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 SCARB1 949 broad.mit.edu 37 12 125292412 125292412 + Missense_Mutation SNP C C G TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr12:125292412C>G ENST00000339570.5 - 7 1100 c.904G>C c.(904-906)Gtg>Ctg p.V302L SCARB1_ENST00000544327.1_Missense_Mutation_p.V248L|SCARB1_ENST00000261693.6_Missense_Mutation_p.V302L|SCARB1_ENST00000546215.1_Missense_Mutation_p.V302L|SCARB1_ENST00000541205.1_Missense_Mutation_p.V261L|SCARB1_ENST00000540495.1_Missense_Mutation_p.V265L|SCARB1_ENST00000535005.1_5'UTR|SCARB1_ENST00000415380.2_Missense_Mutation_p.V302L|SCARB1_ENST00000376788.1_Missense_Mutation_p.V202L NM_001082959.1 NP_001076428.1 Q8WTV0 SCRB1_HUMAN scavenger receptor class B, member 1 302 adhesion to symbiont|cell adhesion|cholesterol efflux|cholesterol homeostasis|cholesterol import|detection of lipopolysaccharide|high-density lipoprotein particle clearance|high-density lipoprotein particle remodeling|lipopolysaccharide transport|lipoprotein metabolic process|positive regulation of cholesterol storage|positive regulation of endothelial cell migration|positive regulation of nitric-oxide synthase activity|recognition of apoptotic cell|reverse cholesterol transport|triglyceride homeostasis|wound healing caveola 1-phosphatidylinositol binding|apolipoprotein A-I binding|high-density lipoprotein particle receptor activity|lipopolysaccharide receptor activity|low-density lipoprotein particle binding|phosphatidylserine binding|transporter activity endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|prostate(1) 17 all_neural(191;0.101)|Medulloblastoma(191;0.163) OV - Ovarian serous cystadenocarcinoma(86;0.000116)|Epithelial(86;0.000415)|all cancers(50;0.00395) Phosphatidylserine(DB00144) TTGGGAGCCACGAAGCGATAG 0.567000 16 40 0 0 1 0 0 NBPF9 400818 broad.mit.edu 37 1 144828545 144828545 + Missense_Mutation SNP A A T TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr1:144828545A>T ENST00000338347.4 + 14 1591 c.1591A>T c.(1591-1593)Aac>Tac p.N531Y NBPF9_ENST00000468645.1_3'UTR|NBPF9_ENST00000281815.8_Missense_Mutation_p.N129Y|NBPF9_ENST00000440491.2_Silent_p.S604S neuroblastoma breakpoint family, member 9 p.N531Y(1) NS(2)|prostate(1) 3 TTCCAGGCTCAACGGCGTGCT 0.453000 5 185 0 0 1 0 0 AGAP10 728127 broad.mit.edu 37 10 47207813 47207813 + Splice_Site SNP T T C TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr10:47207813T>C ENST00000355232.3 - 5 3482 c.471_splice c.e5+1 p.H157_splice AGAP10_ENST00000413193.2_Splice_Site_p.H228_splice|RP11-144G6.12_ENST00000605970.1_RNA|AGAP10_ENST00000452145.2_Splice_Site_p.H132_splice ArfGAP with GTPase domain, ankyrin repeat and PH domain 10 p.H228R(20) endometrium(5)|kidney(3)|lung(1)|prostate(2)|urinary_tract(1) 12 TTTACTTACATGGTTTGTACA 0.294000 3 26 0 0 1 0 0 CYFIP2 26999 broad.mit.edu 37 5 156787349 156787349 + Silent SNP C C T TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr5:156787349C>T ENST00000347377.6 + 25 3308 c.2877C>T c.(2875-2877)tgC>tgT p.C959C CYFIP2_ENST00000521420.1_Silent_p.C933C|CYFIP2_ENST00000522463.1_Silent_p.C763C|CYFIP2_ENST00000541131.1_Silent_p.C884C|CYFIP2_ENST00000318218.6_Silent_p.C984C|CYFIP2_ENST00000435847.2_Silent_p.C658C|CYFIP2_ENST00000442283.2_3'UTR|CYFIP2_ENST00000377576.3_Silent_p.C959C NM_001037332.2 NP_001032409.2 Q96F07 CYFP2_HUMAN cytoplasmic FMR1 interacting protein 2 984 apoptosis|cell-cell adhesion cell junction|perinuclear region of cytoplasm|synapse|synaptosome protein binding breast(1)|endometrium(12)|kidney(2)|lung(23) 38 Renal(175;0.00212) Medulloblastoma(196;0.0306)|all_neural(177;0.0897) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) CCAAGATATGCCGCTTGCCCC 0.517000 4 121 0 0 1 0 0 MAML3 55534 broad.mit.edu 37 4 140811108 140811108 + Silent SNP C C T TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr4:140811108C>T ENST00000509479.2 - 2 2338 c.1482G>A c.(1480-1482)caG>caA p.Q494Q MAML3_ENST00000327122.5_Silent_p.Q338Q|MAML3_ENST00000398940.1_Silent_p.Q33Q NM_018717.4 NP_061187.2 Q96JK9 MAML3_HUMAN mastermind-like 3 (Drosophila) 494 Gln-rich. Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nuclear speck transcription coactivator activity breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2) 25 all_hematologic(180;0.162) gctgctgctgctgctgctgct 0.537000 3 30 0 0 1 0 0 NRL 4901 broad.mit.edu 37 14 24551759 24551759 + Missense_Mutation SNP T T C TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr14:24551759T>C ENST00000561028.1 - 2 618 c.299A>G c.(298-300)cAg>cGg p.Q100R NRL_ENST00000397002.2_Missense_Mutation_p.Q100R|NRL_ENST00000396997.1_Missense_Mutation_p.Q100R P54845 NRL_HUMAN neural retina leucine zipper 100 response to stimulus|transcription from RNA polymerase II promoter|visual perception nucleus leucine zipper domain binding|sequence-specific DNA binding lung(2) 2 GBM - Glioblastoma multiforme(265;0.0181) GCCCTGACCCTGCAGCAGCTC 0.657000 3 40 0 0 1 0 0 MEGF10 84466 broad.mit.edu 37 5 126754828 126754828 + Missense_Mutation SNP C C T TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr5:126754828C>T ENST00000274473.6 + 12 1589 c.1322C>T c.(1321-1323)aCc>aTc p.T441I MEGF10_ENST00000508365.1_Missense_Mutation_p.T441I|MEGF10_ENST00000503335.2_Missense_Mutation_p.T441I|MEGF10_ENST00000418761.2_Missense_Mutation_p.T441I NM_032446.2 NP_115822.1 Q96KG7 MEG10_HUMAN multiple EGF-like-domains 10 441 Necessary for interaction with AP2M1, self-assembly and formation of the irregular, mosaic-like adhesion pattern. cell adhesion|phagocytosis basolateral plasma membrane|cell projection|integral to membrane|phagocytic cup breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(28)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1) 68 Prostate(80;0.165) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123) GACTGCTCTACCCCATGCCCT 0.443000 58 57 0 0 1 0 0 PDE4A 5141 broad.mit.edu 37 19 10577609 10577609 + Missense_Mutation SNP C C T TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr19:10577609C>T ENST00000380702.2 + 16 1907 c.1907C>T c.(1906-1908)gCg>gTg p.A636V PDE4A_ENST00000344979.3_Missense_Mutation_p.A419V|PDE4A_ENST00000592685.1_Missense_Mutation_p.A636V|PDE4A_ENST00000440014.2_Missense_Mutation_p.A597V|PDE4A_ENST00000352831.6_Missense_Mutation_p.A658V|PDE4A_ENST00000293683.5_Missense_Mutation_p.A632V P27815 PDE4A_HUMAN phosphodiesterase 4A, cAMP-specific 658 Catalytic. signal transduction cytosol|membrane fraction|perinuclear region of cytoplasm|ruffle membrane|soluble fraction 3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|protein binding NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1) 27 OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06) Cilostazol(DB01166)|Dipyridamole(DB00975)|Dyphylline(DB00651)|Enprofylline(DB00824)|Iloprost(DB01088)|Milrinone(DB00235)|Pentoxifylline(DB00806)|Phentolamine(DB00692)|Tadalafil(DB00820)|Theophylline(DB00277) GAGACCTGGGCGGACCTTGTC 0.572000 39 74 0 0 1 0 0 GPR50 9248 broad.mit.edu 37 X 150349267 150349267 + Missense_Mutation SNP C C G TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chrX:150349267C>G ENST00000218316.3 + 2 1281 c.1212C>G c.(1210-1212)caC>caG p.H404Q NM_004224.3 NP_004215.2 Q13585 MTR1L_HUMAN G protein-coupled receptor 50 404 Pro-rich. cell-cell signaling integral to plasma membrane melatonin receptor activity p.H404Q(2) breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|stomach(1) 38 Acute lymphoblastic leukemia(192;6.56e-05) CTACCCACCACAAGTCTGTCT 0.602000 5 63 0 0 1 0 0 DLC1 10395 broad.mit.edu 37 8 12958214 12958214 + Missense_Mutation SNP G G T TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr8:12958214G>T ENST00000276297.4 - 9 2041 c.1632C>A c.(1630-1632)agC>agA p.S544R DLC1_ENST00000358919.2_Missense_Mutation_p.S107R|DLC1_ENST00000520226.1_Missense_Mutation_p.S33R|DLC1_ENST00000512044.2_Missense_Mutation_p.S141R NM_182643.2 NP_872584.2 Q96QB1 RHG07_HUMAN deleted in liver cancer 1 544 actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction caveola|cytosol|focal adhesion|nucleus Rho GTPase activator activity|SH2 domain binding NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1) 110 ACCACCTCTTGCTGTCCCTTT 0.552000 3 37 1 1 1 1 0 RNPS1 10921 broad.mit.edu 37 16 2314324 2314324 + Missense_Mutation SNP G G A TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr16:2314324G>A ENST00000565678.1 - 3 625 c.80C>T c.(79-81)tCa>tTa p.S27L RNPS1_ENST00000566458.1_Missense_Mutation_p.S4L|RNPS1_ENST00000566397.1_5'UTR|RNPS1_ENST00000561718.1_5'UTR|RNPS1_ENST00000569598.2_Intron|RNPS1_ENST00000568631.1_Missense_Mutation_p.S27L|RNPS1_ENST00000397086.2_Missense_Mutation_p.S27L|RNPS1_ENST00000567147.1_Missense_Mutation_p.S4L|RNPS1_ENST00000301730.8_Missense_Mutation_p.S27L|RNPS1_ENST00000320225.5_Missense_Mutation_p.S27L Q15287 RNPS1_HUMAN RNA binding protein S1, serine-rich domain 27 Lys-rich.|Necessary for interaction with SRP54, nuclear localization and exon-skipping.|Necessary for interaction with the cleaved p110 isoform of CDC2L1. mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|termination of RNA polymerase II transcription cytosol|nuclear speck mRNA 3'-UTR binding|nucleotide binding|protein binding endometrium(1)|large_intestine(1)|lung(4)|ovary(2)|urinary_tract(1) 9 TTTGGTAGGTGAAGGAGCCCT 0.557000 8 116 0 0 1 0 0 CRIPAK 285464 broad.mit.edu 37 4 1389323 1389323 + Missense_Mutation SNP G G A rs71299249 byFrequency TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr4:1389323G>A ENST00000324803.4 + 1 3984 c.1024G>A c.(1024-1026)Gcc>Acc p.A342T NM_175918.3 NP_787114.2 Q8N1N5 CRPAK_HUMAN cysteine-rich PAK1 inhibitor 342 ER-nucleus signaling pathway|negative regulation of protein kinase activity|regulation of cytoskeleton organization|response to estrogen stimulus endoplasmic reticulum|nucleus|plasma membrane protein binding NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1) 35 OV - Ovarian serous cystadenocarcinoma(23;0.0106) TGGAGTGCCCGCCTGCTCACA 0.667000 7 409 0 0 1 0 0 TMEM132B 114795 broad.mit.edu 37 12 126138738 126138738 + Missense_Mutation SNP G G A TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr12:126138738G>A ENST00000299308.3 + 9 2727 c.2719G>A c.(2719-2721)Gtc>Atc p.V907I TMEM132B_ENST00000535886.1_Missense_Mutation_p.V419I NM_052907.2 NP_443139.2 Q14DG7 T132B_HUMAN transmembrane protein 132B 907 integral to membrane NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1) 107 all_neural(191;0.101)|Medulloblastoma(191;0.163) OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362) CTTGCTCTGCGTCTTCTGTCT 0.522000 4 96 0 0 1 0 0 RFTN1 23180 broad.mit.edu 37 3 16419524 16419524 + Missense_Mutation SNP G G A TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr3:16419524G>A ENST00000334133.4 - 5 799 c.527C>T c.(526-528)gCt>gTt p.A176V RFTN1_ENST00000432519.1_Missense_Mutation_p.A140V NM_015150.1 NP_055965.1 Q14699 RFTN1_HUMAN raftlin, lipid raft linker 1 176 plasma membrane central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(8)|lung(8)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(2) 38 AGACACCGGAGCACTGCTGCC 0.552000 3 34 0 0 1 0 0 SEMA6D 80031 broad.mit.edu 37 15 48063896 48063896 + Missense_Mutation SNP C C T TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr15:48063896C>T ENST00000316364.5 + 19 3575 c.3136C>T c.(3136-3138)Ccg>Tcg p.P1046S SEMA6D_ENST00000558816.1_3'UTR|SEMA6D_ENST00000389428.3_Missense_Mutation_p.P971S|SEMA6D_ENST00000536845.2_Missense_Mutation_p.P1046S|SEMA6D_ENST00000558014.1_Missense_Mutation_p.P984S|SEMA6D_ENST00000354744.4_Missense_Mutation_p.P990S|SEMA6D_ENST00000355997.3_3'UTR|SEMA6D_ENST00000358066.4_Missense_Mutation_p.P984S|SEMA6D_ENST00000389432.2_Missense_Mutation_p.P1003S|SEMA6D_ENST00000537942.1_Missense_Mutation_p.P984S|SEMA6D_ENST00000389433.2_Missense_Mutation_p.P1027S NM_153618.1 NP_705871.1 Q8NFY4 SEM6D_HUMAN sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D 1046 axon guidance cytoplasm|integral to membrane|plasma membrane receptor activity biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4) 77 all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18) all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06) AAAGAGGACGCCGTCCTTAAA 0.512000 20 171 0 0 1 0 0 PTCRA 171558 broad.mit.edu 37 6 42890951 42890951 + Missense_Mutation SNP C C T TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr6:42890951C>T ENST00000304672.1 + 2 326 c.245C>T c.(244-246)aCg>aTg p.T82M PTCRA_ENST00000446507.1_Intron|PTCRA_ENST00000441198.1_Missense_Mutation_p.T57M NM_001243168.1|NM_138296.2 NP_001230097.1|NP_612153.2 Q6ISU1 PTCRA_HUMAN pre T-cell antigen receptor alpha 82 integral to membrane receptor activity large_intestine(2)|lung(4)|ovary(2) 8 Colorectal(47;0.196) all cancers(41;0.000731)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|OV - Ovarian serous cystadenocarcinoma(102;0.0218)|Kidney(15;0.0388) TCCCCAGCAACGGATGGCACC 0.622000 14 55 0 0 1 0 0 TFAP4 7023 broad.mit.edu 37 16 4312678 4312678 + Silent SNP G G C TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr16:4312678G>C ENST00000204517.6 - 2 442 c.114C>G c.(112-114)ccC>ccG p.P38P NM_003223.2 NP_003214.1 Q01664 TFAP4_HUMAN transcription factor AP-4 (activating enhancer binding protein 4) 38 DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|negative regulation by host of viral transcription|negative regulation of cell cycle arrest|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|negative regulation of DNA binding|negative regulation of transcription, DNA-dependent|positive regulation by host of viral transcription|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein complex assembly|regulation of S phase of mitotic cell cycle transcriptional repressor complex E-box binding|histone deacetylase binding|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity NS(1)|endometrium(2)|lung(8)|ovary(1)|prostate(1)|skin(1) 14 GCTGAGTCTCGGGGGTTAGTG 0.622000 4 69 0 0 1 0 0 CHEK2 11200 broad.mit.edu 37 22 29091840 29091840 + Missense_Mutation SNP T T C rs142470496 byFrequency TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr22:29091840T>C ENST00000544772.1 - 12 1890 c.454A>G c.(454-456)Aag>Gag p.K152E CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000328354.6_Missense_Mutation_p.K373E|CHEK2_ENST00000405598.1_Missense_Mutation_p.K373E|CHEK2_ENST00000402731.1_Missense_Mutation_p.K344E|CHEK2_ENST00000348295.3_Missense_Mutation_p.K344E|CHEK2_ENST00000403642.1_Missense_Mutation_p.K282E|CHEK2_ENST00000382580.2_Missense_Mutation_p.K416E|CHEK2_ENST00000404276.1_Missense_Mutation_p.K373E|CHEK2_ENST00000382578.1_Missense_Mutation_p.K282E|CHEK2_ENST00000382566.1_3'UTR NM_001257387.1 NP_001244316.1 O96017 CHK2_HUMAN checkpoint kinase 2 373 FHA. cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence PML body ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity p.K373E(9) central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2) 50 CCCAAAATCTTGGAGTGCCCA 0.418000 F breast Direct reversal of damage;Other conserved DNA damage response genes 3 71 0 0 1 0 0 ECT2 1894 broad.mit.edu 37 3 172480266 172480266 + Missense_Mutation SNP T T G TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr3:172480266T>G ENST00000417960.1 + 9 1200 c.723T>G c.(721-723)gaT>gaG p.D241E ECT2_ENST00000441497.2_Missense_Mutation_p.D242E|ECT2_ENST00000540509.1_Missense_Mutation_p.D273E|ECT2_ENST00000427830.1_Missense_Mutation_p.D242E|ECT2_ENST00000392692.3_Missense_Mutation_p.D273E|ECT2_ENST00000232458.5_Missense_Mutation_p.D242E NM_001258316.1 NP_001245245.1 Q9H8V3 ECT2_HUMAN epithelial cell transforming sequence 2 oncogene 242 BRCT 2. apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol Rho guanyl-nucleotide exchange factor activity|signal transducer activity breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 37 Ovarian(172;0.00197)|Breast(254;0.158) Lung(28;1.33e-14)|LUSC - Lung squamous cell carcinoma(14;1.48e-14) CATTTCAAGATTGTATTTTAA 0.294000 5 34 0 0 1 0 0 ZP1 22917 broad.mit.edu 37 11 60637317 60637317 + Missense_Mutation SNP C C T TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr11:60637317C>T ENST00000278853.5 + 3 626 c.626C>T c.(625-627)gCt>gTt p.A209V NM_207341.2 NP_997224.2 P60852 ZP1_HUMAN zona pellucida glycoprotein 1 (sperm receptor) 209 single fertilization integral to membrane|plasma membrane|proteinaceous extracellular matrix breast(3)|endometrium(2)|large_intestine(8)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1) 26 GCCACCCTGGCTCAACCCCAC 0.587000 3 37 0 0 1 0 0 ADAMTSL3 57188 broad.mit.edu 37 15 84611672 84611672 + Silent SNP C C T TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr15:84611672C>T ENST00000286744.5 + 19 2552 c.2328C>T c.(2326-2328)ggC>ggT p.G776G ADAMTSL3_ENST00000567476.1_Silent_p.G776G NM_207517.2 NP_997400.2 P82987 ATL3_HUMAN ADAMTS-like 3 776 TSP type-1 6. proteinaceous extracellular matrix metallopeptidase activity|zinc ion binding NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4) 130 BRCA - Breast invasive adenocarcinoma(143;0.211) GGACTTGTGGCGGGGGAACTC 0.537000 3 29 0 0 1 0 0 COL11A2 1302 broad.mit.edu 37 6 33134291 33134291 + Splice_Site SNP G G C TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr6:33134291G>C ENST00000341947.2 - 60 4618 c.4392_splice c.e60+1 p.P1464_splice COL11A2_ENST00000477772.1_Intron|COL11A2_ENST00000374712.1_Splice_Site_p.P1383_splice|COL11A2_ENST00000374713.1_Splice_Site_p.P1417_splice|COL11A2_ENST00000395197.1_Splice_Site_p.P1404_splice|COL11A2_ENST00000361917.1_Splice_Site_p.P1357_splice|COL11A2_ENST00000357486.1_Splice_Site_p.P1443_splice|COL11A2_ENST00000374714.1_Splice_Site_p.P1438_splice|COL11A2_ENST00000374708.4_Splice_Site_p.P1378_splice NM_080680.2 NP_542411.2 P13942 COBA2_HUMAN collagen, type XI, alpha 2 1464 Triple-helical region. cartilage development|cell adhesion|collagen fibril organization|sensory perception of sound|soft palate development collagen type XI extracellular matrix structural constituent conferring tensile strength|protein binding, bridging biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6) 68 AGTACTCACGGGGAGGCCGGG 0.612000 3 42 0 0 1 0 0 ING1 3621 broad.mit.edu 37 13 111366587 111366587 + Missense_Mutation SNP C C G TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr13:111366587C>G ENST00000333219.7 + 1 963 c.91C>G c.(91-93)Cag>Gag p.Q31E ING1_ENST00000375775.3_Intron|ING1_ENST00000338450.7_Intron NM_001267728.1|NM_198219.2 NP_001254657.1|NP_937862.1 Q9UK53 ING1_HUMAN inhibitor of growth family, member 1 0 cell cycle|negative regulation of cell growth|negative regulation of cell proliferation nucleus zinc ion binding endometrium(4)|large_intestine(6)|lung(1)|ovary(1) 12 all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148) BRCA - Breast invasive adenocarcinoma(86;0.188) TTTCGACTTGCAGAGAAATGT 0.627000 12 34 0 0 1 0 0 GCKR 2646 broad.mit.edu 37 2 27728649 27728649 + Missense_Mutation SNP C C G TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr2:27728649C>G ENST00000264717.2 + 10 878 c.815C>G c.(814-816)aCc>aGc p.T272S GCKR_ENST00000424318.2_Missense_Mutation_p.T82S NM_001486.3 NP_001477.2 Q14397 GCKR_HUMAN glucokinase (hexokinase 4) regulator 272 SIS 1. carbohydrate metabolic process|glucose transport|negative regulation of glucokinase activity|positive regulation of gene expression|protein import into nucleus, translocation|regulation of glucose transport|response to fructose stimulus|transmembrane transport|triglyceride homeostasis|urate metabolic process cytosol|nucleoplasm fructose-6-phosphate binding|protein binding breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(2) 29 Acute lymphoblastic leukemia(172;0.155) CTGCTGGAAACCCTGTTATTA 0.542000 5 65 0 0 1 0 0 PHB 5245 broad.mit.edu 37 17 47486440 47486440 + Silent SNP G G A TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr17:47486440G>A ENST00000300408.3 - 5 546 c.474C>T c.(472-474)gcC>gcT p.A158A RP11-81K2.1_ENST00000576461.1_Intron|PHB_ENST00000511832.1_Intron|PHB_ENST00000508009.1_5'UTR NM_002634.2 NP_002625.1 P35232 PHB_HUMAN prohibitin 158 cellular response to interleukin-6|DNA replication|glucocorticoid receptor signaling pathway|histone deacetylation|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of transcription by competitive promoter binding|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|progesterone receptor signaling pathway|regulation of apoptosis integral to plasma membrane|mitochondrial inner membrane|nucleoplasm histone deacetylase binding|transcription regulatory region DNA binding endometrium(4)|large_intestine(2)|lung(4) 10 all_cancers(4;2.62e-14)|Breast(4;4.21e-29)|all_epithelial(4;6.9e-18) Epithelial(5;8.1e-06)|all cancers(6;7.71e-05) CAAAGGTGGCGGCTCGCTCTG 0.587000 11 41 0 0 1 0 0 KIAA1324 57535 broad.mit.edu 37 1 109656849 109656849 + Frame_Shift_Del DEL G G - TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr1:109656849delG ENST00000369939.3 + 1 227 c.44delG c.(43-45)agfs p.R15fs KIAA1324_ENST00000529753.1_Frame_Shift_Del_p.R15fs NM_020775.4 NP_065826.2 Q6UXG2 K1324_HUMAN KIAA1324 15 macroautophagy|positive regulation of vacuole organization|regulation of apoptosis integral to plasma membrane NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1) 34 all_epithelial(167;0.000102)|all_lung(203;0.000323)|Lung NSC(277;0.00063) Colorectal(144;0.0188)|Lung(183;0.0527)|COAD - Colon adenocarcinoma(174;0.14)|Epithelial(280;0.21)|all cancers(265;0.249) GCCAGAGTCAGGGGAAGAACT 0.662 2 4 --- --- --- --- PMS2CL 441194 broad.mit.edu 37 7 6775132 6775133 + RNA INS - - T rs72390141 TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr7:6775132_6775133insT ENST00000486256.1 + 0 833 NR_002217.1 GGTCATGTAAGTTTTTTTTTTT 0.401 3 6 --- --- --- --- PLEC 5339 broad.mit.edu 37 8 145000031 145000031 + Frame_Shift_Del DEL C C - TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr8:145000031delC ENST00000322810.4 - 31 4646 c.4477delG c.(4477-4479)cafs p.A1493fs PLEC_ENST00000436759.2_Frame_Shift_Del_p.A1383fs|PLEC_ENST00000345136.3_Frame_Shift_Del_p.A1356fs|PLEC_ENST00000356346.3_Frame_Shift_Del_p.A1342fs|PLEC_ENST00000527096.1_Frame_Shift_Del_p.A1379fs|PLEC_ENST00000357649.2_Frame_Shift_Del_p.A1360fs|PLEC_ENST00000398774.2_Frame_Shift_Del_p.A1324fs|PLEC_ENST00000354589.3_Frame_Shift_Del_p.A1356fs|PLEC_ENST00000354958.2_Frame_Shift_Del_p.A1334fs NM_201380.2 NP_958782.1 Q15149 PLEC_HUMAN plectin 1493 Central fibrous rod domain. cellular component disassembly involved in apoptosis|hemidesmosome assembly cytosol|focal adhesion|hemidesmosome|intermediate filament cytoskeleton|sarcolemma actin binding|structural constituent of muscle NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10) 137 CGCTCCTCTGCCCGCTGCTGC 0.701 2 4 --- --- --- --- PHOSPHO1 162466 broad.mit.edu 37 17 47302390 47302392 + In_Frame_Del DEL AGG AGG - TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr17:47302390_47302392delAGG ENST00000413580.1 - 3 512_514 c.95_97delCCT c.(94-99)tgc>t p.SC32del PHOSPHO1_ENST00000310544.4_Intron|PHOSPHO1_ENST00000514112.1_In_Frame_Del_p.SC32del NM_001143804.1|NM_178500.3 NP_001137276.1|NP_848595.1 Q8TCT1 PHOP1_HUMAN phosphatase, orphan 1 0 regulation of bone mineralization metal ion binding|phosphoethanolamine/phosphocholine phosphatase activity Epithelial(5;8.1e-06)|all cancers(6;7.71e-05) Choline(DB00122) ggagagcagcaggaggaggagga 0.700 3 5 --- --- --- --- CTD-2369P2.5 0 broad.mit.edu 37 19 10377498 10377498 + RNA DEL T T - TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chr19:10377498delT ENST00000592893.1 - 0 141 TCCATAGCCCTTTTTTTTTCC 0.428 3 6 --- --- --- --- KANTR 102723508 broad.mit.edu 37 X 53142506 53142507 + RNA INS - - A rs146094031 TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chrX:53142506_53142507insA ENST00000604849.1 + 0 96 AAAACACACACACAAAAAAAAA 0.356 3 4 --- --- --- --- NRK 203447 broad.mit.edu 37 X 105149314 105149314 + Frame_Shift_Del DEL C C - TCGA-WB-A80K-01A-11D-A35I-08 TCGA-WB-A80K-10A-01D-A35G-08 Untested Somatic Phase_I WXS none Illumina GAIIx 8a1af203-5d3f-48c4-88bd-be808fe0f6f8 731b0a29-9ad3-4daf-98c1-7cf7ba584796 g.chrX:105149314delC ENST00000428173.2 + 10 1126 c.823delC c.(823-825)ccfs p.P275fs NRK_ENST00000243300.9_Frame_Shift_Del_p.P275fs Q7Z2Y5 NRK_HUMAN Nik related kinase 275 Protein kinase. ATP binding|protein serine/threonine kinase activity|small GTPase regulator activity breast(8)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(14)|lung(36)|ovary(3)|prostate(1)|skin(2) 76 GGAATCTGCTCCCACAGTCAA 0.368 HNSCC(51;0.14) 2 4 --- --- --- ---