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 PPCS 79717 broad.mit.edu 37 1 42922269 42922269 + Silent SNP C C T TCGA-ET-A39S-01A-11D-A19J-08 TCGA-ET-A39S-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4715aaf8-bfde-4f8c-9099-6b87ed6f3fba 1330fdd2-5fa2-4f99-b8ed-a9b278650139 g.chr1:42922269C>T ENST00000372561.3 + 1 40 c.33C>T c.(31-33)ccC>ccT p.P11P PPCS_ENST00000372562.1_Intron|PPCS_ENST00000472013.1_3'UTR|PPCS_ENST00000455780.1_5'UTR|PPCS_ENST00000372556.3_Silent_p.P11P|PPCS_ENST00000372560.3_Silent_p.P11P NM_024664.2 NP_078940.2 Q9HAB8 PPCS_HUMAN phosphopantothenoylcysteine synthetase 11 coenzyme biosynthetic process|pantothenate metabolic process cytosol phosphopantothenate--cysteine ligase activity breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|skin(3) 12 Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0333) CCGAGTTCCCCCAGCCTCCCG 0.726000 3 17 0 0 0.000248 0 0 STARD8 9754 broad.mit.edu 37 X 67940175 67940175 + Silent SNP A A C TCGA-ET-A39S-01A-11D-A19J-08 TCGA-ET-A39S-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4715aaf8-bfde-4f8c-9099-6b87ed6f3fba 1330fdd2-5fa2-4f99-b8ed-a9b278650139 g.chrX:67940175A>C ENST00000252336.6 + 7 2091 c.1719A>C c.(1717-1719)ccA>ccC p.P573P STARD8_ENST00000374597.3_Silent_p.P573P|STARD8_ENST00000374599.3_Silent_p.P653P NM_014725.4 NP_055540.2 Q92502 STAR8_HUMAN StAR-related lipid transfer (START) domain containing 8 573 Rho-GAP. regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction cytosol|focal adhesion GTPase activator activity p.P573P(4)|p.P653P(2) NS(2)|breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2) 50 TTGGGGTGCCACCCCTCATCC 0.577000 5 19 0 0 0.000602 0 0 BRAF 673 broad.mit.edu 37 7 140453136 140453136 + Missense_Mutation SNP A A T rs121913377 TCGA-ET-A39S-01A-11D-A19J-08 TCGA-ET-A39S-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4715aaf8-bfde-4f8c-9099-6b87ed6f3fba 1330fdd2-5fa2-4f99-b8ed-a9b278650139 g.chr7:140453136A>T ENST00000288602.6 - 15 1859 c.1799T>A c.(1798-1800)gTg>gAg p.V600E NM_004333.4 NP_004324.2 P15056 BRAF_HUMAN v-raf murine sarcoma viral oncogene homolog B 600 Protein kinase. V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis). activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission cytosol|nucleus|plasma membrane ATP binding|metal ion binding p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1) SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2) NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3) 27380 Melanoma(164;0.00956) Sorafenib(DB00398) TCGAGATTTCACTGTAGCTAG 0.368000 V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN) 61 """Mis, T, O""" """AKAP9, KIAA1549""" """melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma""" Cardio-facio-cutaneous syndrome Cardiofaciocutaneous syndrome 27 56 0 0 0.007291 0 0 RUNX2 860 broad.mit.edu 37 6 45390445 45390445 + Silent SNP A A G TCGA-ET-A39S-01A-11D-A19J-08 TCGA-ET-A39S-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4715aaf8-bfde-4f8c-9099-6b87ed6f3fba 1330fdd2-5fa2-4f99-b8ed-a9b278650139 g.chr6:45390445A>G ENST00000371438.1 + 2 532 c.174A>G c.(172-174)caA>caG p.Q58Q RUNX2_ENST00000359524.5_Silent_p.Q44Q|RUNX2_ENST00000541979.1_Silent_p.Q126Q|RUNX2_ENST00000371432.3_Silent_p.Q44Q|RUNX2_ENST00000371436.6_Silent_p.Q58Q|RUNX2_ENST00000465038.2_Silent_p.Q58Q|RUNX2_ENST00000576263.1_Silent_p.Q58Q|RUNX2_ENST00000352853.5_Silent_p.Q126Q NM_001024630.3 NP_001019801.3 Q13950 RUNX2_HUMAN runt-related transcription factor 2 58 Poly-Gln. negative regulation of transcription, DNA-dependent|osteoblast differentiation|positive regulation of transcription, DNA-dependent nucleus ATP binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 34 agcagcagcaacagcagcagc 0.731000 4 53 0 0 0.000602 0 0 MARS2 92935 broad.mit.edu 37 2 198571775 198571775 + Missense_Mutation SNP G G T TCGA-ET-A39S-01A-11D-A19J-08 TCGA-ET-A39S-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4715aaf8-bfde-4f8c-9099-6b87ed6f3fba 1330fdd2-5fa2-4f99-b8ed-a9b278650139 g.chr2:198571775G>T ENST00000282276.6 + 1 1689 c.1646G>T c.(1645-1647)gGa>gTa p.G549V AC011997.1_ENST00000409845.1_Intron NM_138395.3 NP_612404.1 Q96GW9 SYMM_HUMAN methionyl-tRNA synthetase 2, mitochondrial 549 methionyl-tRNA aminoacylation mitochondrial matrix ATP binding|methionine-tRNA ligase activity breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1) 22 L-Methionine(DB00134) AGGAGTCTTGGAGAGCTCTAT 0.532000 48 148 4.29476e-34 5.63687e-34 0.003610 1 0 DNAH1 25981 broad.mit.edu 37 3 52356519 52356519 + Missense_Mutation SNP A A G TCGA-ET-A39S-01A-11D-A19J-08 TCGA-ET-A39S-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4715aaf8-bfde-4f8c-9099-6b87ed6f3fba 1330fdd2-5fa2-4f99-b8ed-a9b278650139 g.chr3:52356519A>G ENST00000420323.2 + 2 322 c.61A>G c.(61-63)Agc>Ggc p.S21G NM_015512.4 NP_056327.4 Q9P2D7 DYH1_HUMAN dynein, axonemal, heavy chain 1 21 Stem (By similarity). ciliary or flagellar motility|microtubule-based movement|response to mechanical stimulus axonemal dynein complex|cilium axoneme|cytoplasm|microtubule ATP binding|ATPase activity|microtubule motor activity cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1) 62 BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245) CCCAGAGTGCAGCAGTGCTCC 0.582000 10 46 0 0 0.000978 0 0 RP11-1166P10.6 0 broad.mit.edu 37 16 32070612 32070612 + RNA SNP A A C TCGA-ET-A39S-01A-11D-A19J-08 TCGA-ET-A39S-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4715aaf8-bfde-4f8c-9099-6b87ed6f3fba 1330fdd2-5fa2-4f99-b8ed-a9b278650139 g.chr16:32070612A>C ENST00000566806.1 - 0 499 GGTCTCCTGCAAGGCTTCTGG 0.552000 5 96 0 0 0.001984 0 0 SHPK 23729 broad.mit.edu 37 17 3518731 3518731 + Silent SNP T T C TCGA-ET-A39S-01A-11D-A19J-08 TCGA-ET-A39S-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4715aaf8-bfde-4f8c-9099-6b87ed6f3fba 1330fdd2-5fa2-4f99-b8ed-a9b278650139 g.chr17:3518731T>C ENST00000225519.3 - 6 1026 c.924A>G c.(922-924)ccA>ccG p.P308P NM_013276.2 NP_037408.2 Q9UHJ6 SHPK_HUMAN sedoheptulokinase 308 carbohydrate metabolic process cytoplasm ATP binding|sedoheptulokinase activity breast(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 16 COAD - Colon adenocarcinoma(5;0.0828) TGTTGAAGTATGGGAAGTAGG 0.592000 20 47 0 0 0.008871 0 0 PRSS3P2 0 broad.mit.edu 37 7 142479940 142479940 + RNA SNP C C T rs58649169 by1000genomes TCGA-ET-A39S-01A-11D-A19J-08 TCGA-ET-A39S-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4715aaf8-bfde-4f8c-9099-6b87ed6f3fba 1330fdd2-5fa2-4f99-b8ed-a9b278650139 g.chr7:142479940C>T ENST00000603901.1 + 0 72 NR_001296.3 ATGACAAGATCGTTGGGGGCT 0.557000 4 58 0 0 0.000248 0 0 PKHD1L1 93035 broad.mit.edu 37 8 110455173 110455174 + Splice_Site INS - - G TCGA-ET-A39S-01A-11D-A19J-08 TCGA-ET-A39S-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4715aaf8-bfde-4f8c-9099-6b87ed6f3fba 1330fdd2-5fa2-4f99-b8ed-a9b278650139 g.chr8:110455173_110455174insG ENST00000378402.5 + 36 4497 c.e36-1 NM_177531.4 NP_803875.2 Q86WI1 PKHL1_HUMAN polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1 immune response cytosol|extracellular space|integral to membrane receptor activity NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4) 263 OV - Ovarian serous cystadenocarcinoma(57;9.88e-13) ATTTTATGGCAGGTTCATTTTC 0.322 HNSCC(38;0.096) 7 123 --- --- --- --- INA 9118 broad.mit.edu 37 10 105048271 105048273 + In_Frame_Del DEL GAG GAG - TCGA-ET-A39S-01A-11D-A19J-08 TCGA-ET-A39S-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4715aaf8-bfde-4f8c-9099-6b87ed6f3fba 1330fdd2-5fa2-4f99-b8ed-a9b278650139 g.chr10:105048271_105048273delGAG ENST00000369849.4 + 3 1394_1396 c.1345_1347delGAG c.(1345-1347)del p.E454del NM_032727.3 NP_116116.1 Q16352 AINX_HUMAN internexin neuronal intermediate filament protein, alpha 454 Poly-Glu.|Tail. cell differentiation|nervous system development neurofilament structural constituent of cytoskeleton p.E449_E450delEE(1) breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(2) 13 Epithelial(162;3.45e-09)|all cancers(201;9.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198) ACTTAAGAAAGAGGAGGAGGAGG 0.458 8 120 --- --- --- --- TRAV9-2 0 broad.mit.edu 37 14 22409533 22409539 + RNA DEL CTCTCTC CTCTCTC - rs57759840 TCGA-ET-A39S-01A-11D-A19J-08 TCGA-ET-A39S-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4715aaf8-bfde-4f8c-9099-6b87ed6f3fba 1330fdd2-5fa2-4f99-b8ed-a9b278650139 g.chr14:22409533_22409539delCTCTCTC ENST00000390441.2 + 0 102 ctctctctctctctctctTTTTTTTTT 0.415 7 10 --- --- --- --- RP11-160E2.17 0 broad.mit.edu 37 17 18988562 18988562 + RNA DEL T T - TCGA-ET-A39S-01A-11D-A19J-08 TCGA-ET-A39S-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4715aaf8-bfde-4f8c-9099-6b87ed6f3fba 1330fdd2-5fa2-4f99-b8ed-a9b278650139 g.chr17:18988562delT ENST00000442355.2 + 0 272 CTGATGTGTGTTTTTTTTTTT 0.279 2 4 --- --- --- --- SALL3 27164 broad.mit.edu 37 18 76753025 76753025 + Frame_Shift_Del DEL C C - TCGA-ET-A39S-01A-11D-A19J-08 TCGA-ET-A39S-10A-01D-A19M-08 Untested Somatic Phase_I WXS none Illumina GAIIx 4715aaf8-bfde-4f8c-9099-6b87ed6f3fba 1330fdd2-5fa2-4f99-b8ed-a9b278650139 g.chr18:76753025delC ENST00000536229.3 + 1 1344 c.635delC c.(634-636)gcfs p.A212fs SALL3_ENST00000575389.2_Frame_Shift_Del_p.A345fs|SALL3_ENST00000537592.2_Frame_Shift_Del_p.A345fs Q9BXA9 SALL3_HUMAN spalt-like transcription factor 3 345 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2) 74 Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167) OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256) ACGCCGCCTGCCCTGGCCCCG 0.781 2 4 --- --- --- ---