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 C12orf71 728858 broad.mit.edu 37 12 27234398 27234398 + Missense_Mutation SNP C C A TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr12:27234398C>A ENST00000429849.2 - 2 549 c.519G>T c.(517-519)atG>atT p.M173I NM_001080406.1 NP_001073875.1 A8MTZ7 CL071_HUMAN chromosome 12 open reading frame 71 173 endometrium(2)|large_intestine(1)|lung(4)|skin(1) 8 CCTGGCTTATCATCTGCCATG 0.463000 38 61 4.92203e-23 5.20599e-23 1 1 0 TP53 7157 broad.mit.edu 37 17 7578542 7578542 + Missense_Mutation SNP G G C TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr17:7578542G>C ENST00000420246.2 - 5 520 c.388C>G c.(388-390)Ctc>Gtc p.L130V TP53_ENST00000445888.2_Missense_Mutation_p.L130V|TP53_ENST00000455263.2_Missense_Mutation_p.L130V|TP53_ENST00000269305.4_Missense_Mutation_p.L130V|TP53_ENST00000413465.2_Missense_Mutation_p.L130V|TP53_ENST00000359597.4_Missense_Mutation_p.L130V NM_001126114.2|NM_001276696.1 NP_001119586.1|NP_001263625.1 P04637 P53_HUMAN tumor protein p53 130 Interaction with AXIN1 (By similarity).|Interaction with HIPK1 (By similarity).|Required for interaction with FBXO42. L -> F (in sporadic cancers; somatic mutation).|L -> H (in sporadic cancers; somatic mutation).|L -> I (in a sporadic cancer; somatic mutation).|L -> P (in sporadic cancers; somatic mutation).|L -> R (in sporadic cancers; somatic mutation).|L -> V (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.L130F(16)|p.L130V(11)|p.0?(8)|p.Y126_K132delYSPALNK(6)|p.L37F(3)|p.Y126_N131delYSPALN(3)|p.L130fs*19(2)|p.Y126fs*11(1)|p.S127_Q136del10(1)|p.A129_L130insXX(1)|p.A129_N131delALN(1)|p.V73fs*9(1)|p.Y126fs*18(1)|p.L130fs*39(1)|p.L130fs*16(1)|p.A129_K132delALNK(1)|p.L130_M133delLNKM(1)|p.N131fs*27(1)|p.P13fs*18(1)|p.S127fs*36(1)|p.L130del(1)|p.L130fs*40(1)|p.L130fs*41(1) NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) ATCTTGTTGAGGGCAGGGGAG 0.552000 111 """Mis, N, F""" """breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types""" """breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types""" Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) 30 3 0 0 1 0 0 ARHGEF2 9181 broad.mit.edu 37 1 155931587 155931587 + Missense_Mutation SNP T T C TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr1:155931587T>C ENST00000368316.1 - 15 1719 c.1249A>G c.(1249-1251)Atc>Gtc p.I417V ARHGEF2_ENST00000368315.3_Missense_Mutation_p.I446V|ARHGEF2_ENST00000361247.4_Missense_Mutation_p.I445V|ARHGEF2_ENST00000313695.7_Missense_Mutation_p.I417V|ARHGEF2_ENST00000313667.4_Missense_Mutation_p.I444V Q92974 ARHG2_HUMAN Rho/Rac guanine nucleotide exchange factor (GEF) 2 445 DH. actin filament organization|apoptosis|cell division|cell morphogenesis|induction of apoptosis by extracellular signals|intracellular protein transport|mitosis|negative regulation of microtubule depolymerization|nerve growth factor receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|regulation of cell proliferation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol|Golgi apparatus|microtubule|ruffle membrane|spindle|tight junction microtubule binding|Rac GTPase binding|Rac guanyl-nucleotide exchange factor activity|zinc ion binding breast(4)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|skin(2) 40 Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195) CGGTTGTAGATCTCCTGCAGA 0.607000 43 48 0 0 1 0 0 IFI16 3428 broad.mit.edu 37 1 158988254 158988254 + Missense_Mutation SNP C C T TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr1:158988254C>T ENST00000295809.7 + 5 1040 c.785C>T c.(784-786)tCa>tTa p.S262L IFI16_ENST00000368131.4_Missense_Mutation_p.S262L|IFI16_ENST00000368132.3_Missense_Mutation_p.S262L|IFI16_ENST00000359709.3_Missense_Mutation_p.S206L|IFI16_ENST00000340979.6_Missense_Mutation_p.S262L|IFI16_ENST00000448393.2_Missense_Mutation_p.S262L|IFI16_ENST00000430894.2_Missense_Mutation_p.S210L Q16666 IF16_HUMAN interferon, gamma-inducible protein 16 262 HIN-200 1. cell proliferation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|monocyte differentiation|negative regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent cytoplasm|nuclear speck|nucleolus double-stranded DNA binding|protein binding cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 29 all_hematologic(112;0.0429) ATCATCATATCAGATTATTTG 0.368000 10 65 0 0 1 0 0 OR10G3 26533 broad.mit.edu 37 14 22038134 22038134 + Missense_Mutation SNP C C T rs142649226 byFrequency TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr14:22038134C>T ENST00000303532.1 - 1 741 c.742G>A c.(742-744)Gtg>Atg p.V248M NM_001005465.1 NP_001005465.1 Q8NGC4 O10G3_HUMAN olfactory receptor, family 10, subfamily G, member 3 248 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity p.V248M(1)|p.V248L(1) central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7) 15 all_cancers(95;0.000987) GBM - Glioblastoma multiforme(265;0.0139) ACGGTGACCACGGTTACATGG 0.577000 20 110 0 0 1 0 0 PTER 9317 broad.mit.edu 37 10 16553190 16553190 + Missense_Mutation SNP A A C TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr10:16553190A>C ENST00000378000.1 + 6 1231 c.985A>C c.(985-987)Ata>Cta p.I329L PTER_ENST00000535784.2_Missense_Mutation_p.I329L|PTER_ENST00000298942.3_Missense_Mutation_p.I329L|PTER_ENST00000423462.2_Missense_Mutation_p.I282L NM_001001484.2|NM_001261838.1|NM_030664.4 NP_001001484.1|NP_001248767.1|NP_109589.2 Q96BW5 PTER_HUMAN phosphotriesterase related 329 catabolic process hydrolase activity, acting on ester bonds|zinc ion binding endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(2) 15 GCTGAGAGGCATAACTGAGAA 0.383000 7 136 0 0 1 0 0 SCGB2A2 4250 broad.mit.edu 37 11 62037739 62037739 + Silent SNP C C T rs137975337 byFrequency TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr11:62037739C>T ENST00000525380.1 + 1 110 c.51C>T c.(49-51)taC>taT p.Y17Y SCGB2A2_ENST00000227918.2_Silent_p.Y17Y Q13296 SG2A2_HUMAN secretoglobin, family 2A, member 2 17 extracellular region steroid binding large_intestine(1)|lung(4)|ovary(1)|prostate(1) 7 AGCACTGCTACGCAGGTGAGT 0.592000 94 109 0 0 1 0 0 CROCCP2 0 broad.mit.edu 37 1 16946434 16946434 + RNA SNP C C T rs367060 TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr1:16946434C>T ENST00000412962.1 - 0 1085 CTCAGCCTTCCGCCGGGCCAG 0.672000 4 19 0 0 1 0 0 CYP2D7P1 0 broad.mit.edu 37 22 42537597 42537597 + RNA SNP A A G rs1800754 by1000genomes TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr22:42537597A>G ENST00000435101.1 - 0 108 CYP2D7P1_ENST00000358097.4_RNA|CYP2D7P1_ENST00000433992.1_RNA endometrium(1) 1 CAGCGTGGTCAAGGTGGTCAC 0.627000 4 32 0 0 1 0 0 CTD-3092A11.1 0 broad.mit.edu 37 15 30776907 30776907 + RNA SNP G G A TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr15:30776907G>A ENST00000564861.1 + 0 143 CGCTCAGAGCGGCTTTCTTTT 0.408000 2 2 0 0 1 0 0 MBD1 4152 broad.mit.edu 37 18 47796399 47796399 + Missense_Mutation SNP A A C TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr18:47796399A>C ENST00000339998.6 - 14 1773 c.1635T>G c.(1633-1635)atT>atG p.I545M MBD1_ENST00000269471.5_Intron|MBD1_ENST00000591416.1_3'UTR|MBD1_ENST00000590208.1_Intron|MBD1_ENST00000436910.1_Intron|MBD1_ENST00000424334.2_Intron|MBD1_ENST00000587605.1_Intron|MBD1_ENST00000382948.5_Intron|MBD1_ENST00000353909.3_Intron|MBD1_ENST00000349085.2_Intron|MBD1_ENST00000347968.3_Intron|MBD1_ENST00000588937.1_Intron|MBD1_ENST00000585672.1_Intron|MBD1_ENST00000269468.5_Intron|MBD1_ENST00000585595.1_Intron NM_001204142.1 NP_001191071.1 Q9UIS9 MBD1_HUMAN methyl-CpG binding domain protein 1 0 TRD. negative regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter chromosome|nuclear speck methyl-CpG binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2) 36 CAATCAAATAAATTTCATATA 0.378000 5 79 0 0 1 0 0 CCNJL 79616 broad.mit.edu 37 5 159707584 159707584 + Silent SNP G G A TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr5:159707584G>A ENST00000393977.3 - 3 513 c.228C>T c.(226-228)gtC>gtT p.V76V CCNJL_ENST00000257536.7_Silent_p.V76V|CCNJL_ENST00000505287.2_Silent_p.V121V|CCNJL_ENST00000519673.1_Silent_p.V76V|CCNJL_ENST00000377503.2_5'UTR|CCNJL_ENST00000541762.1_Silent_p.V75V NM_024565.5 NP_078841.3 Q8IV13 CCNJL_HUMAN cyclin J-like 76 Cyclin N-terminal. nucleus endometrium(2)|kidney(5)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1) 17 Renal(175;0.00196) Medulloblastoma(196;0.0354)|all_neural(177;0.116) Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) TGGAGGTGGTGACGTTGTAGC 0.622000 5 99 0 0 1 0 0 RP11-423O2.5 0 broad.mit.edu 37 1 142803543 142803543 + RNA SNP C C T TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr1:142803543C>T ENST00000423385.1 - 0 1422 TGTTGGAATTCCTGATGAATC 0.269000 5 102 0 0 1 0 0 RHOH 399 broad.mit.edu 37 4 40245505 40245505 + Missense_Mutation SNP G G A TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr4:40245505G>A ENST00000381799.4 + 3 1223 c.499G>A c.(499-501)Gtc>Atc p.V167I RHOH_ENST00000505618.1_Missense_Mutation_p.V167I NM_001278363.1|NM_001278365.1|NM_004310.3 NP_001265292.1|NP_001265294.1|NP_004301.1 Q15669 RHOH_HUMAN ras homolog family member H 167 negative regulation of I-kappaB kinase/NF-kappaB cascade|regulation of small GTPase mediated signal transduction|regulation of transcription, DNA-dependent|small GTPase mediated signal transduction|T cell differentiation cytosol|mitochondrion|plasma membrane GTP binding|GTPase inhibitor activity|kinase inhibitor activity|Rho GTPase binding kidney(1)|large_intestine(3)|lung(7)|ovary(1) 12 TGAGTGCGCCGTCCGAACTGC 0.542000 34 26 0 0 1 0 0 IL18R1 8809 broad.mit.edu 37 2 102984511 102984511 + Silent SNP T T A TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr2:102984511T>A ENST00000409599.1 + 4 641 c.285T>A c.(283-285)tcT>tcA p.S95S IL18R1_ENST00000233957.1_Silent_p.S95S|IL18R1_ENST00000334376.3_Silent_p.S95S Q13478 IL18R_HUMAN interleukin 18 receptor 1 95 Ig-like C2-type 1. innate immune response integral to membrane|plasma membrane interleukin-1 receptor activity breast(1)|endometrium(3)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1) 34 ACACAGGATCTTACTTTTTCC 0.403000 12 128 0 0 1 0 0 IDH1 3417 broad.mit.edu 37 2 209113113 209113113 + Missense_Mutation SNP G G A rs121913499 TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr2:209113113G>A ENST00000415913.1 - 4 775 c.394C>T c.(394-396)Cgt>Tgt p.R132C IDH1_ENST00000345146.2_Missense_Mutation_p.R132C|IDH1_ENST00000446179.1_Missense_Mutation_p.R132C O75874 IDHC_HUMAN isocitrate dehydrogenase 1 (NADP+), soluble 132 R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). 2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle cytosol|peroxisomal matrix isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity p.R132C(446)|p.R132G(125)|p.R132S(106)|p.G131_R132>VL(1)|p.R132V(1) NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1) 4887 Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136) TAAGCATGACGACCTATGATG 0.398000 Mis gliobastoma 40 47 0 0 1 0 0 SLC12A2 6558 broad.mit.edu 37 5 127449952 127449952 + Missense_Mutation SNP T T C TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr5:127449952T>C ENST00000262461.2 + 3 1114 c.925T>C c.(925-927)Tca>Cca p.S309P SLC12A2_ENST00000343225.4_Missense_Mutation_p.S309P NM_001046.2 NP_001037.1 P55011 S12A2_HUMAN solute carrier family 12 (sodium/potassium/chloride transporter), member 2 309 potassium ion transport|sodium ion transport|transepithelial ammonium transport|transepithelial chloride transport integral to plasma membrane|membrane fraction ammonia transmembrane transporter activity|sodium:potassium:chloride symporter activity breast(3)|endometrium(5)|kidney(5)|large_intestine(12)|lung(16)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 48 all_cancers(142;0.0972)|Prostate(80;0.151) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978) Bumetanide(DB00887)|Potassium Chloride(DB00761) CATTAGATTGTCATGGATTGT 0.373000 51 128 0 0 1 0 0 TMPRSS6 164656 broad.mit.edu 37 22 37469676 37469676 + Missense_Mutation SNP G G C TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr22:37469676G>C ENST00000381792.2 - 13 1591 c.1451C>G c.(1450-1452)gCc>gGc p.A484G TMPRSS6_ENST00000406856.1_Missense_Mutation_p.A484G|TMPRSS6_ENST00000346753.3_Missense_Mutation_p.A493G|TMPRSS6_ENST00000406725.1_Missense_Mutation_p.A484G Q8IU80 TMPS6_HUMAN transmembrane protease, serine 6 493 LDL-receptor class A 1. angiogenesis|extracellular matrix organization|fibrinolysis|intracellular signal transduction|proteolysis integral to membrane|intracellular|plasma membrane serine-type endopeptidase activity breast(5)|central_nervous_system(4)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3) 40 CTGGAATGTGGCTCTGCAAAC 0.587000 11 96 0 0 1 0 0 ICAM3 3385 broad.mit.edu 37 19 10445307 10445307 + Silent SNP A A G TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr19:10445307A>G ENST00000589261.1 - 5 1390 c.858T>C c.(856-858)aaT>aaC p.N286N ICAM3_ENST00000160262.5_Silent_p.N363N P32942 ICAM3_HUMAN intercellular adhesion molecule 3 363 Ig-like C2-type 3. cell-cell adhesion|regulation of immune response integral to plasma membrane integrin binding central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(2) 13 OV - Ovarian serous cystadenocarcinoma(20;6.13e-09)|Epithelial(33;9.69e-06)|all cancers(31;2.05e-05) TCTCGGTAGCATTTAGCTGAA 0.632000 35 55 0 0 1 0 0 ACAT2 39 broad.mit.edu 37 6 160199292 160199292 + Missense_Mutation SNP C C G TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr6:160199292C>G ENST00000367048.4 + 8 2763 c.1003C>G c.(1003-1005)Ctt>Gtt p.L335V ACAT2_ENST00000541436.1_Missense_Mutation_p.L364V|ACAT2_ENST00000472052.1_3'UTR NM_005891.2 NP_005882.2 Q9BWD1 THIC_HUMAN acetyl-CoA acetyltransferase 2 335 mitochondrion|nucleolus acetyl-CoA C-acetyltransferase activity|protein binding breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(1) 9 Breast(66;0.000776)|Ovarian(120;0.0303) OV - Ovarian serous cystadenocarcinoma(65;1.51e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06) AGTTAAAGAACTTGGATTAAA 0.388000 13 21 0 0 1 0 0 SLC28A2 9153 broad.mit.edu 37 15 45561537 45561537 + Splice_Site SNP T T C TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr15:45561537T>C ENST00000347644.3 + 14 1435 c.1368_splice c.e14-1 p.V457_splice CTD-2651B20.3_ENST00000560344.1_RNA|CTD-2651B20.3_ENST00000561404.1_RNA NM_004212.3 NP_004203.2 O43868 S28A2_HUMAN solute carrier family 28 (concentrative nucleoside transporter), member 2 457 nucleobase, nucleoside and nucleotide metabolic process integral to plasma membrane|membrane fraction nucleoside binding|nucleoside:sodium symporter activity|purine nucleoside transmembrane transporter activity NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(4)|skin(1) 26 all_cancers(109;8.53e-07)|all_epithelial(112;1.39e-05)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417) all cancers(107;3.77e-16)|GBM - Glioblastoma multiforme(94;2.71e-06) TTCACTCAGGTCATCTGCTCC 0.478000 32 112 0 0 1 0 0 MYO1F 4542 broad.mit.edu 37 19 8620581 8620581 + Missense_Mutation SNP C C T TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr19:8620581C>T ENST00000338257.8 - 2 370 c.103G>A c.(103-105)Gcc>Acc p.A35T NM_012335.3 NP_036467.2 O00160 MYO1F_HUMAN myosin IF 35 Myosin head-like. unconventional myosin complex actin binding|ATP binding|calmodulin binding|motor activity breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(7)|lung(13)|ovary(3)|prostate(3)|skin(3)|urinary_tract(1) 42 CGGAGGTTGGCGGCAATGGCG 0.617000 26 61 0 0 1 0 0 SLC6A3 6531 broad.mit.edu 37 5 1422122 1422122 + Missense_Mutation SNP C C T rs138948519 TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr5:1422122C>T ENST00000270349.9 - 5 788 c.661G>A c.(661-663)Gtg>Atg p.V221M SLC6A3_ENST00000453492.2_Missense_Mutation_p.V221M NM_001044.4 NP_001035.1 Q01959 SC6A3_HUMAN solute carrier family 6 (neurotransmitter transporter), member 3 221 cell death|neurotransmitter biosynthetic process axon|cytoplasm|integral to plasma membrane|neuronal cell body p.V221M(1) breast(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(19)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1) 38 OV - Ovarian serous cystadenocarcinoma(19;0.00928)|all cancers(22;0.0262) Amphetamine(DB00182)|Benztropine(DB00245)|Bupropion(DB01156)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dextroamphetamine(DB01576)|Diethylpropion(DB00937)|Duloxetine(DB00476)|Fencamfamine(DB01463)|Mazindol(DB00579)|Methylphenidate(DB00422)|Modafinil(DB00745)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Procaine(DB00721) AGGTGCAGCACGCCACGTCTG 0.662000 7 86 0 0 1 0 0 EID2B 126272 broad.mit.edu 37 19 40023429 40023429 + Missense_Mutation SNP G G C TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr19:40023429G>C ENST00000326282.4 - 1 65 c.14C>G c.(13-15)aCt>aGt p.T5S CTB-60E11.9_ENST00000594676.1_RNA|EID2B_ENST00000601837.1_5'UTR NM_152361.1 NP_689574.1 Q96D98 EID2B_HUMAN EP300 interacting inhibitor of differentiation 2B 5 cell differentiation|muscle organ development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus endometrium(1)|lung(1)|urinary_tract(1) 3 all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159) Epithelial(26;8.61e-26)|all cancers(26;2.76e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657) CAACAGCCCAGTCGGCTCCGC 0.647000 OREG0025463 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 10 19 0 0 1 0 0 IPO9 55705 broad.mit.edu 37 1 201817721 201817721 + Splice_Site SNP A A G TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr1:201817721A>G ENST00000361565.4 + 4 582 c.514_splice c.e4+1 p.T171_splice IPO9_ENST00000464348.1_3'UTR NM_018085.4 NP_060555.2 Q96P70 IPO9_HUMAN importin 9 171 protein import into nucleus cytoplasm|nucleus histone binding|protein transporter activity cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1) 38 GTGTGCTGACAGGTACCAGAA 0.512000 19 25 0 0 1 0 0 BMP6 654 broad.mit.edu 37 6 7727731 7727731 + Silent SNP G G A TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr6:7727731G>A ENST00000283147.6 + 1 702 c.543G>A c.(541-543)ccG>ccA p.P181P NM_001718.4 NP_001709.1 P22004 BMP6_HUMAN bone morphogenetic protein 6 181 BMP signaling pathway|cartilage development|growth|immune response|positive regulation of aldosterone biosynthetic process|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of transcription from RNA polymerase II promoter|SMAD protein signal transduction extracellular space BMP receptor binding|cytokine activity|growth factor activity|protein heterodimerization activity breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(6)|ovary(1)|prostate(1) 23 Ovarian(93;0.0721) CCGCGCACCCGCTCAACCGCA 0.741000 3 13 0 0 1 0 0 OR51B2 79345 broad.mit.edu 37 11 5345181 5345181 + Missense_Mutation SNP A A G TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr11:5345181A>G ENST00000328813.2 - 1 401 c.347T>C c.(346-348)aTg>aCg p.M116T HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron NM_033180.4 NP_149420.4 Q9Y5P1 O51B2_HUMAN olfactory receptor, family 51, subfamily B, member 2 116 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity NS(1)|biliary_tract(1)|central_nervous_system(1)|large_intestine(6)|lung(21)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1) 35 Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212) Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135) ATCATATGCCATTGCCAGGAG 0.458000 7 85 0 0 1 0 0 RRN3P2 0 broad.mit.edu 37 16 29110458 29110458 + RNA SNP T T C rs151074589 by1000genomes TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr16:29110458T>C ENST00000564580.1 + 0 1131 p.W375R(25) GAATTTTGAGTGGATAGTGAT 0.328000 4 57 0 0 1 0 0 CROCCP2 0 broad.mit.edu 37 1 16946438 16946438 + RNA SNP G G A rs28392876 by1000genomes TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr1:16946438G>A ENST00000412962.1 - 0 1081 GCCTTCCGCCGGGCCAGCAGC 0.672000 4 15 0 0 1 0 0 ABCA12 26154 broad.mit.edu 37 2 215843555 215843555 + Silent SNP G G A TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr2:215843555G>A ENST00000272895.7 - 32 5169 c.4950C>T c.(4948-4950)taC>taT p.Y1650Y ABCA12_ENST00000389661.4_Silent_p.Y1332Y NM_173076.2 NP_775099.2 Q86UK0 ABCAC_HUMAN ATP-binding cassette, sub-family A (ABC1), member 12 1650 cellular homeostasis|lipid transport integral to membrane ATP binding|ATPase activity NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1) 139 Renal(323;0.127) Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011) CTGAAATGCCGTAGCACCCGA 0.458000 7 135 0 0 1 0 0 SLCO2A1 6578 broad.mit.edu 37 3 133654661 133654661 + Nonsense_Mutation SNP G G A TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr3:133654661G>A ENST00000310926.4 - 13 2044 c.1771C>T c.(1771-1773)Cga>Tga p.R591* SLCO2A1_ENST00000493729.1_Nonsense_Mutation_p.R515* NM_005630.2 NP_005621.2 Q92959 SO2A1_HUMAN solute carrier organic anion transporter family, member 2A1 591 sodium-independent organic anion transport integral to plasma membrane|membrane fraction prostaglandin transmembrane transporter activity|protein binding breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(2) 30 CAGGCCCCTCGCCTCCCCAAG 0.602000 4 28 0 0 1 0 0 FBXO33 254170 broad.mit.edu 37 14 39870639 39870639 + Silent SNP G G A rs144987416 TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr14:39870639G>A ENST00000298097.7 - 3 1474 c.1137C>T c.(1135-1137)atC>atT p.I379I FBXO33_ENST00000554190.1_Intron NM_203301.3 NP_976046.1 Q7Z6M2 FBX33_HUMAN F-box protein 33 379 endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|urinary_tract(1) 9 Hepatocellular(127;0.213) LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00121)|Epithelial(34;0.169) GBM - Glioblastoma multiforme(112;0.0425) CTTCACTCTTGATATCAAAAG 0.398000 43 53 0 0 1 0 0 KIAA0556 23247 broad.mit.edu 37 16 27640072 27640072 + Silent SNP T T C TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr16:27640072T>C ENST00000261588.4 + 4 250 c.231T>C c.(229-231)aaT>aaC p.N77N NM_015202.2 NP_056017.2 O60303 K0556_HUMAN KIAA0556 77 breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3) 76 ACGGTGCCAATTCGGAGCTGA 0.522000 43 142 0 0 1 0 0 ATP13A5 344905 broad.mit.edu 37 3 193081122 193081122 + Missense_Mutation SNP G G T rs12637558 byFrequency TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr3:193081122G>T ENST00000342358.4 - 3 404 c.287C>A c.(286-288)tCc>tAc p.S96Y NM_198505.2 NP_940907.2 Q4VNC0 AT135_HUMAN ATPase type 13A5 96 S -> Y (in dbSNP:rs12637558). ATP biosynthetic process|cation transport integral to membrane ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding p.S96F(1)|p.S96Y(1) NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 76 all_cancers(143;1.08e-08)|Ovarian(172;0.0386) OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06) GBM - Glioblastoma multiforme(46;0.000307) CTTCAGTGTGGATAAGTAGAG 0.398000 5 60 0.014758 0.0150313 1 1 0 STK31 56164 broad.mit.edu 37 7 23871943 23871943 + Nonsense_Mutation SNP T T A TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr7:23871943T>A ENST00000354639.3 + 24 3413 c.2949T>A c.(2947-2949)tgT>tgA p.C983* STK31_ENST00000405627.3_3'UTR|STK31_ENST00000355870.3_Nonsense_Mutation_p.C1006*|STK31_ENST00000428484.1_Nonsense_Mutation_p.C983*|STK31_ENST00000433467.2_Nonsense_Mutation_p.C983* NM_001260504.1|NM_032944.3 NP_001247433.1|NP_116562.2 Q9BXU1 STK31_HUMAN serine/threonine kinase 31 1006 Protein kinase. ATP binding|nucleic acid binding|protein serine/threonine kinase activity breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 67 TGGATAAATGTATGGAGAAGA 0.333000 55 50 0 0 1 0 0 FLG 2312 broad.mit.edu 37 1 152284999 152284999 + Missense_Mutation SNP C C T rs142483068 byFrequency TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr1:152284999C>T ENST00000368799.1 - 3 2398 c.2363G>A c.(2362-2364)cGa>cAa p.R788Q FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA NM_002016.1 NP_002007.1 P20930 FILA_HUMAN filaggrin 788 Ser-rich. keratinocyte differentiation cytoplasmic membrane-bounded vesicle|intermediate filament calcium ion binding|structural molecule activity autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12) 424 Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127) LUSC - Lung squamous cell carcinoma(543;0.206) CCCTGAACGTCGAGACCTTTC 0.567000 Ichthyosis 147 385 0 0 1 0 0 C5orf34 375444 broad.mit.edu 37 5 43488036 43488036 + Silent SNP T T C TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr5:43488036T>C ENST00000306862.2 - 12 2070 c.1695A>G c.(1693-1695)gaA>gaG p.E565E RP11-159F24.3_ENST00000505645.1_RNA NM_198566.2 NP_940968.1 Q96MH7 CE034_HUMAN chromosome 5 open reading frame 34 565 breast(2)|endometrium(2)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|stomach(2) 21 Lung NSC(6;2.07e-05) TCTTTTCAAGTTCAGAAGCAA 0.318000 3 15 0 0 1 0 0 TCEB3 6924 broad.mit.edu 37 1 24077560 24077561 + Frame_Shift_Del DEL AA AA - TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr1:24077560_24077561delAA ENST00000418390.2 + 4 814_815 c.543_544delAA c.(541-546)agagfs p.RK181fs NM_003198.2 NP_003189.2 Q14241 ELOA1_HUMAN transcription elongation factor B (SIII), polypeptide 3 (110kDa, elongin A) 181 positive regulation of viral transcription|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|viral reproduction integral to membrane DNA binding breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1) 19 Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.42e-24)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;4.74e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|KIRC - Kidney renal clear cell carcinoma(1967;0.00334)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187) GAGATGAGAGAAAGAGGTGTCA 0.480 50 121 --- --- --- --- GBP2 2634 broad.mit.edu 37 1 89578261 89578263 + In_Frame_Del DEL TCT TCT - rs142287187 TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr1:89578261_89578263delTCT ENST00000370466.3 - 8 1522_1524 c.1254_1256delAGA c.(1252-1257)gat>ga p.ED418del GBP2_ENST00000463660.1_5'UTR NM_004120.3 NP_004111.2 P32456 GBP2_HUMAN guanylate binding protein 2, interferon-inducible 418 interferon-gamma-mediated signaling pathway|type I interferon-mediated signaling pathway plasma membrane GTP binding|GTPase activity p.E418delE(1) endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(1) 20 Lung NSC(277;0.0908) all cancers(265;0.0151)|Epithelial(280;0.0284) CTGCTTGACATCTTCTTCTAAAG 0.438 40 192 --- --- --- --- GBP7 388646 broad.mit.edu 37 1 89615082 89615083 + Frame_Shift_Del DEL GT GT - TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr1:89615082_89615083delGT ENST00000294671.2 - 7 1182_1183 c.1044_1045delAC c.(1042-1047)actcfs p.TL348fs NM_207398.2 NP_997281.2 Q8N8V2 GBP7_HUMAN guanylate binding protein 7 348 integral to membrane GTP binding|GTPase activity NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 27 Lung NSC(277;0.0908) all cancers(265;0.00835)|Epithelial(280;0.0322) AGCTCCTGGAGTGTGTCTGTGG 0.535 11 147 --- --- --- --- UXS1 80146 broad.mit.edu 37 2 106710502 106710505 + Frame_Shift_Del DEL CTTT CTTT - TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr2:106710502_106710505delCTTT ENST00000283148.7 - 15 1352_1355 c.1255_1258delAAAG c.(1255-1260)gafs p.KG419fs UXS1_ENST00000409032.1_Frame_Shift_Del_p.KG246fs|UXS1_ENST00000540130.1_Frame_Shift_Del_p.KG357fs|UXS1_ENST00000409501.3_Frame_Shift_Del_p.KG414fs NM_001253875.1|NM_025076.4 NP_001240804.1|NP_079352.2 Q8NBZ7 UXS1_HUMAN UDP-glucuronate decarboxylase 1 414 cellular metabolic process Golgi cisterna membrane|integral to membrane coenzyme binding|UDP-glucuronate decarboxylase activity cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2) 17 CGAGTCCGTCCTTTCTTTATTCTG 0.412 35 32 --- --- --- --- CCNYL1 151195 broad.mit.edu 37 2 208605430 208605433 + Splice_Site DEL AGTA AGTA - TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr2:208605430_208605433delAGTA ENST00000295414.3 + 6 730 c.519_splice c.e6+1 p.173_splice CCNYL1_ENST00000339882.5_Intron|CCNYL1_ENST00000392209.3_Splice_Site_p.103_splice Q8N7R7 CCYL1_HUMAN cyclin Y-like 1 173 Cyclin N-terminal. regulation of cyclin-dependent protein kinase activity protein kinase binding endometrium(1)|large_intestine(1)|lung(3) 5 LUSC - Lung squamous cell carcinoma(261;0.0731)|Epithelial(149;0.139)|Lung(261;0.14) ATCCACTTACAGTAAGTGTCACTT 0.289 7 37 --- --- --- --- SEC22A 26984 broad.mit.edu 37 3 122944084 122944085 + Frame_Shift_Ins INS - - CCGATGGAGT TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr3:122944084_122944085insCCGATGGAGT ENST00000309934.4 + 3 1377_1378 c.481_482insCCGATGGAGT c.(481-483)caafs p.Q161fs SEC22A_ENST00000477063.1_3'UTR|SEC22A_ENST00000481965.2_Intron|SEC22A_ENST00000492595.1_Frame_Shift_Ins_p.Q161fs NM_012430.4 NP_036562.2 Q96IW7 SC22A_HUMAN SEC22 vesicle trafficking protein homolog A (S. cerevisiae) 161 ER to Golgi vesicle-mediated transport|protein transport endoplasmic reticulum membrane|integral to membrane transporter activity NS(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1) 10 GBM - Glioblastoma multiforme(114;0.0548) ACTGGGGTCAGCCAATGGAGTC 0.396 18 164 --- --- --- --- ZXDC 79364 broad.mit.edu 37 3 126191130 126191133 + Frame_Shift_Del DEL ATAA ATAA - TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr3:126191130_126191133delATAA ENST00000389709.3 - 2 976_979 c.923_926delTTAT c.(922-927)tcfs p.FI308fs ZXDC_ENST00000336332.5_Frame_Shift_Del_p.FI308fs NM_025112.4 NP_079388.3 Q2QGD7 ZXDC_HUMAN ZXD family zinc finger C 308 positive regulation of transcription, DNA-dependent nucleus C2H2 zinc finger domain binding|identical protein binding|LRR domain binding|nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(1) 17 GBM - Glioblastoma multiforme(114;0.155) ACTCACTGTGATAAATGTCTTCTC 0.475 44 77 --- --- --- --- RP11-680B3.2 0 broad.mit.edu 37 3 148582960 148582960 + RNA DEL A A - rs143382113 TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr3:148582960delA ENST00000488190.1 - 0 304 CTCCAGCTGGAAAAAAAAAAC 0.438 3 6 --- --- --- --- YTHDC1 91746 broad.mit.edu 37 4 69203308 69203310 + In_Frame_Del DEL AGG AGG - TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr4:69203308_69203310delAGG ENST00000344157.4 - 3 774_776 c.439_441delCCT c.(439-441)del p.P147del YTHDC1_ENST00000355665.3_In_Frame_Del_p.P147del|YTHDC1_ENST00000579690.1_In_Frame_Del_p.P147del NM_001031732.2 NP_001026902.1 Q96MU7 YTDC1_HUMAN YTH domain containing 1 147 NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2) 30 CATCTGGCGTAGGAGATTTGGCC 0.404 21 37 --- --- --- --- ANK2 287 broad.mit.edu 37 4 114277079 114277080 + Frame_Shift_Del DEL CT CT - TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr4:114277079_114277080delCT ENST00000357077.4 + 38 7358_7359 c.7305_7306delCT c.(7303-7308)gactfs p.DS2435fs ANK2_ENST00000510275.2_Intron|ANK2_ENST00000264366.6_Frame_Shift_Del_p.DS2402fs|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000506722.1_Intron NM_001148.4 NP_001139.3 Q01484 ANK2_HUMAN ankyrin 2, neuronal 2402 axon guidance|signal transduction apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere protein binding NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10) 248 Ovarian(17;0.0448)|Hepatocellular(203;0.218) OV - Ovarian serous cystadenocarcinoma(123;4.92e-05) GCCACAAAGACTCTCTGGAAGC 0.510 45 66 --- --- --- --- RELL2 285613 broad.mit.edu 37 5 141018562 141018564 + In_Frame_Del DEL AGG AGG - TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr5:141018562_141018564delAGG ENST00000297164.3 + 3 1491_1493 c.291_293delAGG c.(289-294)gaa>ga p.EG99del RELL2_ENST00000521367.1_In_Frame_Del_p.EG33del|RELL2_ENST00000518856.1_In_Frame_Del_p.EG33del|RELL2_ENST00000518025.1_Intron|RELL2_ENST00000444782.1_In_Frame_Del_p.EG99del NM_173828.4 NP_776189.3 Q8NC24 RELL2_HUMAN RELT-like 2 99 integral to membrane|plasma membrane large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1) 9 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) GGGACAGTGAAGGAGAAGGGACA 0.557 7 31 --- --- --- --- GEMIN5 25929 broad.mit.edu 37 5 154315435 154315438 + Frame_Shift_Del DEL AAGT AAGT - TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr5:154315435_154315438delAAGT ENST00000285873.7 - 3 547_550 c.472_475delACTT c.(472-477)gtfs p.TC158fs NM_001252156.1|NM_015465.4 NP_001239085.1|NP_056280.2 Q8TEQ6 GEMI5_HUMAN gem (nuclear organelle) associated protein 5 158 ncRNA metabolic process|protein complex assembly|spliceosomal snRNP assembly Cajal body|cytosol|spliceosomal complex protein binding|snRNA binding breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1) 38 Renal(175;0.00488) Medulloblastoma(196;0.0354)|all_neural(177;0.147) KIRC - Kidney renal clear cell carcinoma(527;0.00112) TGAGGTGAACAAGTAAGACAGAAA 0.353 7 90 --- --- --- --- STAG3L4 0 broad.mit.edu 37 7 66772495 66772495 + RNA DEL T T - TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr7:66772495delT ENST00000416602.2 + 0 362 NR_040586.1 Q8TBR4 STG34_HUMAN endometrium(2)|lung(5) 7 Lung NSC(55;0.0839)|all_lung(88;0.181) GCTTGATTCCTTTTTTTTTTT 0.423 3 4 --- --- --- --- PABPC1 26986 broad.mit.edu 37 8 101724994 101724995 + Frame_Shift_Ins INS - - A rs140822921 by1000genomes TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr8:101724994_101724995insA ENST00000318607.5 - 6 1889_1890 c.761_762insT c.(760-762)agafs p.R254fs PABPC1_ENST00000522387.1_Frame_Shift_Ins_p.R222fs|PABPC1_ENST00000519596.1_5'UTR|PABPC1_ENST00000519004.1_Frame_Shift_Ins_p.R209fs NM_002568.3 NP_002559.2 P11940 PABP1_HUMAN poly(A) binding protein, cytoplasmic 1 254 CSDE1-binding.|RRM 3. mRNA polyadenylation|mRNA stabilization|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|translation catalytic step 2 spliceosome|cytosol nucleotide binding|poly(A) RNA binding|protein C-terminus binding|translation activator activity breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1) 40 all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125) Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206) CATTGAGCTCCTTTCCGTTCAT 0.371 8 85 --- --- --- --- OR1J4 26219 broad.mit.edu 37 9 125281597 125281599 + In_Frame_Del DEL TTC TTC - TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr9:125281597_125281599delTTC ENST00000340750.1 + 1 178_180 c.178_180delTTC c.(178-180)del p.F62del NM_001004452.1 NP_001004452.1 Q8NGS1 OR1J4_HUMAN olfactory receptor, family 1, subfamily J, member 4 62 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity large_intestine(5)|lung(11)|skin(3)|upper_aerodigestive_tract(1) 20 CACCCCCATGTTCTTCTTCCTCA 0.498 133 175 --- --- --- --- ZDHHC5 25921 broad.mit.edu 37 11 57466855 57466857 + In_Frame_Del DEL AGA AGA - TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr11:57466855_57466857delAGA ENST00000287169.3 + 11 3309_3311 c.1947_1949delAGA c.(1945-1950)aca>ac p.TE649del ZDHHC5_ENST00000527985.1_In_Frame_Del_p.TE596del NM_015457.2 NP_056272.2 Q9C0B5 ZDHC5_HUMAN zinc finger, DHHC-type containing 5 649 integral to membrane acyltransferase activity|zinc ion binding endometrium(6)|kidney(3)|large_intestine(3)|lung(5)|skin(1) 18 TCTCTGAGACAGAAGAAGTGGCC 0.512 11 107 --- --- --- --- CALCOCO1 57658 broad.mit.edu 37 12 54110173 54110175 + In_Frame_Del DEL CTC CTC - TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr12:54110173_54110175delCTC ENST00000548263.1 - 8 922_924 c.874_876delGAG c.(874-876)del p.E292del CALCOCO1_ENST00000430117.2_Intron|CALCOCO1_ENST00000262059.4_In_Frame_Del_p.E292del|CALCOCO1_ENST00000550804.1_In_Frame_Del_p.E292del Q9P1Z2 CACO1_HUMAN calcium binding and coiled-coil domain 1 292 steroid hormone receptor signaling pathway|transcription, DNA-dependent|Wnt receptor signaling pathway cytoplasm armadillo repeat domain binding|beta-catenin binding|ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|sequence-specific DNA binding|transcription regulatory region DNA binding NS(2)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1) 28 AGTGATGGTTCTCCTGTTGTGCC 0.542 40 50 --- --- --- --- HERC2P9 0 broad.mit.edu 37 15 28913367 28913367 + RNA DEL T T - TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr15:28913367delT ENST00000528584.1 + 0 1224 NR_036443.1 TGAGTTCTCCTTTTTTTTTTT 0.308 4 7 --- --- --- --- SMARCA4 6597 broad.mit.edu 37 19 11106926 11106928 + In_Frame_Del DEL AGA AGA - TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chr19:11106926_11106928delAGA ENST00000358026.2 + 10 1915_1917 c.1631_1633delAGA c.(1630-1635)cag>c p.QK544del SMARCA4_ENST00000590574.1_In_Frame_Del_p.QK544del|SMARCA4_ENST00000541122.2_In_Frame_Del_p.QK544del|SMARCA4_ENST00000589677.1_In_Frame_Del_p.QK544del|SMARCA4_ENST00000450717.3_In_Frame_Del_p.QK544del|SMARCA4_ENST00000444061.3_In_Frame_Del_p.QK544del|SMARCA4_ENST00000413806.3_In_Frame_Del_p.QK544del|SMARCA4_ENST00000429416.3_In_Frame_Del_p.QK544del|SMARCA4_ENST00000344626.4_In_Frame_Del_p.QK544del NM_001128849.1 NP_001122321.1 P51532 SMCA4_HUMAN SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 544 chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity p.?(1) adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2) 163 all_lung(6;0.0512)|Lung NSC(9;0.0568) CTCATCGACCAGAAGAAGGACAA 0.576 """F, N, Mis""" NSCLC 42 160 --- --- --- --- ATRX 546 broad.mit.edu 37 X 76918950 76918951 + Frame_Shift_Del DEL CA CA - TCGA-HT-7855-01A-11D-2395-08 TCGA-HT-7855-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx 1bc9fea0-cb11-47c4-bfe6-a813ee66a3eb 0ba77c15-05f7-4769-8070-6a2a63a9f466 g.chrX:76918950_76918951delCA ENST00000373344.5 - 12 4254_4255 c.4040_4041delTG c.(4039-4041)gfs p.V1347fs ATRX_ENST00000395603.3_Frame_Shift_Del_p.V1309fs|ATRX_ENST00000480283.1_5'UTR NM_000489.3 NP_000480.2 P46100 ATRX_HUMAN alpha thalassemia/mental retardation syndrome X-linked 1347 DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent nuclear heterochromatin ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding p.?(1) bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2) 145 Phosphatidylserine(DB00144) CTCCGTCACTCACAGTCAATTT 0.361 """Mis, F, N""" """Pancreatic neuroendocrine tumors, paediatric GBM""" ATR-X (alpha thalassemia/mental retardation) syndrome 27 5 --- --- --- ---