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 MAGEC1 9947 broad.mit.edu 37 X 140995008 140995008 + Missense_Mutation SNP G G A TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chrX:140995008G>A ENST00000285879.4 + 4 2104 c.1818G>A c.(1816-1818)atG>atA p.M606I MAGEC1_ENST00000406005.2_Intron NM_005462.4 NP_005453.2 O60732 MAGC1_HUMAN melanoma antigen family C, 1 606 protein binding breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1) 127 Acute lymphoblastic leukemia(192;6.56e-05) AGGACTCCATGTCTCCTCTCT 0.572000 HNSCC(15;0.026) 5 218 0 0 0.014758 0 0 PGBD2 0 broad.mit.edu 37 1 249211207 249211207 + Missense_Mutation SNP G G T TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr1:249211207G>T ENST00000539153.1 + 4 670 c.415G>T c.(415-417)Gtg>Ttg p.V139L PGBD2_ENST00000462488.1_Intron|PGBD2_ENST00000355360.4_Intron|PGBD2_ENST00000329291.5_Missense_Mutation_p.V142L Q6P3X8 PGBD2_HUMAN piggyBac transposable element derived 2 142 NS(1)|endometrium(3)|lung(6)|ovary(1)|skin(3) 14 all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199) all_cancers(173;0.012) OV - Ovarian serous cystadenocarcinoma(106;0.00989) GCTGAGTCCCGTGGGCCTTTT 0.398000 13 35 1.99824e-07 2.37885e-07 0.033300 1 0 IRX2 153572 broad.mit.edu 37 5 2748624 2748624 + Missense_Mutation SNP C C A TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr5:2748624C>A ENST00000382611.6 - 3 1446 c.1198G>T c.(1198-1200)Gcg>Tcg p.A400S IRX2_ENST00000302057.5_Missense_Mutation_p.A400S NM_001134222.1 NP_001127694.1 Q9BZI1 IRX2_HUMAN iroquois homeobox 2 400 nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity breast(1)|central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2) 26 GBM - Glioblastoma multiforme(108;0.204) TGCAGCGCCGCGTTCAAGTTC 0.706000 40 78 5.73435e-26 7.35173e-26 0.048971 1 0 TXNDC2 0 broad.mit.edu 37 18 9887095 9887095 + Missense_Mutation SNP G G A TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr18:9887095G>A ENST00000306084.6 + 2 818 c.619G>A c.(619-621)Ggt>Agt p.G207S TXNDC2_ENST00000357775.4_Missense_Mutation_p.G140S|TXNDC2_ENST00000536353.2_Intron NM_001098529.1 NP_001091999.1 Q86VQ3 TXND2_HUMAN thioredoxin domain containing 2 (spermatozoa) 207 22 X 15 AA approximate tandem repeat of Q-P-K-X-G-D-I-P-K-S-[PS]-E-[KE]-X-I. cell differentiation|cell redox homeostasis|glycerol ether metabolic process|multicellular organismal development|spermatogenesis cytoplasm electron carrier activity|nutrient reservoir activity|protein disulfide oxidoreductase activity|thioredoxin-disulfide reductase activity NS(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(7)|urinary_tract(1) 31 GCCCAAAGAGGGTGACATCCC 0.567000 4 220 0 0 0.009096 0 0 NBPF10 100132406 broad.mit.edu 37 1 145295505 145295505 + Silent SNP G G C TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr1:145295505G>C ENST00000342960.5 + 2 293 c.258G>C c.(256-258)ctG>ctC p.L86L NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000369339.2_Intron|RP11-458D21.5_ENST00000468030.1_3'UTR NM_001039703.4 NP_001034792.4 A6NDV3 A6NDV3_HUMAN neuroblastoma breakpoint family, member 10 86 p.L86L(1) NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2) 73 all_hematologic(923;0.032) Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258) CAGAGCAGCTGAAGCAAGCTG 0.512000 5 239 0 0 0.093190 0 0 BAGE2 85319 broad.mit.edu 37 21 11039406 11039406 + RNA SNP T T C rs8134740 by1000genomes TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr21:11039406T>C ENST00000470054.1 - 0 797 B melanoma antigen family, member 2 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) TCATTAGAAATCTGTTTTTCC 0.299000 10 62 0 0 0.069234 0 0 CACNA1A 773 broad.mit.edu 37 19 13565980 13565980 + Missense_Mutation SNP C C T TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr19:13565980C>T ENST00000360228.5 - 2 339 c.340G>A c.(340-342)Gtc>Atc p.V114I CACNA1A_ENST00000573710.2_Missense_Mutation_p.V114I NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2 NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2 O00555 CAC1A_HUMAN calcium channel, voltage-dependent, P/Q type, alpha 1A subunit 114 cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion cytoplasm|nucleus syntaxin binding breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1) 42 OV - Ovarian serous cystadenocarcinoma(19;5.07e-21) Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230) AGTGCGAGGACGATGCAATTC 0.453000 64 185 0 0 0.048971 0 0 TTN 7273 broad.mit.edu 37 2 179402314 179402314 + Missense_Mutation SNP T T C TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr2:179402314T>C ENST00000589042.1 - 355 99844 c.99620A>G c.(99619-99621)tAt>tGt p.Y33207C TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.Y24142C|TTN_ENST00000342175.6_Missense_Mutation_p.Y24334C|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.Y24267C|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000591111.1_Missense_Mutation_p.Y31566C|TTN-AS1_ENST00000588804.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.Y30639C|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000585358.1_RNA NM_001267550.1 NP_001254479.1 Q8WZ42 TITIN_HUMAN titin 31566 ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26) 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) CACAGCTCCATAATATTTCTC 0.458000 3 37 0 0 0.009096 0 0 E2F3 1871 broad.mit.edu 37 6 20486987 20486987 + Missense_Mutation SNP G G T TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr6:20486987G>T ENST00000346618.3 + 5 1018 c.952G>T c.(952-954)Gtg>Ttg p.V318L E2F3_ENST00000535432.1_Missense_Mutation_p.V187L NM_001949.4 NP_001940.1 O00716 E2F3_HUMAN E2F transcription factor 3 318 Dimerization (Potential). G1 phase of mitotic cell cycle|G2 phase of mitotic cell cycle|transcription initiation from RNA polymerase II promoter transcription factor complex DNA binding|protein binding|sequence-specific DNA binding transcription factor activity central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(3) 7 all_cancers(95;0.154)|all_epithelial(95;0.0585)|Breast(50;0.146)|Ovarian(93;0.148) OV - Ovarian serous cystadenocarcinoma(7;0.0068)|all cancers(50;0.0148)|Epithelial(50;0.0562) TGTTATAGTTGTGAAAGCCCC 0.383000 11 39 3.27435e-08 4.09294e-08 0.020292 1 0 HYPK 25764 broad.mit.edu 37 15 44093364 44093364 + Missense_Mutation SNP A A G TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr15:44093364A>G ENST00000406925.1 + 3 4332 c.221A>G c.(220-222)gAg>gGg p.E74G SERF2_ENST00000600633.1_Missense_Mutation_p.E74G|HYPK_ENST00000458412.1_Intron|SERF2_ENST00000594896.1_Missense_Mutation_p.E120G|HYPK_ENST00000498605.1_3'UTR|HYPK_ENST00000442995.2_Missense_Mutation_p.E74G huntingtin interacting protein K all_cancers(109;3.26e-11)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.61e-06)|all_lung(180;1.5e-05)|Melanoma(134;0.0417) GBM - Glioblastoma multiforme(94;8.1e-07) AGGTCCCGGGAGCAGAAAGCC 0.493000 16 83 0 0 0.069288 0 0 AC024560.3 0 broad.mit.edu 37 3 197348646 197348646 + RNA SNP T T C rs138265355 by1000genomes TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr3:197348646T>C ENST00000418868.1 - 0 613 NR_003266.2 TGGGCCTGCCTGCCCTTTCCA 0.532000 4 112 0 0 0.029380 0 0 LRRC37A16P 0 broad.mit.edu 37 17 66126418 66126418 + RNA SNP A A G TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr17:66126418A>G ENST00000590019.1 - 0 343 CCTCAATGCTATTTTTAAATT 0.413000 3 178 0 0 0.004672 0 0 CD3D 915 broad.mit.edu 37 11 118209888 118209888 + Missense_Mutation SNP G G A TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr11:118209888G>A ENST00000300692.4 - 5 641 c.505C>T c.(505-507)Cgg>Tgg p.R169W CD3D_ENST00000392884.2_Missense_Mutation_p.R125W|CD3D_ENST00000529594.1_Missense_Mutation_p.R96W NM_000732.4 NP_000723.1 P04234 CD3D_HUMAN CD3d molecule, delta (CD3-TCR complex) 169 positive thymic T cell selection|T cell costimulation|T cell receptor signaling pathway cytoplasm|integral to membrane protein heterodimerization activity large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2) 9 all_hematologic(175;0.046) Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234) BRCA - Breast invasive adenocarcinoma(274;3.04e-05) CACTTGTTCCGAGCCCAGTTT 0.502000 31 112 0 0 0.069456 0 0 PITX2 5308 broad.mit.edu 37 4 111539506 111539506 + Nonstop_Mutation SNP A A T TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr4:111539506A>T ENST00000394595.3 - 4 778 c.523T>A c.(523-525)Taa>Aaa p.*175K PITX2_ENST00000394598.2_Missense_Mutation_p.N243K|PITX2_ENST00000306732.3_Missense_Mutation_p.N250K|PITX2_ENST00000354925.2_Missense_Mutation_p.N243K|PITX2_ENST00000355080.5_Missense_Mutation_p.N197K Q99697 PITX2_HUMAN paired-like homeodomain 2 0 determination of left/right symmetry|organ morphogenesis transcription factor complex sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding breast(1)|endometrium(3)|large_intestine(1)|lung(5) 10 Hepatocellular(203;0.217) OV - Ovarian serous cystadenocarcinoma(123;0.00222) TGTTCAAGTTATTCAGGCTGT 0.582000 28 68 0 0 0.030593 0 0 MT-ND1 4535 broad.mit.edu 37 MT 3898 3898 + Missense_Mutation SNP T T C TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chrM:3898T>C ENST00000361390.2 + 1 592 c.592T>C c.(592-594)Ttc>Ctc p.198_198insL mitochondrially encoded NADH dehydrogenase 1 breast(1)|endometrium(13)|kidney(17)|lung(2)|prostate(1) 34 ACCGAACCCCCTTCGACCTTG 0.502000 42 1 0 0 0.048971 0 0 ZIC2 7546 broad.mit.edu 37 13 100637729 100637729 + Silent SNP T T G TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr13:100637729T>G ENST00000376335.3 + 3 1685 c.1392T>G c.(1390-1392)gcT>gcG p.A464A NM_007129.3 NP_009060.2 O95409 ZIC2_HUMAN Zic family member 2 464 Poly-Ala. brain development|negative regulation of transcription, DNA-dependent|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|visual perception cytoplasm|nucleus chromatin DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding large_intestine(2)|liver(2)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 13 all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184) cggcggcggctgcggcggcgg 0.816000 3 33 0 0 0.004672 0 0 AGR2 10551 broad.mit.edu 37 7 16839390 16839390 + Missense_Mutation SNP T T C TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr7:16839390T>C ENST00000419304.2 - 5 460 c.308A>G c.(307-309)cAg>cGg p.Q103R AGR2_ENST00000401412.1_Missense_Mutation_p.Q103R|AGR2_ENST00000419572.2_Missense_Mutation_p.Q123R NM_006408.3 NP_006399.1 O95994 AGR2_HUMAN anterior gradient 2 103 mucus secretion endoplasmic reticulum|extracellular region protein binding endometrium(2)|lung(1)|prostate(1)|skin(2) 6 Lung NSC(10;0.0376)|all_lung(11;0.0855) UCEC - Uterine corpus endometrioid carcinoma (126;0.184) GAGGACAAACTGCTCTGCCAA 0.308000 6 18 0 0 0.038147 0 0 AGAP5 729092 broad.mit.edu 37 10 75451811 75451811 + Missense_Mutation SNP C C T TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr10:75451811C>T ENST00000443782.2 - 3 442 c.317G>A c.(316-318)tGt>tAt p.C106Y RP11-464F9.1_ENST00000399449.3_RNA|AGAP5_ENST00000374094.4_Missense_Mutation_p.C129Y A6NIR3 AGAP5_HUMAN ArfGAP with GTPase domain, ankyrin repeat and PH domain 5 129 regulation of ARF GTPase activity ARF GTPase activator activity|zinc ion binding p.C106Y(1) NS(1)|breast(1)|endometrium(3)|kidney(1)|lung(5)|skin(1) 12 ATGGTTTGTACAGTTGCTTCT 0.284000 3 5 0 0 0.014758 0 0 CDH11 1009 broad.mit.edu 37 16 64984728 64984728 + Silent SNP G G A TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr16:64984728G>A ENST00000394156.3 - 12 2289 c.1836C>T c.(1834-1836)aaC>aaT p.N612N CDH11_ENST00000268603.4_Silent_p.N612N|CDH11_ENST00000566827.1_Silent_p.N486N P55287 CAD11_HUMAN cadherin 11, type 2, OB-cadherin (osteoblast) 612 Cadherin 5. adherens junction organization|cell junction assembly|homophilic cell adhesion|ossification|skeletal system development integral to membrane|plasma membrane calcium ion binding|protein binding NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2) 88 Ovarian(137;0.0973) OV - Ovarian serous cystadenocarcinoma(108;0.205) TCAGGCCGGCGTTCAGAATGT 0.632000 T USP6 aneurysmal bone cysts TSP Lung(24;0.17) 27 61 0 0 0.050027 0 0 ECM2 1842 broad.mit.edu 37 9 95277148 95277148 + Missense_Mutation SNP C C A TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr9:95277148C>A ENST00000344604.5 - 4 968 c.819G>T c.(817-819)gaG>gaT p.E273D ECM2_ENST00000444490.2_Missense_Mutation_p.E251D|CENPP_ENST00000375587.3_Intron NM_001197295.1|NM_001393.3 NP_001184224.1|NP_001384.1 O94769 ECM2_HUMAN extracellular matrix protein 2, female organ and adipocyte specific 273 Poly-Glu. cell-matrix adhesion integrin binding breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 27 cctcctcatcctcctcctcct 0.607000 4 118 2.0095e-06 2.33663e-06 0.029380 1 0 RANBP9 10048 broad.mit.edu 37 6 13711709 13711709 + Missense_Mutation SNP G G T TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr6:13711709G>T ENST00000011619.3 - 1 87 c.29C>A c.(28-30)cCg>cAg p.P10Q NM_005493.2 NP_005484.2 Q96S59 RANB9_HUMAN RAN binding protein 9 10 Poly-Pro. axon guidance|microtubule nucleation|protein complex assembly cytosol|microtubule associated complex|nucleus Ran GTPase binding breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1) 16 Breast(50;0.00669)|Ovarian(93;0.0634) all_hematologic(90;0.117) Epithelial(50;0.223) ctgctgctgcggcggcggcgg 0.761000 3 35 0.00909568 0.00988661 0.009096 1 0 COL4A4 1286 broad.mit.edu 37 2 227875182 227875182 + Missense_Mutation SNP C C G TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr2:227875182C>G ENST00000396625.3 - 46 4576 c.4369G>C c.(4369-4371)Ggg>Cgg p.G1457R COL4A4_ENST00000329662.7_Missense_Mutation_p.G1454R NM_000092.4 NP_000083.3 P53420 CO4A4_HUMAN collagen, type IV, alpha 4 1457 Triple-helical region. axon guidance|glomerular basement membrane development basal lamina|collagen type IV extracellular matrix structural constituent|protein binding breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3) 98 Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242) Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181) GGGCCAAACCCTTTGGGCCCA 0.572000 6 21 0 0 0.029380 0 0 ZNF207 7756 broad.mit.edu 37 17 30687706 30687706 + Missense_Mutation SNP C C A TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr17:30687706C>A ENST00000394670.4 + 4 566 c.397C>A c.(397-399)Caa>Aaa p.Q133K ZNF207_ENST00000577908.1_Missense_Mutation_p.Q133K|ZNF207_ENST00000321233.6_Missense_Mutation_p.Q133K|RP11-227G15.3_ENST00000581915.1_RNA|ZNF207_ENST00000341711.6_Intron|ZNF207_ENST00000342555.6_Missense_Mutation_p.Q136K|ZNF207_ENST00000394673.2_Missense_Mutation_p.Q133K NM_001098507.1 NP_001091977.1 O43670 ZN207_HUMAN zinc finger protein 207 133 nucleus DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding breast(1)|endometrium(2)|kidney(2)|lung(3)|urinary_tract(2) 10 Breast(31;0.116)|Ovarian(249;0.182) BRCA - Breast invasive adenocarcinoma(9;0.239) ACAGCCTGTTCAACCTCAGCA 0.443000 4 61 0.014758 0.0157 0.014758 1 0 AP005901.1 0 broad.mit.edu 37 18 15323276 15323276 + RNA SNP A A T TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr18:15323276A>T ENST00000455308.2 - 0 572 NR_027417.1 ATCAACTGCAATTGCATTTGC 0.308000 5 9 0 0 0.058154 0 0 AC112229.4 0 broad.mit.edu 37 2 111144370 111144370 + RNA SNP T T C TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr2:111144370T>C ENST00000606848.1 - 0 1370 GGCAGCACCATAGTGGCGGCC 0.622000 3 8 0 0 0.009096 0 0 FAM182B 0 broad.mit.edu 37 20 25848614 25848614 + Translation_Start_Site SNP C C A rs144456407 by1000genomes TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr20:25848614C>A ENST00000376404.2 - 0 172 FAM182B_ENST00000478164.1_5'UTR lung(1) 1 ccgggcaggcctgaggctggg 0.667000 3 19 0.00909568 0.00988661 0.009096 1 0 RRN3P2 0 broad.mit.edu 37 16 29110458 29110458 + RNA SNP T T C rs151074589 by1000genomes TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr16:29110458T>C ENST00000564580.1 + 0 1131 p.W375R(25) GAATTTTGAGTGGATAGTGAT 0.328000 3 44 0 0 0.021553 0 0 PPP1R35 221908 broad.mit.edu 37 7 100033362 100033362 + Silent SNP G G C TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr7:100033362G>C ENST00000292330.2 - 3 670 c.480C>G c.(478-480)ctC>ctG p.L160L RP11-758P17.2_ENST00000492523.1_RNA|PPP1R35_ENST00000476185.1_Intron NM_145030.2 NP_659467.1 Q8TAP8 CG047_HUMAN protein phosphatase 1, regulatory subunit 35 160 GGTCCCGGAAGAGCCGCTTGG 0.721000 3 8 0 0 0.014758 0 0 BRAF 673 broad.mit.edu 37 7 140453136 140453136 + Missense_Mutation SNP A A T rs121913377 TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr7:140453136A>T ENST00000288602.6 - 15 1859 c.1799T>A c.(1798-1800)gTg>gAg p.V600E NM_004333.4 NP_004324.2 P15056 BRAF_HUMAN v-raf murine sarcoma viral oncogene homolog B 600 Protein kinase. V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis). activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission cytosol|nucleus|plasma membrane ATP binding|metal ion binding p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1) SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2) NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3) 27380 Melanoma(164;0.00956) Sorafenib(DB00398) TCGAGATTTCACTGTAGCTAG 0.368000 V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN) 61 """Mis, T, O""" """AKAP9, KIAA1549""" """melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma""" Cardio-facio-cutaneous syndrome Cardiofaciocutaneous syndrome 12 38 0 0 0.105934 0 0 AC024560.3 0 broad.mit.edu 37 3 197348739 197348739 + RNA SNP G G C TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr3:197348739G>C ENST00000418868.1 - 0 520 NR_003266.2 TAATTTTCTAGCTGTGAAAGA 0.398000 4 95 0 0 0.021553 0 0 FAM208B 54906 broad.mit.edu 37 10 5781833 5781833 + Missense_Mutation SNP A A C TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr10:5781833A>C ENST00000328090.5 + 13 2325 c.1700A>C c.(1699-1701)gAt>gCt p.D567A RP11-336A10.2_ENST00000411512.2_RNA NM_017782.4 NP_060252.4 Q5VWN6 CJ018_HUMAN family with sequence similarity 208, member B 567 CCACAAAATGATGTTTTGCTC 0.378000 21 43 0 0 0.108266 0 0 ITSN2 50618 broad.mit.edu 37 2 24550934 24550934 + Silent SNP G G T TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr2:24550934G>T ENST00000355123.4 - 2 461 c.18C>A c.(16-18)ccC>ccA p.P6P ITSN2_ENST00000407704.1_5'UTR|ITSN2_ENST00000361999.3_Silent_p.P6P|ITSN2_ENST00000406921.3_Silent_p.P6P NM_006277.2 NP_006268.2 Q9NZM3 ITSN2_HUMAN intersectin 2 6 endocytosis|regulation of Rho protein signal transduction cytoplasm calcium ion binding|Rho guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1) 61 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) TCATAGCTGTGGGAAACTGAG 0.373000 4 57 3.59834e-05 4.08902e-05 0.021553 1 0 NBPF9 400818 broad.mit.edu 37 1 144815953 144815953 + Missense_Mutation SNP A A G TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr1:144815953A>G ENST00000440491.2 + 4 550 c.550A>G c.(550-552)Aat>Gat p.N184D NBPF9_ENST00000281815.8_5'UTR|NBPF9_ENST00000468645.1_3'UTR|NBPF9_ENST00000338347.4_Missense_Mutation_p.N184D NM_001037675.2 NP_001032764.1 neuroblastoma breakpoint family, member 9 p.N184D(2) NS(2)|prostate(1) 3 CAACGATGACAATGAAGATGT 0.423000 5 110 0 0 0.021553 0 0 TACC2 10579 broad.mit.edu 37 10 123842613 123842613 + Missense_Mutation SNP A A G TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr10:123842613A>G ENST00000369005.1 + 4 938 c.598A>G c.(598-600)Atg>Gtg p.M200V TACC2_ENST00000513429.1_Intron|TACC2_ENST00000515273.1_Missense_Mutation_p.M200V|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515603.1_Missense_Mutation_p.M200V|TACC2_ENST00000453444.2_Missense_Mutation_p.M200V|TACC2_ENST00000334433.3_Missense_Mutation_p.M200V NM_206862.2 NP_996744.2 O95359 TACC2_HUMAN transforming, acidic coiled-coil containing protein 2 200 microtubule organizing center|nucleus nuclear hormone receptor binding NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3) 83 all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197) GTCACCTGGAATGTCGCCAGT 0.582000 17 33 0 0 0.055883 0 0 FAM120B 84498 broad.mit.edu 37 6 170628184 170628184 + Missense_Mutation SNP C C T TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr6:170628184C>T ENST00000476287.1 + 2 1814 c.1706C>T c.(1705-1707)aCc>aTc p.T569I FAM120B_ENST00000540480.1_Missense_Mutation_p.T581I|FAM120B_ENST00000537664.1_Missense_Mutation_p.T592I|FAM120B_ENST00000252510.9_Intron NM_032448.1 NP_115824.1 Q96EK7 F120B_HUMAN family with sequence similarity 120B 569 cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus protein binding endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2) 44 Breast(66;0.000338)|Esophageal squamous(34;0.241) OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899) CAACAAGTAACCATGGTTTCA 0.388000 10 27 0 0 0.069234 0 0 PTCH2 8643 broad.mit.edu 37 1 45288194 45288194 + Frame_Shift_Del DEL G G - TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr1:45288194delG ENST00000372192.3 - 22 3635 c.3505delC c.(3505-3507)tgfs p.L1169fs PTCH2_ENST00000447098.2_Intron NM_003738.4 NP_003729.3 Q9Y6C5 PTC2_HUMAN patched 2 1169 protein complex assembly|spermatogenesis integral to plasma membrane hedgehog receptor activity NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1) 50 Acute lymphoblastic leukemia(166;0.155) GCACCAGGCAGGGGGGGTGGG 0.657 Basal Cell Nevus syndrome 7 173 --- --- --- --- PBXIP1 57326 broad.mit.edu 37 1 154917508 154917510 + In_Frame_Del DEL GGT GGT - rs143592003 TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr1:154917508_154917510delGGT ENST00000368463.3 - 11 2257_2259 c.2186_2188delACC c.(2185-2190)cgg>c p.HR729del PBXIP1_ENST00000368465.1_In_Frame_Del_p.HR700del|PBXIP1_ENST00000539880.1_In_Frame_Del_p.HR556del|PBXIP1_ENST00000542459.1_In_Frame_Del_p.HR574del NM_020524.2 NP_065385.2 Q96AQ6 PBIP1_HUMAN pre-B-cell leukemia homeobox interacting protein 1 729 His-rich. cell differentiation|multicellular organismal development|negative regulation of transcription, DNA-dependent cytosol|microtubule|nucleus protein binding|transcription corepressor activity breast(1)|kidney(2)|large_intestine(6)|lung(13)|prostate(1)|urinary_tract(1) 24 all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245) BRCA - Breast invasive adenocarcinoma(34;0.00034) TGTCAGCCCCGGTGGTGGTGGTG 0.640 8 201 --- --- --- --- ANKRD36 375248 broad.mit.edu 37 2 97847365 97847368 + Splice_Site DEL TAAT TAAT - TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr2:97847365_97847368delTAAT ENST00000420699.2 + 25 2008 c.e25+2 ANKRD36_ENST00000461153.2_Splice_Site NM_001164315.1 NP_001157787.1 A6QL64 AN36A_HUMAN ankyrin repeat domain 36 endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1) 23 GCTGAGAAGGTAATTAAAGTCTCA 0.314 4 8 --- --- --- --- CRIPAK 285464 broad.mit.edu 37 4 1388441 1388442 + Frame_Shift_Ins INS - - CG rs144787346 byFrequency TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr4:1388441_1388442insCG ENST00000324803.4 + 1 3102_3103 c.142_143insCG c.(142-144)gccfs p.A48fs NM_175918.3 NP_787114.2 Q8N1N5 CRPAK_HUMAN cysteine-rich PAK1 inhibitor 48 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) CTGCTCACACATGCCCATGTGG 0.644 12 1206 --- --- --- --- TNIP2 79155 broad.mit.edu 37 4 2757866 2757866 + Frame_Shift_Del DEL G G - TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr4:2757866delG ENST00000315423.7 - 1 237 c.151delC c.(151-153)gcfs p.R51fs TNIP2_ENST00000510267.1_5'UTR|TNIP2_ENST00000503235.1_Frame_Shift_Del_p.R51fs NM_024309.3 NP_077285.3 Q8NFZ5 TNIP2_HUMAN TNFAIP3 interacting protein 2 51 cytosol protein binding breast(2)|central_nervous_system(1)|large_intestine(4)|lung(6)|prostate(1) 14 UCEC - Uterine corpus endometrioid carcinoma (64;0.168) GCGGCCAGGCGGGCGCGGAGG 0.761 2 4 --- --- --- --- PCDH10 57575 broad.mit.edu 37 4 134073569 134073571 + In_Frame_Del DEL CTG CTG - TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr4:134073569_134073571delCTG ENST00000264360.4 + 1 3100_3102 c.2274_2276delCTG c.(2272-2277)ctc>ct p.LC758del NM_032961.1 NP_116586.1 Q9P2E7 PCD10_HUMAN protocadherin 10 758 Cys-rich. homophilic cell adhesion integral to membrane|plasma membrane calcium ion binding NS(2)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(30)|liver(1)|lung(72)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(2) 136 LUSC - Lung squamous cell carcinoma(193;0.227) ATTGCTGCCTCTGCTGCTGCTGC 0.581 8 92 --- --- --- --- SFRP1 6422 broad.mit.edu 37 8 41166638 41166640 + In_Frame_Del DEL GCT GCT - rs3055861 TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr8:41166638_41166640delGCT ENST00000220772.3 - 1 376_378 c.39_41delAGC c.(37-42)gcc>gc p.AA13del NM_003012.4 NP_003003.3 Q8N474 SFRP1_HUMAN secreted frizzled-related protein 1 13 brain development|canonical Wnt receptor signaling pathway|cellular response to BMP stimulus|cellular response to estradiol stimulus|cellular response to fibroblast growth factor stimulus|cellular response to heparin|cellular response to hypoxia|cellular response to interleukin-1|cellular response to prostaglandin E stimulus|cellular response to starvation|cellular response to transforming growth factor beta stimulus|cellular response to tumor necrosis factor|cellular response to vitamin D|DNA fragmentation involved in apoptotic nuclear change|dorsal/ventral axis specification|hemopoietic progenitor cell differentiation|hemopoietic stem cell differentiation|menstrual cycle phase|negative regulation of androgen receptor signaling pathway|negative regulation of B cell differentiation|negative regulation of bone remodeling|negative regulation of canonical Wnt receptor signaling pathway involved in controlling type B pancreatic cell proliferation|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cysteine-type endopeptidase activity|negative regulation of epithelial cell proliferation|negative regulation of epithelial to mesenchymal transition|negative regulation of fibroblast apoptosis|negative regulation of fibroblast proliferation|negative regulation of insulin secretion|negative regulation of ossification|negative regulation of osteoblast proliferation|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway involved in dorsal/ventral axis specification|osteoblast differentiation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell growth|positive regulation of epithelial cell proliferation|positive regulation of fat cell differentiation|positive regulation of fibroblast apoptosis|positive regulation of focal adhesion assembly|positive regulation of non-canonical Wnt receptor signaling pathway|positive regulation of Rac GTPase activity|positive regulation of smoothened signaling pathway|positive regulation of stress fiber assembly|positive regulation of transcription, DNA-dependent|regulation of angiogenesis|regulation of cell cycle process|response to drug|response to organic cyclic compound|vasculature development cell surface|cytosol|extracellular space|plasma membrane|proteinaceous extracellular matrix cysteine-type endopeptidase activity|drug binding|frizzled binding|heparin binding|identical protein binding|PDZ domain binding|Wnt receptor activity|Wnt-protein binding breast(1)|central_nervous_system(1)|large_intestine(2)|liver(1)|lung(1)|skin(1) 7 Breast(1;9.19e-13)|Ovarian(28;0.00769)|Colorectal(14;0.0305)|Lung SC(25;0.211) all_lung(54;0.0034)|Lung NSC(58;0.0134)|Hepatocellular(245;0.023)|Esophageal squamous(32;0.0559) BRCA - Breast invasive adenocarcinoma(1;1.11e-10)|LUSC - Lung squamous cell carcinoma(45;0.00894)|COAD - Colon adenocarcinoma(11;0.0174) CACGCCCAGGGCTGCCCCGCGGC 0.764 7 6 --- --- --- --- PRB2 653247 broad.mit.edu 37 12 11546506 11546508 + In_Frame_Del DEL TTG TTG - TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr12:11546506_11546508delTTG ENST00000389362.4 - 3 539_541 c.504_506delCAA c.(502-507)aag>aa p.NK168del PRB1_ENST00000546254.1_Intron NM_006248.3 NP_006239.3 proline-rich protein BstNI subfamily 2 NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(5)|skin(4)|stomach(2)|urinary_tract(1) 37 all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09) OV - Ovarian serous cystadenocarcinoma(49;0.185) ACTTCGGGACTTGTTGTCTCCTT 0.596 13 672 --- --- --- --- RP11-438N16.1 0 broad.mit.edu 37 12 114200310 114200311 + RNA INS - - C TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr12:114200310_114200311insC ENST00000547963.1 - 0 69 CTCCAGCGGTGCCCCCTCCCCC 0.589 4 3 --- --- --- --- ECSIT 51295 broad.mit.edu 37 19 11618821 11618821 + Frame_Shift_Del DEL G G - TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr19:11618821delG ENST00000270517.7 - 5 916 c.781delC c.(781-783)agfs p.Q261fs ECSIT_ENST00000591352.1_5'UTR|ECSIT_ENST00000592312.1_Frame_Shift_Del_p.Q145fs|ECSIT_ENST00000417981.2_Frame_Shift_Del_p.Q47fs|ECSIT_ENST00000591104.1_Frame_Shift_Del_p.Q261fs|ECSIT_ENST00000588998.1_Frame_Shift_Del_p.Q47fs|ECSIT_ENST00000252440.7_Frame_Shift_Del_p.Q261fs NM_016581.4 NP_057665.2 Q9BQ95 ECSIT_HUMAN ECSIT signalling integrator 261 innate immune response|regulation of oxidoreductase activity mitochondrion oxidoreductase activity, acting on NADH or NADPH|protein binding kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1) 11 ATGTGGGGCTGGGGGGGATCT 0.582 7 244 --- --- --- --- KCNN4 3783 broad.mit.edu 37 19 44284861 44284861 + Frame_Shift_Del DEL C C - TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chr19:44284861delC ENST00000262888.3 - 1 548 c.153delG c.(151-153)ggfs p.G51fs NM_002250.2 NP_002241.1 O15554 KCNN4_HUMAN potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4 51 defense response voltage-gated potassium channel complex calcium-activated potassium channel activity|calmodulin binding biliary_tract(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1) 15 Prostate(69;0.0352) Clotrimazole(DB00257)|Halothane(DB01159)|Quinine(DB00468) TCACCGAGCACCCCCCGAACC 0.652 8 271 --- --- --- --- USP9X 8239 broad.mit.edu 37 X 41043681 41043682 + Frame_Shift_Ins INS - - A TCGA-EL-A3MY-01A-11D-A21A-08 TCGA-EL-A3MY-11A-12D-A21A-08 Untested Somatic Phase_I WXS none Illumina GAIIx a9c29edd-2ef1-46ef-93c6-796cf0332a2b 8b4e9b9d-c2d3-4b38-b7a1-3642e56555d3 g.chrX:41043681_41043682insA ENST00000324545.7 + 23 3944_3945 c.3311_3312insA c.(3310-3312)gccfs p.A1104fs USP9X_ENST00000378308.2_Frame_Shift_Ins_p.A1104fs NM_001039590.2|NM_001039591.2 NP_001034679.2|NP_001034680.2 Q93008 USP9X_HUMAN ubiquitin specific peptidase 9, X-linked 1104 BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process cytoplasm co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 87 CCTGCTGGTGCACCTCTGGCTG 0.401 20 41 --- --- --- ---