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 PSAT1 29968 broad.mit.edu 37 9 80919787 80919787 + Missense_Mutation SNP A A C TCGA-ET-A39N-01A-11D-A19J-08 TCGA-ET-A39N-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5904b857-04c7-404e-83b5-0d000ae43a35 5ab942e6-6a35-4b33-a4fa-8061207d8ec4 g.chr9:80919787A>C ENST00000376588.3 + 4 396 c.328A>C c.(328-330)Aag>Cag p.K110Q PSAT1_ENST00000347159.2_Missense_Mutation_p.K110Q NM_058179.2 NP_478059.1 Q9Y617 SERC_HUMAN phosphoserine aminotransferase 1 110 L-serine biosynthetic process|pyridoxine biosynthetic process O-phospho-L-serine:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1) 20 L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165) TTGGTCAGCTAAGGCCGCAGA 0.507000 4 50 0 0 1 0 0 MAP3K1 4214 broad.mit.edu 37 5 56180602 56180602 + Nonsense_Mutation SNP G G T TCGA-ET-A39N-01A-11D-A19J-08 TCGA-ET-A39N-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5904b857-04c7-404e-83b5-0d000ae43a35 5ab942e6-6a35-4b33-a4fa-8061207d8ec4 g.chr5:56180602G>T ENST00000399503.3 + 16 3931 c.3931G>T c.(3931-3933)Gga>Tga p.G1311* NM_005921.1 NP_005912.1 Q13233 M3K1_HUMAN mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase 1311 Protein kinase. cellular response to mechanical stimulus|innate immune response|MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway cytosol ATP binding|zinc ion binding NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1) 57 Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223) OV - Ovarian serous cystadenocarcinoma(10;6.08e-40) TAGGATGTTGGGAGCCACGTG 0.363000 3 49 0.00909568 0.00979535 1 1 0 ARAP2 116984 broad.mit.edu 37 4 36069767 36069767 + Missense_Mutation SNP C C T rs149183264 TCGA-ET-A39N-01A-11D-A19J-08 TCGA-ET-A39N-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5904b857-04c7-404e-83b5-0d000ae43a35 5ab942e6-6a35-4b33-a4fa-8061207d8ec4 g.chr4:36069767C>T ENST00000303965.4 - 33 5366 c.4877G>A c.(4876-4878)cGa>cAa p.R1626Q NM_015230.3 NP_056045.2 Q8WZ64 ARAP2_HUMAN ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2 1626 regulation of ARF GTPase activity|small GTPase mediated signal transduction cytosol ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|zinc ion binding breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1) 82 TTTTCGGGGTCGATTTCGAAG 0.502000 5 100 0 0 1 0 0 OR5D18 219438 broad.mit.edu 37 11 55587399 55587399 + Missense_Mutation SNP C C G rs147156620 by1000genomes TCGA-ET-A39N-01A-11D-A19J-08 TCGA-ET-A39N-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5904b857-04c7-404e-83b5-0d000ae43a35 5ab942e6-6a35-4b33-a4fa-8061207d8ec4 g.chr11:55587399C>G ENST00000333976.4 + 1 314 c.294C>G c.(292-294)tgC>tgG p.C98W NM_001001952.1 NP_001001952.1 Q8NGL1 OR5DI_HUMAN olfactory receptor, family 5, subfamily D, member 18 98 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 55 all_epithelial(135;0.208) TTTTAGGATGCGTAGTACAAT 0.433000 39 156 0 0 1 0 0 CSPG4 1464 broad.mit.edu 37 15 75969141 75969141 + Missense_Mutation SNP C C T TCGA-ET-A39N-01A-11D-A19J-08 TCGA-ET-A39N-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5904b857-04c7-404e-83b5-0d000ae43a35 5ab942e6-6a35-4b33-a4fa-8061207d8ec4 g.chr15:75969141C>T ENST00000308508.5 - 10 5811 c.5719G>A c.(5719-5721)Gtg>Atg p.V1907M CTD-2026K11.1_ENST00000569467.1_RNA NM_001897.4 NP_001888.2 Q6UVK1 CSPG4_HUMAN chondroitin sulfate proteoglycan 4 1907 Cysteine-containing.|Neurite growth inhibition (By similarity). angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane protein kinase binding|signal transducer activity breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4) 48 CCGTTGGCCACGAAGGCCAGC 0.672000 4 11 0 0 1 0 0 WDR96 80217 broad.mit.edu 37 10 105945732 105945732 + Splice_Site SNP C C A TCGA-ET-A39N-01A-11D-A19J-08 TCGA-ET-A39N-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5904b857-04c7-404e-83b5-0d000ae43a35 5ab942e6-6a35-4b33-a4fa-8061207d8ec4 g.chr10:105945732C>A ENST00000357060.3 - 15 2125 c.2010_splice c.e15+1 p.L670_splice WDR96_ENST00000278064.2_Splice_Site_p.L601_splice|WDR96_ENST00000428666.1_Splice_Site_p.L671_splice NM_025145.5 NP_079421.5 Q8NDM7 WDR96_HUMAN WD repeat domain 96 670 NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3) 72 AGCAGCTTACCAAAGTATAAA 0.318000 3 44 1 1 1 1 0 RP11-24M17.5 0 broad.mit.edu 37 15 76067911 76067911 + RNA SNP A A G rs12101948 by1000genomes TCGA-ET-A39N-01A-11D-A19J-08 TCGA-ET-A39N-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5904b857-04c7-404e-83b5-0d000ae43a35 5ab942e6-6a35-4b33-a4fa-8061207d8ec4 g.chr15:76067911A>G ENST00000395215.3 + 0 18 CAGGTGCCTGATACGTGACTG 0.547000 3 34 0 0 1 0 0 DCAF12L2 340578 broad.mit.edu 37 X 125299431 125299431 + Silent SNP G G A TCGA-ET-A39N-01A-11D-A19J-08 TCGA-ET-A39N-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5904b857-04c7-404e-83b5-0d000ae43a35 5ab942e6-6a35-4b33-a4fa-8061207d8ec4 g.chrX:125299431G>A ENST00000538699.1 - 2 557 c.477C>T c.(475-477)ccC>ccT p.P159P DCAF12L2_ENST00000360028.2_Silent_p.P159P NM_001013628.2 NP_001013650.1 Q5VW00 DC122_HUMAN DDB1 and CUL4 associated factor 12-like 2 159 NS(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(36)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(3) 64 GCGTCTTGGAGGGATTCAGCT 0.687000 6 142 0 0 1 0 0 UBQLN3 50613 broad.mit.edu 37 11 5530553 5530553 + Missense_Mutation SNP C C T TCGA-ET-A39N-01A-11D-A19J-08 TCGA-ET-A39N-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5904b857-04c7-404e-83b5-0d000ae43a35 5ab942e6-6a35-4b33-a4fa-8061207d8ec4 g.chr11:5530553C>T ENST00000311659.4 - 2 383 c.236G>A c.(235-237)tGt>tAt p.C79Y HBG2_ENST00000380259.2_Intron NM_017481.2 NP_059509.1 Q9H347 UBQL3_HUMAN ubiquilin 3 79 Ubiquitin-like. NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|prostate(1)|skin(2) 39 Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212) Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135) TCGCACTCCACACTGTGCCAG 0.562000 50 25 0 0 1 0 0 SYNPO2 171024 broad.mit.edu 37 4 119944588 119944588 + Nonsense_Mutation SNP C C T TCGA-ET-A39N-01A-11D-A19J-08 TCGA-ET-A39N-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5904b857-04c7-404e-83b5-0d000ae43a35 5ab942e6-6a35-4b33-a4fa-8061207d8ec4 g.chr4:119944588C>T ENST00000307142.4 + 2 305 c.109C>T c.(109-111)Cga>Tga p.R37* SYNPO2_ENST00000429713.2_Nonsense_Mutation_p.R37*|SYNPO2_ENST00000448416.2_Nonsense_Mutation_p.R37*|SYNPO2_ENST00000434046.2_Nonsense_Mutation_p.R37* NM_133477.2 NP_597734.2 Q9UMS6 SYNP2_HUMAN synaptopodin 2 37 PDZ. nucleus|Z disc 14-3-3 protein binding|actin binding|muscle alpha-actinin binding breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1) 64 CACTCAGATTCGAAATCAGAG 0.428000 10 15 0 0 1 0 0 ULK4 54986 broad.mit.edu 37 3 41723024 41723024 + Missense_Mutation SNP G G A TCGA-ET-A39N-01A-11D-A19J-08 TCGA-ET-A39N-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5904b857-04c7-404e-83b5-0d000ae43a35 5ab942e6-6a35-4b33-a4fa-8061207d8ec4 g.chr3:41723024G>A ENST00000301831.4 - 29 3415 c.2953C>T c.(2953-2955)Ctc>Ttc p.L985F NM_017886.2 NP_060356.2 Q96C45 ULK4_HUMAN unc-51 like kinase 4 985 ATP binding|protein serine/threonine kinase activity breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1) 22 KIRC - Kidney renal clear cell carcinoma(284;0.214) TCTCGAATGAGAGCCAGAAGA 0.473000 3 45 0 0 1 0 0 BAGE2 85319 broad.mit.edu 37 21 11058353 11058353 + RNA SNP T T C rs79433933 by1000genomes TCGA-ET-A39N-01A-11D-A19J-08 TCGA-ET-A39N-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5904b857-04c7-404e-83b5-0d000ae43a35 5ab942e6-6a35-4b33-a4fa-8061207d8ec4 g.chr21:11058353T>C ENST00000470054.1 - 0 324 B melanoma antigen family, member 2 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) GAAATCTCTTTATAAAACCTT 0.343000 6 81 0 0 1 0 0 LETMD1 25875 broad.mit.edu 37 12 51442144 51442144 + Missense_Mutation SNP C C T TCGA-ET-A39N-01A-11D-A19J-08 TCGA-ET-A39N-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5904b857-04c7-404e-83b5-0d000ae43a35 5ab942e6-6a35-4b33-a4fa-8061207d8ec4 g.chr12:51442144C>T ENST00000418425.2 + 1 24 c.5C>T c.(4-6)gCg>gTg p.A2V LETMD1_ENST00000548516.1_3'UTR|LETMD1_ENST00000380123.2_Missense_Mutation_p.A2V|LETMD1_ENST00000550929.1_5'UTR|LETMD1_ENST00000262055.4_Missense_Mutation_p.A2V|LETMD1_ENST00000547008.1_Missense_Mutation_p.A2V|LETMD1_ENST00000552739.1_Missense_Mutation_p.A2V NM_001243689.1 NP_001230618.1 Q6P1Q0 LTMD1_HUMAN LETM1 domain containing 1 2 Required and sufficient for mitochondrial import. integral to membrane|mitochondrial outer membrane protein binding central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(3) 16 GTGAAGATGGCGCTCTCCAGG 0.592000 OREG0021818 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 87 59 0 0 1 0 0 AXIN1 8312 broad.mit.edu 37 16 341240 341240 + Silent SNP C C T TCGA-ET-A39N-01A-11D-A19J-08 TCGA-ET-A39N-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5904b857-04c7-404e-83b5-0d000ae43a35 5ab942e6-6a35-4b33-a4fa-8061207d8ec4 g.chr16:341240C>T ENST00000262320.3 - 9 2615 c.2244G>A c.(2242-2244)ccG>ccA p.P748P AXIN1_ENST00000354866.3_Intron NM_003502.3 NP_003493.1 O15169 AXIN1_HUMAN axin 1 748 Interaction with HIPK2 (By similarity).|Interaction with PPP2CA.|Interaction with RNF111. activation of JUN kinase activity|activation of protein kinase activity|apoptosis|axial mesoderm formation|canonical Wnt receptor signaling pathway involved in neural plate anterior/posterior pattern formation|cellular protein complex assembly|cellular response to organic cyclic compound|cytoplasmic microtubule organization|determination of left/right symmetry|dorsal/ventral axis specification|embryonic eye morphogenesis|embryonic skeletal joint morphogenesis|forebrain anterior/posterior pattern formation|muscle cell development|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fat cell differentiation|olfactory placode formation|optic placode formation|positive regulation of JNK cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of transcription, DNA-dependent|positive regulation of ubiquitin-protein ligase activity|regulation of catenin import into nucleus|tail morphogenesis|Wnt receptor signaling pathway involved in forebrain neuron fate commitment|Wnt receptor signaling pathway involved in somitogenesis APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|cell cortex|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|cytosol|lateral plasma membrane|nucleus|perinuclear region of cytoplasm|postsynaptic density armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|I-SMAD binding|p53 binding|protein complex scaffold|protein homodimerization activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2) 221 all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187) CGTGCAGCACCGGCGCGCACG 0.692000 3 7 0 0 1 0 0 KARS 3735 broad.mit.edu 37 16 75662486 75662486 + Missense_Mutation SNP G G A TCGA-ET-A39N-01A-11D-A19J-08 TCGA-ET-A39N-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5904b857-04c7-404e-83b5-0d000ae43a35 5ab942e6-6a35-4b33-a4fa-8061207d8ec4 g.chr16:75662486G>A ENST00000319410.5 - 14 1881 c.1760C>T c.(1759-1761)aCg>aTg p.T587M KARS_ENST00000568378.1_Intron|KARS_ENST00000302445.3_Missense_Mutation_p.T559M NM_001130089.1 NP_001123561.1 Q15046 SYK_HUMAN lysyl-tRNA synthetase 559 interspecies interaction between organisms|lysyl-tRNA aminoacylation|tRNA processing cytosol|extracellular region|mitochondrial matrix|nucleus|plasma membrane|soluble fraction ATP binding|lysine-tRNA ligase activity|metal ion binding|tRNA binding kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1) 18 L-Lysine(DB00123) GTTGGAGTCCGTGAGAAACAT 0.552000 3 53 0 0 1 0 0 AC074391.1 0 broad.mit.edu 37 2 65738862 65738863 + RNA DEL TG TG - TCGA-ET-A39N-01A-11D-A19J-08 TCGA-ET-A39N-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5904b857-04c7-404e-83b5-0d000ae43a35 5ab942e6-6a35-4b33-a4fa-8061207d8ec4 g.chr2:65738862_65738863delTG ENST00000377977.3 + 0 862 TTTTTTTTTTTGTCCAGGAGGC 0.302 3 4 --- --- --- --- CCDC144CP 0 broad.mit.edu 37 17 20227624 20227624 + RNA DEL A A - TCGA-ET-A39N-01A-11D-A19J-08 TCGA-ET-A39N-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5904b857-04c7-404e-83b5-0d000ae43a35 5ab942e6-6a35-4b33-a4fa-8061207d8ec4 g.chr17:20227624delA ENST00000340196.4 + 0 568 AAAAAGAAGTAAGAGTCAGGA 0.318 7 13 --- --- --- --- RP4-777D9.2 0 broad.mit.edu 37 20 21196191 21196192 + RNA INS - - T TCGA-ET-A39N-01A-11D-A19J-08 TCGA-ET-A39N-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 5904b857-04c7-404e-83b5-0d000ae43a35 5ab942e6-6a35-4b33-a4fa-8061207d8ec4 g.chr20:21196191_21196192insT ENST00000591761.1 - 0 119 PLK1S1_ENST00000457464.1_RNA|RP4-777D9.2_ENST00000443753.1_RNA|RP4-777D9.2_ENST00000433213.2_RNA CTTTGAAATACTTTTTTTTTAT 0.322 2 4 --- --- --- ---