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 KAT6A 7994 broad.mit.edu 37 8 41790659 41790659 + Silent SNP T T G TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr8:41790659T>G ENST00000396930.3 - 18 5622 c.5079A>C c.(5077-5079)ccA>ccC p.P1693P KAT6A_ENST00000406337.1_Silent_p.P1693P|KAT6A_ENST00000265713.2_Silent_p.P1693P NM_001099412.1 NP_001092882.1 Q92794 MYST3_HUMAN K(lysine) acetyltransferase 6A 1693 Gln/Pro-rich. histone H3 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription coactivator activity|transcription factor binding|zinc ion binding ggggagggggtgggggtggag 0.627000 15 118 0 0 1 0 0 TBC1D4 9882 broad.mit.edu 37 13 75884223 75884223 + Silent SNP C C T TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr13:75884223C>T ENST00000377636.3 - 14 2794 c.2448G>A c.(2446-2448)ccG>ccA p.P816P TBC1D4_ENST00000431480.2_Silent_p.P808P|TBC1D4_ENST00000377625.2_Silent_p.P753P|TBC1D4_ENST00000425511.1_Silent_p.P33P NM_014832.2 NP_055647.2 O60343 TBCD4_HUMAN TBC1 domain family, member 4 816 cytoplasm Rab GTPase activator activity breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 50 Prostate(6;0.014)|Breast(118;0.0982) GBM - Glioblastoma multiforme(99;0.0116) ATACAACCAGCGGTTCCTCCT 0.493000 20 232 0 0 1 0 0 MALAT1 0 broad.mit.edu 37 11 65268712 65268712 + RNA SNP T T G TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr11:65268712T>G ENST00000534336.1 + 0 3480 NR_002819.2 TTTGTGGGGGTGGGGGCAAAA 0.393000 44 173 0 0 1 0 0 ARHGEF10L 55160 broad.mit.edu 37 1 18023723 18023723 + Missense_Mutation SNP G G A TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr1:18023723G>A ENST00000361221.3 + 29 3847 c.3688G>A c.(3688-3690)Gcc>Acc p.A1230T ARHGEF10L_ENST00000452522.1_Missense_Mutation_p.A1191T|ARHGEF10L_ENST00000375415.1_Missense_Mutation_p.A1191T|ARHGEF10L_ENST00000167825.4_Missense_Mutation_p.A933T|ARHGEF10L_ENST00000469726.1_3'UTR|ARHGEF10L_ENST00000375408.3_Missense_Mutation_p.A1003T NM_018125.3 NP_060595.3 Q9HCE6 ARGAL_HUMAN Rho guanine nucleotide exchange factor (GEF) 10-like 1230 regulation of Rho protein signal transduction cytoplasm Rho guanyl-nucleotide exchange factor activity NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1) 43 Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204) CGCCCGCGACGCCCACCGCAA 0.677000 16 243 0 0 1 0 0 RP11-50E11.3 0 broad.mit.edu 37 10 52390836 52390836 + RNA SNP A A G rs7904101 by1000genomes TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr10:52390836A>G ENST00000443374.1 + 0 1529 TTCCGTATCCATATTCTACAA 0.512000 8 88 0 0 1 0 0 PCYT2 5833 broad.mit.edu 37 17 79866486 79866486 + Missense_Mutation SNP C C T TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr17:79866486C>T ENST00000538936.2 - 4 473 c.365G>A c.(364-366)gGc>gAc p.G122D PCYT2_ENST00000331285.3_Missense_Mutation_p.G44D|PCYT2_ENST00000538721.2_Missense_Mutation_p.G122D|PCYT2_ENST00000571105.1_Missense_Mutation_p.G122D|PCYT2_ENST00000570388.1_Missense_Mutation_p.G44D|PCYT2_ENST00000570391.1_Missense_Mutation_p.G90D NM_001256435.1|NM_002861.3 NP_001243364.1|NP_002852.1 Q99447 PCY2_HUMAN phosphate cytidylyltransferase 2, ethanolamine 122 Catalytic 1 (Potential). phospholipid biosynthetic process ethanolamine-phosphate cytidylyltransferase activity breast(2)|endometrium(1)|lung(4)|ovary(1) 8 all_neural(118;0.0878)|Ovarian(332;0.12) BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382) GGTGTCCCGGCCATCTACAGT 0.597000 13 171 0 0 1 0 0 CSHL1 1444 broad.mit.edu 37 17 61987405 61987405 + Silent SNP A A T rs2006122 by1000genomes TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr17:61987405A>T ENST00000450719.3 - 3 543 c.306T>A c.(304-306)ccT>ccA p.P102P CSHL1_ENST00000309894.5_Intron|CSHL1_ENST00000346606.6_Intron|CSHL1_ENST00000561003.1_Silent_p.P113P|CSHL1_ENST00000438387.2_Intron|CSHL1_ENST00000558099.1_5'UTR|CSHL1_ENST00000259003.10_Intron|CSHL1_ENST00000392824.4_3'UTR Q14406 CSHL_HUMAN chorionic somatomammotropin hormone-like 1 0 extracellular region hormone activity|metal ion binding endometrium(3)|lung(6) 9 ATGAAGAATAAGGTGAGTTCT 0.547000 35 673 0 0 1 0 0 HMGN2P46 0 broad.mit.edu 37 15 45848224 45848224 + RNA SNP G G T TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr15:45848224G>T ENST00000409454.1 + 0 1219 TGCAGATTTTGTTTAGCTTTT 0.318000 20 108 9.22233e-05 9.22233e-05 1 1 0 D86994.2 0 broad.mit.edu 37 22 23006961 23006961 + RNA SNP C C T TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr22:23006961C>T ENST00000385099.1 + 0 64 GGCTCTGCTCCTCCTCACCCT 0.627000 7 55 0 0 1 0 0 SPAG4 6676 broad.mit.edu 37 20 34204182 34204182 + Missense_Mutation SNP A A G TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr20:34204182A>G ENST00000374273.3 + 1 369 c.257A>G c.(256-258)aAc>aGc p.N86S NM_003116.1 NP_003107.1 Q9NPE6 SPAG4_HUMAN sperm associated antigen 4 86 spermatogenesis cilium|flagellar axoneme|integral to membrane structural molecule activity NS(1)|cervix(5)|kidney(1)|large_intestine(3)|lung(10)|ovary(1) 21 Lung NSC(9;0.0053)|all_lung(11;0.00785) BRCA - Breast invasive adenocarcinoma(18;0.0127) CGGAGCCACAACTGGCAGACA 0.736000 6 52 0 0 1 0 0 GRIN2A 0 broad.mit.edu 37 16 10274206 10274206 + Silent SNP C C T TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr16:10274206C>T ENST00000396573.2 - 3 372 c.63G>A c.(61-63)ccG>ccA p.P21P GRIN2A_ENST00000330684.3_Silent_p.P21P|GRIN2A_ENST00000562109.1_Silent_p.P21P|GRIN2A_ENST00000396575.2_Silent_p.P21P|GRIN2A_ENST00000404927.2_Silent_p.P21P NM_000833.3 NP_000824.1 Q12879 NMDE1_HUMAN glutamate receptor, ionotropic, N-methyl D-aspartate 2A 21 response to ethanol cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1) 198 Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043) CGCTCGGCGCCGGACCGCGCC 0.647000 16 220 0 0 1 0 0 SLC9A7P1 0 broad.mit.edu 37 12 98849029 98849029 + RNA SNP G G T TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr12:98849029G>T ENST00000554295.1 - 0 1894 NR_033801.1 GGGAGCCGCTGTGTCTCCACC 0.592000 11 47 7.07596e-05 7.30422e-05 1 1 0 KRTAP4-9 100132386 broad.mit.edu 37 17 39261693 39261693 + Missense_Mutation SNP A A T rs113059833 by1000genomes TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr17:39261693A>T ENST00000391415.1 + 1 110 c.53A>T c.(52-54)gAc>gTc p.D18V NM_001146041.1 NP_001139513.1 Q9BYQ8 KRA49_HUMAN keratin associated protein 4-9 18 keratin filament p.D18V(1) central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3) 14 TGCGGCCAAGACCTCTGTCAG 0.627000 28 260 0 0 1 0 0 GLB1L3 112937 broad.mit.edu 37 11 134182352 134182352 + Missense_Mutation SNP G G A TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr11:134182352G>A ENST00000431683.2 + 14 1397 c.1397G>A c.(1396-1398)cGc>cAc p.R466H NM_001080407.2 NP_001073876.2 Q8NCI6 GLBL3_HUMAN galactosidase, beta 1-like 3 466 carbohydrate metabolic process cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|pancreas(1) 13 all_hematologic(175;0.127) all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559) Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222) TCCGGAGGCCGCCTCCGTGCC 0.607000 18 213 0 0 1 0 0 ATXN3L 92552 broad.mit.edu 37 X 13337260 13337260 + Missense_Mutation SNP T T C TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chrX:13337260T>C ENST00000380622.2 - 1 1258 c.794A>G c.(793-795)gAt>gGt p.D265G GS1-600G8.3_ENST00000431486.1_RNA NM_001135995.1 NP_001129467.1 Q9H3M9 ATX3L_HUMAN ataxin 3-like 265 protein deubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus ubiquitin-specific protease activity endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1) 28 CTTTGGAAGATCTTGCGATGT 0.428000 69 941 0 0 1 0 0 ADAMTS4 9507 broad.mit.edu 37 1 161166457 161166457 + Missense_Mutation SNP G G A TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr1:161166457G>A ENST00000367996.4 - 2 1275 c.847C>T c.(847-849)Ccc>Tcc p.P283S ADAMTS4_ENST00000367995.3_Missense_Mutation_p.P283S NM_005099.4 NP_005090.3 O75173 ATS4_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 4 283 Peptidase M12B. proteolysis|skeletal system development extracellular space|proteinaceous extracellular matrix metalloendopeptidase activity|protease binding|zinc ion binding central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(20)|ovary(4)|prostate(3)|skin(1)|urinary_tract(1) 43 all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093) BRCA - Breast invasive adenocarcinoma(70;0.00275) GCAGCACTGGGCCCCACTTGG 0.632000 46 515 0 0 1 0 0 D86994.2 0 broad.mit.edu 37 22 23006960 23006960 + RNA SNP C C A TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr22:23006960C>A ENST00000385099.1 + 0 63 GGGCTCTGCTCCTCCTCACCC 0.627000 7 56 2.74318e-10 2.92606e-10 1 1 0 CHD6 0 broad.mit.edu 37 20 40127944 40127944 + Silent SNP A A G TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr20:40127944A>G ENST00000373233.3 - 6 1083 c.906T>C c.(904-906)acT>acC p.T302T CHD6_ENST00000373222.3_Silent_p.T337T|CHD6_ENST00000309279.7_Silent_p.T302T NM_032221.3 NP_115597.3 Q8TD26 CHD6_HUMAN chromodomain helicase DNA binding protein 6 302 Chromo 1. chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9) 129 Myeloproliferative disorder(115;0.00425) CCTCCTGGACAGTCTTAGATG 0.398000 7 66 0 0 1 0 0 RRN3P2 0 broad.mit.edu 37 16 29110458 29110458 + RNA SNP T T C rs151074589 by1000genomes TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr16:29110458T>C ENST00000564580.1 + 0 1131 p.W375R(25) GAATTTTGAGTGGATAGTGAT 0.328000 20 217 0 0 1 0 0 TRIOBP 11078 broad.mit.edu 37 22 38120431 38120431 + Missense_Mutation SNP A A T TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr22:38120431A>T ENST00000406386.3 + 7 2123 c.1868A>T c.(1867-1869)aAc>aTc p.N623I RP1-37E16.12_ENST00000455236.1_RNA NM_001039141.2 NP_001034230.1 Q9H2D6 TARA_HUMAN TRIO and F-actin binding protein 623 actin modification|barbed-end actin filament capping actin cytoskeleton|cytoplasm|nucleus actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 12 Melanoma(58;0.0574) ACACGAGATAACCCCAGAACA 0.587000 54 821 0 0 1 0 0 AP005901.1 0 broad.mit.edu 37 18 15316755 15316755 + RNA SNP G G C TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr18:15316755G>C ENST00000455308.2 - 0 668 NR_027417.1 TGTTCCTTCAGATGTTCCTTC 0.433000 6 68 0 0 1 0 0 VAMP3 9341 broad.mit.edu 37 1 7838212 7838214 + In_Frame_Del DEL TCA TCA - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr1:7838212_7838214delTCA ENST00000054666.6 + 4 381_383 c.266_268delTCA c.(265-270)ttc>t p.FI89del VAMP3_ENST00000470357.1_In_Frame_Del_p.FI61del NM_004781.3 NP_004772.1 Q15836 VAMP3_HUMAN vesicle-associated membrane protein 3 89 cellular membrane fusion|positive regulation of receptor recycling|protein complex assembly|protein transport|retrograde transport, endosome to Golgi|substrate adhesion-dependent cell spreading|vesicle docking involved in exocytosis cell junction|clathrin-coated vesicle|integral to membrane|recycling endosome|synapse|synaptosome protein binding breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3) 6 Ovarian(185;0.0634)|all_lung(157;0.178) all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;6.33e-69)|GBM - Glioblastoma multiforme(8;2.07e-34)|Colorectal(212;1.36e-07)|COAD - Colon adenocarcinoma(227;1.38e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000805)|KIRC - Kidney renal clear cell carcinoma(229;0.000917)|STAD - Stomach adenocarcinoma(132;0.000985)|READ - Rectum adenocarcinoma(331;0.0642) CTGGTTATCTTCATCATCATCAT 0.365 7 968 --- --- --- --- C1orf172 126695 broad.mit.edu 37 1 27277240 27277241 + Frame_Shift_Del DEL TG TG - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr1:27277240_27277241delTG ENST00000320567.5 - 3 1134_1135 c.1046_1047delCA c.(1045-1047)afs p.T349fs NM_152365.2 NP_689578.2 Q8NAX2 CA172_HUMAN chromosome 1 open reading frame 172 349 NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 17 all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.37e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.22e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419) AGATCTGCACTGTCAGCTCTAG 0.569 10 621 --- --- --- --- ZMYM4 9202 broad.mit.edu 37 1 35846959 35846960 + Frame_Shift_Ins INS - - A TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr1:35846959_35846960insA ENST00000314607.6 + 8 1361_1362 c.1281_1282insA c.(1279-1284)ctaaaafs p.LK427fs ZMYM4_ENST00000373297.2_Frame_Shift_Ins_p.LK427fs NM_005095.2 NP_005086.2 Q5VZL5 ZMYM4_HUMAN zinc finger, MYM-type 4 427 multicellular organismal development DNA binding|zinc ion binding breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2) 54 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887) CATATGAACTGAAAAAAAAACC 0.342 11 406 --- --- --- --- LRRIQ3 127255 broad.mit.edu 37 1 74575212 74575213 + Frame_Shift_Ins INS - - T TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr1:74575212_74575213insT ENST00000354431.4 - 5 923_924 c.732_733insA c.(730-735)aaagcafs p.A245fs LRRIQ3_ENST00000468759.1_5'UTR|LRRIQ3_ENST00000395089.1_Frame_Shift_Ins_p.A245fs|LRRIQ3_ENST00000370909.2_Frame_Shift_Ins_p.A137fs NM_001105659.1 NP_001099129.1 A6PVS8 LRIQ3_HUMAN leucine-rich repeats and IQ motif containing 3 245 QQEKII -> TAGKNY (in Ref. 1; BAD18621). NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5) 73 TTTTCCTGCTGTTTTTTTTTGT 0.327 20 379 --- --- --- --- TNNI3K 51086 broad.mit.edu 37 1 74957824 74957826 + In_Frame_Del DEL CTT CTT - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr1:74957824_74957826delCTT ENST00000370891.2 + 25 2544_2546 c.2528_2530delCTT c.(2527-2532)cct>c p.PS843del FPGT-TNNI3K_ENST00000557284.1_In_Frame_Del_p.PS843del|TNNI3K_ENST00000326637.3_In_Frame_Del_p.PS742del|LRRC53_ENST00000294635.4_Intron NM_001112808.2 NP_001106279.1 TNNI3 interacting kinase cervix(1)|endometrium(3)|kidney(5)|large_intestine(21)|lung(31)|ovary(4)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3) 76 TCTCTCTCACCTTCTTCTTCTTC 0.473 9 1149 --- --- --- --- BCL10 8915 broad.mit.edu 37 1 85736511 85736511 + Frame_Shift_Del DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr1:85736511delT ENST00000370580.1 - 2 873 c.136delA c.(136-138)tafs p.I46fs NM_003921.4 NP_003912.1 O95999 BCL10_HUMAN B-cell CLL/lymphoma 10 46 CARD. apoptosis|cellular response to mechanical stimulus|innate immune response|interleukin-6 biosynthetic process|lymphotoxin A biosynthetic process|negative regulation of mature B cell apoptosis|neural tube closure|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-8 biosynthetic process|positive regulation of mast cell cytokine production|positive regulation of NF-kappaB transcription factor activity|positive regulation of phosphorylation|positive regulation of protein ubiquitination|positive regulation of transcription, DNA-dependent|protein homooligomerization|response to molecule of bacterial origin|T cell receptor signaling pathway CBM complex|cytosol|lysosome|membrane raft|nucleus|perinuclear region of cytoplasm NF-kappaB binding|protease binding|protein C-terminus binding|protein kinase B binding|protein self-association|transcription coactivator activity|ubiquitin binding|ubiquitin protein ligase binding p.I46fs*4(1) haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1) 19 all cancers(265;0.0114)|Epithelial(280;0.0311) CTACTGAGTATTTTTTTTGCA 0.343 T IGH@ MALT 17 551 --- --- --- --- RP11-343N15.1 0 broad.mit.edu 37 1 121116645 121116645 + RNA DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr1:121116645delT ENST00000437515.1 - 0 329 CAAGCCCCCCTTTAAAAAAAA 0.393 12 300 --- --- --- --- ANKRD20A12P 0 broad.mit.edu 37 1 142716575 142716578 + RNA DEL AAAC AAAC - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr1:142716575_142716578delAAAC ENST00000595144.1 - 0 418 catctcagaaaaacaaacaaacaa 0.422 16 601 --- --- --- --- MCL1 4170 broad.mit.edu 37 1 150551492 150551494 + In_Frame_Del DEL TCC TCC - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr1:150551492_150551494delTCC ENST00000369026.2 - 1 572_574 c.513_515delGGA c.(511-516)gac>ga p.ED171del MCL1_ENST00000307940.3_In_Frame_Del_p.ED171del NM_001197320.1|NM_021960.4 NP_001184249.1|NP_068779.1 Q07820 MCL1_HUMAN myeloid cell leukemia sequence 1 (BCL2-related) 171 PEST-like. anti-apoptosis|apoptosis|cell fate determination|cellular homeostasis|multicellular organismal development|response to cytokine stimulus integral to membrane|mitochondrial outer membrane|nucleoplasm BH3 domain binding|protein binding|protein channel activity|protein heterodimerization activity endometrium(2)|large_intestine(1)|lung(4)|prostate(1) 8 all_cancers(9;1.69e-53)|all_epithelial(9;1.95e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171) UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206) GTACAACTCGTCCTCCTCCTCCT 0.635 12 587 --- --- --- --- TCHH 7062 broad.mit.edu 37 1 152082957 152082959 + In_Frame_Del DEL CTC CTC - rs143222885 by1000genomes TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr1:152082957_152082959delCTC ENST00000368804.1 - 2 2733_2735 c.2734_2736delGAG c.(2734-2736)del p.E912del NM_007113.2 NP_009044.2 Q07283 TRHY_HUMAN trichohyalin 912 10 X 30 AA tandem repeats. keratinization cytoskeleton calcium ion binding NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4) 105 Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127) LUSC - Lung squamous cell carcinoma(543;0.206) CTCTCTGTAGCTCCTCCTCCTCC 0.586 11 1276 --- --- --- --- KLHL12 59349 broad.mit.edu 37 1 202862508 202862508 + Frame_Shift_Del DEL C C - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr1:202862508delC ENST00000367261.3 - 11 1657 c.1439delG c.(1438-1440)gafs p.G480fs KLHL12_ENST00000435533.3_Frame_Shift_Del_p.G518fs|KLHL12_ENST00000367259.1_Intron NM_021633.2 NP_067646.1 Q53G59 KLH12_HUMAN kelch-like family member 12 480 Interaction with DVL3. Wnt receptor signaling pathway protein binding NS(3)|breast(2)|endometrium(1)|large_intestine(1)|lung(6)|stomach(1) 14 BRCA - Breast invasive adenocarcinoma(75;0.166) ACCATCAAATCCCCCCACCAC 0.453 7 1159 --- --- --- --- PTPN14 5784 broad.mit.edu 37 1 214557049 214557051 + In_Frame_Del DEL CCT CCT - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr1:214557049_214557051delCCT ENST00000366956.5 - 13 2341_2343 c.2147_2149delAGG c.(2146-2151)gct>g p.EA716del PTPN14_ENST00000543945.1_3'UTR NM_005401.4 NP_005392.2 Q15678 PTN14_HUMAN protein tyrosine phosphatase, non-receptor type 14 716 Poly-Glu. lymphangiogenesis cytoplasm|cytoskeleton protein tyrosine phosphatase activity|receptor tyrosine kinase binding p.E716delE(1) NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 58 OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155) GATTCTGGAGCCTCCTCCTCCTC 0.626 15 401 --- --- --- --- ATP6V1C2 245973 broad.mit.edu 37 2 10912688 10912688 + Frame_Shift_Del DEL A A - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr2:10912688delA ENST00000381661.3 + 8 699 c.590delA c.(589-591)cafs p.Q197fs ATP6V1C2_ENST00000272238.4_Frame_Shift_Del_p.Q197fs NM_144583.3 NP_653184.2 Q8NEY4 VATC2_HUMAN ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C2 197 ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport cytosol|proton-transporting V-type ATPase, V1 domain endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 19 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191) Epithelial(75;0.15)|OV - Ovarian serous cystadenocarcinoma(76;0.152) TCACAATGGCAAAAAACCTAC 0.512 7 2755 --- --- --- --- SMC6 79677 broad.mit.edu 37 2 17898126 17898126 + Frame_Shift_Del DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr2:17898126delT ENST00000448223.2 - 14 1497 c.1228delA c.(1228-1230)tafs p.I410fs SMC6_ENST00000381272.4_Frame_Shift_Del_p.I436fs|SMC6_ENST00000402989.1_Frame_Shift_Del_p.I410fs|SMC6_ENST00000351948.4_Frame_Shift_Del_p.I410fs NM_001142286.1 NP_001135758.1 Q96SB8 SMC6_HUMAN structural maintenance of chromosomes 6 410 DNA recombination|DNA repair chromosome|nucleus ATP binding NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2) 43 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158) AACCAAGATATTTTTTTTTGT 0.343 10 265 --- --- --- --- APOB 338 broad.mit.edu 37 2 21228602 21228602 + Frame_Shift_Del DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr2:21228602delT ENST00000233242.1 - 26 11265 c.11138delA c.(11137-11139)acfs p.N3713fs NM_000384.2 NP_000375.2 P04114 APOB_HUMAN apolipoprotein B 3713 cholesterol homeostasis|cholesterol metabolic process|leukocyte migration|low-density lipoprotein particle clearance|low-density lipoprotein particle remodeling|platelet activation|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|receptor-mediated endocytosis|response to virus chylomicron remnant|clathrin-coated endocytic vesicle membrane|endoplasmic reticulum lumen|endoplasmic reticulum membrane|endosome lumen|endosome membrane|intermediate-density lipoprotein particle|low-density lipoprotein particle|mature chylomicron|microsome|plasma membrane|very-low-density lipoprotein particle cholesterol transporter activity|enzyme binding|heparin binding|low-density lipoprotein particle receptor binding|phospholipid binding|protein heterodimerization activity NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6) 305 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) Atorvastatin(DB01076) GCCATTGGGGTTTTTGGTGTA 0.398 7 784 --- --- --- --- RTN4 57142 broad.mit.edu 37 2 55253745 55253746 + Frame_Shift_Ins INS - - T TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr2:55253745_55253746insT ENST00000337526.6 - 3 1732_1733 c.1489_1490insA c.(1489-1491)agafs p.R497fs RTN4_ENST00000394611.2_Frame_Shift_Ins_p.R291fs|RTN4_ENST00000354474.6_Frame_Shift_Ins_p.R265fs|RTN4_ENST00000405240.1_Frame_Shift_Ins_p.R291fs|RTN4_ENST00000357376.3_Frame_Shift_Ins_p.R291fs|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000357732.4_Intron|RTN4_ENST00000317610.7_Intron|RTN4_ENST00000404909.1_Frame_Shift_Ins_p.R291fs NM_020532.4 NP_065393.1 Q9NQC3 RTN4_HUMAN reticulon 4 497 apoptosis|axonal fasciculation|cerebral cortex radial glia guided migration|endoplasmic reticulum tubular network organization|negative regulation of anti-apoptosis|negative regulation of axon extension|nerve growth factor receptor signaling pathway|regulation of apoptosis|regulation of branching morphogenesis of a nerve|regulation of cell migration integral to endoplasmic reticulum membrane|nuclear envelope|plasma membrane protein binding NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1) 36 CTTTTCTTCTATTTTTTTTTCA 0.381 12 577 --- --- --- --- HTRA2 27429 broad.mit.edu 37 2 74757185 74757186 + Frame_Shift_Ins INS - - G TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr2:74757185_74757186insG ENST00000258080.3 + 1 682_683 c.52_53insG c.(52-54)ggcfs p.G18fs HTRA2_ENST00000352222.3_Frame_Shift_Ins_p.G18fs|HTRA2_ENST00000467961.1_Intron NM_013247.4 NP_037379.1 O43464 HTRA2_HUMAN HtrA serine peptidase 2 18 apoptosis|proteolysis|response to stress CD40 receptor complex|endoplasmic reticulum membrane|internal side of plasma membrane|mitochondrial intermembrane space|mitochondrial membrane|nucleus serine-type endopeptidase activity|unfolded protein binding endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1) 12 TCGGGCATGGCGGGCTTTGGGG 0.718 45 340 --- --- --- --- AC027612.3 0 broad.mit.edu 37 2 91887905 91887906 + RNA INS - - T TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr2:91887905_91887906insT ENST00000436174.1 - 0 540 GCTATTTTCCATTTTTTTTTTT 0.292 12 222 --- --- --- --- AC027612.3 0 broad.mit.edu 37 2 91899642 91899642 + RNA DEL G G - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr2:91899642delG ENST00000436174.1 - 0 168 AAAAAAAAAAGCAAAGTAGGA 0.269 8 76 --- --- --- --- SLC9A4 389015 broad.mit.edu 37 2 103149137 103149137 + Frame_Shift_Del DEL A A - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr2:103149137delA ENST00000295269.4 + 12 2844 c.2387delA c.(2386-2388)cafs p.Q796fs NM_001011552.3 NP_001011552.2 Q6AI14 SL9A4_HUMAN solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4 796 regulation of pH apical plasma membrane|basolateral plasma membrane|integral to membrane sodium:hydrogen antiporter activity NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 43 CCTTTGCTCCAAAAAAAATAG 0.473 9 280 --- --- --- --- GCC2 9648 broad.mit.edu 37 2 109087883 109087884 + Frame_Shift_Ins INS - - A TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr2:109087883_109087884insA ENST00000309863.6 + 6 2812_2813 c.2098_2099insA c.(2098-2100)aaafs p.K700fs NM_181453.3 NP_852118.1 Q8IWJ2 GCC2_HUMAN GRIP and coiled-coil domain containing 2 700 Golgi ribbon formation|late endosome to Golgi transport|microtubule anchoring|microtubule organizing center organization|protein localization in Golgi apparatus|protein targeting to lysosome|recycling endosome to Golgi transport|regulation of protein exit from endoplasmic reticulum membrane|trans-Golgi network identical protein binding breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3) 54 ACTCAGTTCAGAAAAAAAACAG 0.307 11 1483 --- --- --- --- TTN 7273 broad.mit.edu 37 2 179459104 179459104 + Frame_Shift_Del DEL A A - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr2:179459104delA ENST00000589042.1 - 296 58341 c.58117delT c.(58117-58119)gcfs p.C19373fs TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Frame_Shift_Del_p.C10308fs|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000591111.1_Frame_Shift_Del_p.C17732fs|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342992.6_Frame_Shift_Del_p.C16805fs|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342175.6_Frame_Shift_Del_p.C10500fs|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000359218.5_Frame_Shift_Del_p.C10433fs NM_001267550.1 NP_001254479.1 Q8WZ42 TITIN_HUMAN titin 17732 Fibronectin type-III 40. 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) GGTTTGGTGCAAAATGATGGT 0.373 9 372 --- --- --- --- EDEM1 9695 broad.mit.edu 37 3 5248941 5248941 + Frame_Shift_Del DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr3:5248941delT ENST00000256497.4 + 7 1454 c.1321delT c.(1321-1323)ttfs p.F442fs EDEM1_ENST00000445686.1_Frame_Shift_Del_p.F247fs NM_014674.2 NP_055489.1 Q92611 EDEM1_HUMAN ER degradation enhancer, mannosidase alpha-like 1 442 ER-associated protein catabolic process|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|response to unfolded protein integral to endoplasmic reticulum membrane calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|misfolded protein binding NS(1)|breast(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3) 22 Epithelial(13;0.0588)|OV - Ovarian serous cystadenocarcinoma(96;0.0682) TCTGCAGGCCTTTTTCCCTGG 0.463 7 657 --- --- --- --- QRICH1 54870 broad.mit.edu 37 3 49094314 49094316 + In_Frame_Del DEL TGC TGC - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr3:49094314_49094316delTGC ENST00000395443.2 - 3 1789_1791 c.1317_1319delGCA c.(1315-1320)caa>ca p.QQ439del QRICH1_ENST00000424300.1_In_Frame_Del_p.QQ439del|QRICH1_ENST00000357496.2_In_Frame_Del_p.QQ439del|QRICH1_ENST00000479449.1_5'UTR NM_198880.1 NP_942581.1 Q2TAL8 QRIC1_HUMAN glutamine-rich 1 439 Gln-rich. breast(2)|endometrium(5)|large_intestine(8)|lung(8)|ovary(1)|skin(1) 25 BRCA - Breast invasive adenocarcinoma(193;8.88e-05)|Kidney(197;0.00239)|KIRC - Kidney renal clear cell carcinoma(197;0.00258) AACTTGGAgttgctgctgctgct 0.562 9 453 --- --- --- --- PARP3 10039 broad.mit.edu 37 3 51978150 51978152 + In_Frame_Del DEL AAC AAC - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr3:51978150_51978152delAAC ENST00000417220.2 + 4 717_719 c.229_231delAAC c.(229-231)del p.N80del PARP3_ENST00000431474.1_In_Frame_Del_p.N80del|PARP3_ENST00000398755.3_In_Frame_Del_p.N87del Q9Y6F1 PARP3_HUMAN poly (ADP-ribose) polymerase family, member 3 80 N -> K (in Ref. 2; AAD29855). DNA repair|protein ADP-ribosylation centriole|nucleus NAD+ ADP-ribosyltransferase activity|protein binding ovary(1) 1 BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000541)|KIRC - Kidney renal clear cell carcinoma(197;0.000716) CAACATCGAGAACAACAACAACA 0.596 7 1427 --- --- --- --- LRIG1 26018 broad.mit.edu 37 3 66436625 66436627 + In_Frame_Del DEL GCT GCT - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr3:66436625_66436627delGCT ENST00000383703.3 - 14 2242_2244 c.1639_1641delAGC c.(1639-1641)del p.S548del LRIG1_ENST00000496559.2_5'UTR|LRIG1_ENST00000273261.3_In_Frame_Del_p.S524del|SLC25A26_ENST00000536651.1_3'UTR Q96JA1 LRIG1_HUMAN leucine-rich repeats and immunoglobulin-like domains 1 524 Ig-like C2-type 1. integral to membrane NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1) 42 Lung NSC(201;0.0101) BRCA - Breast invasive adenocarcinoma(55;0.00047) TCATGGGGGAGCTGCTGCTGCTG 0.547 8 1609 --- --- --- --- SIDT1 54847 broad.mit.edu 37 3 113286403 113286403 + Frame_Shift_Del DEL A A - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr3:113286403delA ENST00000264852.4 + 3 1087 c.361delA c.(361-363)acfs p.N121fs SIDT1_ENST00000393830.3_Frame_Shift_Del_p.N121fs NM_017699.2 NP_060169.2 Q9NXL6 SIDT1_HUMAN SID1 transmembrane family, member 1 121 integral to membrane breast(1)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|liver(2)|lung(15)|ovary(3)|pancreas(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1) 50 GAGGAGCTACAACTATCAAGA 0.468 20 547 --- --- --- --- ATR 545 broad.mit.edu 37 3 142241646 142241648 + In_Frame_Del DEL AAT AAT - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr3:142241646_142241648delAAT ENST00000350721.4 - 23 4309_4311 c.4188_4190delATT c.(4186-4191)ttg>tt p.LL1396del ATR_ENST00000383101.3_In_Frame_Del_p.LL1332del NM_001184.3 NP_001175.2 Q13535 ATR_HUMAN ataxia telangiectasia and Rad3 related 1396 cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence PML body ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4) 122 TAGCTCCATCAATAATCCATAGG 0.379 Other conserved DNA damage response genes 12 571 --- --- --- --- WWTR1 25937 broad.mit.edu 37 3 149260194 149260196 + In_Frame_Del DEL CTG CTG - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr3:149260194_149260196delCTG ENST00000465804.1 - 5 953_955 c.697_699delCAG c.(697-699)del p.Q233del WWTR1_ENST00000360632.3_In_Frame_Del_p.Q233del|WWTR1_ENST00000467467.1_In_Frame_Del_p.Q233del NM_001168278.1 NP_001161750.1 Q9GZV5 WWTR1_HUMAN WW domain containing transcription regulator 1 233 Gln-rich. hippo signaling cascade|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of protein kinase activity|negative regulation of protein phosphorylation|positive regulation of cell proliferation|positive regulation of epithelial to mesenchymal transition|regulation of SMAD protein import into nucleus|stem cell division|transcription, DNA-dependent cytoplasm transcription coactivator activity breast(5)|cervix(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1) 23 LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048) GCCGCAGTTTCTGCTGCTGCTGC 0.581 T CAMTA1 epitheliod hemangioendothelioma 8 349 --- --- --- --- ZNF876P 0 broad.mit.edu 37 4 212236 212236 + RNA DEL A A - rs80061878 TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr4:212236delA ENST00000356347.3 + 0 172 NR_027481.1 ctaaaaatacaaaaaaaaaaa 0.493 7 10 --- --- --- --- GABRG1 2565 broad.mit.edu 37 4 46060358 46060358 + Frame_Shift_Del DEL A A - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr4:46060358delA ENST00000295452.4 - 7 959 c.792delT c.(790-792)ttfs p.F264fs NM_173536.3 NP_775807.2 Q8N1C3 GBRG1_HUMAN gamma-aminobutyric acid (GABA) A receptor, gamma 1 264 gamma-aminobutyric acid signaling pathway cell junction|chloride channel complex|postsynaptic membrane chloride channel activity|extracellular ligand-gated ion channel activity p.F264fs*3(1) breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 76 Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23) TGCTCAGGTCAAAAAAAATTG 0.294 9 376 --- --- --- --- PKD2 5311 broad.mit.edu 37 4 88986559 88986559 + Frame_Shift_Del DEL A A - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr4:88986559delA ENST00000237596.2 + 11 2218 c.2152delA c.(2152-2154)aafs p.K719fs PKD2_ENST00000502363.1_Frame_Shift_Del_p.K137fs|PKD2_ENST00000508588.1_Frame_Shift_Del_p.K137fs|PKD2_ENST00000511337.1_3'UTR NM_000297.3 NP_000288.1 Q13563 PKD2_HUMAN polycystic kidney disease 2 (autosomal dominant) 719 EF-hand domain. basal cortex|basal plasma membrane|endoplasmic reticulum|integral to membrane|lamellipodium|microtubule basal body calcium ion binding|cytoskeletal protein binding|voltage-gated chloride channel activity|voltage-gated sodium channel activity breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(2)|lung(15)|skin(4)|upper_aerodigestive_tract(1) 36 Hepatocellular(203;0.114)|Acute lymphoblastic leukemia(40;0.221) OV - Ovarian serous cystadenocarcinoma(123;9.98e-10)|COAD - Colon adenocarcinoma(81;0.0237) ACTAAAACTGAAAAAAAATAC 0.383 9 752 --- --- --- --- NAP1L5 266812 broad.mit.edu 37 4 89618484 89618486 + In_Frame_Del DEL TCC TCC - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr4:89618484_89618486delTCC ENST00000323061.5 - 1 900_902 c.420_422delGGA c.(418-423)gaa>ga p.EE142del HERC3_ENST00000402738.1_Intron|HERC3_ENST00000264345.3_Intron|HERC3_ENST00000543130.1_Intron NM_153757.2 NP_715638.1 Q96NT1 NP1L5_HUMAN nucleosome assembly protein 1-like 5 142 Glu-rich. nucleosome assembly nucleus protein binding endometrium(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1) 7 OV - Ovarian serous cystadenocarcinoma(123;0.000181) gtactcctcttcctcctcctcct 0.606 17 459 --- --- --- --- OTUD4 54726 broad.mit.edu 37 4 146077123 146077125 + In_Frame_Del DEL CAG CAG - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr4:146077123_146077125delCAG ENST00000454497.2 - 8 595_597 c.458_460delCTG c.(457-462)gat>g p.AD153del OTUD4_ENST00000455611.2_5'UTR|OTUD4_ENST00000447906.2_In_Frame_Del_p.AD218del NM_001102653.1 NP_001096123.1 Q01804 OTUD4_HUMAN OTU domain containing 4 218 OTU. protein binding breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2) 33 all_hematologic(180;0.151) CCATTCACATCAGCAGCAGCAGC 0.340 7 427 --- --- --- --- CDH10 1008 broad.mit.edu 37 5 24492973 24492973 + Frame_Shift_Del DEL A A - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr5:24492973delA ENST00000264463.4 - 10 2084 c.1577delT c.(1576-1578)tcfs p.F526fs CDH10_ENST00000502921.1_5'UTR NM_006727.3 NP_006718.2 Q9Y6N8 CAD10_HUMAN cadherin 10, type 2 (T2-cadherin) 526 Cadherin 5. adherens junction organization|cell junction assembly|homophilic cell adhesion integral to membrane|plasma membrane calcium ion binding NS(1)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(29)|lung(111)|ovary(6)|pancreas(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(4) 185 STAD - Stomach adenocarcinoma(35;0.0556) AGCTAAACTGAAAAAAAATTT 0.313 HNSCC(23;0.051) 7 967 --- --- --- --- ZFR 51663 broad.mit.edu 37 5 32419951 32419953 + In_Frame_Del DEL GGT GGT - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr5:32419951_32419953delGGT ENST00000265069.8 - 3 495_497 c.393_395delACC c.(391-396)ccc>cc p.PP131del NM_016107.3 NP_057191.2 Q96KR1 ZFR_HUMAN zinc finger RNA binding protein 131 Ala-rich. multicellular organismal development chromosome|cytoplasm|nucleus DNA binding|RNA binding|zinc ion binding breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|upper_aerodigestive_tract(2) 32 STAD - Stomach adenocarcinoma(35;0.19) AGTAGCTGGGGGTGGTGGTGGTG 0.483 8 1076 --- --- --- --- C1QTNF3 114899 broad.mit.edu 37 5 34042955 34042955 + Frame_Shift_Del DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr5:34042955delT ENST00000382065.3 - 1 982 c.276delA c.(274-276)ctfs p.L92fs C1QTNF3_ENST00000231338.7_Intron NM_181435.5 NP_852100.3 Q9BXJ4 C1QT3_HUMAN C1q and tumor necrosis factor related protein 3 0 Collagen-like. collagen breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|prostate(3)|stomach(1)|urinary_tract(1) 17 all_lung(31;0.0207) TGATCTGGGCTAGGTCATCTA 0.453 15 872 --- --- --- --- FGF10 2255 broad.mit.edu 37 5 44388715 44388717 + In_Frame_Del DEL AGC AGC - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr5:44388715_44388717delAGC ENST00000264664.4 - 1 182_184 c.68_70delGCT c.(67-72)ttt>t p.CF23del NM_004465.1 NP_004456.1 O15520 FGF10_HUMAN fibroblast growth factor 10 23 actin cytoskeleton reorganization|activation of MAPK activity|bud outgrowth involved in lung branching|ERK1 and ERK2 cascade|fibroblast growth factor receptor signaling pathway involved in mammary gland specification|insulin receptor signaling pathway|lacrimal gland development|lung saccule development|mesonephros development|negative regulation of cell cycle arrest|positive regulation of ATPase activity|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of DNA repair|positive regulation of DNA replication|positive regulation of epithelial cell migration|positive regulation of epithelial cell proliferation involved in wound healing|positive regulation of ERK1 and ERK2 cascade|positive regulation of hair follicle cell proliferation|positive regulation of keratinocyte migration|positive regulation of keratinocyte proliferation|positive regulation of lymphocyte proliferation|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of Ras protein signal transduction|positive regulation of transcription, DNA-dependent|positive regulation of urothelial cell proliferation|protein localization at cell surface|radial glial cell differentiation|regulation of saliva secretion|response to protein stimulus|secretion by lung epithelial cell involved in lung growth|tear secretion|thymus development|urothelial cell proliferation cell surface|extracellular space|nucleus|plasma membrane chemoattractant activity|growth factor activity|heparin binding|type 2 fibroblast growth factor receptor binding haematopoietic_and_lymphoid_tissue(1)|lung(11)|skin(1) 13 Lung NSC(6;1.12e-06) AGCAACAAAAAGCAGCAGCAGCA 0.537 7 423 --- --- --- --- GTF2H2B 0 broad.mit.edu 37 5 69730714 69730715 + RNA INS - - T TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr5:69730714_69730715insT ENST00000513202.1 + 0 753 NR_033417.1 CTATGAAGGTGTTTTTTTTTCC 0.322 13 479 --- --- --- --- THBS4 7060 broad.mit.edu 37 5 79372774 79372776 + In_Frame_Del DEL TGA TGA - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr5:79372774_79372776delTGA ENST00000350881.2 + 16 2179_2181 c.1989_1991delTGA c.(1987-1992)tgt>tg p.CD663del CTD-2201I18.1_ENST00000503007.1_RNA|CTD-2201I18.1_ENST00000514042.1_RNA|THBS4_ENST00000511733.1_In_Frame_Del_p.CD572del NM_003248.4 NP_003239.2 P35443 TSP4_HUMAN thrombospondin 4 663 endothelial cell-cell adhesion|myoblast migration|negative regulation of angiogenesis|positive regulation of endothelial cell proliferation|positive regulation of neutrophil chemotaxis|positive regulation of peptidyl-tyrosine phosphorylation basement membrane|extracellular space calcium ion binding|heparin binding|integrin binding|structural molecule activity breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|stomach(3) 34 Lung NSC(167;0.00328)|all_lung(232;0.00355)|Ovarian(174;0.0261) OV - Ovarian serous cystadenocarcinoma(54;6.3e-45)|Epithelial(54;1.77e-39)|all cancers(79;3.2e-34) GTGACGAGTGTGATGATGATGAT 0.562 9 1531 --- --- --- --- MSH3 4437 broad.mit.edu 37 5 79970915 79970915 + Frame_Shift_Del DEL A A - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr5:79970915delA ENST00000265081.6 + 7 1221 c.1141delA c.(1141-1143)aafs p.K383fs NM_002439.4 NP_002430.3 P20585 MSH3_HUMAN mutS homolog 3 383 maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments MutSbeta complex|nuclear chromosome ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2) 29 Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244) OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33) TGTTAGGGACAAAAAAAAGGG 0.348 Mismatch excision repair (MMR) 12 892 --- --- --- --- CSNK1G3 1456 broad.mit.edu 37 5 122881495 122881495 + Frame_Shift_Del DEL A A - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr5:122881495delA ENST00000395412.1 + 2 857 c.138delA c.(136-138)ggfs p.G46fs CSNK1G3_ENST00000361991.2_Frame_Shift_Del_p.G46fs|CSNK1G3_ENST00000360683.2_Frame_Shift_Del_p.G46fs|CSNK1G3_ENST00000512718.3_Intron|CSNK1G3_ENST00000521364.1_Frame_Shift_Del_p.G46fs|CSNK1G3_ENST00000345990.4_Frame_Shift_Del_p.G46fs|CSNK1G3_ENST00000508708.1_3'UTR|CSNK1G3_ENST00000511130.2_Intron|CSNK1G3_ENST00000510842.2_Frame_Shift_Del_p.G46fs|CSNK1G3_ENST00000395411.1_Frame_Shift_Del_p.G46fs NM_001044723.1 NP_001038188.1 Q9Y6M4 KC1G3_HUMAN casein kinase 1, gamma 3 46 Protein kinase. Wnt receptor signaling pathway cytoplasm ATP binding|protein serine/threonine kinase activity autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(3)|prostate(1)|skin(1) 15 all_cancers(142;0.0156)|Prostate(80;0.0322)|Lung NSC(810;0.245) KIRC - Kidney renal clear cell carcinoma(527;0.165)|Kidney(363;0.229) OV - Ovarian serous cystadenocarcinoma(64;0.000121)|Epithelial(69;0.000227)|all cancers(49;0.00176) TTAGAGTTGGAAAAAAAATTG 0.363 8 737 --- --- --- --- ANKHD1 54882 broad.mit.edu 37 5 139905676 139905676 + Frame_Shift_Del DEL A A - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr5:139905676delA ENST00000297183.6 + 26 4712 c.4588delA c.(4588-4590)aafs p.K1531fs ANKHD1-EIF4EBP3_ENST00000532219.1_Frame_Shift_Del_p.K1531fs|ANKHD1_ENST00000360839.2_Frame_Shift_Del_p.K1531fs NM_020690.5 NP_065741.3 ankyrin repeat and KH domain containing 1 breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2) 60 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) TGTGTTTGGGAAAAAAAGGGC 0.423 9 1146 --- --- --- --- PCDHB14 0 broad.mit.edu 37 5 140604247 140604247 + Frame_Shift_Del DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr5:140604247delT ENST00000239449.4 + 1 1170 c.1170delT c.(1168-1170)ccfs p.P390fs PCDHB14_ENST00000515856.2_Frame_Shift_Del_p.P237fs NM_018934.2 NP_061757.1 Q9Y5E9 PCDBE_HUMAN 390 Cadherin 4. calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission integral to membrane|plasma membrane calcium ion binding NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1) 49 KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339) ATAACCTCCCTTTTTTCCTGA 0.443 7 893 --- --- --- --- RBM27 54439 broad.mit.edu 37 5 145647320 145647320 + Frame_Shift_Del DEL A A - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr5:145647320delA ENST00000265271.5 + 15 2606 c.2440delA c.(2440-2442)aafs p.K816fs RBM27_ENST00000506502.1_Frame_Shift_Del_p.K761fs NM_018989.1 NP_061862.1 Q9P2N5 RBM27_HUMAN RNA binding motif protein 27 816 mRNA processing cytoplasm|nuclear speck nucleotide binding|RNA binding|zinc ion binding p.K816fs*5(1) NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1) 39 KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) AGAAGTGCTTAAAAAAAAACA 0.348 9 407 --- --- --- --- PPARGC1B 133522 broad.mit.edu 37 5 149216457 149216459 + In_Frame_Del DEL GGA GGA - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr5:149216457_149216459delGGA ENST00000309241.5 + 8 2471_2473 c.2439_2441delGGA c.(2437-2442)ggg>gg p.GE813del PPARGC1B_ENST00000403750.1_In_Frame_Del_p.GE749del|PPARGC1B_ENST00000360453.4_In_Frame_Del_p.GE774del|PPARGC1B_ENST00000394320.3_In_Frame_Del_p.GE813del NM_133263.3 NP_573570.3 Q86YN6 PRGC2_HUMAN peroxisome proliferator-activated receptor gamma, coactivator 1 beta 813 Glu-rich. estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter mediator complex AF-2 domain binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|receptor activator activity|RNA binding|RNA polymerase II transcription cofactor activity NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(2)|lung(15)|ovary(3)|prostate(2)|stomach(1) 30 KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147) aggaagaaggggaggaggaggag 0.606 8 580 --- --- --- --- STK10 6793 broad.mit.edu 37 5 171583751 171583760 + Frame_Shift_Del DEL GACTTTGGCC GACTTTGGCC - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr5:171583751_171583760delGACTTTGGCC ENST00000176763.5 - 2 532_541 c.189_198delGGCCAAAGTC c.(187-198)gcfs p.AAKV63fs NM_005990.3 NP_005981.3 O94804 STK10_HUMAN serine/threonine kinase 10 63 Protein kinase. ATP binding|protein serine/threonine kinase activity breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2) 47 Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094) Medulloblastoma(196;0.00868)|all_neural(177;0.026) Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516) TGGTTTCAATGACTTTGGCCGCAGCCAAAG 0.552 15 728 --- --- --- --- EDN1 1906 broad.mit.edu 37 6 12292614 12292615 + Frame_Shift_Ins INS - - G TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr6:12292614_12292615insG ENST00000379375.5 + 2 372_373 c.105_106insG c.(103-108)gggggafs p.GG35fs NM_001168319.1|NM_001955.4 NP_001161791.1|NP_001946.3 P05305 EDN1_HUMAN endothelin 1 35 artery smooth muscle contraction|calcium-mediated signaling|leukocyte activation|negative regulation of blood coagulation|negative regulation of cellular protein metabolic process|negative regulation of nitric-oxide synthase biosynthetic process|negative regulation of transcription from RNA polymerase II promoter|nitric oxide transport|peptide hormone secretion|phosphatidylinositol 3-kinase cascade|positive regulation of cardiac muscle hypertrophy|positive regulation of cell size|positive regulation of endothelial cell migration|positive regulation of heart rate|positive regulation of hormone secretion|positive regulation of JUN kinase activity|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of prostaglandin-endoperoxide synthase activity|positive regulation of sarcomere organization|positive regulation of smooth muscle cell proliferation|prostaglandin biosynthetic process|protein kinase C deactivation|regulation of systemic arterial blood pressure by endothelin|regulation of vasoconstriction|vein smooth muscle contraction cytoplasm|extracellular space cytokine activity|endothelin A receptor binding|endothelin B receptor binding|hormone activity endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1) 13 all_cancers(95;0.241)|Breast(50;0.0266)|Ovarian(93;0.12) all_hematologic(90;0.117) GTGAGAACGGCGGGGAGAAACC 0.619 7 765 --- --- --- --- HIST1H4K 8362 broad.mit.edu 37 6 27799162 27799163 + Frame_Shift_Ins INS - - A TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr6:27799162_27799163insA ENST00000357549.2 - 1 142_143 c.143_144insT c.(142-144)tggfs p.W48fs NM_003541.2 NP_003532.1 P62805 H4_HUMAN histone cluster 1, H4k 48 CenH3-containing nucleosome assembly at centromere|negative regulation of megakaryocyte differentiation|phosphatidylinositol-mediated signaling|telomere maintenance nucleoplasm|nucleosome DNA binding|protein binding breast(1)|endometrium(1)|lung(3)|ovary(1)|prostate(1) 7 AGATGAGGCCGGAGATGCGCTT 0.644 7 192 --- --- --- --- OR2J2 26707 broad.mit.edu 37 6 29141422 29141422 + Frame_Shift_Del DEL A A - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr6:29141422delA ENST00000377167.2 + 1 112 c.10delA c.(10-12)aafs p.K5fs NM_030905.2 NP_112167.2 O76002 OR2J2_HUMAN olfactory receptor, family 2, subfamily J, member 2 5 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(17)|ovary(1)|upper_aerodigestive_tract(1) 25 AATGATGATTAAAAAAAATGC 0.358 8 634 --- --- --- --- PPP1R10 5514 broad.mit.edu 37 6 30570264 30570266 + In_Frame_Del DEL GGA GGA - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr6:30570264_30570266delGGA ENST00000376511.2 - 19 2712_2714 c.2160_2162delTCC c.(2158-2163)cca>cc p.PP720del NM_002714.3 NP_002705.2 Q96QC0 PP1RA_HUMAN protein phosphatase 1, regulatory subunit 10 720 Gly-rich. protein import into nucleus|transcription, DNA-dependent PTW/PP1 phosphatase complex DNA binding|protein phosphatase inhibitor activity|RNA binding|zinc ion binding cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(3)|skin(1) 25 GCCTCGGAATggaggaggaggag 0.670 7 390 --- --- --- --- STK19 8859 broad.mit.edu 37 6 31939825 31939826 + Frame_Shift_Ins INS - - G TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr6:31939825_31939826insG ENST00000375331.2 + 1 218_219 c.52_53insG c.(52-54)ggcfs p.G18fs STK19_ENST00000375333.2_Frame_Shift_Ins_p.G18fs|DOM3Z_ENST00000375349.3_5'UTR|DOM3Z_ENST00000478221.1_5'UTR|DOM3Z_ENST00000337523.5_5'UTR NM_004197.1 NP_004188.1 P49842 STK19_HUMAN serine/threonine kinase 19 18 nucleus ATP binding|protein binding|protein serine/threonine kinase activity skin(5)|upper_aerodigestive_tract(2) 7 GCGACAGTGGCGGGCAAACCCC 0.634 31 907 --- --- --- --- STK19 8859 broad.mit.edu 37 6 31939829 31939830 + Frame_Shift_Ins INS - - A TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr6:31939829_31939830insA ENST00000375331.2 + 1 222_223 c.56_57insA c.(55-57)gaafs p.E19fs STK19_ENST00000375333.2_Frame_Shift_Ins_p.E19fs|DOM3Z_ENST00000375349.3_5'UTR|DOM3Z_ENST00000478221.1_5'UTR|DOM3Z_ENST00000337523.5_5'UTR NM_004197.1 NP_004188.1 P49842 STK19_HUMAN serine/threonine kinase 19 19 nucleus ATP binding|protein binding|protein serine/threonine kinase activity skin(5)|upper_aerodigestive_tract(2) 7 CAGTGGCGGGCAAACCCCTCCC 0.634 16 780 --- --- --- --- UHRF1BP1 54887 broad.mit.edu 37 6 34804004 34804006 + In_Frame_Del DEL CAG CAG - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr6:34804004_34804006delCAG ENST00000192788.5 + 8 1083_1085 c.912_914delCAG c.(910-915)aac>aa p.NS304del UHRF1BP1_ENST00000452449.2_In_Frame_Del_p.NS304del NM_017754.3 NP_060224.3 Q6BDS2 URFB1_HUMAN UHRF1 binding protein 1 304 breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2) 54 GCAACAGCAACAGCAGCAGCAGC 0.552 7 1299 --- --- --- --- UHRF1BP1 54887 broad.mit.edu 37 6 34826124 34826124 + Frame_Shift_Del DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr6:34826124delT ENST00000192788.5 + 14 2162 c.1991delT c.(1990-1992)ctfs p.L664fs UHRF1BP1_ENST00000452449.2_Frame_Shift_Del_p.L664fs NM_017754.3 NP_060224.3 Q6BDS2 URFB1_HUMAN UHRF1 binding protein 1 664 p.L666fs*15(1) breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2) 54 CTGCACATGCTTTTTTTGCAT 0.502 9 656 --- --- --- --- C6orf89 221477 broad.mit.edu 37 6 36867371 36867371 + Frame_Shift_Del DEL C C - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr6:36867371delC ENST00000480824.2 + 3 445 c.151delC c.(151-153)ccfs p.P53fs C6orf89_ENST00000373685.1_Frame_Shift_Del_p.P53fs|C6orf89_ENST00000510325.2_5'UTR|C6orf89_ENST00000359359.2_5'UTR|C6orf89_ENST00000355190.3_Frame_Shift_Del_p.P60fs Q6UWU4 CF089_HUMAN chromosome 6 open reading frame 89 53 integral to membrane breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(2) 15 ACCTCAGAGACCCCCCCCGCA 0.428 8 502 --- --- --- --- FOXP4 116113 broad.mit.edu 37 6 41555186 41555186 + Frame_Shift_Del DEL C C - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr6:41555186delC ENST00000373060.1 + 7 1266 c.808delC c.(808-810)ccfs p.P271fs FOXP4_ENST00000409208.1_Frame_Shift_Del_p.P271fs|FOXP4_ENST00000307972.4_Frame_Shift_Del_p.P271fs|FOXP4_ENST00000373057.3_Frame_Shift_Del_p.P269fs|FOXP4_ENST00000373063.3_Frame_Shift_Del_p.P270fs NM_001012426.1|NM_001012427.1 NP_001012426.1|NP_001012427.1 Q8IVH2 FOXP4_HUMAN forkhead box P4 271 embryonic foregut morphogenesis|heart development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development cytoplasm|transcription factor complex chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1) 16 Ovarian(28;0.0327)|Colorectal(47;0.196) CAAGGTCTCACCCCCCCTCTC 0.677 OREG0004065 type=REGULATORY REGION|Gene=FOXP4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay 7 701 --- --- --- --- ICK 22858 broad.mit.edu 37 6 52883129 52883129 + Splice_Site DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr6:52883129delT ENST00000356971.3 - 8 1151 c.663_splice c.e8+1 p.K221_splice ICK_ENST00000350082.5_Splice_Site_p.K221_splice NM_016513.4 NP_057597.2 Q9UPZ9 ICK_HUMAN intestinal cell (MAK-like) kinase 221 Protein kinase. intracellular protein kinase cascade|multicellular organismal development cytosol|nucleus ATP binding|cyclin-dependent protein kinase activity|magnesium ion binding breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(3)|stomach(1) 31 Lung NSC(77;0.103) TATCATTACCTTTTTTGGTGT 0.502 9 1400 --- --- --- --- MAP3K7 6885 broad.mit.edu 37 6 91296568 91296570 + In_Frame_Del DEL GAG GAG - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr6:91296568_91296570delGAG ENST00000369329.3 - 1 194_196 c.33_35delCTC c.(31-36)tcg>tc p.SS13del MAP3K7_ENST00000369332.3_In_Frame_Del_p.SS13del|MAP3K7_ENST00000369327.3_In_Frame_Del_p.SS13del|MAP3K7_ENST00000369325.3_In_Frame_Del_p.SS13del NM_145331.2 NP_663304.1 O43318 M3K7_HUMAN mitogen-activated protein kinase kinase kinase 7 13 Poly-Ser. activation of MAPK activity|activation of NF-kappaB-inducing kinase activity|histone H3 acetylation|I-kappaB phosphorylation|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of T cell cytokine production|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transforming growth factor beta receptor signaling pathway Ada2/Gcn5/Ada3 transcription activator complex|cytosol|endosome membrane ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2) 28 all_cancers(76;6.4e-08)|Acute lymphoblastic leukemia(125;1.43e-09)|Prostate(29;9.32e-09)|all_hematologic(105;3.69e-06)|all_epithelial(107;0.000187)|Ovarian(999;0.0164) OV - Ovarian serous cystadenocarcinoma(136;2.05e-11)|all cancers(137;3.25e-11)|GBM - Glioblastoma multiforme(226;0.0416)|BRCA - Breast invasive adenocarcinoma(108;0.0429) GGCCGAAGACGAGGAGGAGGAGG 0.655 7 149 --- --- --- --- ASCC3 10973 broad.mit.edu 37 6 101296336 101296336 + Frame_Shift_Del DEL A A - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr6:101296336delA ENST00000369162.2 - 4 833 c.489delT c.(487-489)ttfs p.F163fs ASCC3_ENST00000522650.1_Frame_Shift_Del_p.F163fs NM_006828.2 NP_006819.2 Q8N3C0 HELC1_HUMAN activating signal cointegrator 1 complex subunit 3 163 regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|microtubule cytoskeleton ATP binding|ATP-dependent helicase activity|nucleic acid binding breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2) 92 all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13) BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199) AATTTTTACCAAAAAAAACCC 0.333 7 363 --- --- --- --- OLIG3 167826 broad.mit.edu 37 6 137815210 137815212 + In_Frame_Del DEL TGG TGG - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr6:137815210_137815212delTGG ENST00000367734.2 - 1 319_321 c.96_98delCCA c.(94-99)cag>ca p.HQ32del NM_175747.2 NP_786923.1 Q7RTU3 OLIG3_HUMAN oligodendrocyte transcription factor 3 32 Poly-His. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding p.Q33K(1) endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1) 11 Breast(32;0.165)|Colorectal(23;0.24) GBM - Glioblastoma multiforme(68;0.00161)|OV - Ovarian serous cystadenocarcinoma(155;0.00447) ACGGCTCTCCtggtggtggtggt 0.596 10 562 --- --- --- --- PHF14 9678 broad.mit.edu 37 7 11075380 11075381 + Frame_Shift_Del DEL AG AG - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr7:11075380_11075381delAG ENST00000403050.3 + 8 2021_2022 c.1569_1570delAG c.(1567-1572)caagfs p.QE523fs PHF14_ENST00000445996.2_Frame_Shift_Del_p.QE238fs NM_014660.3 NP_055475.2 O94880 PHF14_HUMAN PHD finger protein 14 523 zinc ion binding NS(2)|breast(1)|endometrium(4)|kidney(5)|large_intestine(5)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2) 35 UCEC - Uterine corpus endometrioid carcinoma (126;0.205) TGTCTTTGCAAGAGAGAGAGAA 0.376 7 1221 --- --- --- --- PPP1R17 10842 broad.mit.edu 37 7 31735179 31735179 + Frame_Shift_Del DEL A A - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr7:31735179delA ENST00000342032.3 + 3 807 c.179delA c.(178-180)cafs p.Q60fs PPP1R17_ENST00000409146.3_Intron NM_006658.4 NP_006649.2 O96001 GSUB_HUMAN protein phosphatase 1, regulatory subunit 17 60 behavior|central nervous system development|intracellular protein kinase cascade|protein phosphorylation soluble fraction GAGTCAGACCAAAAAAAACCA 0.438 8 990 --- --- --- --- POU6F2 11281 broad.mit.edu 37 7 39379288 39379290 + In_Frame_Del DEL CAG CAG - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr7:39379288_39379290delCAG ENST00000518318.2 + 5 601_603 c.559_561delCAG c.(559-561)del p.Q196del POU6F2_ENST00000517348.1_3'UTR|POU6F2_ENST00000559001.1_In_Frame_Del_p.Q188del|POU6F2_ENST00000403058.1_In_Frame_Del_p.Q196del P78424 PO6F2_HUMAN POU class 6 homeobox 2 196 Gln-rich. Q -> QQ (in Ref. 1; AAB49727/AAB49728). central nervous system development|ganglion mother cell fate determination|transcription from RNA polymerase II promoter|visual perception sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity NS(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2) 42 gctccagctccagcagcagcagc 0.616 10 208 --- --- --- --- INHBA 3624 broad.mit.edu 37 7 41729741 41729743 + In_Frame_Del DEL TTC TTC - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr7:41729741_41729743delTTC ENST00000242208.4 - 3 1032_1034 c.786_788delGAA c.(784-789)aaa>aa p.KK262del INHBA_ENST00000442711.1_In_Frame_Del_p.KK262del|INHBA_ENST00000464515.1_5'UTR|AC005027.3_ENST00000416150.1_RNA NM_002192.2 NP_002183.1 P08476 INHBA_HUMAN inhibin, beta A 262 cell cycle arrest|cell surface receptor linked signaling pathway|defense response|erythrocyte differentiation|eyelid development in camera-type eye|G1/S transition of mitotic cell cycle|growth|hair follicle development|hemoglobin biosynthetic process|hemopoietic progenitor cell differentiation|induction of apoptosis|male gonad development|negative regulation of B cell differentiation|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of follicle-stimulating hormone secretion|negative regulation of interferon-gamma biosynthetic process|negative regulation of macrophage differentiation|negative regulation of phosphorylation|nervous system development|odontogenesis|ovarian follicle development|palate development|positive regulation of erythrocyte differentiation|positive regulation of follicle-stimulating hormone secretion|positive regulation of ovulation|positive regulation of transcription from RNA polymerase II promoter|progesterone secretion|regulation of activin receptor signaling pathway activin A complex|inhibin A complex cytokine activity|follistatin binding|growth factor activity|hormone activity|identical protein binding|signal transducer activity biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(15)|lung(26)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 55 ctcctcttctttcttcttcttct 0.581 TSP Lung(11;0.080) 8 283 --- --- --- --- DTX2 113878 broad.mit.edu 37 7 76112249 76112249 + Frame_Shift_Del DEL A A - rs147779783 byFrequency TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr7:76112249delA ENST00000324432.5 + 5 1203 c.693delA c.(691-693)ccfs p.P231fs DTX2_ENST00000413936.2_Frame_Shift_Del_p.P231fs|DTX2_ENST00000446600.1_Frame_Shift_Del_p.P140fs|DTX2_ENST00000307569.8_Frame_Shift_Del_p.P231fs|DTX2_ENST00000430490.2_Frame_Shift_Del_p.P231fs|DTX2_ENST00000446820.2_Frame_Shift_Del_p.P231fs NM_020892.2 NP_065943.2 Q86UW9 DTX2_HUMAN deltex homolog 2 (Drosophila) 231 Notch signaling pathway cytoplasm|nucleus protein binding|zinc ion binding NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(1)|skin(1)|stomach(2) 27 AGCACCCCCCACACAGGACCG 0.657 8 2045 --- --- --- --- TMEM60 85025 broad.mit.edu 37 7 77423460 77423460 + Frame_Shift_Del DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr7:77423460delT ENST00000257663.3 - 2 607 c.231delA c.(229-231)aafs p.K77fs NM_032936.3 NP_116325.1 Q9H2L4 TMM60_HUMAN transmembrane protein 60 77 integral to membrane endometrium(1)|large_intestine(1)|lung(2) 4 GGTACCAGGCTTTTTTTTTAA 0.408 20 756 --- --- --- --- PCLO 27445 broad.mit.edu 37 7 82595385 82595385 + Frame_Shift_Del DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr7:82595385delT ENST00000423517.2 - 4 4056 c.3719delA c.(3718-3720)agfs p.K1240fs PCLO_ENST00000333891.8_Frame_Shift_Del_p.K1240fs NM_014510.2 NP_055325.2 Q9Y6V0 PCLO_HUMAN piccolo presynaptic cytomatrix protein 1179 cytoskeleton organization|synaptic vesicle exocytosis cell junction|cytoskeleton|synaptic vesicle calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2) 259 AGGGGTTGGCTTTTTTTCTTC 0.383 8 1917 --- --- --- --- SRRT 51593 broad.mit.edu 37 7 100479332 100479332 + Frame_Shift_Del DEL G G - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr7:100479332delG ENST00000388793.4 + 4 524 c.304delG c.(304-306)ggfs p.G106fs SRRT_ENST00000347433.4_Frame_Shift_Del_p.G106fs|SRRT_ENST00000432932.1_Frame_Shift_Del_p.G106fs|SRRT_ENST00000457580.2_Frame_Shift_Del_p.G106fs NM_001128852.1|NM_015908.5 NP_001122324.1|NP_056992.4 Q9BXP5 SRRT_HUMAN serrate RNA effector molecule homolog (Arabidopsis) 106 G -> GG (in Ref. 3; CAB46374). cell proliferation|primary miRNA processing|response to arsenic-containing substance cytoplasm|nucleoplasm protein binding p.G104fs*45(1) breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1) 40 GCCCTATGCTGGGGGGGGTGG 0.607 8 301 --- --- --- --- WASL 8976 broad.mit.edu 37 7 123332873 123332875 + In_Frame_Del DEL GGA GGA - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr7:123332873_123332875delGGA ENST00000223023.4 - 9 1205_1207 c.873_875delTCC c.(871-876)ccc>cc p.PP293del NM_003941.2 NP_003932.3 O00401 WASL_HUMAN Wiskott-Aldrich syndrome-like 293 Pro-rich. actin polymerization or depolymerization|axon guidance|cellular component movement|nitric oxide metabolic process|protein complex assembly|regulation of nitric-oxide synthase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent actin cytoskeleton|cytosol|nucleolus|plasma membrane actin binding|small GTPase regulator activity endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 29 gtgtggagggggaggaggaggag 0.567 8 499 --- --- --- --- CNOT4 4850 broad.mit.edu 37 7 135047688 135047688 + Frame_Shift_Del DEL G G - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr7:135047688delG ENST00000541284.1 - 12 2421 c.2091delC c.(2089-2091)ccfs p.P697fs CNOT4_ENST00000451834.1_Frame_Shift_Del_p.P694fs|CNOT4_ENST00000361528.4_Frame_Shift_Del_p.P623fs|CNOT4_ENST00000423368.2_Frame_Shift_Del_p.P626fs NM_001190849.1|NM_001190850.1 NP_001177778.1|NP_001177779.1 O95628 CNOT4_HUMAN CCR4-NOT transcription complex, subunit 4 366 nuclear-transcribed mRNA poly(A) tail shortening|protein autoubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|nucleus nucleotide binding|protein binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1) 22 GGGTTTTGCTGGGGGGTCTGA 0.532 7 2164 --- --- --- --- MCPH1 79648 broad.mit.edu 37 8 6289099 6289099 + Frame_Shift_Del DEL A A - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr8:6289099delA ENST00000344683.5 + 4 389 c.313delA c.(313-315)aafs p.K107fs MCPH1_ENST00000522905.1_Frame_Shift_Del_p.K107fs|MCPH1_ENST00000519480.1_Frame_Shift_Del_p.K107fs NM_024596.3 NP_078872.2 Q8NEM0 MCPH1_HUMAN microcephalin 1 107 microtubule organizing center AGPAT5/MCPH1(2) central_nervous_system(1)|large_intestine(4)|skin(1) 6 Hepatocellular(245;0.0663) Colorectal(4;0.0505) AAGCCTAATTAAAAAAAAAGT 0.274 10 484 --- --- --- --- FAM66B 0 broad.mit.edu 37 8 7196263 7196264 + RNA DEL AC AC - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr8:7196263_7196264delAC ENST00000606573.1 - 0 703 ACTGAGGGGTacacacacacac 0.500 8 15 --- --- --- --- DLC1 10395 broad.mit.edu 37 8 12958019 12958019 + Frame_Shift_Del DEL G G - rs145646504 TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr8:12958019delG ENST00000276297.4 - 9 2236 c.1827delC c.(1825-1827)ccfs p.P609fs DLC1_ENST00000512044.2_Frame_Shift_Del_p.P206fs|DLC1_ENST00000520226.1_Frame_Shift_Del_p.P98fs|DLC1_ENST00000358919.2_Frame_Shift_Del_p.P172fs NM_182643.2 NP_872584.2 Q96QB1 RHG07_HUMAN deleted in liver cancer 1 609 actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction caveola|cytosol|focal adhesion|nucleus Rho GTPase activator activity|SH2 domain binding NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1) 110 CATCCTCGCTGGGGGGCGCGT 0.672 7 662 --- --- --- --- NUGGC 389643 broad.mit.edu 37 8 27888776 27888776 + Frame_Shift_Del DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr8:27888776delT ENST00000413272.2 - 15 2034 c.1892delA c.(1891-1893)atfs p.N631fs NUGGC_ENST00000341513.6_Frame_Shift_Del_p.N631fs NM_001010906.1 NP_001010906.1 nuclear GTPase, germinal center associated GATCAGGAAATTTTTTTTGCA 0.453 9 1163 --- --- --- --- TEX15 56154 broad.mit.edu 37 8 30695491 30695491 + Frame_Shift_Del DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr8:30695491delT ENST00000256246.2 - 3 7234 c.7160delA c.(7159-7161)agfs p.K2387fs NM_031271.3 NP_112561.2 Q9BXT5 TEX15_HUMAN testis expressed 15 2387 NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1) 138 KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111) CATTTCAACCTTTTTTGGCGT 0.388 7 910 --- --- --- --- FGFR1 2260 broad.mit.edu 37 8 38285914 38285916 + In_Frame_Del DEL TCA TCA - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr8:38285914_38285916delTCA ENST00000447712.2 - 4 1337_1339 c.396_398delTGA c.(394-399)gac>ga p.DD132del FGFR1_ENST00000532791.1_In_Frame_Del_p.DD132del|FGFR1_ENST00000341462.5_In_Frame_Del_p.DD135del|FGFR1_ENST00000425967.3_In_Frame_Del_p.DD165del|FGFR1_ENST00000397091.5_In_Frame_Del_p.DD132del|FGFR1_ENST00000397103.1_In_Frame_Del_p.DD43del|FGFR1_ENST00000335922.5_In_Frame_Del_p.DD124del|FGFR1_ENST00000397108.4_In_Frame_Del_p.DD132del|FGFR1_ENST00000397113.2_In_Frame_Del_p.DD132del|FGFR1_ENST00000356207.5_In_Frame_Del_p.DD43del|FGFR1_ENST00000326324.6_In_Frame_Del_p.DD43del NM_001174063.1|NM_015850.3|NM_023110.2 NP_001167534.1|NP_056934.2|NP_075598.2 P11362 FGFR1_HUMAN fibroblast growth factor receptor 1 132 axon guidance|cell growth|insulin receptor signaling pathway|MAPKKK cascade|positive regulation of cell proliferation|skeletal system development extracellular region|integral to plasma membrane|membrane fraction ATP binding|fibroblast growth factor receptor activity|heparin binding|protein homodimerization activity p.D133N(3)|p.D44N(1) FGFR1/ZNF703(2) breast(2)|central_nervous_system(7)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2) 50 all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442) Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065) Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24) Palifermin(DB00039) TGAAGAGGAGtcatcatcatcat 0.498 1 T """BCR, FOP, ZNF198, CEP1""" """MPD, NHL""" """Pfeiffer syndrome, Kallman syndrome""" 13 277 --- --- --- --- PRKDC 5591 broad.mit.edu 37 8 48746799 48746799 + Frame_Shift_Del DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr8:48746799delT ENST00000314191.2 - 60 8163 c.8107delA c.(8107-8109)ggfs p.R2703fs PRKDC_ENST00000338368.3_Frame_Shift_Del_p.R2703fs|PRKDC_ENST00000523565.1_5'UTR NM_006904.6 NP_008835.5 P78527 PRKDC_HUMAN protein kinase, DNA-activated, catalytic polypeptide 2704 KIP-binding. cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7) 147 all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391) AGGCCCAGCCTTTTTTTCCCA 0.498 Non-homologous end-joining 10 2001 --- --- --- --- TERF1 7013 broad.mit.edu 37 8 73921284 73921286 + In_Frame_Del DEL GAG GAG - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr8:73921284_73921286delGAG ENST00000276602.6 + 1 186_188 c.163_165delGAG c.(163-165)del p.E62del TERF1_ENST00000276603.5_In_Frame_Del_p.E62del NM_003218.3 NP_003209.2 P54274 TERF1_HUMAN telomeric repeat binding factor (NIMA-interacting) 1 62 Asp/Glu-rich (acidic).|Poly-Glu.|TRFH dimerization. age-dependent telomere shortening|cell division|G2/M transition of mitotic cell cycle|induction of apoptosis|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of telomere maintenance via semi-conservative replication|negative regulation of telomere maintenance via telomerase|positive regulation of microtubule polymerization|positive regulation of mitosis|positive regulation of mitotic cell cycle|protein homooligomerization|regulation of transcription, DNA-dependent|telomere maintenance via telomerase|telomere maintenance via telomere shortening chromosome, telomeric region|cytoplasm|nuclear telomere cap complex|nucleoplasm|nucleus|spindle caspase activator activity|DNA bending activity|double-stranded telomeric DNA binding|identical protein binding|microtubule binding|protein heterodimerization activity|protein homodimerization activity|telomerase inhibitor activity|telomeric DNA binding central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1) 9 Breast(64;0.218) Epithelial(68;0.0984) GGGGGCCCCCgaggaggaggagg 0.650 11 175 --- --- --- --- TP53INP1 0 broad.mit.edu 37 8 95952409 95952411 + In_Frame_Del DEL TCT TCT - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr8:95952409_95952411delTCT ENST00000342697.4 - 3 557_559 c.150_152delAGA c.(148-153)gag>ga p.EE50del TP53INP1_ENST00000378776.4_In_Frame_Del_p.EE50del|TP53INP1_ENST00000448464.2_In_Frame_Del_p.EE50del|NDUFAF6_ENST00000396113.1_Intron NM_033285.3 NP_150601.1 Q96A56 T53I1_HUMAN tumor protein p53 inducible nuclear protein 1 50 Glu-rich. apoptosis PML body p.E50E(1) kidney(2)|large_intestine(3)|lung(2)|prostate(1)|skin(1) 9 Breast(36;8.75e-07) GATGTCCTCCTCTTCTTCTTCTT 0.458 9 297 --- --- --- --- DPYS 1807 broad.mit.edu 37 8 105440214 105440214 + Frame_Shift_Del DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr8:105440214delT ENST00000351513.2 - 6 1218 c.1086delA c.(1084-1086)aafs p.K362fs NM_001385.2 NP_001376.1 Q14117 DPYS_HUMAN dihydropyrimidinase 362 protein homotetramerization|pyrimidine nucleoside catabolic process|thymine catabolic process|uracil catabolic process cytosol dihydropyrimidinase activity|zinc ion binding NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 41 OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229) CCACCACGCCTTTTTCCCATA 0.478 19 1644 --- --- --- --- PKHD1L1 93035 broad.mit.edu 37 8 110455173 110455174 + Splice_Site INS - - G TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr8:110455173_110455174insG ENST00000378402.5 + 36 4497 c.e36-1 NM_177531.4 NP_803875.2 Q86WI1 PKHL1_HUMAN polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1 immune response cytosol|extracellular space|integral to membrane receptor activity NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4) 263 OV - Ovarian serous cystadenocarcinoma(57;9.88e-13) ATTTTATGGCAGGTTCATTTTC 0.322 HNSCC(38;0.096) 11 529 --- --- --- --- ATAD2 29028 broad.mit.edu 37 8 124384893 124384893 + Frame_Shift_Del DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr8:124384893delT ENST00000287394.5 - 3 461 c.354delA c.(352-354)aafs p.K118fs ATAD2_ENST00000521903.1_5'UTR NM_014109.3 NP_054828.2 Q6PL18 ATAD2_HUMAN ATPase family, AAA domain containing 2 118 regulation of transcription, DNA-dependent|transcription, DNA-dependent mitochondrion|nucleus ATP binding|ATPase activity p.E119fs*8(1) breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2) 48 Lung NSC(37;1.25e-09)|Ovarian(258;0.00838) STAD - Stomach adenocarcinoma(47;0.00288) TGTGCTCTTCTTTTTTTTTAT 0.269 9 878 --- --- --- --- PLEC 5339 broad.mit.edu 37 8 145000951 145000953 + Splice_Site DEL CCT CCT - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr8:145000951_145000953delCCT ENST00000322810.4 - 30 4623_4625 c.4455_splice c.e30+1 p.G1485_splice PLEC_ENST00000354958.2_Splice_Site_p.G1326_splice|PLEC_ENST00000356346.3_Splice_Site_p.G1334_splice|PLEC_ENST00000354589.3_Splice_Site_p.G1348_splice|PLEC_ENST00000527096.1_Splice_Site_p.G1371_splice|PLEC_ENST00000436759.2_Splice_Site_p.G1375_splice|PLEC_ENST00000357649.2_Splice_Site_p.G1352_splice|PLEC_ENST00000398774.2_Splice_Site_p.G1316_splice|PLEC_ENST00000345136.3_Splice_Site_p.G1348_splice NM_201380.2 NP_958782.1 Q15149 PLEC_HUMAN plectin 1485 Central fibrous rod domain. cellular component disassembly involved in apoptosis|hemidesmosome assembly cytosol|focal adhesion|hemidesmosome|intermediate filament cytoskeleton|sarcolemma actin binding|structural constituent of muscle NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10) 137 ACGGGCTGTACCTCCTCCTCCTC 0.621 7 763 --- --- --- --- KIFC2 90990 broad.mit.edu 37 8 145692926 145692926 + Frame_Shift_Del DEL G G - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr8:145692926delG ENST00000301332.2 + 5 905 c.528delG c.(526-528)ctfs p.L176fs NM_145754.2 NP_665697.1 Q96AC6 KIFC2_HUMAN kinesin family member C2 176 microtubule-based movement cytoplasm|microtubule ATP binding|microtubule motor activity|protein binding central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(3)|prostate(3)|skin(2)|urinary_tract(1) 19 all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055) GCGAGCCACTGGGGGATGAGA 0.627 OREG0019057 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 7 852 --- --- --- --- NOL6 65083 broad.mit.edu 37 9 33466944 33466944 + Frame_Shift_Del DEL C C - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr9:33466944delC ENST00000379471.2 - 15 2003 c.1916delG c.(1915-1917)gcfs p.G639fs NOL6_ENST00000464829.1_Intron|NOL6_ENST00000455041.2_Frame_Shift_Del_p.G587fs Q9H6R4 NOL6_HUMAN nucleolar protein 6 (RNA-associated) 639 rRNA processing condensed nuclear chromosome|nucleolus RNA binding endometrium(4)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|skin(2) 27 LUSC - Lung squamous cell carcinoma(29;0.00788) GBM - Glioblastoma multiforme(74;0.152) ATCCAGGGGGCCCCCCACATA 0.517 OREG0019137 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 9 2257 --- --- --- --- VCP 7415 broad.mit.edu 37 9 35062983 35062985 + In_Frame_Del DEL AAG AAG - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr9:35062983_35062985delAAG ENST00000358901.6 - 7 1696_1698 c.801_803delCTT c.(799-804)ttg>tt p.FL267del NM_007126.3 NP_009057.1 P55072 TERA_HUMAN valosin containing protein 267 activation of caspase activity|double-strand break repair|endoplasmic reticulum unfolded protein response|ER-associated protein catabolic process|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination|retrograde protein transport, ER to cytosol cytosol|endoplasmic reticulum|microsome|nucleus|proteasome complex ATP binding|ATPase activity|lipid binding|polyubiquitin binding|protein domain specific binding|protein phosphatase binding breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|stomach(2)|upper_aerodigestive_tract(1) 24 LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778) ACCATTGATCAAGAAGAAGAAGG 0.463 7 1010 --- --- --- --- RP11-204M4.2 0 broad.mit.edu 37 9 41962602 41962602 + RNA DEL G G - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr9:41962602delG ENST00000454645.1 - 0 902 NR_003670.1 TTCTTTCTTTGTTTTTTTTCC 0.373 13 321 --- --- --- --- ECM2 1842 broad.mit.edu 37 9 95277132 95277134 + In_Frame_Del DEL CCT CCT - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr9:95277132_95277134delCCT ENST00000344604.5 - 4 982_984 c.833_835delAGG c.(832-837)ggt>g p.EG278del CENPP_ENST00000375587.3_Intron|ECM2_ENST00000444490.2_In_Frame_Del_p.EG256del NM_001197295.1|NM_001393.3 NP_001184224.1|NP_001384.1 O94769 ECM2_HUMAN extracellular matrix protein 2, female organ and adipocyte specific 278 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 ccctcctcaccctcctcctcctc 0.611 7 758 --- --- --- --- HABP4 22927 broad.mit.edu 37 9 99250415 99250416 + Frame_Shift_Ins INS - - C TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr9:99250415_99250416insC ENST00000375249.4 + 7 1119_1120 c.1044_1045insC c.(1042-1047)aaccgcfs p.R349fs HABP4_ENST00000466976.1_3'UTR|HABP4_ENST00000375251.3_Frame_Shift_Ins_p.R244fs NM_014282.2 NP_055097.2 Q5JVS0 HABP4_HUMAN hyaluronan binding protein 4 349 platelet activation|platelet degranulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|extracellular region|nucleus protein binding NS(1)|cervix(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(2) 13 Acute lymphoblastic leukemia(62;0.0169)|all_hematologic(171;0.214) TTTTCCGGAAACCCGCCAATGA 0.530 15 767 --- --- --- --- WDR5 11091 broad.mit.edu 37 9 137019598 137019598 + Frame_Shift_Del DEL C C - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr9:137019598delC ENST00000358625.3 + 10 813 c.642delC c.(640-642)aafs p.N214fs WDR5_ENST00000425041.1_Frame_Shift_Del_p.N214fs NM_017588.2 NP_060058.1 P61964 WDR5_HUMAN WD repeat domain 5 214 histone H3 acetylation|histone H3-K4 methylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent Ada2/Gcn5/Ada3 transcription activator complex|MLL1 complex|Set1C/COMPASS complex protein binding endometrium(1)|kidney(1)|large_intestine(2)|lung(5) 9 Myeloproliferative disorder(178;0.0255)|Medulloblastoma(224;0.123) Epithelial(140;6.61e-13)|all cancers(34;5.66e-12)|OV - Ovarian serous cystadenocarcinoma(145;3.93e-08)|GBM - Glioblastoma multiforme(294;0.00326)|READ - Rectum adenocarcinoma(205;0.154) ATGACGACAACCCCCCCGTGT 0.627 10 2139 --- --- --- --- ANK3 288 broad.mit.edu 37 10 61828745 61828747 + In_Frame_Del DEL GTG GTG - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr10:61828745_61828747delGTG ENST00000280772.1 - 37 12083_12085 c.11892_11894delCAC c.(11890-11895)act>ac p.TT3964del ANK3_ENST00000373827.2_Intron|ANK3_ENST00000503366.1_Intron|ANK3_ENST00000355288.2_Intron NM_020987.3 NP_066267.2 Q12955 ANK3_HUMAN ankyrin 3, node of Ranvier (ankyrin G) 3964 Thr-rich. establishment of protein localization|signal transduction basolateral plasma membrane|cytoplasm|cytoskeleton protein binding NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7) 196 ggtggtggcagtggtggtggtgg 0.498 7 769 --- --- --- --- RUFY2 55680 broad.mit.edu 37 10 70156583 70156583 + Frame_Shift_Del DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr10:70156583delT ENST00000388768.2 - 4 783 c.457delA c.(457-459)tgfs p.M153fs RUFY2_ENST00000602465.1_Frame_Shift_Del_p.M118fs|RUFY2_ENST00000342616.4_Frame_Shift_Del_p.M118fs|RUFY2_ENST00000454950.2_Frame_Shift_Del_p.M60fs|RUFY2_ENST00000399200.2_Intron|RUFY2_ENST00000472394.2_5'UTR NM_017987.4 NP_060457.4 Q8WXA3 RUFY2_HUMAN RUN and FYVE domain containing 2 167 RUN. nucleus metal ion binding NS(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(2) 20 TAATCGGCCATTTTTTTTTGC 0.398 21 358 --- --- --- --- PSD 5662 broad.mit.edu 37 10 104176574 104176574 + Frame_Shift_Del DEL G G - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr10:104176574delG ENST00000020673.5 - 2 748 c.222delC c.(220-222)ccfs p.P74fs PSD_ENST00000406432.1_Frame_Shift_Del_p.P74fs|PSD_ENST00000492902.2_5'UTR NM_001270966.1|NM_002779.3 NP_001257895.1|NP_002770.3 A5PKW4 PSD1_HUMAN pleckstrin and Sec7 domain containing 74 Pro-rich. regulation of ARF protein signal transduction cytoplasm|plasma membrane|ruffle ARF guanyl-nucleotide exchange factor activity|signal transducer activity p.S75fs*127(1) breast(4)|endometrium(2)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 34 Epithelial(162;1.27e-08)|all cancers(201;2.85e-07) CACGGGGTGAGGGGGGGCCAC 0.672 8 633 --- --- --- --- SLK 9748 broad.mit.edu 37 10 105727547 105727549 + In_Frame_Del DEL AGA AGA - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr10:105727547_105727549delAGA ENST00000369755.3 + 1 589_591 c.44_46delAGA c.(43-48)gag>g p.EK15del SLK_ENST00000335753.4_In_Frame_Del_p.EK15del NM_014720.2 NP_055535.2 Q9H2G2 SLK_HUMAN STE20-like kinase 15 apoptosis|nucleotide-excision repair cytoplasm|plasma membrane ATP binding|DNA binding|nuclease activity|protein serine/threonine kinase activity kidney(1)|lung(1)|ovary(2)|skin(2)|stomach(2) 8 Colorectal(252;0.178) Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165) TTGGGGAGCGAGAAGAAGAAGAA 0.448 9 711 --- --- --- --- IKZF5 64376 broad.mit.edu 37 10 124758126 124758127 + Frame_Shift_Ins INS - - T TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr10:124758126_124758127insT ENST00000368886.5 - 3 335_336 c.15_16insA c.(13-18)aacagafs p.NR5fs IKZF5_ENST00000479103.1_5'UTR NM_001271840.1 NP_001258769.1 Q9H5V7 IKZF5_HUMAN IKAROS family zinc finger 5 (Pegasus) 5 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding endometrium(2)|lung(3)|prostate(1) 6 all_neural(114;0.169)|Colorectal(57;0.178)|Glioma(114;0.222) Colorectal(40;0.0701)|COAD - Colon adenocarcinoma(40;0.0754) AAAGGCTCTGGTTTTTTTTCAC 0.371 7 496 --- --- --- --- CPXM2 119587 broad.mit.edu 37 10 125528165 125528167 + In_Frame_Del DEL CAG CAG - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr10:125528165_125528167delCAG ENST00000241305.3 - 9 1328_1330 c.1174_1176delCTG c.(1174-1176)del p.L392del CPXM2_ENST00000368854.3_5'UTR NM_198148.2 NP_937791.2 Q8N436 CPXM2_HUMAN carboxypeptidase X (M14 family), member 2 392 Poly-Leu. cell adhesion|proteolysis extracellular space metallocarboxypeptidase activity|zinc ion binding NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3) 47 all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233) COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237) CGAACTGCACCAGCAGCAGCAGC 0.626 9 950 --- --- --- --- FRG2B 441581 broad.mit.edu 37 10 135438960 135438960 + Frame_Shift_Del DEL C C - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr10:135438960delC ENST00000443774.1 - 4 532 c.483delG c.(481-483)agfs p.R161fs FRG2B_ENST00000425520.1_Frame_Shift_Del_p.R160fs Q96QU4 FRG2B_HUMAN FSHD region gene 2 family, member B 160 nucleus endometrium(2)|kidney(2)|lung(14)|ovary(1)|prostate(1) 20 all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175) OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06) GGGCCCGAGACCTATGCCGCT 0.557 18 883 --- --- --- --- KRTAP5-5 439915 broad.mit.edu 37 11 1651191 1651199 + In_Frame_Del DEL GGCTGTGGA GGCTGTGGA - rs71025763 TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr11:1651191_1651199delGGCTGTGGA ENST00000399676.2 + 1 159_167 c.121_129delGGCTGTGGA c.(121-129)del p.GCG47del NM_001001480.2 NP_001001480.2 Q701N2 KRA55_HUMAN keratin associated protein 5-5 47 keratin filament endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1) 33 all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229) BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082) ctgtggctccggctgtggaggctgtgggg 0.713 7 599 --- --- --- --- TSSC4 10078 broad.mit.edu 37 11 2424492 2424493 + Frame_Shift_Ins INS - - G TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr11:2424492_2424493insG ENST00000333256.6 + 3 1072_1073 c.629_630insG c.(628-630)gggfs p.G210fs TSSC4_ENST00000380996.5_Frame_Shift_Ins_p.G146fs|TSSC4_ENST00000380992.1_Intron|TSSC4_ENST00000467308.1_Intron|TSSC4_ENST00000451491.2_Frame_Shift_Ins_p.G210fs Q9Y5U2 TSSC4_HUMAN tumor suppressing subtransferable candidate 4 210 endometrium(3)|large_intestine(1)|lung(4) 8 all_epithelial(84;0.000161)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.0137)|Lung NSC(207;0.209) BRCA - Breast invasive adenocarcinoma(625;0.00145)|LUSC - Lung squamous cell carcinoma(625;0.19) AGCTGTGGGGAGGGGAGGGTCA 0.658 8 401 --- --- --- --- NUP98 4928 broad.mit.edu 37 11 3720389 3720389 + Frame_Shift_Del DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr11:3720389delT ENST00000324932.7 - 25 4352 c.3932delA c.(3931-3933)acfs p.N1311fs NUP98_ENST00000355260.3_Frame_Shift_Del_p.N1311fs|NUP98_ENST00000359171.4_Frame_Shift_Del_p.N1311fs NM_016320.4|NM_139132.3 NP_057404.2|NP_624358.2 P52948 NUP98_HUMAN nucleoporin 98kDa 1328 carbohydrate metabolic process|DNA replication|glucose transport|interspecies interaction between organisms|mitotic prometaphase|mRNA transport|nuclear pore organization|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction cytosol|nuclear membrane|nucleoplasm|Nup107-160 complex protein binding|structural constituent of nuclear pore|transporter activity NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 66 Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227) BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199) CACAGGGCTGTTTTTTTGGGT 0.512 T """HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11""" AML 14 1520 --- --- --- --- DENND5A 23258 broad.mit.edu 37 11 9167317 9167317 + Frame_Shift_Del DEL C C - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr11:9167317delC ENST00000328194.3 - 17 3223 c.2903delG c.(2902-2904)gcfs p.G968fs DENND5A_ENST00000527700.1_Frame_Shift_Del_p.G311fs|DENND5A_ENST00000530044.1_Frame_Shift_Del_p.G968fs NM_001243254.1|NM_015213.3 NP_001230183.1|NP_056028.2 Q6IQ26 DEN5A_HUMAN DENN/MADD domain containing 5A 968 PLAT. breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(16)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 39 GAACATGGAGCCCCCCAGCTT 0.478 8 2136 --- --- --- --- SLC1A2 6506 broad.mit.edu 37 11 35313881 35313881 + Frame_Shift_Del DEL A A - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr11:35313881delA ENST00000278379.3 - 7 1326 c.1044delT c.(1042-1044)ttfs p.F348fs SLC1A2_ENST00000395753.1_Frame_Shift_Del_p.F339fs|SLC1A2_ENST00000606205.1_Frame_Shift_Del_p.F348fs|SLC1A2_ENST00000395750.1_Frame_Shift_Del_p.F339fs NM_004171.3 NP_004162.2 P43004 EAA2_HUMAN solute carrier family 1 (glial high affinity glutamate transporter), member 2 348 D-aspartate import|L-glutamate import|synaptic transmission integral to membrane|membrane fraction high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|urinary_tract(1) 24 all_lung(20;0.211)|all_epithelial(35;0.234) all_hematologic(20;0.109) STAD - Stomach adenocarcinoma(6;0.00731) L-Glutamic Acid(DB00142) AAATGCCAGCAAAAAAGGAGA 0.468 7 1678 --- --- --- --- RPLP0P2 0 broad.mit.edu 37 11 61405017 61405019 + RNA DEL CTG CTG - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr11:61405017_61405019delCTG ENST00000496593.1 + 0 1621_1623 NR_002775.2 acagctgctcctgctgctgctgc 0.557 9 194 --- --- --- --- SLC3A2 6520 broad.mit.edu 37 11 62649529 62649529 + Frame_Shift_Del DEL A A - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr11:62649529delA ENST00000377892.1 + 6 1209 c.985delA c.(985-987)aafs p.K331fs SLC3A2_ENST00000538682.1_3'UTR|SLC3A2_ENST00000536981.1_5'UTR|SLC3A2_ENST00000535296.1_Frame_Shift_Del_p.K269fs|SLC3A2_ENST00000338663.7_Frame_Shift_Del_p.K199fs|SLC3A2_ENST00000377891.2_Frame_Shift_Del_p.K301fs|SLC3A2_ENST00000377889.2_Frame_Shift_Del_p.K238fs|SLC3A2_ENST00000377890.2_Frame_Shift_Del_p.K300fs P08195 4F2_HUMAN solute carrier family 3 (amino acid transporter heavy chain), member 2 300 blood coagulation|carbohydrate metabolic process|cell growth|cellular nitrogen compound metabolic process|leucine import|leukocyte migration|tryptophan transport apical plasma membrane|cell surface|integral to membrane|melanosome calcium:sodium antiporter activity|catalytic activity|cation binding|neutral amino acid transmembrane transporter activity|protein binding p.K331fs*31(1) endometrium(1)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2) 22 GCAATCGGCTAAAAAAAAGAG 0.463 7 508 --- --- --- --- KRTAP5-7 440050 broad.mit.edu 37 11 71238416 71238436 + In_Frame_Del DEL TGTGGCTCTGGCTGTGGGGGA TGTGGCTCTGGCTGTGGGGGA - rs71931178 TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr11:71238416_71238436delTGTGGCTCTGGCTGTGGGGGA ENST00000398536.4 + 1 104_124 c.70_90delTGTGGCTCTGGCTGTGGGGGA c.(70-90)del p.CGSGCGG24del NM_001012503.1 NP_001012521.1 Q6L8G8 KRA57_HUMAN keratin associated protein 5-7 24 keratin filament p.G30G(1) breast(1)|endometrium(1)|kidney(3)|lung(6)|ovary(1) 12 CTGTGGGGGCTGTGGCTCTGGCTGTGGGGGATGTGGCTCCA 0.665 8 1479 --- --- --- --- GDPD4 220032 broad.mit.edu 37 11 76928312 76928315 + Splice_Site DEL ATCT ATCT - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr11:76928312_76928315delATCT ENST00000376217.2 - 17 1791_1792 c.1540_splice c.e17-1 p.514_splice GDPD4_ENST00000315938.4_3'UTR Q6W3E5 GDPD4_HUMAN glycerophosphodiester phosphodiesterase domain containing 4 514 glycerol metabolic process|lipid metabolic process integral to membrane glycerophosphodiester phosphodiesterase activity|metal ion binding breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1) 20 CTATGTGCAAatctatctatctat 0.471 9 427 --- --- --- --- NOX4 50507 broad.mit.edu 37 11 89106662 89106663 + Splice_Site INS - - A rs56022003 TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr11:89106662_89106663insA ENST00000535633.1 - 12 1313 c.e12-2 NOX4_ENST00000375979.3_Splice_Site|NOX4_ENST00000527626.1_Splice_Site|NOX4_ENST00000525196.1_Intron|NOX4_ENST00000528341.1_Splice_Site|NOX4_ENST00000343727.5_Splice_Site|NOX4_ENST00000531342.1_Splice_Site|NOX4_ENST00000527956.1_Splice_Site|NOX4_ENST00000263317.4_Splice_Site|NOX4_ENST00000424319.1_Splice_Site|NOX4_ENST00000413594.2_Splice_Site|NOX4_ENST00000542487.1_Splice_Site|NOX4_ENST00000532825.1_Splice_Site|NOX4_ENST00000534731.1_Splice_Site NM_001143836.1|NM_016931.3 NP_001137308.1|NP_058627.1 Q9NPH5 NOX4_HUMAN NADPH oxidase 4 cell aging|cell morphogenesis|inflammatory response|negative regulation of cell proliferation|superoxide anion generation endoplasmic reticulum membrane|focal adhesion|integral to membrane|nucleus electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|nucleotide binding|oxygen sensor activity p.?(1) NS(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(20)|ovary(2)|prostate(3)|skin(2) 44 Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011) AGTTGGACACTAAAAAAAAATA 0.292 13 690 --- --- --- --- MMP12 4321 broad.mit.edu 37 11 102738793 102738794 + RNA INS - - T rs35342965 by1000genomes TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr11:102738793_102738794insT ENST00000532855.1 - 0 727_728 P39900 MMP12_HUMAN matrix metallopeptidase 12 (macrophage elastase) positive regulation of epithelial cell proliferation involved in wound healing|proteolysis|wound healing, spreading of epidermal cells proteinaceous extracellular matrix calcium ion binding|metalloendopeptidase activity|zinc ion binding autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(5)|skin(1)|upper_aerodigestive_tract(1) 26 all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967) BRCA - Breast invasive adenocarcinoma(274;0.014) Acetohydroxamic Acid(DB00551) TGAGGAACAAGTGGTGCCTAAG 0.416 7 58 --- --- --- --- CD3G 917 broad.mit.edu 37 11 118220583 118220583 + Frame_Shift_Del DEL A A - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr11:118220583delA ENST00000532917.1 + 3 273 c.205delA c.(205-207)aafs p.K71fs CD3G_ENST00000532903.1_3'UTR|CD3G_ENST00000392883.2_Frame_Shift_Del_p.K11fs NM_000073.2 NP_000064.1 P09693 CD3G_HUMAN CD3g molecule, gamma (CD3-TCR complex) 71 Ig-like. establishment or maintenance of cell polarity|protein complex assembly|protein transport|regulation of apoptosis|T cell activation|T cell costimulation|T cell receptor signaling pathway integral to plasma membrane|T cell receptor complex protein heterodimerization activity|receptor signaling complex scaffold activity|T cell receptor binding|transmembrane receptor activity breast(2)|kidney(1)|large_intestine(2)|skin(1) 6 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) AACTGAAGATAAAAAAAAATG 0.403 9 476 --- --- --- --- CCDC153 283152 broad.mit.edu 37 11 119061043 119061043 + Frame_Shift_Del DEL G G - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr11:119061043delG ENST00000503566.2 - 6 598 c.599delC c.(598-600)ctfs p.P200fs CCDC153_ENST00000415318.1_Frame_Shift_Del_p.P200fs Q494R4 CC153_HUMAN coiled-coil domain containing 153 200 lung(3)|stomach(1) 4 CAAAGATCCAGGGGGGGTGAG 0.567 8 833 --- --- --- --- FAM118B 79607 broad.mit.edu 37 11 126131333 126131335 + In_Frame_Del DEL AGA AGA - rs138767340 TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr11:126131333_126131335delAGA ENST00000533050.1 + 8 1489_1491 c.996_998delAGA c.(994-999)aga>ag p.RE332del FAM118B_ENST00000360194.4_In_Frame_Del_p.RE331del NM_024556.3 NP_078832.1 Q9BPY3 F118B_HUMAN family with sequence similarity 118, member B 332 breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1) 13 all_hematologic(175;0.145) Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0784) GGATGGTGAGAGAAGGTCAGCTA 0.379 7 277 --- --- --- --- ACSM4 341392 broad.mit.edu 37 12 7456935 7456935 + Frame_Shift_Del DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr12:7456935delT ENST00000399422.4 + 1 56 c.8delT c.(7-9)atfs p.I3fs NM_001080454.1 NP_001073923.1 P0C7M7 ACSM4_HUMAN acyl-CoA synthetase medium-chain family member 4 3 fatty acid metabolic process mitochondrial matrix ATP binding|butyrate-CoA ligase activity|metal ion binding endometrium(6)|kidney(1)|lung(14) 21 ACCATGAAGATTTTTTTCCGC 0.473 7 1013 --- --- --- --- RP11-377D9.3 0 broad.mit.edu 37 12 13154583 13154583 + RNA DEL G G - rs75373880 TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr12:13154583delG ENST00000543321.1 + 0 31 HTR7P1_ENST00000535469.1_RNA TCTGCTGAGCGGGGGCCCCCG 0.731 9 17 --- --- --- --- SCAF11 9169 broad.mit.edu 37 12 46318575 46318577 + In_Frame_Del DEL GGT GGT - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr12:46318575_46318577delGGT ENST00000465950.1 - 2 4104_4106 c.2895_2897delACC c.(2893-2898)ccc>cc p.PP969del SCAF11_ENST00000419565.2_In_Frame_Del_p.PP1284del|SCAF11_ENST00000549162.1_In_Frame_Del_p.PP1092del|SCAF11_ENST00000369367.3_In_Frame_Del_p.PP1284del Q99590 SCAFB_HUMAN SR-related CTD-associated factor 11 1284 Arg-rich. spliceosome assembly nucleus protein binding|zinc ion binding breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(17)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3) 69 TGGGGGAGGGGGTGGTGGTGGTG 0.483 7 443 --- --- --- --- TUBA1A 7846 broad.mit.edu 37 12 49580272 49580274 + In_Frame_Del DEL GGA GGA - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr12:49580272_49580274delGGA ENST00000546918.1 - 2 432_434 c.346_348delTCC c.(346-348)del p.S116del TUBA1A_ENST00000550767.1_Intron|TUBA1A_ENST00000295766.5_Intron|TUBA1A_ENST00000301071.7_Intron Q71U36 TBA1A_HUMAN tubulin, alpha 1a 0 'de novo' posttranslational protein folding|G2/M transition of mitotic cell cycle|microtubule-based movement|protein polymerization cytosol|microtubule GTP binding|GTPase activity|structural molecule activity stomach(1)|upper_aerodigestive_tract(1) 2 ggagcaggggggaggaggaggag 0.621 7 475 --- --- --- --- PRPF40B 25766 broad.mit.edu 37 12 50025258 50025258 + Frame_Shift_Del DEL C C - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr12:50025258delC ENST00000261897.1 + 2 626 c.75delC c.(73-75)atfs p.I25fs PRPF40B_ENST00000548825.2_Frame_Shift_Del_p.I53fs|PRPF40B_ENST00000380281.1_Frame_Shift_Del_p.I31fs Q6NWY9 PR40B_HUMAN PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae) 31 Pro-rich. mRNA processing|RNA splicing nuclear speck breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1) 34 CACCAGCTATCCCCCCCATGC 0.607 7 1028 --- --- --- --- OR10A7 121364 broad.mit.edu 37 12 55615114 55615116 + In_Frame_Del DEL CTT CTT - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr12:55615114_55615116delCTT ENST00000326258.1 + 1 306_308 c.306_308delCTT c.(304-309)tac>ta p.YF102del NM_001005280.1 NP_001005280.1 Q8NGE5 O10A7_HUMAN olfactory receptor, family 10, subfamily A, member 7 102 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity endometrium(3)|kidney(1)|lung(11)|ovary(4)|prostate(2)|skin(3) 24 CCCAGATGTACTTCTTCTTCTTC 0.414 8 1193 --- --- --- --- OR6C75 390323 broad.mit.edu 37 12 55759486 55759486 + Frame_Shift_Del DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr12:55759486delT ENST00000343399.3 + 1 592 c.592delT c.(592-594)ttfs p.F199fs NM_001005497.1 NP_001005497.1 A6NL08 O6C75_HUMAN olfactory receptor, family 6, subfamily C, member 75 199 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity p.L200fs*1(1) endometrium(2)|large_intestine(5)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(2) 25 ACTCATGGCATTTTTTTTAGC 0.393 7 539 --- --- --- --- RP11-74M13.4 0 broad.mit.edu 37 12 57255299 57255300 + RNA INS - - A rs139092727 by1000genomes TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr12:57255299_57255300insA ENST00000557452.1 + 0 720 ATGGAAGAAGGAAaaaaaaata 0.426 7 228 --- --- --- --- R3HDM2 22864 broad.mit.edu 37 12 57674205 57674207 + In_Frame_Del DEL TGC TGC - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr12:57674205_57674207delTGC ENST00000402412.1 - 14 1668_1670 c.1278_1280delGCA c.(1276-1281)caa>ca p.QQ426del RP11-123K3.4_ENST00000548184.1_RNA|R3HDM2_ENST00000358907.2_In_Frame_Del_p.QQ412del|R3HDM2_ENST00000393811.2_In_Frame_Del_p.QQ139del|R3HDM2_ENST00000441731.2_In_Frame_Del_p.QQ73del|R3HDM2_ENST00000347140.3_In_Frame_Del_p.QQ412del|R3HDM2_ENST00000413953.2_In_Frame_Del_p.QQ139del|R3HDM2_ENST00000403821.2_In_Frame_Del_p.QQ412del Q9Y2K5 R3HD2_HUMAN R3H domain containing 2 412 Gln-rich. nucleus nucleic acid binding breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1) 22 AGCAGGAAGTtgctgctgctgct 0.576 15 599 --- --- --- --- LRIG3 121227 broad.mit.edu 37 12 59268350 59268351 + Frame_Shift_Ins INS - - G TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr12:59268350_59268351insG ENST00000320743.3 - 17 2986_2987 c.2700_2701insC c.(2698-2703)acgccafs p.P901fs LRIG3_ENST00000379141.4_Frame_Shift_Ins_p.P841fs NM_153377.4 NP_700356.2 Q6UXM1 LRIG3_HUMAN leucine-rich repeats and immunoglobulin-like domains 3 901 integral to membrane LRIG3/ROS1(2) breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 48 GBM - Glioblastoma multiforme(1;1.17e-18) TCAATATGGCAGGTCCCTTTGA 0.401 T ROS1 NSCLC 9 486 --- --- --- --- ZFC3H1 196441 broad.mit.edu 37 12 72057256 72057258 + In_Frame_Del DEL GCT GCT - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr12:72057256_72057258delGCT ENST00000378743.3 - 1 491_493 c.133_135delAGC c.(133-135)del p.S45del THAP2_ENST00000308086.2_5'UTR|ZFC3H1_ENST00000548100.1_In_Frame_Del_p.S45del|ZFC3H1_ENST00000552037.1_In_Frame_Del_p.S45del NM_144982.4 NP_659419.3 O60293 ZC3H1_HUMAN zinc finger, C3H1-type containing 45 Ser-rich. RNA processing intracellular metal ion binding NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2) 69 GCCCGCCGCCGCTGCTGCTGCTG 0.631 OREG0021993 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 16 907 --- --- --- --- RP11-114H23.1 0 broad.mit.edu 37 12 76082490 76082491 + RNA INS - - T rs141632958 TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr12:76082490_76082491insT ENST00000552856.1 - 0 401 cattctTTTTCTTTTTTTTTTT 0.361 13 18 --- --- --- --- CUX2 23316 broad.mit.edu 37 12 111785948 111785948 + Frame_Shift_Del DEL C C - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr12:111785948delC ENST00000261726.6 + 22 4434 c.4280delC c.(4279-4281)gcfs p.A1427fs NM_015267.3 NP_056082.2 O14529 CUX2_HUMAN cut-like homeobox 2 1427 Pro-rich. nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2) 55 CCACCTGGCGCCCCCCCTGCC 0.657 7 728 --- --- --- --- GCN1L1 10985 broad.mit.edu 37 12 120595737 120595739 + In_Frame_Del DEL CTC CTC - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr12:120595737_120595739delCTC ENST00000300648.6 - 26 3013_3015 c.3001_3003delGAG c.(3001-3003)del p.E1001del NM_006836.1 NP_006827.1 Q92616 GCN1L_HUMAN GCN1 general control of amino-acid synthesis 1-like 1 (yeast) 1001 regulation of translation ribosome protein binding|translation factor activity, nucleic acid binding NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2) 94 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) GGGCCATCCACTCCTCCTCCTCC 0.631 9 335 --- --- --- --- ZMYM5 9205 broad.mit.edu 37 13 20426143 20426145 + In_Frame_Del DEL CAT CAT - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr13:20426143_20426145delCAT ENST00000337963.4 - 3 440_442 c.176_178delATG c.(175-180)gtt>g p.DV59del ZMYM5_ENST00000382907.4_In_Frame_Del_p.DV59del|ZMYM5_ENST00000382905.4_In_Frame_Del_p.DV59del NM_001142684.1 NP_001136156.1 Q9UJ78 ZMYM5_HUMAN zinc finger, MYM-type 5 59 Poly-Asp. nucleus zinc ion binding kidney(1)|large_intestine(5)|lung(9) 15 all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162) all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431) ATAAACACAAcatcatcatcatc 0.379 8 495 --- --- --- --- TPTE2P6 0 broad.mit.edu 37 13 25157747 25157748 + RNA INS - - T rs144668552 by1000genomes TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr13:25157747_25157748insT ENST00000453498.1 + 0 554 AAAATGGGAGGTTTTTTTAGGG 0.411 7 75 --- --- --- --- WASF3 10810 broad.mit.edu 37 13 27255386 27255387 + Frame_Shift_Ins INS - - C rs141429361 TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr13:27255386_27255387insC ENST00000361042.4 + 8 1128_1129 c.903_904insC c.(901-906)ccccccfs p.PP301fs WASF3_ENST00000335327.5_Frame_Shift_Ins_p.PP304fs Q9UPY6 WASF3_HUMAN WAS protein family, member 3 304 actin filament polymerization cytoplasm|cytoskeleton actin binding breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|pancreas(1)|prostate(2)|skin(2) 22 Colorectal(5;0.000247) Lung SC(185;0.0156)|Breast(139;0.147) all cancers(112;0.0114)|Epithelial(112;0.046)|OV - Ovarian serous cystadenocarcinoma(117;0.0547)|Lung(94;0.105)|LUSC - Lung squamous cell carcinoma(192;0.155) CTCAGCAGCCGCCCCCCCCGCC 0.678 9 513 --- --- --- --- KIAA1704 0 broad.mit.edu 37 13 45580365 45580367 + In_Frame_Del DEL GAT GAT - rs138421508 TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr13:45580365_45580367delGAT ENST00000361121.2 + 3 285_287 c.250_252delGAT c.(250-252)del p.D88del RP11-321C24.1_ENST00000437748.2_lincRNA|KIAA1704_ENST00000357537.3_De_novo_Start_InFrame|KIAA1704_ENST00000379151.4_In_Frame_Del_p.D88del Q8IXQ4 K1704_HUMAN 88 Poly-Asp. breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|prostate(2)|skin(1) 12 Lung NSC(96;0.00143)|Prostate(109;0.0137)|Breast(139;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.133) KIRC - Kidney renal clear cell carcinoma(16;0.234) GBM - Glioblastoma multiforme(144;0.000313)|BRCA - Breast invasive adenocarcinoma(63;0.126) Ggatgatgacgatgatgatgatg 0.335 13 1286 --- --- --- --- PIBF1 10464 broad.mit.edu 37 13 73357634 73357634 + Frame_Shift_Del DEL A A - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr13:73357634delA ENST00000326291.6 + 2 365 c.27delA c.(25-27)tcfs p.S9fs NM_006346.2 NP_006337.2 Q8WXW3 PIBF1_HUMAN progesterone immunomodulatory binding factor 1 9 centrosome breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1) 24 Prostate(6;0.00191)|Breast(118;0.0736)|Acute lymphoblastic leukemia(28;0.0865) GBM - Glioblastoma multiforme(99;0.000664) CAAAGGAGTCAAAAAAAGTGA 0.303 8 501 --- --- --- --- SLITRK5 26050 broad.mit.edu 37 13 88330019 88330021 + In_Frame_Del DEL GCA GCA - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr13:88330019_88330021delGCA ENST00000325089.6 + 2 2595_2597 c.2376_2378delGCA c.(2374-2379)ctg>ct p.LQ792del SLITRK5_ENST00000400028.3_In_Frame_Del_p.LQ551del NM_015567.1 NP_056382.1 O94991 SLIK5_HUMAN SLIT and NTRK-like family, member 5 792 integral to membrane breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4) 81 all_neural(89;0.101)|Medulloblastoma(90;0.163) ACCACCACCTgcagcagcagcag 0.655 8 395 --- --- --- --- TEP1 7011 broad.mit.edu 37 14 20852647 20852647 + Frame_Shift_Del DEL C C - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr14:20852647delC ENST00000262715.5 - 23 3282 c.3242delG c.(3241-3243)gtfs p.G1081fs TEP1_ENST00000556935.1_Frame_Shift_Del_p.G973fs NM_007110.4 NP_009041.2 Q99973 TEP1_HUMAN telomerase-associated protein 1 1081 telomere maintenance via recombination chromosome, telomeric region|cytoplasm|nuclear matrix|soluble fraction|telomerase holoenzyme complex ATP binding|RNA binding p.V1082fs*47(1) NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1) 96 all_cancers(95;0.00123) all_lung(585;0.235) Epithelial(56;7.42e-08)|all cancers(55;6.46e-07) GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233) AGCTGCCACACCCCCCCACTC 0.587 11 1445 --- --- --- --- CHD8 57680 broad.mit.edu 37 14 21884031 21884031 + Frame_Shift_Del DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr14:21884031delT ENST00000399982.2 - 5 1816 c.1752delA c.(1750-1752)aafs p.K584fs CHD8_ENST00000557364.1_Frame_Shift_Del_p.K584fs|CHD8_ENST00000555962.1_Intron|CHD8_ENST00000430710.3_Frame_Shift_Del_p.K305fs NM_001170629.1 NP_001164100.1 Q9HCK8 CHD8_HUMAN chromodomain helicase DNA binding protein 8 584 ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent MLL1 complex ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2) 85 all_cancers(95;0.00121) Epithelial(56;2.55e-06)|all cancers(55;1.73e-05) GBM - Glioblastoma multiforme(265;0.00424) CCTCTGTATATTTTTTTCGCT 0.398 7 899 --- --- --- --- RP11-407N17.3 0 broad.mit.edu 37 14 39746242 39746243 + Frame_Shift_Ins INS - - T rs75842899 byFrequency TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr14:39746242_39746243insT ENST00000553728.1 + 6 1986_1987 c.1773_1774insT c.(1771-1776)ctttttfs p.LF591fs CTAGE5_ENST00000280083.3_Frame_Shift_Ins_p.LF56fs|CTAGE5_ENST00000557038.1_5'UTR|CTAGE5_ENST00000348007.3_Frame_Shift_Ins_p.LF56fs|CTAGE5_ENST00000556148.1_Intron|CTAGE5_ENST00000396158.2_Frame_Shift_Ins_p.LF56fs|RP11-407N17.3_ENST00000603904.1_Frame_Shift_Ins_p.LF27fs|CTAGE5_ENST00000396165.4_Frame_Shift_Ins_p.LF27fs|CTAGE5_ENST00000553352.1_Frame_Shift_Ins_p.LF27fs|CTAGE5_ENST00000341502.5_Frame_Shift_Ins_p.LF56fs|CTAGE5_ENST00000341749.3_Frame_Shift_Ins_p.LF44fs TTGCTGTTCTCTTTTTTTTGTG 0.371 12 391 --- --- --- --- MAP3K9 4293 broad.mit.edu 37 14 71275774 71275776 + In_Frame_Del DEL CCT CCT - rs3832971 TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr14:71275774_71275776delCCT ENST00000554752.2 - 1 112_114 c.113_115delAGG c.(112-117)gcg>g p.EA38del MAP3K9_ENST00000555993.2_In_Frame_Del_p.EA38del|MAP3K9_ENST00000381250.4_In_Frame_Del_p.EA38del P80192 M3K9_HUMAN mitogen-activated protein kinase kinase kinase 9 38 Ala-rich.|Poly-Glu. activation of JUN kinase activity|protein autophosphorylation ATP binding|JUN kinase kinase kinase activity|MAP kinase kinase activity|protein homodimerization activity p.E38delE(1) breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2) 46 all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08) GCCGCCGCCGcctcctcctcctc 0.773 7 32 --- --- --- --- SIPA1L1 26037 broad.mit.edu 37 14 72190482 72190484 + In_Frame_Del DEL TCC TCC - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr14:72190482_72190484delTCC ENST00000555818.1 + 16 4738_4740 c.4390_4392delTCC c.(4390-4392)del p.S1468del SIPA1L1_ENST00000537413.1_In_Frame_Del_p.S922del|SIPA1L1_ENST00000358550.2_In_Frame_Del_p.S1447del|SIPA1L1_ENST00000554874.1_3'UTR|SIPA1L1_ENST00000381232.3_In_Frame_Del_p.S1447del NM_015556.1 NP_056371.1 O43166 SI1L1_HUMAN signal-induced proliferation-associated 1 like 1 1468 Ser-rich. actin cytoskeleton reorganization|activation of Rap GTPase activity|regulation of dendritic spine morphogenesis cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane|synaptosome GTPase activator activity NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1) 78 all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109) ctcctcctcttcctcctcctcct 0.552 9 829 --- --- --- --- INF2 64423 broad.mit.edu 37 14 105174270 105174271 + Frame_Shift_Ins INS - - G TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr14:105174270_105174271insG ENST00000392634.4 + 8 1778_1779 c.1666_1667insG c.(1666-1668)ggtfs p.G556fs INF2_ENST00000330634.7_Frame_Shift_Ins_p.G556fs NM_022489.3 NP_071934.3 Q27J81 INF2_HUMAN inverted formin, FH2 and WH2 domain containing 556 FH2. actin cytoskeleton organization endoplasmic reticulum|nucleus|perinuclear region of cytoplasm actin binding|Rho GTPase binding large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 8 all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172) all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116) Epithelial(152;0.176) CAGCCATCGGCGGGTGAACCCA 0.663 13 356 --- --- --- --- SNHG14 0 broad.mit.edu 37 15 25324325 25324325 + RNA DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr15:25324325delT ENST00000549804.2 + 0 1377 ACAACTGTCATTTTTTTTGAT 0.478 8 386 --- --- --- --- SNHG14 0 broad.mit.edu 37 15 25432666 25432666 + RNA DEL G G - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr15:25432666delG ENST00000424208.1 + 0 761 NR_003305.1 TGTGTGTGGTGGGGGGTGCCC 0.552 8 1698 --- --- --- --- HERC2P9 0 broad.mit.edu 37 15 28913367 28913367 + RNA DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr15:28913367delT ENST00000528584.1 + 0 1224 NR_036443.1 TGAGTTCTCCTTTTTTTTTTT 0.308 8 45 --- --- --- --- CGNL1 84952 broad.mit.edu 37 15 57744359 57744360 + Frame_Shift_Del DEL AG AG - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr15:57744359_57744360delAG ENST00000281282.5 + 6 2004_2005 c.1926_1927delAG c.(1924-1929)gaagfs p.EE642fs NM_001252335.1|NM_032866.4 NP_001239264.1|NP_116255.2 Q0VF96 CGNL1_HUMAN cingulin-like 1 642 myosin complex|tight junction motor activity autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(14)|ovary(4)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(1) 60 all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186) ACATTAAAGAAGAGAGAGAGAG 0.441 9 406 --- --- --- --- NARG2 79664 broad.mit.edu 37 15 60745782 60745782 + Frame_Shift_Del DEL A A - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr15:60745782delA ENST00000561114.1 - 9 1307 c.1145delT c.(1144-1146)tcfs p.F382fs NARG2_ENST00000261520.4_Intron|NARG2_ENST00000439632.1_Intron NM_001276385.1 NP_001263314.1 Q659A1 NARG2_HUMAN NMDA receptor regulated 2 0 nucleus breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2) 32 CCCTTAGGGGAAAAAAAAAGC 0.338 10 213 --- --- --- --- UBE2Q2P1 0 broad.mit.edu 37 15 85077360 85077360 + RNA DEL A A - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr15:85077360delA ENST00000339094.1 - 0 1678 NR_003661.2 tttttaaactaaaaaaaaaaa 0.373 13 55 --- --- --- --- DNM1P47 0 broad.mit.edu 37 15 102292783 102292786 + RNA DEL CTCA CTCA - rs61084368 TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr15:102292783_102292786delCTCA ENST00000561463.1 + 0 829_832 p.Q125E(1) GATGCTGCTTCTCAGAGCTGCTGT 0.603 7 293 --- --- --- --- RRN3P2 0 broad.mit.edu 37 16 29113498 29113498 + RNA DEL T T - rs11366120 TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr16:29113498delT ENST00000564580.1 + 0 1360 AGGAGGTGGAttttttttttc 0.542 11 196 --- --- --- --- RP11-44F14.1 0 broad.mit.edu 37 16 53404542 53404543 + RNA INS - - A TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr16:53404542_53404543insA ENST00000565421.1 - 0 410 TCTCCTTTCTCAAACTTAACCT 0.327 17 236 --- --- --- --- MT1JP 0 broad.mit.edu 37 16 56670304 56670306 + RNA DEL CTT CTT - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr16:56670304_56670306delCTT ENST00000564564.1 + 0 630_632 ACTGCTGTACCTTCTTCATCTCA 0.581 8 311 --- --- --- --- RANBP10 57610 broad.mit.edu 37 16 67763279 67763281 + In_Frame_Del DEL GAG GAG - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr16:67763279_67763281delGAG ENST00000317506.3 - 10 1369_1371 c.1254_1256delCTC c.(1252-1257)tcg>tc p.SS420del RANBP10_ENST00000536251.1_In_Frame_Del_p.SS191del|RANBP10_ENST00000602677.1_In_Frame_Del_p.SS420del|RANBP10_ENST00000448631.2_In_Frame_Del_p.SS364del|RANBP10_ENST00000411657.2_In_Frame_Del_p.SS303del NM_020850.1 NP_065901.1 Q6VN20 RBP10_HUMAN RAN binding protein 10 420 Ser-rich. p.S418S(2) endometrium(5)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|skin(1) 23 Acute lymphoblastic leukemia(13;4.34e-06)|all_hematologic(13;0.000643)|Ovarian(137;0.192) OV - Ovarian serous cystadenocarcinoma(108;0.00522)|Epithelial(162;0.025)|all cancers(182;0.157) ggaagaggacgaggaggaggagg 0.567 9 258 --- --- --- --- SPG7 6687 broad.mit.edu 37 16 89613072 89613073 + Frame_Shift_Ins INS - - G rs111475461 byFrequency TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr16:89613072_89613073insG ENST00000268704.2 + 11 1471_1472 c.1456_1457insG c.(1456-1458)ggafs p.G486fs NM_003119.2 NP_003110.1 Q9UQ90 SPG7_HUMAN spastic paraplegia 7 (pure and complicated autosomal recessive) 486 R -> Q. cell death|nervous system development|protein catabolic process|proteolysis integral to membrane|mitochondrial membrane ATP binding|metalloendopeptidase activity|nucleoside-triphosphatase activity|unfolded protein binding|zinc ion binding autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|urinary_tract(1) 20 all_hematologic(23;0.00824)|Colorectal(91;0.102) all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015) GCAGGAGAGGCGGGAGATTTTT 0.594 14 840 --- --- --- --- MYH10 4628 broad.mit.edu 37 17 8415820 8415822 + In_Frame_Del DEL TTC TTC - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr17:8415820_8415822delTTC ENST00000360416.3 - 24 3037_3039 c.2899_2901delGAA c.(2899-2901)del p.E967del MYH10_ENST00000269243.4_In_Frame_Del_p.E936del|MYH10_ENST00000396239.1_In_Frame_Del_p.E957del|MYH10_ENST00000379980.4_In_Frame_Del_p.E952del NM_001256012.1 NP_001242941.1 P35580 MYH10_HUMAN myosin, heavy chain 10, non-muscle 936 actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape cell cortex|cleavage furrow|midbody|myosin complex|stress fiber actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1) 52 TTTGGTTTCTTTCTTCTTCTTCT 0.350 8 307 --- --- --- --- AC005863.1 0 broad.mit.edu 37 17 14673542 14673543 + RNA INS - - T TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr17:14673542_14673543insT ENST00000379640.1 - 0 354_355 GCTGGTCCCAGTTTTTTTTTCT 0.450 9 235 --- --- --- --- SNORD3A 0 broad.mit.edu 37 17 19091512 19091517 + RNA DEL GGGAGT GGGAGT - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr17:19091512_19091517delGGGAGT ENST00000365494.1 + 0 184_189 ctccgtattggggagtgagagggaga 0.539 13 1151 --- --- --- --- RP11-178C3.2 0 broad.mit.edu 37 17 58050857 58050857 + RNA DEL G G - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr17:58050857delG ENST00000586209.1 + 0 158 TTTTTTTTTTGGCAGTTTTTA 0.423 9 112 --- --- --- --- LRRC37A16P 0 broad.mit.edu 37 17 66141017 66141017 + RNA DEL C C - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr17:66141017delC ENST00000590019.1 - 0 70 AAGATTTCTACAAAAAAAAAA 0.323 8 271 --- --- --- --- RNF213 57674 broad.mit.edu 37 17 78354713 78354713 + Frame_Shift_Del DEL C C - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr17:78354713delC ENST00000582970.1 + 56 13866 c.13723delC c.(13723-13725)ccfs p.P4576fs CTD-2047H16.4_ENST00000575034.1_RNA|CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000508628.2_Frame_Shift_Del_p.P4625fs|RNF213_ENST00000336301.6_Frame_Shift_Del_p.P2649fs NM_001256071.1 NP_001243000.1 Q9HCF4 ALO17_HUMAN ring finger protein 213 0 NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3) 130 all_neural(118;0.0538) BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057) CCGAGGGCTGCCCCCAGTGGT 0.587 7 2081 --- --- --- --- SLC25A10 1468 broad.mit.edu 37 17 79686865 79686865 + Frame_Shift_Del DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr17:79686865delT ENST00000331531.5 + 10 857 c.737delT c.(736-738)gtfs p.V246fs SLC25A10_ENST00000350690.5_Frame_Shift_Del_p.V237fs|SLC25A10_ENST00000541223.1_Frame_Shift_Del_p.V392fs|SLC25A10_ENST00000545862.1_Frame_Shift_Del_p.V194fs|SLC25A10_ENST00000571730.1_Frame_Shift_Del_p.V392fs NM_001270888.1 NP_001257817.1 Q9UBX3 DIC_HUMAN solute carrier family 25 (mitochondrial carrier; dicarboxylate transporter), member 10 237 gluconeogenesis|mitochondrial transport integral to membrane|mitochondrial inner membrane|nucleus protein binding endometrium(1)|lung(9)|ovary(1)|prostate(1)|skin(2) 14 all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.23) BRCA - Breast invasive adenocarcinoma(99;0.0117)|OV - Ovarian serous cystadenocarcinoma(97;0.0955) Succinic acid(DB00139) CTGCAGGGCGTTTTCCACTGC 0.617 7 2209 --- --- --- --- RBBP8 5932 broad.mit.edu 37 18 20572852 20572853 + Frame_Shift_Ins INS - - A TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr18:20572852_20572853insA ENST00000399722.2 + 11 1413_1414 c.1062_1063insA c.(1060-1065)ggaaaafs p.GK354fs RBBP8_ENST00000360790.5_Frame_Shift_Ins_p.GK354fs|RBBP8_ENST00000327155.5_Frame_Shift_Ins_p.GK354fs|RBBP8_ENST00000399725.2_Frame_Shift_Ins_p.GK354fs NM_203291.1 NP_976036.1 Q99708 COM1_HUMAN retinoblastoma binding protein 8 354 cell cycle checkpoint|DNA double-strand break processing involved in repair via single-strand annealing|meiosis|regulation of transcription from RNA polymerase II promoter nucleus damaged DNA binding|protein binding|single-stranded DNA specific endodeoxyribonuclease activity p.K357fs*3(2)|p.K355E(2)|p.G354G(2) central_nervous_system(1)|cervix(2)|endometrium(5)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1) 24 all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19) OV - Ovarian serous cystadenocarcinoma(1;0.00196) TACAGCCTGGGAAAAAAAAACA 0.361 Homologous recombination 13 487 --- --- --- --- CCDC178 374864 broad.mit.edu 37 18 30913143 30913143 + Frame_Shift_Del DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr18:30913143delT ENST00000383096.3 - 10 1056 c.874delA c.(874-876)tgfs p.M292fs CCDC178_ENST00000402325.1_Frame_Shift_Del_p.M292fs|CCDC178_ENST00000579916.1_Intron|CCDC178_ENST00000403303.1_Frame_Shift_Del_p.M292fs|CCDC178_ENST00000583930.1_Frame_Shift_Del_p.M292fs|CCDC178_ENST00000406524.2_Frame_Shift_Del_p.M292fs|CCDC178_ENST00000579947.1_Frame_Shift_Del_p.M292fs|CCDC178_ENST00000300227.8_Frame_Shift_Del_p.M292fs coiled-coil domain containing 178 p.M292fs*3(2) TTTACCTCCATTTTTTTTTTA 0.318 10 215 --- --- --- --- LMAN1 3998 broad.mit.edu 37 18 57013193 57013194 + Frame_Shift_Ins INS - - T TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr18:57013193_57013194insT ENST00000251047.5 - 8 1629_1630 c.912_913insA c.(910-915)aaaggafs p.G305fs NM_005570.3 NP_005561.1 P49257 LMAN1_HUMAN lectin, mannose-binding, 1 305 blood coagulation|ER to Golgi vesicle-mediated transport|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|protein transport endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane mannose binding|metal ion binding|unfolded protein binding breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1) 16 Colorectal(73;0.0946) Antihemophilic Factor(DB00025) TGGAATTCCTCTTTTTTTTTAT 0.455 10 601 --- --- --- --- CYP4F3 4051 broad.mit.edu 37 19 15769322 15769322 + Frame_Shift_Del DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr19:15769322delT ENST00000221307.7 + 11 1319 c.1271delT c.(1270-1272)gtfs p.V424fs CYP4F3_ENST00000591058.1_Frame_Shift_Del_p.V424fs|CYP4F3_ENST00000586182.1_Frame_Shift_Del_p.V424fs|CYP4F3_ENST00000585846.1_Frame_Shift_Del_p.V424fs NM_000896.2 NP_000887.2 Q08477 CP4F3_HUMAN cytochrome P450, family 4, subfamily F, polypeptide 3 424 leukotriene metabolic process|xenobiotic metabolic process endoplasmic reticulum membrane|integral to membrane|microsome electron carrier activity|heme binding|leukotriene-B4 20-monooxygenase activity|oxygen binding endometrium(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|stomach(1) 34 CTCATCAGTGTTTTTGGAACC 0.622 7 1620 --- --- --- --- ZNF43 7594 broad.mit.edu 37 19 22002025 22002026 + Splice_Site INS - - A TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr19:22002025_22002026insA ENST00000594012.1 - 5 500 c.e5-2 ZNF43_ENST00000598288.1_Splice_Site|ZNF43_ENST00000598381.1_Splice_Site|ZNF43_ENST00000354959.4_Splice_Site|ZNF43_ENST00000595461.1_Splice_Site NM_001256649.1|NM_001256651.1|NM_001256653.1|NM_001256654.1 NP_001243578.1|NP_001243580.1|NP_001243582.1|NP_001243583.1 P17038 ZNF43_HUMAN zinc finger protein 43 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding p.?(1) autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2) 51 Renal(1328;0.000219)|Hepatocellular(1079;0.121) GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127) CAATGGTCCCTAAAAAAAACAA 0.386 8 938 --- --- --- --- HAUS5 23354 broad.mit.edu 37 19 36108990 36108990 + Frame_Shift_Del DEL C C - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr19:36108990delC ENST00000203166.5 + 10 739 c.714delC c.(712-714)cafs p.H238fs HAUS5_ENST00000379045.2_Frame_Shift_Del_p.H238fs NM_015302.1 NP_056117.1 O94927 HAUS5_HUMAN HAUS augmin-like complex, subunit 5 238 cell division|centrosome organization|mitosis|spindle assembly centrosome|HAUS complex|microtubule|spindle NS(1)|breast(2)|cervix(3)|endometrium(1)|large_intestine(2)|lung(5)|skin(2) 16 TGACAAACCACCCCCCAGGCC 0.642 7 1081 --- --- --- --- WDR62 284403 broad.mit.edu 37 19 36583666 36583668 + In_Frame_Del DEL GCA GCA - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr19:36583666_36583668delGCA ENST00000401500.2 + 19 2321_2323 c.2286_2288delGCA c.(2284-2289)cgg>cg p.RQ762del WDR62_ENST00000270301.7_In_Frame_Del_p.RQ762del NM_001083961.1|NM_173636.4 NP_001077430.1|NP_775907.4 O43379 WDR62_HUMAN WD repeat domain 62 762 cerebral cortex development nucleus cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3) 43 Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.06) TTGACCACCGGCAGCAGCAGCAG 0.616 7 889 --- --- --- --- LYPD3 27076 broad.mit.edu 37 19 43969653 43969655 + In_Frame_Del DEL AGC AGC - rs141441894 byFrequency TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr19:43969653_43969655delAGC ENST00000244333.3 - 1 157_159 c.69_71delGCT c.(67-72)ctt>ct p.LL23del NM_014400.2 NP_055215.2 O95274 LYPD3_HUMAN LY6/PLAUR domain containing 3 23 anchored to plasma membrane cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|upper_aerodigestive_tract(2) 11 Prostate(69;0.0153) ACCTCCGCGAAGCAGCAGCAGCA 0.675 9 843 --- --- --- --- PNMAL1 55228 broad.mit.edu 37 19 46973195 46973197 + In_Frame_Del DEL CTT CTT - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr19:46973195_46973197delCTT ENST00000313683.10 - 2 1401_1403 c.1096_1098delAAG c.(1096-1098)del p.K366del PNMAL1_ENST00000602246.1_Intron|PNMAL1_ENST00000438932.2_Splice_Site_p.K366_splice NM_001103149.1|NM_018215.3 NP_001096619.1|NP_060685.2 Q86V59 PNML1_HUMAN paraneoplastic Ma antigen family-like 1 366 cervix(1)|endometrium(2)|large_intestine(8)|lung(8)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 25 Ovarian(192;0.00965)|all_neural(266;0.0459) OV - Ovarian serous cystadenocarcinoma(262;0.000166)|all cancers(93;0.0014)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427) CCAAGCTCACCTTCTTCTTCTTC 0.562 8 1193 --- --- --- --- MAMSTR 284358 broad.mit.edu 37 19 49218105 49218106 + Frame_Shift_Ins INS - - G TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr19:49218105_49218106insG ENST00000318083.6 - 6 548_549 c.485_486insC c.(484-486)ccafs p.P162fs MAMSTR_ENST00000377367.3_Frame_Shift_Ins_p.P59fs|MAMSTR_ENST00000419611.1_Frame_Shift_Ins_p.P59fs|MAMSTR_ENST00000594582.1_Frame_Shift_Ins_p.P59fs|MAMSTR_ENST00000356751.4_Frame_Shift_Ins_p.P59fs Q6ZN01 MASTR_HUMAN MEF2 activating motif and SAP domain containing transcriptional regulator 162 Pro-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus nucleic acid binding endometrium(1)|ovary(1) 2 CCAACTTGTGTGGGGGGGGCGA 0.569 8 580 --- --- --- --- AC008984.2 0 broad.mit.edu 37 19 54843564 54843565 + RNA INS - - C rs144647366 by1000genomes TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr19:54843564_54843565insC ENST00000507363.1 - 0 430 CGGCTGCTCCTCCCCAGGCTGC 0.723 10 16 --- --- --- --- ZNF134 7693 broad.mit.edu 37 19 58132432 58132432 + Frame_Shift_Del DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr19:58132432delT ENST00000396161.5 + 3 1255 c.945delT c.(943-945)ccfs p.P315fs NM_003435.3 NP_003426.3 P52741 ZN134_HUMAN zinc finger protein 134 315 nucleus DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(3)|prostate(1) 11 Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156) UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265) GAGAAAATCCTTATGATTGCA 0.413 44 1060 --- --- --- --- FRG1B 0 broad.mit.edu 37 20 29625899 29625900 + Frame_Shift_Ins INS - - AT TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr20:29625899_29625900insAT ENST00000278882.3 + 5 523_524 c.143_144insAT c.(142-144)atafs p.I48fs FRG1B_ENST00000358464.4_Frame_Shift_Ins_p.I48fs|FRG1B_ENST00000439954.2_Frame_Shift_Ins_p.I53fs endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9) 53 GGCTATGGAAAATATCTTGGTA 0.342 28 691 --- --- --- --- LPIN3 64900 broad.mit.edu 37 20 39977799 39977799 + Frame_Shift_Del DEL C C - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr20:39977799delC ENST00000373257.3 + 5 716 c.625delC c.(625-627)ccfs p.P210fs NM_022896.1 NP_075047.1 Q9BQK8 LPIN3_HUMAN lipin 3 210 fatty acid metabolic process nucleus phosphatidate phosphatase activity breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(7)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 31 Myeloproliferative disorder(115;0.000739) TGGCGAGTGGCCCCCCCAGGC 0.537 7 634 --- --- --- --- AC005220.3 0 broad.mit.edu 37 20 52557949 52557950 + RNA INS - - TT rs72548465 by1000genomes TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr20:52557949_52557950insTT ENST00000450473.1 + 0 550 gtgtgtgtgtgtgtgtgtgcgc 0.500 6 11 --- --- --- --- DIDO1 11083 broad.mit.edu 37 20 61512380 61512381 + Frame_Shift_Ins INS - - G TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr20:61512380_61512381insG ENST00000266070.4 - 16 5252_5253 c.4927_4928insC c.(4927-4929)cccfs p.P1643fs DIDO1_ENST00000395343.1_Frame_Shift_Ins_p.P1643fs NM_033081.2 NP_149072.2 Q9BTC0 DIDO1_HUMAN death inducer-obliterator 1 1643 apoptosis|transcription, DNA-dependent cytoplasm|nucleus zinc ion binding NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1) 99 Breast(26;5.68e-08) CGTGGCGGGGCGGGTGCCCTCC 0.728 10 139 --- --- --- --- ANKRD20A11P 0 broad.mit.edu 37 21 15343608 15343609 + RNA INS - - A TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr21:15343608_15343609insA ENST00000344693.5 - 0 736 NR_027270.1 TAAAACAGCAGAAAAAATTAAT 0.272 15 507 --- --- --- --- ADAMTS5 11096 broad.mit.edu 37 21 28296615 28296615 + Frame_Shift_Del DEL A A - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr21:28296615delA ENST00000284987.5 - 8 2671 c.2550delT c.(2548-2550)ttfs p.F850fs AP001601.2_ENST00000426771.1_RNA NM_007038.3 NP_008969.2 Q9UNA0 ATS5_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 5 850 Spacer. proteolysis proteinaceous extracellular matrix integrin binding|metalloendopeptidase activity|zinc ion binding breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3) 72 TCTTGGGAACAAAAAAGCTAT 0.478 7 745 --- --- --- --- MED15 51586 broad.mit.edu 37 22 20918817 20918819 + In_Frame_Del DEL CAG CAG - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr22:20918817_20918819delCAG ENST00000263205.7 + 6 601_603 c.532_534delCAG c.(532-534)del p.Q188del MED15_ENST00000292733.7_In_Frame_Del_p.Q188del|MED15_ENST00000425759.2_In_Frame_Del_p.Q77del|MED15_ENST00000406969.1_In_Frame_Del_p.Q162del|MED15_ENST00000542773.1_5'UTR|MED15_ENST00000541476.1_In_Frame_Del_p.Q162del|MED15_ENST00000382974.2_In_Frame_Del_p.Q117del NM_001003891.1 NP_001003891.1 Q96RN5 MED15_HUMAN mediator complex subunit 15 188 Poly-Gln. regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent Golgi apparatus|mediator complex protein binding central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1) 25 all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209) ggcggcgctacagcagcagcagc 0.626 OREG0026319 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 8 187 --- --- --- --- IGLV4-60 0 broad.mit.edu 37 22 22516884 22516884 + RNA DEL C C - rs34221567 TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr22:22516884delC ENST00000390284.2 + 0 172 CGCATGGCATCAGCAGCAGCC 0.567 7 251 --- --- --- --- SH3BP1 23616 broad.mit.edu 37 22 38039752 38039754 + In_Frame_Del DEL AGG AGG - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr22:38039752_38039754delAGG ENST00000599616.1 + 5 383_385 c.383_385delAGG c.(382-387)aag>a p.KE128del SH3BP1_ENST00000442465.2_In_Frame_Del_p.KE192del|SH3BP1_ENST00000336738.5_In_Frame_Del_p.KE192del|SH3BP1_ENST00000495174.1_3'UTR|SH3BP1_ENST00000357436.4_In_Frame_Del_p.KE192del|Z83844.1_ENST00000456099.1_RNA Q9Y3L3 3BP1_HUMAN SH3-domain binding protein 1 192 BAR. signal transduction cytoplasm GTPase activator activity|SH3 domain binding breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 13 Melanoma(58;0.0574) GAGACGCTGAAGGAGGAGGAGGA 0.606 OREG0026546 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 7 560 --- --- --- --- SERHL 94009 broad.mit.edu 37 22 42898665 42898666 + RNA INS - - C TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr22:42898665_42898666insC ENST00000359906.2 + 0 409 NR_027786.1 serine hydrolase-like endometrium(1)|large_intestine(1) 2 CCCATATGGTGCCCCCCCCCCA 0.589 7 26 --- --- --- --- ARFGAP3 26286 broad.mit.edu 37 22 43213780 43213780 + Frame_Shift_Del DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr22:43213780delT ENST00000263245.5 - 10 1115 c.896delA c.(895-897)atfs p.N299fs ARFGAP3_ENST00000429508.2_Frame_Shift_Del_p.N227fs|ARFGAP3_ENST00000437119.2_Frame_Shift_Del_p.N255fs NM_001142293.1|NM_014570.4 NP_001135765.1|NP_055385.3 Q9NP61 ARFG3_HUMAN ADP-ribosylation factor GTPase activating protein 3 299 intracellular protein transport|protein secretion|regulation of ARF GTPase activity|vesicle-mediated transport cytosol|Golgi membrane ARF GTPase activator activity|protein transporter activity|zinc ion binding breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1) 11 TGAGTCAACATTTTTTTTGCC 0.363 8 878 --- --- --- --- SMC1B 27127 broad.mit.edu 37 22 45802384 45802384 + Frame_Shift_Del DEL T T - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr22:45802384delT ENST00000357450.4 - 4 571 c.572delA c.(571-573)atfs p.N191fs SMC1B_ENST00000404354.3_Frame_Shift_Del_p.N191fs NM_148674.3 NP_683515.3 Q8NDV3 SMC1B_HUMAN structural maintenance of chromosomes 1B 191 chromosome organization|meiosis chromosome, centromeric region|cytoplasm|meiotic cohesin complex|nucleus ATP binding breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2) 37 Ovarian(80;0.00965)|all_neural(38;0.0416) UCEC - Uterine corpus endometrioid carcinoma (28;0.0182) TGCCGCTATATTTTTTTTCTT 0.343 8 444 --- --- --- --- MLC1 23209 broad.mit.edu 37 22 50502593 50502595 + In_Frame_Del DEL AGC AGC - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chr22:50502593_50502595delAGC ENST00000311597.5 - 11 1533_1535 c.927_929delGCT c.(925-930)cta>ct p.LL309del MLC1_ENST00000538737.1_In_Frame_Del_p.LL275del|MLC1_ENST00000535444.1_In_Frame_Del_p.LL230del|MLC1_ENST00000483836.1_5'UTR|MLC1_ENST00000431262.2_In_Frame_Del_p.LL279del|MLC1_ENST00000395876.2_In_Frame_Del_p.LL309del|MLC1_ENST00000450140.2_In_Frame_Del_p.LL257del NM_015166.3 NP_055981.1 Q15049 MLC1_HUMAN megalencephalic leukoencephalopathy with subcortical cysts 1 309 L -> M (in a pedigree affected by schizophrenia). basolateral plasma membrane|endosome|integral to membrane|integral to membrane of membrane fraction ion channel activity endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(3) 18 all_cancers(38;7.69e-11)|all_epithelial(38;9.52e-10)|all_lung(38;3.67e-05)|Breast(42;0.000776)|Lung NSC(38;0.000946)|Ovarian(80;0.0365)|Lung SC(80;0.113) READ - Rectum adenocarcinoma(2;0.000669)|Colorectal(2;0.00242)|LUAD - Lung adenocarcinoma(64;0.0695)|BRCA - Breast invasive adenocarcinoma(115;0.216) caggagcactagcagcagcagca 0.655 7 118 --- --- --- --- NUDT11 0 broad.mit.edu 37 X 51239296 51239309 + Translation_Start_Site DEL TCCTCGAGGCAGCC TCCTCGAGGCAGCC - rs78182391 TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chrX:51239296_51239309delTCCTCGAGGCAGCC ENST00000375992.3 - 0 139_152 NM_018159.3 NP_060629.2 Q96G61 NUD11_HUMAN nudix (nucleoside diphosphate linked moiety X)-type motif 11 cytoplasm diphosphoinositol-polyphosphate diphosphatase activity|metal ion binding p.?(5) breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|prostate(1)|upper_aerodigestive_tract(2) 9 Ovarian(276;0.236) TTGCACTTCATCCTCGAGGCAGCCTCCTCGAGGC 0.692 HNSCC(48;0.14) 14 36 --- --- --- --- ATRX 546 broad.mit.edu 37 X 76907782 76907784 + In_Frame_Del DEL TCC TCC - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chrX:76907782_76907784delTCC ENST00000373344.5 - 15 4591_4593 c.4377_4379delGGA c.(4375-4380)gaa>ga p.EE1463del ATRX_ENST00000395603.3_In_Frame_Del_p.EE1425del|ATRX_ENST00000480283.1_5'UTR NM_000489.3 NP_000480.2 P46100 ATRX_HUMAN alpha thalassemia/mental retardation syndrome X-linked 1463 Poly-Glu. 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) ctcctcctcttcctcctcctcct 0.389 """Mis, F, N""" """Pancreatic neuroendocrine tumors, paediatric GBM""" ATR-X (alpha thalassemia/mental retardation) syndrome 10 376 --- --- --- --- PAK3 5063 broad.mit.edu 37 X 110406206 110406208 + In_Frame_Del DEL GAA GAA - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chrX:110406206_110406208delGAA ENST00000519681.1 + 10 1037_1039 c.595_597delGAA c.(595-597)del p.E203del PAK3_ENST00000372010.1_In_Frame_Del_p.E197del|PAK3_ENST00000446737.1_In_Frame_Del_p.E182del|PAK3_ENST00000262836.4_In_Frame_Del_p.E197del|PAK3_ENST00000425146.1_In_Frame_Del_p.E182del|PAK3_ENST00000372007.4_In_Frame_Del_p.E182del|PAK3_ENST00000417227.1_In_Frame_Del_p.E203del|PAK3_ENST00000360648.4_In_Frame_Del_p.E218del|PAK3_ENST00000518291.1_In_Frame_Del_p.E218del O75914 PAK3_HUMAN p21 protein (Cdc42/Rac)-activated kinase 3 197 Linker. multicellular organismal development ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(15)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4) 41 agatgaagaggaagaagaagaag 0.394 TSP Lung(19;0.15) 8 444 --- --- --- --- CUL4B 8450 broad.mit.edu 37 X 119694117 119694119 + In_Frame_Del DEL GAG GAG - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chrX:119694117_119694119delGAG ENST00000371322.5 - 1 436_438 c.375_377delCTC c.(373-378)tca>tc p.SS127del CUL4B_ENST00000336592.6_In_Frame_Del_p.SS132del|CUL4B_ENST00000404115.3_In_Frame_Del_p.SS145del NM_001079872.1 NP_001073341.1 Q13620 CUL4B_HUMAN cullin 4B 145 Ser-rich. cell cycle|DNA repair|ubiquitin-dependent protein catabolic process Cul4B-RING ubiquitin ligase complex|nucleus protein binding|ubiquitin protein ligase binding NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 36 TGGTGAAGATgaggaggaggagg 0.488 9 239 --- --- --- --- MAMLD1 10046 broad.mit.edu 37 X 149639325 149639327 + In_Frame_Del DEL CAG CAG - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chrX:149639325_149639327delCAG ENST00000370401.2 + 4 1790_1792 c.1480_1482delCAG c.(1480-1482)del p.Q502del MAMLD1_ENST00000432680.2_In_Frame_Del_p.Q477del|MAMLD1_ENST00000262858.5_In_Frame_Del_p.Q502del|MAMLD1_ENST00000455522.2_5'UTR|MAMLD1_ENST00000426613.2_In_Frame_Del_p.Q477del Q13495 MAMD1_HUMAN mastermind-like domain containing 1 502 Poly-Gln. male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus p.Q469Q(1)|p.Q494Q(1)|p.Q421Q(1) breast(1)|endometrium(4)|kidney(3)|large_intestine(12)|lung(14)|ovary(1)|prostate(2) 37 Acute lymphoblastic leukemia(192;6.56e-05) AAGCcagcaacagcagcagcagc 0.532 10 249 --- --- --- --- PASD1 139135 broad.mit.edu 37 X 150817142 150817144 + In_Frame_Del DEL GCT GCT - TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chrX:150817142_150817144delGCT ENST00000370357.4 + 9 930_932 c.685_687delGCT c.(685-687)del p.A236del NM_173493.2 NP_775764.2 Q8IV76 PASD1_HUMAN PAS domain containing 1 236 Poly-Ala. nucleus signal transducer activity p.A229A(2) breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1) 48 Acute lymphoblastic leukemia(192;6.56e-05) CGTTGAACCCgctgctgctgctg 0.433 12 508 --- --- --- --- UBL4A 8266 broad.mit.edu 37 X 153714159 153714160 + Frame_Shift_Ins INS - - G rs150392222 TCGA-HZ-8519-01A-11D-2396-08 TCGA-HZ-8519-10A-01D-2396-08 Untested Somatic Phase_I WXS none Illumina GAIIx a5e71fad-3b79-47f8-b3c7-3aa289972191 63b831aa-a874-4e47-b5e9-b75522bb6e66 g.chrX:153714159_153714160insG ENST00000369660.4 - 3 398_399 c.313_314insC c.(313-315)ccafs p.P105fs UBL4A_ENST00000477777.1_5'UTR|UBL4A_ENST00000369653.4_Frame_Shift_Ins_p.P105fs NM_014235.3 NP_055050.1 P11441 UBL4A_HUMAN ubiquitin-like 4A 105 protein modification process|tail-anchored membrane protein insertion into ER membrane|transport BAT3 complex small conjugating protein ligase activity endometrium(5)|lung(1)|urinary_tract(1) 7 all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176) ACTGAAGTGGCGGGCCAAGACT 0.629 10 615 --- --- --- ---