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 PTEN 5728 broad.mit.edu 37 10 89690828 89690828 + Missense_Mutation SNP G G A TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr10:89690828G>A ENST00000371953.3 + 4 1592 c.235G>A c.(235-237)Gcc>Acc p.A79T NM_000314.4 NP_000305.3 P60484 PTEN_HUMAN phosphatase and tensin homolog 79 Phosphatase tensin-type. activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway cytosol|internal side of plasma membrane|PML body anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity p.0?(37)|p.?(5)|p.R55fs*1(5)|p.L70fs*7(4)|p.C71fs*6(2)|p.Y27fs*1(2)|p.A79T(2)|p.F56fs*2(1) NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17) 2771 all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132) KIRC - Kidney renal clear cell carcinoma(1;0.214) UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218) TTATGACACCGCCAAATTTAA 0.303000 31 """D, Mis, N, F, S""" """glioma, prostate, endometrial""" """harmartoma, glioma, prostate, endometrial""" Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18) 6 256 0 0 1 0 0 RBM15 64783 broad.mit.edu 37 1 110883698 110883698 + Silent SNP A A C TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr1:110883698A>C ENST00000369784.3 + 1 2571 c.1671A>C c.(1669-1671)gcA>gcC p.A557A RBM15_ENST00000487146.2_Silent_p.A557A|RBM15_ENST00000602849.1_Silent_p.A557A NM_022768.4 NP_073605.4 Q96T37 RBM15_HUMAN RNA binding motif protein 15 557 interspecies interaction between organisms nucleus nucleotide binding|protein binding|RNA binding ovary(3) 3 all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634) BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135) GACATCGGGCACCAGACCCTT 0.532000 T MKL1 acute megakaryocytic leukemia 10 342 0 0 1 0 0 DLX6 1750 broad.mit.edu 37 7 96635385 96635385 + Splice_Site SNP G G A TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr7:96635385G>A ENST00000007660.5 + 1 95 c.e1+1 DLX6-AS1_ENST00000458352.2_RNA|DLX6-AS1_ENST00000605417.1_RNA|DLX6-AS1_ENST00000452769.2_RNA|DLX6-AS1_ENST00000437331.2_RNA|DLX6-AS1_ENST00000430404.2_RNA|DLX6-AS1_ENST00000430027.2_RNA|DLX6-AS1_ENST00000437541.1_RNA|DLX6_ENST00000518156.2_Silent_p.Q32Q NM_005222.3 NP_005213.3 P56179 DLX6_HUMAN distal-less homeobox 6 nervous system development|skeletal system development nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity central_nervous_system(1)|kidney(1)|large_intestine(1)|liver(2)|lung(4)|ovary(2)|urinary_tract(1) 12 all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858) agcagcagcagcaacagcagc 0.657000 3 45 0 0 1 0 0 LL22NC03-80A10.6 0 broad.mit.edu 37 22 22661721 22661721 + RNA SNP G G T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr22:22661721G>T ENST00000426066.1 + 0 500 NR_027293.1 TTTTAGCTTTGTGCTTTTCCT 0.378000 9 138 2.27111e-07 2.31437e-07 1 1 0 PADI1 29943 broad.mit.edu 37 1 17570638 17570638 + Missense_Mutation SNP A A T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr1:17570638A>T ENST00000375471.4 + 16 1984 c.1892A>T c.(1891-1893)gAt>gTt p.D631V PADI1_ENST00000537499.1_Missense_Mutation_p.D188V|PADI1_ENST00000413717.2_Missense_Mutation_p.D146V|PADI1_ENST00000536552.1_Missense_Mutation_p.D102V|PADI1_ENST00000460293.1_3'UTR NM_013358.2 NP_037490.2 Q9ULC6 PADI1_HUMAN peptidyl arginine deiminase, type I 631 peptidyl-citrulline biosynthetic process from peptidyl-arginine cytoplasm calcium ion binding|protein-arginine deiminase activity haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1) 28 Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.00522)|BRCA - Breast invasive adenocarcinoma(304;1.3e-05)|COAD - Colon adenocarcinoma(227;1.31e-05)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(196;0.0069)|READ - Rectum adenocarcinoma(331;0.0681)|Lung(427;0.197) L-Citrulline(DB00155) ATCTTCATTGATGACTACTTG 0.592000 12 423 0 0 1 0 0 SDHAP1 0 broad.mit.edu 37 3 195698264 195698264 + RNA SNP T T C rs12485654 by1000genomes TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr3:195698264T>C ENST00000427841.1 - 0 1608 NR_003264.2 TTTGTCAACATTCGTGACAGA 0.413000 7 278 0 0 1 0 0 MLLT3 4300 broad.mit.edu 37 9 20414373 20414373 + Silent SNP G G A TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr9:20414373G>A ENST00000380338.4 - 5 757 c.471C>T c.(469-471)agC>agT p.S157S MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S154S|MLLT3_ENST00000475957.1_5'UTR NM_004529.2 NP_004520.2 P42568 AF9_HUMAN myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 157 Poly-Ser. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus protein binding p.S157S(5) central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7) 66 GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05) tgctgctgctgctactgctgc 0.527000 T MLL ALL 11 414 0 0 1 0 0 FAT3 120114 broad.mit.edu 37 11 92533399 92533399 + Missense_Mutation SNP C C T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr11:92533399C>T ENST00000298047.6 + 9 7237 c.7220C>T c.(7219-7221)gCc>gTc p.A2407V FAT3_ENST00000409404.2_Missense_Mutation_p.A2407V|FAT3_ENST00000525166.1_Missense_Mutation_p.A2257V Q8TDW7 FAT3_HUMAN FAT atypical cadherin 3 2407 Cadherin 22. homophilic cell adhesion|multicellular organismal development integral to membrane|plasma membrane calcium ion binding NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5) 85 Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858) AGTGAATTAGCCCCCCGGGGC 0.443000 TCGA Ovarian(4;0.039) 13 616 0 0 1 0 0 HSD17B7P2 0 broad.mit.edu 37 10 38654432 38654432 + RNA SNP A A G rs2257765 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr10:38654432A>G ENST00000494540.1 + 0 599 NR_003086.1 TCATCTCGCAATGCAAGGAAA 0.453000 10 322 0 0 1 0 0 PSD 5662 broad.mit.edu 37 10 104170669 104170669 + Silent SNP G G A TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr10:104170669G>A ENST00000020673.5 - 10 2563 c.2037C>T c.(2035-2037)atC>atT p.I679I PSD_ENST00000406432.1_Silent_p.I679I NM_001270966.1|NM_002779.3 NP_001257895.1|NP_002770.3 A5PKW4 PSD1_HUMAN pleckstrin and Sec7 domain containing 679 SEC7. regulation of ARF protein signal transduction cytoplasm|plasma membrane|ruffle ARF guanyl-nucleotide exchange factor activity|signal transducer activity 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) CCAGGTTCCCGATGAAGTCCC 0.632000 30 600 0 0 1 0 0 ZNF284 342909 broad.mit.edu 37 19 44590411 44590411 + Missense_Mutation SNP T T G TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr19:44590411T>G ENST00000421176.3 + 5 996 c.780T>G c.(778-780)atT>atG p.I260M ZNF223_ENST00000591793.1_3'UTR NM_001037813.2 NP_001032902.1 Q2VY69 ZN284_HUMAN zinc finger protein 284 260 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1) 15 Prostate(69;0.0435) AACCTCATATTTGTGAGGAAT 0.408000 14 585 0 0 1 0 0 NSUN5P1 0 broad.mit.edu 37 7 75044209 75044209 + RNA SNP T T C rs71255231 by1000genomes TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr7:75044209T>C ENST00000393633.2 + 0 3473 large_intestine(1)|lung(1) 2 TCTCCTGGACTCCTTGATGCC 0.547000 6 156 0 0 1 0 0 B9D1 27077 broad.mit.edu 37 17 19247075 19247075 + Missense_Mutation SNP G G A rs4924987 by1000genomes TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr17:19247075G>A ENST00000477478.2 - 6 760 c.427C>T c.(427-429)Cat>Tat p.H143Y B9D1_ENST00000395616.3_Intron|B9D1_ENST00000395615.1_Intron|B9D1_ENST00000575403.1_Intron|B9D1_ENST00000261499.4_Intron|B9D1_ENST00000461069.2_Intron Q9UPM9 B9D1_HUMAN B9 protein domain 1 125 cilium assembly centrosome|microtubule basal body protein binding large_intestine(3)|urinary_tract(1) 4 all_cancers(12;2.04e-05)|all_epithelial(12;0.000806)|Hepatocellular(7;0.00345)|Breast(13;0.143) TATGGGGGATGGGGGTAAGAG 0.642000 9 361 0 0 1 0 0 ZNF733P 0 broad.mit.edu 37 7 62752443 62752443 + RNA SNP G G C TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr7:62752443G>C ENST00000331425.6 - 0 992 NR_003952.1 CTTATGTCTAGTAAGGTTTGA 0.438000 12 189 0 0 1 0 0 GLUD1P2 0 broad.mit.edu 37 10 48968566 48968566 + RNA SNP A A G TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr10:48968566A>G ENST00000594520.1 + 0 723 ACAGGATAACAAACTGGAAAA 0.318000 16 355 0 0 1 0 0 KRTAP4-9 100132386 broad.mit.edu 37 17 39262039 39262039 + Missense_Mutation SNP C C G TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr17:39262039C>G ENST00000391415.1 + 1 456 c.399C>G c.(397-399)agC>agG p.S133R NM_001146041.1 NP_001139513.1 Q9BYQ8 KRA49_HUMAN keratin associated protein 4-9 133 29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP]. keratin filament p.S133R(1)|p.S121R(1) central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3) 14 gtgtgtccagctgctgcaagc 0.652000 5 142 0 0 1 0 0 DOT1L 84444 broad.mit.edu 37 19 2210769 2210769 + Silent SNP C C T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr19:2210769C>T ENST00000398665.3 + 14 1302 c.1266C>T c.(1264-1266)ccC>ccT p.P422P NM_032482.2 NP_115871.1 Q8TEK3 DOT1L_HUMAN DOT1-like histone H3K79 methyltransferase 422 nucleus DNA binding|histone-lysine N-methyltransferase activity|protein binding NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9) 42 Hepatocellular(1079;0.137) UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18) CTGCGAACCCCGAGCGGAAGC 0.632000 75 394 0 0 1 0 0 MLLT3 4300 broad.mit.edu 37 9 20414346 20414346 + Silent SNP G G A TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr9:20414346G>A ENST00000380338.4 - 5 784 c.498C>T c.(496-498)agC>agT p.S166S MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S163S|MLLT3_ENST00000475957.1_5'UTR NM_004529.2 NP_004520.2 P42568 AF9_HUMAN myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 166 Poly-Ser. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus protein binding p.S166S(4) central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7) 66 GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05) tgctgctactgctgctgctgc 0.527000 T MLL ALL 15 474 0 0 1 0 0 ACSM2A 123876 broad.mit.edu 37 16 20491925 20491925 + Nonsense_Mutation SNP C C T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr16:20491925C>T ENST00000573854.1 + 11 1426 c.1312C>T c.(1312-1314)Cga>Tga p.R438* ACSM2A_ENST00000536134.1_Nonsense_Mutation_p.R210*|ACSM2A_ENST00000219054.6_Nonsense_Mutation_p.R438*|ACSM2A_ENST00000575690.1_Nonsense_Mutation_p.R438*|ACSM2A_ENST00000396104.2_Nonsense_Mutation_p.R438*|ACSM2A_ENST00000417235.2_Nonsense_Mutation_p.R359*|ACSM2A_ENST00000575558.1_3'UTR NM_001010845.2 NP_001010845.1 Q08AH3 ACS2A_HUMAN acyl-CoA synthetase medium-chain family member 2A 438 fatty acid metabolic process mitochondrial matrix ATP binding|butyrate-CoA ligase activity|metal ion binding breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(34)|ovary(1)|skin(6)|stomach(1) 51 AGCCAACATTCGAGGAGACTT 0.512000 16 836 0 0 1 0 0 CDK5RAP2 55755 broad.mit.edu 37 9 123253652 123253652 + Missense_Mutation SNP A A C TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr9:123253652A>C ENST00000349780.4 - 13 1594 c.1415T>G c.(1414-1416)tTg>tGg p.L472W CDK5RAP2_ENST00000359309.3_Missense_Mutation_p.L472W|CDK5RAP2_ENST00000360822.3_Missense_Mutation_p.L472W|CDK5RAP2_ENST00000360190.4_Missense_Mutation_p.L472W NM_018249.4 NP_060719.4 Q96SN8 CK5P2_HUMAN CDK5 regulatory subunit associated protein 2 472 brain development|centrosome organization|chromosome segregation|G2/M transition of mitotic cell cycle|microtubule bundle formation|negative regulation of centriole replication|positive regulation of transcription, DNA-dependent|regulation of neuron differentiation|regulation of spindle checkpoint cytosol|Golgi apparatus|microtubule|pericentriolar material|perinuclear region of cytoplasm|spindle pole calmodulin binding|microtubule binding|neuronal Cdc2-like kinase binding|transcription regulatory region DNA binding breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1) 58 TTGATTGTGCAATTTTTTATT 0.318000 36 250 0 0 1 0 0 ADAMTS12 81792 broad.mit.edu 37 5 33616037 33616037 + Missense_Mutation SNP T T G TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr5:33616037T>G ENST00000504830.1 - 15 2619 c.2284A>C c.(2284-2286)Aac>Cac p.N762H ADAMTS12_ENST00000352040.3_Missense_Mutation_p.N677H|ADAMTS12_ENST00000504582.1_5'UTR NM_030955.2 NP_112217.2 P58397 ATS12_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 12 762 Spacer 1. proteolysis proteinaceous extracellular matrix metalloendopeptidase activity|zinc ion binding NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5) 216 TAGTTCCCGTTCCACTGGATA 0.468000 HNSCC(64;0.19) 18 627 0 0 1 0 0 MLLT3 4300 broad.mit.edu 37 9 20414340 20414340 + Silent SNP G G A TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr9:20414340G>A ENST00000380338.4 - 5 790 c.504C>T c.(502-504)agC>agT p.S168S MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S165S|MLLT3_ENST00000475957.1_5'UTR NM_004529.2 NP_004520.2 P42568 AF9_HUMAN myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 168 Poly-Ser. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus protein binding p.S168S(5) central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7) 66 GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05) tgctgctgctgctactgctgc 0.537000 T MLL ALL 17 495 0 0 1 0 0 RP11-156P1.3 0 broad.mit.edu 37 17 45128812 45128812 + RNA SNP C C T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr17:45128812C>T ENST00000575173.1 - 0 418 AGTCCTGTTTCTGTGTGGATT 0.373000 6 203 0 0 1 0 0 ADAMTS12 81792 broad.mit.edu 37 5 33616038 33616038 + Nonsense_Mutation SNP C C T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr5:33616038C>T ENST00000504830.1 - 15 2618 c.2283G>A c.(2281-2283)tgG>tgA p.W761* ADAMTS12_ENST00000352040.3_Nonsense_Mutation_p.W676*|ADAMTS12_ENST00000504582.1_5'UTR NM_030955.2 NP_112217.2 P58397 ATS12_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 12 761 Spacer 1. proteolysis proteinaceous extracellular matrix metalloendopeptidase activity|zinc ion binding p.W761*(1) NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5) 216 AGTTCCCGTTCCACTGGATAA 0.468000 HNSCC(64;0.19) 18 628 0 0 1 0 0 NBPF14 25832 broad.mit.edu 37 1 148012531 148012531 + Silent SNP C C T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr1:148012531C>T ENST00000369219.1 - 12 1444 c.1428G>A c.(1426-1428)aaG>aaA p.K476K Q5TI25 NBPFE_HUMAN neuroblastoma breakpoint family, member 14 476 NBPF 5. cytoplasm p.K476K(2)|p.K476N(1) NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(23)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1) 42 all_hematologic(923;0.032) AGCCAACATGCTTTTCCTCCA 0.443000 5 54 0 0 1 0 0 KRTAP4-9 100132386 broad.mit.edu 37 17 39262047 39262047 + Missense_Mutation SNP A A G TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr17:39262047A>G ENST00000391415.1 + 1 464 c.407A>G c.(406-408)aAg>aGg p.K136R NM_001146041.1 NP_001139513.1 Q9BYQ8 KRA49_HUMAN keratin associated protein 4-9 136 29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP]. keratin filament central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3) 14 agctgctgcaagccccagtgc 0.652000 5 140 0 0 1 0 0 DMAP1 55929 broad.mit.edu 37 1 44680450 44680450 + Silent SNP G G A TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr1:44680450G>A ENST00000372289.2 + 3 536 c.273G>A c.(271-273)aaG>aaA p.K91K DMAP1_ENST00000361745.6_Silent_p.K91K|DMAP1_ENST00000315913.5_Silent_p.K91K NM_019100.4 NP_061973.1 Q9NPF5 DMAP1_HUMAN DNA methyltransferase 1 associated protein 1 91 DNA methylation|histone H2A acetylation|histone H4 acetylation|negative regulation of transcription, DNA-dependent|regulation of growth|transcription, DNA-dependent NuA4 histone acetyltransferase complex DNA binding|protein binding breast(1)|cervix(1)|endometrium(6)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 16 Acute lymphoblastic leukemia(166;0.155) GCTCCAAGAAGGTGCGGCCTT 0.612000 10 415 0 0 1 0 0 RFX6 222546 broad.mit.edu 37 6 117248259 117248259 + Missense_Mutation SNP G G A TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr6:117248259G>A ENST00000332958.2 + 17 1971 c.1955G>A c.(1954-1956)cGa>cAa p.R652Q NM_173560.3 NP_775831.2 Q8HWS3 RFX6_HUMAN regulatory factor X, 6 652 glucose homeostasis|pancreatic A cell differentiation|pancreatic D cell differentiation|pancreatic E cell differentiation|positive regulation of transcription, DNA-dependent|regulation of insulin secretion|transcription, DNA-dependent|type B pancreatic cell differentiation nucleus protein binding|transcription regulatory region DNA binding cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(29)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1) 59 ATGGCAAGCCGAGGAAGTGTC 0.512000 12 732 0 0 1 0 0 NAA40 79829 broad.mit.edu 37 11 63720021 63720021 + Missense_Mutation SNP G G A TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr11:63720021G>A ENST00000377793.4 + 5 495 c.394G>A c.(394-396)Gat>Aat p.D132N NAA40_ENST00000456907.2_Missense_Mutation_p.D92N|NAA40_ENST00000536939.1_3'UTR|NAA40_ENST00000539656.1_Intron|NAA40_ENST00000542163.1_Missense_Mutation_p.D111N NM_024771.2 NP_079047.2 Q86UY6 NAA40_HUMAN N(alpha)-acetyltransferase 40, NatD catalytic subunit 132 N-acetyltransferase. N-acetyltransferase activity NS(1)|endometrium(1)|lung(2)|prostate(1) 5 GGAGTGTGGGGATGAAGTCCT 0.582000 8 338 0 0 1 0 0 CPNE6 9362 broad.mit.edu 37 14 24546432 24546432 + Missense_Mutation SNP G G A TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr14:24546432G>A ENST00000397016.2 + 16 1680 c.1369G>A c.(1369-1371)Gtg>Atg p.V457M CPNE6_ENST00000537691.1_Missense_Mutation_p.V512M|CPNE6_ENST00000216775.2_Missense_Mutation_p.V457M O95741 CPNE6_HUMAN copine VI (neuronal) 457 VWFA. lipid metabolic process|nervous system development|synaptic transmission|vesicle-mediated transport calcium ion binding|transporter activity endometrium(4)|large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1) 22 GBM - Glioblastoma multiforme(265;0.0184) CACTGCTATCGTGCGTGCCTC 0.617000 35 354 0 0 1 0 0 TSSC2 0 broad.mit.edu 37 11 3427845 3427845 + RNA SNP C C T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr11:3427845C>T ENST00000529482.1 + 0 962 CTTCAAGTGGCAGGAGCAGAA 0.587000 17 252 0 0 1 0 0 MST1 4485 broad.mit.edu 37 3 49723551 49723551 + Missense_Mutation SNP A A G TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr3:49723551A>G ENST00000449682.2 - 9 1452 c.1091T>C c.(1090-1092)aTg>aCg p.M364T MST1_ENST00000383728.3_3'UTR NM_020998.3 NP_066278.3 P26927 HGFL_HUMAN macrophage stimulating 1 (hepatocyte growth factor-like) 350 proteolysis extracellular region serine-type endopeptidase activity p.M350T(3) NS(4)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|skin(9)|stomach(1)|urinary_tract(2) 41 BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244) GGCCGCGCGCATGCCGGGCCG 0.667000 6 103 0 0 1 0 0 ANKHD1 54882 broad.mit.edu 37 5 139916985 139916985 + Missense_Mutation SNP C C T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr5:139916985C>T ENST00000297183.6 + 31 7163 c.7039C>T c.(7039-7041)Cca>Tca p.P2347S ANKHD1-EIF4EBP3_ENST00000532219.1_Missense_Mutation_p.P2347S|ANKHD1_ENST00000360839.2_Missense_Mutation_p.P2347S|ANKHD1_ENST00000544120.1_Missense_Mutation_p.P671S 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) CACTTCTGCCCCACCAACGTT 0.473000 10 596 0 0 1 0 0 ZNF761 388561 broad.mit.edu 37 19 53945909 53945909 + RNA SNP T T C rs28727441 by1000genomes TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr19:53945909T>C ENST00000454407.1 + 0 55 TPM3P9_ENST00000424846.3_RNA Q86XN6 ZN761_HUMAN zinc finger protein 761 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1) 30 GBM - Glioblastoma multiforme(134;0.00786) ACCCTGACTCTGCCTGAGGCC 0.562000 15 251 0 0 1 0 0 CCT6P1 0 broad.mit.edu 37 7 65222986 65222986 + RNA SNP G G T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr7:65222986G>T ENST00000442266.1 + 0 578 GAATTCTGGCGTTTTTTACAA 0.289000 7 98 1.06961e-07 1.10047e-07 1 1 0 HS6ST2 90161 broad.mit.edu 37 X 131762528 131762528 + Missense_Mutation SNP C C T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chrX:131762528C>T ENST00000370836.2 - 4 1956 c.1541G>A c.(1540-1542)cGt>cAt p.R514H HS6ST2_ENST00000406696.3_Missense_Mutation_p.R240H|HS6ST2_ENST00000370833.2_Missense_Mutation_p.R408H|HS6ST2_ENST00000370837.1_Missense_Mutation_p.R368H|HS6ST2_ENST00000521489.1_Missense_Mutation_p.R554H NM_147175.3 NP_671704.3 Q96MM7 H6ST2_HUMAN heparan sulfate 6-O-sulfotransferase 2 514 integral to membrane sulfotransferase activity central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(2) 9 Acute lymphoblastic leukemia(192;0.000127) TTGTTCCTGACGCTTTCGCCT 0.483000 15 714 0 0 1 0 0 MLLT3 4300 broad.mit.edu 37 9 20414343 20414343 + Silent SNP A A G TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr9:20414343A>G ENST00000380338.4 - 5 787 c.501T>C c.(499-501)agT>agC p.S167S MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S164S|MLLT3_ENST00000475957.1_5'UTR NM_004529.2 NP_004520.2 P42568 AF9_HUMAN myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 167 Poly-Ser. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus protein binding p.S167S(19) central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7) 66 GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05) tgctgctgctactgctgctgc 0.532000 T MLL ALL 32 469 0 0 1 0 0 ZNF532 55205 broad.mit.edu 37 18 56586416 56586416 + Silent SNP G G A TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr18:56586416G>A ENST00000336078.4 + 4 1673 c.897G>A c.(895-897)ccG>ccA p.P299P ZNF532_ENST00000591808.1_Silent_p.P299P|ZNF532_ENST00000591083.1_Silent_p.P299P|ZNF532_ENST00000589288.1_Silent_p.P299P|ZNF532_ENST00000591230.1_Silent_p.P299P NM_018181.4 NP_060651.2 Q9HCE3 ZN532_HUMAN zinc finger protein 532 299 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding breast(5)|central_nervous_system(1)|cervix(2)|endometrium(14)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(4)|urinary_tract(1) 52 AATCCTCCCCGTTACCAAAAG 0.542000 14 766 0 0 1 0 0 PI4KAP1 0 broad.mit.edu 37 22 20386816 20386816 + RNA SNP A A G TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr22:20386816A>G ENST00000430523.3 - 0 1696 NR_003563.1 GTTTTCTTGGAGACAGTGATG 0.597000 5 17 0 0 1 0 0 GSN 2934 broad.mit.edu 37 9 124062285 124062285 + Splice_Site SNP T T G TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr9:124062285T>G ENST00000373818.4 + 1 213 c.e1+2 GSN_ENST00000394353.2_Intron|GSN_ENST00000545652.1_Intron|GSN_ENST00000341272.2_Intron|GSN_ENST00000436847.1_Intron|GSN_ENST00000373808.2_Intron|GSN_ENST00000449733.1_Intron|GSN_ENST00000412819.1_Intron|GSN_ENST00000373823.3_Intron NM_000177.4|NM_001258029.1 NP_000168.1|NP_001244958.1 P06396 GELS_HUMAN gelsolin actin filament polymerization|actin filament severing|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|cilium morphogenesis actin cytoskeleton|cytosol actin binding|calcium ion binding|protein binding NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(1) 21 gaggcgcgggtgagtgcccgg 0.697000 34 117 0 0 1 0 0 ANKRD36C 400986 broad.mit.edu 37 2 96521777 96521777 + Missense_Mutation SNP T T C rs77768218 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr2:96521777T>C ENST00000456556.1 - 63 4316 c.4232A>G c.(4231-4233)cAt>cGt p.H1411R ANKRD36C_ENST00000419039.2_Missense_Mutation_p.H438R|ANKRD36C_ENST00000420871.2_Missense_Mutation_p.H662R ankyrin repeat domain 36C p.H662R(6)|p.H1411R(3) breast(1)|endometrium(8)|kidney(5)|lung(4) 18 AAGGTCTTCATGCTTTCTTTT 0.383000 7 159 0 0 1 0 0 FAM5C 0 broad.mit.edu 37 1 190067264 190067264 + Missense_Mutation SNP G G A TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr1:190067264G>A ENST00000367462.3 - 8 2416 c.2185C>T c.(2185-2187)Cgt>Tgt p.R729C FAM5C_ENST00000534846.1_Missense_Mutation_p.R627C|FAM5C_ENST00000484105.1_5'UTR NM_199051.1 NP_950252.1 Q76B58 FAM5C_HUMAN 729 extracellular region NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(18)|lung(98)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(7)|urinary_tract(2) 164 Prostate(682;0.198) AGTCTATGACGAAGCAAGCAA 0.463000 33 663 0 0 1 0 0 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C A rs121913529 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr12:25398284C>A ENST00000311936.3 - 2 226 c.35G>T c.(34-36)gGt>gTt p.G12V KRAS_ENST00000256078.4_Missense_Mutation_p.G12V|KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V NM_004985.3 NP_004976.2 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog 12 G -> A (in a colorectal cancer sample; somatic mutation).|G -> C (in lung carcinoma; somatic mutation).|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation).|G -> R (in lung cancer and bladder cancer; somatic mutation).|G -> S (in lung carcinoma and GASC; somatic mutation).|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation). activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction plasma membrane GTP binding|GTPase activity|protein binding p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis """pancreatic, colorectal, lung, thyroid, AML, others""" Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) 15 98 1.3612e-06 1.37404e-06 1 1 0 EP400 57634 broad.mit.edu 37 12 132547087 132547087 + Silent SNP G G A rs12366766 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr12:132547087G>A ENST00000333577.4 + 48 8392 c.8283G>A c.(8281-8283)caG>caA p.Q2761Q EP400_ENST00000330386.6_Silent_p.Q2644Q|EP400_ENST00000389561.2_Silent_p.Q2725Q|EP400_ENST00000332482.4_Silent_p.Q2688Q|EP400_ENST00000389562.2_Silent_p.Q2724Q Q96L91 EP400_HUMAN E1A binding protein p400 2761 Interaction with ZNF42 (By similarity).|Poly-Gln. histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity p.Q2724Q(16)|p.Q2725Q(1) NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3) 161 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) agcagcagcagcaacaacagc 0.562000 18 339 0 0 1 0 0 FAM47A 158724 broad.mit.edu 37 X 34149477 34149477 + Missense_Mutation SNP C C T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chrX:34149477C>T ENST00000346193.3 - 1 970 c.919G>A c.(919-921)Gag>Aag p.E307K NM_203408.3 NP_981953.2 Q5JRC9 FA47A_HUMAN family with sequence similarity 47, member A 307 NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2) 97 AGTGGAGTCTCGAAAGGCCGA 0.612000 36 197 0 0 1 0 0 ZBTB22 0 broad.mit.edu 37 6 33284203 33284203 + Missense_Mutation SNP G G A TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr6:33284203G>A ENST00000431845.2 - 2 642 c.491C>T c.(490-492)aCc>aTc p.T164I ZBTB22_ENST00000418724.1_Missense_Mutation_p.T164I NM_005453.4 NP_005444.4 O15209 ZBT22_HUMAN zinc finger and BTB domain containing 22 164 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(3) 21 AGTGACAGAGGTGGCTGCAGC 0.642000 17 584 0 0 1 0 0 MST1 4485 broad.mit.edu 37 3 49723545 49723545 + Missense_Mutation SNP G G A rs4052562 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr3:49723545G>A ENST00000449682.2 - 9 1458 c.1097C>T c.(1096-1098)gCg>gTg p.A366V MST1_ENST00000383728.3_3'UTR NM_020998.3 NP_066278.3 P26927 HGFL_HUMAN macrophage stimulating 1 (hepatocyte growth factor-like) 352 proteolysis extracellular region serine-type endopeptidase activity NS(4)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|skin(9)|stomach(1)|urinary_tract(2) 41 BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244) GCAAAAGGCCGCGCGCATGCC 0.667000 5 101 0 0 1 0 0 GRM1 2911 broad.mit.edu 37 6 146720262 146720262 + Missense_Mutation SNP G G A TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr6:146720262G>A ENST00000392299.2 + 8 2557 c.2087G>A c.(2086-2088)cGg>cAg p.R696Q GRM1_ENST00000355289.4_Missense_Mutation_p.R696Q|GRM1_ENST00000507907.1_Missense_Mutation_p.R696Q|GRM1_ENST00000492807.2_Missense_Mutation_p.R696Q|GRM1_ENST00000282753.1_Missense_Mutation_p.R696Q|GRM1_ENST00000361719.2_Missense_Mutation_p.R696Q Q13255 GRM1_HUMAN glutamate receptor, metabotropic 1 696 R -> W (in a colorectal cancer sample; somatic mutation). synaptic transmission integral to plasma membrane G-protein coupled receptor activity|glutamate receptor activity NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1) 126 Ovarian(120;0.0387) OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762) Acamprosate(DB00659)|L-Glutamic Acid(DB00142) ATCTGCACCCGGAAGCCCAGG 0.512000 17 842 0 0 1 0 0 NRSN1 140767 broad.mit.edu 37 6 24134622 24134622 + Missense_Mutation SNP C C T rs143725119 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr6:24134622C>T ENST00000378491.4 + 3 368 c.67C>T c.(67-69)Cgc>Tgc p.R23C NRSN1_ENST00000378475.1_Missense_Mutation_p.R23C|NRSN1_ENST00000378478.1_Missense_Mutation_p.R23C NM_080723.4 NP_542454.3 Q8IZ57 NRSN1_HUMAN neurensin 1 23 nervous system development growth cone|integral to membrane|neuronal cell body|transport vesicle breast(1)|endometrium(2)|large_intestine(2)|lung(15)|skin(1)|upper_aerodigestive_tract(1) 22 TGGTTACCAGCGCTATGGAGT 0.517000 10 313 0 0 1 0 0 ATP10B 23120 broad.mit.edu 37 5 160034027 160034027 + Missense_Mutation SNP G G A TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr5:160034027G>A ENST00000327245.5 - 19 3751 c.2905C>T c.(2905-2907)Cca>Tca p.P969S NM_025153.2 NP_079429.2 O94823 AT10B_HUMAN ATPase, class V, type 10B 969 ATP biosynthetic process integral to membrane ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1) 75 Renal(175;0.00196) Medulloblastoma(196;0.0377)|all_neural(177;0.121) Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) TTGCGGTCTGGCTTCTGTAGT 0.443000 67 543 0 0 1 0 0 CELF3 11189 broad.mit.edu 37 1 151678725 151678725 + Silent SNP C C T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr1:151678725C>T ENST00000290583.4 - 10 1894 c.1101G>A c.(1099-1101)caG>caA p.Q367Q RP11-98D18.1_ENST00000457548.1_RNA|CELF3_ENST00000392706.3_Silent_p.Q162Q|CELF3_ENST00000290585.4_Silent_p.Q317Q|CELF3_ENST00000470688.1_5'UTR NM_001172648.1|NM_007185.4 NP_001166119.1|NP_009116.3 Q5SZQ8 CELF3_HUMAN CUGBP, Elav-like family member 3 367 Gln-rich. nuclear mRNA splicing, via spliceosome|regulation of alternative nuclear mRNA splicing, via spliceosome cytoplasm|nucleus mRNA binding|nucleotide binding p.Q367Q(1) central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1) 21 gctgctgttgctgctgctgct 0.657000 4 57 0 0 1 0 0 MOV10L1 54456 broad.mit.edu 37 22 50553049 50553049 + Missense_Mutation SNP C C T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr22:50553049C>T ENST00000262794.5 + 7 1207 c.1124C>T c.(1123-1125)cCa>cTa p.P375L MOV10L1_ENST00000395858.3_Missense_Mutation_p.P375L|MOV10L1_ENST00000545383.1_Missense_Mutation_p.P375L|MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000540615.1_Missense_Mutation_p.P355L NM_018995.2 NP_061868.1 Q9BXT6 M10L1_HUMAN Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse) 375 germ cell development|multicellular organismal development|spermatogenesis ATP binding|ATP-dependent RNA helicase activity|magnesium ion binding|RNA binding breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3) 67 all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114) LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24) GGAATCTCTCCAGGTAGTGGA 0.512000 9 346 0 0 1 0 0 GRIK3 2899 broad.mit.edu 37 1 37324731 37324731 + Missense_Mutation SNP C C T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr1:37324731C>T ENST00000373091.3 - 7 1098 c.1082G>A c.(1081-1083)cGc>cAc p.R361H GRIK3_ENST00000373093.4_Missense_Mutation_p.R361H|GRIK3_ENST00000462621.1_5'UTR NM_000831.3 NP_000822.2 Q13003 GRIK3_HUMAN glutamate receptor, ionotropic, kainate 3 361 negative regulation of synaptic transmission, glutamatergic|regulation of membrane potential|synaptic transmission cell junction|dendrite cytoplasm|integral to plasma membrane|perikaryon|postsynaptic membrane|terminal button adenylate cyclase inhibiting metabotropic glutamate receptor activity|extracellular-glutamate-gated ion channel activity|G-protein-coupled receptor binding|kainate selective glutamate receptor activity p.R361H(2) breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(27)|lung(35)|ovary(5)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1) 89 Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169) L-Glutamic Acid(DB00142) GTTCATGAAGCGGCCGCCAAA 0.627000 83 434 0 0 1 0 0 MST1 4485 broad.mit.edu 37 3 49723542 49723542 + Missense_Mutation SNP G G C rs2087732 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr3:49723542G>C ENST00000449682.2 - 9 1461 c.1100C>G c.(1099-1101)gCc>gGc p.A367G MST1_ENST00000383728.3_3'UTR NM_020998.3 NP_066278.3 P26927 HGFL_HUMAN macrophage stimulating 1 (hepatocyte growth factor-like) 353 proteolysis extracellular region serine-type endopeptidase activity NS(4)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|skin(9)|stomach(1)|urinary_tract(2) 41 BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244) GTAGCAAAAGGCCGCGCGCAT 0.672000 4 105 0 0 1 0 0 ZNF761 388561 broad.mit.edu 37 19 53945837 53945837 + RNA SNP T T C rs17855120 by1000genomes TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr19:53945837T>C ENST00000454407.1 + 0 55 TPM3P9_ENST00000424846.3_RNA Q86XN6 ZN761_HUMAN zinc finger protein 761 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1) 30 GBM - Glioblastoma multiforme(134;0.00786) GGACCAGACTTTGCTTGACCT 0.512000 37 236 0 0 1 0 0 LINC00303 0 broad.mit.edu 37 1 204006440 204006440 + RNA SNP C C T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr1:204006440C>T ENST00000367207.3 - 0 580 AGTCTCGGGGCGGGGGTATGG 0.522000 12 68 0 0 1 0 0 NCOA6 23054 broad.mit.edu 37 20 33345744 33345744 + Silent SNP C C T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr20:33345744C>T ENST00000374796.2 - 8 3377 c.807G>A c.(805-807)caG>caA p.Q269Q NCOA6_ENST00000359003.2_Silent_p.Q269Q Q14686 NCOA6_HUMAN nuclear receptor coactivator 6 269 CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region. brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter transcription factor complex chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding p.Q269Q(15) NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1) 107 gctgctgctgctgttgttgtt 0.537000 7 283 0 0 1 0 0 VAMP3 9341 broad.mit.edu 37 1 7838212 7838214 + In_Frame_Del DEL TCA TCA - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 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 12 1152 --- --- --- --- AADACL3 126767 broad.mit.edu 37 1 12785492 12785493 + Frame_Shift_Ins INS - - T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr1:12785492_12785493insT ENST00000332530.3 + 3 598_599 c.372_373insT c.(370-375)tagtttfs p.*F124fs AADACL3_ENST00000359318.5_Frame_Shift_Ins_p.*F194fs NM_001103169.1 NP_001096639.1 Q5VUY0 ADCL3_HUMAN arylacetamide deacetylase-like 3 194 hydrolase activity breast(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1) 15 Ovarian(185;0.249) Lung NSC(185;8.27e-05)|all_lung(284;9.47e-05)|Renal(390;0.000147)|Colorectal(325;0.000583)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00217)|KIRC - Kidney renal clear cell carcinoma(229;0.00579)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649) TCATCTGCTACTGTTTTTTTCA 0.455 7 1444 --- --- --- --- EXTL1 2134 broad.mit.edu 37 1 26349533 26349535 + In_Frame_Del DEL CCT CCT - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr1:26349533_26349535delCCT ENST00000374280.3 + 1 1263_1265 c.396_398delCCT c.(394-399)tgc>tg p.CL132del NM_004455.2 NP_004446.2 Q92935 EXTL1_HUMAN exostosin-like glycosyltransferase 1 132 skeletal system development integral to membrane|intrinsic to endoplasmic reticulum membrane glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity|protein binding central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|stomach(1)|urinary_tract(1) 23 Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298) UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00594)|READ - Rectum adenocarcinoma(331;0.0649) CTGGGGCCTGCCTCCTCCTCCTC 0.606 8 347 --- --- --- --- C1orf122 127687 broad.mit.edu 37 1 38274674 38274674 + Frame_Shift_Del DEL C C - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr1:38274674delC ENST00000373043.1 + 2 1779 c.73delC c.(73-75)ccfs p.P26fs C1orf122_ENST00000468084.1_Frame_Shift_Del_p.P26fs|C1orf122_ENST00000525096.2_Intron|C1orf122_ENST00000446260.2_Frame_Shift_Del_p.R116fs|C1orf122_ENST00000373042.4_Frame_Shift_Del_p.P89fs Q6ZSJ8 CA122_HUMAN chromosome 1 open reading frame 122 89 kidney(2)|lung(2) 4 Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197) Myeloproliferative disorder(586;0.0393) ACCTGGAGCGCCCCCCCAGCC 0.592 7 963 --- --- --- --- PTPRF 5792 broad.mit.edu 37 1 44071946 44071948 + In_Frame_Del DEL GCG GCG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr1:44071946_44071948delGCG ENST00000359947.4 + 20 3859_3861 c.3519_3521delGCG c.(3517-3522)cag>ca p.QR1173del PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000438120.1_In_Frame_Del_p.QR1164del|PTPRF_ENST00000372413.3_In_Frame_Del_p.QR1164del|PTPRF_ENST00000372414.3_In_Frame_Del_p.QR1173del|PTPRF_ENST00000422171.2_In_Frame_Del_p.QR521del NM_002840.3 NP_002831.2 P10586 PTPRF_HUMAN protein tyrosine phosphatase, receptor type, F 1173 transmembrane receptor protein tyrosine phosphatase signaling pathway integral to plasma membrane transmembrane receptor protein tyrosine phosphatase activity NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3) 72 all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0333) GAGAGGAGCAGCGGCGGCGGCGG 0.631 13 835 --- --- --- --- BCL10 8915 broad.mit.edu 37 1 85736511 85736511 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 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 10 725 --- --- --- --- CLCC1 23155 broad.mit.edu 37 1 109477407 109477407 + Frame_Shift_Del DEL T T - rs150759040 by1000genomes TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr1:109477407delT ENST00000369971.2 - 11 1670 c.1541delA c.(1540-1542)agfs p.K514fs CLCC1_ENST00000348264.2_Frame_Shift_Del_p.K329fs|CLCC1_ENST00000302500.4_Frame_Shift_Del_p.K393fs|CLCC1_ENST00000356970.2_Frame_Shift_Del_p.K514fs|AKNAD1_ENST00000357393.4_Intron|CLCC1_ENST00000482889.1_Intron|CLCC1_ENST00000415331.1_Frame_Shift_Del_p.K464fs|CLCC1_ENST00000369968.2_Frame_Shift_Del_p.K329fs|CLCC1_ENST00000369969.2_Frame_Shift_Del_p.K393fs|CLCC1_ENST00000369970.3_Frame_Shift_Del_p.K464fs|CLCC1_ENST00000369976.1_Intron NM_001048210.1 NP_001041675.1 Q96S66 CLCC1_HUMAN chloride channel CLIC-like 1 514 endoplasmic reticulum|Golgi apparatus|integral to membrane|nucleus autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|liver(1)|skin(1) 14 all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626) Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.231) GAGCTGGGCCTTTTCCGCTGC 0.597 7 883 --- --- --- --- SYCP1 6847 broad.mit.edu 37 1 115469134 115469134 + Frame_Shift_Del DEL A A - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr1:115469134delA ENST00000369522.3 + 23 2116 c.1876delA c.(1876-1878)aafs p.K628fs SYCP1_ENST00000369518.1_Frame_Shift_Del_p.K628fs NM_003176.2 NP_003167.2 Q15431 SYCP1_HUMAN synaptonemal complex protein 1 628 cell division|reciprocal meiotic recombination|spermatogenesis|synaptonemal complex assembly DNA binding RGS22/SYCP1(2) NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(1) 48 Lung SC(450;0.211) all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221) Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133) TAAGGCCTTGAAAAAAAAAGG 0.264 7 144 --- --- --- --- RP11-343N15.1 0 broad.mit.edu 37 1 121137698 121137699 + RNA INS - - TT rs57730437 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr1:121137698_121137699insTT ENST00000437515.1 - 0 329 CTACTTACATCTTTTTGTCTTT 0.441 16 173 --- --- --- --- ANKRD20A12P 0 broad.mit.edu 37 1 142716575 142716578 + RNA DEL AAAC AAAC - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr1:142716575_142716578delAAAC ENST00000595144.1 - 0 418 catctcagaaaaacaaacaaacaa 0.422 15 544 --- --- --- --- RP11-782C8.2 0 broad.mit.edu 37 1 143210446 143210446 + RNA DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr1:143210446delT ENST00000412204.2 - 0 624 RP11-782C8.1_ENST00000438000.1_lincRNA GTCCATATACTAAAAAGGTTA 0.284 14 135 --- --- --- --- LINGO4 339398 broad.mit.edu 37 1 151773603 151773603 + Frame_Shift_Del DEL A A - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr1:151773603delA ENST00000368820.3 - 2 2515 c.1578delT c.(1576-1578)ttfs p.F526fs NM_001004432.2 NP_001004432.1 Q6UY18 LIGO4_HUMAN leucine rich repeat and Ig domain containing 4 526 integral to membrane breast(2)|cervix(1)|endometrium(4)|large_intestine(5)|lung(4)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1) 21 Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14) LUSC - Lung squamous cell carcinoma(543;0.181) TGCTATCCAGAAAAAAAGGCC 0.582 9 1291 --- --- --- --- ASH1L 55870 broad.mit.edu 37 1 155307999 155308000 + Frame_Shift_Ins INS - - T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr1:155307999_155308000insT ENST00000368346.3 - 27 9337_9338 c.8698_8699insA c.(8698-8700)agafs p.R2900fs ASH1L_ENST00000392403.3_Frame_Shift_Ins_p.R2895fs Q9NR48 ASH1L_HUMAN ash1 (absent, small, or homeotic)-like (Drosophila) 2900 cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter chromosome|Golgi apparatus|nucleus|tight junction DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding p.T2895fs*44(1) autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4) 124 Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145) Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021) ACTTTCCTCTGTTTTTTTTTCA 0.520 23 821 --- --- --- --- ARHGEF2 9181 broad.mit.edu 37 1 155922481 155922481 + Frame_Shift_Del DEL A A - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr1:155922481delA ENST00000368316.1 - 19 2308 c.1838delT c.(1837-1839)tcfs p.F613fs ARHGEF2_ENST00000361247.4_Frame_Shift_Del_p.F641fs|ARHGEF2_ENST00000368315.3_Frame_Shift_Del_p.F642fs|ARHGEF2_ENST00000313667.4_Frame_Shift_Del_p.F640fs|ARHGEF2_ENST00000313695.7_Frame_Shift_Del_p.F613fs Q92974 ARHG2_HUMAN Rho/Rac guanine nucleotide exchange factor (GEF) 2 641 actin filament organization|apoptosis|cell division|cell morphogenesis|induction of apoptosis by extracellular signals|intracellular protein transport|mitosis|negative regulation of microtubule depolymerization|nerve growth factor receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|regulation of cell proliferation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction cytosol|Golgi apparatus|microtubule|ruffle membrane|spindle|tight junction microtubule binding|Rac GTPase binding|Rac guanyl-nucleotide exchange factor activity|zinc ion binding breast(4)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|skin(2) 40 Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195) CTCAGAGCGGAAAAGGCCCCT 0.642 7 458 --- --- --- --- SCYL3 57147 broad.mit.edu 37 1 169833511 169833511 + Splice_Site DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr1:169833511delT ENST00000367772.4 - 9 1151 c.955_splice c.e9+1 p.K318_splice SCYL3_ENST00000367771.5_Splice_Site_p.K318_splice|SCYL3_ENST00000470238.1_5'UTR|SCYL3_ENST00000367770.1_Splice_Site_p.K318_splice NM_181093.3 NP_851607.2 Q8IZE3 PACE1_HUMAN SCY1-like 3 (S. cerevisiae) 318 cell migration Golgi apparatus|lamellipodium ATP binding|protein binding|protein kinase activity breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 27 all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181) AGCATTCACCTTTTTTGGGGC 0.393 9 736 --- --- --- --- IPO9 55705 broad.mit.edu 37 1 201843998 201844000 + In_Frame_Del DEL GAG GAG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr1:201843998_201844000delGAG ENST00000361565.4 + 22 2941_2943 c.2872_2874delGAG c.(2872-2874)del p.E962del NM_018085.4 NP_060555.2 Q96P70 IPO9_HUMAN importin 9 962 protein import into nucleus cytoplasm|nucleus histone binding|protein transporter activity cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1) 38 ggaggaggaagaggaggaggagg 0.443 7 599 --- --- --- --- C1orf131 128061 broad.mit.edu 37 1 231362513 231362513 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr1:231362513delT ENST00000318906.2 - 5 693 c.665delA c.(664-666)agfs p.K222fs C1orf131_ENST00000366649.2_Frame_Shift_Del_p.K222fs|C1orf131_ENST00000366651.3_Frame_Shift_Del_p.K221fs Q8NDD1 CA131_HUMAN chromosome 1 open reading frame 131 222 Lys-rich. breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1) 8 Breast(184;0.0871) all_cancers(173;0.2)|Prostate(94;0.183) CTTTGCTGCCTTTTTTTCTTT 0.373 7 944 --- --- --- --- SMC6 79677 broad.mit.edu 37 2 17898126 17898126 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr2:17898126delT ENST00000448223.2 - 14 1497 c.1228delA c.(1228-1230)tafs p.I410fs SMC6_ENST00000402989.1_Frame_Shift_Del_p.I410fs|SMC6_ENST00000351948.4_Frame_Shift_Del_p.I410fs|SMC6_ENST00000381272.4_Frame_Shift_Del_p.I436fs 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 12 293 --- --- --- --- ASXL2 55252 broad.mit.edu 37 2 26022304 26022306 + In_Frame_Del DEL CTG CTG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr2:26022304_26022306delCTG ENST00000435504.4 - 5 644_646 c.351_353delCAG c.(349-354)agt>ag p.SS117del ASXL2_ENST00000336112.4_In_Frame_Del_p.SS89del|ASXL2_ENST00000272341.4_5'UTR|ASXL2_ENST00000497092.1_5'UTR Q76L83 ASXL2_HUMAN additional sex combs like 2 (Drosophila) 117 Ser-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus metal ion binding|protein binding NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(3) 33 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) GCCACCATCACTGCTGCTGCTGC 0.463 11 846 --- --- --- --- OTOF 9381 broad.mit.edu 37 2 26693554 26693556 + In_Frame_Del DEL CTT CTT - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr2:26693554_26693556delCTT ENST00000272371.2 - 32 4054_4056 c.3928_3930delAAG c.(3928-3930)del p.K1310del OTOF_ENST00000339598.3_In_Frame_Del_p.K543del|OTOF_ENST00000338581.6_In_Frame_Del_p.K543del|OTOF_ENST00000403946.3_In_Frame_Del_p.K1310del|OTOF_ENST00000402415.3_In_Frame_Del_p.K620del NM_194248.2 NP_919224.1 Q9HC10 OTOF_HUMAN otoferlin 1310 Poly-Lys. cellular membrane fusion|sensory perception of sound|synaptic vesicle exocytosis basolateral plasma membrane|cell junction|cytosol|endoplasmic reticulum membrane|integral to membrane|membrane fraction|synaptic vesicle membrane calcium ion binding NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1) 106 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) CCGCAGTGCCcttcttcttcttc 0.576 8 544 --- --- --- --- RMDN2 151393 broad.mit.edu 37 2 38178783 38178783 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr2:38178783delT ENST00000407257.1 + 2 572 c.425delT c.(424-426)atfs p.I142fs RMDN2-AS1_ENST00000414365.2_RNA|RMDN2_ENST00000354545.2_Intron|RMDN2_ENST00000417700.2_Intron|RMDN2_ENST00000406384.1_Intron|RMDN2_ENST00000402091.3_Frame_Shift_Del_p.I142fs|RMDN2_ENST00000234195.3_Frame_Shift_Del_p.I142fs regulator of microtubule dynamics 2 AAGAGTGCCATTTTTTTTGAT 0.333 15 617 --- --- --- --- USP34 9736 broad.mit.edu 37 2 61575023 61575025 + In_Frame_Del DEL TGG TGG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr2:61575023_61575025delTGG ENST00000398571.2 - 15 2341_2343 c.2265_2267delCCA c.(2263-2268)cat>ca p.HH759del NM_014709.3 NP_055524.3 Q70CQ2 UBP34_HUMAN ubiquitin specific peptidase 34 759 positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2) 138 Epithelial(17;0.229) gtggtggtgatggtggtggtggt 0.389 8 476 --- --- --- --- AC027612.3 0 broad.mit.edu 37 2 91887905 91887906 + RNA INS - - T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr2:91887905_91887906insT ENST00000436174.1 - 0 540 GCTATTTTCCATTTTTTTTTTT 0.292 8 316 --- --- --- --- ANKRD20A8P 0 broad.mit.edu 37 2 95513688 95513689 + RNA INS - - TA TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr2:95513688_95513689insTA ENST00000432432.2 - 0 850 NR_040113.1 CTCACCTAATGTATAAGATGGA 0.327 20 755 --- --- --- --- TMEM131 23505 broad.mit.edu 37 2 98427639 98427639 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr2:98427639delT ENST00000186436.5 - 18 2148 c.1920delA c.(1918-1920)aafs p.K640fs NM_015348.1 NP_056163.1 Q92545 TM131_HUMAN transmembrane protein 131 640 integral to membrane NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1) 57 TCCCCTCTAATTTTTTTGCAG 0.393 14 1601 --- --- --- --- LIPT1 51601 broad.mit.edu 37 2 99778781 99778781 + Frame_Shift_Del DEL A A - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr2:99778781delA ENST00000393477.3 + 4 713 c.361delA c.(361-363)aafs p.K123fs LIPT1_ENST00000393471.2_Frame_Shift_Del_p.K123fs|LIPT1_ENST00000393473.2_Frame_Shift_Del_p.K123fs|LIPT1_ENST00000393474.3_Frame_Shift_Del_p.K123fs|LIPT1_ENST00000340066.1_Frame_Shift_Del_p.K123fs|MRPL30_ENST00000410042.1_Intron NM_145197.2 NP_660198.1 Q9Y234 LIPT_HUMAN lipoyltransferase 1 123 lipid metabolic process|protein lipoylation mitochondrion acyltransferase activity large_intestine(6)|lung(1) 7 Lipoic Acid(DB00166) CTTTACAACCAAAAAAAAGTA 0.388 9 414 --- --- --- --- SLC20A1 6574 broad.mit.edu 37 2 113416607 113416608 + Frame_Shift_Del DEL AG AG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr2:113416607_113416608delAG ENST00000272542.3 + 7 1523_1524 c.984_985delAG c.(982-987)ccagfs p.PE328fs SLC20A1_ENST00000480984.1_3'UTR NM_005415.4 NP_005406.3 Q8WUM9 S20A1_HUMAN solute carrier family 20 (phosphate transporter), member 1 328 phosphate metabolic process|positive regulation of I-kappaB kinase/NF-kappaB cascade integral to plasma membrane inorganic phosphate transmembrane transporter activity|receptor activity|sodium-dependent phosphate transmembrane transporter activity p.R332fs*14(1) breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|skin(1)|urinary_tract(3) 28 AGGAAGCTCCAGAGAGAGAGAG 0.515 10 463 --- --- --- --- CCDC93 54520 broad.mit.edu 37 2 118705727 118705727 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr2:118705727delT ENST00000376300.2 - 15 1315 c.1178delA c.(1177-1179)atfs p.N393fs CCDC93_ENST00000319432.5_Frame_Shift_Del_p.N392fs NM_019044.4 NP_061917.3 Q567U6 CCD93_HUMAN coiled-coil domain containing 93 393 breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(2) 29 CAGATTTTCATTCATGGCTAC 0.373 177 1137 --- --- --- --- ANKRD44 91526 broad.mit.edu 37 2 197943383 197943384 + Frame_Shift_Del DEL TG TG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr2:197943383_197943384delTG ENST00000409153.1 - 16 1875_1876 c.1693_1694delCA c.(1693-1695)tfs p.H565fs ANKRD44_ENST00000337207.5_Intron|ANKRD44_ENST00000450567.1_Intron|ANKRD44_ENST00000282272.8_Intron|ANKRD44_ENST00000539527.1_Frame_Shift_Del_p.H493fs|ANKRD44_ENST00000328737.2_Intron Q8N8A2 ANR44_HUMAN ankyrin repeat domain 44 811 protein binding NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2) 45 OV - Ovarian serous cystadenocarcinoma(117;0.246) ATTTGGGGTATGTGTGTGTGTG 0.411 9 98 --- --- --- --- AC073321.4 0 broad.mit.edu 37 2 217475032 217475032 + RNA DEL A A - rs71401156 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr2:217475032delA ENST00000441803.1 + 0 195 ATTTTATTTCAAAAAAAAAAA 0.373 17 28 --- --- --- --- IRS1 3667 broad.mit.edu 37 2 227660808 227660810 + In_Frame_Del DEL GCT GCT - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr2:227660808_227660810delGCT ENST00000305123.4 - 1 3665_3667 c.2645_2647delAGC c.(2644-2649)ccc>c p.QP882del NM_005544.2 NP_005535.1 P35568 IRS1_HUMAN insulin receptor substrate 1 882 Poly-Gln. fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity caveola|cytosol|insulin receptor complex|microsome|nucleus insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(10)|lung(33)|ovary(6)|pancreas(1)|prostate(1)|urinary_tract(2) 69 Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23) Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137) TGCAGCAAGGgctgctgctgctg 0.626 13 465 --- --- --- --- EFHD1 80303 broad.mit.edu 37 2 233546363 233546365 + In_Frame_Del DEL GGA GGA - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr2:233546363_233546365delGGA ENST00000264059.3 + 4 1131_1133 c.654_656delGGA c.(652-657)cgg>cg p.RE218del EFHD1_ENST00000409708.1_In_Frame_Del_p.RE106del|EFHD1_ENST00000409613.1_In_Frame_Del_p.RE122del|EFHD1_ENST00000410095.1_In_Frame_Del_p.RE106del NM_025202.3 NP_079478.1 Q9BUP0 EFHD1_HUMAN EF-hand domain family, member D1 218 calcium ion binding|protein binding NS(1)|breast(1)|large_intestine(2)|lung(3) 7 all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Breast(86;0.0199)|Renal(207;0.025) Epithelial(121;2.08e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00825)|Lung(119;0.0101) AGCGGAAGCGGGAGGAGGAGGAG 0.547 8 627 --- --- --- --- GAL3ST2 64090 broad.mit.edu 37 2 242738494 242738496 + In_Frame_Del DEL TCC TCC - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr2:242738494_242738496delTCC ENST00000192314.6 + 2 175_177 c.44_46delTCC c.(43-48)atc>a p.IL15del NM_022134.2 NP_071417.2 Q9H3Q3 G3ST2_HUMAN galactose-3-O-sulfotransferase 2 15 biosynthetic process Golgi cisterna membrane|integral to membrane galactosylceramide sulfotransferase activity p.L16I(1) endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|prostate(1)|skin(1) 14 all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244) Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833) TTCCGGGTCATCCTCCTCCTCCT 0.631 9 454 --- --- --- --- CLASP2 23122 broad.mit.edu 37 3 33602361 33602361 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr3:33602361delT ENST00000399362.4 - 28 3243 c.2890delA c.(2890-2892)tgfs p.M964fs CLASP2_ENST00000359576.5_Frame_Shift_Del_p.M956fs|CLASP2_ENST00000307312.7_Frame_Shift_Del_p.M446fs|CLASP2_ENST00000468888.2_Frame_Shift_Del_p.M965fs|CLASP2_ENST00000461133.3_Frame_Shift_Del_p.M724fs|CLASP2_ENST00000539981.1_Frame_Shift_Del_p.M734fs|CLASP2_ENST00000480013.1_Frame_Shift_Del_p.M744fs NM_015097.2 NP_055912.2 B2RTR1 B2RTR1_HUMAN cytoplasmic linker associated protein 2 966 breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1) 48 TCAGCACCCATTTTTTTTAGT 0.343 7 913 --- --- --- --- PDCD6IP 10015 broad.mit.edu 37 3 33866811 33866811 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr3:33866811delT ENST00000307296.3 + 5 972 c.595delT c.(595-597)ttfs p.F200fs PDCD6IP_ENST00000457054.2_Frame_Shift_Del_p.F200fs Q8WUM4 PDC6I_HUMAN programmed cell death 6 interacting protein 200 BRO1.|Interaction with CHMP4A, CHMP4B and CHMP4C.|Interaction with EIAV p9. apoptosis|cell cycle|cell division|interspecies interaction between organisms|protein transport cytosol|melanosome|microtubule organizing center calcium-dependent protein binding central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1) 23 TCAAGAAGTATTTTTTTTAAA 0.368 7 728 --- --- --- --- NKTR 4820 broad.mit.edu 37 3 42679486 42679486 + Frame_Shift_Del DEL A A - rs150528581 byFrequency TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr3:42679486delA ENST00000232978.8 + 13 2478 c.2290delA c.(2290-2292)aafs p.K765fs RP4-613B23.1_ENST00000445452.1_RNA|RP4-613B23.1_ENST00000438017.1_RNA|RP4-613B23.1_ENST00000434363.1_RNA NM_005385.3 NP_005376.2 P30414 NKTR_HUMAN natural killer-tumor recognition sequence 765 Arg/Ser-rich. protein folding membrane cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity breast(3)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4) 41 KIRC - Kidney renal clear cell carcinoma(284;0.24) ATCCAGTGGGAAAAAAAATAG 0.378 8 602 --- --- --- --- SETD2 29072 broad.mit.edu 37 3 47103755 47103756 + Frame_Shift_Del DEL TC TC - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr3:47103755_47103756delTC ENST00000409792.3 - 14 6232_6233 c.6190_6191delGA c.(6190-6192)cfs p.D2064fs SETD2_ENST00000492397.1_5'UTR NM_014159.6 NP_054878.5 Q9BYW2 SETD2_HUMAN SET domain containing 2 2064 regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome|nucleus DNA binding|histone-lysine N-methyltransferase activity|oxidoreductase activity|transition metal ion binding breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5) 141 Acute lymphoblastic leukemia(5;0.0169) BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844) CTTGTCTGGGTCTCTCTCTCTT 0.485 """N, F, S, Mis""" clear cell renal carcinoma 8 2093 --- --- --- --- RP11-325B23.2 0 broad.mit.edu 37 3 98031434 98031434 + RNA DEL A A - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr3:98031434delA ENST00000508616.1 + 0 149 OR5H8P_ENST00000394191.2_RNA TTACAATCTTAAAAAAAAAAG 0.333 8 183 --- --- --- --- SLCO2A1 6578 broad.mit.edu 37 3 133670082 133670083 + Frame_Shift_Ins INS - - A rs141736851 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr3:133670082_133670083insA ENST00000310926.4 - 6 1103_1104 c.830_831insT c.(829-831)tttfs p.F277fs SLCO2A1_ENST00000493729.1_Frame_Shift_Ins_p.F201fs NM_005630.2 NP_005621.2 Q92959 SO2A1_HUMAN solute carrier organic anion transporter family, member 2A1 277 sodium-independent organic anion transport integral to plasma membrane|membrane fraction prostaglandin transmembrane transporter activity|protein binding breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(2) 30 CTCGAGGGAAGAAAAAAAAGGG 0.490 7 633 --- --- --- --- DBR1 51163 broad.mit.edu 37 3 137880741 137880743 + In_Frame_Del DEL TCG TCG - rs2622736 byFrequency TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr3:137880741_137880743delTCG ENST00000260803.4 - 8 1776_1778 c.1623_1625delCGA c.(1621-1626)gat>ga p.DD541del DBR1_ENST00000505015.2_In_Frame_Del_p.DD307del NM_016216.3 NP_057300.2 Q9UK59 DBR1_HUMAN debranching RNA lariats 1 541 nucleus metal ion binding|RNA lariat debranching enzyme activity NS(1)|kidney(1)|large_intestine(4)|lung(8)|skin(1) 15 TTAAGCTGCATCGTCATCATCAT 0.394 10 711 --- --- --- --- WWTR1 25937 broad.mit.edu 37 3 149260194 149260196 + In_Frame_Del DEL CTG CTG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr3:149260194_149260196delCTG ENST00000465804.1 - 5 953_955 c.697_699delCAG c.(697-699)del p.Q233del WWTR1_ENST00000467467.1_In_Frame_Del_p.Q233del|WWTR1_ENST00000360632.3_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 8 374 --- --- --- --- DHX36 170506 broad.mit.edu 37 3 154032977 154032978 + Frame_Shift_Ins INS - - T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr3:154032977_154032978insT ENST00000496811.1 - 3 540_541 c.460_461insA c.(460-462)gttfs p.V154fs DHX36_ENST00000308361.6_Frame_Shift_Ins_p.V154fs|DHX36_ENST00000329463.5_Frame_Shift_Ins_p.V154fs|DHX36_ENST00000544526.1_Frame_Shift_Ins_p.V154fs NM_020865.2 NP_065916.2 Q9H2U1 DHX36_HUMAN DEAH (Asp-Glu-Ala-His) box polypeptide 36 154 cytoplasm|nucleus ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(11)|prostate(2)|skin(1)|urinary_tract(1) 35 LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173) GATTCTAAACATTTTTTTTTCT 0.337 11 391 --- --- --- --- PHC3 80012 broad.mit.edu 37 3 169896635 169896637 + In_Frame_Del DEL TGG TGG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr3:169896635_169896637delTGG ENST00000494943.1 - 2 136_138 c.68_70delCCA c.(67-72)atc>a p.TI23del PHC3_ENST00000467570.1_In_Frame_Del_p.TI35del|PHC3_ENST00000474275.1_In_Frame_Del_p.TI23del|PHC3_ENST00000497658.1_In_Frame_Del_p.TI35del|PHC3_ENST00000481639.1_In_Frame_Del_p.TI35del|PHC3_ENST00000495893.1_In_Frame_Del_p.TI35del Q8NDX5 PHC3_HUMAN polyhomeotic homolog 3 (Drosophila) 23 Poly-Thr. multicellular organismal development PcG protein complex DNA binding|zinc ion binding breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|upper_aerodigestive_tract(2) 26 all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169) Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655) GAAgtggtgatggtggtggtggt 0.493 7 1455 --- --- --- --- EIF4G1 1981 broad.mit.edu 37 3 184039744 184039746 + In_Frame_Del DEL GAA GAA - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr3:184039744_184039746delGAA ENST00000342981.4 + 9 1786_1788 c.1372_1374delGAA c.(1372-1374)del p.E465del EIF4G1_ENST00000346169.2_In_Frame_Del_p.E465del|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000434061.2_In_Frame_Del_p.E269del|EIF4G1_ENST00000411531.1_In_Frame_Del_p.E425del|EIF4G1_ENST00000414031.1_In_Frame_Del_p.E425del|EIF4G1_ENST00000352767.3_In_Frame_Del_p.E472del|EIF4G1_ENST00000392537.2_In_Frame_Del_p.E378del|EIF4G1_ENST00000441154.1_In_Frame_Del_p.E301del|EIF4G1_ENST00000427845.1_In_Frame_Del_p.E378del|EIF4G1_ENST00000382330.3_In_Frame_Del_p.E472del|EIF4G1_ENST00000350481.5_In_Frame_Del_p.E301del|EIF4G1_ENST00000424196.1_In_Frame_Del_p.E472del|EIF4G1_ENST00000435046.2_In_Frame_Del_p.E269del|EIF4G1_ENST00000319274.6_In_Frame_Del_p.E465del NM_182917.4 NP_886553.3 Q04637 IF4G1_HUMAN eukaryotic translation initiation factor 4 gamma, 1 465 Poly-Glu. insulin receptor signaling pathway|interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation cytosol|eukaryotic translation initiation factor 4F complex protein binding|translation initiation factor activity central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1) 75 all_cancers(143;1.06e-10)|Ovarian(172;0.0339) Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22) GGAGGAAATGgaagaagaagaag 0.562 7 597 --- --- --- --- FETUB 26998 broad.mit.edu 37 3 186362544 186362544 + Frame_Shift_Del DEL A A - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr3:186362544delA ENST00000265029.3 + 4 530 c.429delA c.(427-429)tcfs p.S143fs FETUB_ENST00000382136.3_Frame_Shift_Del_p.S106fs|FETUB_ENST00000382134.3_Frame_Shift_Del_p.S78fs|FETUB_ENST00000450521.1_Frame_Shift_Del_p.S143fs|FETUB_ENST00000539949.1_5'UTR|FETUB_ENST00000488561.1_3'UTR|RP11-134F2.2_ENST00000455926.1_RNA|RP11-134F2.2_ENST00000428501.1_RNA NM_014375.2 NP_055190.2 Q9UGM5 FETUB_HUMAN fetuin B 143 extracellular space cysteine-type endopeptidase inhibitor activity endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1) 20 all_cancers(143;6.64e-12)|Ovarian(172;0.0339) OV - Ovarian serous cystadenocarcinoma(80;5.73e-20) GBM - Glioblastoma multiforme(93;0.0479) CAACAGTTTCAAAAAAAAAGA 0.418 11 755 --- --- --- --- ATP13A3 79572 broad.mit.edu 37 3 194181471 194181473 + In_Frame_Del DEL GAG GAG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr3:194181471_194181473delGAG ENST00000439040.1 - 4 930_932 c.139_141delCTC c.(139-141)del p.L47del ATP13A3_ENST00000256031.4_In_Frame_Del_p.L47del Q9H7F0 AT133_HUMAN ATPase type 13A3 47 ATP biosynthetic process|cation transport integral to membrane ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding NS(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1) 24 all_cancers(143;6.01e-09)|Ovarian(172;0.0634) Melanoma(1037;0.211) OV - Ovarian serous cystadenocarcinoma(49;3.83e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06) GBM - Glioblastoma multiforme(46;5.98e-05) GCATCCAATAGAGGAGGAGGAGG 0.463 9 789 --- --- --- --- LINC00969 0 broad.mit.edu 37 3 195395356 195395357 + RNA DEL TG TG - rs113879828 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr3:195395356_195395357delTG ENST00000445430.1 + 0 796 CGTGGGCCACTGTGTGCAGTCA 0.604 17 238 --- --- --- --- PDE6B 5158 broad.mit.edu 37 4 661763 661765 + In_Frame_Del DEL AGG AGG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr4:661763_661765delAGG ENST00000255622.6 + 21 2514_2516 c.2471_2473delAGG c.(2470-2475)aag>a p.KE824del PDE6B_ENST00000429163.2_In_Frame_Del_p.KE545del|PDE6B_ENST00000496514.1_In_Frame_Del_p.KE824del NM_000283.3|NM_001145291.1 NP_000274.2|NP_001138763.1 P35913 PDE6B_HUMAN phosphodiesterase 6B, cGMP-specific, rod, beta 824 cytosolic calcium ion homeostasis|GMP metabolic process|phototransduction, visible light|platelet activation|visual perception cytosol|membrane 3',5'-cyclic-GMP phosphodiesterase activity|metal ion binding NS(1)|breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|urinary_tract(1) 30 CTGGAGGAGAAGGAGGAGGAGGA 0.562 11 942 --- --- --- --- FGFRL1 53834 broad.mit.edu 37 4 1019055 1019056 + Frame_Shift_Del DEL CA CA - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr4:1019055_1019056delCA ENST00000398484.2 + 8 2015_2016 c.1435_1436delCA c.(1435-1437)cfs p.H479fs FGFRL1_ENST00000504138.1_Frame_Shift_Del_p.H479fs|FGFRL1_ENST00000264748.6_Frame_Shift_Del_p.H479fs|FGFRL1_ENST00000510644.1_Frame_Shift_Del_p.H479fs Q8N441 FGRL1_HUMAN fibroblast growth factor receptor-like 1 479 His-rich. regulation of cell growth integral to membrane|plasma membrane fibroblast growth factor receptor activity|heparin binding endometrium(1)|lung(9)|ovary(1)|prostate(1)|skin(1) 13 OV - Ovarian serous cystadenocarcinoma(23;0.0158) cacagacatccacacacacaca 0.584 7 48 --- --- --- --- PROM1 8842 broad.mit.edu 37 4 15995680 15995680 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr4:15995680delT ENST00000505450.1 - 15 2282 c.1670delA c.(1669-1671)atfs p.N557fs PROM1_ENST00000543373.1_Frame_Shift_Del_p.N557fs|PROM1_ENST00000508167.1_Frame_Shift_Del_p.N557fs|PROM1_ENST00000539194.1_Frame_Shift_Del_p.N566fs|PROM1_ENST00000510224.1_Frame_Shift_Del_p.N566fs|PROM1_ENST00000447510.2_Frame_Shift_Del_p.N566fs|PROM1_ENST00000540805.1_Frame_Shift_Del_p.N566fs NM_001145848.1 NP_001139320.1 O43490 PROM1_HUMAN prominin 1 566 camera-type eye photoreceptor cell differentiation|photoreceptor cell maintenance|retina layer formation apical plasma membrane|cell surface|integral to plasma membrane|microvillus membrane|photoreceptor outer segment membrane|plasma membrane beta-actinin binding|cadherin binding breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2) 35 AGTGCCTCTATTTTTTTTGCA 0.428 13 574 --- --- --- --- GABRG1 2565 broad.mit.edu 37 4 46060358 46060358 + Frame_Shift_Del DEL A A - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 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 10 421 --- --- --- --- UTP3 57050 broad.mit.edu 37 4 71554620 71554622 + In_Frame_Del DEL GAG GAG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr4:71554620_71554622delGAG ENST00000254803.2 + 1 425_427 c.226_228delGAG c.(226-228)del p.E81del NM_020368.2 NP_065101.1 Q9NQZ2 SAS10_HUMAN UTP3, small subunit (SSU) processome component, homolog (S. cerevisiae) 81 Glu-rich. brain development|chromatin modification|gene silencing nucleolus endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(4) 18 Lung(101;0.235) ggaggatggcgaggaggaggagg 0.567 14 286 --- --- --- --- BMP2K 55589 broad.mit.edu 37 4 79792161 79792169 + In_Frame_Del DEL CAGCACCAC CAGCACCAC - rs2114202 byFrequency TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr4:79792161_79792169delCAGCACCAC ENST00000335016.5 + 11 1622_1630 c.1456_1464delCAGCACCAC c.(1456-1464)del p.QHH486del BMP2K_ENST00000502871.1_In_Frame_Del_p.QHH486del NM_198892.1 NP_942595.1 Q9NSY1 BMP2K_HUMAN BMP2 inducible kinase 486 Gln/His-rich. Q -> H (in dbSNP:rs2114202). Missing (in Ref. 2; CAB70863). nucleus ATP binding|protein serine/threonine kinase activity NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1) 13 gcagcagcagcagcaccaccaccaccacc 0.488 22 368 --- --- --- --- PRDM8 56978 broad.mit.edu 37 4 81123250 81123252 + In_Frame_Del DEL CAG CAG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr4:81123250_81123252delCAG ENST00000339711.4 + 10 1865_1867 c.634_636delCAG c.(634-636)del p.Q217del PRDM8_ENST00000415738.2_In_Frame_Del_p.Q217del|PRDM8_ENST00000504452.1_In_Frame_Del_p.Q217del NM_020226.3 NP_064611.3 Q9NQV8 PRDM8_HUMAN PR domain containing 8 217 Gly-rich.|Poly-Gln. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(2) 10 tggcaaagaccagcagcagcagc 0.655 OREG0016246 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 8 389 --- --- --- --- FAT4 79633 broad.mit.edu 37 4 126398522 126398522 + Frame_Shift_Del DEL A A - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr4:126398522delA ENST00000335110.5 + 12 7295 c.7295delA c.(7294-7296)gafs p.E2432fs FAT4_ENST00000394329.3_Intron Q6V0I7 FAT4_HUMAN FAT atypical cadherin 4 4185 Cadherin 23. homophilic cell adhesion integral to membrane|plasma membrane calcium ion binding NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6) 355 TGTTTTAAAGAAAAAAAATGC 0.343 7 427 --- --- --- --- IRX4 50805 broad.mit.edu 37 5 1879669 1879671 + In_Frame_Del DEL CCT CCT - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr5:1879669_1879671delCCT ENST00000505790.1 - 5 1139_1141 c.683_685delAGG c.(682-687)ggg>g p.EG228del IRX4_ENST00000231357.2_In_Frame_Del_p.EG228del|IRX4_ENST00000513692.1_In_Frame_Del_p.EG228del|IRX4_ENST00000505938.1_5'UTR NM_001278634.1 NP_001265563.1 P78413 IRX4_HUMAN iroquois homeobox 4 228 Poly-Glu. heart development nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity endometrium(1)|lung(7)|ovary(1)|prostate(1) 10 GBM - Glioblastoma multiforme(108;0.242) tcctcgcccccctcctcctcctc 0.685 8 272 --- --- --- --- AC026703.1 0 broad.mit.edu 37 5 32789822 32789823 + Frame_Shift_Del DEL GT GT - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr5:32789822_32789823delGT ENST00000326958.1 + 1 878_879 c.315_316delGT c.(313-318)gggtfs p.GC105fs NPR3_ENST00000265074.8_3'UTR CTGATTTTGGGTGTGTGTGTGT 0.421 7 560 --- --- --- --- THBS4 7060 broad.mit.edu 37 5 79372774 79372776 + In_Frame_Del DEL TGA TGA - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr5:79372774_79372776delTGA ENST00000350881.2 + 16 2179_2181 c.1989_1991delTGA c.(1987-1992)tgt>tg p.CD663del CTD-2201I18.1_ENST00000514042.1_RNA|THBS4_ENST00000511733.1_In_Frame_Del_p.CD572del|CTD-2201I18.1_ENST00000503007.1_RNA 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 7 1607 --- --- --- --- MEGF10 84466 broad.mit.edu 37 5 126792989 126792991 + In_Frame_Del DEL CAG CAG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr5:126792989_126792991delCAG ENST00000274473.6 + 26 3669_3671 c.3402_3404delCAG c.(3400-3405)aac>aa p.NS1134del MEGF10_ENST00000503335.2_In_Frame_Del_p.NS1134del NM_032446.2 NP_115822.1 Q96KG7 MEG10_HUMAN multiple EGF-like-domains 10 1134 Necessary for formation of large intracellular vacuoles.|Ser-rich. cell adhesion|phagocytosis basolateral plasma membrane|cell projection|integral to membrane|phagocytic cup breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(28)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1) 68 Prostate(80;0.165) KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488) OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123) gcagcagcaacagcagcagcagc 0.512 8 316 --- --- --- --- HMMR 3161 broad.mit.edu 37 5 162917425 162917426 + Frame_Shift_Ins INS - - A TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr5:162917425_162917426insA ENST00000416990.2 + 17 2144_2145 c.1647_1648insA c.(1645-1650)gcaaaafs p.AK549fs HMMR_ENST00000353866.3_Frame_Shift_Ins_p.AK648fs|HMMR_ENST00000432118.2_Frame_Shift_Ins_p.AK577fs|RP11-80G7.1_ENST00000521666.1_RNA|RP11-80G7.1_ENST00000514724.2_RNA|HMMR_ENST00000393915.4_Frame_Shift_Ins_p.AK664fs|HMMR_ENST00000358715.3_Frame_Shift_Ins_p.AK663fs O75330 HMMR_HUMAN hyaluronan-mediated motility receptor (RHAMM) 663 cell surface|cytoplasm hyaluronic acid binding cervix(1)|kidney(3)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(1) 23 Renal(175;0.000281) Medulloblastoma(196;0.00853)|all_neural(177;0.0408) Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848) GTCAGCTTGCTAAAAAAAAACA 0.307 8 432 --- --- --- --- BTNL8 79908 broad.mit.edu 37 5 180374632 180374633 + Frame_Shift_Del DEL GA GA - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr5:180374632_180374633delGA ENST00000231229.4 + 4 1028_1029 c.794_795delGA c.(793-795)cfs p.R265fs BTNL8_ENST00000340184.4_Intron|BTNL8_ENST00000508408.1_Frame_Shift_Del_p.R265fs|BTNL8_ENST00000511704.1_Intron|BTNL8_ENST00000400707.3_Intron|BTNL8_ENST00000505126.1_Intron|BTNL8_ENST00000533815.2_Intron NM_001159708.1|NM_024850.2 NP_001153180.1|NP_079126.1 Q6UX41 BTNL8_HUMAN butyrophilin-like 8 265 integral to membrane breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|prostate(3)|skin(1)|upper_aerodigestive_tract(1) 28 all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114) all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) CAGTGTAAGCGAGAGAGAGAAG 0.495 9 1919 --- --- --- --- DEK 7913 broad.mit.edu 37 6 18264079 18264081 + In_Frame_Del DEL TCC TCC - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr6:18264079_18264081delTCC ENST00000397239.3 - 2 585_587 c.138_140delGGA c.(136-141)gaa>ga p.EE46del DEK_ENST00000244776.7_In_Frame_Del_p.EE46del NM_003472.3 NP_003463.1 P35659 DEK_HUMAN DEK oncogene 46 Asp/Glu-rich (highly acidic). chromatin modification|regulation of transcription from RNA polymerase II promoter|signal transduction|transcription from RNA polymerase II promoter|viral genome replication nucleus DNA binding|histone binding endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|upper_aerodigestive_tract(1) 7 Ovarian(93;0.00769)|Breast(50;0.0495) all_hematologic(90;0.053) OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332) CCCACCTTTTtcctcctcctcct 0.532 T NUP214 AML 8 493 --- --- --- --- HIST1H1A 3024 broad.mit.edu 37 6 26017448 26017448 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr6:26017448delT ENST00000244573.3 - 1 592 c.513delA c.(511-513)aafs p.K171fs NM_005325.3 NP_005316.1 Q02539 H11_HUMAN histone cluster 1, H1a 171 nucleosome assembly|spermatogenesis nucleosome|nucleus DNA binding cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|ovary(3)|prostate(1) 13 CAGTTTTGGGTTTTTTTGGAT 0.483 8 1721 --- --- --- --- BTN2A2 10385 broad.mit.edu 37 6 26384091 26384093 + In_Frame_Del DEL CCT CCT - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr6:26384091_26384093delCCT ENST00000356709.4 + 2 153_155 c.42_44delCCT c.(40-45)tcc>tc p.SL14del BTN2A2_ENST00000469230.1_In_Frame_Del_p.SL14del|BTN2A2_ENST00000352867.2_In_Frame_Del_p.SL14del|BTN2A2_ENST00000432533.2_In_Frame_Del_p.SL14del|BTN2A2_ENST00000416795.2_In_Frame_Del_p.SL14del|BTN2A2_ENST00000482536.1_In_Frame_Del_p.SL14del NM_001197240.1|NM_006995.4 NP_001184169.1|NP_008926.2 Q8WVV5 BT2A2_HUMAN butyrophilin, subfamily 2, member A2 14 negative regulation of activated T cell proliferation|negative regulation of cellular metabolic process|negative regulation of cytokine secretion integral to membrane breast(2)|endometrium(3)|large_intestine(5)|lung(13) 23 TGCCAGCCTCcctcctcctcctc 0.581 7 616 --- --- --- --- NKAPL 222698 broad.mit.edu 37 6 28227860 28227860 + Frame_Shift_Del DEL G G - rs3734564 byFrequency TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr6:28227860delG ENST00000343684.3 + 1 763 c.711delG c.(709-711)aafs p.K240fs NM_001007531.1 NP_001007532.1 Q5M9Q1 NKAPL_HUMAN NFKB activating protein-like 240 Lys-rich. breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 31 acaaaacaaagaaaaagaaga 0.368 11 123 --- --- --- --- UHRF1BP1 54887 broad.mit.edu 37 6 34804004 34804006 + In_Frame_Del DEL CAG CAG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 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 13 1608 --- --- --- --- PHF3 23469 broad.mit.edu 37 6 64394097 64394097 + Frame_Shift_Del DEL A A - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr6:64394097delA ENST00000262043.3 + 4 814 c.474delA c.(472-474)acfs p.T158fs PHF3_ENST00000393387.1_Frame_Shift_Del_p.T158fs|PHF3_ENST00000509330.1_Frame_Shift_Del_p.T158fs Q92576 PHF3_HUMAN PHD finger protein 3 158 multicellular organismal development|transcription, DNA-dependent nucleus zinc ion binding breast(7)|cervix(2)|endometrium(8)|kidney(7)|large_intestine(18)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(6) 75 all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121) LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148) TAAGTAACACAAAAAAAGCAT 0.383 7 1257 --- --- --- --- MDN1 23195 broad.mit.edu 37 6 90372572 90372574 + In_Frame_Del DEL TCA TCA - rs36040566 byFrequency TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr6:90372572_90372574delTCA ENST00000369393.3 - 86 14464_14466 c.14349_14351delTGA c.(14347-14352)gag>ga p.DE4783del MDN1_ENST00000428876.1_In_Frame_Del_p.DE4783del Q9NU22 MDN1_HUMAN MDN1, midasin homolog (yeast) 4783 D -> E (in dbSNP:rs36040566). protein complex assembly|regulation of protein complex assembly nucleus ATP binding|ATPase activity|unfolded protein binding NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2) 218 all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246) BRCA - Breast invasive adenocarcinoma(108;0.0193) atcttcctcctcatcATCATCAC 0.458 8 743 --- --- --- --- PNISR 25957 broad.mit.edu 37 6 99856015 99856015 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr6:99856015delT ENST00000369239.5 - 7 1010 c.806delA c.(805-807)agfs p.K269fs PNISR_ENST00000438806.1_Frame_Shift_Del_p.K269fs NM_032870.2 NP_116259.2 Q8TF01 PNISR_HUMAN PNN-interacting serine/arginine-rich protein 269 nuclear speck p.K269R(1) breast(2)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 24 TTCTGTGGCCTTTTTTTCTTT 0.393 8 712 --- --- --- --- MED23 9439 broad.mit.edu 37 6 131919846 131919846 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr6:131919846delT ENST00000403834.3 - 19 2467 c.2294delA c.(2293-2295)atfs p.N765fs MED23_ENST00000368068.3_Frame_Shift_Del_p.N759fs|MED23_ENST00000368053.4_Frame_Shift_Del_p.N765fs|MED23_ENST00000354577.4_Frame_Shift_Del_p.N765fs|MED23_ENST00000540546.1_Frame_Shift_Del_p.N765fs|MED23_ENST00000368058.1_Frame_Shift_Del_p.N765fs|MED23_ENST00000545957.1_Frame_Shift_Del_p.N400fs|MED23_ENST00000368060.3_Frame_Shift_Del_p.N759fs Q9ULK4 MED23_HUMAN mediator complex subunit 23 759 regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter transcription factor complex protein binding|transcription coactivator activity p.N759fs*7(1)|p.N765fs*7(1) NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(12)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2) 44 Breast(56;0.0753) GBM - Glioblastoma multiforme(226;0.0115)|OV - Ovarian serous cystadenocarcinoma(155;0.0608) CTCCTCCACATTTTTTTTCAG 0.378 10 615 --- --- --- --- PHACTR2 9749 broad.mit.edu 37 6 144086414 144086414 + Frame_Shift_Del DEL A A - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr6:144086414delA ENST00000427704.2 + 6 808 c.678delA c.(676-678)tcfs p.S226fs PHACTR2_ENST00000440869.2_Frame_Shift_Del_p.S237fs|PHACTR2_ENST00000367582.3_Frame_Shift_Del_p.S157fs|PHACTR2_ENST00000305766.6_Frame_Shift_Del_p.S146fs|PHACTR2_ENST00000367584.4_Frame_Shift_Del_p.S214fs NM_001100166.1|NM_014721.2 NP_001093636.1|NP_055536.2 O75167 PHAR2_HUMAN phosphatase and actin regulator 2 226 actin binding|protein phosphatase inhibitor activity NS(3)|breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2) 30 OV - Ovarian serous cystadenocarcinoma(155;1.58e-05)|GBM - Glioblastoma multiforme(68;0.0386) CCTCTCATTCAAAAAAAACAA 0.398 10 813 --- --- --- --- SHPRH 257218 broad.mit.edu 37 6 146264834 146264836 + In_Frame_Del DEL ATC ATC - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr6:146264834_146264836delATC ENST00000367503.3 - 9 2079_2081 c.1681_1683delGAT c.(1681-1683)del p.D561del SHPRH_ENST00000438092.2_In_Frame_Del_p.D561del|SHPRH_ENST00000367505.2_In_Frame_Del_p.D561del|SHPRH_ENST00000275233.7_In_Frame_Del_p.D561del NM_001042683.2 NP_001036148.2 Q149N8 SHPRH_HUMAN SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase 561 DNA repair|nucleosome assembly nucleosome|nucleus ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1) 79 Ovarian(120;0.0365) OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124) AATAGTAAGGATCATCATCATCA 0.360 7 765 --- --- --- --- GRM1 2911 broad.mit.edu 37 6 146755219 146755221 + In_Frame_Del DEL GAG GAG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr6:146755219_146755221delGAG ENST00000361719.2 + 9 3342_3344 c.2872_2874delGAG c.(2872-2874)del p.E961del GRM1_ENST00000507907.1_3'UTR|GRM1_ENST00000355289.4_3'UTR|GRM1_ENST00000492807.2_3'UTR|GRM1_ENST00000282753.1_In_Frame_Del_p.E961del|GRM1_ENST00000392299.2_3'UTR NM_001278064.1 NP_001264993.1 Q13255 GRM1_HUMAN glutamate receptor, metabotropic 1 961 synaptic transmission integral to plasma membrane G-protein coupled receptor activity|glutamate receptor activity NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1) 126 Ovarian(120;0.0387) OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762) Acamprosate(DB00659)|L-Glutamic Acid(DB00142) TTACAACGTAGAGGAGGAGGAGG 0.586 8 922 --- --- --- --- HOXA1 3198 broad.mit.edu 37 7 27135314 27135316 + In_Frame_Del DEL CGA CGA - rs10951154 byFrequency TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr7:27135314_27135316delCGA ENST00000343060.4 - 1 277_279 c.216_218delTCG c.(214-219)cac>ca p.HR72del HOXA1_ENST00000355633.5_In_Frame_Del_p.HR72del|HOTAIRM1_ENST00000495032.1_RNA NM_005522.4 NP_005513.1 P49639 HXA1_HUMAN homeobox A1 72 Poly-His. nucleus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(14)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 31 Ctgggggtggcgatggtggtggt 0.650 OREG0003750 type=REGULATORY REGION|Gene=BC031342|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay 15 407 --- --- --- --- BBS9 27241 broad.mit.edu 37 7 33312723 33312723 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr7:33312723delT ENST00000242067.6 + 8 1323 c.802delT c.(802-804)ttfs p.F269fs BBS9_ENST00000355070.2_Frame_Shift_Del_p.F269fs|BBS9_ENST00000425508.2_Frame_Shift_Del_p.F224fs|BBS9_ENST00000354265.4_Frame_Shift_Del_p.F269fs|BBS9_ENST00000350941.3_Frame_Shift_Del_p.F269fs|BBS9_ENST00000396127.2_Frame_Shift_Del_p.F269fs NM_198428.2 NP_940820.1 Q3SYG4 PTHB1_HUMAN Bardet-Biedl syndrome 9 269 fat cell differentiation|response to stimulus|visual perception BBSome|cilium membrane|microtubule organizing center|nucleus protein binding BBS9/PKD1L1(2) NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1) 50 GBM - Glioblastoma multiforme(11;0.0894) TGAGAGAAACTTTTTTTGCCT 0.393 Bardet-Biedl syndrome 9 1186 --- --- --- --- POU6F2 11281 broad.mit.edu 37 7 39379288 39379290 + In_Frame_Del DEL CAG CAG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr7:39379288_39379290delCAG ENST00000518318.2 + 5 601_603 c.559_561delCAG c.(559-561)del p.Q196del POU6F2_ENST00000559001.1_In_Frame_Del_p.Q188del|POU6F2_ENST00000517348.1_3'UTR|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 14 168 --- --- --- --- CCT6P3 0 broad.mit.edu 37 7 64528813 64528814 + RNA INS - - T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr7:64528813_64528814insT ENST00000426828.1 + 0 621 NR_033416.1 CTTTCTGTAACTTTTTTTTTTT 0.317 10 83 --- --- --- --- GTF2IRD2P1 0 broad.mit.edu 37 7 72683455 72683456 + RNA INS - - T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr7:72683455_72683456insT ENST00000425256.1 - 0 120 NR_002164.1 CGTTCTACCAgtttttttttgt 0.441 9 424 --- --- --- --- HIP1 3092 broad.mit.edu 37 7 75168684 75168684 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr7:75168684delT ENST00000336926.6 - 30 3046 c.3020delA c.(3019-3021)agfs p.K1007fs HIP1_ENST00000434438.2_Frame_Shift_Del_p.K956fs NM_005338.5 NP_005329.3 O00291 HIP1_HUMAN huntingtin interacting protein 1 1007 I/LWEQ. activation of caspase activity|cell differentiation|clathrin coat assembly|endocytosis|induction of apoptosis|positive regulation of receptor-mediated endocytosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent clathrin coated vesicle membrane|cytoskeleton|Golgi apparatus|membrane fraction|nucleus actin binding|clathrin binding|phosphatidylinositol binding|structural constituent of cytoskeleton breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 51 CTCGTAGTGCTTTTTCCGAAG 0.507 T PDGFRB CMML 8 2414 --- --- --- --- PEX1 5189 broad.mit.edu 37 7 92146721 92146721 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr7:92146721delT ENST00000248633.4 - 5 1203 c.1108delA c.(1108-1110)ttfs p.I370fs PEX1_ENST00000438045.1_Intron|PEX1_ENST00000541751.1_5'UTR|PEX1_ENST00000428214.1_Frame_Shift_Del_p.I370fs NM_000466.2 NP_000457.1 O43933 PEX1_HUMAN peroxisomal biogenesis factor 1 370 microtubule-based peroxisome localization|protein import into peroxisome matrix cytosol|nucleus|peroxisomal membrane ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1) 41 all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592) Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123) GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23) TCTGACCTAATTTTTTTTTGA 0.353 21 956 --- --- --- --- MEPCE 56257 broad.mit.edu 37 7 100028823 100028825 + In_Frame_Del DEL CCA CCA - rs71555278 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr7:100028823_100028825delCCA ENST00000310512.2 + 1 1570_1572 c.1182_1184delCCA c.(1180-1185)cgc>cg p.RH394del MEPCE_ENST00000414441.1_5'UTR NM_019606.5 NP_062552.2 Q7L2J0 MEPCE_HUMAN methylphosphate capping enzyme 394 methyltransferase activity breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(2)|lung(9)|prostate(4)|skin(1)|upper_aerodigestive_tract(1) 24 Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439) GGGGAGGCCGCCACCACCACCAC 0.581 7 474 --- --- --- --- TRBV7-8 0 broad.mit.edu 37 7 142099832 142099833 + RNA DEL CA CA - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr7:142099832_142099833delCA ENST00000390359.3 - 0 88 accactctctcacacacacaca 0.455 10 423 --- --- --- --- PRSS3P2 0 broad.mit.edu 37 7 142482025 142482025 + RNA DEL A A - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr7:142482025delA ENST00000603901.1 + 0 591 NR_001296.3 TGCAGTGCCCACATGGAGAAG 0.572 14 124 --- --- --- --- FAM66D 0 broad.mit.edu 37 8 11994579 11994580 + RNA DEL TG TG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr8:11994579_11994580delTG ENST00000434078.2 + 0 608 NR_027425.1 TGTTCgtgtttgtgtgtgtgtg 0.505 8 139 --- --- --- --- PABPC1 26986 broad.mit.edu 37 8 101724994 101724995 + Frame_Shift_Ins INS - - A rs140822921 by1000genomes TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr8:101724994_101724995insA ENST00000318607.5 - 6 1889_1890 c.761_762insT c.(760-762)agafs p.R254fs PABPC1_ENST00000519004.1_Frame_Shift_Ins_p.R209fs|PABPC1_ENST00000522387.1_Frame_Shift_Ins_p.R222fs|PABPC1_ENST00000519596.1_5'UTR NM_002568.3 NP_002559.2 P11940 PABP1_HUMAN poly(A) binding protein, cytoplasmic 1 254 CSDE1-binding.|RRM 3. mRNA polyadenylation|mRNA stabilization|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|translation catalytic step 2 spliceosome|cytosol nucleotide binding|poly(A) RNA binding|protein C-terminus binding|translation activator activity breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1) 40 all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125) Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206) CATTGAGCTCCTTTCCGTTCAT 0.371 13 445 --- --- --- --- PKHD1L1 93035 broad.mit.edu 37 8 110455173 110455174 + Splice_Site INS - - G TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 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) 7 584 --- --- --- --- KANK1 23189 broad.mit.edu 37 9 732475 732477 + In_Frame_Del DEL GAG GAG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr9:732475_732477delGAG ENST00000382303.1 + 10 3755_3757 c.3103_3105delGAG c.(3103-3105)del p.E1039del KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382293.3_In_Frame_Del_p.E881del|KANK1_ENST00000382297.2_In_Frame_Del_p.E1039del NM_001256876.1 NP_001243805.1 Q14678 KANK1_HUMAN KN motif and ankyrin repeat domains 1 1039 negative regulation of actin filament polymerization cytoplasm autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1) 43 Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128) Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222) TCTTGAAGAAGAGGAGGAGGAGG 0.463 11 722 --- --- --- --- GLIS3 169792 broad.mit.edu 37 9 4286057 4286057 + Frame_Shift_Del DEL A A - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr9:4286057delA ENST00000381971.3 - 2 962 c.369delT c.(367-369)ttfs p.F123fs NM_001042413.1 NP_001035878.1 Q8NEA6 GLIS3_HUMAN GLIS family zinc finger 3 297 Ser-rich. negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter DNA binding|zinc ion binding NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1) 26 Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148) Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148) GATTTGGAGGAAAAGGGCTTC 0.473 8 833 --- --- --- --- RLN2 6019 broad.mit.edu 37 9 5304560 5304561 + Frame_Shift_Ins INS - - A TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr9:5304560_5304561insA ENST00000381627.3 - 1 408_409 c.20_21insT c.(19-21)tcafs p.S7fs RLN2_ENST00000308420.3_Frame_Shift_Ins_p.S7fs NM_134441.2 NP_604390.1 P04090 REL2_HUMAN relaxin 2 7 female pregnancy extracellular region hormone activity endometrium(2)|kidney(1)|large_intestine(2)|lung(6) 11 all_hematologic(13;0.137) Acute lymphoblastic leukemia(23;0.158) GBM - Glioblastoma multiforme(50;0.0201)|Lung(218;0.0987) CTAGCAGGTGGAAAAAAAACAG 0.535 8 531 --- --- --- --- RANBP6 26953 broad.mit.edu 37 9 6012690 6012690 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr9:6012690delT ENST00000259569.5 - 1 2928 c.2918delA c.(2917-2919)atfs p.N973fs NM_001243202.1|NM_001243203.1|NM_012416.3 NP_001230131.1|NP_001230132.1|NP_036548.1 O60518 RNBP6_HUMAN RAN binding protein 6 973 protein transport cytoplasm|nucleus binding p.N973fs*12(1) NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(5)|large_intestine(8)|lung(9)|ovary(7)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1) 51 Acute lymphoblastic leukemia(23;0.158) GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101) AGCAATGACATTTTTTTTGGT 0.358 7 469 --- --- --- --- MLLT3 4300 broad.mit.edu 37 9 20413952 20413952 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr9:20413952delT ENST00000380338.4 - 5 1178 c.892delA c.(892-894)ggfs p.R298fs MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Frame_Shift_Del_p.R295fs|MLLT3_ENST00000475957.1_5'UTR NM_004529.2 NP_004520.2 P42568 AF9_HUMAN myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 298 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus protein binding central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7) 66 GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05) CTCTTTTTCCTTTTTTTGGCT 0.393 T MLL ALL 8 1239 --- --- --- --- HRCT1 646962 broad.mit.edu 37 9 35906348 35906350 + In_Frame_Del DEL CTG CTG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr9:35906348_35906350delCTG ENST00000354323.2 + 1 160_162 c.64_66delCTG c.(64-66)del p.L28del NM_001039792.1 NP_001034881.1 Q6UXD1 HRCT1_HUMAN histidine rich carboxyl terminus 1 28 integral to membrane NS(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(1) 4 TGTGGCGGTCctgctgctgctgc 0.670 8 173 --- --- --- --- CNTNAP3B 728577 broad.mit.edu 37 9 43844265 43844265 + Frame_Shift_Del DEL G G - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr9:43844265delG ENST00000377564.3 + 10 1992 c.1599delG c.(1597-1599)gcfs p.A533fs NM_001201380.1 NP_001188309.1 Q96NU0 CNT3B_HUMAN contactin associated protein-like 3B 533 Laminin G-like 2. cell adhesion|signal transduction integral to membrane receptor binding central_nervous_system(1)|endometrium(2)|lung(3)|pancreas(1)|prostate(3) 10 AGCAGGGGGCGCTGGGGAGTT 0.542 8 145 --- --- --- --- WDR5 11091 broad.mit.edu 37 9 137019597 137019598 + Frame_Shift_Ins INS - - C TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr9:137019597_137019598insC ENST00000358625.3 + 10 812_813 c.641_642insC c.(640-642)accfs p.T214fs WDR5_ENST00000425041.1_Frame_Shift_Ins_p.T214fs 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) GATGACGACAACCCCCCCGTGT 0.624 9 1807 --- --- --- --- TUBBP5 0 broad.mit.edu 37 9 141070013 141070014 + RNA INS - - GCG rs76591329 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr9:141070013_141070014insGCG ENST00000503395.1 + 0 1132 CTCCTGGGAACGCGGCCCTCCC 0.728 18 166 --- --- --- --- EGR2 1959 broad.mit.edu 37 10 64573487 64573489 + In_Frame_Del DEL GCT GCT - rs112474655 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr10:64573487_64573489delGCT ENST00000242480.3 - 2 1234_1236 c.909_911delAGC c.(907-912)gcc>gc p.AA307del EGR2_ENST00000439032.1_In_Frame_Del_p.AA307del|EGR2_ENST00000411732.1_In_Frame_Del_p.AA257del NM_000399.3|NM_001136177.1 NP_000390.2|NP_001129649.1 P11161 EGR2_HUMAN early growth response 2 307 Poly-Ala. fat cell differentiation|protein export from nucleus|transcription from RNA polymerase II promoter cytoplasm|nucleus chromatin binding|RNA polymerase II activating transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|ubiquitin protein ligase binding|zinc ion binding endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(13)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1) 36 Prostate(12;0.0297)|all_hematologic(501;0.228) GGCGGCGGCGGCTGCTGCTGCTG 0.695 7 262 --- --- --- --- JMJD1C 221037 broad.mit.edu 37 10 64952699 64952699 + Splice_Site DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr10:64952699delT ENST00000399262.2 - 16 6293 c.6076_splice c.e16+1 p.K2025_splice JMJD1C_ENST00000542921.1_Splice_Site_p.K1843_splice|JMJD1C_ENST00000402544.1_Splice_Site_p.K1788_splice|JMJD1C_ENST00000399251.1_3'UTR NM_032776.1 NP_116165.1 Q15652 JHD2C_HUMAN jumonji domain containing 1C 2025 blood coagulation|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleoplasm histone demethylase activity (H3-K9 specific)|metal ion binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|thyroid hormone receptor binding breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3) 77 Prostate(12;0.0119)|all_hematologic(501;0.191) TATGTTTACCTTTTTTTTCCT 0.373 7 784 --- --- --- --- ADD3 120 broad.mit.edu 37 10 111893350 111893350 + Frame_Shift_Del DEL A A - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr10:111893350delA ENST00000277900.8 + 14 2364 c.1999delA c.(1999-2001)aafs p.K669fs ADD3_ENST00000356080.4_Frame_Shift_Del_p.K701fs|ADD3_ENST00000360162.3_Frame_Shift_Del_p.K669fs NM_001121.2 NP_001112.2 Q9UEY8 ADDG_HUMAN adducin 3 (gamma) 701 cytoskeleton actin binding|calmodulin binding|metal ion binding|structural constituent of cytoskeleton central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(3) 29 Breast(234;0.052)|Lung NSC(174;0.223) Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742) GAAAAAGAACAAAAAAAAGGA 0.333 7 729 --- --- --- --- DCLRE1A 9937 broad.mit.edu 37 10 115608957 115608957 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr10:115608957delT ENST00000361384.2 - 2 2824 c.1907delA c.(1906-1908)agfs p.K636fs DCLRE1A_ENST00000369305.1_Frame_Shift_Del_p.K636fs NM_014881.3 NP_055696.3 Q6PJP8 DCR1A_HUMAN DNA cross-link repair 1A 636 cell division|mitosis nucleus hydrolase activity breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(2)|urinary_tract(1) 31 Epithelial(162;0.0157)|all cancers(201;0.0171) TCTACATCTCTTTTTTTGACG 0.368 Other identified genes with known or suspected DNA repair function 7 1401 --- --- --- --- NUP98 4928 broad.mit.edu 37 11 3720389 3720389 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr11:3720389delT ENST00000324932.7 - 25 4352 c.3932delA c.(3931-3933)acfs p.N1311fs NUP98_ENST00000359171.4_Frame_Shift_Del_p.N1311fs|NUP98_ENST00000355260.3_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 9 1519 --- --- --- --- SLC22A9 114571 broad.mit.edu 37 11 63149668 63149669 + Frame_Shift_Ins INS - - A TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr11:63149668_63149669insA ENST00000279178.3 + 6 1241_1242 c.992_993insA c.(991-993)gcafs p.A331fs SLC22A9_ENST00000310969.4_3'UTR NM_080866.2 NP_543142.2 Q8IVM8 S22A9_HUMAN solute carrier family 22 (organic anion transporter), member 9 331 transmembrane transport integral to membrane breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1) 18 CTGGAGGCAGCACAAAAAAAAA 0.406 8 1016 --- --- --- --- SYTL2 54843 broad.mit.edu 37 11 85422269 85422270 + Frame_Shift_Ins INS - - A TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr11:85422269_85422270insA ENST00000359152.5 - 5 4253_4254 c.4254_4255insT c.(4252-4257)gaacagfs p.EQ1418fs SYTL2_ENST00000389958.3_Frame_Shift_Ins_p.EQ3fs|SYTL2_ENST00000389960.4_Intron|SYTL2_ENST00000316356.4_Frame_Shift_Ins_p.EQ573fs|SYTL2_ENST00000525702.1_Frame_Shift_Ins_p.EQ14fs|SYTL2_ENST00000525423.1_Frame_Shift_Ins_p.EQ894fs|SYTL2_ENST00000533892.1_Intron|SYTL2_ENST00000528231.1_Frame_Shift_Ins_p.EQ572fs|SYTL2_ENST00000527523.1_Frame_Shift_Ins_p.EQ540fs|SYTL2_ENST00000529581.1_Frame_Shift_Ins_p.EQ14fs|SYTL2_ENST00000524452.1_Intron|SYTL2_ENST00000354566.3_Frame_Shift_Ins_p.EQ910fs NM_206928.2 NP_996811.1 Q9HCH5 SYTL2_HUMAN synaptotagmin-like 2 572 intracellular protein transport|vesicle docking involved in exocytosis exocytic vesicle|extrinsic to plasma membrane|melanosome|membrane fraction neurexin binding|phosphatidylinositol-4,5-bisphosphate binding|phosphatidylserine binding|Rab GTPase binding breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 52 Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033) KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237) GTTTCTCTGTCATCACTCTACA 0.401 9 511 --- --- --- --- MMP12 4321 broad.mit.edu 37 11 102738793 102738794 + RNA INS - - T rs35342965 by1000genomes TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 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 69 --- --- --- --- CASP1 834 broad.mit.edu 37 11 104897656 104897656 + Frame_Shift_Del DEL G G - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr11:104897656delG ENST00000533400.1 - 8 1064 c.1029delC c.(1027-1029)ccfs p.P343fs CASP1_ENST00000525825.1_Frame_Shift_Del_p.P322fs|CASP1_ENST00000598974.1_Frame_Shift_Del_p.P343fs|CASP1_ENST00000415981.2_Frame_Shift_Del_p.P27fs|CASP1_ENST00000534497.1_Frame_Shift_Del_p.P202fs|CASP1_ENST00000446369.1_Frame_Shift_Del_p.P202fs|CASP1_ENST00000436863.3_Frame_Shift_Del_p.P343fs|CASP1_ENST00000531166.1_Frame_Shift_Del_p.P27fs|CASP1_ENST00000527979.1_Frame_Shift_Del_p.P306fs|CASP1_ENST00000353247.5_Frame_Shift_Del_p.P27fs|CASP1_ENST00000594519.1_Frame_Shift_Del_p.P202fs|CASP1_ENST00000526568.1_Frame_Shift_Del_p.P250fs|CASP1_ENST00000593315.1_Frame_Shift_Del_p.P322fs|CASP1_ENST00000393136.4_Frame_Shift_Del_p.P322fs|CASP1_ENST00000528974.1_3'UTR NM_001257118.1 NP_001244047.1 P29466 CASP1_HUMAN caspase 1, apoptosis-related cysteine peptidase 343 cellular response to mechanical stimulus|cellular response to organic substance|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis|signal transduction cytosol caspase activator activity|cysteine-type endopeptidase activity|protein binding haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2) 5 Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047) BRCA - Breast invasive adenocarcinoma(274;0.000525)|Epithelial(105;0.0128)|all cancers(92;0.0482) Minocycline(DB01017)|Penicillamine(DB00859) AGCCCATTGTGGGATGTCTCC 0.393 13 526 --- --- --- --- SIK3 23387 broad.mit.edu 37 11 116729014 116729016 + In_Frame_Del DEL TGC TGC - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr11:116729014_116729016delTGC ENST00000375300.1 - 20 3026_3028 c.3021_3023delGCA c.(3019-3024)caa>ca p.QQ1011del SIK3_ENST00000292055.4_In_Frame_Del_p.QQ953del|SIK3_ENST00000446921.2_In_Frame_Del_p.QQ951del|SIK3_ENST00000375288.1_In_Frame_Del_p.QQ288del|SIK3_ENST00000542607.1_In_Frame_Del_p.QQ893del|SIK3_ENST00000434315.2_In_Frame_Del_p.QQ792del|SIK3_ENST00000488337.1_5'UTR Q9Y2K2 SIK3_HUMAN SIK family kinase 3 953 cytoplasm ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1) 57 ttgctgctgttgctgctgctgct 0.591 7 226 --- --- --- --- PVRL1 5818 broad.mit.edu 37 11 119535678 119535680 + In_Frame_Del DEL CCT CCT - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr11:119535678_119535680delCCT ENST00000264025.3 - 6 1861_1863 c.1331_1333delAGG c.(1330-1335)ggc>g p.EG444del PVRL1_ENST00000341398.2_Intron NM_002855.4 NP_002846.3 Q15223 PVRL1_HUMAN poliovirus receptor-related 1 (herpesvirus entry mediator C) 444 Poly-Glu. adherens junction organization|cell junction assembly|entry of virus into host cell|heterophilic cell-cell adhesion|homophilic cell adhesion|immune response cell-cell adherens junction|extracellular region|integral to membrane cell adhesion molecule binding|coreceptor activity|protein homodimerization activity p.E444fs*>73(1) breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 27 Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) BRCA - Breast invasive adenocarcinoma(274;4.29e-05) CCTCCACCGCcctcctcctcctc 0.660 11 249 --- --- --- --- NTF3 4908 broad.mit.edu 37 12 5603608 5603609 + Frame_Shift_Ins INS - - C TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr12:5603608_5603609insC ENST00000423158.3 + 2 479_480 c.267_268insC c.(265-270)ggccgcfs p.R90fs NTF3_ENST00000535299.1_Intron|NTF3_ENST00000331010.6_Frame_Shift_Ins_p.R77fs NM_001102654.1 NP_001096124.1 P20783 NTF3_HUMAN neurotrophin 3 77 signal transduction extracellular region growth factor activity|neurotrophin receptor binding endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(3)|upper_aerodigestive_tract(1) 22 AGCGGGGAGGGCCCGCCAAGTC 0.579 29 507 --- --- --- --- CHD4 1108 broad.mit.edu 37 12 6711546 6711546 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr12:6711546delT ENST00000309577.6 - 3 381 c.218delA c.(217-219)agfs p.K73fs CHD4_ENST00000544484.1_Frame_Shift_Del_p.K70fs|CHD4_ENST00000544040.1_Frame_Shift_Del_p.K73fs|CHD4_ENST00000357008.2_Frame_Shift_Del_p.K73fs Q14839 CHD4_HUMAN chromodomain helicase DNA binding protein 4 73 chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent microtubule organizing center|NuRD complex ATP binding|ATP-dependent DNA helicase activity|DNA binding|zinc ion binding central_nervous_system(2) 2 ACTCACCTCCTTTTTTTGGCG 0.468 10 1737 --- --- --- --- KLHL42 57542 broad.mit.edu 37 12 27950769 27950769 + Frame_Shift_Del DEL G G - rs145908611 byFrequency TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr12:27950769delG ENST00000381271.2 + 3 1499 c.1188delG c.(1186-1188)gtfs p.V396fs NM_020782.1 NP_065833.1 kelch-like family member 42 TCTACATCGTGGGGGGGTGTC 0.592 7 1011 --- --- --- --- SCAF11 9169 broad.mit.edu 37 12 46318575 46318577 + In_Frame_Del DEL GGT GGT - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 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 7 548 --- --- --- --- SCAF11 9169 broad.mit.edu 37 12 46320707 46320708 + Frame_Shift_Del DEL TC TC - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr12:46320707_46320708delTC ENST00000465950.1 - 1 3040_3041 c.1831_1832delGA c.(1831-1833)afs p.E611fs SCAF11_ENST00000419565.2_Frame_Shift_Del_p.E926fs|SCAF11_ENST00000549162.1_Frame_Shift_Del_p.E734fs|SCAF11_ENST00000369367.3_Frame_Shift_Del_p.E926fs Q99590 SCAFB_HUMAN SR-related CTD-associated factor 11 926 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 GGTTCTCCTTTCTCTCTCTCTC 0.446 21 1065 --- --- --- --- CBX5 23468 broad.mit.edu 37 12 54645832 54645832 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr12:54645832delT ENST00000209875.4 - 3 453 c.317delA c.(316-318)agfs p.K106fs CBX5_ENST00000439541.2_Frame_Shift_Del_p.K106fs|CBX5_ENST00000550411.1_Frame_Shift_Del_p.K106fs NM_012117.2 NP_036249.1 P45973 CBX5_HUMAN chromobox homolog 5 106 blood coagulation|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent cytoplasm|histone deacetylase complex|histone methyltransferase complex|nuclear centromeric heterochromatin|nuclear envelope|nucleolus|transcriptional repressor complex methylated histone residue binding|protein binding, bridging|repressing transcription factor binding endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2) 8 TACCTCTCTCTTTTTTTTAGA 0.323 8 1253 --- --- --- --- XPOT 11260 broad.mit.edu 37 12 64812755 64812755 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr12:64812755delT ENST00000332707.5 + 6 899 c.370delT c.(370-372)ttfs p.F126fs NM_007235.4 NP_009166.2 O43592 XPOT_HUMAN exportin, tRNA 126 Necessary for interaction with Ran, nuclear localization and nuclear import. intracellular protein transport|tRNA export from nucleus cytoplasm|nucleoplasm protein transporter activity|tRNA binding p.F126fs*6(1) NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(7)|lung(12)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 45 GBM - Glioblastoma multiforme(28;0.0404) GTGGCCCAAGTTTTTTTTTGA 0.443 7 711 --- --- --- --- GNPTAB 79158 broad.mit.edu 37 12 102158002 102158002 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr12:102158002delT ENST00000299314.7 - 13 2955 c.2693delA c.(2692-2694)agfs p.K898fs NM_024312.4 NP_077288.2 Q3T906 GNPTA_HUMAN N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits 898 cell differentiation Golgi membrane|integral to membrane|nucleus metal ion binding|transcription factor binding|UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1) 37 TTGGAAATACTTTTTTTTCTC 0.373 10 1258 --- --- --- --- NCOR2 9612 broad.mit.edu 37 12 124848228 124848228 + Frame_Shift_Del DEL G G - rs12321697 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr12:124848228delG ENST00000356219.3 - 22 3080 c.2925delC c.(2923-2925)ccfs p.P975fs NCOR2_ENST00000404621.1_Frame_Shift_Del_p.P957fs|NCOR2_ENST00000404121.2_Frame_Shift_Del_p.P528fs|NCOR2_ENST00000397355.1_Frame_Shift_Del_p.P958fs|NCOR2_ENST00000405201.1_Frame_Shift_Del_p.P975fs|NCOR2_ENST00000429285.2_Frame_Shift_Del_p.P957fs NM_006312.5 NP_006303.4 Q9Y618 NCOR2_HUMAN nuclear receptor corepressor 2 975 cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent nuclear body|nucleus|transcriptional repressor complex DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2) 69 all_neural(191;0.0804)|Medulloblastoma(191;0.163) Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764) CACTCACGATGGGGGGGATGG 0.652 7 1190 --- --- --- --- ZMYM5 9205 broad.mit.edu 37 13 20426143 20426145 + In_Frame_Del DEL CAT CAT - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 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 10 614 --- --- --- --- PABPC3 5042 broad.mit.edu 37 13 25671333 25671333 + Frame_Shift_Del DEL A A - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr13:25671333delA ENST00000281589.3 + 1 1034 c.997delA c.(997-999)aafs p.K333fs NM_030979.2 NP_112241.2 Q9H361 PABP3_HUMAN poly(A) binding protein, cytoplasmic 3 333 RRM 4. mRNA metabolic process cytoplasm nucleotide binding|poly(A) RNA binding p.F335fs*19(1) breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|pancreas(1)|skin(3) 47 Lung SC(185;0.0225)|Breast(139;0.0602) all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241) TGGTCGCAGCAAAGGGTTTGG 0.428 11 1396 --- --- --- --- HSPH1 10808 broad.mit.edu 37 13 31715381 31715382 + Frame_Shift_Ins INS - - T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr13:31715381_31715382insT ENST00000320027.5 - 13 2075_2076 c.1731_1732insA c.(1729-1734)aattgafs p.N*577fs HSPH1_ENST00000445273.2_Frame_Shift_Ins_p.N*579fs|HSPH1_ENST00000380405.4_Frame_Shift_Ins_p.N*533fs|HSPH1_ENST00000429785.2_Frame_Shift_Ins_p.N*396fs|HSPH1_ENST00000380406.5_Frame_Shift_Ins_p.N*536fs NM_006644.2 NP_006635.2 Q92598 HS105_HUMAN heat shock 105kDa/110kDa protein 1 577 positive regulation of MHC class I biosynthetic process|positive regulation of NK T cell activation|response to unfolded protein cytoplasm|extracellular region ATP binding breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1) 27 Lung SC(185;0.0257) all cancers(112;0.00385)|Epithelial(112;0.0328)|OV - Ovarian serous cystadenocarcinoma(117;0.0375)|GBM - Glioblastoma multiforme(144;0.125) GGCTGGTCAACTTTTTTTTCAT 0.376 7 733 --- --- --- --- PDS5B 23047 broad.mit.edu 37 13 33344580 33344580 + Frame_Shift_Del DEL A A - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr13:33344580delA ENST00000315596.10 + 32 4132 c.3946delA c.(3946-3948)aafs p.K1318fs NM_015032.3 NP_055847.1 Q9NTI5 PDS5B_HUMAN PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae) 1318 cell division|cell proliferation|mitotic sister chromatid cohesion|negative regulation of cell proliferation chromatin|nucleus ATP binding|DNA binding|identical protein binding p.K1318fs*76(1) NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|lung(14)|ovary(5)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1) 62 Lung SC(185;0.0367) all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204) AAAAGGAAGCAAAAAAAAATC 0.443 8 283 --- --- --- --- KBTBD6 89890 broad.mit.edu 37 13 41705686 41705688 + In_Frame_Del DEL CTG CTG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr13:41705686_41705688delCTG ENST00000379485.1 - 1 1194_1196 c.960_962delCAG c.(958-963)agt>ag p.SS322del KBTBD6_ENST00000499385.2_In_Frame_Del_p.SS256del NM_152903.4 NP_690867.3 Q86V97 KBTB6_HUMAN kelch repeat and BTB (POZ) domain containing 6 322 protein binding NS(1)|breast(1)|endometrium(8)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|skin(4)|urinary_tract(4) 43 Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114) all cancers(112;4.08e-09)|Epithelial(112;4.74e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000131)|GBM - Glioblastoma multiforme(144;0.000876)|BRCA - Breast invasive adenocarcinoma(63;0.0673) gctgctgctactgctgctgctgc 0.522 7 257 --- --- --- --- ZC3H13 23091 broad.mit.edu 37 13 46549613 46549614 + Frame_Shift_Del DEL CT CT - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr13:46549613_46549614delCT ENST00000242848.4 - 12 2620_2621 c.2272_2273delAG c.(2272-2274)gfs p.R758fs ZC3H13_ENST00000282007.3_Frame_Shift_Del_p.R758fs Q5T200 ZC3HD_HUMAN zinc finger CCCH-type containing 13 758 Arg/Glu-rich. nucleic acid binding|zinc ion binding cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 79 Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262) KIRC - Kidney renal clear cell carcinoma(16;0.234) GBM - Glioblastoma multiforme(144;4.18e-05) ctctctctccctctctctctct 0.530 7 455 --- --- --- --- RBM26 64062 broad.mit.edu 37 13 79918806 79918807 + Frame_Shift_Ins INS - - T TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr13:79918806_79918807insT ENST00000438737.2 - 15 2621_2622 c.2181_2182insA c.(2179-2184)aaaggafs p.G728fs RBM26_ENST00000267229.7_Frame_Shift_Ins_p.G701fs|RBM26_ENST00000438724.1_Frame_Shift_Ins_p.G704fs Q5T8P6 RBM26_HUMAN RNA binding motif protein 26 728 mRNA processing nucleotide binding|protein binding|RNA binding|zinc ion binding NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(6)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1) 33 Acute lymphoblastic leukemia(28;0.0279) GBM - Glioblastoma multiforme(99;0.0188) GTACTTACCTGTTTTTTTTTCT 0.332 8 313 --- --- --- --- RP11-597A11.1 0 broad.mit.edu 37 14 20086237 20086237 + RNA DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr14:20086237delT ENST00000548261.1 + 0 51 GGTGTGTGTGTGGGGGGGTAT 0.388 21 88 --- --- --- --- RP11-597A11.1 0 broad.mit.edu 37 14 20086382 20086383 + RNA INS - - AAAA TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr14:20086382_20086383insAAAA ENST00000548261.1 + 0 135 TCTTACAAGGTAAAAAAAATGA 0.312 9 86 --- --- --- --- LRP10 26020 broad.mit.edu 37 14 23341527 23341529 + In_Frame_Del DEL CCT CCT - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr14:23341527_23341529delCCT ENST00000359591.4 + 1 706_708 c.15_17delCCT c.(13-18)acc>ac p.TL5del LRP10_ENST00000546834.1_In_Frame_Del_p.TL5del NM_014045.3 NP_054764.2 Q7Z4F1 LRP10_HUMAN low density lipoprotein receptor-related protein 10 5 endocytosis coated pit|integral to membrane central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(2) 32 all_cancers(95;4.69e-05) GBM - Glioblastoma multiforme(265;0.00549) TGTTGGCCACCCTCCTCCTCCTC 0.670 8 455 --- --- --- --- ACIN1 22985 broad.mit.edu 37 14 23528607 23528609 + In_Frame_Del DEL TCT TCT - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr14:23528607_23528609delTCT ENST00000262710.1 - 19 4101_4103 c.3774_3776delAGA c.(3772-3777)gag>ga p.EE1258del ACIN1_ENST00000457657.1_In_Frame_Del_p.EE1218del|ACIN1_ENST00000555053.1_In_Frame_Del_p.EE1245del|ACIN1_ENST00000605057.1_In_Frame_Del_p.EE1200del|ACIN1_ENST00000557515.1_In_Frame_Del_p.EE499del|ACIN1_ENST00000397341.3_In_Frame_Del_p.EE500del|ACIN1_ENST00000338631.6_In_Frame_Del_p.EE531del|ACIN1_ENST00000357481.2_In_Frame_Del_p.EE500del NM_001164814.1|NM_014977.3 NP_001158286.1|NP_055792.1 Q9UKV3 ACINU_HUMAN apoptotic chromatin condensation inducer 1 1258 Arg/Asp/Glu/Lys-rich. apoptotic chromosome condensation|erythrocyte differentiation|positive regulation of monocyte differentiation cytosol ATPase activity|enzyme binding|nucleic acid binding|nucleotide binding breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1) 37 all_cancers(95;1.36e-05) GBM - Glioblastoma multiforme(265;0.00816) ctccttttgctcttcttcttctt 0.601 7 331 --- --- --- --- RBM25 58517 broad.mit.edu 37 14 73572607 73572608 + Frame_Shift_Del DEL AG AG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr14:73572607_73572608delAG ENST00000261973.7 + 11 1480_1481 c.1195_1196delAG c.(1195-1197)afs p.R399fs RBM25_ENST00000527432.1_Frame_Shift_Del_p.R399fs NM_021239.2 NP_067062.1 P49756 RBM25_HUMAN RNA binding motif protein 25 399 Arg-rich.|Glu-rich.|Necessary for nuclear speckle localization. apoptosis|mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome|RNA splicing cytoplasm|nuclear speck mRNA binding|nucleotide binding|protein binding breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(6)|ovary(2)|pancreas(1) 31 BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688) agagcgggaaagagagagagag 0.446 23 238 --- --- --- --- GPR65 0 broad.mit.edu 37 14 88477555 88477555 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr14:88477555delT ENST00000267549.3 + 2 922 c.364delT c.(364-366)ttfs p.F124fs RP11-300J18.2_ENST00000554433.1_RNA NM_003608.3 NP_003599.2 Q8IYL9 PSYR_HUMAN G protein-coupled receptor 65 124 actin cytoskeleton reorganization|activation of Rho GTPase activity|apoptosis|immune response|multicellular organismal development|positive regulation of cAMP biosynthetic process|positive regulation of stress fiber assembly|response to acidity integral to plasma membrane G-protein coupled receptor activity central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|prostate(1) 16 CCCTTTGAAGTTTTTTTTCCT 0.428 7 1478 --- --- --- --- PTPN21 11099 broad.mit.edu 37 14 88945628 88945630 + In_Frame_Del DEL TCC TCC - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr14:88945628_88945630delTCC ENST00000556564.1 - 13 2429_2431 c.2145_2147delGGA c.(2143-2148)gac>ga p.ED717del PTPN21_ENST00000328736.3_In_Frame_Del_p.ED717del NM_007039.3 NP_008970.2 Q16825 PTN21_HUMAN protein tyrosine phosphatase, non-receptor type 21 717 Poly-Glu. cytoplasm|cytoskeleton binding|protein tyrosine phosphatase activity breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|liver(1)|lung(7)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1) 45 GAAGTCCTCGTCCTCCTCCTCCT 0.704 10 277 --- --- --- --- EML1 2009 broad.mit.edu 37 14 100367334 100367334 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr14:100367334delT ENST00000262233.6 + 9 1105 c.966delT c.(964-966)ggfs p.G322fs EML1_ENST00000334192.4_Frame_Shift_Del_p.G341fs|EML1_ENST00000327921.9_Frame_Shift_Del_p.G310fs NM_004434.2 NP_004425.2 O00423 EMAL1_HUMAN echinoderm microtubule associated protein like 1 322 cytoplasm|microtubule|microtubule associated complex calcium ion binding|protein binding breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1) 42 Melanoma(154;0.0879)|all_epithelial(191;0.216) TTGGAATAGGTTTTTTTGACC 0.428 11 848 --- --- --- --- SNHG14 0 broad.mit.edu 37 15 25324325 25324325 + RNA DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr15:25324325delT ENST00000549804.2 + 0 1377 ACAACTGTCATTTTTTTTGAT 0.478 7 383 --- --- --- --- PIGB 9488 broad.mit.edu 37 15 55621922 55621922 + Splice_Site DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr15:55621922delT ENST00000164305.5 + 5 814 c.522_splice c.e5-1 p.F176_splice PIGB_ENST00000539642.1_5'UTR NM_004855.4 NP_004846.4 Q92521 PIGB_HUMAN phosphatidylinositol glycan anchor biosynthesis, class B 176 C-terminal protein lipidation|preassembly of GPI anchor in ER membrane integral to membrane|intrinsic to endoplasmic reticulum membrane glycolipid mannosyltransferase activity endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1) 11 all cancers(107;0.0255) TTTTTCTTAGTTTTTTTGCCA 0.338 7 789 --- --- --- --- SLC24A1 9187 broad.mit.edu 37 15 65918177 65918179 + In_Frame_Del DEL CTG CTG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr15:65918177_65918179delCTG ENST00000261892.6 + 2 2046_2048 c.1759_1761delCTG c.(1759-1761)del p.L591del SLC24A1_ENST00000399033.4_In_Frame_Del_p.L591del|SLC24A1_ENST00000339868.6_In_Frame_Del_p.L591del|SLC24A1_ENST00000546330.1_In_Frame_Del_p.L591del|SLC24A1_ENST00000544319.2_In_Frame_Del_p.L591del|SLC24A1_ENST00000537259.1_In_Frame_Del_p.L591del NM_001254740.1|NM_004727.2 NP_001241669.1|NP_004718.1 O60721 NCKX1_HUMAN solute carrier family 24 (sodium/potassium/calcium exchanger), member 1 591 response to light intensity|visual perception integral to plasma membrane|membrane fraction|outer membrane calcium, potassium:sodium antiporter activity|protein binding|symporter activity breast(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 23 GTGGGAGAGCCTGCTGCTGCTGC 0.547 22 604 --- --- --- --- ADAMTS7 11173 broad.mit.edu 37 15 79058183 79058184 + Frame_Shift_Ins INS - - TGGGTCC TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr15:79058183_79058184insTGGGTCC ENST00000388820.4 - 19 4279_4280 c.4069_4070insGGACCCA c.(4069-4071)gggfs p.-1357fs NM_014272.3 NP_055087.2 Q9UKP4 ATS7_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 7 proteolysis proteinaceous extracellular matrix metalloendopeptidase activity|zinc ion binding NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9) 54 AGGCTGACCCTTGGGTCCTGGG 0.653 15 158 --- --- --- --- VPS33B 26276 broad.mit.edu 37 15 91550236 91550238 + In_Frame_Del DEL TCC TCC - rs147271815 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr15:91550236_91550238delTCC ENST00000333371.3 - 9 995_997 c.642_644delGGA c.(640-645)gat>ga p.ED214del VPS33B_ENST00000535906.1_In_Frame_Del_p.ED187del|VPS33B_ENST00000535843.1_In_Frame_Del_p.ED123del NM_018668.3 NP_061138.3 Q9H267 VP33B_HUMAN vacuolar protein sorting 33 homolog B (yeast) 214 cellular membrane fusion|lysosome localization|melanosome localization|platelet alpha granule organization|protein transport|vesicle docking involved in exocytosis late endosome membrane|lysosomal membrane|perinuclear region of cytoplasm|platelet alpha granule protein binding central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|stomach(2) 16 Lung NSC(78;0.0987)|all_lung(78;0.175) GGTTTCGCCATCCTCCTCCTCCT 0.522 10 785 --- --- --- --- RP11-266O8.1 0 broad.mit.edu 37 15 93974509 93974510 + RNA DEL TC TC - rs57286078 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr15:93974509_93974510delTC ENST00000543286.1 + 0 545 TTGGCTGGGTTCtttttttttt 0.431 10 187 --- --- --- --- RP11-266O8.1 0 broad.mit.edu 37 15 93974510 93974510 + RNA DEL C C - rs57286078 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr15:93974510delC ENST00000543286.1 + 0 545 TGGCTGGGTTCtttttttttt 0.433 16 172 --- --- --- --- Z97634.5 0 broad.mit.edu 37 16 437259 437260 + RNA DEL AT AT - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr16:437259_437260delAT ENST00000412293.1 + 0 521 NR_024453.2 CTAATTCTAAATATATATATAT 0.421 20 146 --- --- --- --- RP11-420N3.2 0 broad.mit.edu 37 16 5313074 5313076 + RNA DEL GGT GGT - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr16:5313074_5313076delGGT ENST00000569895.1 + 0 304 GCAGggtgacggtggtggtggtg 0.483 9 424 --- --- --- --- RP11-368J21.3 0 broad.mit.edu 37 16 22579763 22579764 + RNA DEL TT TT - rs112473041 by1000genomes TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr16:22579763_22579764delTT ENST00000550753.1 + 0 1976 NR_003676.2 tgtgtgtgtgtttgtttgtTTT 0.505 7 564 --- --- --- --- TNRC6A 27327 broad.mit.edu 37 16 24807240 24807240 + Frame_Shift_Del DEL A A - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr16:24807240delA ENST00000395799.3 + 9 3670 c.3541delA c.(3541-3543)aafs p.K1182fs TNRC6A_ENST00000315183.7_Frame_Shift_Del_p.K1182fs NM_014494.2 NP_055309.2 Q8NDV7 TNR6A_HUMAN trinucleotide repeat containing 6A 1182 Sufficient for interaction with EIF2C1 and EIF2C4. negative regulation of translation involved in gene silencing by miRNA cytoplasmic mRNA processing body|micro-ribonucleoprotein complex nucleotide binding|RNA binding breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 64 GBM - Glioblastoma multiforme(48;0.0394) TCTGAGTGGCAAAAAAAGGAG 0.398 17 1174 --- --- --- --- TAOK2 9344 broad.mit.edu 37 16 29994531 29994533 + In_Frame_Del DEL GAG GAG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr16:29994531_29994533delGAG ENST00000308893.4 + 12 2181_2183 c.1138_1140delGAG c.(1138-1140)del p.E392del TAOK2_ENST00000279394.3_In_Frame_Del_p.E392del|TAOK2_ENST00000416441.2_In_Frame_Del_p.E219del|TAOK2_ENST00000543033.1_In_Frame_Del_p.E392del NM_001252043.1|NM_016151.3 NP_001238972.1|NP_057235.2 Q9UL54 TAOK2_HUMAN TAO kinase 2 392 Glu-rich. actin cytoskeleton organization|activation of MAPKK activity|apoptosis|cell migration|focal adhesion assembly|positive regulation of JNK cascade|protein targeting to membrane|regulation of cell growth|regulation of cell shape|response to stress cytoplasmic vesicle membrane|cytoskeleton|dendrite|integral to membrane|nucleolus ATP binding|protein serine/threonine kinase activity breast(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(3)|skin(1) 22 CAACgaggaagaggaggaggagg 0.611 8 445 --- --- --- --- SETD1A 9739 broad.mit.edu 37 16 30982809 30982811 + In_Frame_Del DEL TCC TCC - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr16:30982809_30982811delTCC ENST00000262519.8 + 13 3813_3815 c.3127_3129delTCC c.(3127-3129)del p.S1058del NM_014712.1 NP_055527.1 O15047 SET1A_HUMAN SET domain containing 1A 1058 Ser-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome|nuclear speck|Set1C/COMPASS complex histone-lysine N-methyltransferase activity|nucleotide binding|protein binding|RNA binding NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1) 59 CAGctcctcatcctcctcctcct 0.547 7 589 --- --- --- --- RP11-439I14.2 0 broad.mit.edu 37 16 64770704 64770705 + RNA INS - - CCAGTGATGGTCACCT rs140029302 by1000genomes TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr16:64770704_64770705insCCAGTGATGGTCACCT ENST00000564293.1 + 0 453_454 TGTCACCACTGCCACCTTGTTC 0.371 9 36 --- --- --- --- EDC4 23644 broad.mit.edu 37 16 67913786 67913788 + In_Frame_Del DEL AGC AGC - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr16:67913786_67913788delAGC ENST00000358933.5 + 16 2094_2096 c.1855_1857delAGC c.(1855-1857)del p.S629del NM_014329.4 NP_055144.3 Q6P2E9 EDC4_HUMAN enhancer of mRNA decapping 4 629 Ser-rich. exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay cytoplasmic mRNA processing body|cytosol|nucleus protein binding breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(2) 41 Ovarian(137;0.0563) OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121) cagcagcggtagcagcagcagca 0.616 7 426 --- --- --- --- NPIPB15 440348 broad.mit.edu 37 16 74425400 74425402 + In_Frame_Del DEL CAA CAA - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr16:74425400_74425402delCAA ENST00000429990.1 + 7 850_852 c.754_756delCAA c.(754-756)del p.Q253del nuclear pore complex interacting protein family, member B15 TCCTCCAACTCAACAACATTCTA 0.517 11 559 --- --- --- --- WDR81 124997 broad.mit.edu 37 17 1631634 1631634 + Frame_Shift_Del DEL G G - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr17:1631634delG ENST00000409644.1 + 1 3381 c.3381delG c.(3379-3381)gafs p.E1127fs WDR81_ENST00000309182.5_Frame_Shift_Del_p.E76fs|WDR81_ENST00000446363.1_Intron|WDR81_ENST00000419248.1_Intron|WDR81_ENST00000437219.2_Intron|RP11-961A15.1_ENST00000576540.1_RNA NM_001163809.1 NP_001157281.1 B3KXU1 B3KXU1_HUMAN WD repeat domain 81 0 cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1) 16 UCEC - Uterine corpus endometrioid carcinoma (25;0.0822) CTCCAGACGAGGGGGGTGCCC 0.662 7 647 --- --- --- --- NUP88 4927 broad.mit.edu 37 17 5290964 5290964 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr17:5290964delT ENST00000573584.1 - 13 2305 c.1796delA c.(1795-1797)agfs p.K600fs NM_002532.4 NP_002523.2 Q99567 NUP88_HUMAN nucleoporin 88kDa 600 carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction cytosol|nuclear pore transporter activity endometrium(4)|kidney(4)|large_intestine(4)|lung(3) 15 TAGTTGTTTCTTTTTTTGGTC 0.363 7 1605 --- --- --- --- MYH10 4628 broad.mit.edu 37 17 8397095 8397097 + In_Frame_Del DEL CCT CCT - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr17:8397095_8397097delCCT ENST00000360416.3 - 32 4301_4303 c.4163_4165delAGG c.(4162-4167)gcc>g p.EA1388del MYH10_ENST00000379980.4_In_Frame_Del_p.EA1373del|MYH10_ENST00000396239.1_In_Frame_Del_p.EA1378del|MYH10_ENST00000269243.4_In_Frame_Del_p.EA1357del NM_001256012.1 NP_001242941.1 P35580 MYH10_HUMAN myosin, heavy chain 10, non-muscle 1357 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 TTCTTCCTGGCCTCCTCCTCCTC 0.596 7 343 --- --- --- --- SNORD3B-2 0 broad.mit.edu 37 17 18967428 18967429 + RNA INS - - A TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr17:18967428_18967429insA ENST00000364880.1 - 0 20_21 actatagaaatgatccctgaaa 0.475 22 45 --- --- --- --- DHRS7B 25979 broad.mit.edu 37 17 21094331 21094333 + In_Frame_Del DEL GAA GAA - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr17:21094331_21094333delGAA ENST00000395511.3 + 7 1163_1165 c.843_845delGAA c.(841-846)ggg>gg p.GK281del DHRS7B_ENST00000579303.1_In_Frame_Del_p.GK266del|DHRS7B_ENST00000581463.1_Intron NM_015510.4 NP_056325.2 Q6IAN0 DRS7B_HUMAN dehydrogenase/reductase (SDR family) member 7B 281 integral to membrane|peroxisomal membrane binding|oxidoreductase activity endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|pancreas(2) 7 CTGCTGTGGGGAAGAAGAAGAAA 0.507 7 1253 --- --- --- --- POLDIP2 26073 broad.mit.edu 37 17 26684394 26684395 + Splice_Site INS - - G rs113730440 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr17:26684394_26684395insG ENST00000540200.1 - 1 78 c.e1+1 POLDIP2_ENST00000003607.4_5'UTR NM_015584.3 NP_056399.1 Q9Y2S7 PDIP2_HUMAN polymerase (DNA-directed), delta interacting protein 2 mitochondrial nucleoid|nucleus all_lung(13;0.000354)|Lung NSC(42;0.00115) UCEC - Uterine corpus endometrioid carcinoma (53;0.154) AGAGCGGCTTTGCCACCGGGCC 0.762 13 28 --- --- --- --- RP11-115K3.2 0 broad.mit.edu 37 17 36214141 36214141 + RNA DEL A A - rs76035088 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr17:36214141delA ENST00000590732.1 - 0 325 NR_024178.1 CAGCaaaattaaaaaaaaaaa 0.328 8 142 --- --- --- --- KRTAP4-1 85285 broad.mit.edu 37 17 39340796 39340852 + In_Frame_Del DEL CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG - rs483929 by1000genomes TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr17:39340796_39340852delCGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG ENST00000398472.1 - 1 742_798 c.255_311delCCCACTCTGCTGTCAGACCACCTGCCACCCCAGCTGTGGTATGTCCAGCTGCTGCCG c.(253-312)cgt>cg p.RPLCCQTTCHPSCGMSSCCR85del Q9BYQ7 KRA41_HUMAN keratin associated protein 4-1 85 18 X 5 AA repeats of C-C-[GRQC]-[SPT]- [VSTL]. Missing (in allele KAP4.10). keratin filament p.H90_C108delHPSCGMSSCCRPLCCQTTC(2)|p.H94_C112delHPSCGMSSCCRPLCCQTTC(2) kidney(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1) 5 Breast(137;0.000496) STAD - Stomach adenocarcinoma(17;0.000449) ACAGAGTGGACGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGGCGGCAGCAGC 0.646 8 472 --- --- --- --- STAT5B 6777 broad.mit.edu 37 17 40370236 40370236 + Frame_Shift_Del DEL G G - rs144993426 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr17:40370236delG ENST00000293328.3 - 9 1270 c.1102delC c.(1102-1104)agfs p.Q368fs NM_012448.3 NP_036580.2 P51692 STA5B_HUMAN signal transducer and activator of transcription 5B 368 2-oxoglutarate metabolic process|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|fatty acid metabolic process|isoleucine metabolic process|JAK-STAT cascade involved in growth hormone signaling pathway|oxaloacetate metabolic process|response to estradiol stimulus|succinate metabolic process|taurine metabolic process|valine metabolic process cytosol|nucleoplasm calcium ion binding|glucocorticoid receptor binding|sequence-specific DNA binding transcription factor activity breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 27 all_cancers(22;4.15e-07)|all_epithelial(22;2.83e-05)|Breast(137;0.000143) BRCA - Breast invasive adenocarcinoma(366;0.135) Dasatinib(DB01254) GCCTTCACCTGGGGGGGGTTC 0.577 9 297 --- --- --- --- STAT3 6774 broad.mit.edu 37 17 40489864 40489864 + Frame_Shift_Del DEL G G - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr17:40489864delG ENST00000264657.5 - 7 874 c.562delC c.(562-564)tgfs p.L188fs STAT3_ENST00000389272.3_Frame_Shift_Del_p.L90fs|STAT3_ENST00000585517.1_Frame_Shift_Del_p.L188fs|STAT3_ENST00000588969.1_Frame_Shift_Del_p.L188fs|STAT3_ENST00000404395.3_Frame_Shift_Del_p.L188fs NM_003150.3|NM_139276.2 NP_003141.2|NP_644805.1 P40763 STAT3_HUMAN signal transducer and activator of transcription 3 (acute-phase response factor) 188 cellular component movement|eating behavior|eye photoreceptor cell differentiation|glucose homeostasis|interleukin-6-mediated signaling pathway|interspecies interaction between organisms|JAK-STAT cascade involved in growth hormone signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|protein import into nucleus|response to estradiol stimulus|sexual reproduction|temperature homeostasis cytosol|nucleus|plasma membrane calcium ion binding|ligand-regulated transcription factor activity|protein dimerization activity|protein kinase binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription factor binding|transcription regulatory region DNA binding breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 35 all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135) BRCA - Breast invasive adenocarcinoma(366;0.139) TTTCCATTCAGATCTTGCATG 0.517 Hyperimmunoglobulin E Recurrent Infection Syndrome 9 271 --- --- --- --- RP11-798G7.5 0 broad.mit.edu 37 17 43596433 43596433 + RNA DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr17:43596433delT ENST00000253803.2 + 0 267 TTTTTGCCGGTTTTGGCCTAC 0.478 11 4502 --- --- --- --- CDC27 996 broad.mit.edu 37 17 45219612 45219612 + Frame_Shift_Del DEL A A - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr17:45219612delA ENST00000066544.3 - 11 1454 c.1361delT c.(1360-1362)cafs p.L454fs CDC27_ENST00000531206.1_Frame_Shift_Del_p.L460fs|CDC27_ENST00000527547.1_Frame_Shift_Del_p.L454fs|CDC27_ENST00000446365.2_Frame_Shift_Del_p.L393fs NM_001114091.1|NM_001256.3 NP_001107563.1|NP_001247.3 P30260 CDC27_HUMAN cell division cycle 27 454 anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule protein phosphatase binding NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2) 90 TGCTTTTTGTAGATTAAAGGC 0.308 43 246 --- --- --- --- RP11-178C3.2 0 broad.mit.edu 37 17 58050857 58050857 + RNA DEL G G - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr17:58050857delG ENST00000586209.1 + 0 158 TTTTTTTTTTGGCAGTTTTTA 0.423 7 121 --- --- --- --- FTSJ3 117246 broad.mit.edu 37 17 61899155 61899157 + In_Frame_Del DEL CTC CTC - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr17:61899155_61899157delCTC ENST00000427159.2 - 15 2167_2169 c.1522_1524delGAG c.(1522-1524)del p.E508del NM_017647.3 NP_060117.3 Q8IY81 RRMJ3_HUMAN FtsJ homolog 3 (E. coli) 508 RNA methylation|rRNA processing nucleolus methyltransferase activity|nucleic acid binding breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1) 27 GCAGTGGATTCTCCTCCTCCTCC 0.537 7 1166 --- --- --- --- SRP68 6730 broad.mit.edu 37 17 74068528 74068530 + In_Frame_Del DEL GCC GCC - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr17:74068528_74068530delGCC ENST00000307877.2 - 1 204_206 c.43_45delGGC c.(43-45)del p.G15del SRP68_ENST00000355113.5_5'UTR|SRP68_ENST00000539137.1_In_Frame_Del_p.G15del NM_014230.3 NP_055045.2 Q9UHB9 SRP68_HUMAN signal recognition particle 68kDa 15 Poly-Gly. Missing (in Ref. 1). response to drug cytosol|endoplasmic reticulum|nucleolus|ribosome|signal recognition particle, endoplasmic reticulum targeting RNA binding|signal recognition particle binding NS(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|lung(4)|ovary(2)|prostate(3) 23 cgccgccactgccgccgccgccg 0.709 7 387 --- --- --- --- RAB40B 10966 broad.mit.edu 37 17 80615785 80615786 + Frame_Shift_Ins INS - - G rs111549422 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr17:80615785_80615786insG ENST00000571995.1 - 6 921_922 c.790_791insC c.(790-792)gagfs p.E264fs RAB40B_ENST00000269347.6_Frame_Shift_Ins_p.E85fs|RAB40B_ENST00000538809.2_IGR NM_006822.2 NP_006813.1 Q12829 RB40B_HUMAN RAB40B, member RAS oncogene family 264 protein transport|small GTPase mediated signal transduction plasma membrane GTP binding p.Q264P(1)|p.Q264fs*>15(1) central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(2) 10 Breast(20;0.00132)|all_neural(118;0.0952) all_cancers(8;0.072)|all_epithelial(8;0.139) BRCA - Breast invasive adenocarcinoma(99;0.0262)|OV - Ovarian serous cystadenocarcinoma(97;0.061) GGGGGGGCTCTGGGGGGGGCGG 0.569 9 1271 --- --- --- --- RBBP8 5932 broad.mit.edu 37 18 20572852 20572853 + Frame_Shift_Ins INS - - A TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 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 10 685 --- --- --- --- CXXC1 30827 broad.mit.edu 37 18 47812275 47812277 + In_Frame_Del DEL CTG CTG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr18:47812275_47812277delCTG ENST00000285106.6 - 5 1195_1197 c.481_483delCAG c.(481-483)del p.Q161del CXXC1_ENST00000589940.1_In_Frame_Del_p.Q161del|CXXC1_ENST00000412036.2_In_Frame_Del_p.Q161del NM_001101654.1|NM_014593.3 NP_001095124.1|NP_055408.2 Q9P0U4 CXXC1_HUMAN CXXC finger protein 1 161 histone H3-K4 methylation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent nuclear speck|Set1C/COMPASS complex protein binding|unmethylated CpG binding|zinc ion binding autonomic_ganglia(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2) 24 ACCGTTTGATctgctgctgctgc 0.557 7 275 --- --- --- --- NEDD4L 0 broad.mit.edu 37 18 55992284 55992286 + In_Frame_Del DEL TCC TCC - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr18:55992284_55992286delTCC ENST00000456986.1 + 9 807_809 c.207_209delTCC c.(205-210)ctt>ct p.LP69del NEDD4L_ENST00000456173.2_In_Frame_Del_p.LP69del|NEDD4L_ENST00000256832.7_In_Frame_Del_p.LP69del|NEDD4L_ENST00000357895.5_In_Frame_Del_p.LP182del|NEDD4L_ENST00000586263.1_In_Frame_Del_p.LP182del|NEDD4L_ENST00000431212.2_In_Frame_Del_p.LP69del|NEDD4L_ENST00000589054.1_Intron|NEDD4L_ENST00000256830.9_In_Frame_Del_p.LP190del|NEDD4L_ENST00000382850.4_In_Frame_Del_p.LP190del|NEDD4L_ENST00000435432.2_In_Frame_Del_p.LP69del|NEDD4L_ENST00000356462.6_In_Frame_Del_p.LP190del|NEDD4L_ENST00000400345.3_In_Frame_Del_p.LP190del NM_001144964.1 NP_001138436.1 Q96PU5 NED4L_HUMAN neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase 190 C2. cellular sodium ion homeostasis|excretion|interspecies interaction between organisms|positive regulation of endocytosis|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of protein catabolic process|response to metal ion|sodium ion transport|water homeostasis cytoplasm protein binding|sodium channel regulator activity|ubiquitin-protein ligase activity breast(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(11)|ovary(1)|prostate(4) 37 AAGAGGAACTTCCTCCTCCTCCT 0.498 13 1150 --- --- --- --- UBXN6 80700 broad.mit.edu 37 19 4454085 4454085 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr19:4454085delT ENST00000301281.6 - 2 213 c.89delA c.(88-90)agfs p.K30fs CTB-50L17.9_ENST00000592034.1_RNA|UBXN6_ENST00000394765.3_5'UTR NM_025241.2 NP_079517.1 Q9BZV1 UBXN6_HUMAN UBX domain protein 6 30 microtubule organizing center|nucleus protein binding NS(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1) 12 TTTGTGGGCCTTTTCCCTGGG 0.667 7 1208 --- --- --- --- TNFSF9 8744 broad.mit.edu 37 19 6531149 6531151 + In_Frame_Del DEL GCT GCT - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr19:6531149_6531151delGCT ENST00000245817.3 + 1 140_142 c.102_104delGCT c.(100-105)ggg>gg p.GL34del NM_003811.3 NP_003802.1 P41273 TNFL9_HUMAN tumor necrosis factor (ligand) superfamily, member 9 34 apoptosis|cell proliferation|cell-cell signaling|immune response|signal transduction extracellular space|integral to membrane cytokine activity|tumor necrosis factor receptor binding central_nervous_system(1)|lung(1)|ovary(1)|prostate(1)|skin(1) 5 TGGTCGCGGGgctgctgctgctg 0.768 9 386 --- --- --- --- DNMT1 1786 broad.mit.edu 37 19 10262139 10262139 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr19:10262139delT ENST00000340748.4 - 23 2387 c.2152delA c.(2152-2154)tgfs p.M718fs DNMT1_ENST00000359526.4_Frame_Shift_Del_p.M734fs|DNMT1_ENST00000540357.1_Frame_Shift_Del_p.M718fs P26358 DNMT1_HUMAN DNA (cytosine-5-)-methyltransferase 1 718 chromatin modification|maintenance of DNA methylation|negative regulation of histone H3-K9 methylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene expression|positive regulation of histone H3-K4 methylation|transcription, DNA-dependent nucleus DNA (cytosine-5-)-methyltransferase activity|DNA binding|transcription factor binding breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1) 70 OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06) Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Ifosfamide(DB01181)|Procainamide(DB01035) CCCTGGTGCATTTTTTTGGGT 0.507 12 1062 --- --- --- --- DNM2 1785 broad.mit.edu 37 19 10940882 10940882 + Frame_Shift_Del DEL C C - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr19:10940882delC ENST00000314646.5 + 20 2535 c.2371delC c.(2371-2373)ccfs p.P792fs DNM2_ENST00000408974.4_Frame_Shift_Del_p.P788fs|DNM2_ENST00000389253.4_Frame_Shift_Del_p.P792fs|DNM2_ENST00000359692.6_Frame_Shift_Del_p.P788fs|DNM2_ENST00000355667.6_Frame_Shift_Del_p.P792fs|DNM2_ENST00000585892.1_Frame_Shift_Del_p.P792fs P50570 DYN2_HUMAN dynamin 2 792 Pro-rich. G2/M transition of mitotic cell cycle|positive regulation of apoptosis|positive regulation of transcription, DNA-dependent|post-Golgi vesicle-mediated transport|receptor internalization|signal transduction|synaptic vesicle transport|transferrin transport cell junction|cytosol|Golgi membrane|microtubule|postsynaptic density|postsynaptic membrane GTP binding|GTPase activity|microtubule binding breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2) 42 Epithelial(33;4.17e-05)|all cancers(31;8.48e-05) CACTCCAGGGCCCCCCCTGAT 0.692 """F, N, Splice, Mis, O""" ETP ALL 7 692 --- --- --- --- YIPF2 78992 broad.mit.edu 37 19 11038362 11038364 + In_Frame_Del DEL GCT GCT - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr19:11038362_11038364delGCT ENST00000586748.1 - 4 393_395 c.221_223delAGC c.(220-225)ccg>c p.QP74del YIPF2_ENST00000253031.2_In_Frame_Del_p.QP74del|YIPF2_ENST00000590329.1_In_Frame_Del_p.QP74del Q9BWQ6 YIPF2_HUMAN Yip1 domain family, member 2 74 integral to membrane|transport vesicle cervix(1)|endometrium(1)|lung(3)|ovary(2) 7 CAGAATCCCGgctgctgctgctg 0.621 7 396 --- --- --- --- CEP89 84902 broad.mit.edu 37 19 33370155 33370155 + Frame_Shift_Del DEL G G - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr19:33370155delG ENST00000305768.4 - 19 2353 c.2265delC c.(2263-2265)ccfs p.P755fs NM_032816.3 NP_116205.3 Q96ST8 CEP89_HUMAN centrosomal protein 89kDa 755 centrosome|spindle pole breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1) 35 CATTGAGGCTGGGGGCAACCA 0.587 7 984 --- --- --- --- ATP4A 495 broad.mit.edu 37 19 36054349 36054351 + In_Frame_Del DEL CTT CTT - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr19:36054349_36054351delCTT ENST00000262623.3 - 2 119_121 c.91_93delAAG c.(91-93)del p.K31del NM_000704.2 NP_000695.2 P20648 ATP4A_HUMAN ATPase, H+/K+ exchanging, alpha polypeptide 31 ATP biosynthetic process|ATP hydrolysis coupled proton transport integral to plasma membrane ATP binding|hydrogen:potassium-exchanging ATPase activity|magnesium ion binding breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(26)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1) 53 all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0724) Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)|Trifluoperazine(DB00831) CGCCACCCGCCTTCTTCTTCTTG 0.601 8 1909 --- --- --- --- PSG7 5676 broad.mit.edu 37 19 43428981 43428982 + RNA INS - - G TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr19:43428981_43428982insG ENST00000406070.2 - 0 1340 NM_002783.2 NP_002774.2 Q13046 PSG7_HUMAN pregnancy specific beta-1-glycoprotein 7 (gene/pseudogene) female pregnancy extracellular region Prostate(69;0.00682) tccagtctacagtggataataa 0.406 19 262 --- --- --- --- PLAUR 5329 broad.mit.edu 37 19 44174235 44174237 + In_Frame_Del DEL AGC AGC - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr19:44174235_44174237delAGC ENST00000221264.4 - 1 462_464 c.36_38delGCT c.(34-39)ctc>ct p.LL12del PLAUR_ENST00000340093.3_In_Frame_Del_p.LL12del|PLAUR_ENST00000339082.3_In_Frame_Del_p.LL12del|PLAUR_ENST00000601723.1_In_Frame_Del_p.LL12del NM_001005377.2 NP_001005377.1 Q03405 UPAR_HUMAN plasminogen activator, urokinase receptor 12 attachment of GPI anchor to protein|blood coagulation|C-terminal protein lipidation|cellular component movement|chemotaxis|fibrinolysis|regulation of proteolysis anchored to membrane|cell surface|endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region|extrinsic to membrane|integral to membrane|plasma membrane enzyme binding|U-plasminogen activator receptor activity endometrium(1)|kidney(4)|large_intestine(5)|lung(5)|ovary(1)|stomach(1)|urinary_tract(3) 20 Prostate(69;0.0153) Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Urokinase(DB00013) GCAGGTGTGGagcagcagcagca 0.660 7 871 --- --- --- --- MAMSTR 284358 broad.mit.edu 37 19 49218105 49218106 + Frame_Shift_Ins INS - - G TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr19:49218105_49218106insG ENST00000318083.6 - 6 548_549 c.485_486insC c.(484-486)ccafs p.P162fs MAMSTR_ENST00000419611.1_Frame_Shift_Ins_p.P59fs|MAMSTR_ENST00000377367.3_Frame_Shift_Ins_p.P59fs|MAMSTR_ENST00000356751.4_Frame_Shift_Ins_p.P59fs|MAMSTR_ENST00000594582.1_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 9 644 --- --- --- --- SIGLEC8 27181 broad.mit.edu 37 19 51961617 51961619 + In_Frame_Del DEL GCA GCA - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr19:51961617_51961619delGCA ENST00000321424.3 - 1 89_91 c.23_25delTGC c.(22-27)ccc>c p.LP8del SIGLEC8_ENST00000340550.5_In_Frame_Del_p.LP8del|SIGLEC8_ENST00000430817.1_In_Frame_Del_p.LP8del NM_014442.2 NP_055257.2 Q9NYZ4 SIGL8_HUMAN sialic acid binding Ig-like lectin 8 8 cell adhesion integral to membrane sugar binding|transmembrane receptor activity NS(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(11)|liver(3)|lung(15)|ovary(2)|skin(4)|stomach(3)|urinary_tract(2) 50 all_neural(266;0.0199) GBM - Glioblastoma multiforme(134;0.000627)|OV - Ovarian serous cystadenocarcinoma(262;0.00979) CAGagcaggggcagcagcagcag 0.596 14 484 --- --- --- --- LILRB5 0 broad.mit.edu 37 19 54754838 54754839 + Frame_Shift_Ins INS - - G rs11375503 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr19:54754838_54754839insG ENST00000450632.1 - 13 1873_1874 c.1796_1797insC c.(1795-1797)cccfs p.P599fs LILRB5_ENST00000345866.6_Intron|LILRB5_ENST00000449561.2_Intron|LILRB5_ENST00000316219.5_Intron O75023 LIRB5_HUMAN leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5 424 cell surface receptor linked signaling pathway|defense response integral to membrane transmembrane receptor activity NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 56 all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19) GBM - Glioblastoma multiforme(193;0.105) GTGGTGGGGGTGGGGAGGCCTG 0.604 31 187 --- --- --- --- BFSP1 631 broad.mit.edu 37 20 17474884 17474884 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr20:17474884delT ENST00000377873.3 - 8 1872 c.1833delA c.(1831-1833)aafs p.K611fs BFSP1_ENST00000377868.2_Frame_Shift_Del_p.K486fs|BFSP1_ENST00000544874.1_Frame_Shift_Del_p.K472fs|BFSP1_ENST00000536626.1_Frame_Shift_Del_p.K472fs NM_001195.3 NP_001186.1 Q12934 BFSP1_HUMAN beaded filament structural protein 1, filensin 611 Tail. cytoplasm|intermediate filament|membrane structural constituent of cytoskeleton|structural constituent of eye lens central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)|stomach(1) 18 TGGGAGGGCCTTTTTCTGGCA 0.527 7 1105 --- --- --- --- GINS1 9837 broad.mit.edu 37 20 25422397 25422397 + Frame_Shift_Del DEL A A - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr20:25422397delA ENST00000262460.4 + 6 601 c.507delA c.(505-507)ttfs p.L169fs GINS1_ENST00000429262.2_3'UTR NM_021067.3 NP_066545.3 Q14691 PSF1_HUMAN GINS complex subunit 1 (Psf1 homolog) 169 DNA strand elongation involved in DNA replication|S phase of mitotic cell cycle cytoplasm|nucleoplasm p.N172fs*14(1) central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|urinary_tract(1) 7 CAGTCCTATTAAAAAAAAATA 0.299 9 441 --- --- --- --- ZNF337 26152 broad.mit.edu 37 20 25657231 25657232 + Frame_Shift_Del DEL TG TG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr20:25657231_25657232delTG ENST00000376436.1 - 4 1231_1232 c.692_693delCA c.(691-693)afs p.T231fs ZNF337_ENST00000252979.5_Frame_Shift_Del_p.T231fs|ZNF337_ENST00000538750.1_Frame_Shift_Del_p.T199fs|RP4-694B14.5_ENST00000414393.1_RNA|RP4-694B14.5_ENST00000455791.1_RNA|RP4-694B14.5_ENST00000439498.1_RNA zinc finger protein 337 breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 32 ACTTCTCTCCTGTGTGTGTGTT 0.510 9 607 --- --- --- --- NCOA6 23054 broad.mit.edu 37 20 33330968 33330970 + In_Frame_Del DEL TGC TGC - rs140426729 byFrequency TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr20:33330968_33330970delTGC ENST00000374796.2 - 12 5660_5662 c.3090_3092delGCA c.(3088-3093)caa>ca p.QQ1030del NCOA6_ENST00000359003.2_In_Frame_Del_p.QQ1030del Q14686 NCOA6_HUMAN nuclear receptor coactivator 6 1030 CREBBP-binding region.|Gln-rich.|NCOA1-binding region. brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter transcription factor complex chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1) 107 CATCATTtgttgctgctgctgct 0.576 9 638 --- --- --- --- ZHX3 23051 broad.mit.edu 37 20 39832962 39832962 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr20:39832962delT ENST00000309060.3 - 4 1010 c.595delA c.(595-597)ttfs p.I199fs ZHX3_ENST00000560361.1_Frame_Shift_Del_p.I199fs|ZHX3_ENST00000557816.1_Frame_Shift_Del_p.I199fs|ZHX3_ENST00000559234.1_Frame_Shift_Del_p.I199fs|ZHX3_ENST00000432768.2_Frame_Shift_Del_p.I199fs|ZHX3_ENST00000558993.1_Frame_Shift_Del_p.I199fs|ZHX3_ENST00000540170.1_Frame_Shift_Del_p.I199fs|ZHX3_ENST00000544979.2_Frame_Shift_Del_p.I199fs Q9H4I2 ZHX3_HUMAN zinc fingers and homeoboxes 3 199 negative regulation of transcription, DNA-dependent cytoplasm|nucleolus protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding endometrium(2)|kidney(5)|large_intestine(8)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2) 31 Myeloproliferative disorder(115;0.00425) AGTGTATGAATTTTTTTGGCT 0.488 8 691 --- --- --- --- BAGE2 85319 broad.mit.edu 37 21 11049306 11049307 + RNA INS - - T rs57143135 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr21:11049306_11049307insT ENST00000470054.1 - 0 659 B melanoma antigen family, member 2 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247) ATATCCAGTAATTTTTTTAAGT 0.272 37 396 --- --- --- --- ANKRD20A11P 0 broad.mit.edu 37 21 15343608 15343609 + RNA INS - - A TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr21:15343608_15343609insA ENST00000344693.5 - 0 736 NR_027270.1 TAAAACAGCAGAAAAAATTAAT 0.272 12 600 --- --- --- --- LINC00478 0 broad.mit.edu 37 21 17443416 17443417 + RNA DEL TG TG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr21:17443416_17443417delTG ENST00000458468.1 + 0 27 NR_027790.1 TTTTTCTTTTTGTGTGTGTGTG 0.431 16 949 --- --- --- --- APP 351 broad.mit.edu 37 21 27394182 27394184 + In_Frame_Del DEL GTG GTG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr21:27394182_27394184delGTG ENST00000358918.3 - 6 1036_1038 c.837_839delCAC c.(835-840)aca>ac p.TT279del APP_ENST00000354192.3_In_Frame_Del_p.TT223del|APP_ENST00000440126.3_In_Frame_Del_p.TT274del|APP_ENST00000348990.5_In_Frame_Del_p.TT279del|APP_ENST00000448388.2_In_Frame_Del_p.TT244del|APP_ENST00000357903.3_In_Frame_Del_p.TT279del|APP_ENST00000474136.1_5'UTR|APP_ENST00000346798.3_In_Frame_Del_p.TT279del|APP_ENST00000439274.2_In_Frame_Del_p.TT223del|APP_ENST00000359726.3_In_Frame_Del_p.TT279del NM_001204301.1|NM_001204302.1 NP_001191230.1|NP_001191231.1 P05067 A4_HUMAN amyloid beta (A4) precursor protein 279 Poly-Thr. adult locomotory behavior|axon cargo transport|axon midline choice point recognition|cell adhesion|cellular copper ion homeostasis|collateral sprouting in absence of injury|dendrite development|endocytosis|extracellular matrix organization|G2 phase of mitotic cell cycle|innate immune response|ionotropic glutamate receptor signaling pathway|mating behavior|mRNA polyadenylation|neuron apoptosis|neuron remodeling|Notch signaling pathway|platelet activation|platelet degranulation|positive regulation of mitotic cell cycle|protein phosphorylation|regulation of epidermal growth factor receptor activity|regulation of multicellular organism growth|regulation of synapse structure and activity|regulation of translation|visual learning axon|cell surface|coated pit|dendritic shaft|dendritic spine|extracellular region|Golgi apparatus|integral to plasma membrane|platelet alpha granule lumen acetylcholine receptor binding|DNA binding|heparin binding|identical protein binding|metal ion binding|protein binding|PTB domain binding|serine-type endopeptidase inhibitor activity endometrium(5)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1) 22 Breast(209;0.00295) CACAGACTCTgtggtggtggtgg 0.522 7 203 --- --- --- --- APP 351 broad.mit.edu 37 21 27394297 27394299 + In_Frame_Del DEL CTT CTT - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr21:27394297_27394299delCTT ENST00000358918.3 - 6 921_923 c.722_724delAAG c.(721-726)gcc>g p.EA241del APP_ENST00000354192.3_In_Frame_Del_p.EA185del|APP_ENST00000440126.3_In_Frame_Del_p.EA236del|APP_ENST00000348990.5_In_Frame_Del_p.EA241del|APP_ENST00000448388.2_In_Frame_Del_p.EA206del|APP_ENST00000357903.3_In_Frame_Del_p.EA241del|APP_ENST00000474136.1_5'UTR|APP_ENST00000346798.3_In_Frame_Del_p.EA241del|APP_ENST00000439274.2_In_Frame_Del_p.EA185del|APP_ENST00000359726.3_In_Frame_Del_p.EA241del NM_001204301.1|NM_001204302.1 NP_001191230.1|NP_001191231.1 P05067 A4_HUMAN amyloid beta (A4) precursor protein 241 Asp/Glu-rich (acidic). adult locomotory behavior|axon cargo transport|axon midline choice point recognition|cell adhesion|cellular copper ion homeostasis|collateral sprouting in absence of injury|dendrite development|endocytosis|extracellular matrix organization|G2 phase of mitotic cell cycle|innate immune response|ionotropic glutamate receptor signaling pathway|mating behavior|mRNA polyadenylation|neuron apoptosis|neuron remodeling|Notch signaling pathway|platelet activation|platelet degranulation|positive regulation of mitotic cell cycle|protein phosphorylation|regulation of epidermal growth factor receptor activity|regulation of multicellular organism growth|regulation of synapse structure and activity|regulation of translation|visual learning axon|cell surface|coated pit|dendritic shaft|dendritic spine|extracellular region|Golgi apparatus|integral to plasma membrane|platelet alpha granule lumen acetylcholine receptor binding|DNA binding|heparin binding|identical protein binding|metal ion binding|protein binding|PTB domain binding|serine-type endopeptidase inhibitor activity endometrium(5)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1) 22 Breast(209;0.00295) tcatcatcggcttcttcttcttc 0.473 7 531 --- --- --- --- PIGP 51227 broad.mit.edu 37 21 38444815 38444815 + Translation_Start_Site DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr21:38444815delT ENST00000399098.1 - 0 193 PIGP_ENST00000464265.1_Frame_Shift_Del_p.M25fs|PIGP_ENST00000399102.1_Start_Codon_Del|PIGP_ENST00000329667.3_5'UTR|PIGP_ENST00000360525.3_Start_Codon_Del|PIGP_ENST00000399103.1_Start_Codon_Del P57054 PIGP_HUMAN phosphatidylinositol glycan anchor biosynthesis, class P C-terminal protein lipidation|preassembly of GPI anchor in ER membrane endoplasmic reticulum membrane|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex|integral to membrane phosphatidylinositol N-acetylglucosaminyltransferase activity kidney(1)|urinary_tract(1) 2 Myeloproliferative disorder(46;0.0412) TTTTCCACCATTTTTCCTGGG 0.488 8 1668 --- --- --- --- TPTEP1 0 broad.mit.edu 37 22 17131430 17131432 + RNA DEL CAC CAC - rs142037179 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr22:17131430_17131432delCAC ENST00000426585.1 + 0 2456_2458 caccatccatcaccaacagaaac 0.443 8 12 --- --- --- --- AC008103.5 0 broad.mit.edu 37 22 18843723 18843724 + RNA INS - - A TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr22:18843723_18843724insA ENST00000412938.1 + 0 2337 AGGGGCACCCCACGGCCTGGAG 0.619 8 111 --- --- --- --- MED15 51586 broad.mit.edu 37 22 20918817 20918819 + In_Frame_Del DEL CAG CAG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 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_ENST00000382974.2_In_Frame_Del_p.Q117del|MED15_ENST00000406969.1_In_Frame_Del_p.Q162del|MED15_ENST00000425759.2_In_Frame_Del_p.Q77del|MED15_ENST00000542773.1_5'UTR|MED15_ENST00000541476.1_In_Frame_Del_p.Q162del 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) 9 181 --- --- --- --- CRKL 1399 broad.mit.edu 37 22 21304075 21304075 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr22:21304075delT ENST00000354336.3 + 3 1363 c.854delT c.(853-855)ctfs p.L285fs NM_005207.3 NP_005198.1 P46109 CRKL_HUMAN v-crk avian sarcoma virus CT10 oncogene homolog-like 285 SH3 2. JNK cascade|Ras protein signal transduction cytosol protein tyrosine kinase activity|SH3/SH2 adaptor activity|signal transducer activity endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7) 14 all_cancers(11;1.16e-25)|all_epithelial(7;3.37e-24)|Lung NSC(8;7.25e-16)|all_lung(8;1.37e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142) Lung SC(17;0.0262) LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.176) CGCAAAGGGCTTTTCCCCTTT 0.468 7 1732 --- --- --- --- LL22NC03-80A10.6 0 broad.mit.edu 37 22 22661172 22661173 + RNA INS - - C rs7410785 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr22:22661172_22661173insC ENST00000426066.1 + 0 264_265 NR_027293.1 CATACAGGTTTTCCCCCCCCAC 0.411 7 249 --- --- --- --- MYH9 4627 broad.mit.edu 37 22 36696948 36696950 + In_Frame_Del DEL CTC CTC - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr22:36696948_36696950delCTC ENST00000216181.5 - 22 3015_3017 c.2785_2787delGAG c.(2785-2787)del p.E929del NM_002473.4 NP_002464.1 P35579 MYH9_HUMAN myosin, heavy chain 9, non-muscle 929 actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3) 86 GCTGGCAGCGCTCCTCCTCCTCC 0.665 T ALK ALCL """Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome""" Hereditary Macrothrombocytopenia, MYH9-associated 9 670 --- --- --- --- TCF20 6942 broad.mit.edu 37 22 42610776 42610778 + In_Frame_Del DEL TGC TGC - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chr22:42610776_42610778delTGC ENST00000359486.3 - 1 670_672 c.534_536delGCA c.(532-537)caa>ca p.QQ178del TCF20_ENST00000335626.4_In_Frame_Del_p.QQ178del NM_005650.1 NP_005641.1 Q9UGU0 TCF20_HUMAN transcription factor 20 (AR1) 178 Poly-Gln. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|transcription coactivator activity|zinc ion binding breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5) 66 CTGCTGGACTTGCTGCTGCTGCT 0.571 12 438 --- --- --- --- CNKSR2 22866 broad.mit.edu 37 X 21627678 21627680 + In_Frame_Del DEL GAG GAG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chrX:21627678_21627680delGAG ENST00000425654.2 + 19 3025_3027 c.2545_2547delGAG c.(2545-2547)del p.E856del CNKSR2_ENST00000543067.1_In_Frame_Del_p.E837del|CNKSR2_ENST00000279451.4_In_Frame_Del_p.E886del|CNKSR2_ENST00000379510.3_In_Frame_Del_p.E886del NM_001168647.1 NP_001162118.1 Q8WXI2 CNKR2_HUMAN connector enhancer of kinase suppressor of Ras 2 886 regulation of signal transduction cytoplasm|membrane protein binding breast(3)|endometrium(8)|kidney(2)|large_intestine(15)|lung(28)|prostate(2)|upper_aerodigestive_tract(3) 61 ggtggaggaagaggaggaggagg 0.517 16 289 --- --- --- --- SRPX 8406 broad.mit.edu 37 X 38079976 38079978 + In_Frame_Del DEL GCA GCA - rs72445954 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chrX:38079976_38079978delGCA ENST00000378533.3 - 1 174_176 c.68_70delTGC c.(67-72)cgc>c p.LR23del SRPX_ENST00000538295.1_In_Frame_Del_p.LR23del|TM4SF2_ENST00000465127.1_Intron|SRPX_ENST00000544439.1_In_Frame_Del_p.LR23del|SRPX_ENST00000432886.2_In_Frame_Del_p.LR23del|SRPX_ENST00000343800.6_Intron NM_006307.4 NP_006298.1 P78539 SRPX_HUMAN sushi-repeat containing protein, X-linked 23 Missing. cell adhesion cell surface|membrane p.L23delL(2) autonomic_ganglia(1)|breast(2)|endometrium(5)|large_intestine(5)|lung(10)|prostate(2) 25 GGCGGGACGCgcagcagcagcag 0.729 OREG0019726 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 19 44 --- --- --- --- TFE3 7030 broad.mit.edu 37 X 48887952 48887952 + Frame_Shift_Del DEL C C - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chrX:48887952delC ENST00000315869.7 - 10 1704 c.1445delG c.(1444-1446)gafs p.G482fs TFE3_ENST00000493583.1_5'UTR NM_006521.4 NP_006512.2 P19532 TFE3_HUMAN transcription factor binding to IGHM enhancer 3 482 humoral immune response|positive regulation of transcription from RNA polymerase II promoter cytoplasm|nucleus sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding NONO/TFE3(2)|PRCC/TFE3(25)|SFPQ/TFE3(6)|CLTC/TFE3(2)|ASPSCR1/TFE3(167) central_nervous_system(1) 1 CTGGGCAGGTCCCCCCCCTAC 0.647 T """SFPQ, ASPSCR1, PRCC, NONO, CLTC""" """papillary renal, alveolar soft part sarcoma, renal""" 9 792 --- --- --- --- GAGE2D 729408 broad.mit.edu 37 X 49208295 49208296 + In_Frame_Ins INS - - TAT TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chrX:49208295_49208296insTAT ENST00000404720.2 + 2 96_97 c.24_25insTAT c.(22-27)acatcg>acTATatcg p.8_9TS>TIS NM_001098407.1|NM_012196.1 NP_001091877.1|NP_036328.1 G antigen 2D GAAGATCGACCTATCGGCCTAG 0.465 51 208 --- --- --- --- PHF8 23133 broad.mit.edu 37 X 54011405 54011407 + In_Frame_Del DEL CTC CTC - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chrX:54011405_54011407delCTC ENST00000338154.6 - 18 2887_2889 c.2383_2385delGAG c.(2383-2385)del p.E795del PHF8_ENST00000338946.6_In_Frame_Del_p.E694del|PHF8_ENST00000357988.5_In_Frame_Del_p.E831del|PHF8_ENST00000322659.8_In_Frame_Del_p.E778del NM_015107.2 NP_055922.1 Q9UPP1 PHF8_HUMAN PHD finger protein 8 831 Ser-rich. brain development|G1/S transition of mitotic cell cycle|negative regulation of chromatin silencing at rDNA|positive regulation of transcription from RNA polymerase I promoter|transcription, DNA-dependent nucleolus chromatin binding|histone demethylase activity (H3-K27 specific)|histone demethylase activity (H3-K36 specific)|histone demethylase activity (H3-K9 specific)|histone demethylase activity (H4-K20 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1) 40 GACTGGCGTTCTCCTCCTCCTCC 0.591 11 893 --- --- --- --- MED12 9968 broad.mit.edu 37 X 70360589 70360591 + In_Frame_Del DEL AGC AGC - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chrX:70360589_70360591delAGC ENST00000333646.6 + 42 6357_6359 c.6158_6160delAGC c.(6157-6162)gag>g p.EQ2053del MED12_ENST00000374080.3_In_Frame_Del_p.EQ2050del|MED12_ENST00000374102.1_In_Frame_Del_p.EQ2049del|MED12_ENST00000478889.1_3'UTR NM_005120.2 NP_005111.2 Q93074 MED12_HUMAN mediator complex subunit 12 2050 Gln-rich. androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter mediator complex ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3) 420 Renal(35;0.156) ATCCTACCTGagcagcagcagca 0.586 """M, S""" uterine leiomyoma Opitz-Kaveggia Syndrome 8 702 --- --- --- --- ATRX 546 broad.mit.edu 37 X 76907782 76907784 + In_Frame_Del DEL TCC TCC - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chrX:76907782_76907784delTCC ENST00000373344.5 - 15 4591_4593 c.4377_4379delGGA c.(4375-4380)gaa>ga p.EE1463del ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_In_Frame_Del_p.EE1425del 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 10 902 --- --- --- --- CUL4B 8450 broad.mit.edu 37 X 119694117 119694119 + In_Frame_Del DEL GAG GAG - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 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 12 448 --- --- --- --- IGSF1 3547 broad.mit.edu 37 X 130408667 130408667 + Frame_Shift_Del DEL T T - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chrX:130408667delT ENST00000370904.1 - 24 4540 c.3630delA c.(3628-3630)aafs p.K1210fs IGSF1_ENST00000370903.3_Frame_Shift_Del_p.K1224fs|IGSF1_ENST00000361420.3_Frame_Shift_Del_p.K1219fs|IGSF1_ENST00000370910.1_Frame_Shift_Del_p.K1210fs Q8N6C5 IGSF1_HUMAN immunoglobulin superfamily, member 1 1219 Ig-like C2-type 12. regulation of transcription, DNA-dependent extracellular region|integral to membrane inhibin beta-A binding|inhibin beta-B binding breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|liver(1)|lung(37)|ovary(4)|skin(3)|upper_aerodigestive_tract(2) 78 TTCCAATGCCTTTTCCTTCTA 0.517 7 2099 --- --- --- --- SPANXN4 441525 broad.mit.edu 37 X 142121809 142121811 + Splice_Site DEL AGA AGA - rs78094296 TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chrX:142121809_142121811delAGA ENST00000446864.1 + 2 175_176 c.78_splice c.e2-1 p.K28_splice SPANXN4_ENST00000370504.3_Intron NM_001009613.2 NP_001009613.1 Q5MJ08 SPXN4_HUMAN SPANX family, member N4 28 endometrium(2)|large_intestine(2)|lung(3)|ovary(1) 8 Acute lymphoblastic leukemia(192;6.56e-05) TTTTTTTACCAGAAGAAGAAGAA 0.414 13 22 --- --- --- --- AFF2 2334 broad.mit.edu 37 X 147733548 147733548 + Frame_Shift_Del DEL A A - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chrX:147733548delA ENST00000370460.2 + 2 555 c.76delA c.(76-78)aafs p.K27fs AFF2_ENST00000370457.5_Frame_Shift_Del_p.K27fs|AFF2_ENST00000342251.3_Frame_Shift_Del_p.K27fs|AFF2_ENST00000370458.1_Frame_Shift_Del_p.K27fs NM_001169123.1|NM_002025.3 NP_001162594.1|NP_002016.2 P51816 AFF2_HUMAN AF4/FMR2 family, member 2 27 brain development|mRNA processing|regulation of RNA splicing|RNA splicing nuclear speck G-quadruplex RNA binding|protein binding breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1) 109 Acute lymphoblastic leukemia(192;6.56e-05) TAGTGCACTTAAAAAAAGGGA 0.378 7 1369 --- --- --- --- RNA5-8SP6 0 broad.mit.edu 37 Y 10037863 10037863 + RNA DEL C C - TCGA-HZ-A49H-01A-11D-A26I-08 TCGA-HZ-A49H-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 23635060-618f-4272-9a34-284c65318d9a 27fb1352-19ad-417f-acbe-a2af1c099544 g.chrY:10037863delC ENST00000515896.1 + 0 100 ATCGACACTTCGAACGCACTT 0.552 12 95 --- --- --- ---