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 Tumor_Sample_UUID Matched_Norm_Sample_UUID 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 ref_context gc_content CCLE_ONCOMAP_overlapping_mutations CCLE_ONCOMAP_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 t_alt_count t_ref_count validation_alt_allele validation_method validation_status validation_tumor_sample pox qox pox_cutoff isArtifactMode oxoGCut LMBRD2 92255 broad.mit.edu 37 5 36111293 36111293 + Missense_Mutation SNP C C T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr5:36111293C>T ENST00000296603.4 - 14 2170 c.1708G>A c.(1708-1710)Gac>Aac p.D570N NM_001007527.1 NP_001007528.1 Q68DH5 LMBD2_HUMAN LMBR1 domain containing 2 570 integral to membrane breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 35 all_lung(31;0.000146) Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202) TTAACTAAGTCTGATGTCATA 0.308000 17 33 0 0 1 0 0 FAM170A 340069 broad.mit.edu 37 5 118970106 118970106 + Silent SNP G G A TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr5:118970106G>A ENST00000515256.1 + 3 835 c.663G>A c.(661-663)ctG>ctA p.L221L A1A519 F170A_HUMAN family with sequence similarity 170, member A 221 intracellular zinc ion binding breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(7)|prostate(2)|skin(3)|upper_aerodigestive_tract(1) 24 CTGACTGGCTGGTGACCATGG 0.592000 53 88 0 0 1 0 0 TRIM56 81844 broad.mit.edu 37 7 100731813 100731813 + Missense_Mutation SNP G G T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr7:100731813G>T ENST00000306085.6 + 3 1517 c.1220G>T c.(1219-1221)gGa>gTa p.G407V NM_030961.1 NP_112223.1 Q9BRZ2 TRI56_HUMAN tripartite motif containing 56 407 defense response to virus|interferon-beta production|protein K63-linked ubiquitination|response to type I interferon cytoplasm ubiquitin-protein ligase activity|zinc ion binding breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 18 Lung NSC(181;0.136)|all_lung(186;0.182) AGACAGGGTGGAGTCCAGCCC 0.627000 17 24 6.49762e-13 6.75752e-13 1 1 0 DNM1P47 100216544 broad.mit.edu 37 15 102292726 102292726 + RNA SNP G G A rs150565409 by1000genomes TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr15:102292726G>A ENST00000561463.1 + 0 772 TGGGAACAAGGAGACACTCCT 0.582000 6 28 0 0 1 0 0 TINAG 27283 broad.mit.edu 37 6 54191662 54191662 + Missense_Mutation SNP G G A TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr6:54191662G>A ENST00000259782.4 + 4 668 c.572G>A c.(571-573)cGc>cAc p.R191H TINAG_ENST00000370869.3_Missense_Mutation_p.R187H|TINAG_ENST00000370864.3_Missense_Mutation_p.R173H NM_014464.3 NP_055279.3 Q9UJW2 TINAG_HUMAN tubulointerstitial nephritis antigen 191 cell adhesion|immune response|Malpighian tubule morphogenesis|proteolysis basement membrane cysteine-type endopeptidase activity|nucleotide binding|polysaccharide binding|scavenger receptor activity p.R191H(1)|p.R191L(1) NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(1) 34 Lung NSC(77;0.0518) LUSC - Lung squamous cell carcinoma(124;0.246) TTTAAATTTCGCCTTGGCACT 0.373000 19 47 0 0 1 0 0 SGIP1 84251 broad.mit.edu 37 1 67147598 67147598 + Silent SNP C C T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr1:67147598C>T ENST00000371037.4 + 15 938 c.861C>T c.(859-861)tcC>tcT p.S287S SGIP1_ENST00000237247.6_Silent_p.S291S|SGIP1_ENST00000371039.1_Intron|SGIP1_ENST00000371035.3_Intron|SGIP1_ENST00000371036.3_Intron NM_032291.2 NP_115667.2 Q9BQI5 SGIP1_HUMAN SH3-domain GRB2-like (endophilin) interacting protein 1 287 Pro-rich. 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 breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(43)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1) 71 AACTACCATCCATCAATGACT 0.403000 14 152 0 0 1 0 0 TACC3 10460 broad.mit.edu 37 4 1746695 1746695 + Silent SNP G G T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr4:1746695G>T ENST00000313288.4 + 16 2578 c.2472G>T c.(2470-2472)ctG>ctT p.L824L NM_006342.2 NP_006333.1 Q9Y6A5 TACC3_HUMAN transforming, acidic coiled-coil containing protein 3 824 centrosome central_nervous_system(1)|endometrium(4)|large_intestine(1)|lung(10)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2) 25 Breast(71;0.212)|all_epithelial(65;0.241) OV - Ovarian serous cystadenocarcinoma(23;0.00765)|Epithelial(3;0.0126) ACGAGGAGCTGACCAGGATCT 0.607000 3 12 0.004672 0.00473268 1 1 0 PAFAH2 5051 broad.mit.edu 37 1 26308867 26308867 + Silent SNP C C T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr1:26308867C>T ENST00000374282.3 - 7 833 c.654G>A c.(652-654)ctG>ctA p.L218L PAFAH2_ENST00000374284.1_Silent_p.L218L|PAFAH2_ENST00000493892.1_5'UTR NM_000437.3 NP_000428.2 Q99487 PAFA2_HUMAN platelet-activating factor acetylhydrolase 2, 40kDa 218 lipid catabolic process cytoplasm 1-alkyl-2-acetylglycerophosphocholine esterase activity|phospholipid binding NS(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(2)|urinary_tract(1) 9 Colorectal(325;3.47e-05)|Lung NSC(340;6.23e-05)|all_lung(284;9.48e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-25)|Colorectal(126;3.57e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00155)|GBM - Glioblastoma multiforme(114;0.00717)|READ - Rectum adenocarcinoma(331;0.0649) TCAAAGTCATCAGATCCAAGC 0.473000 23 40 0 0 1 0 0 SPTAN1 6709 broad.mit.edu 37 9 131386673 131386673 + Nonsense_Mutation SNP G G T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr9:131386673G>T ENST00000372739.3 + 46 6009 c.5899G>T c.(5899-5901)Gag>Tag p.E1967* SPTAN1_ENST00000372731.4_Nonsense_Mutation_p.E1962*|SPTAN1_ENST00000358161.5_Nonsense_Mutation_p.E1967* NM_001130438.2 NP_001123910.1 Q13813 SPTA2_HUMAN spectrin, alpha, non-erythrocytic 1 1962 actin filament capping|axon guidance|cellular component disassembly involved in apoptosis cytosol|intracellular membrane-bounded organelle|membrane fraction|microtubule cytoskeleton|spectrin actin binding|calcium ion binding|calmodulin binding|structural constituent of cytoskeleton NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2) 87 GTCAGACCTGGAGAAAGCTGC 0.547000 6 21 3.59834e-05 3.69303e-05 1 1 0 CNNM2 54805 broad.mit.edu 37 10 104679304 104679304 + Missense_Mutation SNP G G A TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr10:104679304G>A ENST00000369878.4 + 1 1255 c.1067G>A c.(1066-1068)gGa>gAa p.G356E CNNM2_ENST00000369875.3_Missense_Mutation_p.G356E|CNNM2_ENST00000433628.2_Missense_Mutation_p.G356E NM_017649.4 NP_060119.3 Q9H8M5 CNNM2_HUMAN cyclin M2 DUF21. ion transport integral to membrane central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1) 19 Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198) Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215) GTCATCTTCGGAGAGATCGTG 0.607000 28 66 0 0 1 0 0 LIPE 3991 broad.mit.edu 37 19 42930736 42930736 + Missense_Mutation SNP G G A TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr19:42930736G>A ENST00000244289.4 - 1 842 c.566C>T c.(565-567)aCg>aTg p.T189M LIPE-AS1_ENST00000594688.1_RNA|LIPE-AS1_ENST00000594624.2_RNA|LIPE-AS1_ENST00000593740.2_RNA|LIPE-AS1_ENST00000457234.2_RNA|LIPE-AS1_ENST00000597203.1_RNA NM_005357.2 NP_005348.2 Q05469 LIPS_HUMAN lipase, hormone-sensitive 189 cholesterol metabolic process|protein phosphorylation|triglyceride catabolic process caveola|cytosol hormone-sensitive lipase activity|protein binding breast(2)|endometrium(4)|kidney(7)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1) 32 Prostate(69;0.00682) CTGGACTGGCGTTGTTTGCTT 0.527000 38 73 0 0 1 0 0 INTS1 26173 broad.mit.edu 37 7 1542571 1542571 + Silent SNP C C T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr7:1542571C>T ENST00000389470.4 - 4 698 c.699G>A c.(697-699)ccG>ccA p.P233P INTS1_ENST00000404767.3_Silent_p.P105P Q8N201 INT1_HUMAN integrator complex subunit 1 105 snRNA processing integral to membrane|integrator complex|nuclear membrane autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2) 62 Ovarian(82;0.0253) UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15) CTTTAATCGACGGAGAAATGG 0.582000 41 135 0 0 1 0 0 CHD1L 9557 broad.mit.edu 37 1 146726621 146726621 + Missense_Mutation SNP G G C TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr1:146726621G>C ENST00000369258.4 + 3 357 c.337G>C c.(337-339)Gaa>Caa p.E113Q CHD1L_ENST00000467213.1_3'UTR|CHD1L_ENST00000369259.3_Intron|CHD1L_ENST00000361293.5_Intron|CHD1L_ENST00000431239.1_Missense_Mutation_p.E113Q NM_001256336.1|NM_004284.4|NM_024568.2 NP_001243265.1|NP_004275.4|NP_078844.2 Q86WJ1 CHD1L_HUMAN chromodomain helicase DNA binding protein 1-like 113 Helicase ATP-binding. chromatin remodeling|DNA repair cytoplasm|nucleus|plasma membrane ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2) 33 all_hematologic(923;0.0487) CTGGAAAGAAGAAATGCAGAG 0.328000 24 52 0 0 1 0 0 KRT12 3859 broad.mit.edu 37 17 39023318 39023318 + Missense_Mutation SNP C C T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr17:39023318C>T ENST00000251643.4 - 1 144 c.121G>A c.(121-123)Ggt>Agt p.G41S NM_000223.3 NP_000214.1 Q99456 K1C12_HUMAN keratin 12 41 Gly-rich.|Head. visual perception intermediate filament structural molecule activity central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(2) 15 Breast(137;0.000301) CCCCCATAACCACTTCCAACA 0.602000 15 49 0 0 1 0 0 FGFR3 2261 broad.mit.edu 37 4 1803568 1803568 + Missense_Mutation SNP C C G rs121913483 TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr4:1803568C>G ENST00000340107.4 + 7 1002 c.746C>G c.(745-747)tCc>tGc p.S249C FGFR3_ENST00000412135.2_Missense_Mutation_p.S249C|FGFR3_ENST00000474521.1_3'UTR|FGFR3_ENST00000440486.2_Missense_Mutation_p.S249C|FGFR3_ENST00000481110.2_Missense_Mutation_p.S249C|FGFR3_ENST00000352904.1_Missense_Mutation_p.S249C|FGFR3_ENST00000260795.2_Missense_Mutation_p.S249C NM_001163213.1 NP_001156685.1 P22607 FGFR3_HUMAN fibroblast growth factor receptor 3 249 S -> C (in KERSEB, bladder cancer, cervical cancer and TD1). bone maturation|cell growth|insulin receptor signaling pathway|JAK-STAT cascade|MAPKKK cascade|negative regulation of developmental growth|positive regulation of cell proliferation integral to plasma membrane ATP binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|identical protein binding p.S249C(1204)|p.R248_S249del(1) NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607) 3091 Breast(71;0.212)|all_epithelial(65;0.241) all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234) Palifermin(DB00039) ACAGAGCGCTCCCCGCACCGG 0.736000 1 """Mis, T""" """IGH@, ETV6""" """bladder, MM, T-cell lymphoma""" """Hypochondroplasia, Thanatophoric dysplasia""" Saethre-Chotzen syndrome;Muenke syndrome 8 13 0 0 1 0 0 PTCHD2 57540 broad.mit.edu 37 1 11561875 11561875 + Missense_Mutation SNP G G A TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr1:11561875G>A ENST00000294484.6 + 2 964 c.826G>A c.(826-828)Gag>Aag p.E276K PTCHD2_ENST00000389575.3_Missense_Mutation_p.E276K NM_020780.1 NP_065831.1 Q9P2K9 PTHD2_HUMAN patched domain containing 2 276 cholesterol homeostasis|regulation of lipid transport|smoothened signaling pathway endoplasmic reticulum|integral to membrane|nuclear membrane hedgehog receptor activity NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3) 76 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) CTGGCGCATCGAGCTCATCTT 0.657000 10 18 0 0 1 0 0 UHRF1BP1L 23074 broad.mit.edu 37 12 100452269 100452269 + Missense_Mutation SNP G G A TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr12:100452269G>A ENST00000279907.7 - 14 2998 c.2786C>T c.(2785-2787)tCa>tTa p.S929L UHRF1BP1L_ENST00000545232.2_Missense_Mutation_p.S579L NM_015054.1 NP_055869.1 A0JNW5 UH1BL_HUMAN UHRF1 binding protein 1-like 929 breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(21)|ovary(3)|skin(1)|upper_aerodigestive_tract(1) 50 TCTGTTGTCTGACATATGATT 0.318000 17 52 0 0 1 0 0 KRT15 3866 broad.mit.edu 37 17 39674669 39674669 + Silent SNP G G T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr17:39674669G>T ENST00000254043.3 - 1 3996 c.411C>A c.(409-411)atC>atA p.I137I KRT15_ENST00000393981.3_5'UTR|KRT15_ENST00000393976.2_Silent_p.I137I|KRT15_ENST00000393974.3_5'UTR NM_002275.3 NP_002266 P19012 K1C15_HUMAN keratin 15 137 Coil 1A.|Rod. epidermis development intermediate filament protein binding|structural constituent of cytoskeleton NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 16 Breast(137;0.000286) ACCAGTCATGGATCTTCACCT 0.542000 46 110 5.48756e-27 6.02859e-27 1 1 0 AGBL1 123624 broad.mit.edu 37 15 87066137 87066137 + Silent SNP C C G TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr15:87066137C>G ENST00000441037.2 + 18 2609 c.2514C>G c.(2512-2514)ctC>ctG p.L838L AGBL1_ENST00000421325.2_Silent_p.L838L|AGBL1_ENST00000389298.3_Silent_p.L569L NM_152336.2 NP_689549.2 Q96MI9 CBPC4_HUMAN ATP/GTP binding protein-like 1 838 C-terminal protein deglutamylation|protein side chain deglutamylation|proteolysis cytosol metallocarboxypeptidase activity|tubulin binding|zinc ion binding NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 62 AAGGCCTCCTCTACCACCTGA 0.537000 32 60 0 0 1 0 0 TTF2 8458 broad.mit.edu 37 1 117617996 117617996 + Missense_Mutation SNP C C G TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr1:117617996C>G ENST00000369466.4 + 5 834 c.790C>G c.(790-792)Caa>Gaa p.Q264E NM_003594.3 NP_003585.3 Q9UNY4 TTF2_HUMAN transcription termination factor, RNA polymerase II mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|termination of RNA polymerase II transcription cytoplasm|spliceosomal complex|transcription elongation factor complex ATP binding|ATP-dependent helicase activity|DNA binding|DNA-dependent ATPase activity|protein binding|zinc ion binding NS(1)|autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(24)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2) 50 Lung SC(450;0.225) all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05) Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19) GCTTTTGCCTCAAAATGTTCA 0.453000 64 113 0 0 1 0 0 FAM193A 8603 broad.mit.edu 37 4 2695412 2695412 + Missense_Mutation SNP C C T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr4:2695412C>T ENST00000324666.5 + 14 2381 c.2030C>T c.(2029-2031)tCg>tTg p.S677L FAM193A_ENST00000505311.1_Missense_Mutation_p.S677L|FAM193A_ENST00000382839.3_Missense_Mutation_p.S677L|FAM193A_ENST00000502458.1_Missense_Mutation_p.S699L|FAM193A_ENST00000545951.1_Missense_Mutation_p.S677L NM_001256666.1 NP_001243595.1 P78312 F193A_HUMAN family with sequence similarity 193, member A 677 NS(2)|breast(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(12)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3) 40 CCAGCGCTCTCGCCTGCTGCG 0.627000 32 83 0 0 1 0 0 FAM214A 56204 broad.mit.edu 37 15 52905938 52905938 + Missense_Mutation SNP G G C TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr15:52905938G>C ENST00000261844.7 - 3 285 c.133C>G c.(133-135)Cat>Gat p.H45D FAM214A_ENST00000546305.2_Missense_Mutation_p.H52D NM_019600.2 NP_062546.2 Q32MH5 K1370_HUMAN family with sequence similarity 214, member A 45 GGAGGGCAATGAAAGCTTTCT 0.428000 13 15 0 0 1 0 0 ZNF423 23090 broad.mit.edu 37 16 49672361 49672361 + Silent SNP G G A TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr16:49672361G>A ENST00000561648.1 - 4 755 c.702C>T c.(700-702)acC>acT p.T234T ZNF423_ENST00000535559.1_Silent_p.T117T|ZNF423_ENST00000262383.2_Silent_p.T234T|ZNF423_ENST00000562520.1_Silent_p.T174T|ZNF423_ENST00000563137.2_Silent_p.T174T|ZNF423_ENST00000567169.1_Silent_p.T117T|ZNF423_ENST00000562871.1_Silent_p.T174T NM_001271620.1 NP_001258549.1 Q2M1K9 ZN423_HUMAN zinc finger protein 423 234 cell differentiation|negative regulation of transcription, DNA-dependent|nervous system development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus zinc ion binding breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2) 89 all_cancers(37;0.0155) GCAGCGAGCTGGTGGAGGAGA 0.577000 17 30 0 0 1 0 0 BRINP3 339479 broad.mit.edu 37 1 190068042 190068042 + Silent SNP G G A TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr1:190068042G>A ENST00000367462.3 - 8 1638 c.1407C>T c.(1405-1407)ctC>ctT p.L469L BRINP3_ENST00000534846.1_Silent_p.L367L NM_199051.1 NP_950252.1 bone morphogenetic protein/retinoic acid inducible neural-specific 3 469 GCCCCTGGCTGAGCATGTAGC 0.592000 52 78 0 0 1 0 0 ZNF804A 91752 broad.mit.edu 37 2 185802577 185802577 + Silent SNP A A G TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr2:185802577A>G ENST00000302277.6 + 4 3048 c.2454A>G c.(2452-2454)agA>agG p.R818R NM_194250.1 NP_919226.1 Q7Z570 Z804A_HUMAN zinc finger protein 804A 818 intracellular zinc ion binding NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1) 146 AAAGAGGCAGATTCCACCCCG 0.393000 14 17 0 0 1 0 0 DCLK1 9201 broad.mit.edu 37 13 36445426 36445426 + Missense_Mutation SNP C C T rs56185003 TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr13:36445426C>T ENST00000255448.4 - 5 1086 c.875G>A c.(874-876)cGc>cAc p.R292H DCLK1_ENST00000360631.3_Missense_Mutation_p.R292H|DCLK1_ENST00000379892.4_Missense_Mutation_p.R292H NM_004734.4 NP_004725.1 O15075 DCLK1_HUMAN doublecortin-like kinase 1 292 Pro/Ser-rich. R -> H (in dbSNP:rs56185003). cell differentiation|central nervous system development|endosome transport|intracellular signal transduction|response to virus integral to plasma membrane ATP binding|protein serine/threonine kinase activity|receptor signaling protein activity breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1) 64 Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122) KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169) all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638) GGTGCTCCTGCGGGATGATGA 0.507000 31 77 0 0 1 0 0 ZBTB32 27033 broad.mit.edu 37 19 36207413 36207413 + Missense_Mutation SNP A A T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr19:36207413A>T ENST00000392197.2 + 7 1541 c.1223A>T c.(1222-1224)cAg>cTg p.Q408L ZBTB32_ENST00000262630.3_Missense_Mutation_p.Q408L Q9Y2Y4 ZBT32_HUMAN zinc finger and BTB domain containing 32 408 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 large_intestine(5)|lung(1)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2) 14 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) CTTTGTCCTCAGCGCTCCCGG 0.667000 OREG0025433 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 37 77 0 0 1 0 0 PCDHA13 56136 broad.mit.edu 37 5 140264082 140264082 + Silent SNP C C T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr5:140264082C>T ENST00000289272.2 + 1 2229 c.2229C>T c.(2227-2229)agC>agT p.S743S PCDHA5_ENST00000529619.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA13_ENST00000409494.1_Silent_p.S743S NM_018904.2|NM_031865.1 NP_061727.1|NP_114071.1 NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2) 95 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) TGTGCTCCAGCGCGGCAGGGA 0.677000 7 122 0 0 1 0 0 HTR6 3362 broad.mit.edu 37 1 20005443 20005443 + Missense_Mutation SNP T T A TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr1:20005443T>A ENST00000289753.1 + 3 1372 c.905T>A c.(904-906)tTc>tAc p.F302Y NM_000871.1 NP_000862.1 P50406 5HT6R_HUMAN 5-hydroxytryptamine (serotonin) receptor 6, G protein-coupled 302 G-protein signaling, coupled to cyclic nucleotide second messenger|synaptic transmission integral to plasma membrane histamine receptor activity|protein binding endometrium(1)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 13 Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439) UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;5.81e-05)|Kidney(64;0.00017)|GBM - Glioblastoma multiforme(114;0.00117)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182) Granisetron(DB00889)|Ondansetron(DB00904)|Sertindole(DB06144) CCAGGCCTCTTCGATGTCCTC 0.617000 43 79 0 0 1 0 0 SLC6A19 340024 broad.mit.edu 37 5 1201811 1201811 + Missense_Mutation SNP C C T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr5:1201811C>T ENST00000304460.10 + 1 102 c.46C>T c.(46-48)Ccg>Tcg p.P16S NM_001003841.2 NP_001003841.1 Q695T7 S6A19_HUMAN solute carrier family 6 (neutral amino acid transporter), member 19 16 cellular nitrogen compound metabolic process integral to plasma membrane amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(25)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2) 44 all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10) Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185) CGCCCGGATCCCGTCCCTGGC 0.677000 12 19 0 0 1 0 0 GPRIN3 285513 broad.mit.edu 37 4 90169782 90169782 + Missense_Mutation SNP C C T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr4:90169782C>T ENST00000609438.1 - 2 1998 c.1480G>A c.(1480-1482)Gag>Aag p.E494K GPRIN3_ENST00000333209.4_Missense_Mutation_p.E494K NM_198281.2 NP_938022.2 Q6ZVF9 GRIN3_HUMAN GPRIN family member 3 breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|prostate(2)|skin(1) 36 Hepatocellular(203;0.114) OV - Ovarian serous cystadenocarcinoma(123;5.67e-05) TCTGCAAACTCAGATGGCCTG 0.453000 40 103 0 0 1 0 0 PLXNB1 5364 broad.mit.edu 37 3 48462746 48462746 + Silent SNP T T C TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr3:48462746T>C ENST00000358536.4 - 8 1970 c.1701A>G c.(1699-1701)tcA>tcG p.S567S PLXNB1_ENST00000358459.4_Silent_p.S567S|PLXNB1_ENST00000456774.1_Silent_p.S567S|PLXNB1_ENST00000296440.6_Silent_p.S567S|PLXNB1_ENST00000448774.2_Intron NM_002673.4 NP_002664.2 O43157 PLXB1_HUMAN plexin B1 567 axon guidance|cell migration|intracellular signal transduction|regulation of cell shape|regulation of cytoskeleton organization|regulation of small GTPase mediated signal transduction|semaphorin-plexin signaling pathway extracellular region|integral to plasma membrane|intracellular|semaphorin receptor complex GTPase activator activity|semaphorin receptor activity|semaphorin receptor binding NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3) 47 BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619) GGCAGGAATATGACTCCCCTG 0.612000 14 49 0 0 1 0 0 CYP8B1 1582 broad.mit.edu 37 3 42917160 42917160 + Missense_Mutation SNP C C T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr3:42917160C>T ENST00000316161.4 - 1 473 c.149G>A c.(148-150)cGg>cAg p.R50Q CYP8B1_ENST00000437102.1_Missense_Mutation_p.R50Q|KRBOX1_ENST00000426937.1_Intron|RP11-141M3.5_ENST00000471537.1_RNA NM_004391.2 NP_004382.2 Q9UNU6 CP8B1_HUMAN cytochrome P450, family 8, subfamily B, polypeptide 1 50 bile acid biosynthetic process|xenobiotic metabolic process endoplasmic reticulum membrane|integral to membrane|microsome 7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity|electron carrier activity|heme binding|oxygen binding|sterol 12-alpha-hydroxylase activity NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(5) 23 KIRC - Kidney renal clear cell carcinoma(284;0.213)|Kidney(284;0.249) CATATTCTTCCGGAAAGCCAT 0.582000 22 57 0 0 1 0 0 ARHGEF3 50650 broad.mit.edu 37 3 56779360 56779360 + Missense_Mutation SNP C C T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr3:56779360C>T ENST00000413728.2 - 7 1304 c.761G>A c.(760-762)cGc>cAc p.R254H ARHGEF3_ENST00000495373.1_Missense_Mutation_p.R248H|ARHGEF3_ENST00000338458.4_Missense_Mutation_p.R280H|ARHGEF3_ENST00000497267.1_Missense_Mutation_p.R219H|ARHGEF3_ENST00000496106.1_Missense_Mutation_p.R254H|ARHGEF3_ENST00000296315.3_Missense_Mutation_p.R248H NM_001128616.1 NP_001122088.1 Q9NR81 ARHG3_HUMAN Rho guanine nucleotide exchange factor (GEF) 3 248 DH. apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|Rho protein signal transduction cytosol Rho guanyl-nucleotide exchange factor activity cervix(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(1) 25 KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193) ATCTAGTTTGCGGCTAAAGGG 0.468000 4 173 0 0 1 0 0 SMURF1 57154 broad.mit.edu 37 7 98649958 98649958 + Silent SNP G G A TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr7:98649958G>A ENST00000361125.1 - 7 910 c.591C>T c.(589-591)ttC>ttT p.F197F SMURF1_ENST00000361368.2_Silent_p.F197F|SMURF1_ENST00000480055.1_5'UTR NM_020429.2 NP_065162.1 Q9HCE7 SMUF1_HUMAN SMAD specific E3 ubiquitin protein ligase 1 197 BMP signaling pathway|cell differentiation|ectoderm development|negative regulation of BMP signaling pathway|negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of protein ubiquitination|proteasomal ubiquitin-dependent protein catabolic process|protein export from nucleus|protein localization at cell surface|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|receptor catabolic process|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process cytosol|plasma membrane activin binding|I-SMAD binding|R-SMAD binding|ubiquitin-protein ligase activity endometrium(3)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|urinary_tract(1) 25 all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274) STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224) GGGACTCCACGAACCTGCAAT 0.597000 27 47 0 0 1 0 0 ZMYM4 9202 broad.mit.edu 37 1 35858283 35858283 + Missense_Mutation SNP G G T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr1:35858283G>T ENST00000314607.6 + 17 2844 c.2764G>T c.(2764-2766)Gat>Tat p.D922Y ZMYM4_ENST00000373297.2_Missense_Mutation_p.D833Y NM_005095.2 NP_005086.2 Q5VZL5 ZMYM4_HUMAN zinc finger, MYM-type 4 922 multicellular organismal development DNA binding|zinc ion binding breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2) 54 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887) AATCATCGGTGATGTAAGTTT 0.264000 37 71 2.66277e-13 2.8067e-13 1 1 0 RMI2 116028 broad.mit.edu 37 16 11444539 11444539 + Silent SNP C C T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr16:11444539C>T ENST00000572173.1 + 5 792 c.147C>T c.(145-147)agC>agT p.S49S RMI2_ENST00000381820.2_Silent_p.S49S|RMI2_ENST00000576027.1_3'UTR|RMI2_ENST00000312499.5_Silent_p.S112S Q96E14 RMI2_HUMAN RecQ mediated genome instability 2 112 DNA replication nucleus DNA binding endometrium(1)|kidney(1)|ovary(1) 3 AGGCCTGCAGCCCTGAGCCCT 0.428000 40 88 0 0 1 0 0 CCDC27 148870 broad.mit.edu 37 1 3677874 3677874 + Silent SNP G G A TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr1:3677874G>A ENST00000294600.2 + 5 825 c.741G>A c.(739-741)caG>caA p.Q247Q NM_152492.2 NP_689705.2 Q2M243 CCD27_HUMAN coiled-coil domain containing 27 247 breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(2)|lung(17)|prostate(1)|skin(2)|urinary_tract(2) 36 all_cancers(77;0.0385)|Ovarian(185;0.0634)|Lung NSC(156;0.21)|all_lung(157;0.218) all_epithelial(116;5.52e-17)|all_lung(118;1.04e-06)|Lung NSC(185;0.000214)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Lung SC(97;0.0367)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127) Epithelial(90;1.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.35e-22)|GBM - Glioblastoma multiforme(42;3.46e-16)|Colorectal(212;1.17e-05)|COAD - Colon adenocarcinoma(227;5.76e-05)|Kidney(185;0.00036)|BRCA - Breast invasive adenocarcinoma(365;0.000696)|KIRC - Kidney renal clear cell carcinoma(229;0.00558)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203) TGGAGATACAGGTTCAGAAGA 0.577000 12 33 0 0 1 0 0 GRIN2A 2903 broad.mit.edu 37 16 9984937 9984937 + Nonsense_Mutation SNP C C T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr16:9984937C>T ENST00000396573.2 - 5 1337 c.1028G>A c.(1027-1029)tGg>tAg p.W343* GRIN2A_ENST00000330684.3_Nonsense_Mutation_p.W343*|GRIN2A_ENST00000562109.1_Nonsense_Mutation_p.W343*|GRIN2A_ENST00000535259.1_Nonsense_Mutation_p.W186*|GRIN2A_ENST00000404927.2_Nonsense_Mutation_p.W343*|GRIN2A_ENST00000396575.2_Nonsense_Mutation_p.W343* NM_000833.3 NP_000824.1 Q12879 NMDE1_HUMAN glutamate receptor, ionotropic, N-methyl D-aspartate 2A 343 response to ethanol cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding p.W343*(1) NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1) 198 Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043) TTTGCCATCCCATGTAACATT 0.438000 23 43 0 0 1 0 0 KATNA1 11104 broad.mit.edu 37 6 149918645 149918645 + Missense_Mutation SNP G G A TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr6:149918645G>A ENST00000367411.2 - 9 1406 c.1148C>T c.(1147-1149)tCa>tTa p.S383L KATNA1_ENST00000335643.8_Missense_Mutation_p.S307L|KATNA1_ENST00000335647.5_Missense_Mutation_p.S383L|KATNA1_ENST00000494504.1_5'UTR NM_007044.3 NP_008975.1 O75449 KTNA1_HUMAN katanin p60 (ATPase containing) subunit A 1 383 cell division|interphase of mitotic cell cycle|mitosis microtubule|microtubule organizing center|spindle pole ATP binding|microtubule binding|microtubule-severing ATPase activity|protein heterodimerization activity endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|urinary_tract(1) 12 Ovarian(120;0.0164) OV - Ovarian serous cystadenocarcinoma(155;2.95e-12)|GBM - Glioblastoma multiforme(68;0.173) GAAGATACCTGACGGCAAAGG 0.358000 19 47 0 0 1 0 0 BRF2 55290 broad.mit.edu 37 8 37706159 37706159 + Nonsense_Mutation SNP G G A TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr8:37706159G>A ENST00000220659.6 - 2 289 c.169C>T c.(169-171)Cga>Tga p.R57* BRF2_ENST00000520601.1_Nonsense_Mutation_p.R57*|BRF2_ENST00000521170.1_Nonsense_Mutation_p.R57* NM_018310.3 NP_060780.2 Q9HAW0 BRF2_HUMAN BRF2, RNA polymerase III transcription initiation factor 50 kDa subunit 57 regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter|transcription initiation, DNA-dependent nucleoplasm protein binding|zinc ion binding breast(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(5)|ovary(1) 12 Lung NSC(58;0.118)|all_lung(54;0.195) BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;1.81e-10) CCTGTGCTTCGGGAATATGTT 0.443000 29 49 0 0 1 0 0 ZNF733P 643955 broad.mit.edu 37 7 62752443 62752443 + RNA SNP G G C TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr7:62752443G>C ENST00000331425.6 - 0 992 NR_003952.1 CTTATGTCTAGTAAGGTTTGA 0.438000 5 42 0 0 1 0 0 COIL 8161 broad.mit.edu 37 17 55019443 55019443 + Missense_Mutation SNP C C T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr17:55019443C>T ENST00000240316.4 - 6 1634 c.1600G>A c.(1600-1602)Gaa>Aaa p.E534K NM_004645.2 NP_004636.1 P38432 COIL_HUMAN coilin 534 Cajal body|nucleolus protein C-terminus binding NS(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|urinary_tract(1) 15 Breast(9;6.15e-08) GCTCCATTTTCATTGTGATAA 0.418000 30 48 0 0 1 0 0 ESPNP 284729 broad.mit.edu 37 1 17023143 17023143 + RNA SNP C C T rs559507 by1000genomes TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr1:17023143C>T ENST00000492551.1 - 0 1720 NR_026567.1 TGTGGGGCTCCGGACTGGTAA 0.692000 6 18 0 0 1 0 0 CD27 939 broad.mit.edu 37 12 6559751 6559751 + Missense_Mutation SNP G G A TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr12:6559751G>A ENST00000266557.3 + 4 722 c.493G>A c.(493-495)Gac>Aac p.D165N CD27-AS1_ENST00000545339.1_RNA|CD27-AS1_ENST00000399492.2_RNA|CD27_ENST00000541233.1_3'UTR NM_001242.4 NP_001233 P26842 CD27_HUMAN CD27 molecule 165 anti-apoptosis|apoptosis|cell surface receptor linked signaling pathway|immunoglobulin mediated immune response|induction of apoptosis|positive regulation of B cell differentiation|positive regulation of JNK cascade|release of cytoplasmic sequestered NF-kappaB extracellular region|integral to plasma membrane caspase inhibitor activity|protein binding|transmembrane receptor activity kidney(1)|large_intestine(5)|lung(1)|urinary_tract(3) 10 GACTCTGGCTGACTTCAGGCA 0.572000 27 51 0 0 1 0 0 AFF4 27125 broad.mit.edu 37 5 132219228 132219228 + Silent SNP A A G TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr5:132219228A>G ENST00000265343.5 - 20 3547 c.3168T>C c.(3166-3168)ccT>ccC p.P1056P NM_014423.3 NP_055238.1 Q9UHB7 AFF4_HUMAN AF4/FMR2 family, member 4 1056 transcription from RNA polymerase II promoter mitochondrion|nucleolus protein binding|sequence-specific DNA binding transcription factor activity SEPT8/AFF4(2) breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2) 43 all_cancers(142;0.145)|Breast(839;0.198) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) TTGGAGAAACAGGGGAAGGCA 0.438000 11 30 0 0 1 0 0 OR7D4 125958 broad.mit.edu 37 19 9324997 9324997 + Missense_Mutation SNP C C T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr19:9324997C>T ENST00000308682.2 - 1 545 c.517G>A c.(517-519)Gag>Aag p.E173K NM_001005191.2 NP_001005191.1 Q8NG98 OR7D4_HUMAN olfactory receptor, family 7, subfamily D, member 4 173 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity p.E173K(1) breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|skin(3)|stomach(1) 26 TGCGGAATCTCAGTGCCTGTG 0.507000 23 55 0 0 1 0 0 RASSF1 11186 broad.mit.edu 37 3 50368087 50368087 + Silent SNP G G T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr3:50368087G>T ENST00000359365.4 - 6 1054 c.948C>A c.(946-948)ctC>ctA p.L316L RASSF1_ENST00000327761.3_Silent_p.L246L|RASSF1_ENST00000395126.3_Silent_p.L165L|RASSF1_ENST00000357043.2_Silent_p.L320L NM_001206957.1|NM_007182.4|NM_170714.1 NP_001193886.1|NP_009113.3|NP_733832.1 Q9NS23 RASF1_HUMAN Ras association (RalGDS/AF-6) domain family member 1 320 MOAP1-binding.|SARAH. cell cycle arrest|negative regulation of cell cycle arrest|positive regulation of protein ubiquitination|protein stabilization|Ras protein signal transduction|response to DNA damage stimulus microtubule|microtubule cytoskeleton|microtubule organizing center|nucleus|spindle pole identical protein binding|protein binding|protein N-terminus binding|zinc ion binding lung(2)|ovary(1)|skin(1)|urinary_tract(1) 5 BRCA - Breast invasive adenocarcinoma(193;0.000278)|OV - Ovarian serous cystadenocarcinoma(275;0.0015)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621) GGATCTGGCGGAGGTGCTCCT 0.597000 26 58 8.58068e-18 9.29574e-18 1 1 0 SMAD7 4092 broad.mit.edu 37 18 46448213 46448213 + Silent SNP C C T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr18:46448213C>T ENST00000262158.2 - 4 1096 c.810G>A c.(808-810)aaG>aaA p.K270K SMAD7_ENST00000591805.1_Silent_p.K55K|SMAD7_ENST00000585986.1_5'UTR|SMAD7_ENST00000589634.1_Silent_p.K269K NM_001190821.1|NM_005904.3 NP_001177750.1|NP_005895.1 O15105 SMAD7_HUMAN SMAD family member 7 270 MH2. adherens junction assembly|artery morphogenesis|BMP signaling pathway|cellular protein complex localization|negative regulation of BMP signaling pathway|negative regulation of cell migration|negative regulation of epithelial to mesenchymal transition|negative regulation of pathway-restricted SMAD protein phosphorylation|negative regulation of peptidyl-serine phosphorylation|negative regulation of peptidyl-threonine phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription by competitive promoter binding|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transforming growth factor beta receptor signaling pathway|negative regulation of ubiquitin-protein ligase activity|pathway-restricted SMAD protein phosphorylation|positive regulation of anti-apoptosis|positive regulation of cell-cell adhesion|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein stabilization|regulation of activin receptor signaling pathway|response to laminar fluid shear stress|transforming growth factor beta receptor signaling pathway|ventricular cardiac muscle tissue morphogenesis|ventricular septum morphogenesis centrosome|cytosol|nucleolus|plasma membrane|transcription factor complex activin binding|beta-catenin binding|I-SMAD binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity|type I transforming growth factor beta receptor binding|ubiquitin protein ligase binding breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1) 10 Colorectal(1;0.0518) CCACTCTCGTCTTCTCCTCCC 0.542000 25 25 0 0 1 0 0 TXLNA 200081 broad.mit.edu 37 1 32650145 32650145 + Silent SNP G G A TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr1:32650145G>A ENST00000373609.1 + 3 806 c.525G>A c.(523-525)ctG>ctA p.L175L TXLNA_ENST00000373610.3_Silent_p.L175L P40222 TXLNA_HUMAN taxilin alpha 175 cell proliferation|exocytosis cytoplasm|extracellular region cytokine activity|high molecular weight B cell growth factor receptor binding endometrium(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 13 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174) TCACGTTGCTGATGCAGACAT 0.557000 35 82 0 0 1 0 0 COL3A1 1281 broad.mit.edu 37 2 189871696 189871696 + Missense_Mutation SNP G G A TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr2:189871696G>A ENST00000304636.3 + 44 3405 c.3235G>A c.(3235-3237)Gct>Act p.A1079T COL3A1_ENST00000317840.5_Intron NM_000090.3 NP_000081 P02461 CO3A1_HUMAN collagen, type III, alpha 1 1079 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 NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3) 126 OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141) Collagenase(DB00048)|Palifermin(DB00039) TCCCGGTCCTGCTGGTTCCCG 0.388000 10 12 0 0 1 0 0 POLR3A 11128 broad.mit.edu 37 10 79745871 79745871 + Missense_Mutation SNP G G T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr10:79745871G>T ENST00000372371.3 - 22 3085 c.2948C>A c.(2947-2949)aCc>aAc p.T983N NM_007055.3 NP_008986.2 O14802 RPC1_HUMAN polymerase (RNA) III (DNA directed) polypeptide A, 155kDa 983 innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter DNA-directed RNA polymerase III complex DNA binding|DNA-directed RNA polymerase activity|ribonucleoside binding|zinc ion binding breast(1)|endometrium(7)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 59 all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095) Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646) TTTATCTCTGGTTTTCTTGAT 0.413000 50 138 2.74695e-27 3.06089e-27 1 1 0 ABCA4 24 broad.mit.edu 37 1 94496055 94496055 + Silent SNP G G A TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr1:94496055G>A ENST00000370225.3 - 29 4367 c.4281C>T c.(4279-4281)ttC>ttT p.F1427F NM_000350.2 NP_000341.2 P78363 ABCA4_HUMAN ATP-binding cassette, sub-family A (ABC1), member 4 1427 phototransduction, visible light|visual perception integral to plasma membrane|membrane fraction ATP binding|ATPase activity, coupled to transmembrane movement of substances NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2) 147 all_lung(203;0.000757)|Lung NSC(277;0.00335) all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171) CAAGTACCGTGAACTGCTCAC 0.557000 28 51 0 0 1 0 0 SHROOM1 134549 broad.mit.edu 37 5 132160030 132160030 + Silent SNP G G C TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr5:132160030G>C ENST00000378679.3 - 7 2127 c.1323C>G c.(1321-1323)ctC>ctG p.L441L SHROOM1_ENST00000378676.1_Silent_p.L372L|SHROOM1_ENST00000319854.3_Silent_p.L441L NM_001172700.1 NP_001166171.1 Q2M3G4 SHRM1_HUMAN shroom family member 1 441 actin filament bundle assembly|cell morphogenesis cytoplasm|microtubule actin filament binding endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 17 KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) GACACTCATGGAGCGGGTACT 0.572000 17 19 0 0 1 0 0 TFAP2E 339488 broad.mit.edu 37 1 36055608 36055608 + Missense_Mutation SNP G G A TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr1:36055608G>A ENST00000373235.3 + 5 1071 c.863G>A c.(862-864)cGc>cAc p.R288H NM_178548.3 NP_848643.2 Q6VUC0 AP2E_HUMAN transcription factor AP-2 epsilon (activating enhancer binding protein 2 epsilon) 288 H-S-H (helix-span-helix), dimerization. nucleus DNA binding|sequence-specific DNA binding transcription factor activity endometrium(1)|large_intestine(1) 2 Myeloproliferative disorder(586;0.0393)|all_neural(195;0.196) GCTGGCCGTCGCAAGGCCGCC 0.577000 3 33 0 0 1 0 0 REG1P 5969 broad.mit.edu 37 2 79363900 79363900 + RNA SNP G G A TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr2:79363900G>A ENST00000444841.1 - 0 438 GGAGGTAGAAGATGCAGCAGA 0.463000 10 9 0 0 1 0 0 SHROOM1 134549 broad.mit.edu 37 5 132160503 132160503 + Missense_Mutation SNP G G C TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr5:132160503G>C ENST00000378679.3 - 6 1849 c.1045C>G c.(1045-1047)Cag>Gag p.Q349E SHROOM1_ENST00000378676.1_Intron|SHROOM1_ENST00000319854.3_Missense_Mutation_p.Q349E NM_001172700.1 NP_001166171.1 Q2M3G4 SHRM1_HUMAN shroom family member 1 349 actin filament bundle assembly|cell morphogenesis cytoplasm|microtubule actin filament binding endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 17 KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) GCCTCTTTCTGAGGCAAGAAC 0.537000 9 14 0 0 1 0 0 DENND1A 57706 broad.mit.edu 37 9 126144610 126144610 + Missense_Mutation SNP C C T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr9:126144610C>T ENST00000373624.2 - 22 2332 c.2131G>A c.(2131-2133)Ggc>Agc p.G711S DENND1A_ENST00000542603.1_Missense_Mutation_p.G496S|DENND1A_ENST00000473039.1_5'UTR|DENND1A_ENST00000394219.3_Missense_Mutation_p.G722S NM_020946.1 NP_065997.1 Q8TEH3 DEN1A_HUMAN DENN/MADD domain containing 1A 711 Pro-rich. cell junction|clathrin coated vesicle membrane|presynaptic membrane guanyl-nucleotide exchange factor activity breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|liver(2)|lung(18)|ovary(2)|prostate(1)|skin(1)|stomach(1) 43 GGCACGATGCCCAGCTCTGGG 0.682000 7 18 0 0 1 0 0 ACACB 32 broad.mit.edu 37 12 109577201 109577201 + Splice_Site SNP G G C TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr12:109577201G>C ENST00000338432.7 + 2 110 c.e2-1 ACACB_ENST00000377854.5_5'Flank|ACACB_ENST00000377848.3_5'Flank O00763 ACACB_HUMAN acetyl-CoA carboxylase beta acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation cytosol|endomembrane system|Golgi apparatus|membrane acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 95 Biotin(DB00121) TCTCCTTACAGATTTTCTGAA 0.418000 23 55 0 0 1 0 0 MTUS2 23281 broad.mit.edu 37 13 29599705 29599705 + Silent SNP G G C TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr13:29599705G>C ENST00000431530.3 + 1 958 c.900G>C c.(898-900)tcG>tcC p.S300S NM_001033602.2 NP_001028774.2 Q5JR59 MTUS2_HUMAN microtubule associated tumor suppressor candidate 2 290 cytoplasm|microtubule microtubule binding|protein homodimerization activity p.S300S(1) NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1) 20 CTTTGGCATCGAAGGAAATCC 0.512000 8 20 0 0 1 0 0 RIF1 55183 broad.mit.edu 37 2 152276858 152276858 + Missense_Mutation SNP G G A TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr2:152276858G>A ENST00000243326.5 + 6 1141 c.658G>A c.(658-660)Gaa>Aaa p.E220K RIF1_ENST00000433166.2_Missense_Mutation_p.E220K|RIF1_ENST00000430328.2_Missense_Mutation_p.E220K|RIF1_ENST00000444746.2_Missense_Mutation_p.E220K|RIF1_ENST00000428287.2_Missense_Mutation_p.E220K|RIF1_ENST00000453091.2_Missense_Mutation_p.E220K Q5UIP0 RIF1_HUMAN RAP1 interacting factor homolog (yeast) cell cycle|response to DNA damage stimulus chromosome, telomeric region|cytoplasm|nucleus|spindle binding NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 97 BRCA - Breast invasive adenocarcinoma(221;0.0429) GAAACAGCAAGAAATAGCATC 0.413000 28 34 0 0 1 0 0 LAMA3 3909 broad.mit.edu 37 18 21508633 21508633 + Silent SNP C C T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr18:21508633C>T ENST00000313654.9 + 64 8581 c.8340C>T c.(8338-8340)ttC>ttT p.F2780F LAMA3_ENST00000399516.3_Silent_p.F2724F|LAMA3_ENST00000269217.6_Silent_p.F1171F|LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000587184.1_Silent_p.F1115F NM_198129.1 NP_937762.1 Q16787 LAMA3_HUMAN laminin, alpha 3 2780 Laminin G-like 3. 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 NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4) 128 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) AATTGAGTTTCACTGATTTGG 0.423000 43 90 0 0 1 0 0 MFSD6L 162387 broad.mit.edu 37 17 8701572 8701572 + Silent SNP G G T TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr17:8701572G>T ENST00000329805.4 - 1 1095 c.867C>A c.(865-867)gtC>gtA p.V289V NM_152599.3 NP_689812.3 Q8IWD5 MFS6L_HUMAN major facilitator superfamily domain containing 6-like 289 integral to membrane central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(7)|skin(4) 17 GCAACCTCCAGACCCACAGGC 0.607000 20 42 6.33239e-15 6.76611e-15 1 1 0 APOB 338 broad.mit.edu 37 2 21247750 21247751 + Splice_Site INS - - A rs35442885 TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr2:21247750_21247751insA ENST00000399256.4 - 17 2421 c.e17-2 APOB_ENST00000233242.1_Intron P04114 APOB_HUMAN apolipoprotein B cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6) 305 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) Atorvastatin(DB01076) CTGGGCGATCTAAAAAAAAACC 0.530 8 60 --- --- --- --- CDKN1A 1026 broad.mit.edu 37 6 36651956 36651957 + Frame_Shift_Ins INS - - A TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr6:36651956_36651957insA ENST00000405375.1 + 2 313_314 c.78_79insA c.(79-81)agcfs p.S27fs CDKN1A_ENST00000448526.2_Frame_Shift_Ins_p.S61fs|CDKN1A_ENST00000244741.5_Frame_Shift_Ins_p.S27fs|CDKN1A_ENST00000373711.2_Frame_Shift_Ins_p.S27fs|CDKN1A_ENST00000478800.1_3'UTR NM_001220778.1 NP_001207707.1 P38936 CDN1A_HUMAN cyclin-dependent kinase inhibitor 1A (p21, Cip1) 27 cell cycle arrest|cellular response to extracellular stimulus|cellular response to ionizing radiation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|induction of apoptosis by intracellular signals|negative regulation of cell growth|negative regulation of cell proliferation|positive regulation of fibroblast proliferation|positive regulation of reactive oxygen species metabolic process|Ras protein signal transduction|S phase of mitotic cell cycle|stress-induced premature senescence cyclin-dependent protein kinase holoenzyme complex|cytosol|nucleoplasm|PCNA-p21 complex cyclin-dependent protein kinase activating kinase activity|cyclin-dependent protein kinase inhibitor activity|metal ion binding breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|urinary_tract(5) 15 GCCCAGTGGACAGCGAGCAGCT 0.634 15 34 --- --- --- --- CCT6P1 643253 broad.mit.edu 37 7 65222951 65222951 + RNA DEL T T - TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr7:65222951delT ENST00000442266.1 + 0 561 TTTCTGTAACTTTTTTTTTTT 0.323 2 4 --- --- --- --- CACFD1 11094 broad.mit.edu 37 9 136325291 136325291 + Frame_Shift_Del DEL G G - TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr9:136325291delG ENST00000316948.4 + 1 183 c.103delG c.(103-105)gggfs p.G35fs CACFD1_ENST00000291722.7_Frame_Shift_Del_p.G35fs|CACFD1_ENST00000540581.1_Frame_Shift_Del_p.G35fs|CACFD1_ENST00000542192.1_Frame_Shift_Del_p.G35fs|CACFD1_ENST00000489519.1_3'UTR NM_017586.3 NP_060056.1 Q9UGQ2 FLOWR_HUMAN calcium channel flower domain containing 1 35 integral to membrane TCGCCTGTCTGGGGTGCTGGG 0.766 2 4 --- --- --- --- LRRC37A16P 651250 broad.mit.edu 37 17 66141015 66141016 + RNA INS - - A TCGA-CF-A7I0-01A-22D-A34U-08 TCGA-CF-A7I0-10A-01D-A34X-08 Untested Somatic Phase_I WXS none Illumina GAIIx 111978f9-3761-4265-8166-7d5d60c51cff d5d1e64d-dcbc-48d7-9dcc-574a09af4eab g.chr17:66141015_66141016insA ENST00000590019.1 - 0 70 CCAAGATTTCTACAAAAAAAAA 0.322 7 72 --- --- --- ---