus DNA binding|protein binding|transcription cofactor activity 0 Lung NSC(201;0.0193)|Prostate(884;0.174) BRCA - Breast invasive adenocarcinoma(55;4.48e-05)|Epithelial(33;0.000274)|LUSC - Lung squamous cell carcinoma(21;0.0123)|KIRC - Kidney renal clear cell carcinoma(39;0.211)|Kidney(39;0.247) 0.5 221.699675 221.699675 68 68 KEEP --- --- --- --- EPHA6 285220 broad.mit.edu 37 3 97194224 97194224 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:97194224G>A uc010how.1 + 8 1966 c.1923G>A c.(1921-1923)CAG>CAA p.Q641Q EPHA6_uc011bgo.1_RNA|EPHA6_uc011bgp.1_Silent_p.Q7Q|EPHA6_uc003drs.3_Silent_p.Q33Q|EPHA6_uc003drr.3_Silent_p.Q33Q|EPHA6_uc003drt.2_Silent_p.Q33Q|EPHA6_uc010hox.1_RNA NM_001080448 NP_001073917 Q9UF33 EPHA6_HUMAN EPH receptor A6 isoform a 546 Extracellular (Potential). integral to plasma membrane ATP binding|ephrin receptor activity stomach(5)|lung(4)|central_nervous_system(3)|breast(1)|skin(1)|ovary(1)|kidney(1) 16 480 0.5 23.12565 23.12565 7 7 KEEP --- --- --- --- ABI3BP 25890 broad.mit.edu 37 3 100617797 100617797 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:100617797C>T uc003dun.2 - ABI3BP_uc003duo.2_Intron|ABI3BP_uc003dup.3_Intron NM_015429 NP_056244 ABI gene family, member 3 (NESH) binding protein extracellular space ovary(2)|large_intestine(1)|haematopoietic_and_lymphoid_tissue(1) 4 0.406593 115.05798 115.751634 37 54 KEEP --- --- --- --- IMPG2 50939 broad.mit.edu 37 3 100950067 100950067 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:100950067G>A uc003duq.1 - IMPG2_uc011bhe.1_Intron|IMPG2_uc010hpj.1_Intron NM_016247 NP_057331 interphotoreceptor matrix proteoglycan 2 visual perception integral to membrane|proteinaceous extracellular matrix extracellular matrix structural constituent|heparin binding|hyaluronic acid binding|receptor activity ovary(2)|haematopoietic_and_lymphoid_tissue(1) 3 0.709677 74.259387 75.479396 22 9 KEEP --- --- --- --- IMPG2 50939 broad.mit.edu 37 3 101010251 101010251 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:101010251G>A uc003duq.1 - IMPG2_uc011bhe.1_Intron NM_016247 NP_057331 interphotoreceptor matrix proteoglycan 2 visual perception integral to membrane|proteinaceous extracellular matrix extracellular matrix structural constituent|heparin binding|hyaluronic acid binding|receptor activity ovary(2)|haematopoietic_and_lymphoid_tissue(1) 3 0.5 29.847353 29.847353 10 10 KEEP --- --- --- --- FLJ25363 401082 broad.mit.edu 37 3 109190140 109190140 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:109190140G>A uc003dxr.1 + NM_001145553 NP_001139025 hypothetical protein LOC401082 0 0.444444 24.19703 24.24555 8 10 KEEP --- --- --- --- FLJ25363 401082 broad.mit.edu 37 3 109190218 109190218 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:109190218C>T uc003dxr.1 + NM_001145553 NP_001139025 hypothetical protein LOC401082 0 0.518519 47.550489 47.558495 14 13 KEEP --- --- --- --- WDR52 55779 broad.mit.edu 37 3 113099775 113099775 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:113099775G>A uc003eae.1 - 16 2069 c.2023C>T c.(2023-2025)CAT>TAT p.H675Y NM_018338 NP_060808 Q96MT7 WDR52_HUMAN WD repeat domain 52 isoform 2 675 central_nervous_system(1) 1 0.387097 115.177739 116.217106 36 57 KEEP --- --- --- --- KIAA2018 205717 broad.mit.edu 37 3 113380309 113380309 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:113380309G>A uc003eam.2 - KIAA2018_uc003eal.2_Intron NM_001009899 NP_001009899 hypothetical protein LOC205717 regulation of transcription, DNA-dependent membrane|nucleus calcium ion binding|DNA binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity skin(2)|ovary(1) 3 0.466667 24.224203 24.238682 7 8 KEEP --- --- --- --- HGD 3081 broad.mit.edu 37 3 120347491 120347491 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:120347491G>A uc003edw.2 - HGD_uc003edv.2_Intron NM_000187 NP_000178 homogentisate 1,2-dioxygenase L-phenylalanine catabolic process|tyrosine catabolic process cytosol homogentisate 1,2-dioxygenase activity|metal ion binding 0 GBM - Glioblastoma multiforme(114;0.158) 0.5 17.674988 17.674988 5 5 KEEP --- --- --- --- STXBP5L 9515 broad.mit.edu 37 3 120959424 120959424 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:120959424C>T uc003eec.3 + STXBP5L_uc011bji.1_Intron NM_014980 NP_055795 syntaxin binding protein 5-like exocytosis|protein transport cytoplasm|integral to membrane|plasma membrane ovary(7)|skin(2) 9 GBM - Glioblastoma multiforme(114;0.0694) 0.44 35.421328 35.499842 11 14 KEEP --- --- --- --- ARGFX 503582 broad.mit.edu 37 3 121304943 121304943 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:121304943C>T uc003eef.2 + 5 539 c.444C>T c.(442-444)ATC>ATT p.I148I NM_001012659 NP_001012677 A6NJG6 ARGFX_HUMAN arginine-fifty homeobox 148 nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity skin(2)|ovary(1) 3 GBM - Glioblastoma multiforme(114;0.152) 0.493976 130.068748 130.07143 41 42 KEEP --- --- --- --- FBXO40 51725 broad.mit.edu 37 3 121340573 121340573 + Nonsense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:121340573G>A uc003eeg.2 + 3 507 c.297G>A c.(295-297)TGG>TGA p.W99* NM_016298 NP_057382 Q9UH90 FBX40_HUMAN F-box protein 40 99 TRAF-type. muscle cell differentiation centrosome|nucleus ubiquitin-protein ligase activity|zinc ion binding ovary(2)|lung(1)|breast(1)|central_nervous_system(1) 5 GBM - Glioblastoma multiforme(114;0.189) 0.480519 124.383033 124.407631 37 40 KEEP --- --- --- --- SLC15A2 6565 broad.mit.edu 37 3 121616299 121616299 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:121616299C>T uc003eep.2 + 3 411 c.258C>T c.(256-258)TAC>TAT p.Y86Y SLC15A2_uc011bjn.1_Silent_p.Y86Y NM_021082 NP_066568 Q16348 S15A2_HUMAN peptide transporter 2 isoform a 86 protein transport integral to plasma membrane peptide:hydrogen symporter activity|protein binding skin(1) 1 GBM - Glioblastoma multiforme(114;0.0967) Cefadroxil(DB01140) 0.425287 107.437578 107.865146 37 50 KEEP --- --- --- --- CD86 942 broad.mit.edu 37 3 121774458 121774458 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:121774458G>A uc003eet.2 + CD86_uc011bjo.1_Intron|CD86_uc011bjp.1_Intron NM_175862 NP_787058 CD86 antigen isoform 1 interspecies interaction between organisms|positive regulation of cell proliferation|positive regulation of interleukin-2 biosynthetic process|positive regulation of interleukin-4 biosynthetic process|positive regulation of lymphotoxin A biosynthetic process|positive regulation of T-helper 2 cell differentiation|positive regulation of transcription, DNA-dependent|T cell costimulation coreceptor activity|protein binding pancreas(1)|skin(1) 2 GBM - Glioblastoma multiforme(114;0.156) Abatacept(DB01281) GBM(67;1379 1389 36064 39806) 0.230769 7.817949 8.681632 3 10 KEEP --- --- --- --- CD86 942 broad.mit.edu 37 3 121822611 121822611 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:121822611G>A uc003eet.2 + 3 433 c.317G>A c.(316-318)GGC>GAC p.G106D CD86_uc011bjo.1_Missense_Mutation_p.G24D|CD86_uc011bjp.1_Intron|CD86_uc003eeu.2_Missense_Mutation_p.G100D NM_175862 NP_787058 P42081 CD86_HUMAN CD86 antigen isoform 1 106 Ig-like V-type.|Extracellular (Potential). interspecies interaction between organisms|positive regulation of cell proliferation|positive regulation of interleukin-2 biosynthetic process|positive regulation of interleukin-4 biosynthetic process|positive regulation of lymphotoxin A biosynthetic process|positive regulation of T-helper 2 cell differentiation|positive regulation of transcription, DNA-dependent|T cell costimulation coreceptor activity|protein binding pancreas(1)|skin(1) 2 GBM - Glioblastoma multiforme(114;0.156) Abatacept(DB01281) GBM(67;1379 1389 36064 39806) 0.564885 242.478178 242.962767 74 57 KEEP --- --- --- --- WDR5B 54554 broad.mit.edu 37 3 122133735 122133735 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:122133735G>A uc003efa.1 - 1 1148 c.641C>T c.(640-642)TCT>TTT p.S214F NM_019069 NP_061942 Q86VZ2 WDR5B_HUMAN WD repeat domain 5B 214 WD 5. ovary(3) 3 GBM - Glioblastoma multiforme(114;0.0704) 0.396396 143.376768 144.419566 44 67 KEEP --- --- --- --- ADCY5 111 broad.mit.edu 37 3 123016029 123016029 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:123016029C>T uc003egh.1 - ADCY5_uc003egg.1_Intron NM_183357 NP_899200 adenylate cyclase 5 activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport integral to membrane|plasma membrane adenylate cyclase activity|ATP binding|metal ion binding ovary(4) 4 GBM - Glioblastoma multiforme(114;0.0342) 0.548387 59.377344 59.440404 17 14 KEEP --- --- --- --- CCDC14 64770 broad.mit.edu 37 3 123666026 123666026 + Silent SNP A T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:123666026A>T uc011bjx.1 - 8 1060 c.969T>A c.(967-969)ATT>ATA p.I323I CCDC14_uc003egv.3_Intron|CCDC14_uc003egx.3_Silent_p.I123I|CCDC14_uc010hrt.2_Silent_p.I282I|CCDC14_uc003egy.3_Silent_p.I123I|CCDC14_uc003egz.2_Silent_p.I123I NM_022757 NP_073594 Q49A88 CCD14_HUMAN coiled-coil domain containing 14 323 centrosome 0 Lung NSC(201;0.0371)|Prostate(884;0.0405)|Myeloproliferative disorder(1037;0.205) Lung(219;0.00942)|GBM - Glioblastoma multiforme(114;0.159) 0.561224 176.038385 176.359328 55 43 KEEP --- --- --- --- SLC12A8 84561 broad.mit.edu 37 3 124802787 124802787 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:124802787G>A uc003ehv.3 - 14 2203 c.2092C>T c.(2092-2094)CGC>TGC p.R698C SLC12A8_uc003ehw.3_Missense_Mutation_p.R727C|SLC12A8_uc003eht.3_Missense_Mutation_p.R499C|SLC12A8_uc003ehu.3_Missense_Mutation_p.R451C|SLC12A8_uc010hry.2_3'UTR NM_024628 NP_078904 A0AV02 S12A8_HUMAN solute carrier family 12, member 8 698 R -> H (in Ref. 2; AAO49174). potassium ion transport integral to membrane symporter activity 0 0.2 9.18878 10.862715 4 16 KEEP --- --- --- --- Unknown broad.mit.edu 37 3 125534946 125534946 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:125534946G>A MIR548I1 (25551 upstream) : LOC100125556 (100498 downstream) 0.25 6.246745 6.700774 2 6 KEEP --- --- --- --- UROC1 131669 broad.mit.edu 37 3 126211219 126211219 + Intron SNP A T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:126211219A>T uc003eiz.1 - UROC1_uc010hsi.1_Intron NM_144639 NP_653240 urocanase domain containing 1 isoform 1 histidine catabolic process cytosol urocanate hydratase activity ovary(1) 1 GBM - Glioblastoma multiforme(114;0.17) 0.4375 21.522608 21.577118 7 9 KEEP --- --- --- --- broad.mit.edu 37 3 126915900 126915900 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:126915900C>T uc003eji.1 + 2 612 c.372C>T c.(370-372)GCC>GCT p.A124A RecName: Full=Putative uncharacterized protein C3orf56; 0.465812 341.875915 342.109593 109 125 KEEP --- --- --- --- ACAD9 28976 broad.mit.edu 37 3 128603514 128603514 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:128603514C>T uc003ela.3 + 2 371 c.169C>T c.(169-171)CCA>TCA p.P57S ACAD9_uc010hsw.1_Intron|ACAD9_uc011bks.1_5'UTR|ACAD9_uc003elb.2_Intron NM_014049 NP_054768 Q9H845 ACAD9_HUMAN acyl-Coenzyme A dehydrogenase family, member 9 57 mitochondrion acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding ovary(2)|central_nervous_system(1) 3 0.472222 113.145948 113.194267 34 38 KEEP --- --- --- --- RAB43 339122 broad.mit.edu 37 3 128813899 128813899 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:128813899G>A uc003eln.1 - 2 605 c.318C>T c.(316-318)TTC>TTT p.F106F RAB43_uc003elo.1_Missense_Mutation_p.S322F|RAB43_uc010hsy.1_Silent_p.F106F NM_198490 NP_940892 Q86YS6 RAB43_HUMAN RAB43 protein 106 protein transport|small GTPase mediated signal transduction plasma membrane GTP binding lung(1) 1 0.457143 102.078496 102.191892 32 38 KEEP --- --- --- --- C3orf37 56941 broad.mit.edu 37 3 129020763 129020763 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:129020763C>T uc003elt.2 + C3orf37_uc003elu.2_Intron|C3orf37_uc003elv.2_Intron|C3orf37_uc003elw.2_Intron NM_020187 NP_064572 hypothetical protein LOC56941 ovary(1) 1 0.538462 166.180974 166.297797 49 42 KEEP --- --- --- --- COL29A1 256076 broad.mit.edu 37 3 130095609 130095609 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:130095609C>T uc010htj.1 + 3 1091 c.597C>T c.(595-597)TCC>TCT p.S199S COL29A1_uc010hti.1_RNA NM_153264 NP_694996 A8TX70 CO6A5_HUMAN collagen, type XXIX, alpha 1 199 Nonhelical region.|VWFA 1. axon guidance|cell adhesion collagen 0 0.454545 50.922385 50.981654 15 18 KEEP --- --- --- --- Unknown broad.mit.edu 37 3 133878213 133878213 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:133878213G>A RYK (-91373 upstream) : RYK (-2235 downstream) 0.580645 59.454112 59.6298 18 13 KEEP --- --- --- --- NMNAT3 349565 broad.mit.edu 37 3 139279927 139279927 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:139279927C>T uc003etj.2 - 4 724 c.684G>A c.(682-684)AAG>AAA p.K228K NMNAT3_uc003etk.2_Silent_p.K191K|NMNAT3_uc003etl.2_RNA|NMNAT3_uc010hul.2_Silent_p.K139K NM_178177 NP_835471 Q96T66 NMNA3_HUMAN nicotinamide mononucleotide adenylyltransferase 228 water-soluble vitamin metabolic process cytosol|mitochondrion ATP binding|nicotinamide-nucleotide adenylyltransferase activity|nicotinate-nucleotide adenylyltransferase activity 0 0.502732 314.096622 314.097774 92 91 KEEP --- --- --- --- GRK7 131890 broad.mit.edu 37 3 141499493 141499493 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:141499493C>T uc011bnd.1 + 2 974 c.890C>T c.(889-891)TCG>TTG p.S297L NM_139209 NP_631948 Q8WTQ7 GRK7_HUMAN G-protein-coupled receptor kinase 7 precursor 297 Protein kinase. visual perception membrane ATP binding|G-protein coupled receptor kinase activity|signal transducer activity lung(2)|stomach(1)|ovary(1)|skin(1) 5 p.S297L(P12ICHIKAWA-Tumor) 174 0.5 100.320609 100.320609 31 31 KEEP --- --- --- --- GRK7 131890 broad.mit.edu 37 3 141499646 141499646 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:141499646C>T uc011bnd.1 + 2 1127 c.1043C>T c.(1042-1044)ACC>ATC p.T348I NM_139209 NP_631948 Q8WTQ7 GRK7_HUMAN G-protein-coupled receptor kinase 7 precursor 348 Protein kinase. visual perception membrane ATP binding|G-protein coupled receptor kinase activity|signal transducer activity lung(2)|stomach(1)|ovary(1)|skin(1) 5 174 0.454545 29.946356 29.986072 10 12 KEEP --- --- --- --- XRN1 54464 broad.mit.edu 37 3 142052059 142052059 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:142052059G>A uc003eus.2 - XRN1_uc010huu.2_Intron|XRN1_uc003eut.2_Intron|XRN1_uc003euu.2_Intron NM_019001 NP_061874 5'-3' exoribonuclease 1 isoform a exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|nuclear mRNA surveillance|rRNA catabolic process cytosol|Golgi apparatus|intermediate filament cytoskeleton|plasma membrane 5'-3' exonuclease activity|DNA binding|protein binding|RNA binding ovary(3) 3 0.4 6.849037 6.89277 2 3 KEEP --- --- --- --- ATR 545 broad.mit.edu 37 3 142212085 142212085 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:142212085G>A uc003eux.3 - 35 6089 c.5967C>T c.(5965-5967)ACC>ACT p.T1989T NM_001184 NP_001175 Q13535 ATR_HUMAN ataxia telangiectasia and Rad3 related protein 1989 FAT. cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence PML body ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity lung(5)|skin(5)|breast(4)|ovary(3)|stomach(1)|central_nervous_system(1)|liver(1) 20 936 Other_conserved_DNA_damage_response_genes 0.507692 111.861978 111.865148 33 32 KEEP --- --- --- --- ATR 545 broad.mit.edu 37 3 142281696 142281696 + Missense_Mutation SNP T G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:142281696T>G uc003eux.3 - 4 670 c.548A>C c.(547-549)GAT>GCT p.D183A NM_001184 NP_001175 Q13535 ATR_HUMAN ataxia telangiectasia and Rad3 related protein 183 cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence PML body ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity lung(5)|skin(5)|breast(4)|ovary(3)|stomach(1)|central_nervous_system(1)|liver(1) 20 936 Other_conserved_DNA_damage_response_genes 0.084337 6.463547 21.015849 7 76 KEEP --- --- --- --- TRPC1 7220 broad.mit.edu 37 3 142496478 142496478 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:142496478C>T uc003evc.2 + 5 773 c.637C>T c.(637-639)CGT>TGT p.R213C TRPC1_uc003evb.2_Missense_Mutation_p.R179C NM_003304 NP_003295 P48995 TRPC1_HUMAN transient receptor potential cation channel, 213 Cytoplasmic (Potential). axon guidance|cytosolic calcium ion homeostasis|positive regulation of release of sequestered calcium ion into cytosol|response to calcium ion cytosol|integral to plasma membrane protein binding|store-operated calcium channel activity ovary(2) 2 0.439024 56.84241 56.975595 18 23 KEEP --- --- --- --- PLOD2 5352 broad.mit.edu 37 3 145820558 145820558 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:145820558C>T uc003evs.1 - 7 1267 c.761G>A c.(760-762)GGA>GAA p.G254E PLOD2_uc011bnm.1_Missense_Mutation_p.G199E|PLOD2_uc003evr.1_Missense_Mutation_p.G254E NM_000935 NP_000926 O00469 PLOD2_HUMAN procollagen-lysine, 2-oxoglutarate 5-dioxygenase 254 protein modification process|response to hypoxia rough endoplasmic reticulum membrane iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-lysine 5-dioxygenase activity|protein binding ovary(1)|skin(1) 2 Vitamin C(DB00126) 0.275 30.707074 32.531057 11 29 KEEP --- --- --- --- CP 1356 broad.mit.edu 37 3 148925105 148925105 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:148925105C>T uc003ewy.3 - CP_uc011bnr.1_Intron|CP_uc003ewx.3_Intron|CP_uc003ewz.2_Intron|CP_uc010hvf.1_Intron NM_000096 NP_000087 ceruloplasmin precursor cellular iron ion homeostasis|copper ion transport|transmembrane transport extracellular space chaperone binding|ferroxidase activity ovary(1) 1 Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152) LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607) Drotrecogin alfa(DB00055) 0.37037 91.828642 93.024922 30 51 KEEP --- --- --- --- PFN2 5217 broad.mit.edu 37 3 149686037 149686037 + Intron SNP C A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:149686037C>A uc003ext.1 - PFN2_uc003exs.1_Intron|PFN2_uc003exu.1_Intron|PFN2_uc011bnu.1_Intron NM_053024 NP_444252 profilin 2 isoform a actin cytoskeleton organization|regulation of actin polymerization or depolymerization actin cytoskeleton|cytoplasm actin binding|phosphatidylinositol-4,5-bisphosphate binding 0 LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066) 0.090909 2.636209 11.914247 5 50 KEEP --- --- --- --- IGSF10 285313 broad.mit.edu 37 3 151174723 151174723 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:151174723C>T uc011bod.1 - NM_178822 NP_849144 immunoglobulin superfamily, member 10 precursor cell differentiation|multicellular organismal development|ossification extracellular region skin(7)|ovary(5)|central_nervous_system(1) 13 LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517) 0.644444 99.586895 100.413621 29 16 KEEP --- --- --- --- AADACL2 344752 broad.mit.edu 37 3 151475007 151475007 + Silent SNP G T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:151475007G>T uc003ezc.2 + 5 951 c.831G>T c.(829-831)CTG>CTT p.L277L AADACL2_uc010hvn.2_Silent_p.L64L NM_207365 NP_997248 Q6P093 ADCL2_HUMAN arylacetamide deacetylase-like 2 precursor 277 extracellular region|integral to membrane carboxylesterase activity 0 LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813) 0.435897 167.693611 168.115037 51 66 KEEP --- --- --- --- KCNAB1 7881 broad.mit.edu 37 3 156181549 156181549 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:156181549C>T uc003far.2 + KCNAB1_uc011bon.1_Intron|KCNAB1_uc003fas.2_Intron|KCNAB1_uc003fat.2_Intron|KCNAB1_uc010hvt.1_Intron|KCNAB1_uc011boo.1_Intron NM_172160 NP_751892 potassium voltage-gated channel, shaker-related cytoplasm|integral to membrane oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity ovary(3)|skin(1) 4 LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465) 0.470588 102.397881 102.448761 32 36 KEEP --- --- --- --- OTOL1 131149 broad.mit.edu 37 3 161214892 161214892 + Missense_Mutation SNP G T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:161214892G>T uc011bpb.1 + 1 297 c.297G>T c.(295-297)TTG>TTT p.L99F NM_001080440 NP_001073909 A6NHN0 OTOL1_HUMAN otolin-1 precursor 99 collagen 0 0.448276 240.149738 240.551175 78 96 KEEP --- --- --- --- SI 6476 broad.mit.edu 37 3 164754141 164754141 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:164754141G>A uc003fei.2 - NM_001041 NP_001032 sucrase-isomaltase carbohydrate metabolic process|polysaccharide digestion apical plasma membrane|brush border|Golgi apparatus|integral to membrane carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1) 14 Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199) Acarbose(DB00284) HNSCC(35;0.089) 0.395349 56.366344 56.778463 17 26 KEEP --- --- --- --- SI 6476 broad.mit.edu 37 3 164792339 164792339 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:164792339G>A uc003fei.2 - 3 297 c.235C>T c.(235-237)CCA>TCA p.P79S NM_001041 NP_001032 P14410 SUIS_HUMAN sucrase-isomaltase 79 Lumenal.|P-type 1. carbohydrate metabolic process|polysaccharide digestion apical plasma membrane|brush border|Golgi apparatus|integral to membrane carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1) 14 Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199) Acarbose(DB00284) HNSCC(35;0.089) 0.44186 61.928547 62.053131 19 24 KEEP --- --- --- --- Unknown broad.mit.edu 37 3 166904176 166904176 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:166904176G>A None (None upstream) : ZBBX (53905 downstream) 0.666667 14.101993 14.249532 4 2 KEEP --- --- --- --- WDR49 151790 broad.mit.edu 37 3 167293834 167293835 + Missense_Mutation DNP GG AA AA MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:167293834_167293835GG>AA uc003fev.1 - 4 663_664 c.357_358CC>TT c.(355-360)GCCCAT>GCTTAT p.H120Y WDR49_uc003feu.1_5'Flank|WDR49_uc011bpd.1_Missense_Mutation_p.H173Y|WDR49_uc003few.1_Missense_Mutation_p.H461Y NM_178824 NP_849146 Q8IV35 WDR49_HUMAN WD repeat domain 49 120 large_intestine(1)|ovary(1)|skin(1) 3 0.531915 167.55519 167.638314 50 44 KEEP --- --- --- --- LRRC31 79782 broad.mit.edu 37 3 169572881 169572881 + Intron SNP C G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:169572881C>G uc003fgc.1 - LRRC31_uc010hwp.1_Intron NM_024727 NP_079003 leucine rich repeat containing 31 ovary(2)|skin(1) 3 all_cancers(22;2.76e-22)|all_epithelial(15;4.73e-27)|all_lung(20;9.24e-17)|Lung NSC(18;3.85e-16)|Ovarian(172;0.000223)|Breast(254;0.197) Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00943) 0.555556 35.751135 35.799391 10 8 KEEP --- --- --- --- SLC2A2 6514 broad.mit.edu 37 3 170724921 170724921 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:170724921G>A uc003fhe.1 - SLC2A2_uc003fhf.1_Intron|SLC2A2_uc011bpu.1_Intron NM_000340 NP_000331 solute carrier family 2 (facilitated glucose carbohydrate metabolic process|cellular lipid metabolic process|endocrine pancreas development|energy reserve metabolic process|regulation of insulin secretion integral to plasma membrane|membrane fraction D-glucose transmembrane transporter activity ovary(1)|central_nervous_system(1) 2 all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122) LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14) 0.451613 44.743651 44.807164 14 17 KEEP --- --- --- --- PLD1 5337 broad.mit.edu 37 3 171338100 171338100 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:171338100G>A uc003fhs.2 - PLD1_uc003fht.2_Intron|PLD1_uc003fhu.3_Intron NM_002662 NP_002653 phospholipase D1 isoform a cell communication|chemotaxis|Ras protein signal transduction endoplasmic reticulum membrane|Golgi membrane|late endosome membrane|perinuclear region of cytoplasm NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity ovary(2)|lung(1) 3 all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186) LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14) Choline(DB00122) NSCLC(149;2174 3517 34058) 595 0.441176 44.516723 44.619736 15 19 KEEP --- --- --- --- PLD1 5337 broad.mit.edu 37 3 171452709 171452710 + Missense_Mutation DNP AC TT TT MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:171452709_171452710AC>TT uc003fhs.2 - 5 601_602 c.485_486GT>AA c.(484-486)AGT>AAA p.S162K PLD1_uc003fht.2_Missense_Mutation_p.S162K NM_002662 NP_002653 Q13393 PLD1_HUMAN phospholipase D1 isoform a 162 PX. cell communication|chemotaxis|Ras protein signal transduction endoplasmic reticulum membrane|Golgi membrane|late endosome membrane|perinuclear region of cytoplasm NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity ovary(2)|lung(1) 3 all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186) LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14) Choline(DB00122) NSCLC(149;2174 3517 34058) 595 0.42236 223.376892 224.223079 68 93 KEEP --- --- --- --- Unknown broad.mit.edu 37 3 175785824 175785824 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:175785824G>A NAALADL2 (262398 upstream) : TBL1XR1 (952719 downstream) 0.4 12.498102 12.585539 4 6 KEEP --- --- --- --- MCCC1 56922 broad.mit.edu 37 3 182804511 182804511 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:182804511G>A uc003fle.2 - 4 476 c.339C>T c.(337-339)ATC>ATT p.I113I MCCC1_uc010hxi.2_RNA|MCCC1_uc011bqo.1_Intron|MCCC1_uc003flf.2_Missense_Mutation_p.S37L|MCCC1_uc003flg.2_Silent_p.I4I|MCCC1_uc011bqp.1_Silent_p.I66I|MCCC1_uc011bqq.1_Silent_p.I4I NM_020166 NP_064551 Q96RQ3 MCCA_HUMAN methylcrotonoyl-Coenzyme A carboxylase 1 (alpha) 113 Biotin carboxylation. biotin metabolic process|leucine catabolic process mitochondrial inner membrane|mitochondrial matrix ATP binding|biotin binding|biotin carboxylase activity|metal ion binding|methylcrotonoyl-CoA carboxylase activity ovary(1)|central_nervous_system(1)|skin(1) 3 all_cancers(143;1.84e-14)|Ovarian(172;0.0355) all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21) Biotin(DB00121) 0.465517 84.516317 84.576699 27 31 KEEP --- --- --- --- KNG1 3827 broad.mit.edu 37 3 186450409 186450409 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:186450409G>A uc011bsa.1 + 7 1088 c.876G>A c.(874-876)GAG>GAA p.E292E KNG1_uc003fqr.2_Silent_p.E292E NM_001102416 NP_001095886 P01042 KNG1_HUMAN kininogen 1 isoform 1 292 Cystatin 3. blood coagulation, intrinsic pathway|elevation of cytosolic calcium ion concentration|inflammatory response|negative regulation of blood coagulation|negative regulation of cell adhesion|platelet activation|platelet degranulation|positive regulation of apoptosis|positive regulation of renal sodium excretion|positive regulation of urine volume|smooth muscle contraction|vasodilation extracellular space|plasma membrane|platelet alpha granule lumen cysteine-type endopeptidase inhibitor activity|heparin binding|receptor binding|zinc ion binding skin(1) 1 all_cancers(143;8.96e-12)|Ovarian(172;0.0339) OV - Ovarian serous cystadenocarcinoma(80;4.12e-20) GBM - Glioblastoma multiforme(93;0.0798) Ouabain(DB01092) 0.520661 212.209168 212.253106 63 58 KEEP --- --- --- --- TPRG1 285386 broad.mit.edu 37 3 188707642 188707642 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:188707642C>T uc003frv.1 + NM_198485 NP_940887 tumor protein p63 regulated 1 0 all_cancers(143;6.12e-12)|all_hematologic(3;0.0359)|Ovarian(172;0.0925) all_lung(153;8.23e-09)|Lung NSC(153;3.55e-06)|all_neural(597;0.0019)|Myeloproliferative disorder(1037;0.0255) Lung(62;6.93e-06) GBM - Glioblastoma multiforme(93;4.77e-14) 0.692308 31.279856 31.708417 9 4 KEEP --- --- --- --- FGF12 2257 broad.mit.edu 37 3 191861769 191861769 + 3'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:191861769G>A uc003fsx.2 - 5 FGF12_uc003fsy.2_3'UTR NM_021032 NP_066360 fibroblast growth factor 12 isoform 1 cell-cell signaling|heart development|JNK cascade|nervous system development|signal transduction extracellular space|nucleus growth factor activity|heparin binding ovary(1)|skin(1)|lung(1)|pancreas(1) 4 all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247) Lung NSC(153;0.21) LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06) GBM - Glioblastoma multiforme(46;0.00032) 0.517544 180.211159 180.241004 59 55 KEEP --- --- --- --- ATP13A4 84239 broad.mit.edu 37 3 193132279 193132279 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:193132279G>A uc003ftd.2 - ATP13A4_uc010hzi.2_Intron NM_032279 NP_115655 ATPase type 13A4 ATP biosynthetic process|cation transport integral to membrane ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding ovary(2) 2 all_cancers(143;1.76e-08)|Ovarian(172;0.0386) OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06) GBM - Glioblastoma multiforme(46;0.000109) 0.421053 24.996607 25.100027 8 11 KEEP --- --- --- --- ATP13A4 84239 broad.mit.edu 37 3 193188501 193188501 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:193188501G>A uc003ftd.2 - ATP13A4_uc003fte.1_Intron|ATP13A4_uc011bsr.1_Intron|ATP13A4_uc003ftf.3_Intron NM_032279 NP_115655 ATPase type 13A4 ATP biosynthetic process|cation transport integral to membrane ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding ovary(2) 2 all_cancers(143;1.76e-08)|Ovarian(172;0.0386) OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06) GBM - Glioblastoma multiforme(46;0.000109) 0.583333 21.620941 21.69275 7 5 KEEP --- --- --- --- Unknown broad.mit.edu 37 3 195724500 195724500 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:195724500G>A SDHAP1 (7350 upstream) : TFRC (51656 downstream) 0.5 9.62482 9.62482 3 3 KEEP --- --- --- --- KIAA0226 9711 broad.mit.edu 37 3 197402081 197402081 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr3:197402081G>A uc003fyc.2 - KIAA0226_uc003fyd.3_Intron|MIR922_hsa-mir-922|MI0005714_5'Flank NM_014687 NP_055502 hypothetical protein LOC9711 isoform 2. autophagy|endocytosis|negative regulation of autophagy|negative regulation of endocytosis early endosome|late endosome|lysosome protein binding 0 all_cancers(143;8.26e-10)|Ovarian(172;0.0418)|Breast(254;0.0976) Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06) GBM - Glioblastoma multiforme(93;0.0446) Esophageal Squamous(3;167 355 3763 15924) 0.357143 59.886131 60.892022 20 36 KEEP --- --- --- --- ZNF595 152687 broad.mit.edu 37 4 53377 53377 + 5'UTR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:53377C>T uc003fzv.1 + 1 ZNF595_uc003fzu.1_RNA|ZNF718_uc003fzt.3_5'UTR|ZNF595_uc010iay.1_RNA|ZNF595_uc011bus.1_5'UTR|ZNF595_uc011but.1_5'UTR NM_182524 NP_872330 zinc finger protein 595 regulation of transcription, DNA-dependent intracellular nucleic acid binding|zinc ion binding 0 all_cancers(4;0.0738)|all_epithelial(65;0.139) Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173) 0.125 25.73898 44.372884 17 119 KEEP --- --- --- --- ZNF732 654254 broad.mit.edu 37 4 265837 265837 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:265837C>T uc011buu.1 - 3 820 c.806G>A c.(805-807)AGA>AAA p.R269K ZNF732_uc010ibb.1_Intron NM_001137608 NP_001131080 B4DXR9 ZN732_HUMAN zinc finger protein 732 270 C2H2-type 5; degenerate. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding 0 1 39.870686 39.869709 10 0 KEEP --- --- --- --- HTT 3064 broad.mit.edu 37 4 3117889 3117889 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:3117889C>T uc011bvq.1 + 9 1118 c.973C>T c.(973-975)CCC>TCC p.P325S NM_002111 NP_002102 P42858 HD_HUMAN huntingtin 323 HEAT 3. establishment of mitotic spindle orientation|Golgi organization|retrograde vesicle-mediated transport, Golgi to ER|vesicle transport along microtubule autophagic vacuole|axon|cytoplasmic vesicle membrane|cytosol|dendrite|endoplasmic reticulum|Golgi apparatus|late endosome|membrane fraction|nucleus|protein complex beta-tubulin binding|dynactin binding|dynein intermediate chain binding|p53 binding|transcription factor binding skin(2)|ovary(1)|lung(1) 4 all_epithelial(65;0.18) UCEC - Uterine corpus endometrioid carcinoma (64;0.187) 0.984375 223.012867 224.955022 63 1 KEEP --- --- --- --- Unknown broad.mit.edu 37 4 3904139 3904139 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:3904139C>T ADRA2C (133888 upstream) : LOC348926 (39531 downstream) 0.916667 39.575438 41.45203 11 1 KEEP --- --- --- --- Unknown broad.mit.edu 37 4 4896407 4896407 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:4896407C>T MSX1 (30749 upstream) : CYTL1 (119909 downstream) 1 40.183771 40.183257 11 0 KEEP --- --- --- --- SORCS2 57537 broad.mit.edu 37 4 7725652 7725652 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:7725652G>A uc003gkb.3 + SORCS2_uc011bwi.1_Intron NM_020777 NP_065828 VPS10 domain receptor protein SORCS 2 precursor integral to membrane neuropeptide receptor activity ovary(1)|central_nervous_system(1) 2 1 27.646559 27.63877 7 0 KEEP --- --- --- --- ACOX3 8310 broad.mit.edu 37 4 8368619 8368619 + 3'UTR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:8368619G>A uc010idk.2 - 18 ACOX3_uc003glc.3_3'UTR|ACOX3_uc003gld.3_3'UTR NM_003501 NP_003492 acyl-Coenzyme A oxidase 3 isoform a bile acid metabolic process|fatty acid beta-oxidation using acyl-CoA oxidase peroxisomal matrix acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|pristanoyl-CoA oxidase activity central_nervous_system(1) 1 1 66.404535 66.404527 17 0 KEEP --- --- --- --- Unknown broad.mit.edu 37 4 9385891 9385891 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:9385891C>T USP17L6P (15097 upstream) : DEFB131 (60369 downstream) 0.987342 303.024537 304.477964 78 1 KEEP --- --- --- --- BST1 683 broad.mit.edu 37 4 15713505 15713505 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:15713505C>T uc003goh.3 + 4 722 c.527C>T c.(526-528)TCC>TTC p.S176F NM_004334 NP_004325 Q10588 BST1_HUMAN bone marrow stromal cell antigen 1 precursor 176 humoral immune response|multicellular organismal development anchored to membrane|extrinsic to membrane|plasma membrane binding|NAD+ nucleosidase activity central_nervous_system(1) 1 1 135.890364 135.890364 35 0 KEEP --- --- --- --- SLIT2 9353 broad.mit.edu 37 4 20611844 20611844 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:20611844G>A uc003gpr.1 + SLIT2_uc003gps.1_Intron NM_004787 NP_004778 slit homolog 2 precursor apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development cell surface|cytoplasm|extracellular space|plasma membrane calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding central_nervous_system(4)|skin(4)|ovary(3) 11 1 38.367454 38.366474 10 0 KEEP --- --- --- --- SLIT2 9353 broad.mit.edu 37 4 20618587 20618587 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:20618587G>A uc003gpr.1 + 35 4106 c.3902G>A c.(3901-3903)GGA>GAA p.G1301E SLIT2_uc003gps.1_Missense_Mutation_p.G1293E NM_004787 NP_004778 O94813 SLIT2_HUMAN slit homolog 2 precursor 1301 Laminin G-like. apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development cell surface|cytoplasm|extracellular space|plasma membrane calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding central_nervous_system(4)|skin(4)|ovary(3) 11 1 70.08441 70.084406 18 0 KEEP --- --- --- --- SLIT2 9353 broad.mit.edu 37 4 20618882 20618882 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:20618882G>A uc003gpr.1 + SLIT2_uc003gps.1_Intron NM_004787 NP_004778 slit homolog 2 precursor apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|Roundabout signaling pathway|ureteric bud development cell surface|cytoplasm|extracellular space|plasma membrane calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding central_nervous_system(4)|skin(4)|ovary(3) 11 1 27.346383 27.338593 7 0 KEEP --- --- --- --- Unknown broad.mit.edu 37 4 25625007 25625007 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:25625007G>A ANAPC4 (204888 upstream) : SLC34A2 (32428 downstream) 1 21.575701 21.560167 6 0 KEEP --- --- --- --- Unknown broad.mit.edu 37 4 37823112 37823112 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:37823112G>A RELL1 (135113 upstream) : PGM2 (5170 downstream) 0.533333 53.701782 53.730724 16 14 KEEP --- --- --- --- TLR10 81793 broad.mit.edu 37 4 38775733 38775733 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:38775733C>T uc003gti.2 - 2 1858 c.1479G>A c.(1477-1479)CTG>CTA p.L493L TLR10_uc003gtj.2_Silent_p.L493L|TLR10_uc003gtk.2_Silent_p.L493L NM_030956 NP_112218 Q9BXR5 TLR10_HUMAN toll-like receptor 10 precursor 493 Extracellular (Potential).|LRR 15. inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway integral to membrane|plasma membrane transmembrane receptor activity lung(1)|breast(1) 2 0.504673 176.947617 176.949594 54 53 KEEP --- --- --- --- NSUN7 79730 broad.mit.edu 37 4 40778145 40778145 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:40778145G>A uc003gvj.3 + 7 1400 c.905G>A c.(904-906)GGC>GAC p.G302D NSUN7_uc003gvi.3_Missense_Mutation_p.G302D NM_024677 NP_078953 NOL1/NOP2/Sun domain family, member 7 0 0.125 8.115402 14.711581 6 42 KEEP --- --- --- --- LIMCH1 22998 broad.mit.edu 37 4 41607878 41607878 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:41607878G>A uc003gvu.3 + LIMCH1_uc003gvt.1_Intron|LIMCH1_uc003gvv.3_Intron|LIMCH1_uc003gvw.3_Intron|LIMCH1_uc003gvx.3_Intron|LIMCH1_uc003gwe.3_Intron|LIMCH1_uc003gvy.3_Intron|LIMCH1_uc003gwa.3_Intron|LIMCH1_uc003gvz.3_Intron NM_014988 NP_055803 LIM and calponin homology domains 1 isoform a actomyosin structure organization actin binding|zinc ion binding ovary(2)|pancreas(1)|skin(1) 4 0.277778 13.528748 14.29175 5 13 KEEP --- --- --- --- LIMCH1 22998 broad.mit.edu 37 4 41621129 41621129 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:41621129C>T uc003gvu.3 + LIMCH1_uc003gvt.1_Intron|LIMCH1_uc003gvv.3_Intron|LIMCH1_uc003gvw.3_Intron|LIMCH1_uc003gvx.3_Intron|LIMCH1_uc003gwe.3_Intron|LIMCH1_uc003gvy.3_Intron|LIMCH1_uc003gwa.3_Intron|LIMCH1_uc003gvz.3_Intron|LIMCH1_uc011byu.1_Intron|LIMCH1_uc003gwc.3_Intron|LIMCH1_uc003gwd.3_Intron|LIMCH1_uc011byv.1_Intron|LIMCH1_uc003gwb.1_Intron NM_014988 NP_055803 LIM and calponin homology domains 1 isoform a actomyosin structure organization actin binding|zinc ion binding ovary(2)|pancreas(1)|skin(1) 4 0.617978 946.681273 952.107458 275 170 KEEP --- --- --- --- GABRA2 2555 broad.mit.edu 37 4 46312234 46312234 + Missense_Mutation SNP T A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:46312234T>A uc003gxc.3 - 5 1188 c.515A>T c.(514-516)GAT>GTT p.D172V GABRA2_uc010igc.2_Missense_Mutation_p.D172V|GABRA2_uc011bzc.1_Missense_Mutation_p.D117V|GABRA2_uc003gxe.2_Missense_Mutation_p.D172V NM_001114175 NP_001107647 P47869 GBRA2_HUMAN gamma-aminobutyric acid A receptor, alpha 2 172 Extracellular (Probable). gamma-aminobutyric acid signaling pathway|neurotransmitter transport|regulation of neurotransmitter levels cell junction|chloride channel complex|integral to synaptic vesicle membrane|postsynaptic membrane benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity ovary(2)|skin(2) 4 Alprazolam(DB00404)|Bromazepam(DB01558)|Diazepam(DB00829)|Ethchlorvynol(DB00189)|Fludiazepam(DB01567)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683) 0.117647 8.4133 15.742067 6 45 KEEP --- --- --- --- Unknown broad.mit.edu 37 4 49240185 49240185 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:49240185C>T CWH43 (176092 upstream) : None (None downstream) 0.269231 18.712265 19.962485 7 19 KEEP --- --- --- --- Unknown broad.mit.edu 37 4 49505114 49505115 + IGR DNP CT TC TC MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:49505114_49505115CT>TC CWH43 (441021 upstream) : None (None downstream) 0.209091 58.060479 66.680173 23 87 KEEP --- --- --- --- SPATA18 132671 broad.mit.edu 37 4 52928564 52928564 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:52928564C>T uc003gzl.2 + SPATA18_uc010igl.1_Intron|SPATA18_uc011bzq.1_Intron|SPATA18_uc003gzk.1_Intron NM_145263 NP_660306 spermatogenesis associated 18 homolog mitochondrial protein catabolic process|mitochondrion degradation by induced vacuole formation|response to DNA damage stimulus mitochondrial outer membrane protein binding ovary(2)|skin(2) 4 GBM - Glioblastoma multiforme(4;1.77e-13)|LUSC - Lung squamous cell carcinoma(32;0.00204) 0.315789 17.64359 18.216812 6 13 KEEP --- --- --- --- SPATA18 132671 broad.mit.edu 37 4 52928569 52928569 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:52928569G>A uc003gzl.2 + SPATA18_uc010igl.1_Intron|SPATA18_uc011bzq.1_Intron|SPATA18_uc003gzk.1_Intron NM_145263 NP_660306 spermatogenesis associated 18 homolog mitochondrial protein catabolic process|mitochondrion degradation by induced vacuole formation|response to DNA damage stimulus mitochondrial outer membrane protein binding ovary(2)|skin(2) 4 GBM - Glioblastoma multiforme(4;1.77e-13)|LUSC - Lung squamous cell carcinoma(32;0.00204) 0.6875 40.43122 40.931937 11 5 KEEP --- --- --- --- PDGFRA 5156 broad.mit.edu 37 4 55133441 55133442 + Intron DNP CC TT TT MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:55133441_55133442CC>TT uc003han.3 + PDGFRA_uc003haa.2_Intron|PDGFRA_uc010igq.1_Intron|PDGFRA_uc003ham.2_Intron NM_006206 NP_006197 platelet-derived growth factor receptor alpha cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye cytoplasm|integral to plasma membrane|nucleus ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1) 674 all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08) GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256) Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268) Pancreas(151;208 1913 7310 23853 37092) 1045 Mis|O|T FIP1L1 GIST|idiopathic hypereosinophilic syndrome Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis TSP Lung(21;0.16) 0.463415 126.34432 126.439728 38 44 KEEP --- --- --- --- TMPRSS11B 132724 broad.mit.edu 37 4 69094825 69094825 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:69094825G>A uc003hdw.3 - NM_182502 NP_872308 transmembrane protease, serine 11B proteolysis extracellular region|integral to plasma membrane serine-type endopeptidase activity ovary(1) 1 0.714286 16.377556 16.665837 5 2 KEEP --- --- --- --- UGT2B4 7363 broad.mit.edu 37 4 70361469 70361469 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:70361469C>T uc003hek.3 - 1 158 c.111G>A c.(109-111)ATG>ATA p.M37I UGT2B4_uc011cap.1_Intron|UGT2B4_uc003hel.3_Missense_Mutation_p.M37I NM_021139 NP_066962 P06133 UD2B4_HUMAN UDP glucuronosyltransferase 2B4 precursor 37 estrogen catabolic process|xenobiotic metabolic process endoplasmic reticulum membrane|integral to membrane|microsome glucuronosyltransferase activity skin(2) 2 0.507463 221.69628 221.702639 68 66 KEEP --- --- --- --- ALB 213 broad.mit.edu 37 4 74284104 74284104 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:74284104C>T uc003hgs.3 + ALB_uc003hgw.3_Intron|ALB_uc011cbe.1_Intron|ALB_uc003hgt.3_Intron|ALB_uc010iii.2_Intron|ALB_uc003hgu.3_Intron|ALB_uc003hgv.3_Intron|ALB_uc011cbf.1_Intron|ALB_uc010iij.2_Intron|ALB_uc003hgx.3_Intron NM_000477 NP_000468 albumin preproprotein bile acid and bile salt transport|bile acid metabolic process|cellular response to starvation|hemolysis by symbiont of host erythrocytes|lipoprotein metabolic process|maintenance of mitochondrion location|negative regulation of apoptosis|platelet activation|platelet degranulation|sodium-independent organic anion transport|transmembrane transport extracellular space|platelet alpha granule lumen|protein complex antioxidant activity|chaperone binding|copper ion binding|DNA binding|drug binding|fatty acid binding|pyridoxal phosphate binding|toxin binding ovary(3)|skin(3) 6 Breast(15;0.00102) Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154) Acenocoumarol(DB01418)|Acitretin(DB00459)|Alfentanil(DB00802)|Aluminium(DB01370)|Auranofin(DB00995)|Bismuth(DB01402)|Captopril(DB01197)|Carboplatin(DB00958)|Cefalotin(DB00456)|Cefazolin(DB01327)|Cefonicid(DB01328)|Cefoperazone(DB01329)|Chlorpheniramine(DB01114)|Chlorpromazine(DB00477)|Ciprofloxacin(DB00537)|Clonazepam(DB01068)|Cloxacillin(DB01147)|Cytarabine(DB00987)|Dantrolene(DB01219)|Diclofenac(DB00586)|Diflunisal(DB00861)|Digitoxin(DB01396)|Estrone(DB00655)|Ethacrynic acid(DB00903)|Etodolac(DB00749)|Flurbiprofen(DB00712)|Gadobenate Dimeglumine(DB00743)|Gatifloxacin(DB01044)|Gliclazide(DB01120)|Halothane(DB01159)|Human Serum Albumin(DB00062)|Hyaluronidase(DB00070)|Ibuprofen(DB01050)|Insulin-detemir(DB01307)|Insulin-glargine(DB01308)|Iodipamide(DB04711)|Ketoprofen(DB01009)|Levamisole(DB00848)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Mefenamic acid(DB00784)|Mephenytoin(DB00532)|Methotrexate(DB00563)|Nortriptyline(DB00540)|Oxazepam(DB00842)|Paclitaxel(DB01229)|Phenprocoumon(DB00946)|Probenecid(DB01032)|Propofol(DB00818)|Pyridoxine(DB00165)|Salicyclic acid(DB00936)|Saquinavir(DB01232)|Serum albumin(DB00096)|Serum albumin iodonated(DB00064)|Sodium lauryl sulfate(DB00815)|Sucralfate(DB00364)|Sulfamethizole(DB00576)|Sulindac(DB00605)|Suprofen(DB00870)|Testosterone(DB00624)|Xanthophyll(DB00137) 0.571429 15.001596 15.032888 4 3 KEEP --- --- --- --- Unknown broad.mit.edu 37 4 74952297 74952297 + IGR SNP A C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:74952297A>C PPBPL2 (31181 upstream) : CXCL2 (10467 downstream) 0.354839 31.314859 31.891077 11 20 KEEP --- --- --- --- CCDC158 339965 broad.mit.edu 37 4 77274351 77274351 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:77274351C>T uc003hkb.3 - 15 2523 c.2370G>A c.(2368-2370)GGG>GGA p.G790G NM_001042784 NP_001036249 Q5M9N0 CD158_HUMAN coiled-coil domain containing 158 790 Potential. skin(3)|ovary(2)|pancreas(1) 6 0.4 68.547644 69.025823 22 33 KEEP --- --- --- --- Unknown broad.mit.edu 37 4 78909682 78909682 + IGR SNP G T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:78909682G>T MRPL1 (35738 upstream) : FRAS1 (69042 downstream) 0.230769 7.117537 7.981607 3 10 KEEP --- --- --- --- PAQR3 152559 broad.mit.edu 37 4 79860255 79860255 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:79860255C>T uc003hlp.1 - 1 328 c.124G>A c.(124-126)GAC>AAC p.D42N PAQR3_uc003hlm.2_RNA|PAQR3_uc003hln.2_RNA|PAQR3_uc003hlq.1_5'UTR NM_001040202 NP_001035292 Q6TCH7 PAQR3_HUMAN progestin and adipoQ receptor family member III 42 Cytoplasmic (Potential). Golgi membrane|integral to membrane receptor activity 0 9 0.494253 132.70543 132.708126 43 44 KEEP --- --- --- --- BMP3 651 broad.mit.edu 37 4 81967167 81967167 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:81967167C>T uc003hmg.3 + 2 912 c.592C>T c.(592-594)CTG>TTG p.L198L NM_001201 NP_001192 P12645 BMP3_HUMAN bone morphogenetic protein 3 preproprotein 198 cartilage development|cell differentiation|cell-cell signaling|growth|ossification extracellular space BMP receptor binding|cytokine activity|growth factor activity ovary(4)|central_nervous_system(1) 5 0.425926 218.747714 219.523468 69 93 KEEP --- --- --- --- ARHGAP24 83478 broad.mit.edu 37 4 86844984 86844984 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:86844984C>T uc003hpk.2 + ARHGAP24_uc003hpj.2_Intron|ARHGAP24_uc003hpl.2_Intron|ARHGAP24_uc010ikf.2_Intron NM_001025616 NP_001020787 Rho GTPase activating protein 24 isoform 1 angiogenesis|cell differentiation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction cell projection|cytoskeleton|cytosol|focal adhesion GTPase activator activity|protein binding 0 Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242) OV - Ovarian serous cystadenocarcinoma(123;0.000571) 0.40625 41.668923 41.914772 13 19 KEEP --- --- --- --- HERC5 51191 broad.mit.edu 37 4 89389622 89389622 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:89389622C>T uc003hrt.2 + HERC5_uc011cdm.1_Intron NM_016323 NP_057407 hect domain and RLD 5 innate immune response|ISG15-protein conjugation|negative regulation of type I interferon production|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of cyclin-dependent protein kinase activity|regulation of defense response to virus|response to virus cytosol|perinuclear region of cytoplasm ISG15 ligase activity|protein binding|ubiquitin-protein ligase activity ovary(4)|lung(3)|skin(2) 9 Hepatocellular(203;0.114) OV - Ovarian serous cystadenocarcinoma(123;0.000209) Esophageal Squamous(39;887 1012 34045 50514) 0.409091 28.970608 29.129576 9 13 KEEP --- --- --- --- HERC3 8916 broad.mit.edu 37 4 89576923 89576923 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:89576923G>A uc003hrw.1 + HERC3_uc003hrv.2_Intron|HERC3_uc011cdn.1_Intron|HERC3_uc011cdo.1_5'Flank NM_014606 NP_055421 hect domain and RLD 3 protein ubiquitination involved in ubiquitin-dependent protein catabolic process cytoplasmic membrane-bounded vesicle ubiquitin-protein ligase activity lung(2)|prostate(1)|skin(1) 4 OV - Ovarian serous cystadenocarcinoma(123;0.000319) 0.695652 59.609453 60.395012 16 7 KEEP --- --- --- --- ADH1C 126 broad.mit.edu 37 4 100265971 100265971 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:100265971C>T uc003huu.2 - NM_000669 NP_000660 class I alcohol dehydrogenase, gamma subunit ethanol oxidation|xenobiotic metabolic process cytosol alcohol dehydrogenase (NAD) activity|zinc ion binding 0 OV - Ovarian serous cystadenocarcinoma(123;1.08e-07) Fomepizole(DB01213)|NADH(DB00157) Naso-/Oropharyngeal/Laryngeal_Cancer_Familial_Clustering_of 0.428571 66.867171 67.085302 21 28 KEEP --- --- --- --- NHEDC1 150159 broad.mit.edu 37 4 103822252 103822252 + 3'UTR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:103822252C>T uc003hww.2 - 12 NHEDC1_uc003hwu.2_Intron|NHEDC1_uc010ilm.2_Intron|NHEDC1_uc003hwv.2_Intron|NHEDC1_uc011cev.1_3'UTR NM_139173 NP_631912 Na+/H+ exchanger domain containing 1 isoform 1 integral to membrane solute:hydrogen antiporter activity ovary(1)|skin(1) 2 Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;1.5e-08) 0.044944 -10.778007 8.926816 4 85 KEEP --- --- --- --- BDH2 56898 broad.mit.edu 37 4 104017453 104017453 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:104017453G>A uc003hwz.2 - BDH2_uc003hxa.2_Intron NM_020139 NP_064524 3-hydroxybutyrate dehydrogenase, type 2 fatty acid beta-oxidation|heme metabolic process|iron ion homeostasis|siderophore biosynthetic process cytoplasm 3-hydroxybutyrate dehydrogenase activity|NAD binding|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor 0 Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;2.02e-08) 0.545455 44.20248 44.242033 12 10 KEEP --- --- --- --- TET2 54790 broad.mit.edu 37 4 106157704 106157705 + Missense_Mutation DNP CC TT TT MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:106157704_106157705CC>TT uc003hxk.2 + 3 2991_2992 c.2605_2606CC>TT c.(2605-2607)CCA>TTA p.P869L TET2_uc011cez.1_Missense_Mutation_p.P890L|TET2_uc003hxj.2_RNA|TET2_uc010ilp.1_Missense_Mutation_p.P869L|TET2_uc003hxi.1_Missense_Mutation_p.P869L NM_001127208 NP_001120680 Q6N021 TET2_HUMAN tet oncogene family member 2 isoform a 869 Gln-rich. cell cycle|myeloid cell differentiation metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen p.P869fs*3(1) haematopoietic_and_lymphoid_tissue(732)|pancreas(1) 733 Myeloproliferative disorder(5;0.0393) OV - Ovarian serous cystadenocarcinoma(123;7.18e-08) 111 Mis N|F MDS 0.4 71.438452 71.919676 22 33 KEEP --- --- --- --- COL25A1 84570 broad.mit.edu 37 4 109738485 109738485 + Intron SNP G T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:109738485G>T uc003hze.1 - COL25A1_uc003hzd.2_Intron NM_198721 NP_942014 collagen, type XXV, alpha 1 isoform 1 collagen|extracellular space beta-amyloid binding|heparin binding ovary(2) 2 Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;0.000173) 0.108696 4.638251 11.620372 5 41 KEEP --- --- --- --- ENPEP 2028 broad.mit.edu 37 4 111436691 111436691 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:111436691C>T uc003iab.3 + NM_001977 NP_001968 glutamyl aminopeptidase cell migration|cell proliferation|cell-cell signaling|proteolysis integral to plasma membrane aminopeptidase activity|metalloexopeptidase activity|zinc ion binding skin(3)|ovary(1)|breast(1) 5 Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;0.0031) L-Glutamic Acid(DB00142) 0.571429 26.90146 26.963603 8 6 KEEP --- --- --- --- Unknown broad.mit.edu 37 4 113378374 113378374 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:113378374C>T ALPK1 (14613 upstream) : NEUROG2 (56300 downstream) 0.45 85.516943 85.647701 27 33 KEEP --- --- --- --- C4orf21 55345 broad.mit.edu 37 4 113486394 113486394 + Intron SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:113486394A>G uc003iau.2 - C4orf21_uc003iav.2_Intron NM_018392 NP_060862 prematurely terminated mRNA decay factor-like integral to membrane zinc ion binding 0 Ovarian(17;0.156) OV - Ovarian serous cystadenocarcinoma(123;0.000676) 0.173913 8.286364 10.59424 4 19 KEEP --- --- --- --- LARP7 51574 broad.mit.edu 37 4 113565903 113565903 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:113565903G>A uc003iay.2 + 2 356 c.78G>A c.(76-78)AAG>AAA p.K26K LARP7_uc003iaz.2_Silent_p.K33K|LARP7_uc003iba.2_5'UTR|LARP7_uc003ibb.2_Silent_p.K26K NM_016648 NP_057732 Q4G0J3 LARP7_HUMAN La ribonucleoprotein domain family, member 7 26 RNA processing nucleoplasm|ribonucleoprotein complex nucleotide binding|RNA binding ovary(3) 3 Ovarian(17;0.0443)|Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;0.000603) 0.355932 65.656889 66.736476 21 38 KEEP --- --- --- --- Unknown broad.mit.edu 37 4 113660097 113660097 + IGR SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:113660097C>T LARP7 (81356 upstream) : ANK2 (79142 downstream) 0.52 77.318602 77.334655 26 24 KEEP --- --- --- --- SEC24D 9871 broad.mit.edu 37 4 119745994 119745994 + Intron SNP A C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:119745994A>C uc003ici.3 - SEC24D_uc003icj.3_Intron|SEC24D_uc003icl.2_Intron|SEC24D_uc010imz.1_Intron|SEC24D_uc011cgg.1_Intron NM_014822 NP_055637 Sec24-related protein D COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm zinc ion binding 0 0.16129 9.156011 12.54157 5 26 KEEP --- --- --- --- C4orf3 401152 broad.mit.edu 37 4 120221607 120221607 + Silent SNP G A A rs80269424 byFrequency;by1000genomes MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:120221607G>A uc003icv.3 - 1 362 c.84C>T c.(82-84)TTC>TTT p.F28F NM_001001701 NP_001001701 Q8WVX3 CD003_HUMAN hypothetical protein LOC401152 28 integral to membrane 0 0.504854 177.406469 177.408674 52 51 KEEP --- --- --- --- broad.mit.edu 37 4 120315406 120315406 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:120315406G>A uc003icx.1 + Homo sapiens cDNA FLJ40382 fis, clone TESTI2035775. 0.47541 94.771944 94.803988 29 32 KEEP --- --- --- --- TNIP3 79931 broad.mit.edu 37 4 122063045 122063045 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:122063045C>T uc010ing.2 - 9 1007 c.811G>A c.(811-813)GGC>AGC p.G271S TNIP3_uc010inh.2_Missense_Mutation_p.G271S|TNIP3_uc011cgj.1_Missense_Mutation_p.G329S NM_024873 NP_079149 Q96KP6 TNIP3_HUMAN TNFAIP3 interacting protein 3 271 ovary(1) 1 0.340909 46.412495 47.396301 15 29 KEEP --- --- --- --- KIAA1109 84162 broad.mit.edu 37 4 123168228 123168228 + Intron SNP T G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:123168228T>G uc003ieh.2 + KIAA1109_uc003iek.2_Intron NM_015312 NP_056127 fragile site-associated protein regulation of cell growth|regulation of epithelial cell differentiation integral to membrane|nucleus ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1) 12 0.75 24.754434 25.209072 6 2 KEEP --- --- --- --- FAT4 79633 broad.mit.edu 37 4 126336611 126336611 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:126336611G>A uc003ifj.3 + 5 6493 c.6493G>A c.(6493-6495)GAA>AAA p.E2165K FAT4_uc011cgp.1_Missense_Mutation_p.E463K NM_024582 NP_078858 Q6V0I7 FAT4_HUMAN FAT tumor suppressor homolog 4 precursor 2165 Cadherin 21.|Extracellular (Potential). homophilic cell adhesion integral to membrane|plasma membrane calcium ion binding ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2) 18 0.605263 155.064468 155.801414 46 30 KEEP --- --- --- --- FAT4 79633 broad.mit.edu 37 4 126355392 126355392 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:126355392C>T uc003ifj.3 + FAT4_uc011cgp.1_Intron NM_024582 NP_078858 FAT tumor suppressor homolog 4 precursor homophilic cell adhesion integral to membrane|plasma membrane calcium ion binding ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2) 18 0.402299 111.807264 112.533654 35 52 KEEP --- --- --- --- FAT4 79633 broad.mit.edu 37 4 126389626 126389626 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:126389626C>T uc003ifj.3 + FAT4_uc011cgp.1_Intron|FAT4_uc003ifi.1_Intron NM_024582 NP_078858 FAT tumor suppressor homolog 4 precursor homophilic cell adhesion integral to membrane|plasma membrane calcium ion binding ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2) 18 0.545455 39.000767 39.040172 12 10 KEEP --- --- --- --- FAT4 79633 broad.mit.edu 37 4 126400884 126400884 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:126400884G>A uc003ifj.3 + FAT4_uc011cgp.1_Intron|FAT4_uc003ifi.1_Intron NM_024582 NP_078858 FAT tumor suppressor homolog 4 precursor homophilic cell adhesion integral to membrane|plasma membrane calcium ion binding ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2) 18 0.478261 35.023172 35.032675 11 12 KEEP --- --- --- --- PCDH18 54510 broad.mit.edu 37 4 138452082 138452082 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:138452082C>T uc003ihe.3 - 1 1548 c.1161G>A c.(1159-1161)AAG>AAA p.K387K PCDH18_uc003ihf.3_Silent_p.K380K|PCDH18_uc011cgz.1_Intron|PCDH18_uc003ihg.3_Silent_p.K167K|PCDH18_uc011cha.1_Intron NM_019035 NP_061908 Q9HCL0 PCD18_HUMAN protocadherin 18 precursor 387 Cadherin 4.|Extracellular (Potential). brain development|homophilic cell adhesion integral to membrane|plasma membrane calcium ion binding pancreas(3)|skin(2) 5 all_hematologic(180;0.24) 0.482759 143.845638 143.868214 42 45 KEEP --- --- --- --- IL15 3600 broad.mit.edu 37 4 142653977 142653977 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:142653977C>T uc003iis.2 + 8 834 c.465C>T c.(463-465)GTC>GTT p.V155V IL15_uc003iit.2_Silent_p.V155V|IL15_uc010iol.2_RNA|IL15_uc003iiu.2_RNA NM_000585 NP_000576 P40933 IL15_HUMAN interleukin 15 preproprotein 155 cell-cell signaling|immune response|positive regulation of interleukin-17 production endosome|extracellular space|Golgi apparatus|integral to plasma membrane|membrane fraction|nucleus cytokine activity|cytokine receptor binding|signal transducer activity 0 all_hematologic(180;0.158) Pancreas(10;184 986 25902) 0.293103 49.45143 51.674289 17 41 KEEP --- --- --- --- GYPB 2994 broad.mit.edu 37 4 144920579 144920579 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:144920579G>A uc003ijm.1 - 3 216 c.160C>T c.(160-162)CGT>TGT p.R54C GYPA_uc003ijn.2_Intron|GYPB_uc011chs.1_RNA|GYPB_uc011cht.1_RNA|GYPB_uc011chu.1_RNA|GYPB_uc010ioo.1_RNA|GYPB_uc010iop.2_RNA|GYPB_uc011chv.1_RNA|GYPB_uc011chw.1_RNA|GYPB_uc011chx.1_Intron|GYPB_uc011chy.1_RNA|GYPB_uc011chz.1_RNA NM_002100 NP_002091 P06028 GLPB_HUMAN glycophorin B precursor 54 Extracellular (Potential). R -> H (in Mit antigen). integral to plasma membrane 0 all_hematologic(180;0.158) 0.375 19.546379 19.765762 6 10 KEEP --- --- --- --- ANAPC10 10393 broad.mit.edu 37 4 145916763 145916763 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:145916763G>A uc003iju.3 - ANAPC10_uc003ijv.3_Intron|ANAPC10_uc003ijw.3_Intron NM_014885 NP_055700 anaphase promoting complex subunit 10 anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|G2/M transition of mitotic cell cycle|mitotic anaphase|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination anaphase-promoting complex|cytosol|nucleoplasm ubiquitin-protein ligase activity 0 all_hematologic(180;0.151) 0.607843 113.836723 114.355898 31 20 KEEP --- --- --- --- TTC29 83894 broad.mit.edu 37 4 147741154 147741154 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:147741154C>T uc003ikw.3 - TTC29_uc010ipc.2_Intron|TTC29_uc003ikx.3_Intron|TTC29_uc010ipd.1_Intron NM_031956 NP_114162 tetratricopeptide repeat domain 29 binding 0 all_hematologic(180;0.151) 0.5 46.275256 46.275256 13 13 KEEP --- --- --- --- EDNRA 1909 broad.mit.edu 37 4 148427530 148427530 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:148427530G>A uc003iky.2 + EDNRA_uc011cid.1_Intron|EDNRA_uc010ipe.1_Intron|EDNRA_uc010ipf.1_Intron|EDNRA_uc010ipg.1_Intron NM_001957 NP_001948 endothelin receptor type A isoform a precursor activation of adenylate cyclase activity|artery smooth muscle contraction|cell proliferation|glucose transport|respiratory gaseous exchange integral to plasma membrane endothelin-A receptor activity|phosphatidylinositol phospholipase C activity ovary(1)|breast(1) 2 all_hematologic(180;0.151) GBM - Glioblastoma multiforme(119;0.154) Bosentan(DB00559) 133 0.266667 11.393075 12.130784 4 11 KEEP --- --- --- --- LRBA 987 broad.mit.edu 37 4 151207143 151207143 + Nonsense_Mutation SNP A T T rs146768056 MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:151207143A>T uc010ipj.2 - 55 8568 c.8094T>A c.(8092-8094)TAT>TAA p.Y2698* LRBA_uc010ipi.2_Nonsense_Mutation_p.Y220*|LRBA_uc003ils.3_Nonsense_Mutation_p.Y593*|LRBA_uc003ilt.3_Nonsense_Mutation_p.Y1346*|LRBA_uc003ilu.3_Nonsense_Mutation_p.Y2686*|LRBA_uc003ilr.3_Nonsense_Mutation_p.Y118* NM_006726 NP_006717 P50851 LRBA_HUMAN LPS-responsive vesicle trafficking, beach and 2698 WD 4. endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane protein binding ovary(3)|breast(3)|skin(1) 7 all_hematologic(180;0.151) 0.117647 3.937844 6.380353 2 15 KEEP --- --- --- --- PET112L 5188 broad.mit.edu 37 4 152680205 152680205 + Intron SNP A C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:152680205A>C uc003iml.2 - PET112L_uc003imm.3_Intron NM_004564 NP_004555 PET112-like precursor mitochondrion ATP binding|carbon-nitrogen ligase activity, with glutamine as amido-N-donor|translation factor activity, nucleic acid binding 0 all_hematologic(180;0.093) Acute lymphoblastic leukemia(8;0.138) L-Glutamic Acid(DB00142)|L-Glutamine(DB00130) 0.571429 16.201587 16.232838 4 3 KEEP --- --- --- --- MAP9 79884 broad.mit.edu 37 4 156274501 156274501 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:156274501G>A uc003ios.2 - MAP9_uc011cin.1_Intron|MAP9_uc010iqa.1_Intron|MAP9_uc003iot.1_Intron NM_001039580 NP_001034669 aster-associated protein cell division|mitosis cytoplasm|microtubule|spindle ovary(1)|central_nervous_system(1) 2 all_hematologic(180;0.24) Renal(120;0.0458) COAD - Colon adenocarcinoma(41;0.143) 0.584906 103.429014 103.761611 31 22 KEEP --- --- --- --- RAPGEF2 9693 broad.mit.edu 37 4 160265220 160265220 + Intron SNP T G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:160265220T>G uc003iqg.3 + NM_014247 NP_055062 Rap guanine nucleotide exchange factor 2 cAMP-mediated signaling|MAPKKK cascade|small GTPase mediated signal transduction integral to plasma membrane|intracellular calcium ion binding|diacylglycerol binding|Rap GTPase activator activity|Rap guanyl-nucleotide exchange factor activity|signal transducer activity lung(2)|upper_aerodigestive_tract(1)|skin(1) 4 all_hematologic(180;0.24) COAD - Colon adenocarcinoma(41;0.0817) 322 0.464646 159.740355 159.848087 46 53 KEEP --- --- --- --- RAPGEF2 9693 broad.mit.edu 37 4 160277140 160277140 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:160277140C>T uc003iqg.3 + 23 4614 c.4304C>T c.(4303-4305)TCG>TTG p.S1435L NM_014247 NP_055062 Q9Y4G8 RPGF2_HUMAN Rap guanine nucleotide exchange factor 2 1435 cAMP-mediated signaling|MAPKKK cascade|small GTPase mediated signal transduction integral to plasma membrane|intracellular calcium ion binding|diacylglycerol binding|Rap GTPase activator activity|Rap guanyl-nucleotide exchange factor activity|signal transducer activity lung(2)|upper_aerodigestive_tract(1)|skin(1) 4 all_hematologic(180;0.24) COAD - Colon adenocarcinoma(41;0.0817) 322 0.5 22.924894 22.924894 7 7 KEEP --- --- --- --- Unknown broad.mit.edu 37 4 165864813 165864813 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:165864813G>A MARCH1 (559611 upstream) : TRIM61 (10787 downstream) 0.45098 74.321018 74.427429 23 28 KEEP --- --- --- --- TRIM61 391712 broad.mit.edu 37 4 165891092 165891092 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:165891092G>A uc003iqw.2 - 3 674 c.63C>T c.(61-63)GAC>GAT p.D21D NM_001012414 NP_001012414 Q5EBN2 TRI61_HUMAN tripartite motif-containing 61 21 RING-type. intracellular zinc ion binding skin(1) 1 all_hematologic(180;0.221) Prostate(90;0.109) GBM - Glioblastoma multiforme(119;0.155) 0.564103 75.355819 75.495803 22 17 KEEP --- --- --- --- GK3P 2713 broad.mit.edu 37 4 166200445 166200445 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:166200445C>T uc003ird.3 - 1 731 c.353G>A c.(352-354)AGA>AAA p.R118K KLHL2_uc003irb.2_Intron|KLHL2_uc011cjm.1_Intron|KLHL2_uc003irc.2_Intron|KLHL2_uc010ira.2_Intron NM_000167 NP_000158 glycerol kinase isoform b 0 0.473684 174.041955 174.110721 54 60 KEEP --- --- --- --- CPE 1363 broad.mit.edu 37 4 166327278 166327278 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:166327278C>T uc003irg.3 + NM_001873 NP_001864 carboxypeptidase E preproprotein cardiac left ventricle morphogenesis|neuropeptide signaling pathway|protein modification process extracellular region|nucleus|plasma membrane metallocarboxypeptidase activity|protein binding|zinc ion binding large_intestine(1)|ovary(1)|skin(1) 3 all_hematologic(180;0.221) Prostate(90;0.0962)|Melanoma(52;0.18) GBM - Glioblastoma multiforme(119;0.137) Glucagon recombinant(DB00040)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071) 0.411765 22.722461 22.837929 7 10 KEEP --- --- --- --- TLL1 7092 broad.mit.edu 37 4 166910643 166910643 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:166910643G>A uc003irh.1 + 2 927 c.280G>A c.(280-282)GGT>AGT p.G94S TLL1_uc011cjn.1_Missense_Mutation_p.G94S|TLL1_uc011cjo.1_5'UTR NM_012464 NP_036596 O43897 TLL1_HUMAN tolloid-like 1 precursor 94 cell differentiation|proteolysis|skeletal system development extracellular region calcium ion binding|metalloendopeptidase activity|zinc ion binding skin(3)|ovary(2)|breast(1)|central_nervous_system(1) 7 all_hematologic(180;0.221) Melanoma(52;0.0315)|Prostate(90;0.0405) GBM - Glioblastoma multiforme(119;0.103) 0.483051 200.97221 201.001661 57 61 KEEP --- --- --- --- KIAA1712 80817 broad.mit.edu 37 4 175225447 175225447 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:175225447C>T uc003itr.2 + 6 848 c.434C>T c.(433-435)CCT>CTT p.P145L KIAA1712_uc010iro.2_Missense_Mutation_p.P145L|KIAA1712_uc003its.2_RNA NM_001040157 NP_001035247 Q9C0F1 CEP44_HUMAN HBV PreS1-transactivated protein 3 isoform a 145 centrosome|midbody|spindle pole 0 Prostate(90;0.00276)|Melanoma(52;0.0179)|Renal(120;0.0376)|Breast(14;0.0991)|all_hematologic(60;0.124)|all_neural(102;0.196) all cancers(43;4.06e-18)|Epithelial(43;1.18e-15)|OV - Ovarian serous cystadenocarcinoma(60;4.65e-09)|GBM - Glioblastoma multiforme(59;0.00098)|STAD - Stomach adenocarcinoma(60;0.0029)|LUSC - Lung squamous cell carcinoma(193;0.0949) 0.440678 90.243236 90.424117 26 33 KEEP --- --- --- --- ODZ3 55714 broad.mit.edu 37 4 183651469 183651469 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:183651469G>A uc003ivd.1 + 14 2739 c.2702G>A c.(2701-2703)GGA>GAA p.G901E ODZ3_uc003ive.1_Missense_Mutation_p.G307E NM_001080477 NP_001073946 Q9P273 TEN3_HUMAN odz, odd Oz/ten-m homolog 3 901 Extracellular (Potential). signal transduction integral to membrane 0 all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184) all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487) 0.5 119.799257 119.799257 36 36 KEEP --- --- --- --- ODZ3 55714 broad.mit.edu 37 4 183713862 183713862 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:183713862G>A uc003ivd.1 + 25 6074 c.6037G>A c.(6037-6039)GTA>ATA p.V2013I NM_001080477 NP_001073946 Q9P273 TEN3_HUMAN odz, odd Oz/ten-m homolog 3 2013 YD 12.|Extracellular (Potential). signal transduction integral to membrane 0 all_lung(41;2.69e-14)|Lung NSC(41;1.92e-11)|Melanoma(52;1.74e-05)|Colorectal(36;0.0062)|Breast(14;0.00748)|all_hematologic(60;0.0162)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_neural(102;0.155)|Medulloblastoma(177;0.184) all cancers(43;1.42e-24)|Epithelial(43;6.86e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.16e-11)|Colorectal(24;9.75e-06)|STAD - Stomach adenocarcinoma(60;2.96e-05)|COAD - Colon adenocarcinoma(29;0.00103)|GBM - Glioblastoma multiforme(59;0.00462)|LUSC - Lung squamous cell carcinoma(40;0.0391)|READ - Rectum adenocarcinoma(43;0.0487) 0.532847 489.065006 489.321562 146 128 KEEP --- --- --- --- MLF1IP 79682 broad.mit.edu 37 4 185646062 185646062 + Intron SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:185646062A>G uc003iwq.2 - MLF1IP_uc003iwp.2_Intron|MLF1IP_uc003iwr.1_Intron NM_024629 NP_078905 MLF1 interacting protein CenH3-containing nucleosome assembly at centromere|interspecies interaction between organisms|mitotic prometaphase|regulation of transcription, DNA-dependent|transcription, DNA-dependent centrosome|condensed chromosome kinetochore|cytosol|nucleoplasm 0 all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Hepatocellular(41;0.000519)|Colorectal(36;0.00172)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.0299)|all_hematologic(60;0.0592)|Medulloblastoma(177;0.146) all cancers(43;7.83e-28)|Epithelial(43;2.56e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-11)|Colorectal(24;3.27e-06)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.16e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000252)|COAD - Colon adenocarcinoma(29;0.000512)|LUSC - Lung squamous cell carcinoma(40;0.01)|READ - Rectum adenocarcinoma(43;0.0419) 0.488372 60.867849 60.873053 21 22 KEEP --- --- --- --- ACSL1 2180 broad.mit.edu 37 4 185694278 185694278 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:185694278C>T uc003iww.2 - 10 1166 c.872G>A c.(871-873)CGA>CAA p.R291Q ACSL1_uc011ckm.1_Missense_Mutation_p.R120Q|ACSL1_uc003iwt.1_Missense_Mutation_p.R291Q|ACSL1_uc003iwu.1_Missense_Mutation_p.R291Q|ACSL1_uc011ckn.1_Missense_Mutation_p.R257Q|ACSL1_uc003iwv.1_Missense_Mutation_p.R291Q|ACSL1_uc010ise.1_RNA NM_001995 NP_001986 P33121 ACSL1_HUMAN acyl-CoA synthetase long-chain family member 1 291 Cytoplasmic (Potential). digestion|fatty acid metabolic process|long-chain fatty-acyl-CoA biosynthetic process|regulation of fatty acid oxidation|triglyceride biosynthetic process endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane ATP binding|long-chain fatty acid-CoA ligase activity ovary(2) 2 all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Colorectal(36;0.00172)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0315)|all_neural(102;0.107)|Medulloblastoma(177;0.146) all cancers(43;1.33e-28)|Epithelial(43;5.3e-25)|OV - Ovarian serous cystadenocarcinoma(60;4.88e-11)|Colorectal(24;3.59e-06)|STAD - Stomach adenocarcinoma(60;2.72e-05)|GBM - Glioblastoma multiforme(59;2.83e-05)|BRCA - Breast invasive adenocarcinoma(30;7.66e-05)|COAD - Colon adenocarcinoma(29;0.000538)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.0419) Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171) 0.347826 51.186875 52.126766 16 30 KEEP --- --- --- --- MTNR1A 4543 broad.mit.edu 37 4 187455385 187455385 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:187455385C>T uc003izd.1 - 2 529 c.511G>A c.(511-513)GAC>AAC p.D171N NM_005958 NP_005949 P48039 MTR1A_HUMAN melatonin receptor 1A 171 Extracellular (Potential). circadian rhythm|G-protein signaling, coupled to cyclic nucleotide second messenger|mating behavior integral to plasma membrane melatonin receptor activity ovary(1)|skin(1)|breast(1)|central_nervous_system(1)|pancreas(1) 5 all_cancers(14;6.39e-56)|all_epithelial(14;1.48e-41)|all_lung(41;2.45e-15)|Lung NSC(41;7.26e-15)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00335)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|Renal(120;0.0183)|all_neural(102;0.202) OV - Ovarian serous cystadenocarcinoma(60;7.63e-12)|BRCA - Breast invasive adenocarcinoma(30;6.68e-07)|GBM - Glioblastoma multiforme(59;3.44e-05)|LUSC - Lung squamous cell carcinoma(40;0.000106)|STAD - Stomach adenocarcinoma(60;0.000279)|READ - Rectum adenocarcinoma(43;0.159) Melatonin(DB01065)|Ramelteon(DB00980) 0.541667 167.182574 167.32582 52 44 KEEP --- --- --- --- TRIML1 339976 broad.mit.edu 37 4 189060749 189060749 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr4:189060749G>A uc003izm.1 + 1 152 c.37G>A c.(37-39)GAA>AAA p.E13K NM_178556 NP_848651 Q8N9V2 TRIML_HUMAN tripartite motif family-like 1 13 multicellular organismal development ligase activity|zinc ion binding ovary(1)|pancreas(1)|breast(1)|skin(1) 4 all_cancers(14;1.33e-43)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)|all_hematologic(60;0.062) OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|BRCA - Breast invasive adenocarcinoma(30;4.19e-06)|GBM - Glioblastoma multiforme(59;0.000232)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.156) Melanoma(31;213 1036 16579 23968 32372) 0.534161 278.049516 278.212879 86 75 KEEP --- --- --- --- SLC6A3 6531 broad.mit.edu 37 5 1420857 1420857 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:1420857G>A uc003jck.2 - NM_001044 NP_001035 solute carrier family 6 (neurotransmitter cell death|neurotransmitter biosynthetic process axon|cytoplasm|integral to plasma membrane|neuronal cell body ovary(3)|breast(2)|pancreas(1) 6 OV - Ovarian serous cystadenocarcinoma(19;0.00928)|all cancers(22;0.0262) Amphetamine(DB00182)|Benztropine(DB00245)|Bupropion(DB01156)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dextroamphetamine(DB01576)|Diethylpropion(DB00937)|Duloxetine(DB00476)|Fencamfamine(DB01463)|Mazindol(DB00579)|Methylphenidate(DB00422)|Modafinil(DB00745)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Procaine(DB00721) 0.633333 67.033969 67.50344 19 11 KEEP --- --- --- --- PAPD7 11044 broad.mit.edu 37 5 6748396 6748396 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:6748396C>T uc003jdx.1 + PAPD7_uc011cmn.1_Intron|PAPD7_uc010itl.1_Intron NM_006999 NP_008930 DNA polymerase sigma cell division|DNA replication|double-strand break repair|mitotic chromosome condensation|response to drug|sister chromatid cohesion nucleus DNA binding|DNA-directed DNA polymerase activity|metal ion binding|SMC protein binding ovary(1) 1 NSCLC(7;212 333 5667 23379 46547) 0.565217 40.187709 40.276192 13 10 KEEP --- --- --- --- SEMA5A 9037 broad.mit.edu 37 5 9066644 9066644 + Nonsense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:9066644G>A uc003jek.2 - 17 2900 c.2188C>T c.(2188-2190)CGA>TGA p.R730* NM_003966 NP_003957 Q13591 SEM5A_HUMAN semaphorin 5A precursor 730 TSP type-1 4.|Extracellular (Potential). cell adhesion|cell-cell signaling integral to membrane|plasma membrane ovary(1)|central_nervous_system(1) 2 0.510791 236.563858 236.579745 71 68 KEEP --- --- --- --- DNAH5 1767 broad.mit.edu 37 5 13692230 13692230 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:13692230G>A uc003jfd.2 - 79 13780 c.13738C>T c.(13738-13740)CGG>TGG p.R4580W DNAH5_uc003jfc.2_Missense_Mutation_p.R748W NM_001369 NP_001360 Q8TE73 DYH5_HUMAN dynein, axonemal, heavy chain 5 4580 microtubule-based movement cilium axoneme|cytoplasm|microtubule ATP binding|ATPase activity|microtubule motor activity ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1) 31 Lung NSC(4;0.00476) Kartagener_syndrome 0.433333 82.354033 82.583557 26 34 KEEP --- --- --- --- DNAH5 1767 broad.mit.edu 37 5 13769156 13769156 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:13769156C>T uc003jfd.2 - 58 9852 c.9810G>A c.(9808-9810)GTG>GTA p.V3270V DNAH5_uc003jfc.2_5'UTR NM_001369 NP_001360 Q8TE73 DYH5_HUMAN dynein, axonemal, heavy chain 5 3270 Stalk (By similarity).|Potential. microtubule-based movement cilium axoneme|cytoplasm|microtubule ATP binding|ATPase activity|microtubule motor activity ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1) 31 Lung NSC(4;0.00476) Kartagener_syndrome 0.451515 497.618774 498.296756 149 181 KEEP --- --- --- --- DNAH5 1767 broad.mit.edu 37 5 13900528 13900528 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:13900528G>A uc003jfd.2 - NM_001369 NP_001360 dynein, axonemal, heavy chain 5 microtubule-based movement cilium axoneme|cytoplasm|microtubule ATP binding|ATPase activity|microtubule motor activity ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1) 31 Lung NSC(4;0.00476) Kartagener_syndrome 0.564103 73.84025 73.978035 22 17 KEEP --- --- --- --- DNAH5 1767 broad.mit.edu 37 5 13901403 13901403 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:13901403G>A uc003jfd.2 - 14 2052 c.2010C>T c.(2008-2010)CTC>CTT p.L670L NM_001369 NP_001360 Q8TE73 DYH5_HUMAN dynein, axonemal, heavy chain 5 670 Stem (By similarity). microtubule-based movement cilium axoneme|cytoplasm|microtubule ATP binding|ATPase activity|microtubule motor activity ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1) 31 Lung NSC(4;0.00476) Kartagener_syndrome 0.361702 47.958851 48.792461 17 30 KEEP --- --- --- --- TRIO 7204 broad.mit.edu 37 5 14488204 14488204 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:14488204C>T uc003jff.2 + 48 7473 c.7467C>T c.(7465-7467)ATC>ATT p.I2489I TRIO_uc003jfg.2_Intron|TRIO_uc003jfh.1_Silent_p.I2138I NM_007118 NP_009049 O75962 TRIO_HUMAN triple functional domain (PTPRF interacting) 2489 apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway cytosol ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1) 18 Lung NSC(4;0.000742) p.2486_2490WSSIP>S(REH-Tumor) 1300 0.764706 43.98284 45.071774 13 4 KEEP --- --- --- --- ANKH 56172 broad.mit.edu 37 5 14745985 14745985 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:14745985G>A uc003jfm.3 - 7 1240 c.909C>T c.(907-909)TTC>TTT p.F303F ANKH_uc003jfl.3_Silent_p.F16F NM_054027 NP_473368 Q9HCJ1 ANKH_HUMAN progressive ankylosis protein 303 Cytoplasmic (Potential). locomotory behavior|regulation of bone mineralization|skeletal system development integral to plasma membrane|outer membrane inorganic diphosphate transmembrane transporter activity|inorganic phosphate transmembrane transporter activity upper_aerodigestive_tract(1) 1 0.461538 60.249145 60.299046 18 21 KEEP --- --- --- --- ANKH 56172 broad.mit.edu 37 5 14755892 14755892 + Intron SNP G A A rs113428747 MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:14755892G>A uc003jfm.3 - NM_054027 NP_473368 progressive ankylosis protein locomotory behavior|regulation of bone mineralization|skeletal system development integral to plasma membrane|outer membrane inorganic diphosphate transmembrane transporter activity|inorganic phosphate transmembrane transporter activity upper_aerodigestive_tract(1) 1 0.428571 27.371197 27.464774 9 12 KEEP --- --- --- --- FAM134B 54463 broad.mit.edu 37 5 16478024 16478024 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:16478024C>T uc003jfs.2 - FAM134B_uc003jfr.2_Intron NM_001034850 NP_001030022 hypothetical protein LOC54463 isoform 1 sensory perception of pain cis-Golgi network|endoplasmic reticulum|integral to membrane ovary(2)|breast(1) 3 0.428571 18.747608 18.809971 6 8 KEEP --- --- --- --- CDH18 1016 broad.mit.edu 37 5 19483368 19483368 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:19483368C>T uc003jgc.2 - CDH18_uc003jgd.2_Intron|CDH18_uc011cnm.1_Intron NM_004934 NP_004925 cadherin 18, type 2 preproprotein adherens junction organization|cell junction assembly|homophilic cell adhesion integral to membrane|plasma membrane calcium ion binding ovary(5)|large_intestine(1)|skin(1) 7 Lung NSC(1;0.00734)|all_lung(1;0.0197) 0.391304 26.868508 27.106909 9 14 KEEP --- --- --- --- CDH18 1016 broad.mit.edu 37 5 19612694 19612694 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:19612694G>A uc003jgc.2 - 5 1037 c.660C>T c.(658-660)GCC>GCT p.A220A CDH18_uc003jgd.2_Silent_p.A220A|CDH18_uc011cnm.1_Silent_p.A220A NM_004934 NP_004925 Q13634 CAD18_HUMAN cadherin 18, type 2 preproprotein 220 Extracellular (Potential).|Cadherin 2. adherens junction organization|cell junction assembly|homophilic cell adhesion integral to membrane|plasma membrane calcium ion binding ovary(5)|large_intestine(1)|skin(1) 7 Lung NSC(1;0.00734)|all_lung(1;0.0197) 0.52381 76.251674 76.272329 22 20 KEEP --- --- --- --- CDH6 1004 broad.mit.edu 37 5 31322844 31322844 + Intron SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:31322844T>C uc003jhe.1 + NM_004932 NP_004923 cadherin 6, type 2 preproprotein adherens junction organization|cell junction assembly|homophilic cell adhesion cytoplasm|integral to membrane|nucleus|plasma membrane calcium ion binding ovary(4)|skin(2)|large_intestine(1) 7 0.395833 66.663077 67.10297 19 29 KEEP --- --- --- --- ZFR 51663 broad.mit.edu 37 5 32403492 32403492 + Missense_Mutation SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:32403492A>G uc003jhr.1 - 8 1315 c.1235T>C c.(1234-1236)TTA>TCA p.L412S NM_016107 NP_057191 Q96KR1 ZFR_HUMAN zinc finger RNA binding protein 412 multicellular organismal development chromosome|cytoplasm|nucleus DNA binding|RNA binding|zinc ion binding 0 STAD - Stomach adenocarcinoma(35;0.19) 0.419355 138.212376 138.739632 39 54 KEEP --- --- --- --- ADAMTS12 81792 broad.mit.edu 37 5 33588863 33588863 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:33588863C>T uc003jia.1 - 18 2869 c.2706G>A c.(2704-2706)GGG>GGA p.G902G ADAMTS12_uc010iuq.1_Silent_p.G817G NM_030955 NP_112217 P58397 ATS12_HUMAN ADAM metallopeptidase with thrombospondin type 1 902 TSP type-1 3. proteolysis proteinaceous extracellular matrix metalloendopeptidase activity|zinc ion binding ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1) 9 HNSCC(64;0.19) OREG0016553 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0.506849 122.374746 122.377705 37 36 KEEP --- --- --- --- SPEF2 79925 broad.mit.edu 37 5 35779256 35779256 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:35779256G>A uc003jjo.2 + 30 4366 c.4255G>A c.(4255-4257)GAA>AAA p.E1419K SPEF2_uc003jjp.1_Missense_Mutation_p.E905K|SPEF2_uc003jjr.2_5'UTR NM_024867 NP_079143 Q9C093 SPEF2_HUMAN KPL2 protein isoform 1 1419 nucleobase, nucleoside, nucleotide and nucleic acid metabolic process ATP binding|nucleobase, nucleoside, nucleotide kinase activity|protein dimerization activity skin(2)|ovary(1)|central_nervous_system(1) 4 all_lung(31;7.56e-05) Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202) 0.408163 63.490334 63.851644 20 29 KEEP --- --- --- --- C5orf42 65250 broad.mit.edu 37 5 37211516 37211516 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:37211516C>T uc011cpa.1 - C5orf42_uc003jks.2_Intron|C5orf42_uc011coz.1_Intron|C5orf42_uc011cpb.1_Intron NM_023073 NP_075561 hypothetical protein LOC65250 ovary(4)|breast(2)|skin(1) 7 all_lung(31;0.000616) COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202) 0.563636 100.721998 100.914795 31 24 KEEP --- --- --- --- EGFLAM 133584 broad.mit.edu 37 5 38407868 38407868 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:38407868G>A uc003jlc.1 + EGFLAM_uc003jlb.1_Intron|EGFLAM_uc003jle.1_Intron|EGFLAM_uc003jlf.1_Intron NM_152403 NP_689616 EGF-like, fibronectin type III and laminin G cell junction|proteinaceous extracellular matrix|synapse pancreas(3)|skin(3)|ovary(1) 7 all_lung(31;0.000385) Colon(62;485 1295 3347 17454) 0.512821 66.300376 66.305908 20 19 KEEP --- --- --- --- RICTOR 253260 broad.mit.edu 37 5 38946642 38946642 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:38946642G>A uc003jlp.2 - 33 4351 c.4327C>T c.(4327-4329)CCC>TCC p.P1443S RICTOR_uc003jlo.2_Missense_Mutation_p.P1467S|RICTOR_uc010ivf.2_Missense_Mutation_p.P1158S NM_152756 NP_689969 Q6R327 RICTR_HUMAN rapamycin-insensitive companion of mTOR 1443 actin cytoskeleton reorganization|embryo development|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of TOR signaling cascade|regulation of protein kinase B signaling cascade|T cell costimulation cytosol|TORC2 complex protein binding ovary(3)|lung(3)|skin(2)|kidney(1)|central_nervous_system(1) 10 all_lung(31;0.000396) 698 0.53211 194.956022 195.05356 58 51 KEEP --- --- --- --- C7 730 broad.mit.edu 37 5 40936549 40936549 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:40936549C>T uc003jmh.2 + 5 504 c.390C>T c.(388-390)ATC>ATT p.I130I C7_uc011cpn.1_RNA NM_000587 NP_000578 P10643 CO7_HUMAN complement component 7 precursor 130 MACPF. complement activation, alternative pathway|complement activation, classical pathway|cytolysis extracellular region|membrane attack complex 0 Ovarian(839;0.0112) 0.586207 58.381843 58.570913 17 12 KEEP --- --- --- --- C6 729 broad.mit.edu 37 5 41142989 41142989 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:41142989C>T uc003jmk.2 - 18 2953 c.2743G>A c.(2743-2745)GGA>AGA p.G915R C6_uc003jml.1_Missense_Mutation_p.G915R NM_000065 NP_000056 P13671 CO6_HUMAN complement component 6 precursor 915 Complement control factor I module 2.|C5b-binding domain.|Kazal-like 2. complement activation, classical pathway|cytolysis|innate immune response membrane attack complex protein binding ovary(3)|central_nervous_system(2)|skin(2) 7 Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157) 0.418367 132.260291 132.82988 41 57 KEEP --- --- --- --- C6 729 broad.mit.edu 37 5 41159246 41159246 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:41159246C>T uc003jmk.2 - 12 2004 c.1794G>A c.(1792-1794)GGG>GGA p.G598G C6_uc003jml.1_Silent_p.G598G NM_000065 NP_000056 P13671 CO6_HUMAN complement component 6 precursor 598 TSP type-1 3. complement activation, classical pathway|cytolysis|innate immune response membrane attack complex protein binding ovary(3)|central_nervous_system(2)|skin(2) 7 Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157) 0.469697 203.653159 203.757282 62 70 KEEP --- --- --- --- PLCXD3 345557 broad.mit.edu 37 5 41382604 41382604 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:41382604C>T uc003jmm.1 - 2 238 c.136G>A c.(136-138)GAA>AAA p.E46K NM_001005473 NP_001005473 Q63HM9 PLCX3_HUMAN phosphatidylinositol-specific phospholipase C, X 46 PI-PLC X-box. intracellular signal transduction|lipid catabolic process phospholipase C activity|signal transducer activity skin(2)|urinary_tract(1)|ovary(1)|lung(1)|central_nervous_system(1) 6 0.655172 125.264063 126.496286 38 20 KEEP --- --- --- --- C5orf51 285636 broad.mit.edu 37 5 41917369 41917369 + Missense_Mutation SNP A C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:41917369A>C uc003jmo.2 + 6 853 c.853A>C c.(853-855)ATT>CTT p.I285L NM_175921 NP_787117 A6NDU8 CE051_HUMAN hypothetical protein LOC285636 285 0 0.6 100.722025 101.113578 27 18 KEEP --- --- --- --- PAIP1 10605 broad.mit.edu 37 5 43556172 43556172 + Intron SNP A T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:43556172A>T uc003job.2 - PAIP1_uc003joa.2_Intron|PAIP1_uc010ivp.2_Intron|PAIP1_uc010ivo.2_Intron|PAIP1_uc003joc.2_Intron NM_006451 NP_006442 poly(A) binding protein interacting protein 1 mRNA stabilization|nuclear-transcribed mRNA poly(A) tail shortening|translational initiation cytosol protein binding|RNA binding|translation activator activity ovary(1) 1 Lung NSC(6;2.07e-05) 0.478261 100.269423 100.297861 33 36 KEEP --- --- --- --- HCN1 348980 broad.mit.edu 37 5 45262173 45262173 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:45262173G>A uc003jok.2 - 8 2548 c.2523C>T c.(2521-2523)CTC>CTT p.L841L NM_021072 NP_066550 O60741 HCN1_HUMAN hyperpolarization activated cyclic 841 Cytoplasmic (Potential). L -> F (in Ref. 2; AAC39759). integral to membrane cAMP binding|sodium channel activity|voltage-gated potassium channel activity ovary(1) 1 0.485714 110.647162 110.659615 34 36 KEEP --- --- --- --- ISL1 3670 broad.mit.edu 37 5 50683484 50683484 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:50683484C>T uc003jor.2 + 3 927 c.379C>T c.(379-381)CTC>TTC p.L127F NM_002202 NP_002193 P61371 ISL1_HUMAN islet-1 127 LIM zinc-binding 2. generation of precursor metabolites and energy|multicellular organismal development nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding central_nervous_system(2)|ovary(1) 3 Lung NSC(810;0.000845)|Breast(144;0.0411) 0.571429 108.997619 109.245253 32 24 KEEP --- --- --- --- DDX4 54514 broad.mit.edu 37 5 55059949 55059949 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:55059949G>A uc003jqg.3 + DDX4_uc010ivz.2_Intron|DDX4_uc003jqh.3_Intron|DDX4_uc003jqj.2_5'Flank NM_001136034 NP_001129506 DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 isoform multicellular organismal development|sperm motility perinuclear region of cytoplasm|pi-body|piP-body ATP binding|ATP-dependent helicase activity|nucleic acid binding ovary(1)|skin(1) 2 Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223) 0.510638 79.699868 79.704447 24 23 KEEP --- --- --- --- DDX4 54514 broad.mit.edu 37 5 55081449 55081449 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:55081449G>A uc003jqg.3 + DDX4_uc010ivz.2_Intron|DDX4_uc003jqh.3_Intron|DDX4_uc003jqj.2_Intron NM_001136034 NP_001129506 DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 isoform multicellular organismal development|sperm motility perinuclear region of cytoplasm|pi-body|piP-body ATP binding|ATP-dependent helicase activity|nucleic acid binding ovary(1)|skin(1) 2 Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223) 0.37037 29.742175 30.141205 10 17 KEEP --- --- --- --- NSA2 10412 broad.mit.edu 37 5 74065115 74065115 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:74065115C>T uc003kdk.1 + 3 351 c.268C>T c.(268-270)CTG>TTG p.L90L GFM2_uc003kdh.1_5'Flank|GFM2_uc003kdi.1_5'Flank|GFM2_uc010izj.1_5'Flank|GFM2_uc010izk.1_5'Flank|GFM2_uc003kdj.1_5'Flank|GFM2_uc010izl.1_5'Flank NM_014886 NP_055701 O95478 NSA2_HUMAN NSA2 ribosome biogenesis homolog 90 Lys-rich. rRNA processing nucleolus|ribonucleoprotein complex ovary(1) 1 0.483607 202.520315 202.548901 59 63 KEEP --- --- --- --- GCNT4 51301 broad.mit.edu 37 5 74325799 74325799 + Missense_Mutation SNP T A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:74325799T>A uc003kdn.2 - 1 926 c.64A>T c.(64-66)ACC>TCC p.T22S NM_016591 NP_057675 Q9P109 GCNT4_HUMAN core 2 beta-1,6-N-acetylglucosaminyltransferase 22 Helical; Signal-anchor for type II membrane protein; (Potential). protein O-linked glycosylation Golgi membrane|integral to membrane beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity ovary(2)|skin(1) 3 all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798) OV - Ovarian serous cystadenocarcinoma(47;8.44e-57) 0.129944 37.203945 60.787449 23 154 KEEP --- --- --- --- AGGF1 55109 broad.mit.edu 37 5 76358997 76358997 + Missense_Mutation SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:76358997T>C uc003ket.2 + 14 2425 c.2065T>C c.(2065-2067)TTT>CTT p.F689L NM_018046 NP_060516 Q8N302 AGGF1_HUMAN angiogenic factor VG5Q 689 angiogenesis|cell adhesion|positive regulation of angiogenesis|positive regulation of endothelial cell proliferation|RNA processing|vasculogenesis extracellular region|perinuclear region of cytoplasm eukaryotic cell surface binding|nucleic acid binding|protein binding ovary(1)|central_nervous_system(1)|skin(1) 3 all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11) OV - Ovarian serous cystadenocarcinoma(54;4.51e-51)|Epithelial(54;2.2e-45)|all cancers(79;6.68e-41) 0.45 253.973618 254.322383 72 88 KEEP --- --- --- --- DHFR 1719 broad.mit.edu 37 5 79929697 79929697 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:79929697C>T uc003kgy.1 - 5 976 c.484G>A c.(484-486)GAA>AAA p.E162K DHFR_uc011ctl.1_Intron|DHFR_uc011ctm.1_Missense_Mutation_p.E110K|DHFR_uc010jap.1_RNA|DHFR_uc003kgx.1_Missense_Mutation_p.E311K NM_000791 NP_000782 P00374 DYR_HUMAN dihydrofolate reductase 162 DHFR. folic acid metabolic process|glycine biosynthetic process|nucleotide biosynthetic process|one-carbon metabolic process|regulation of transcription involved in G1/S phase of mitotic cell cycle|response to methotrexate|tetrahydrofolate metabolic process cytosol dihydrofolate reductase activity|drug binding|folate reductase activity|NADP binding 0 Lung NSC(167;0.00475)|all_lung(232;0.00502)|Ovarian(174;0.0261) OV - Ovarian serous cystadenocarcinoma(54;2.69e-46)|Epithelial(54;7.49e-41)|all cancers(79;1.54e-35) Dapsone(DB00250)|Dimethyl sulfoxide(DB01093)|Lamotrigine(DB00555)|Methotrexate(DB00563)|NADH(DB00157)|Pemetrexed(DB00642)|Proguanil(DB01131)|Pyrimethamine(DB00205)|Trimethoprim(DB00440)|Trimetrexate(DB01157) 302 0.55814 81.204071 81.330397 24 19 KEEP --- --- --- --- MSH3 4437 broad.mit.edu 37 5 79968019 79968019 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:79968019C>T uc003kgz.2 + NM_002439 NP_002430 mutS homolog 3 maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding lung(2)|ovary(1)|breast(1) 4 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) Melanoma(88;1010 1399 13793 26548 36275) 1101 MMR 0.333333 9.021864 9.243337 3 6 KEEP --- --- --- --- GPR98 84059 broad.mit.edu 37 5 89975275 89975275 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:89975275C>T uc003kju.2 + GPR98_uc003kjt.2_Intron NM_032119 NP_115495 G protein-coupled receptor 98 precursor cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance cell surface|cytoplasm|integral to membrane|plasma membrane calcium ion binding|G-protein coupled receptor activity ovary(11)|central_nervous_system(3)|pancreas(2) 16 all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192) OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20) 0.533333 27.300889 27.315347 8 7 KEEP --- --- --- --- GPR98 84059 broad.mit.edu 37 5 90103558 90103559 + Intron DNP AG TA TA MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:90103558_90103559AG>TA uc003kju.2 + GPR98_uc003kjt.2_Intron|GPR98_uc003kjw.2_Intron NM_032119 NP_115495 G protein-coupled receptor 98 precursor cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance cell surface|cytoplasm|integral to membrane|plasma membrane calcium ion binding|G-protein coupled receptor activity ovary(11)|central_nervous_system(3)|pancreas(2) 16 all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192) OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20) 0.322581 58.878123 60.611075 20 42 KEEP --- --- --- --- MCTP1 79772 broad.mit.edu 37 5 94245101 94245101 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:94245101C>T uc003kkx.2 - MCTP1_uc003kkv.2_Intron|MCTP1_uc003kkw.2_Intron|MCTP1_uc003kkz.2_Intron|MCTP1_uc003kku.2_Intron NM_024717 NP_078993 multiple C2 domains, transmembrane 1 isoform L calcium-mediated signaling integral to membrane|membrane fraction calcium ion binding ovary(2) 2 all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207) all cancers(79;9.1e-17) 0.533333 77.501581 77.544914 24 21 KEEP --- --- --- --- ARSK 153642 broad.mit.edu 37 5 94936442 94936442 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:94936442C>T uc003kld.2 + ARSK_uc010jbg.2_Intron|ARSK_uc011cum.1_Intron NM_198150 NP_937793 arylsulfatase K precursor extracellular region arylsulfatase activity|metal ion binding pancreas(1) 1 all_cancers(142;3.38e-06)|all_epithelial(76;6.57e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473) all cancers(79;6.5e-16) 0.571429 13.100592 13.131646 4 3 KEEP --- --- --- --- Unknown broad.mit.edu 37 5 98015882 98015882 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:98015882G>A None (None upstream) : RGMB (89117 downstream) 0.413793 36.395757 36.583671 12 17 KEEP --- --- --- --- SLCO4C1 353189 broad.mit.edu 37 5 101582931 101582931 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:101582931G>A uc003knm.2 - NM_180991 NP_851322 solute carrier organic anion transporter family, cell differentiation|multicellular organismal development|sodium-independent organic anion transport|spermatogenesis basolateral plasma membrane|integral to membrane sodium-independent organic anion transmembrane transporter activity upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)|pancreas(1) 4 all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486) Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986) 0.390244 45.586787 46.020642 16 25 KEEP --- --- --- --- PAM 5066 broad.mit.edu 37 5 102249814 102249814 + Intron SNP T G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:102249814T>G uc003knw.2 + PAM_uc003kns.2_Intron|PAM_uc003knt.2_Intron|PAM_uc003knu.2_Intron|PAM_uc003knv.2_Intron|PAM_uc011cuz.1_Intron NM_000919 NP_000910 peptidylglycine alpha-amidating monooxygenase peptide metabolic process|protein modification process extracellular region|integral to membrane|stored secretory granule L-ascorbic acid binding|peptidylamidoglycolate lyase activity|peptidylglycine monooxygenase activity|protein binding 0 all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284) Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127) Vitamin C(DB00126) 0.416667 35.64652 35.791914 10 14 KEEP --- --- --- --- CAMK4 814 broad.mit.edu 37 5 110784890 110784890 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:110784890C>T uc011cvj.1 + 8 713 c.614C>T c.(613-615)CCA>CTA p.P205L CAMK4_uc003kpf.2_Missense_Mutation_p.P205L|CAMK4_uc010jbv.2_Missense_Mutation_p.P8L NM_001744 NP_001735 Q16566 KCC4_HUMAN calcium/calmodulin-dependent protein kinase IV 205 Protein kinase. activation of phospholipase C activity|nerve growth factor receptor signaling pathway|synaptic transmission cytosol|nucleoplasm ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity ovary(3)|lung(2) 5 all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244) OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109) 687 0.485714 53.471769 53.478055 17 18 KEEP --- --- --- --- CAMK4 814 broad.mit.edu 37 5 110820008 110820008 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:110820008G>A uc011cvj.1 + 12 1365 c.1266G>A c.(1264-1266)GAG>GAA p.E422E CAMK4_uc003kpf.2_Silent_p.E422E|CAMK4_uc010jbv.2_Silent_p.E225E|CAMK4_uc003kpg.2_Silent_p.E113E NM_001744 NP_001735 Q16566 KCC4_HUMAN calcium/calmodulin-dependent protein kinase IV 422 activation of phospholipase C activity|nerve growth factor receptor signaling pathway|synaptic transmission cytosol|nucleoplasm ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity ovary(3)|lung(2) 5 all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244) OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109) 687 0.4375 70.369496 70.532769 21 27 KEEP --- --- --- --- EPB41L4A 64097 broad.mit.edu 37 5 111600808 111600808 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:111600808C>T uc003kpv.1 - EPB41L4A_uc003kpw.1_Intron NM_022140 NP_071423 erythrocyte protein band 4.1-like 4 cytoplasm|cytoskeleton|extrinsic to membrane cytoskeletal protein binding ovary(1) 1 all_cancers(142;4.93e-06)|all_epithelial(76;2.28e-08)|Prostate(80;0.000244)|Colorectal(10;0.000788)|Ovarian(225;0.0448)|Lung NSC(167;0.126)|all_lung(232;0.135) OV - Ovarian serous cystadenocarcinoma(64;6.24e-09)|Epithelial(69;1.43e-07)|all cancers(49;2.78e-05)|COAD - Colon adenocarcinoma(37;0.0467)|Colorectal(14;0.0791) 0.5 34.423948 34.423948 11 11 KEEP --- --- --- --- FEM1C 56929 broad.mit.edu 37 5 114860738 114860738 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:114860738G>A uc003krb.1 - 3 1683 c.1121C>T c.(1120-1122)CCT>CTT p.P374L NM_020177 NP_064562 Q96JP0 FEM1C_HUMAN feminization 1 homolog a 374 cytoplasm breast(2)|ovary(1) 3 all_cancers(142;0.000575)|all_epithelial(76;9.98e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195) OV - Ovarian serous cystadenocarcinoma(64;2.5e-07)|Epithelial(69;2.66e-07)|all cancers(49;1.39e-05) 0.541176 162.264912 162.391484 46 39 KEEP --- --- --- --- HSD17B4 3295 broad.mit.edu 37 5 118832401 118832401 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:118832401C>T uc003ksj.2 + HSD17B4_uc011cwg.1_Intron|HSD17B4_uc011cwh.1_Intron|HSD17B4_uc011cwi.1_Intron|HSD17B4_uc003ksk.3_Intron|HSD17B4_uc011cwj.1_Intron|HSD17B4_uc010jcn.1_Intron NM_000414 NP_000405 hydroxysteroid (17-beta) dehydrogenase 4 bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase peroxisomal matrix 3-hydroxyacyl-CoA dehydrogenase activity|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity|estradiol 17-beta-dehydrogenase activity|isomerase activity|long-chain-enoyl-CoA hydratase activity|protein binding|sterol binding|sterol transporter activity ovary(1)|pancreas(1) 2 all_cancers(142;0.0206)|Prostate(80;0.0322) OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122) NADH(DB00157) Colon(35;490 801 34689 41394 43344) 0.547619 151.251455 151.416518 46 38 KEEP --- --- --- --- SNCAIP 9627 broad.mit.edu 37 5 121786096 121786096 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:121786096G>A uc003ksw.1 + SNCAIP_uc011cwl.1_Intron|SNCAIP_uc003ksx.1_Intron|SNCAIP_uc003ksy.1_Intron|SNCAIP_uc003ksz.1_Intron|SNCAIP_uc010jcu.2_Intron|SNCAIP_uc011cwm.1_Intron|SNCAIP_uc003kta.1_Intron|SNCAIP_uc010jcv.1_Intron|SNCAIP_uc010jcw.1_Intron|SNCAIP_uc010jcx.1_Intron|uc003ktb.1_Intron|SNCAIP_uc003ktc.1_Intron NM_005460 NP_005451 synuclein alpha interacting protein cell death|dopamine metabolic process|regulation of inclusion body assembly|regulation of neurotransmitter secretion cytoplasm|neuronal cell body|nucleolus|presynaptic membrane ubiquitin protein ligase binding ovary(1)|pancreas(1) 2 all_cancers(142;0.00787)|Prostate(80;0.0327) KIRC - Kidney renal clear cell carcinoma(527;0.206) OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232) 0.25 14.265013 15.401363 5 15 KEEP --- --- --- --- SNCAIP 9627 broad.mit.edu 37 5 121786283 121786283 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:121786283G>A uc003ksw.1 + 10 1947 c.1741G>A c.(1741-1743)GAT>AAT p.D581N SNCAIP_uc011cwl.1_Missense_Mutation_p.D139N|SNCAIP_uc003ksx.1_Missense_Mutation_p.D628N|SNCAIP_uc003ksy.1_Missense_Mutation_p.D215N|SNCAIP_uc003ksz.1_Missense_Mutation_p.D215N|SNCAIP_uc010jcu.2_Missense_Mutation_p.D177N|SNCAIP_uc011cwm.1_Missense_Mutation_p.D215N|SNCAIP_uc003kta.1_Missense_Mutation_p.D213N|SNCAIP_uc010jcv.1_RNA|SNCAIP_uc010jcw.1_Missense_Mutation_p.D275N|SNCAIP_uc010jcx.1_Missense_Mutation_p.D521N|uc003ktb.1_RNA|SNCAIP_uc003ktc.1_Missense_Mutation_p.D97N NM_005460 NP_005451 Q9Y6H5 SNCAP_HUMAN synuclein alpha interacting protein 581 cell death|dopamine metabolic process|regulation of inclusion body assembly|regulation of neurotransmitter secretion cytoplasm|neuronal cell body|nucleolus|presynaptic membrane ubiquitin protein ligase binding ovary(1)|pancreas(1) 2 all_cancers(142;0.00787)|Prostate(80;0.0327) KIRC - Kidney renal clear cell carcinoma(527;0.206) OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232) 0.543689 180.506623 180.677733 56 47 KEEP --- --- --- --- FBN2 2201 broad.mit.edu 37 5 127674737 127674737 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:127674737C>T uc003kuu.2 - 26 3799 c.3360G>A c.(3358-3360)AGG>AGA p.R1120R FBN2_uc003kuv.2_Silent_p.R1087R NM_001999 NP_001990 P35556 FBN2_HUMAN fibrillin 2 precursor 1120 EGF-like 16; calcium-binding. bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation microfibril calcium ion binding|extracellular matrix structural constituent ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1) 15 all_cancers(142;0.0216)|Prostate(80;0.0551) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146) 1552 0.52439 142.827553 142.869812 43 39 KEEP --- --- --- --- ADAMTS19 171019 broad.mit.edu 37 5 128797440 128797440 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:128797440G>A uc003kvb.1 + 2 719 c.719G>A c.(718-720)GGA>GAA p.G240E ADAMTS19_uc003kvc.1_RNA NM_133638 NP_598377 Q8TE59 ATS19_HUMAN ADAM metallopeptidase with thrombospondin type 1 240 proteolysis proteinaceous extracellular matrix metalloendopeptidase activity|zinc ion binding ovary(5)|breast(2)|lung(1)|skin(1) 9 all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) OV - Ovarian serous cystadenocarcinoma(64;0.222) 425 0.463158 132.226067 132.343647 44 51 KEEP --- --- --- --- CCNI2 645121 broad.mit.edu 37 5 132083946 132083946 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:132083946C>T uc003kxq.1 + CCNI2_uc011cxg.1_Intron|CCNI2_uc011cxh.1_Intron NM_001039780 NP_001034869 cyclin I family, member 2 regulation of cyclin-dependent protein kinase activity protein kinase binding 0 KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) 0.285714 9.582331 10.168069 4 10 KEEP --- --- --- --- AFF4 27125 broad.mit.edu 37 5 132270089 132270089 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:132270089G>A uc003kyd.2 - 3 1076 c.668C>T c.(667-669)CCT>CTT p.P223L AFF4_uc011cxk.1_5'UTR|AFF4_uc003kye.1_Missense_Mutation_p.P223L|AFF4_uc003kyf.3_Missense_Mutation_p.P223L NM_014423 NP_055238 Q9UHB7 AFF4_HUMAN ALL1 fused gene from 5q31 223 Ser-rich. transcription from RNA polymerase II promoter mitochondrion|nucleolus protein binding|sequence-specific DNA binding transcription factor activity ovary(2)|kidney(2)|skin(1) 5 all_cancers(142;0.145)|Breast(839;0.198) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) Ovarian(126;889 1733 2942 10745 11605) 374 0.461538 143.443349 143.560434 42 49 KEEP --- --- --- --- SEC24A 10802 broad.mit.edu 37 5 134060611 134060611 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:134060611C>T uc003kzs.2 + SEC24A_uc011cxu.1_Intron NM_021982 NP_068817 SEC24 related gene family, member A COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm zinc ion binding 0 KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) 0.538462 23.125796 23.142488 7 6 KEEP --- --- --- --- C5orf20 140947 broad.mit.edu 37 5 134782052 134782052 + 3'UTR SNP A G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:134782052A>G uc003lav.2 - 1 NM_130848 NP_570900 dendritic cell nuclear protein 1 nucleus 0 KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233) 0.56383 170.779723 171.112688 53 41 KEEP --- --- --- --- FBXL21 26223 broad.mit.edu 37 5 135277051 135277051 + Silent SNP G A A rs149332163 by1000genomes MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:135277051G>A uc010jec.1 + 5 1017 c.996G>A c.(994-996)CGG>CGA p.R332R FBXL21_uc003lbc.2_Intron NM_012159 NP_036291 Q9UKT6 FXL21_HUMAN F-box and leucine-rich repeat protein 21 332 LRR 5. rhythmic process ubiquitin ligase complex ubiquitin-protein ligase activity lung(1) 1 KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233) 0.531646 144.650589 144.719107 42 37 KEEP --- --- --- --- TRPC7 57113 broad.mit.edu 37 5 135583045 135583045 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:135583045C>T uc003lbn.1 - TRPC7_uc010jef.1_Intron|TRPC7_uc010jeg.1_Intron|TRPC7_uc010jeh.1_Intron|TRPC7_uc010jei.1_Intron|TRPC7_uc010jej.1_Intron NM_020389 NP_065122 transient receptor potential cation channel, axon guidance|platelet activation integral to membrane|plasma membrane calcium channel activity|protein binding 0 KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233) 0.6 10.025848 10.069526 3 2 KEEP --- --- --- --- TRPC7 57113 broad.mit.edu 37 5 135692381 135692381 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:135692381G>A uc003lbn.1 - 1 695 c.692C>T c.(691-693)TCC>TTC p.S231F TRPC7_uc010jef.1_Missense_Mutation_p.S223F|TRPC7_uc010jeg.1_RNA|TRPC7_uc010jeh.1_Missense_Mutation_p.S223F|TRPC7_uc010jei.1_Missense_Mutation_p.S223F|TRPC7_uc010jej.1_5'UTR NM_020389 NP_065122 Q9HCX4 TRPC7_HUMAN transient receptor potential cation channel, 232 Cytoplasmic (Potential). axon guidance|platelet activation integral to membrane|plasma membrane calcium channel activity|protein binding 0 KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233) 0.473684 26.86513 26.877049 9 10 KEEP --- --- --- --- SIL1 64374 broad.mit.edu 37 5 138371022 138371022 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:138371022G>A uc003ldm.2 - SIL1_uc003ldn.2_Intron|SIL1_uc003ldo.2_Intron|SIL1_uc003ldp.2_Intron|SIL1_uc003ldq.1_Intron NM_022464 NP_071909 SIL1 protein precursor intracellular protein transport|protein folding|transmembrane transport endoplasmic reticulum lumen unfolded protein binding 0 KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325) Marinesco-Sj_gren_syndrome 0.566667 56.377754 56.493682 17 13 KEEP --- --- --- --- PCDHA12 56137 broad.mit.edu 37 5 140256006 140256006 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:140256006G>A uc003lic.2 + 1 1076 c.949G>A c.(949-951)GAA>AAA p.E317K PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc011daf.1_Missense_Mutation_p.E317K NM_018903 NP_061726 Q9UN75 PCDAC_HUMAN protocadherin alpha 12 isoform 1 precursor 317 Cadherin 3.|Extracellular (Potential). homophilic cell adhesion integral to membrane|plasma membrane calcium ion binding|protein binding 0 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) Pancreas(113;759 1672 13322 24104 50104) 0.394495 134.799395 135.862339 43 66 KEEP --- --- --- --- PCDHAC1 56135 broad.mit.edu 37 5 140308628 140308628 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:140308628C>T uc003lih.2 + 1 2327 c.2151C>T c.(2149-2151)AGC>AGT p.S717S PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Intron|PCDHA13_uc003lif.2_Intron|PCDHAC1_uc003lig.1_Silent_p.S717S NM_018898 NP_061721 Q9H158 PCDC1_HUMAN protocadherin alpha subfamily C, 1 isoform 1 717 Cytoplasmic (Potential). homophilic cell adhesion|nervous system development integral to plasma membrane calcium ion binding skin(3)|ovary(2) 5 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) 0.47561 262.440184 262.525178 78 86 KEEP --- --- --- --- PCDHAC2 56134 broad.mit.edu 37 5 140348695 140348695 + Nonsense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:140348695C>T uc003lii.2 + 1 2584 c.2344C>T c.(2344-2346)CGA>TGA p.R782* PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc003lic.2_Intron|PCDHA13_uc003lie.1_Intron|PCDHA13_uc003lif.2_Intron|PCDHAC1_uc003lih.2_Intron|PCDHAC2_uc011dag.1_Nonsense_Mutation_p.R782* NM_018899 NP_061722 Q9Y5I4 PCDC2_HUMAN protocadherin alpha subfamily C, 2 isoform 1 782 Cytoplasmic (Potential). homophilic cell adhesion|nervous system development integral to plasma membrane calcium ion binding ovary(2)|skin(2) 4 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) Melanoma(190;638 2083 3390 11909 52360) 0.431818 120.436945 120.793625 38 50 KEEP --- --- --- --- PCDHB1 29930 broad.mit.edu 37 5 140431934 140431934 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:140431934G>A uc003lik.1 + 1 956 c.879G>A c.(877-879)CAG>CAA p.Q293Q NM_013340 NP_037472 Q9Y5F3 PCDB1_HUMAN protocadherin beta 1 precursor 293 Cadherin 3.|Extracellular (Potential). homophilic cell adhesion integral to membrane|plasma membrane calcium ion binding 0 KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339) 0.5 103.44994 103.44994 30 30 KEEP --- --- --- --- PCDHB2 56133 broad.mit.edu 37 5 140475825 140475825 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:140475825C>T uc003lil.2 + 1 1589 c.1451C>T c.(1450-1452)ACC>ATC p.T484I PCDHB2_uc003lim.1_Missense_Mutation_p.T145I NM_018936 NP_061759 Q9Y5E7 PCDB2_HUMAN protocadherin beta 2 precursor 484 Extracellular (Potential).|Cadherin 5. calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission integral to plasma membrane calcium ion binding ovary(3)|upper_aerodigestive_tract(2)|pancreas(1) 6 KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339) 0.088235 2.524469 14.155399 6 62 KEEP --- --- --- --- PCDHB8 56128 broad.mit.edu 37 5 140559101 140559101 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:140559101G>A uc011dai.1 + 1 1672 c.1486G>A c.(1486-1488)GAT>AAT p.D496N PCDHB16_uc003liv.2_5'Flank|PCDHB16_uc010jfw.1_5'Flank NM_019120 NP_061993 Q9UN66 PCDB8_HUMAN protocadherin beta 8 precursor 496 Cadherin 5.|Extracellular (Potential). homophilic cell adhesion integral to membrane|plasma membrane calcium ion binding skin(4) 4 KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339) 0.270833 33.853527 36.127846 13 35 KEEP --- --- --- --- PCDHB12 56124 broad.mit.edu 37 5 140590037 140590037 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:140590037G>A uc003liz.2 + 1 1747 c.1558G>A c.(1558-1560)GAC>AAC p.D520N PCDHB12_uc011dak.1_Missense_Mutation_p.D183N NM_018932 NP_061755 Q9Y5F1 PCDBC_HUMAN protocadherin beta 12 precursor 520 Extracellular (Potential).|Cadherin 5. homophilic cell adhesion|nervous system development integral to plasma membrane calcium ion binding skin(2)|ovary(1) 3 KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339) 0.43299 126.93277 127.312639 42 55 KEEP --- --- --- --- PCDHGA4 56111 broad.mit.edu 37 5 140737028 140737028 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:140737028C>T uc003ljq.1 + 1 2261 c.2261C>T c.(2260-2262)TCC>TTC p.S754F PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGB2_uc003ljs.1_5'Flank|PCDHGA4_uc003ljp.1_Missense_Mutation_p.S754F|PCDHGB2_uc011dar.1_5'Flank NM_018917 NP_061740 Q9Y5G9 PCDG4_HUMAN protocadherin gamma subfamily A, 4 isoform 1 754 Cytoplasmic (Potential). homophilic cell adhesion integral to membrane|plasma membrane calcium ion binding 0 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) 0.486111 112.884939 112.898152 35 37 KEEP --- --- --- --- PCDHGA9 56107 broad.mit.edu 37 5 140784076 140784076 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:140784076C>T uc003lkh.1 + 1 1557 c.1557C>T c.(1555-1557)TCC>TCT p.S519S PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc011dax.1_Silent_p.S519S NM_018921 NP_061744 Q9Y5G4 PCDG9_HUMAN protocadherin gamma subfamily A, 9 isoform 1 519 Extracellular (Potential).|Cadherin 5. homophilic cell adhesion integral to membrane|plasma membrane calcium ion binding 0 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) 0.492754 117.448945 117.452107 34 35 KEEP --- --- --- --- SH3RF2 153769 broad.mit.edu 37 5 145393643 145393643 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:145393643G>A uc003lnt.2 + SH3RF2_uc011dbl.1_Intron NM_152550 NP_689763 SH3 domain containing ring finger 2 ligase activity|protein phosphatase 1 binding|zinc ion binding ovary(1)|skin(1) 2 KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) 0.4625 128.583229 128.679206 37 43 KEEP --- --- --- --- GPR151 134391 broad.mit.edu 37 5 145895533 145895533 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:145895533C>T uc003lod.1 - 1 144 c.144G>A c.(142-144)CTG>CTA p.L48L NM_194251 NP_919227 Q8TDV0 GP151_HUMAN G protein-coupled receptor 151 48 Helical; Name=1; (Potential). integral to membrane|plasma membrane G-protein coupled receptor activity ovary(1)|pancreas(1) 2 KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) Pancreas(78;420 1386 18535 37114 49710) 0.535354 177.940373 178.056334 53 46 KEEP --- --- --- --- FBXO38 81545 broad.mit.edu 37 5 147794026 147794026 + Intron SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:147794026T>C uc003lpf.1 + FBXO38_uc003lpg.1_Intron|FBXO38_uc003lph.2_Intron NM_205836 NP_995308 F-box protein 38 isoform b cytoplasm|nucleus ovary(4)|skin(2) 6 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) 0.428571 11.424215 11.45532 3 4 KEEP --- --- --- --- HTR4 3360 broad.mit.edu 37 5 147928467 147928467 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:147928467G>A uc003lpn.2 - HTR4_uc010jgu.1_Intron|HTR4_uc003lpi.1_Intron|HTR4_uc003lpj.1_Intron|HTR4_uc003lpk.2_Intron|HTR4_uc011dby.1_Intron|HTR4_uc003lpl.2_Intron|HTR4_uc003lpm.2_Intron|HTR4_uc010jgv.2_Intron|HTR4_uc003lpo.1_Intron NM_000870 NP_000861 serotonin 5-HT4 receptor isoform b G-protein signaling, coupled to cyclic nucleotide second messenger|positive regulation of cell proliferation endosome|integral to plasma membrane|membrane fraction serotonin receptor activity ovary(1) 1 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) Cisapride(DB00604)|Rizatriptan(DB00953)|Tegaserod(DB01079)|Zolmitriptan(DB00315) GBM(120;370 1604 14007 17804 41573) 0.466667 23.524502 23.538944 7 8 KEEP --- --- --- --- PPARGC1B 133522 broad.mit.edu 37 5 149212301 149212301 + Missense_Mutation SNP C T T rs75266799 by1000genomes MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:149212301C>T uc003lrc.2 + 5 707 c.665C>T c.(664-666)TCG>TTG p.S222L PPARGC1B_uc003lrb.1_Missense_Mutation_p.S222L|PPARGC1B_uc003lrd.2_Missense_Mutation_p.S183L|PPARGC1B_uc003lrf.2_Missense_Mutation_p.S201L|PPARGC1B_uc003lre.1_Missense_Mutation_p.S201L NM_133263 NP_573570 Q86YN6 PRGC2_HUMAN peroxisome proliferator-activated receptor 222 estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter mediator complex AF-2 domain binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|receptor activator activity|RNA binding|RNA polymerase II transcription cofactor activity 0 KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147) 0.469697 188.185127 188.293369 62 70 KEEP --- --- --- --- PDE6A 5145 broad.mit.edu 37 5 149242829 149242829 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:149242829C>T uc003lrg.3 - 21 2479 c.2359G>A c.(2359-2361)GAA>AAA p.E787K NM_000440 NP_000431 P16499 PDE6A_HUMAN phosphodiesterase 6A 787 cytosolic calcium ion homeostasis|GMP metabolic process|platelet activation|signal transduction|visual perception cytosol|plasma membrane 3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding ovary(1)|pancreas(1) 2 KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147) 0.415094 68.45598 68.785204 22 31 KEEP --- --- --- --- PDE6A 5145 broad.mit.edu 37 5 149312173 149312173 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:149312173C>T uc003lrg.3 - NM_000440 NP_000431 phosphodiesterase 6A cytosolic calcium ion homeostasis|GMP metabolic process|platelet activation|signal transduction|visual perception cytosol|plasma membrane 3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding ovary(1)|pancreas(1) 2 KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147) 0.485714 55.173412 55.179636 17 18 KEEP --- --- --- --- CCDC69 26112 broad.mit.edu 37 5 150563796 150563796 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:150563796C>T uc003ltq.2 - CCDC69_uc010jhu.2_Intron|CCDC69_uc011dcq.1_Intron NM_015621 NP_056436 coiled-coil domain containing 69 ovary(2) 2 Medulloblastoma(196;0.091)|all_hematologic(541;0.207) KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) 0.666667 14.902146 15.049734 4 2 KEEP --- --- --- --- SLC36A2 153201 broad.mit.edu 37 5 150726726 150726726 + Intron SNP C A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:150726726C>A uc003lty.2 - GM2A_uc011dcs.1_Intron|SLC36A2_uc003ltz.2_Intron|SLC36A2_uc003lua.2_Intron|SLC36A2_uc010jhv.2_Intron|SLC36A2_uc011dct.1_Intron NM_181776 NP_861441 solute carrier family 36, member 2 cellular nitrogen compound metabolic process cytoplasm|integral to membrane|plasma membrane glycine transmembrane transporter activity ovary(1)|central_nervous_system(1) 2 Medulloblastoma(196;0.109)|all_hematologic(541;0.243) KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) 0.08 1.929134 6.427869 2 23 KEEP --- --- --- --- FAT2 2196 broad.mit.edu 37 5 150911119 150911119 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:150911119C>T uc003lue.3 - GM2A_uc011dcs.1_Intron|FAT2_uc003lud.3_Intron NM_001447 NP_001438 FAT tumor suppressor 2 precursor epithelial cell migration|homophilic cell adhesion cell-cell adherens junction|integral to membrane|nucleus calcium ion binding ovary(4)|upper_aerodigestive_tract(1)|skin(1) 6 Medulloblastoma(196;0.0912)|all_hematologic(541;0.104) KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) 0.1875 13.129607 16.056867 6 26 KEEP --- --- --- --- KIF4B 285643 broad.mit.edu 37 5 154395622 154395622 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:154395622G>A uc010jih.1 + 1 2363 c.2203G>A c.(2203-2205)GGA>AGA p.G735R NM_001099293 NP_001092763 Q2VIQ3 KIF4B_HUMAN kinesin family member 4B 735 Interaction with PRC1 (By similarity).|Potential. HGKEGI -> RGMEGT (in Ref. 1; AF241316). axon guidance|blood coagulation|microtubule-based movement cytosol|microtubule|nuclear matrix ATP binding|DNA binding|microtubule motor activity ovary(1) 1 Renal(175;0.00488) Medulloblastoma(196;0.0523) KIRC - Kidney renal clear cell carcinoma(527;0.00112) 0.463415 64.120242 64.168148 19 22 KEEP --- --- --- --- ITK 3702 broad.mit.edu 37 5 156636048 156636048 + Intron SNP T G G MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:156636048T>G uc003lwo.1 + NM_005546 NP_005537 IL2-inducible T-cell kinase cellular defense response|intracellular signal transduction|T cell receptor signaling pathway cytosol|plasma membrane ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding lung(12)|ovary(8)|skin(4)|stomach(1)|central_nervous_system(1) 26 Renal(175;0.00212) Medulloblastoma(196;0.0354)|all_neural(177;0.1) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) Esophageal Squamous(70;1378 1469 8785 19883) 330 T SYK peripheral T-cell lymphoma 0.565217 46.378432 46.463712 13 10 KEEP --- --- --- --- ITK 3702 broad.mit.edu 37 5 156675867 156675867 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:156675867G>A uc003lwo.1 + 16 1723 c.1641G>A c.(1639-1641)CTG>CTA p.L547L NM_005546 NP_005537 Q08881 ITK_HUMAN IL2-inducible T-cell kinase 547 Protein kinase. cellular defense response|intracellular signal transduction|T cell receptor signaling pathway cytosol|plasma membrane ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding lung(12)|ovary(8)|skin(4)|stomach(1)|central_nervous_system(1) 26 Renal(175;0.00212) Medulloblastoma(196;0.0354)|all_neural(177;0.1) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) Esophageal Squamous(70;1378 1469 8785 19883) 330 T SYK peripheral T-cell lymphoma 0.448276 82.342504 82.477819 26 32 KEEP --- --- --- --- GABRA6 2559 broad.mit.edu 37 5 161119131 161119131 + Silent SNP G A A rs144044129 MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:161119131G>A uc003lyu.2 + 8 1349 c.1011G>A c.(1009-1011)AGG>AGA p.R337R GABRA6_uc003lyv.2_Silent_p.R108R NM_000811 NP_000802 Q16445 GBRA6_HUMAN gamma-aminobutyric acid A receptor, alpha 6 337 Cytoplasmic (Probable). gamma-aminobutyric acid signaling pathway cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane benzodiazepine receptor activity|chloride channel activity p.R337R(1) ovary(7)|skin(3)|large_intestine(1)|central_nervous_system(1) 12 Renal(175;0.00259) Medulloblastoma(196;0.0208)|all_neural(177;0.0672) Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683) TCGA Ovarian(5;0.080) 0.394366 83.681972 84.376306 28 43 KEEP --- --- --- --- GABRA1 2554 broad.mit.edu 37 5 161300259 161300259 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:161300259G>A uc010jiw.2 + 6 860 c.392G>A c.(391-393)GGA>GAA p.G131E GABRA1_uc010jix.2_Missense_Mutation_p.G131E|GABRA1_uc010jiy.2_Missense_Mutation_p.G131E|GABRA1_uc003lyx.3_Missense_Mutation_p.G131E|GABRA1_uc010jiz.2_Missense_Mutation_p.G131E|GABRA1_uc010jja.2_Missense_Mutation_p.G131E|GABRA1_uc010jjb.2_Missense_Mutation_p.G131E NM_000806 NP_000797 P14867 GBRA1_HUMAN gamma-aminobutyric acid (GABA) A receptor, alpha 131 Extracellular (Probable). Missing (in Ref. 4; CAA31925). gamma-aminobutyric acid signaling pathway|synaptic transmission cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity ovary(2)|pancreas(1) 3 Renal(175;0.00259) Medulloblastoma(196;0.0208)|all_neural(177;0.0672) Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) all cancers(165;0.228) Alprazolam(DB00404)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Halazepam(DB00801)|Halothane(DB01159)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Metharbital(DB00463)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Picrotoxin(DB00466)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Zaleplon(DB00962)|Zolpidem(DB00425) 0.627119 128.289737 129.126854 37 22 KEEP --- --- --- --- GABRG2 2566 broad.mit.edu 37 5 161528342 161528342 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:161528342C>T uc003lyz.3 + GABRG2_uc010jjc.2_Intron|GABRG2_uc003lyy.3_Intron|GABRG2_uc011dej.1_Intron NM_000816 NP_000807 gamma-aminobutyric acid A receptor, gamma 2 gamma-aminobutyric acid signaling pathway cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity|protein binding ovary(4)|skin(1) 5 Renal(175;0.000319) Medulloblastoma(196;0.0208)|all_neural(177;0.0672) Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136) 0.5 65.806708 65.806708 20 20 KEEP --- --- --- --- ODZ2 57451 broad.mit.edu 37 5 167419999 167419999 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:167419999C>T uc010jjd.2 + 5 998 c.998C>T c.(997-999)TCT>TTT p.S333F ODZ2_uc003lzq.2_Missense_Mutation_p.S212F|ODZ2_uc003lzr.3_Missense_Mutation_p.S142F NM_001122679 NP_001116151 odz, odd Oz/ten-m homolog 2 ovary(6)|central_nervous_system(4) 10 Renal(175;0.00124)|Lung NSC(126;0.136)|all_lung(126;0.242) Medulloblastoma(196;0.0241)|all_neural(177;0.026) Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) all cancers(165;0.0444)|OV - Ovarian serous cystadenocarcinoma(192;0.0694)|Epithelial(171;0.124) 0.569767 165.083498 165.447716 49 37 KEEP --- --- --- --- SLIT3 6586 broad.mit.edu 37 5 168233726 168233726 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:168233726C>T uc003mab.2 - SLIT3_uc010jjg.2_Intron|SLIT3_uc010jji.2_Intron|SLIT3_uc003mac.1_Intron NM_003062 NP_003053 slit homolog 3 precursor apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway extracellular space|mitochondrion calcium ion binding|Roundabout binding ovary(3)|skin(1) 4 Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392) Medulloblastoma(196;0.0399)|all_neural(177;0.0966) Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) Ovarian(29;311 847 10864 17279 24903) 0.454545 15.708443 15.722654 5 6 KEEP --- --- --- --- UBTD2 92181 broad.mit.edu 37 5 171682588 171682588 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:171682588G>A uc003mbp.1 - NM_152277 NP_689490 dendritic cell-derived ubiquitin-like protein cytoplasm 0 Renal(175;0.000159)|Lung NSC(126;0.00976)|all_lung(126;0.0156) Medulloblastoma(196;0.00853)|all_neural(177;0.026) Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516) 0.631579 42.987039 43.272359 12 7 KEEP --- --- --- --- LMAN2 10960 broad.mit.edu 37 5 176765361 176765361 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:176765361C>T uc003mge.2 - LMAN2_uc003mgd.2_Intron NM_006816 NP_006807 lectin, mannose-binding 2 precursor protein transport endoplasmic reticulum membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane metal ion binding|sugar binding 0 all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152) all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) 0.5 8.723847 8.723847 3 3 KEEP --- --- --- --- RASGEF1C 255426 broad.mit.edu 37 5 179541497 179541497 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:179541497G>A uc003mlq.2 - 10 1425 c.1128C>T c.(1126-1128)TTC>TTT p.F376F RASGEF1C_uc003mlr.2_Silent_p.F376F|RASGEF1C_uc003mlp.3_Silent_p.F225F NM_175062 NP_778232 Q8N431 RGF1C_HUMAN RasGEF domain family, member 1C 376 Ras-GEF. regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction intracellular guanyl-nucleotide exchange factor activity ovary(1) 1 all_cancers(89;3.44e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137) all_cancers(40;0.0242)|Medulloblastoma(196;0.00498)|all_neural(177;0.0137) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) 0.555556 33.65142 33.699672 10 8 KEEP --- --- --- --- FLT4 2324 broad.mit.edu 37 5 180056702 180056702 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:180056702C>T uc003mma.3 - 6 889 c.810G>A c.(808-810)GGG>GGA p.G270G FLT4_uc003mlz.3_Silent_p.G270G|FLT4_uc003mmb.1_5'Flank|FLT4_uc011dgy.1_Silent_p.G270G|FLT4_uc011dgz.1_Silent_p.G270G|FLT4_uc011dha.1_3'UTR NM_002020 NP_002011 P35916 VGFR3_HUMAN fms-related tyrosine kinase 4 isoform 2 270 Ig-like C2-type 3.|Extracellular (Potential). positive regulation of cell proliferation integral to plasma membrane ATP binding|protein phosphatase binding|vascular endothelial growth factor receptor activity lung(7)|skin(2)|ovary(2)|stomach(1)|central_nervous_system(1)|breast(1)|kidney(1) 15 all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114) all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) all cancers(165;0.134) Sorafenib(DB00398)|Sunitinib(DB01268) Colon(97;1075 1466 27033 27547 35871) 2638 Congenital_Hereditary_Lymphedema 0.666667 27.904013 28.199208 8 4 KEEP --- --- --- --- MGAT1 4245 broad.mit.edu 37 5 180219027 180219027 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr5:180219027G>A uc003mmg.3 - 2 1440 c.945C>T c.(943-945)GGC>GGT p.G315G MGAT1_uc010jlf.2_Silent_p.G315G|MGAT1_uc010jlg.2_Silent_p.G315G|MGAT1_uc003mmh.3_Silent_p.G315G|MGAT1_uc010jlh.2_Silent_p.G315G|MGAT1_uc003mmi.3_Silent_p.G315G NM_002406 NP_002397 P26572 MGAT1_HUMAN mannosyl (alpha-1,3-)-glycoprotein 315 Lumenal (Potential). post-translational protein modification|protein N-linked glycosylation via asparagine Golgi membrane|integral to membrane alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity|metal ion binding ovary(1) 1 all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114) all_cancers(40;0.00356)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) 0.468085 67.444098 67.485945 22 25 KEEP --- --- --- --- EXOC2 55770 broad.mit.edu 37 6 632957 632957 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:632957G>A uc003mtd.2 - 3 413 c.279C>T c.(277-279)CTC>CTT p.L93L EXOC2_uc003mte.2_Silent_p.L93L|EXOC2_uc011dho.1_Intron NM_018303 NP_060773 Q96KP1 EXOC2_HUMAN Sec5 protein 93 IPT/TIG. exocytosis|protein transport breast(4)|ovary(2)|pancreas(1) 7 Ovarian(93;0.0733) Breast(5;0.0014)|all_lung(73;0.0697)|all_hematologic(90;0.0897) OV - Ovarian serous cystadenocarcinoma(45;0.0507)|BRCA - Breast invasive adenocarcinoma(62;0.14) 0.316832 91.459656 94.475087 32 69 KEEP --- --- --- --- FARS2 10667 broad.mit.edu 37 6 5545628 5545628 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:5545628C>T uc010jnv.1 + FARS2_uc003mwr.2_Intron NM_006567 NP_006558 phenylalanyl-tRNA synthetase 2 precursor phenylalanyl-tRNA aminoacylation|tRNA processing mitochondrial matrix|soluble fraction ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding 0 Ovarian(93;0.11) all_hematologic(90;0.0104) L-Phenylalanine(DB00120) 0.32 46.483832 47.922388 16 34 KEEP --- --- --- --- Unknown broad.mit.edu 37 6 7517723 7517723 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:7517723G>A RIOK1 (99455 upstream) : DSP (24147 downstream) 0.428571 67.767148 67.985296 21 28 KEEP --- --- --- --- CAP2 10486 broad.mit.edu 37 6 17507554 17507554 + Intron SNP G C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:17507554G>C uc003ncb.2 + CAP2_uc010jpk.1_Intron|CAP2_uc011dja.1_Intron|CAP2_uc011djb.1_Intron|CAP2_uc011djc.1_Intron|CAP2_uc011djd.1_Intron NM_006366 NP_006357 adenylyl cyclase-associated protein 2 activation of adenylate cyclase activity|axon guidance|cytoskeleton organization|establishment or maintenance of cell polarity|signal transduction plasma membrane actin binding ovary(1) 1 Breast(50;0.0333)|Ovarian(93;0.0386) all_hematologic(90;0.0466) all cancers(50;0.194)|Epithelial(50;0.227) 0.441176 107.243741 107.448168 30 38 KEEP --- --- --- --- MBOAT1 154141 broad.mit.edu 37 6 20118733 20118733 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:20118733C>T uc003ncx.1 - 9 1151 c.946G>A c.(946-948)GGA>AGA p.G316R MBOAT1_uc011dji.1_Missense_Mutation_p.G167R NM_001080480 NP_001073949 Q6ZNC8 MBOA1_HUMAN membrane bound O-acyltransferase domain 316 Helical; (Potential). phospholipid biosynthetic process integral to membrane acyltransferase activity 0 all_cancers(95;0.244)|Breast(50;0.0379)|Ovarian(93;0.0473)|all_epithelial(95;0.109) OV - Ovarian serous cystadenocarcinoma(7;0.00392)|all cancers(50;0.0117)|Epithelial(50;0.0454) 0.637931 134.696288 135.670688 37 21 KEEP --- --- --- --- DCDC2 51473 broad.mit.edu 37 6 24175008 24175008 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:24175008C>T uc003ndx.2 - 10 1683 c.1381G>A c.(1381-1383)GAA>AAA p.E461K DCDC2_uc003ndy.2_Missense_Mutation_p.E461K|DCDC2_uc003ndw.2_Missense_Mutation_p.E212K NM_016356 NP_057440 Q9UHG0 DCDC2_HUMAN doublecortin domain containing 2 461 cellular defense response|intracellular signal transduction|neuron migration ovary(1) 1 Ovarian(999;0.101) 0.592593 166.314161 166.920721 48 33 KEEP --- --- --- --- GPLD1 2822 broad.mit.edu 37 6 24437007 24437007 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:24437007C>T uc003ned.1 - NM_001503 NP_001494 glycosylphosphatidylinositol specific extracellular region glycosylphosphatidylinositol phospholipase D activity ovary(2)|kidney(1) 3 0.775 101.541581 104.318833 31 9 KEEP --- --- --- --- SLC17A1 6568 broad.mit.edu 37 6 25826603 25826603 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:25826603C>T uc003nfh.3 - SLC17A1_uc011djy.1_Intron|SLC17A1_uc010jqb.1_Intron|SLC17A1_uc010jqc.1_Intron NM_005074 NP_005065 solute carrier family 17 (sodium phosphate), sodium ion transport|urate metabolic process integral to plasma membrane|membrane fraction sodium-dependent phosphate transmembrane transporter activity|symporter activity ovary(3)|pancreas(1) 4 0.522727 76.425584 76.445228 23 21 KEEP --- --- --- --- HIST1H2BE 8344 broad.mit.edu 37 6 26184321 26184321 + Missense_Mutation SNP C A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:26184321C>A uc003ngt.2 + 1 298 c.298C>A c.(298-300)CGC>AGC p.R100S NM_003523 NP_003514 P62807 H2B1C_HUMAN histone cluster 1, H2be 100 defense response to bacterium|nucleosome assembly nucleosome|nucleus DNA binding|protein binding 0 0.229508 37.426373 41.512478 14 47 KEEP --- --- --- --- HIST1H4D 8360 broad.mit.edu 37 6 26189085 26189085 + Missense_Mutation SNP T C C MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:26189085T>C uc003ngu.2 - 1 220 c.220A>G c.(220-222)ACG>GCG p.T74A NM_003539 NP_003530 P62805 H4_HUMAN histone cluster 1, H4d 74 CenH3-containing nucleosome assembly at centromere|negative regulation of megakaryocyte differentiation|phosphatidylinositol-mediated signaling|telomere maintenance nucleoplasm|nucleosome DNA binding|protein binding 0 all_hematologic(11;0.196) 0.160714 16.43824 22.575579 9 47 KEEP --- --- --- --- HIST1H3I 8354 broad.mit.edu 37 6 27841331 27841331 + 5'Flank SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:27841331G>A uc003njy.2 - HIST1H4L_uc003njz.2_5'Flank NM_003533 NP_003524 histone cluster 1, H3i blood coagulation|nucleosome assembly|regulation of gene silencing|S phase nucleoplasm|nucleosome DNA binding|protein binding ovary(1) 1 0.4 11.497665 11.58521 4 6 KEEP --- --- --- --- TRIM27 5987 broad.mit.edu 37 6 28887951 28887951 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:28887951C>T uc003nlr.2 - 3 944 c.585G>A c.(583-585)GAG>GAA p.E195E TRIM27_uc003nls.2_Silent_p.E195E|TRIM27_uc003nlt.1_Silent_p.E195E NM_006510 NP_006501 P14373 TRI27_HUMAN ret finger protein 195 cell proliferation|negative regulation of gene expression, epigenetic|negative regulation of transcription from RNA polymerase II promoter|protein trimerization|spermatogenesis|transcription, DNA-dependent cytoplasm|integral to plasma membrane|membrane fraction|nuclear membrane|PML body DNA binding|protein binding|transmembrane receptor protein tyrosine kinase activity|zinc ion binding ovary(1) 1 T RET papillary thyroid 0.565574 229.379632 229.835109 69 53 KEEP --- --- --- --- Unknown broad.mit.edu 37 6 29069663 29069663 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:29069663G>A OR2B3 (14573 upstream) : OR2J3 (10005 downstream) 0.545455 40.204624 40.244683 12 10 KEEP --- --- --- --- Unknown broad.mit.edu 37 6 29231207 29231207 + IGR SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:29231207G>A OR2J2 (88857 upstream) : OR14J1 (43260 downstream) 0.571429 13.500851 13.531933 4 3 KEEP --- --- --- --- TRIM39 56658 broad.mit.edu 37 6 30309578 30309578 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:30309578C>T uc010jrz.2 + 9 1411 c.1099C>T c.(1099-1101)CGG>TGG p.R367W TRIM39_uc003npz.2_Missense_Mutation_p.R337W|TRIM39_uc003nqb.2_Missense_Mutation_p.R337W|TRIM39_uc003nqc.2_Missense_Mutation_p.R337W|TRIM39_uc010jsa.1_Missense_Mutation_p.R337W NM_021253 NP_067076 Q9HCM9 TRI39_HUMAN tripartite motif-containing 39 isoform 1 367 B30.2/SPRY. apoptosis cytosol|mitochondrion identical protein binding|zinc ion binding ovary(3) 3 0.512195 69.461472 69.466419 21 20 KEEP --- --- --- --- MDC1 9656 broad.mit.edu 37 6 30672489 30672489 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:30672489G>A uc003nrg.3 - 10 4911 c.4471C>T c.(4471-4473)CCC>TCC p.P1491S MDC1_uc003nrf.3_Intron|MDC1_uc011dmp.1_Missense_Mutation_p.P1098S NM_014641 NP_055456 Q14676 MDC1_HUMAN mediator of DNA-damage checkpoint 1 1491 Interaction with the PRKDC complex. cell cycle|double-strand break repair via homologous recombination|intra-S DNA damage checkpoint focal adhesion|nucleoplasm FHA domain binding|protein C-terminus binding breast(2)|ovary(1)|kidney(1) 4 Other_conserved_DNA_damage_response_genes 0.421875 168.107313 168.793029 54 74 KEEP --- --- --- --- MICB 4277 broad.mit.edu 37 6 31477504 31477504 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:31477504G>A uc003ntn.3 + MICB_uc011dnm.1_Intron|MICB_uc003nto.3_Intron NM_005931 NP_005922 MHC class I polypeptide-related sequence B antigen processing and presentation|cytolysis|gamma-delta T cell activation|immune response|immune response-activating cell surface receptor signaling pathway|interspecies interaction between organisms|negative regulation of defense response to virus by host|response to heat|response to oxidative stress|response to retinoic acid integral to plasma membrane|MHC class I protein complex natural killer cell lectin-like receptor binding 0 0.616667 126.088379 126.80418 37 23 KEEP --- --- --- --- BAT2 7916 broad.mit.edu 37 6 31599470 31599470 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:31599470C>T uc003nvb.3 + 16 3269 c.3020C>T c.(3019-3021)CCA>CTA p.P1007L BAT2_uc011dnv.1_Intron|BAT2_uc003nvc.3_Missense_Mutation_p.P1007L NM_080686 NP_542417 P48634 PRC2A_HUMAN HLA-B associated transcript-2 1007 4 X 57 AA type A repeats. cytoplasm|nucleus protein binding 0 0.5625 29.176188 29.230478 9 7 KEEP --- --- --- --- CSNK2B 1460 broad.mit.edu 37 6 31638831 31638831 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:31638831C>T uc003nvs.1 + LY6G5B_uc003nvt.1_Intron NM_001320 NP_001311 casein kinase 2, beta polypeptide adiponectin-mediated signaling pathway|axon guidance|cellular protein complex assembly|negative regulation of cell proliferation|regulation of DNA binding|Wnt receptor signaling pathway cytosol|nucleus|protein kinase CK2 complex identical protein binding|protein domain specific binding|protein kinase regulator activity|receptor binding|transcription factor binding 0 0.313953 78.50001 81.145593 27 59 KEEP --- --- --- --- LY6G6F 259215 broad.mit.edu 37 6 31675345 31675345 + Missense_Mutation SNP G T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:31675345G>T uc003nwa.1 + 2 163 c.163G>T c.(163-165)GCA>TCA p.A55S BAT5_uc011dnz.1_Intron|LY6G6F_uc003nwb.1_Missense_Mutation_p.A55S NM_001003693 NP_001003693 Q5SQ64 LY66F_HUMAN G6f protein precursor 55 Extracellular (Potential).|Ig-like V-type. integral to membrane|plasma membrane breast(1)|central_nervous_system(1) 2 0.131579 7.84752 12.861009 5 33 KEEP --- --- --- --- C6orf27 80737 broad.mit.edu 37 6 31742316 31742316 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:31742316C>T uc011dog.1 - 5 936 c.698G>A c.(697-699)GGA>GAA p.G233E C6orf27_uc003nxd.2_5'UTR|C6orf27_uc011doh.1_RNA NM_025258 NP_079534 Q9Y334 G7C_HUMAN G7c protein precursor 233 extracellular region ovary(3) 3 0.62963 58.081451 58.480554 17 10 KEEP --- --- --- --- SLC44A4 80736 broad.mit.edu 37 6 31843920 31843920 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:31843920G>A uc010jti.2 - SLC44A4_uc011dol.1_Intron|SLC44A4_uc011dom.1_Intron NM_025257 NP_079533 choline transporter-like protein 4 integral to membrane|plasma membrane choline transmembrane transporter activity large_intestine(2)|ovary(1)|central_nervous_system(1) 4 Choline(DB00122) 0.653846 56.576588 57.118162 17 9 KEEP --- --- --- --- CFB 629 broad.mit.edu 37 6 31912561 31912561 + 5'Flank SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:31912561G>A uc003nyj.3 + C2_uc003nyc.2_Missense_Mutation_p.D441N|C2_uc011doo.1_Missense_Mutation_p.D408N|C2_uc011dop.1_Missense_Mutation_p.D440N|C2_uc003nyf.2_Missense_Mutation_p.D654N|C2_uc010jtk.2_Missense_Mutation_p.D522N|C2_uc011doq.1_Missense_Mutation_p.D625N|C2_uc003nyg.2_Missense_Mutation_p.D431N|CFB_uc011dor.1_Missense_Mutation_p.D501N|C2_uc003nyh.1_Missense_Mutation_p.D305N|CFB_uc011dos.1_5'Flank|CFB_uc003nyi.2_5'Flank NM_001710 NP_001701 complement factor B preproprotein complement activation, alternative pathway|proteolysis extracellular region|plasma membrane complement binding|serine-type endopeptidase activity skin(1) 1 0.561404 108.005419 108.192252 32 25 KEEP --- --- --- --- STK19 8859 broad.mit.edu 37 6 31940123 31940123 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:31940123G>A uc003nyv.2 + 2 393 c.265G>A c.(265-267)GAC>AAC p.D89N DOM3Z_uc003nyo.1_5'Flank|DOM3Z_uc003nyp.1_5'Flank|DOM3Z_uc003nyq.1_5'Flank|DOM3Z_uc003nyr.1_5'Flank|DOM3Z_uc003nys.1_5'Flank|DOM3Z_uc010jtl.1_5'Flank|STK19_uc003nyt.2_Missense_Mutation_p.D46N|DOM3Z_uc003nyu.1_5'Flank|STK19_uc011dow.1_Missense_Mutation_p.D89N|STK19_uc011dox.1_Missense_Mutation_p.D46N|STK19_uc003nyw.2_Missense_Mutation_p.D89N|STK19_uc010jtn.1_RNA NM_032454 NP_115830 P49842 STK19_HUMAN serine/threonine kinase 19 isoform 2 89 D -> N (in a metastatic melanoma sample; somatic mutation). nucleus ATP binding|protein binding|protein serine/threonine kinase activity p.D89N(2) skin(4) 4 p.D89N(COLO829-Tumor) 192 0.327103 99.583806 102.423071 35 72 KEEP --- --- --- --- TNXB 7148 broad.mit.edu 37 6 31978805 31978805 + Silent SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:31978805C>T uc011dpc.1 - 4 1593 c.684G>A c.(682-684)CAG>CAA p.Q228Q STK19_uc003nza.2_5'Flank|STK19_uc003nzb.2_5'Flank NM_032470 NP_115859 P22105 TENX_HUMAN tenascin XB isoform 2 3844 Fibronectin type-III 30. actin cytoskeleton organization|cell adhesion|collagen metabolic process|elastic fiber assembly|signal transduction extracellular space|intracellular|proteinaceous extracellular matrix heparin binding|integrin binding 0 0.207792 38.551807 44.64742 16 61 KEEP --- --- --- --- AGPAT1 10554 broad.mit.edu 37 6 32138018 32138018 + Missense_Mutation SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:32138018G>A uc003oae.2 - 5 848 c.530C>T c.(529-531)CCT>CTT p.P177L PPT2_uc003nzy.1_Intron|AGPAT1_uc011dpj.1_RNA|AGPAT1_uc011dpk.1_Missense_Mutation_p.P141L|AGPAT1_uc003oaf.2_Missense_Mutation_p.P177L|AGPAT1_uc003oag.2_Missense_Mutation_p.P67L|AGPAT1_uc003oah.2_Missense_Mutation_p.P177L|AGPAT1_uc003oai.1_Missense_Mutation_p.P177L|AGPAT1_uc011dpl.1_Missense_Mutation_p.P65L NM_006411 NP_006402 Q99943 PLCA_HUMAN 1-acylglycerol-3-phosphate O-acyltransferase 1 177 energy reserve metabolic process|phosphatidic acid biosynthetic process|positive regulation of cellular metabolic process|positive regulation of cytokine production|triglyceride biosynthetic process endoplasmic reticulum membrane|integral to membrane 1-acylglycerol-3-phosphate O-acyltransferase activity central_nervous_system(1) 1 0.611111 38.528449 38.722887 11 7 KEEP --- --- --- --- HLA-DPA1 3113 broad.mit.edu 37 6 33036355 33036355 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:33036355G>A uc003ocs.1 - HLA-DPA1_uc010juk.2_3'UTR NM_033554 NP_291032 major histocompatibility complex, class II, DP antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway endoplasmic reticulum membrane|endosome membrane|Golgi apparatus|integral to plasma membrane|lysosomal membrane|MHC class II protein complex MHC class II receptor activity skin(1) 1 0.761905 54.709764 56.024823 16 5 KEEP --- --- --- --- PHF1 5252 broad.mit.edu 37 6 33380920 33380920 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:33380920C>T uc003oeh.2 + PHF1_uc011drh.1_Intron|PHF1_uc003oei.2_Intron|PHF1_uc010jux.2_Intron NM_024165 NP_077084 PHD finger protein 1 isoform b chromatin modification nucleus nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding 0 Ovarian(999;0.0443) 0.632353 154.442838 155.489592 43 25 KEEP --- --- --- --- ITPR3 3710 broad.mit.edu 37 6 33645171 33645171 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:33645171C>T uc011drk.1 + NM_002224 NP_002215 inositol 1,4,5-triphosphate receptor, type 3 activation of phospholipase C activity|calcium ion transport into cytosol|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|protein heterooligomerization|protein homooligomerization|regulation of insulin secretion|response to calcium ion apical part of cell|brush border|endoplasmic reticulum membrane|integral to plasma membrane|myelin sheath|neuronal cell body|nuclear outer membrane|platelet dense tubular network membrane inositol 1,3,4,5 tetrakisphosphate binding|inositol 1,4,5 trisphosphate binding|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|inositol hexakisphosphate binding|intracellular ligand-gated calcium channel activity|protein binding ovary(6)|lung(5)|central_nervous_system(5)|breast(2)|kidney(1) 19 0.384615 14.97147 15.123379 5 8 KEEP --- --- --- --- UHRF1BP1 54887 broad.mit.edu 37 6 34839354 34839354 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:34839354C>T uc003oju.3 + UHRF1BP1_uc010jvm.1_Intron|UHRF1BP1_uc010jvn.2_Intron|UHRF1BP1_uc010jvo.2_Intron NM_017754 NP_060224 ICBP90 binding protein 1 ovary(3) 3 0.683333 143.094714 144.886908 41 19 KEEP --- --- --- --- TCP11 6954 broad.mit.edu 37 6 35086193 35086193 + Silent SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:35086193G>A uc003okd.2 - 10 1585 c.1404C>T c.(1402-1404)CTC>CTT p.L468L TCP11_uc003ojz.1_Silent_p.L393L|TCP11_uc003oka.2_Silent_p.L393L|TCP11_uc003okb.2_Silent_p.L392L|TCP11_uc003okc.2_Silent_p.L392L|TCP11_uc011dsu.1_Silent_p.L450L|TCP11_uc011dsv.1_Silent_p.L417L|TCP11_uc011dsw.1_Silent_p.L422L NM_001093728 NP_001087197 Q8WWU5 TCP11_HUMAN t-complex 11 isoform 1 455 cell differentiation|multicellular organismal development|spermatogenesis integral to membrane ovary(3)|skin(2) 5 0.596491 113.354673 113.817303 34 23 KEEP --- --- --- --- SCUBE3 222663 broad.mit.edu 37 6 35209698 35209698 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:35209698G>A uc003okf.1 + SCUBE3_uc003okg.1_Intron|SCUBE3_uc003okh.1_Intron NM_152753 NP_689966 signal peptide, CUB domain, EGF-like 3 protein heterooligomerization|protein homooligomerization cell surface|extracellular region calcium ion binding|protein binding skin(1) 1 OREG0017372 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0.536585 70.951809 70.999453 22 19 KEEP --- --- --- --- DNAH8 1769 broad.mit.edu 37 6 38705844 38705844 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:38705844C>T uc003ooe.1 + NM_001371 NP_001362 dynein, axonemal, heavy polypeptide 8 skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1) 21 2979 0.473684 29.474514 29.485904 9 10 KEEP --- --- --- --- DNAH8 1769 broad.mit.edu 37 6 38758186 38758186 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:38758186G>A uc003ooe.1 + NM_001371 NP_001362 dynein, axonemal, heavy polypeptide 8 skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1) 21 2979 0.294118 28.535306 29.825815 10 24 KEEP --- --- --- --- DNAH8 1769 broad.mit.edu 37 6 38899798 38899798 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:38899798C>T uc003ooe.1 + DNAH8_uc003oog.1_Intron|uc003oof.1_Intron NM_001371 NP_001362 dynein, axonemal, heavy polypeptide 8 skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1) 21 2979 0.543478 88.878676 88.954189 25 21 KEEP --- --- --- --- DNAH8 1769 broad.mit.edu 37 6 38976414 38976414 + Intron SNP G A A MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:38976414G>A uc003ooe.1 + NM_001371 NP_001362 dynein, axonemal, heavy polypeptide 8 skin(8)|ovary(7)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1) 21 2979 1 16.468709 16.408065 4 0 KEEP --- --- --- --- UBR2 23304 broad.mit.edu 37 6 42642058 42642058 + Intron SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:42642058C>T uc011dur.1 + UBR2_uc011dus.1_Intron|UBR2_uc003osh.2_Intron|UBR2_uc011dut.1_Intron NM_015255 NP_056070 ubiquitin protein ligase E3 component n-recognin cellular response to leucine|chromatin silencing|histone H2A ubiquitination|negative regulation of TOR signaling cascade nucleus|plasma membrane leucine binding|zinc ion binding ovary(3)|pancreas(1) 4 Colorectal(47;0.196) Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196) 0.333333 11.99582 12.291117 4 8 KEEP --- --- --- --- POLH 5429 broad.mit.edu 37 6 43582187 43582187 + Missense_Mutation SNP C T T MEL-JWCI-WGS-11-Tumor MEL-JWCI-WGS-11-Normal Phase_I Unspecified Illumina GAIIx g.chr6:43582187C>T uc003ovq.3 + 11 2339 c.2035C>T c.(2035-2037)CAT>TAT p.H679Y POLH_uc010jyu.2_Missense_Mutation_p.H555Y|POLH_uc011dvl.1_RNA|POLH_uc003ovr.3_Missense_Mutation_p.H580Y NM_006502 NP_006493 Q9Y253 POLH_HUMAN DNA-directed DNA polymerase eta 679 DNA replication|DNA synthesis involved in DNA repair|regulation of DNA repair|response to UV-C cytoplasm|nucleoplasm damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding breast(2) 2 all_cancers(18;1.89e-05)|Lung NSC(15;0.00161)|all_lung(25;0.004) all cancers(41;0.000753)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167) DNA_polymerases_(catalytic_subunits) Xeroderma_Pigmentosum 0.626943 407.416957 410.145866 121 72 KEEP --- --- --- --- MUT 45