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 PRTG 283659 broad.mit.edu 37 15 55933315 55933315 + Silent SNP G G A TCGA-P7-A5NY-05A-11D-A35D-08 TCGA-P7-A5NY-10A-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d 87bae02a-0994-4ce5-a27b-72494a4a1b5f g.chr15:55933315G>A ENST00000389286.4 - 12 2180 c.2133C>T c.(2131-2133)tgC>tgT p.C711C NM_173814.4 NP_776175.2 Q2VWP7 PRTG_HUMAN protogenin 711 multicellular organismal development integral to membrane breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 41 all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135) ACTTACACACGCATCCTGGAG 0.448000 3 26 0 0 1 0 0 BTN2A3P 54718 broad.mit.edu 37 6 26422353 26422353 + RNA SNP C C T rs141013110 TCGA-P7-A5NY-05A-11D-A35D-08 TCGA-P7-A5NY-10A-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d 87bae02a-0994-4ce5-a27b-72494a4a1b5f g.chr6:26422353C>T ENST00000466808.2 + 0 7 p.P3S(2) GCTCATGGAACCAGCTGCTGC 0.622000 4 90 0 0 1 0 0 TRPS1 7227 broad.mit.edu 37 8 116599567 116599567 + Silent SNP G G A TCGA-P7-A5NY-05A-11D-A35D-08 TCGA-P7-A5NY-10A-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d 87bae02a-0994-4ce5-a27b-72494a4a1b5f g.chr8:116599567G>A ENST00000395715.3 - 5 2938 c.2361C>T c.(2359-2361)gaC>gaT p.D787D TRPS1_ENST00000220888.5_Silent_p.D774D|TRPS1_ENST00000519076.1_Silent_p.D528D|TRPS1_ENST00000519674.1_Silent_p.D774D|TRPS1_ENST00000520276.1_Silent_p.D778D NM_014112.2 NP_054831.2 Q9UHF7 TRPS1_HUMAN trichorhinophalangeal syndrome I 774 Mediates interaction with GLI3. negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2) 111 all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219) Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12) CTTTGAGCCCGTCCTTCTCTT 0.507000 Langer-Giedion syndrome 4 179 0 0 1 0 0 CRAT 1384 broad.mit.edu 37 9 131860910 131860910 + Missense_Mutation SNP G G A TCGA-P7-A5NY-05A-11D-A35D-08 TCGA-P7-A5NY-10A-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d 87bae02a-0994-4ce5-a27b-72494a4a1b5f g.chr9:131860910G>A ENST00000318080.2 - 9 1399 c.1105C>T c.(1105-1107)Cgg>Tgg p.R369W RP11-247A12.1_ENST00000434250.1_RNA NM_000755.3|NM_001257363.1 NP_000746.2|NP_001244292.1 P43155 CACP_HUMAN carnitine O-acetyltransferase 369 energy derivation by oxidation of organic compounds|fatty acid beta-oxidation using acyl-CoA oxidase|transport endoplasmic reticulum|mitochondrial inner membrane|peroxisomal matrix carnitine O-acetyltransferase activity central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(2) 13 UCEC - Uterine corpus endometrioid carcinoma (4;0.0178) L-Carnitine(DB00583) AGGGGAGACCGCACAAGCTCG 0.607000 4 83 0 0 1 0 0 AMOT 154796 broad.mit.edu 37 X 112058796 112058796 + Silent SNP C C T TCGA-P7-A5NY-05A-11D-A35D-08 TCGA-P7-A5NY-10A-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d 87bae02a-0994-4ce5-a27b-72494a4a1b5f g.chrX:112058796C>T ENST00000371959.3 - 2 1181 c.1182G>A c.(1180-1182)caG>caA p.Q394Q AMOT_ENST00000371958.1_Silent_p.Q162Q|AMOT_ENST00000371962.1_Silent_p.Q162Q|AMOT_ENST00000304758.1_5'UTR|AMOT_ENST00000524145.1_Silent_p.Q394Q NM_001113490.1 NP_001106962.1 Q4VCS5 AMOT_HUMAN angiomotin 394 actin cytoskeleton organization|cell-cell junction assembly|negative regulation of angiogenesis|negative regulation of vascular permeability|positive regulation of blood vessel endothelial cell migration|positive regulation of cell size|positive regulation of stress fiber assembly|regulation of cell migration actin filament|cell surface|cytoplasm|endocytic vesicle|external side of plasma membrane|integral to membrane|lamellipodium|ruffle|stress fiber|tight junction angiostatin binding|protein binding|receptor activity p.Q394Q(1) breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|skin(2)|upper_aerodigestive_tract(1) 43 gctgctgctgctgttgttggt 0.582000 3 43 0 0 1 0 0 UBBP4 23666 broad.mit.edu 37 17 21730916 21730916 + Missense_Mutation SNP G G T rs111245273 by1000genomes TCGA-P7-A5NY-05A-11D-A35D-08 TCGA-P7-A5NY-10A-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d 87bae02a-0994-4ce5-a27b-72494a4a1b5f g.chr17:21730916G>T ENST00000584755.1 + 2 615 c.218G>T c.(217-219)cGg>cTg p.R73L UBBP4_ENST00000578713.1_Missense_Mutation_p.R73L|UBBP4_ENST00000584398.1_Intron|UBBP4_ENST00000583708.1_Intron p.R73L(24) endometrium(9)|kidney(4)|lung(4)|prostate(3)|urinary_tract(4) 24 GTCCTGCGTCGGAGAGGTGGT 0.552000 5 65 1.23904e-05 1.44555e-05 1 1 0 LTBP2 4053 broad.mit.edu 37 14 75022242 75022242 + Nonsense_Mutation SNP G G A TCGA-P7-A5NY-05A-11D-A35D-08 TCGA-P7-A5NY-10A-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d 87bae02a-0994-4ce5-a27b-72494a4a1b5f g.chr14:75022242G>A ENST00000261978.4 - 4 1371 c.985C>T c.(985-987)Cag>Tag p.Q329* LTBP2_ENST00000556690.1_Nonsense_Mutation_p.Q329*|CTD-2207P18.1_ENST00000554552.1_lincRNA|LTBP2_ENST00000557425.1_Intron NM_000428.2 NP_000419.1 Q14767 LTBP2_HUMAN latent transforming growth factor beta binding protein 2 329 protein secretion|protein targeting|transforming growth factor beta receptor signaling pathway extracellular space|proteinaceous extracellular matrix calcium ion binding|growth factor binding breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 58 BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649) GGTACCGCCTGTTGGGTGCCA 0.627000 9 38 0 0 1 0 0 SIRPB1 10326 broad.mit.edu 37 20 1585397 1585397 + Missense_Mutation SNP T T C rs148754551 by1000genomes TCGA-P7-A5NY-05A-11D-A35D-08 TCGA-P7-A5NY-10A-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d 87bae02a-0994-4ce5-a27b-72494a4a1b5f g.chr20:1585397T>C ENST00000279477.7 - 3 806 c.742A>G c.(742-744)Acc>Gcc p.T248A SIRPB1_ENST00000381605.4_Intron|RP4-576H24.4_ENST00000564763.1_Intron|SIRPB1_ENST00000568365.1_Missense_Mutation_p.T248A|SIRPB1_ENST00000381603.3_Intron NM_001135844.2 NP_001129316.1 O00241 SIRB1_HUMAN signal-regulatory protein beta 1 248 cell junction assembly|cell surface receptor linked signaling pathway integral to plasma membrane protein binding p.T248A(5) central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1) 31 CCTCGGATGGTCTCAGACAAG 0.627000 4 22 0 0 1 0 0 OCA2 4948 broad.mit.edu 37 15 28231750 28231750 + Missense_Mutation SNP C C T TCGA-P7-A5NY-05A-11D-A35D-08 TCGA-P7-A5NY-10A-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d 87bae02a-0994-4ce5-a27b-72494a4a1b5f g.chr15:28231750C>T ENST00000354638.3 - 12 1377 c.1222G>A c.(1222-1224)Gat>Aat p.D408N OCA2_ENST00000353809.5_Missense_Mutation_p.D384N|OCA2_ENST00000382996.2_Missense_Mutation_p.D408N NM_000275.2 NP_000266.2 Q04671 P_HUMAN oculocutaneous albinism II 408 eye pigment biosynthetic process endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosomal membrane|melanosome membrane arsenite transmembrane transporter activity|citrate transmembrane transporter activity|L-tyrosine transmembrane transporter activity|protein binding p.D408N(1) NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(48)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 85 all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234) all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045) GCACAATAATCGAAAAATCCC 0.294000 Oculocutaneous Albinism 28 46 0 0 1 0 0 TSHZ3 57616 broad.mit.edu 37 19 31768209 31768209 + Silent SNP G G A TCGA-P7-A5NY-05A-11D-A35D-08 TCGA-P7-A5NY-10A-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d 87bae02a-0994-4ce5-a27b-72494a4a1b5f g.chr19:31768209G>A ENST00000240587.4 - 2 2817 c.2490C>T c.(2488-2490)gtC>gtT p.V830V NM_020856.2 NP_065907.2 Q63HK5 TSH3_HUMAN teashirt zinc finger homeobox 3 830 negative regulation of transcription, DNA-dependent|regulation of respiratory gaseous exchange by neurological system process growth cone|nucleus chromatin binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5) 123 Esophageal squamous(110;0.226) TGAATGATACGACGGCAGATG 0.527000 20 108 0 0 1 0 0 PMS2P3 5387 broad.mit.edu 37 7 75142142 75142142 + RNA DEL A A - rs35519730 TCGA-P7-A5NY-05A-11D-A35D-08 TCGA-P7-A5NY-10A-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d 87bae02a-0994-4ce5-a27b-72494a4a1b5f g.chr7:75142142delA ENST00000418756.1 - 0 991 NR_028059.1 lung(1) 1 tctcaaaaagaaaaaaaaaaa 0.418 2 4 --- --- --- --- FAM66B 100128890 broad.mit.edu 37 8 7196263 7196264 + RNA DEL AC AC - TCGA-P7-A5NY-05A-11D-A35D-08 TCGA-P7-A5NY-10A-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d 87bae02a-0994-4ce5-a27b-72494a4a1b5f g.chr8:7196263_7196264delAC ENST00000606573.1 - 0 703 ACTGAGGGGTacacacacacac 0.500 3 4 --- --- --- --- MYRF 745 broad.mit.edu 37 11 61547022 61547022 + Frame_Shift_Del DEL C C - TCGA-P7-A5NY-05A-11D-A35D-08 TCGA-P7-A5NY-10A-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d 87bae02a-0994-4ce5-a27b-72494a4a1b5f g.chr11:61547022delC ENST00000278836.5 + 16 2323 c.2227delC c.(2227-2229)ccfs p.P744fs MYRF_ENST00000327797.1_Frame_Shift_Del_p.P388fs|TMEM258_ENST00000535042.1_Intron|MYRF_ENST00000389602.4_Frame_Shift_Del_p.P135fs|MYRF_ENST00000265460.5_Frame_Shift_Del_p.P735fs NM_001127392.1 NP_001120864.1 myelin regulatory factor CAAGAAGAGGCCCCCCAAGGT 0.652 2 4 --- --- --- --- HERC2P2 400322 broad.mit.edu 37 15 23312380 23312380 + RNA DEL T T - TCGA-P7-A5NY-05A-11D-A35D-08 TCGA-P7-A5NY-10A-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d 87bae02a-0994-4ce5-a27b-72494a4a1b5f g.chr15:23312380delT ENST00000560464.1 - 0 3118 TGTTAttttcttttttttttt 0.398 3 5 --- --- --- --- DUOX2 50506 broad.mit.edu 37 15 45399034 45399034 + Frame_Shift_Del DEL G G - TCGA-P7-A5NY-05A-11D-A35D-08 TCGA-P7-A5NY-10A-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d 87bae02a-0994-4ce5-a27b-72494a4a1b5f g.chr15:45399034delG ENST00000389039.6 - 15 2212 c.1827delC c.(1825-1827)ccfs p.P609fs DUOX2_ENST00000603300.1_Frame_Shift_Del_p.P609fs Q9NRD8 DUOX2_HUMAN dual oxidase 2 609 cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|response to virus apical plasma membrane|integral to membrane calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|peroxidase activity NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1) 63 all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027) all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068) GCTCACCTAAGGGAAGGCAGC 0.587 2 4 --- --- --- --- UBE2Q2P1 388165 broad.mit.edu 37 15 85081721 85081721 + RNA DEL C C - TCGA-P7-A5NY-05A-11D-A35D-08 TCGA-P7-A5NY-10A-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d 87bae02a-0994-4ce5-a27b-72494a4a1b5f g.chr15:85081721delC ENST00000339094.1 - 0 1678 NR_003661.2 caaatatatacccccattcat 0.323 2 4 --- --- --- --- C16orf74 404550 broad.mit.edu 37 16 85743879 85743881 + In_Frame_Del DEL GCT GCT - TCGA-P7-A5NY-05A-11D-A35D-08 TCGA-P7-A5NY-10A-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d 87bae02a-0994-4ce5-a27b-72494a4a1b5f g.chr16:85743879_85743881delGCT ENST00000602583.1 - 1 575_577 c.25_27delAGC c.(25-27)del p.S9del C16orf74_ENST00000284245.4_In_Frame_Del_p.S21del|C16orf74_ENST00000602675.1_5'UTR|C16orf74_ENST00000602914.1_Intron|C16orf74_ENST00000602719.1_In_Frame_Del_p.S21del|C16orf74_ENST00000602766.1_5'UTR|C16orf74_ENST00000602758.1_Intron Q96GX8 CP074_HUMAN chromosome 16 open reading frame 74 21 CCTCGTCGTGGCTGCTGCTGCTG 0.635 3 6 --- --- --- --- TNPO2 30000 broad.mit.edu 37 19 12830109 12830110 + Frame_Shift_Ins INS - - T TCGA-P7-A5NY-05A-11D-A35D-08 TCGA-P7-A5NY-10A-01D-A35B-08 Untested Somatic Phase_I WXS none Illumina GAIIx 0c4fc0e7-ba0e-49b5-a8b2-0b6ec20b2d8d 87bae02a-0994-4ce5-a27b-72494a4a1b5f g.chr19:12830109_12830110insT ENST00000425528.1 - 4 497_498 c.140_141insA c.(139-141)tctfs p.S47fs TNPO2_ENST00000588216.1_Frame_Shift_Ins_p.S47fs|TNPO2_ENST00000592287.1_Frame_Shift_Ins_p.S47fs|TNPO2_ENST00000450764.2_Frame_Shift_Ins_p.S47fs|TNPO2_ENST00000589956.1_5'UTR|TNPO2_ENST00000356861.5_Frame_Shift_Ins_p.S47fs|TNPO2_ENST00000441499.1_Frame_Shift_Ins_p.S47fs O14787 TNPO2_HUMAN transportin 2 47 Importin N-terminal. intracellular protein transport cytoplasm|nucleus nuclear localization sequence binding|protein binding|protein transporter activity autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 28 CGAAAATCAGGTAGTTGTTGAA 0.545 10 23 --- --- --- ---