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 NCOR1P1 0 broad.mit.edu 37 20 26084094 26084094 + RNA SNP T T C TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr20:26084094T>C ENST00000478176.1 - 0 363 NR_003678.1 aaaacataCATTCTTAGAATA 0.299000 5 101 0 0 1 0 0 HAAO 23498 broad.mit.edu 37 2 42996988 42996988 + Silent SNP G G T TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr2:42996988G>T ENST00000294973.6 - 7 550 c.495C>A c.(493-495)ctC>ctA p.L165L NM_012205.2 NP_036337.2 P46952 3HAO_HUMAN 3-hydroxyanthranilate 3,4-dioxygenase 165 Linker (By similarity). neuron homeostasis|pyridine nucleotide biosynthetic process|quinolinate biosynthetic process|response to cadmium ion|response to zinc ion|tryptophan catabolic process cytosol|soluble fraction 3-hydroxyanthranilate 3,4-dioxygenase activity|electron carrier activity|ferrous iron binding p.L165L(1) breast(2)|cervix(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|urinary_tract(2) 11 GTGGCTCCTTGAGCAGCTGGT 0.637000 15 589 6.72482e-11 7.20517e-11 1 1 0 TPTE2P6 0 broad.mit.edu 37 13 25161457 25161457 + RNA SNP G G A rs1851732 by1000genomes TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr13:25161457G>A ENST00000453498.1 + 0 981 TTATTTATTCGATTCGTGGTA 0.378000 19 132 0 0 1 0 0 RP11-707M1.1 0 broad.mit.edu 37 11 49831862 49831862 + RNA SNP G G A rs10839383 by1000genomes TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr11:49831862G>A ENST00000527477.1 + 0 2087 CCTCTTCCTTGTGCCTTATCA 0.353000 15 524 0 0 1 0 0 GLUD1P2 0 broad.mit.edu 37 10 48968566 48968566 + RNA SNP A A G TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr10:48968566A>G ENST00000594520.1 + 0 723 ACAGGATAACAAACTGGAAAA 0.318000 6 110 0 0 1 0 0 RP11-798G7.5 0 broad.mit.edu 37 17 43587569 43587569 + RNA SNP G G C rs149697015 by1000genomes TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr17:43587569G>C ENST00000253803.2 + 0 267 LRRC37A4P_ENST00000579913.1_RNA aactccgtctgaaaagaaaag 0.443000 8 264 0 0 1 0 0 LRRC30 339291 broad.mit.edu 37 18 7231272 7231272 + Missense_Mutation SNP C C T TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr18:7231272C>T ENST00000383467.2 + 1 150 c.136C>T c.(136-138)Cgg>Tgg p.R46W NM_001105581.1 NP_001099051.1 A6NM36 LRC30_HUMAN leucine rich repeat containing 30 46 central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(1)|skin(3) 31 CCTGCTGAAGCGGGGCATGCA 0.597000 13 508 0 0 1 0 0 CSPP1 79848 broad.mit.edu 37 8 68062082 68062082 + Silent SNP T T C TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr8:68062082T>C ENST00000262210.5 + 16 2056 c.2025T>C c.(2023-2025)taT>taC p.Y675Y CSPP1_ENST00000412460.1_Intron NM_024790.6 NP_079066.5 Q1MSJ5 CSPP1_HUMAN centrosome and spindle pole associated protein 1 710 Poly-Gly. centrosome|microtubule|spindle NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|prostate(3)|skin(1)|urinary_tract(1) 49 Breast(64;0.214) Lung NSC(129;0.0908)|all_lung(136;0.152) Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153) CAAGAACATATGAAGATAAAA 0.358000 32 925 0 0 1 0 0 KRTAP4-9 100132386 broad.mit.edu 37 17 39262039 39262039 + Missense_Mutation SNP C C G TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f 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 6 168 0 0 1 0 0 MLLT3 4300 broad.mit.edu 37 9 20414346 20414346 + Silent SNP G G A TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr9:20414346G>A ENST00000380338.4 - 5 784 c.498C>T c.(496-498)agC>agT p.S166S MLLT3_ENST00000429426.2_Silent_p.S163S|MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000355930.6_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 16 461 0 0 1 0 0 CCT6P1 0 broad.mit.edu 37 7 65222986 65222986 + RNA SNP G G T TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr7:65222986G>T ENST00000442266.1 + 0 578 GAATTCTGGCGTTTTTTACAA 0.289000 4 55 0.00198382 0.00198382 1 1 0 AC008103.5 0 broad.mit.edu 37 22 18844888 18844888 + RNA SNP A A G TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr22:18844888A>G ENST00000412938.1 + 0 3138 GCTCACGGAAATACAGCTTCA 0.587000 16 429 0 0 1 0 0 PARG 8505 broad.mit.edu 37 10 51093329 51093329 + Missense_Mutation SNP C C T TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr10:51093329C>T ENST00000402038.3 - 4 294 c.295G>A c.(295-297)Gca>Aca p.A99T NM_003631.2 NP_003622.2 Q86W56 PARG_HUMAN poly (ADP-ribose) glycohydrolase 584 carbohydrate metabolic process nucleus poly(ADP-ribose) glycohydrolase activity p.A584T(1) endometrium(5)|kidney(2)|lung(1)|ovary(2) 10 Epithelial(53;0.213) TGAGCTTCTGCTTCTTCAAGT 0.318000 10 275 0 0 1 0 0 HSD17B7P2 0 broad.mit.edu 37 10 38654432 38654432 + RNA SNP A A G rs2257765 TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr10:38654432A>G ENST00000494540.1 + 0 599 NR_003086.1 TCATCTCGCAATGCAAGGAAA 0.453000 10 274 0 0 1 0 0 KRTAP4-9 100132386 broad.mit.edu 37 17 39262047 39262047 + Missense_Mutation SNP A A G TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f 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 7 157 0 0 1 0 0 AC008103.5 0 broad.mit.edu 37 22 18844766 18844766 + RNA SNP G G A TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr22:18844766G>A ENST00000412938.1 + 0 3016 CAGCCTCTGAGGGCAGCAGTG 0.557000 14 86 0 0 1 0 0 MLLT3 4300 broad.mit.edu 37 9 20414340 20414340 + Silent SNP G G A TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr9:20414340G>A ENST00000380338.4 - 5 790 c.504C>T c.(502-504)agC>agT p.S168S MLLT3_ENST00000429426.2_Silent_p.S165S|MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000355930.6_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 23 483 0 0 1 0 0 COTL1 23406 broad.mit.edu 37 16 84600451 84600451 + Nonstop_Mutation SNP T T G TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr16:84600451T>G ENST00000262428.4 - 4 591 c.429A>C c.(427-429)taA>taC p.*143Y COTL1_ENST00000567278.1_5'UTR|COTL1_ENST00000564057.1_Nonstop_Mutation_p.*74Y NM_021149.2 NP_066972.1 Q14019 COTL1_HUMAN coactosin-like 1 (Dictyostelium) 0 cytoplasm|cytoskeleton actin binding|enzyme binding endometrium(1)|large_intestine(1)|liver(1)|lung(2)|skin(1) 6 GGGGCTGGGGTTACTCCGTCT 0.622000 11 128 0 0 1 0 0 GABRD 2563 broad.mit.edu 37 1 1956774 1956774 + Splice_Site DEL C C - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr1:1956774delC ENST00000378585.4 + 3 266 c.181_splice c.e3-1 p.G61_splice NM_000815.4 NP_000806.2 O14764 GBRD_HUMAN gamma-aminobutyric acid (GABA) A receptor, delta 61 cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity p.V64fs*365(1) central_nervous_system(2)|endometrium(3)|kidney(2)|lung(8)|ovary(2)|prostate(1)|skin(2) 20 all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;2.7e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128) Epithelial(90;2.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.17e-24)|GBM - Glioblastoma multiforme(42;9.56e-08)|Colorectal(212;4.12e-05)|COAD - Colon adenocarcinoma(227;0.000194)|Kidney(185;0.00231)|BRCA - Breast invasive adenocarcinoma(365;0.00441)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0344)|Lung(427;0.2) TCCTTGCAGGCCCCCCCGTGA 0.647 7 842 --- --- --- --- AADACL3 126767 broad.mit.edu 37 1 12785494 12785494 + Frame_Shift_Del DEL G G - rs7513079 by1000genomes TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr1:12785494delG ENST00000332530.3 + 3 600 c.374delG c.(373-375)ttfs p.C125fs AADACL3_ENST00000359318.5_Frame_Shift_Del_p.C195fs NM_001103169.1 NP_001096639.1 Q5VUY0 ADCL3_HUMAN arylacetamide deacetylase-like 3 195 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) ATCTGCTACTGTTTTTTTCAA 0.458 13 1080 --- --- --- --- CROCCP2 0 broad.mit.edu 37 1 16953827 16953828 + RNA INS - - C rs57007114 TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr1:16953827_16953828insC ENST00000412962.1 - 0 477 TCACTTTCCTGCCCGAACCTCC 0.609 7 217 --- --- --- --- EXTL1 2134 broad.mit.edu 37 1 26349533 26349535 + In_Frame_Del DEL CCT CCT - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f 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 12 344 --- --- --- --- MACF1 23499 broad.mit.edu 37 1 39788668 39788670 + In_Frame_Del DEL GGA GGA - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr1:39788668_39788670delGGA ENST00000564288.1 + 33 5001_5003 c.4224_4226delGGA c.(4222-4227)ctg>ct p.LE1408del MACF1_ENST00000539005.1_In_Frame_Del_p.LE1413del|MACF1_ENST00000545844.1_In_Frame_Del_p.LE1413del|MACF1_ENST00000317713.7_In_Frame_Del_p.LE1413del|MACF1_ENST00000361689.2_In_Frame_Del_p.LE1413del|MACF1_ENST00000567887.1_In_Frame_Del_p.LE1445del|MACF1_ENST00000372915.3_In_Frame_Del_p.LE1413del|MACF1_ENST00000476350.1_3'UTR Q9UPN3 MACF1_HUMAN microtubule-actin crosslinking factor 1 1413 cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing Golgi apparatus|microtubule|ruffle membrane actin filament binding|ATPase activity|calcium ion binding|microtubule binding breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10) 203 Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074) Myeloproliferative disorder(586;0.0255) OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204) TCCGGCGTCTGGAGGAGGAGGAG 0.493 7 712 --- --- --- --- SLC6A9 6536 broad.mit.edu 37 1 44489938 44489938 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr1:44489938delT ENST00000372310.3 - 2 177 c.12delA c.(10-12)aafs p.K4fs SLC6A9_ENST00000372306.3_Frame_Shift_Del_p.K4fs|SLC6A9_ENST00000475075.2_5'UTR|SLC6A9_ENST00000537678.1_5'UTR|SLC6A9_ENST00000492434.2_5'UTR NM_001024845.2 NP_001020016.1 P48067 SC6A9_HUMAN solute carrier family 6 (neurotransmitter transporter, glycine), member 9 335 integral to plasma membrane|membrane fraction glycine:sodium symporter activity|neurotransmitter:sodium symporter activity endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(2) 22 Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0511) Glycine(DB00145) CTTTGGCACCTTTTCCTACCA 0.627 9 1894 --- --- --- --- IPP 3652 broad.mit.edu 37 1 46184897 46184898 + Frame_Shift_Del DEL AC AC - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr1:46184897_46184898delAC ENST00000396478.3 - 6 1265_1266 c.1163_1164delGT c.(1162-1164)tfs p.C388fs NM_005897.2 NP_005888.1 Q9Y573 IPP_HUMAN intracisternal A particle-promoted polypeptide 388 actin cytoskeleton|cytoplasm actin binding central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|stomach(2) 20 Acute lymphoblastic leukemia(166;0.155) TAGCCCCATAACACACACACAC 0.347 14 350 --- --- --- --- WDR78 79819 broad.mit.edu 37 1 67390426 67390426 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr1:67390426delT ENST00000371026.3 - 1 144 c.89delA c.(88-90)agfs p.K30fs WDR78_ENST00000371023.3_Frame_Shift_Del_p.K30fs|WDR78_ENST00000371022.3_Frame_Shift_Del_p.K30fs|WDR78_ENST00000431318.1_5'UTR NM_024763.4 NP_079039.4 Q5VTH9 WDR78_HUMAN WD repeat domain 78 30 NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3) 32 GCACCACCCCTTTTTTTGGCC 0.622 7 903 --- --- --- --- BRDT 676 broad.mit.edu 37 1 92447228 92447230 + In_Frame_Del DEL AGC AGC - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr1:92447228_92447230delAGC ENST00000370389.2 + 12 2623_2625 c.1699_1701delAGC c.(1699-1701)del p.S575del BRDT_ENST00000394530.3_In_Frame_Del_p.S602del|BRDT_ENST00000362005.3_In_Frame_Del_p.S648del|BRDT_ENST00000399546.2_In_Frame_Del_p.S648del|BRDT_ENST00000402388.1_In_Frame_Del_p.S648del NM_001242810.1 NP_001229739.1 Q58F21 BRDT_HUMAN bromodomain, testis-specific 648 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus protein serine/threonine kinase activity|transcription coactivator activity breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(24)|ovary(1)|prostate(4)|skin(2)|stomach(2)|urinary_tract(2) 56 all_lung(203;0.00531)|Lung NSC(277;0.0194) all cancers(265;0.0228)|Epithelial(280;0.133) ACTGAGTGAGagcagcagcagca 0.419 9 438 --- --- --- --- NGF 4803 broad.mit.edu 37 1 115828721 115828722 + Frame_Shift_Del DEL CA CA - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr1:115828721_115828722delCA ENST00000369512.2 - 3 863_864 c.695_696delTG c.(694-696)gfs p.V232fs RP4-663N10.1_ENST00000425449.1_RNA NM_002506.2 NP_002497.2 P01138 NGF_HUMAN nerve growth factor (beta polypeptide) 232 activation of MAPKK activity|activation of phospholipase C activity|anti-apoptosis|apoptosis|induction of apoptosis by extracellular signals|negative regulation of cell cycle|nerve growth factor processing|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|Ras protein signal transduction endosome|Golgi lumen growth factor activity|nerve growth factor receptor binding breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(2) 13 Lung SC(450;0.211) all_cancers(81;1.07e-06)|all_epithelial(167;4.43e-06)|all_lung(203;2.86e-05)|Lung NSC(69;4.99e-05) Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|all cancers(265;0.159)|Epithelial(280;0.179) Clenbuterol(DB01407) TCCTGCTGAGCACACACACACA 0.579 7 548 --- --- --- --- PBXIP1 57326 broad.mit.edu 37 1 154917508 154917510 + In_Frame_Del DEL GGT GGT - rs143592003 TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr1:154917508_154917510delGGT ENST00000368463.3 - 11 2257_2259 c.2186_2188delACC c.(2185-2190)cgg>c p.HR729del PBXIP1_ENST00000539880.1_In_Frame_Del_p.HR556del|PBXIP1_ENST00000542459.1_In_Frame_Del_p.HR574del|PBXIP1_ENST00000368465.1_In_Frame_Del_p.HR700del NM_020524.2 NP_065385.2 Q96AQ6 PBIP1_HUMAN pre-B-cell leukemia homeobox interacting protein 1 729 His-rich. cell differentiation|multicellular organismal development|negative regulation of transcription, DNA-dependent cytosol|microtubule|nucleus protein binding|transcription corepressor activity breast(1)|kidney(2)|large_intestine(6)|lung(13)|prostate(1)|urinary_tract(1) 24 all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245) BRCA - Breast invasive adenocarcinoma(34;0.00034) TGTCAGCCCCGGTGGTGGTGGTG 0.640 11 510 --- --- --- --- DHX9 1660 broad.mit.edu 37 1 182845333 182845333 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr1:182845333delT ENST00000367549.3 + 17 2074 c.1964delT c.(1963-1965)gtfs p.V655fs NM_001357.4 NP_001348.2 Q08211 DHX9_HUMAN DEAH (Asp-Glu-Ala-His) box helicase 9 655 Helicase C-terminal. CRD-mediated mRNA stabilization|nuclear mRNA splicing, via spliceosome centrosome|CRD-mediated mRNA stability complex|nucleolus|nucleoplasm|ribonucleoprotein complex ATP binding|ATP-dependent DNA helicase activity|ATP-dependent RNA helicase activity|DNA binding|double-stranded RNA binding|protein binding NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2) 49 GCTGTGTTGGTTTTTTTGCCT 0.378 10 712 --- --- --- --- DYRK3 8444 broad.mit.edu 37 1 206821441 206821441 + Frame_Shift_Del DEL A A - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr1:206821441delA ENST00000367106.1 + 4 1311 c.838delA c.(838-840)aafs p.K281fs DYRK3_ENST00000489878.1_Intron|DYRK3_ENST00000367108.3_Frame_Shift_Del_p.K281fs|DYRK3_ENST00000367109.2_Frame_Shift_Del_p.K301fs O43781 DYRK3_HUMAN dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3 301 Protein kinase. erythrocyte differentiation nucleus ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(9)|lung(8)|skin(1)|stomach(2) 25 Breast(84;0.183) BRCA - Breast invasive adenocarcinoma(75;0.166) TGAGCTGATTAAAAAAAATAA 0.403 9 690 --- --- --- --- PTPN14 5784 broad.mit.edu 37 1 214557049 214557051 + In_Frame_Del DEL CCT CCT - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr1:214557049_214557051delCCT ENST00000366956.5 - 13 2341_2343 c.2147_2149delAGG c.(2146-2151)gct>g p.EA716del PTPN14_ENST00000543945.1_3'UTR NM_005401.4 NP_005392.2 Q15678 PTN14_HUMAN protein tyrosine phosphatase, non-receptor type 14 716 Poly-Glu. lymphangiogenesis cytoplasm|cytoskeleton protein tyrosine phosphatase activity|receptor tyrosine kinase binding p.E716delE(1) NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 58 OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155) GATTCTGGAGCCTCCTCCTCCTC 0.626 11 381 --- --- --- --- RMDN2 151393 broad.mit.edu 37 2 38178783 38178783 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr2:38178783delT ENST00000407257.1 + 2 572 c.425delT c.(424-426)atfs p.I142fs RMDN2_ENST00000402091.3_Frame_Shift_Del_p.I142fs|RMDN2_ENST00000234195.3_Frame_Shift_Del_p.I142fs|RMDN2_ENST00000406384.1_Intron|RMDN2_ENST00000354545.2_Intron|RMDN2-AS1_ENST00000414365.2_RNA|RMDN2_ENST00000417700.2_Intron regulator of microtubule dynamics 2 AAGAGTGCCATTTTTTTTGAT 0.333 8 425 --- --- --- --- DHX57 90957 broad.mit.edu 37 2 39095411 39095413 + In_Frame_Del DEL CCA CCA - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr2:39095411_39095413delCCA ENST00000295373.6 - 2 261_263 c.135_137delTGG c.(133-138)gga>gg p.GG47del NM_198963.1 NP_945314.1 Q6P158 DHX57_HUMAN DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57 47 Gly-rich. ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding|zinc ion binding NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1) 62 all_hematologic(82;0.248) Gccgccacctccaccaccaccac 0.532 10 606 --- --- --- --- SOS1 6654 broad.mit.edu 37 2 39213243 39213243 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr2:39213243delT ENST00000426016.1 - 24 3810 c.3724delA c.(3724-3726)gtfs p.S1242fs SOS1_ENST00000402219.2_Frame_Shift_Del_p.S1242fs|SOS1_ENST00000395038.2_Frame_Shift_Del_p.S1227fs Q07889 SOS1_HUMAN son of sevenless homolog 1 (Drosophila) 1242 apoptosis|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction cytosol DNA binding|protein binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2) 75 all_hematologic(82;0.21) CCATGGTCACTTTTTTTGCCC 0.517 Noonan syndrome 7 528 --- --- --- --- SOS1 6654 broad.mit.edu 37 2 39222520 39222520 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr2:39222520delT ENST00000426016.1 - 21 3176 c.3090delA c.(3088-3090)aafs p.K1030fs SOS1_ENST00000402219.2_Frame_Shift_Del_p.K1030fs|SOS1_ENST00000395038.2_Frame_Shift_Del_p.K1030fs Q07889 SOS1_HUMAN son of sevenless homolog 1 (Drosophila) 1030 apoptosis|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction cytosol DNA binding|protein binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2) 75 all_hematologic(82;0.21) GATAGCTATATTTTTTTGGCT 0.388 Noonan syndrome 7 494 --- --- --- --- TMEM127 55654 broad.mit.edu 37 2 96919781 96919783 + In_Frame_Del DEL TGC TGC - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr2:96919781_96919783delTGC ENST00000258439.2 - 4 736_738 c.480_482delGCA c.(478-483)cat>ca p.QH160del TMEM127_ENST00000435268.1_In_Frame_Del_p.QH76del|TMEM127_ENST00000432959.1_In_Frame_Del_p.QH160del NM_001193304.2|NM_017849.3 NP_001180233.1|NP_060319.1 O75204 TM127_HUMAN transmembrane protein 127 160 negative regulation of cell proliferation|negative regulation of TOR signaling cascade cytoplasm|integral to membrane|plasma membrane endometrium(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1) 5 GTACTTCTTATGCTGCTGCTGCT 0.557 9 472 --- --- --- --- SLC20A1 6574 broad.mit.edu 37 2 113416607 113416608 + Frame_Shift_Del DEL AG AG - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f 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 7 411 --- --- --- --- FSIP2 401024 broad.mit.edu 37 2 186670480 186670480 + Frame_Shift_Del DEL A A - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr2:186670480delA ENST00000343098.5 + 17 16714 c.16714delA c.(16714-16716)aafs p.K5573fs FSIP2_ENST00000424728.1_Frame_Shift_Del_p.K5484fs NM_173651.2 NP_775922.2 fibrous sheath interacting protein 2 NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2) 69 CACATCAGTGAAAAAAGGTGA 0.363 7 375 --- --- --- --- IRS1 3667 broad.mit.edu 37 2 227660808 227660810 + In_Frame_Del DEL GCT GCT - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f 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 8 463 --- --- --- --- EFHD1 80303 broad.mit.edu 37 2 233546363 233546365 + In_Frame_Del DEL GGA GGA - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr2:233546363_233546365delGGA ENST00000264059.3 + 4 1131_1133 c.654_656delGGA c.(652-657)cgg>cg p.RE218del EFHD1_ENST00000409613.1_In_Frame_Del_p.RE122del|EFHD1_ENST00000410095.1_In_Frame_Del_p.RE106del|EFHD1_ENST00000409708.1_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 9 620 --- --- --- --- TMEM40 55287 broad.mit.edu 37 3 12790198 12790200 + In_Frame_Del DEL GAG GAG - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr3:12790198_12790200delGAG ENST00000314124.7 - 3 521_523 c.165_167delCTC c.(163-168)tct>tc p.SS69del TMEM40_ENST00000431022.2_In_Frame_Del_p.SS85del|TMEM40_ENST00000435575.1_Intron|TMEM40_ENST00000264728.8_In_Frame_Del_p.SS69del|TMEM40_ENST00000435218.2_In_Frame_Del_p.SS69del NM_018306.2 NP_060776.2 Q8WWA1 TMM40_HUMAN transmembrane protein 40 69 Ser-rich. integral to membrane breast(1)|large_intestine(3)|lung(5)|urinary_tract(1) 10 tgaggaggaagaggaggaggagg 0.419 15 1065 --- --- --- --- SATB1 6304 broad.mit.edu 37 3 18391133 18391135 + In_Frame_Del DEL CTG CTG - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr3:18391133_18391135delCTG ENST00000338745.6 - 11 3553_3555 c.1819_1821delCAG c.(1819-1821)del p.Q607del TBC1D5_ENST00000414318.2_Intron|SATB1_ENST00000454909.2_In_Frame_Del_p.Q607del|SATB1_ENST00000417717.2_In_Frame_Del_p.Q639del NM_002971.4 NP_002962.1 Q01826 SATB1_HUMAN SATB homeobox 1 607 Poly-Gln. cellular component disassembly involved in apoptosis|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter nuclear matrix|PML body double-stranded DNA binding|sequence-specific DNA binding NS(2)|breast(2)|endometrium(6)|large_intestine(4)|lung(10)|ovary(1)|skin(5)|upper_aerodigestive_tract(2) 32 GCGGCGGTGCctgctgctgctgc 0.606 7 181 --- --- --- --- SGOL1 151648 broad.mit.edu 37 3 20216050 20216050 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr3:20216050delT ENST00000412997.1 - 6 1324 c.973delA c.(973-975)tgfs p.M325fs SGOL1_ENST00000421451.1_Frame_Shift_Del_p.M325fs|SGOL1_ENST00000306698.2_Intron|SGOL1_ENST00000412868.1_Frame_Shift_Del_p.M325fs|SGOL1-AS1_ENST00000448208.1_RNA|SGOL1_ENST00000263753.4_Frame_Shift_Del_p.M325fs|SGOL1_ENST00000429446.3_Intron|SGOL1_ENST00000442720.1_Intron|SGOL1-AS1_ENST00000441442.1_RNA|SGOL1_ENST00000417364.1_Intron|SGOL1_ENST00000437051.1_Intron|SGOL1_ENST00000383774.1_Intron|SGOL1_ENST00000443724.1_Intron|SGOL1_ENST00000419233.2_Intron|SGOL1_ENST00000452020.1_Intron|SGOL1_ENST00000425061.1_Intron NM_001199251.1 NP_001186180.1 Q5FBB7 SGOL1_HUMAN shugoshin-like 1 (S. pombe) 325 attachment of spindle microtubules to kinetochore|cell division|centriole-centriole cohesion|meiotic chromosome segregation|mitotic prometaphase centrosome|condensed chromosome kinetochore|cytosol|mitotic cohesin complex|spindle pole protein binding kidney(1)|large_intestine(4)|lung(6)|skin(1)|urinary_tract(2) 14 GATTTGTGCATTTTTTTTTGG 0.318 10 185 --- --- --- --- CLASP2 23122 broad.mit.edu 37 3 33602361 33602361 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr3:33602361delT ENST00000399362.4 - 28 3243 c.2890delA c.(2890-2892)tgfs p.M964fs CLASP2_ENST00000539981.1_Frame_Shift_Del_p.M734fs|CLASP2_ENST00000461133.3_Frame_Shift_Del_p.M724fs|CLASP2_ENST00000468888.2_Frame_Shift_Del_p.M965fs|CLASP2_ENST00000307312.7_Frame_Shift_Del_p.M446fs|CLASP2_ENST00000480013.1_Frame_Shift_Del_p.M744fs|CLASP2_ENST00000359576.5_Frame_Shift_Del_p.M956fs 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 8 623 --- --- --- --- CDCP1 64866 broad.mit.edu 37 3 45127479 45127479 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr3:45127479delT ENST00000296129.1 - 9 2296 c.2162delA c.(2161-2163)agfs p.K721fs NM_022842.3 NP_073753.3 Q9H5V8 CDCP1_HUMAN CUB domain containing protein 1 721 extracellular region|integral to membrane|plasma membrane central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|skin(4)|urinary_tract(1) 29 BRCA - Breast invasive adenocarcinoma(193;0.00928)|KIRC - Kidney renal clear cell carcinoma(197;0.0519)|Kidney(197;0.0651) TTTCTGAAACTTTTTTGGCTG 0.468 8 1517 --- --- --- --- QRICH1 54870 broad.mit.edu 37 3 49094314 49094316 + In_Frame_Del DEL TGC TGC - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr3:49094314_49094316delTGC ENST00000395443.2 - 3 1789_1791 c.1317_1319delGCA c.(1315-1320)caa>ca p.QQ439del QRICH1_ENST00000357496.2_In_Frame_Del_p.QQ439del|QRICH1_ENST00000424300.1_In_Frame_Del_p.QQ439del|QRICH1_ENST00000479449.1_5'UTR NM_198880.1 NP_942581.1 Q2TAL8 QRIC1_HUMAN glutamine-rich 1 439 Gln-rich. breast(2)|endometrium(5)|large_intestine(8)|lung(8)|ovary(1)|skin(1) 25 BRCA - Breast invasive adenocarcinoma(193;8.88e-05)|Kidney(197;0.00239)|KIRC - Kidney renal clear cell carcinoma(197;0.00258) AACTTGGAgttgctgctgctgct 0.562 9 471 --- --- --- --- ERC2 26059 broad.mit.edu 37 3 55733470 55733472 + In_Frame_Del DEL TGG TGG - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr3:55733470_55733472delTGG ENST00000288221.6 - 16 3036_3038 c.2781_2783delCCA c.(2779-2784)cat>ca p.HH931del NM_015576.1 NP_056391.1 O15083 ERC2_HUMAN ELKS/RAB6-interacting/CAST family member 2 931 Poly-His. cell junction|cytoplasm|cytoskeleton|growth cone|presynaptic membrane|synaptosome protein binding breast(2)|endometrium(5)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|urinary_tract(1) 31 KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219) gtggtggtgatggtggtggtggt 0.502 10 1331 --- --- --- --- PDE12 201626 broad.mit.edu 37 3 57542768 57542770 + In_Frame_Del DEL CTT CTT - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr3:57542768_57542770delCTT ENST00000311180.8 + 1 765_767 c.662_664delCTT c.(661-666)cct>c p.PS221del PDE12_ENST00000487257.1_In_Frame_Del_p.PS221del NM_177966.5 NP_808881.3 Q6L8Q7 PDE12_HUMAN phosphodiesterase 12 221 hydrolase activity breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|liver(4)|lung(3)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1) 20 KIRC - Kidney renal clear cell carcinoma(284;0.011)|Kidney(284;0.0127) CCCTCCTCACCTTCTTCTTCTTG 0.616 8 1080 --- --- --- --- TMCC1 23023 broad.mit.edu 37 3 129370576 129370578 + In_Frame_Del DEL CTG CTG - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr3:129370576_129370578delCTG ENST00000393238.3 - 6 2048_2050 c.1708_1710delCAG c.(1708-1710)del p.Q570del TMCC1_ENST00000329333.5_In_Frame_Del_p.Q391del|TMCC1_ENST00000432054.2_In_Frame_Del_p.Q246del|TMCC1_ENST00000426664.2_In_Frame_Del_p.Q456del NM_001017395.3 NP_001017395.2 O94876 TMCC1_HUMAN transmembrane and coiled-coil domain family 1 570 integral to membrane PLXND1/TMCC1(4) breast(1)|endometrium(3)|large_intestine(8)|lung(12)|skin(1) 25 GCTGCACCACCTGCTGCTGCTGC 0.581 15 647 --- --- --- --- DBR1 51163 broad.mit.edu 37 3 137880741 137880743 + In_Frame_Del DEL TCG TCG - rs2622736 byFrequency TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f 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 8 596 --- --- --- --- RP11-167H9.4 0 broad.mit.edu 37 3 149769296 149769296 + RNA DEL C C - rs59377959 TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr3:149769296delC ENST00000487840.1 + 0 46 TTCCTGGTGTCtttttttttt 0.463 11 331 --- --- --- --- MED12L 116931 broad.mit.edu 37 3 150877786 150877786 + Frame_Shift_Del DEL C C - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr3:150877786delC ENST00000474524.1 + 7 1043 c.1005delC c.(1003-1005)ggfs p.G335fs MED12L_ENST00000273432.4_Intron|MED12L_ENST00000422248.2_Frame_Shift_Del_p.G335fs|MED12L_ENST00000309237.4_Frame_Shift_Del_p.G335fs NM_053002.4 NP_443728.3 Q86YW9 MD12L_HUMAN mediator complex subunit 12-like 335 regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent mediator complex NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1) 128 LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517) CCAGCCCTGGCCCCCCCGGCC 0.582 7 1018 --- --- --- --- PHC3 80012 broad.mit.edu 37 3 169896635 169896637 + In_Frame_Del DEL TGG TGG - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f 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_ENST00000495893.1_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 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 9 1362 --- --- --- --- FETUB 26998 broad.mit.edu 37 3 186362544 186362544 + Frame_Shift_Del DEL A A - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr3:186362544delA ENST00000265029.3 + 4 530 c.429delA c.(427-429)tcfs p.S143fs FETUB_ENST00000382134.3_Frame_Shift_Del_p.S78fs|RP11-134F2.2_ENST00000428501.1_RNA|FETUB_ENST00000488561.1_3'UTR|FETUB_ENST00000382136.3_Frame_Shift_Del_p.S106fs|FETUB_ENST00000539949.1_5'UTR|FETUB_ENST00000450521.1_Frame_Shift_Del_p.S143fs|RP11-134F2.2_ENST00000455926.1_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 8 590 --- --- --- --- EIF4A2 1974 broad.mit.edu 37 3 186505331 186505331 + Frame_Shift_Del DEL C C - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr3:186505331delC ENST00000323963.5 + 9 1021 c.957delC c.(955-957)ttfs p.F319fs EIF4A2_ENST00000356531.5_Frame_Shift_Del_p.F224fs|EIF4A2_ENST00000440191.2_Frame_Shift_Del_p.F320fs Q14240 IF4A2_HUMAN eukaryotic translation initiation factor 4A2 319 Helicase C-terminal. interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation cytosol|eukaryotic translation initiation factor 4F complex ATP binding|ATP-dependent helicase activity|protein binding|translation initiation factor activity breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|urinary_tract(1) 28 all_cancers(143;2.68e-12)|Ovarian(172;0.0339) OV - Ovarian serous cystadenocarcinoma(80;1.07e-20) GBM - Glioblastoma multiforme(93;0.0704) TGAGGGAATTCCGGTCAGGGT 0.403 T BCL6 NHL 11 759 --- --- --- --- PDE6B 5158 broad.mit.edu 37 4 661763 661765 + In_Frame_Del DEL AGG AGG - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f 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 8 934 --- --- --- --- OTOP1 133060 broad.mit.edu 37 4 4204225 4204229 + Frame_Shift_Del DEL TTGAG TTGAG - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr4:4204225_4204229delTTGAG ENST00000296358.4 - 4 700_704 c.676_680delCTCAA c.(676-681)tfs p.LN226fs NM_177998.1 NP_819056.1 Q7RTM1 OTOP1_HUMAN otopetrin 1 226 biomineral tissue development extracellular space|integral to membrane p.L226fs*1(1) NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1) 34 UCEC - Uterine corpus endometrioid carcinoma (64;0.168) CTTGTGCTCATTGAGTTGGTGCTTT 0.502 14 587 --- --- --- --- PROM1 8842 broad.mit.edu 37 4 15995680 15995680 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr4:15995680delT ENST00000505450.1 - 15 2282 c.1670delA c.(1669-1671)atfs p.N557fs PROM1_ENST00000539194.1_Frame_Shift_Del_p.N566fs|PROM1_ENST00000508167.1_Frame_Shift_Del_p.N557fs|PROM1_ENST00000510224.1_Frame_Shift_Del_p.N566fs|PROM1_ENST00000540805.1_Frame_Shift_Del_p.N566fs|PROM1_ENST00000543373.1_Frame_Shift_Del_p.N557fs|PROM1_ENST00000447510.2_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 10 441 --- --- --- --- KIAA1211 57482 broad.mit.edu 37 4 57179503 57179503 + Frame_Shift_Del DEL A A - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr4:57179503delA ENST00000504228.1 + 5 600 c.495delA c.(493-495)ccfs p.P165fs KIAA1211_ENST00000264229.6_Frame_Shift_Del_p.P165fs|KIAA1211_ENST00000541073.1_Frame_Shift_Del_p.P158fs Q6ZU35 K1211_HUMAN KIAA1211 165 endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1) 65 Glioma(25;0.08)|all_neural(26;0.101) CTGTTAAGCCAAAAAAACAGA 0.572 8 573 --- --- --- --- CDKL2 8999 broad.mit.edu 37 4 76539579 76539580 + Frame_Shift_Ins INS - - T TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr4:76539579_76539580insT ENST00000429927.2 - 3 925_926 c.222_223insA c.(220-225)aagatgfs p.M75fs CDKL2_ENST00000307465.4_Frame_Shift_Ins_p.M75fs NM_003948.3 NP_003939.1 Q92772 CDKL2_HUMAN cyclin-dependent kinase-like 2 (CDC2-related kinase) 75 Protein kinase. sex differentiation|signal transduction cytoplasm|nucleus ATP binding|cyclin-dependent protein kinase activity breast(3)|endometrium(1)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(2)|stomach(2) 22 Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122) AGGTACCATCGTTTTTTTTTCT 0.322 9 274 --- --- --- --- BMP2K 55589 broad.mit.edu 37 4 79792137 79792139 + In_Frame_Del DEL CAG CAG - rs17855588 TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr4:79792137_79792139delCAG ENST00000335016.5 + 11 1598_1600 c.1432_1434delCAG c.(1432-1434)del p.Q486del BMP2K_ENST00000502871.1_In_Frame_Del_p.Q486del 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 gcaacagcaacagcagcagcagc 0.498 7 334 --- --- --- --- NAP1L5 266812 broad.mit.edu 37 4 89618431 89618433 + In_Frame_Del DEL CCT CCT - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr4:89618431_89618433delCCT ENST00000323061.5 - 1 953_955 c.473_475delAGG c.(472-477)gct>g p.EA158del HERC3_ENST00000543130.1_Intron|HERC3_ENST00000264345.3_Intron|HERC3_ENST00000402738.1_Intron NM_153757.2 NP_715638.1 Q96NT1 NP1L5_HUMAN nucleosome assembly protein 1-like 5 158 Glu-rich. nucleosome assembly nucleus protein binding endometrium(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1) 7 OV - Ovarian serous cystadenocarcinoma(123;0.000181) TCTGCCGCAGcctcctcctcctc 0.626 9 847 --- --- --- --- CXXC4 80319 broad.mit.edu 37 4 105412094 105412096 + In_Frame_Del DEL GAG GAG - rs146939312 TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr4:105412094_105412096delGAG ENST00000394767.2 - 2 1314_1316 c.864_866delCTC c.(862-867)tcg>tc p.SS290del CXXC4_ENST00000466963.1_Intron|AC093628.1_ENST00000606234.1_RNA|CXXC4_ENST00000426831.1_In_Frame_Del_p.SS121del NM_025212.2 NP_079488.2 Q9H2H0 CXXC4_HUMAN CXXC finger protein 4 121 negative regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway|zygotic specification of dorsal/ventral axis DNA binding|PDZ domain binding|zinc ion binding p.S120A(1) kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 11 OV - Ovarian serous cystadenocarcinoma(123;3.05e-08) TGAGGAGGACGAGGAGGAGGAGG 0.606 7 487 --- --- --- --- CXXC4 80319 broad.mit.edu 37 4 105412465 105412467 + In_Frame_Del DEL GCC GCC - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr4:105412465_105412467delGCC ENST00000394767.2 - 2 943_945 c.493_495delGGC c.(493-495)del p.G165del AC004053.1_ENST00000500179.1_RNA|CXXC4_ENST00000466963.1_Intron|CXXC4_ENST00000426831.1_5'UTR NM_025212.2 NP_079488.2 Q9H2H0 CXXC4_HUMAN CXXC finger protein 4 0 Interaction with DVL1 (By similarity). negative regulation of Wnt receptor signaling pathway|Wnt receptor signaling pathway|zygotic specification of dorsal/ventral axis DNA binding|PDZ domain binding|zinc ion binding kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 11 OV - Ovarian serous cystadenocarcinoma(123;3.05e-08) TGGTCCTgctgccgccgccgccg 0.695 11 618 --- --- --- --- TET2 54790 broad.mit.edu 37 4 106155778 106155779 + Frame_Shift_Ins INS - - A TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr4:106155778_106155779insA ENST00000513237.1 + 3 1539_1540 c.742_743insA c.(742-744)aaafs p.K248fs TET2_ENST00000545826.1_Frame_Shift_Ins_p.K227fs|TET2_ENST00000380013.4_Frame_Shift_Ins_p.K227fs|TET2_ENST00000413648.2_Frame_Shift_Ins_p.K227fs|TET2_ENST00000394764.1_Frame_Shift_Ins_p.K227fs|TET2_ENST00000305737.2_Frame_Shift_Ins_p.K227fs|TET2_ENST00000540549.1_Frame_Shift_Ins_p.K227fs Q6N021 TET2_HUMAN tet methylcytosine dioxygenase 2 227 cell cycle|myeloid cell differentiation metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen p.E227*(1) NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2) 1314 Myeloproliferative disorder(5;0.0393) OV - Ovarian serous cystadenocarcinoma(123;7.18e-08) TGAACTCCTGGAAAAAACACTG 0.406 """Mis N, F""" MDS 9 289 --- --- --- --- FRG1 2483 broad.mit.edu 37 4 190873437 190873439 + In_Frame_Del DEL AAG AAG - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr4:190873437_190873439delAAG ENST00000226798.4 + 3 476_478 c.254_256delAAG c.(253-258)aaa>a p.KE85del FRG1_ENST00000514482.1_3'UTR NM_004477.2 NP_004468.1 Q14331 FRG1_HUMAN FSHD region gene 1 85 rRNA processing Cajal body|catalytic step 2 spliceosome|nuclear speck|nucleolus NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1) 32 all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147) all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161) GCTCCACACAAAGAAGGTTTGTG 0.414 11 696 --- --- --- --- MYO10 4651 broad.mit.edu 37 5 16694605 16694606 + Frame_Shift_Ins INS - - C TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr5:16694605_16694606insC ENST00000513610.1 - 27 4128_4129 c.3674_3675insG c.(3673-3675)gtcfs p.V1225fs MYO10_ENST00000505695.1_Frame_Shift_Ins_p.V564fs|MYO10_ENST00000515803.1_Frame_Shift_Ins_p.V564fs|MYO10_ENST00000274203.9_Frame_Shift_Ins_p.V582fs|MYO10_ENST00000427430.2_Frame_Shift_Ins_p.V582fs NM_012334.2 NP_036466.2 Q9HD67 MYO10_HUMAN myosin X 1225 PH 1. axon guidance|signal transduction myosin complex actin binding|ATP binding|motor activity p.S1226fs*25(1) NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 86 GCGTGGAGGAGCCCCCCCCTTT 0.564 7 866 --- --- --- --- PDZD2 23037 broad.mit.edu 37 5 32090059 32090061 + In_Frame_Del DEL TCC TCC - rs61744453 by1000genomes TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr5:32090059_32090061delTCC ENST00000438447.1 + 20 6893_6895 c.6505_6507delTCC c.(6505-6507)del p.S2173del PDZD2_ENST00000282493.3_In_Frame_Del_p.S2173del O15018 PDZD2_HUMAN PDZ domain containing 2 2173 Ser-rich. cell adhesion cell-cell junction|endoplasmic reticulum|extracellular region|nucleus NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1) 148 AAAACTGGCGTCCTCCTCCTCCT 0.527 12 822 --- --- --- --- FGF10 2255 broad.mit.edu 37 5 44388715 44388717 + In_Frame_Del DEL AGC AGC - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr5:44388715_44388717delAGC ENST00000264664.4 - 1 182_184 c.68_70delGCT c.(67-72)ttt>t p.CF23del NM_004465.1 NP_004456.1 O15520 FGF10_HUMAN fibroblast growth factor 10 23 actin cytoskeleton reorganization|activation of MAPK activity|bud outgrowth involved in lung branching|ERK1 and ERK2 cascade|fibroblast growth factor receptor signaling pathway involved in mammary gland specification|insulin receptor signaling pathway|lacrimal gland development|lung saccule development|mesonephros development|negative regulation of cell cycle arrest|positive regulation of ATPase activity|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of DNA repair|positive regulation of DNA replication|positive regulation of epithelial cell migration|positive regulation of epithelial cell proliferation involved in wound healing|positive regulation of ERK1 and ERK2 cascade|positive regulation of hair follicle cell proliferation|positive regulation of keratinocyte migration|positive regulation of keratinocyte proliferation|positive regulation of lymphocyte proliferation|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of Ras protein signal transduction|positive regulation of transcription, DNA-dependent|positive regulation of urothelial cell proliferation|protein localization at cell surface|radial glial cell differentiation|regulation of saliva secretion|response to protein stimulus|secretion by lung epithelial cell involved in lung growth|tear secretion|thymus development|urothelial cell proliferation cell surface|extracellular space|nucleus|plasma membrane chemoattractant activity|growth factor activity|heparin binding|type 2 fibroblast growth factor receptor binding haematopoietic_and_lymphoid_tissue(1)|lung(11)|skin(1) 13 Lung NSC(6;1.12e-06) AGCAACAAAAAGCAGCAGCAGCA 0.537 7 389 --- --- --- --- THBS4 7060 broad.mit.edu 37 5 79372774 79372776 + In_Frame_Del DEL TGA TGA - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f 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 1485 --- --- --- --- CSNK1G3 1456 broad.mit.edu 37 5 122881495 122881495 + Frame_Shift_Del DEL A A - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr5:122881495delA ENST00000395412.1 + 2 857 c.138delA c.(136-138)ggfs p.G46fs CSNK1G3_ENST00000345990.4_Frame_Shift_Del_p.G46fs|CSNK1G3_ENST00000521364.1_Frame_Shift_Del_p.G46fs|CSNK1G3_ENST00000361991.2_Frame_Shift_Del_p.G46fs|CSNK1G3_ENST00000360683.2_Frame_Shift_Del_p.G46fs|CSNK1G3_ENST00000510842.2_Frame_Shift_Del_p.G46fs|CSNK1G3_ENST00000395411.1_Frame_Shift_Del_p.G46fs|CSNK1G3_ENST00000511130.2_Intron|CSNK1G3_ENST00000508708.1_3'UTR|CSNK1G3_ENST00000512718.3_Intron NM_001044723.1 NP_001038188.1 Q9Y6M4 KC1G3_HUMAN casein kinase 1, gamma 3 46 Protein kinase. Wnt receptor signaling pathway cytoplasm ATP binding|protein serine/threonine kinase activity autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(3)|prostate(1)|skin(1) 15 all_cancers(142;0.0156)|Prostate(80;0.0322)|Lung NSC(810;0.245) KIRC - Kidney renal clear cell carcinoma(527;0.165)|Kidney(363;0.229) OV - Ovarian serous cystadenocarcinoma(64;0.000121)|Epithelial(69;0.000227)|all cancers(49;0.00176) TTAGAGTTGGAAAAAAAATTG 0.363 7 527 --- --- --- --- SLC22A4 6583 broad.mit.edu 37 5 131676327 131676327 + Frame_Shift_Del DEL T T - rs72552721 TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr5:131676327delT ENST00000200652.3 + 9 1688 c.1514delT c.(1513-1515)ctfs p.L505fs AC034220.3_ENST00000437091.1_RNA|AC034220.3_ENST00000417795.1_RNA NM_003059.2 NP_003050.2 Q9H015 S22A4_HUMAN solute carrier family 22 (organic cation/zwitterion transporter), member 4 505 body fluid secretion|sodium ion transport apical plasma membrane|integral to plasma membrane|mitochondrion ATP binding|carnitine transporter activity|cation:cation antiporter activity|PDZ domain binding|secondary active organic cation transmembrane transporter activity|symporter activity p.E509fs*1(1) endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|urinary_tract(1) 16 all_cancers(142;0.0752)|Breast(839;0.198) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) L-Carnitine(DB00583) ATCCTCACCCTTTTTTTCCCT 0.418 11 1005 --- --- --- --- IK 3550 broad.mit.edu 37 5 140032593 140032594 + Frame_Shift_Del DEL GA GA - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr5:140032593_140032594delGA ENST00000417647.2 + 5 407_408 c.268_269delGA c.(268-270)gfs p.E90fs IK_ENST00000523672.1_3'UTR NM_006083.3 NP_006074.2 Q13123 RED_HUMAN IK cytokine, down-regulator of HLA II 90 cell-cell signaling|immune response extracellular space|nucleus|soluble fraction large_intestine(1) 1 all_hematologic(541;4.8e-07)|all_lung(500;0.000434)|Lung NSC(810;0.00161)|Breast(839;0.128) KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) ACAAGAAATTGAGAGAGAGAGA 0.460 9 301 --- --- --- --- PPARGC1B 133522 broad.mit.edu 37 5 149216457 149216459 + In_Frame_Del DEL GGA GGA - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr5:149216457_149216459delGGA ENST00000309241.5 + 8 2471_2473 c.2439_2441delGGA c.(2437-2442)ggg>gg p.GE813del PPARGC1B_ENST00000360453.4_In_Frame_Del_p.GE774del|PPARGC1B_ENST00000403750.1_In_Frame_Del_p.GE749del|PPARGC1B_ENST00000394320.3_In_Frame_Del_p.GE813del NM_133263.3 NP_573570.3 Q86YN6 PRGC2_HUMAN peroxisome proliferator-activated receptor gamma, coactivator 1 beta 813 Glu-rich. estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter mediator complex AF-2 domain binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|nucleotide binding|receptor activator activity|RNA binding|RNA polymerase II transcription cofactor activity NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(2)|lung(15)|ovary(3)|prostate(2)|stomach(1) 30 KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147) aggaagaaggggaggaggaggag 0.606 11 680 --- --- --- --- BTN2A3P 0 broad.mit.edu 37 6 26422388 26422390 + RNA DEL CCT CCT - rs113134648 TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr6:26422388_26422390delCCT ENST00000466808.2 + 0 42_44 GGCCAGCCTCCCTCCTCCTCCTC 0.586 12 757 --- --- --- --- ABCF1 23 broad.mit.edu 37 6 30545662 30545664 + In_Frame_Del DEL AGC AGC - rs111358819 TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr6:30545662_30545664delAGC ENST00000326195.8 + 3 300_302 c.188_190delAGC c.(187-192)gag>g p.EQ63del ABCF1_ENST00000396515.4_In_Frame_Del_p.EQ63del|ABCF1_ENST00000376545.3_In_Frame_Del_p.EQ63del NM_001025091.1 NP_001020262.1 Q8NE71 ABCF1_HUMAN ATP-binding cassette, sub-family F (GCN20), member 1 63 inflammatory response|translational initiation nuclear envelope|nucleoplasm|polysomal ribosome ATP binding|ATPase activity|protein binding|ribosome binding|translation activator activity|translation factor activity, nucleic acid binding breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|skin(2) 21 AAGGAGAAGGagcagcagcagca 0.512 7 569 --- --- --- --- HLA-DRB6 0 broad.mit.edu 37 6 32522756 32522756 + RNA DEL A A - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr6:32522756delA ENST00000411500.1 - 0 458 NR_001298.1 GGACTAGGAGAAAAAAAGGTA 0.517 8 171 --- --- --- --- DAXX 1616 broad.mit.edu 37 6 33287898 33287900 + In_Frame_Del DEL TCC TCC - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr6:33287898_33287900delTCC ENST00000374542.5 - 5 1557_1559 c.1353_1355delGGA c.(1351-1356)gaa>ga p.EE455del DAXX_ENST00000266000.6_In_Frame_Del_p.EE455del|DAXX_ENST00000414083.2_In_Frame_Del_p.EE380del|DAXX_ENST00000477162.1_5'UTR NM_001141969.1|NM_001141970.1|NM_001350.4 NP_001135441.1|NP_001135442.1|NP_001341.1 Q9UER7 DAXX_HUMAN death-domain associated protein 455 Asp/Glu-rich (acidic).|Necessary for interaction with USP7. activation of JUN kinase activity|androgen receptor signaling pathway|apoptosis|induction of apoptosis via death domain receptors|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|regulation of protein ubiquitination|transcription, DNA-dependent chromosome, centromeric region|cytosol|nucleolus|PML body androgen receptor binding|heat shock protein binding|p53 binding|protein homodimerization activity|protein N-terminus binding|receptor signaling protein activity|transcription factor binding|ubiquitin protein ligase binding p.E451E(2) breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(2)|lung(7)|ovary(3)|pancreas(18)|prostate(3)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1) 55 ctcttcttcttcctcctcctcct 0.552 """Mis, F, N""" Pancreatic neuroendocrine tumors. Paediatric GBM 7 296 --- --- --- --- TULP1 7287 broad.mit.edu 37 6 35478775 35478777 + In_Frame_Del DEL TCC TCC - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr6:35478775_35478777delTCC ENST00000229771.6 - 5 439_441 c.360_362delGGA c.(358-363)gaa>ga p.EE122del TULP1_ENST00000322263.4_In_Frame_Del_p.EE69del NM_003322.3 NP_003313.3 O00294 TULP1_HUMAN tubby like protein 1 122 Poly-Glu. Missing (in RP14). dendrite development|eye photoreceptor cell development|phagocytosis|photoreceptor cell maintenance|positive regulation of phagocytosis cell junction|cytoplasm|extracellular region|photoreceptor inner segment|photoreceptor outer segment|synapse actin filament binding|phosphatidylinositol-4,5-bisphosphate binding central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1) 19 gtcctcctcttcctcctcctcct 0.567 8 709 --- --- --- --- TREML2 79865 broad.mit.edu 37 6 41168714 41168716 + In_Frame_Del DEL CAG CAG - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr6:41168714_41168716delCAG ENST00000483722.1 - 1 216_218 c.31_33delCTG c.(31-33)del p.L11del NM_024807.2 NP_079083.2 Q5T2D2 TRML2_HUMAN triggering receptor expressed on myeloid cells-like 2 11 T cell activation cell surface|integral to membrane|plasma membrane protein binding|receptor activity breast(1)|central_nervous_system(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1) 18 Ovarian(28;0.0418)|Colorectal(47;0.196) CCTGTGGCCACAGCAGCAGCAGC 0.631 12 233 --- --- --- --- SEC63 11231 broad.mit.edu 37 6 108214774 108214774 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr6:108214774delT ENST00000369002.4 - 16 1765 c.1586delA c.(1585-1587)agfs p.K530fs NM_007214.4 NP_009145.1 Q9UGP8 SEC63_HUMAN SEC63 homolog (S. cerevisiae) 530 SEC63 1. protein folding|protein targeting to membrane endoplasmic reticulum membrane|integral to membrane heat shock protein binding|receptor activity|unfolded protein binding p.K529fs*4(1) endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 36 all_cancers(87;5.35e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0294) BRCA - Breast invasive adenocarcinoma(108;0.0079)|Epithelial(106;0.0356)|all cancers(137;0.0525)|OV - Ovarian serous cystadenocarcinoma(136;0.054) TAAAGGTTTCTTTTTTTTTGA 0.368 22 651 --- --- --- --- ZBTB24 9841 broad.mit.edu 37 6 109802729 109802729 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr6:109802729delT ENST00000230122.3 - 2 668 c.501delA c.(499-501)aafs p.K167fs NM_001164313.1|NM_014797.2 NP_001157785.1|NP_055612.2 O43167 ZBT24_HUMAN zinc finger and BTB domain containing 24 167 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|protein binding|zinc ion binding breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1) 22 all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149) Epithelial(106;0.0154)|all cancers(137;0.0216)|OV - Ovarian serous cystadenocarcinoma(136;0.0242)|BRCA - Breast invasive adenocarcinoma(108;0.059) ATGTATTGACTTTTTTTGGTC 0.418 7 1164 --- --- --- --- ARHGAP18 93663 broad.mit.edu 37 6 129959602 129959603 + Frame_Shift_Ins INS - - T TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr6:129959602_129959603insT ENST00000368149.2 - 3 576_577 c.488_489insA c.(487-489)aaafs p.K163fs NM_033515.2 NP_277050.2 Q8N392 RHG18_HUMAN Rho GTPase activating protein 18 163 regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction cytosol GTPase activator activity|protein binding NS(2)|endometrium(1)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(3) 18 OV - Ovarian serous cystadenocarcinoma(136;0.0621)|GBM - Glioblastoma multiforme(226;0.0638)|all cancers(137;0.074) GGTACTGTTTGTTTTTTTTCCT 0.421 9 1075 --- --- --- --- EPB41L2 2037 broad.mit.edu 37 6 131191073 131191075 + In_Frame_Del DEL CTG CTG - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr6:131191073_131191075delCTG ENST00000337057.3 - 15 2416_2418 c.2235_2237delCAG c.(2233-2238)agt>ag p.SS745del EPB41L2_ENST00000524581.1_In_Frame_Del_p.SS123del|EPB41L2_ENST00000525271.1_Intron|EPB41L2_ENST00000445890.2_Intron|EPB41L2_ENST00000530481.1_In_Frame_Del_p.SS675del|EPB41L2_ENST00000525193.1_Intron|EPB41L2_ENST00000529208.1_In_Frame_Del_p.SS675del|EPB41L2_ENST00000531410.1_Intron|EPB41L2_ENST00000530757.1_Intron|EPB41L2_ENST00000368128.2_In_Frame_Del_p.SS745del|EPB41L2_ENST00000528282.1_Intron|EPB41L2_ENST00000527659.1_In_Frame_Del_p.SS675del|EPB41L2_ENST00000527411.1_In_Frame_Del_p.SS675del|EPB41L2_ENST00000392427.3_Intron NM_001431.3 NP_001422.1 O43491 E41L2_HUMAN erythrocyte membrane protein band 4.1-like 2 745 cortical actin cytoskeleton organization extrinsic to membrane|plasma membrane|spectrin actin binding|structural molecule activity autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(23)|prostate(1)|skin(2) 44 Breast(56;0.0639) OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355) CTCACTCTCACTGCTGCTGCTGC 0.562 9 638 --- --- --- --- CPVL 54504 broad.mit.edu 37 7 29070261 29070262 + Frame_Shift_Ins INS - - T rs5883182 TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr7:29070261_29070262insT ENST00000409850.1 - 16 1897_1898 c.1251_1252insA c.(1249-1254)aatttgfs p.NL417fs CPVL_ENST00000396276.3_Frame_Shift_Ins_p.NL417fs|CPVL_ENST00000265394.5_Frame_Shift_Ins_p.NL417fs Q9H3G5 CPVL_HUMAN carboxypeptidase, vitellogenic-like 417 proteolysis protein binding|serine-type carboxypeptidase activity p.V418fs*24(1) NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(1) 28 ATCTTCCAAACTTTTTTTTCTG 0.510 7 849 --- --- --- --- BBS9 27241 broad.mit.edu 37 7 33312723 33312723 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr7:33312723delT ENST00000242067.6 + 8 1323 c.802delT c.(802-804)ttfs p.F269fs BBS9_ENST00000396127.2_Frame_Shift_Del_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 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 7 790 --- --- --- --- TRGC1 0 broad.mit.edu 37 7 38301855 38301856 + RNA DEL GT GT - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr7:38301855_38301856delGT ENST00000443402.2 - 0 330 NM_001003799.1|NM_001003806.1 NP_001003799.1|NP_001003806.1 TCAATTGTTCGTGTGTGTGTGT 0.356 9 500 --- --- --- --- POU6F2 11281 broad.mit.edu 37 7 39379288 39379290 + In_Frame_Del DEL CAG CAG - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f 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 8 168 --- --- --- --- INTS4L2 0 broad.mit.edu 37 7 65150713 65150714 + RNA INS - - A TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr7:65150713_65150714insA ENST00000430126.2 + 0 694_695 CATACCATGAGAAAATCTCTAA 0.436 7 239 --- --- --- --- CCT6P1 0 broad.mit.edu 37 7 65226569 65226569 + RNA DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr7:65226569delT ENST00000442266.1 + 0 1167 gcccggccCCttttttttttt 0.413 9 23 --- --- --- --- AUTS2 26053 broad.mit.edu 37 7 70255577 70255579 + In_Frame_Del DEL CCA CCA - rs35604576 TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr7:70255577_70255579delCCA ENST00000342771.4 + 19 3696_3698 c.3375_3377delCCA c.(3373-3378)agc>ag p.SH1125del AUTS2_ENST00000406775.2_In_Frame_Del_p.SH1101del NM_015570.2 NP_056385.1 Q8WXX7 AUTS2_HUMAN autism susceptibility candidate 2 1125 His-rich. breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1) 50 all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093) LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186) ACGACTACAGccaccaccaccac 0.680 8 117 --- --- --- --- PHTF2 57157 broad.mit.edu 37 7 77569580 77569581 + Frame_Shift_Ins INS - - T TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr7:77569580_77569581insT ENST00000416283.2 + 12 1725_1726 c.1599_1600insT c.(1597-1602)ttttttfs p.FF533fs PHTF2_ENST00000248550.7_Frame_Shift_Ins_p.FF567fs|PHTF2_ENST00000307305.8_Frame_Shift_Ins_p.FF529fs|PHTF2_ENST00000422959.2_Frame_Shift_Ins_p.FF533fs|PHTF2_ENST00000424760.1_Frame_Shift_Ins_p.FF529fs|PHTF2_ENST00000275575.7_Frame_Shift_Ins_p.FF529fs NM_001127357.1|NM_020432.4 NP_001120829.1|NP_065165.3 Q8N3S3 PHTF2_HUMAN putative homeodomain transcription factor 2 567 regulation of transcription, DNA-dependent|transcription, DNA-dependent endoplasmic reticulum|nucleus DNA binding endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1) 19 TGTGGATTTTCTTTTTTTTGCT 0.307 8 483 --- --- --- --- CYP51A1 1595 broad.mit.edu 37 7 91752494 91752494 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr7:91752494delT ENST00000003100.8 - 7 1191 c.1026delA c.(1024-1026)aafs p.K342fs CYP51A1_ENST00000450723.1_Frame_Shift_Del_p.K237fs|LRRD1_ENST00000422722.1_5'UTR NM_000786.3 NP_000777.1 Q16850 CP51A_HUMAN cytochrome P450, family 51, subfamily A, polypeptide 1 336 cholesterol biosynthetic process|xenobiotic metabolic process endoplasmic reticulum membrane|integral to membrane|microsome electron carrier activity|heme binding|sterol 14-demethylase activity endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|skin(1) 10 all_cancers(62;2.16e-09)|all_epithelial(64;3.86e-08)|Breast(17;0.00206)|all_lung(186;0.169)|all_hematologic(106;0.215)|Lung NSC(181;0.227) STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225) Fluconazole(DB00196)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Miconazole(DB01110)|Terconazole(DB00251) CTAAATAACATTTTTTTTGAA 0.398 7 754 --- --- --- --- PTCD1 26024 broad.mit.edu 37 7 99032605 99032607 + In_Frame_Del DEL CTC CTC - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr7:99032605_99032607delCTC ENST00000292478.4 - 2 509_511 c.259_261delGAG c.(259-261)del p.E87del PTCD1_ENST00000485746.1_5'UTR|PTCD1_ENST00000555673.1_In_Frame_Del_p.E136del|ATP5J2-PTCD1_ENST00000413834.1_In_Frame_Del_p.E136del NM_015545.3 NP_056360.2 pentatricopeptide repeat domain 1 p.E87K(1) endometrium(5)|large_intestine(3)|lung(16)|ovary(2)|skin(1) 27 all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166) STAD - Stomach adenocarcinoma(171;0.215) TCCCAAAACTCTCCTCCTCCTCC 0.606 9 869 --- --- --- --- AZGP1P1 0 broad.mit.edu 37 7 99578706 99578706 + RNA DEL A A - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr7:99578706delA ENST00000425474.1 + 0 87 NR_036679.1 cttagtttacagtgaaaacaa 0.522 10 40 --- --- --- --- CNPY4 245812 broad.mit.edu 37 7 99717402 99717402 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr7:99717402delT ENST00000262932.3 + 1 167 c.35delT c.(34-36)ctfs p.L12fs TAF6_ENST00000437822.2_5'UTR|RP11-506M12.1_ENST00000494221.1_RNA NM_152755.1 NP_689968.1 Q8N129 CNPY4_HUMAN canopy FGF signaling regulator 4 12 extracellular region breast(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1) 7 Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439) TTGCTTTTCCTTTTTTTGGCC 0.527 7 285 --- --- --- --- MEPCE 56257 broad.mit.edu 37 7 100028823 100028825 + In_Frame_Del DEL CCA CCA - rs71555278 TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f 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 8 463 --- --- --- --- SRRT 51593 broad.mit.edu 37 7 100482040 100482042 + In_Frame_Del DEL AGG AGG - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr7:100482040_100482042delAGG ENST00000388793.4 + 7 1029_1031 c.809_811delAGG c.(808-813)cag>c p.QE270del SRRT_ENST00000432932.1_In_Frame_Del_p.QE270del|SRRT_ENST00000347433.4_In_Frame_Del_p.QE270del|SRRT_ENST00000457580.2_In_Frame_Del_p.QE270del NM_001128852.1|NM_015908.5 NP_001122324.1|NP_056992.4 Q9BXP5 SRRT_HUMAN serrate RNA effector molecule homolog (Arabidopsis) 270 Glu-rich. cell proliferation|primary miRNA processing|response to arsenic-containing substance cytoplasm|nucleoplasm protein binding breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1) 40 ATCCTGGAGCAGGAGGAGGAGGA 0.596 8 192 --- --- --- --- PUS7 54517 broad.mit.edu 37 7 105122888 105122888 + Splice_Site DEL C C - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr7:105122888delC ENST00000356362.2 - 8 1135 c.e8-1 PUS7_ENST00000469408.1_Splice_Site NM_019042.3 NP_061915.2 Q96PZ0 PUS7_HUMAN pseudouridylate synthase 7 homolog (S. cerevisiae) pseudouridine synthesis|tRNA processing pseudouridine synthase activity|RNA binding breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(8)|pancreas(1)|skin(1) 23 TGCAGTTATTCTTTaaaaaaa 0.348 9 523 --- --- --- --- TRBV7-8 0 broad.mit.edu 37 7 142099805 142099806 + RNA DEL AC AC - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr7:142099805_142099806delAC ENST00000390359.3 - 0 88 TAGTCATcatacacacacacac 0.441 16 307 --- --- --- --- NUGGC 389643 broad.mit.edu 37 8 27888776 27888776 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr8:27888776delT ENST00000413272.2 - 15 2034 c.1892delA c.(1891-1893)atfs p.N631fs NUGGC_ENST00000341513.6_Frame_Shift_Del_p.N631fs NM_001010906.1 NP_001010906.1 nuclear GTPase, germinal center associated GATCAGGAAATTTTTTTTGCA 0.453 7 885 --- --- --- --- KAT6A 7994 broad.mit.edu 37 8 41798420 41798422 + In_Frame_Del DEL CTC CTC - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr8:41798420_41798422delCTC ENST00000396930.3 - 16 3520_3522 c.2977_2979delGAG c.(2977-2979)del p.E993del KAT6A_ENST00000265713.2_In_Frame_Del_p.E993del|KAT6A_ENST00000406337.1_In_Frame_Del_p.E993del NM_001099412.1 NP_001092882.1 Q92794 MYST3_HUMAN K(lysine) acetyltransferase 6A 993 Poly-Glu. histone H3 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent MOZ/MORF histone acetyltransferase complex|nucleosome DNA binding|histone acetyltransferase activity|transcription coactivator activity|transcription factor binding|zinc ion binding GGCTTTCCGGCTCCTCCTCCTCC 0.567 14 1043 --- --- --- --- TERF1 7013 broad.mit.edu 37 8 73921284 73921286 + In_Frame_Del DEL GAG GAG - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr8:73921284_73921286delGAG ENST00000276602.6 + 1 186_188 c.163_165delGAG c.(163-165)del p.E62del TERF1_ENST00000276603.5_In_Frame_Del_p.E62del NM_003218.3 NP_003209.2 P54274 TERF1_HUMAN telomeric repeat binding factor (NIMA-interacting) 1 62 Asp/Glu-rich (acidic).|Poly-Glu.|TRFH dimerization. age-dependent telomere shortening|cell division|G2/M transition of mitotic cell cycle|induction of apoptosis|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of telomere maintenance via semi-conservative replication|negative regulation of telomere maintenance via telomerase|positive regulation of microtubule polymerization|positive regulation of mitosis|positive regulation of mitotic cell cycle|protein homooligomerization|regulation of transcription, DNA-dependent|telomere maintenance via telomerase|telomere maintenance via telomere shortening chromosome, telomeric region|cytoplasm|nuclear telomere cap complex|nucleoplasm|nucleus|spindle caspase activator activity|DNA bending activity|double-stranded telomeric DNA binding|identical protein binding|microtubule binding|protein heterodimerization activity|protein homodimerization activity|telomerase inhibitor activity|telomeric DNA binding central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1) 9 Breast(64;0.218) Epithelial(68;0.0984) GGGGGCCCCCgaggaggaggagg 0.650 7 134 --- --- --- --- DPYS 1807 broad.mit.edu 37 8 105440214 105440214 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr8:105440214delT ENST00000351513.2 - 6 1218 c.1086delA c.(1084-1086)aafs p.K362fs NM_001385.2 NP_001376.1 Q14117 DPYS_HUMAN dihydropyrimidinase 362 protein homotetramerization|pyrimidine nucleoside catabolic process|thymine catabolic process|uracil catabolic process cytosol dihydropyrimidinase activity|zinc ion binding NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 41 OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229) CCACCACGCCTTTTTCCCATA 0.478 8 1384 --- --- --- --- RANBP6 26953 broad.mit.edu 37 9 6012690 6012690 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f 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 11 327 --- --- --- --- HRCT1 646962 broad.mit.edu 37 9 35906348 35906350 + In_Frame_Del DEL CTG CTG - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f 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 9 147 --- --- --- --- ANKRD19P 0 broad.mit.edu 37 9 95599088 95599089 + RNA DEL CA CA - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr9:95599088_95599089delCA ENST00000473204.1 + 0 1169_1170 TTCACGGGCGCACACACACACA 0.421 10 314 --- --- --- --- FOXE1 2304 broad.mit.edu 37 9 100616701 100616706 + In_Frame_Del DEL GCCGCC GCCGCC - rs11279082 TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr9:100616701_100616706delGCCGCC ENST00000375123.3 + 1 1166_1171 c.505_510delGCCGCC c.(505-510)del p.AA177del NM_004473.3 NP_004464.2 O00358 FOXE1_HUMAN forkhead box E1 (thyroid transcription factor 2) 177 Ala-rich.|Poly-Ala. cell migration|embryonic organ morphogenesis|hair follicle morphogenesis|hard palate development|lens morphogenesis in camera-type eye|negative regulation of transcription from RNA polymerase II promoter|pattern specification process|peripheral nervous system development|pharynx development|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|soft palate development|thymus development|thyroid gland development|thyroid hormone generation transcription factor complex DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding central_nervous_system(1)|endometrium(1)|lung(2)|upper_aerodigestive_tract(1) 5 Acute lymphoblastic leukemia(62;0.158) Ggctgccgcagccgccgccgccgccg 0.767 7 49 --- --- --- --- RABL6 55684 broad.mit.edu 37 9 139734633 139734635 + In_Frame_Del DEL AGA AGA - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr9:139734633_139734635delAGA ENST00000371675.3 + 14 2498_2500 c.1613_1615delAGA c.(1612-1617)gag>g p.EK538del RABL6_ENST00000311502.7_In_Frame_Del_p.EK653del|RABL6_ENST00000432842.2_3'UTR|RABL6_ENST00000371663.4_In_Frame_Del_p.EK654del|RABL6_ENST00000357466.2_Intron RAB, member RAS oncogene family-like 6 CCCTCTaaggagaagaagaagaa 0.571 8 339 --- --- --- --- AGAP4 119016 broad.mit.edu 37 10 46342668 46342688 + In_Frame_Del DEL GCTCCTGCCATCCTGTCCCCA GCTCCTGCCATCCTGTCCCCA - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr10:46342668_46342688delGCTCCTGCCATCCTGTCCCCA ENST00000448048.2 - 1 233_253 c.108_128delTGGGGACAGGATGGCAGGAGC c.(106-129)gcg>gc p.AGDRMAGA36del AGAP4_ENST00000430779.2_5'UTR NM_133446.2 NP_597703.2 Q96P64 AGAP4_HUMAN ArfGAP with GTPase domain, ankyrin repeat and PH domain 4 36 regulation of ARF GTPase activity ARF GTPase activator activity|zinc ion binding p.G37_A43delGDRMAGA(1) central_nervous_system(1)|lung(1)|ovary(1) 3 AGCCATGGGCGCTCCTGCCATCCTGTCCCCAGCTCCTGCCT 0.588 7 75 --- --- --- --- ANK3 288 broad.mit.edu 37 10 61828745 61828747 + In_Frame_Del DEL GTG GTG - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr10:61828745_61828747delGTG ENST00000280772.1 - 37 12083_12085 c.11892_11894delCAC c.(11890-11895)act>ac p.TT3964del ANK3_ENST00000373827.2_Intron|ANK3_ENST00000355288.2_Intron|ANK3_ENST00000503366.1_Intron NM_020987.3 NP_066267.2 Q12955 ANK3_HUMAN ankyrin 3, node of Ranvier (ankyrin G) 3964 Thr-rich. establishment of protein localization|signal transduction basolateral plasma membrane|cytoplasm|cytoskeleton protein binding NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7) 196 ggtggtggcagtggtggtggtgg 0.498 9 787 --- --- --- --- PLAU 5328 broad.mit.edu 37 10 75673298 75673298 + Splice_Site DEL A A - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr10:75673298delA ENST00000446342.1 + 6 893 c.409_splice c.e6-1 p.G137_splice PLAU_ENST00000372764.3_Splice_Site_p.G154_splice|PLAU_ENST00000372762.4_Splice_Site_p.G118_splice|C10orf55_ENST00000412307.2_Intron|PLAU_ENST00000494287.1_3'UTR|C10orf55_ENST00000409178.1_Intron NM_001145031.1 NP_001138503.1 P00749 UROK_HUMAN plasminogen activator, urokinase 154 Kringle. blood coagulation|chemotaxis|fibrinolysis|proteolysis|regulation of cell adhesion mediated by integrin|regulation of receptor activity|regulation of smooth muscle cell migration|regulation of smooth muscle cell-matrix adhesion|signal transduction cell surface|extracellular space|plasma membrane serine-type endopeptidase activity cervix(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(3)|ovary(2) 16 Prostate(51;0.0112) Amiloride(DB00594)|Urokinase(DB00013) GTCCTCCAGGAAAAAAGCCCT 0.517 7 2182 --- --- --- --- PANK1 53354 broad.mit.edu 37 10 91359120 91359120 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr10:91359120delT ENST00000307534.4 - 3 1354 c.1199delA c.(1198-1200)agfs p.K400fs PANK1_ENST00000371774.2_Frame_Shift_Del_p.K202fs|PANK1_ENST00000342512.3_Frame_Shift_Del_p.K175fs|PANK1_ENST00000322191.6_Frame_Shift_Del_p.K175fs NM_148977.2 NP_683878.1 Q8TE04 PANK1_HUMAN pantothenate kinase 1 400 coenzyme A biosynthetic process|pantothenate metabolic process cytosol|nucleus ATP binding|pantothenate kinase activity cervix(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2) 11 Bezafibrate(DB01393) GCAGTACGGCTTTTTTTGACA 0.438 7 1025 --- --- --- --- TNKS2 80351 broad.mit.edu 37 10 93601945 93601946 + Frame_Shift_Ins INS - - A TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr10:93601945_93601946insA ENST00000371627.4 + 16 2235_2236 c.1856_1857insA c.(1855-1857)aaafs p.K619fs NM_025235.3 NP_079511.1 Q9H2K2 TNKS2_HUMAN tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2 619 positive regulation of canonical Wnt receptor signaling pathway|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein polyubiquitination|Wnt receptor signaling pathway Golgi membrane|microsome|nuclear envelope|pericentriolar material|perinuclear region of cytoplasm NAD+ ADP-ribosyltransferase activity|protein binding p.N622fs*29(1) biliary_tract(1)|breast(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1) 48 Colorectal(252;0.162) GCAGACCCTACAAAAAAAAACA 0.391 7 239 --- --- --- --- TSPAN4 0 broad.mit.edu 37 11 864443 864445 + In_Frame_Del DEL CTG CTG - rs61867552 byFrequency TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr11:864443_864445delCTG ENST00000397404.1 + 5 521_523 c.262_264delCTG c.(262-264)del p.L92del TSPAN4_ENST00000525201.1_In_Frame_Del_p.L28del|TSPAN4_ENST00000397406.1_In_Frame_Del_p.L92del|TSPAN4_ENST00000409531.1_In_Frame_Del_p.L111del|TSPAN4_ENST00000397396.1_In_Frame_Del_p.L28del|TSPAN4_ENST00000346501.4_In_Frame_Del_p.L92del|TSPAN4_ENST00000409543.2_In_Frame_Del_p.L92del|TSPAN4_ENST00000397397.2_In_Frame_Del_p.L92del|TSPAN4_ENST00000397408.1_In_Frame_Del_p.L92del|TSPAN4_ENST00000397411.2_In_Frame_Del_p.L92del NM_001025237.1 NP_001020408.1 O14817 TSN4_HUMAN tetraspanin 4 92 protein complex assembly integral to plasma membrane breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1) 3 all_cancers(49;2.64e-08)|all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)|all_lung(207;0.24) all cancers(45;4.32e-25)|Epithelial(43;3.29e-24)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703) ACAGTTCTTCCTGCTGCTGCTGC 0.650 8 805 --- --- --- --- UBQLN3 50613 broad.mit.edu 37 11 5529918 5529920 + In_Frame_Del DEL TGG TGG - rs2234451 byFrequency TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr11:5529918_5529920delTGG ENST00000311659.4 - 2 1016_1018 c.869_871delCCA c.(868-873)agc>a p.TS290del HBG2_ENST00000380259.2_Intron NM_017481.2 NP_059509.1 Q9H347 UBQL3_HUMAN ubiquilin 3 290 T -> S (in dbSNP:rs2234451). NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|prostate(1)|skin(2) 39 Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212) Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135) GAAGGTTGGCTGGTGGTGGTGGT 0.537 8 721 --- --- --- --- APBB1 322 broad.mit.edu 37 11 6432090 6432092 + In_Frame_Del DEL TCC TCC - rs145320037 TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr11:6432090_6432092delTCC ENST00000389906.2 - 2 585_587 c.486_488delGGA c.(484-489)gat>ga p.ED162del APBB1_ENST00000533407.1_Intron|APBB1_ENST00000311051.3_In_Frame_Del_p.ED162del|APBB1_ENST00000299402.6_In_Frame_Del_p.ED162del NM_001257325.1 NP_001244254.1 O00213 APBB1_HUMAN amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65) 162 Glu-rich. apoptosis|axonogenesis|cell cycle arrest|histone H4 acetylation|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of thymidylate synthase biosynthetic process|positive regulation of apoptosis|positive regulation of transcription, DNA-dependent|response to DNA damage stimulus|signal transduction|transcription, DNA-dependent cytoplasm|growth cone|lamellipodium|nucleus|plasma membrane|synapse beta-amyloid binding|chromatin binding|histone binding|proline-rich region binding|transcription factor binding p.E162D(1) breast(4)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|prostate(2)|skin(1)|urinary_tract(1) 24 Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029) Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194) atcatcatcatcctcctcctcct 0.635 20 366 --- --- --- --- OR10A5 144124 broad.mit.edu 37 11 6867223 6867225 + In_Frame_Del DEL TTC TTC - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr11:6867223_6867225delTTC ENST00000299454.4 + 1 341_343 c.310_312delTTC c.(310-312)del p.F108del OR10A5_ENST00000379831.2_In_Frame_Del_p.F112del Q9H207 O10A5_HUMAN olfactory receptor, family 10, subfamily A, member 5 108 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(1)|skin(2)|urinary_tract(2) 21 Medulloblastoma(188;0.0523)|all_neural(188;0.236) Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129) TCAGATGTATTTCTTCTTCTTCT 0.517 7 743 --- --- --- --- FADS2 9415 broad.mit.edu 37 11 61607885 61607887 + In_Frame_Del DEL TCC TCC - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr11:61607885_61607887delTCC ENST00000278840.4 + 3 1028_1030 c.398_400delTCC c.(397-402)ttc>t p.FL133del FADS2_ENST00000521849.1_In_Frame_Del_p.FL133del|FADS2_ENST00000522056.1_In_Frame_Del_p.FL102del|FADS2_ENST00000257261.6_In_Frame_Del_p.FL111del NM_004265.2 NP_004256.1 O95864 FADS2_HUMAN fatty acid desaturase 2 133 electron transport chain|transport|unsaturated fatty acid biosynthetic process endoplasmic reticulum membrane|integral to plasma membrane|membrane fraction heme binding breast(2)|kidney(2)|large_intestine(4)|liver(1)|lung(2)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1) 20 Alpha-Linolenic Acid(DB00132) CACGTGTTCTTCCTCCTCCTCCT 0.537 7 1053 --- --- --- --- VEGFB 7423 broad.mit.edu 37 11 64004663 64004663 + Frame_Shift_Del DEL A A - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr11:64004663delA ENST00000309422.2 + 5 675 c.379delA c.(379-381)aafs p.K129fs VEGFB_ENST00000426086.2_Frame_Shift_Del_p.K129fs NM_001243733.1|NM_003377.4 NP_001230662.1|NP_003368.1 P49765 VEGFB_HUMAN vascular endothelial growth factor B 129 anti-apoptosis|induction of positive chemotaxis|negative regulation of gene expression|negative regulation of neuron apoptosis|platelet activation|platelet degranulation|positive regulation of cell division|positive regulation of endothelial cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of mast cell chemotaxis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of protein kinase B signaling cascade|positive regulation of vascular endothelial growth factor receptor signaling pathway|positive regulation of vascular wound healing|vascular endothelial growth factor receptor signaling pathway extracellular region|extracellular space|membrane|platelet alpha granule lumen chemoattractant activity|growth factor activity|heparin binding|vascular endothelial growth factor receptor 1 binding p.K129fs*5(2) endometrium(2)|large_intestine(2)|prostate(1)|stomach(1) 6 TTTCAGACCTAAAAAAAAGGA 0.473 8 561 --- --- --- --- PAK1 5058 broad.mit.edu 37 11 77069990 77069992 + In_Frame_Del DEL CAT CAT - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr11:77069990_77069992delCAT ENST00000356341.3 - 6 1079_1081 c.548_550delATG c.(547-552)gct>g p.DA183del PAK1_ENST00000278568.4_In_Frame_Del_p.DA183del|PAK1_ENST00000525542.1_5'UTR|PAK1_ENST00000528203.1_In_Frame_Del_p.DA85del|PAK1_ENST00000530617.1_In_Frame_Del_p.DA183del NM_002576.4 NP_002567.3 Q13153 PAK1_HUMAN p21 protein (Cdc42/Rac)-activated kinase 1 183 Interaction with CRIPAK. apoptosis|axon guidance|cytoskeleton organization|ER-nucleus signaling pathway|positive regulation of JUN kinase activity|positive regulation of peptidyl-serine phosphorylation|protein autophosphorylation|T cell costimulation|T cell receptor signaling pathway cytosol|focal adhesion|Golgi apparatus ATP binding|collagen binding|protein binding|protein serine/threonine kinase activity NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(13)|skin(2)|stomach(1) 29 all_cancers(14;1.75e-18) GGTGGGGTAGcatcatcatcatc 0.478 16 688 --- --- --- --- SIK3 23387 broad.mit.edu 37 11 116729011 116729013 + In_Frame_Del DEL TGT TGT - rs539858 byFrequency TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr11:116729011_116729013delTGT ENST00000375300.1 - 20 3029_3031 c.3024_3026delACA c.(3022-3027)cag>ca p.QQ1012del SIK3_ENST00000446921.2_In_Frame_Del_p.QQ952del|SIK3_ENST00000292055.4_In_Frame_Del_p.QQ954del|SIK3_ENST00000488337.1_5'UTR|SIK3_ENST00000434315.2_In_Frame_Del_p.QQ793del|SIK3_ENST00000542607.1_In_Frame_Del_p.QQ894del|SIK3_ENST00000375288.1_In_Frame_Del_p.QQ289del Q9Y2K2 SIK3_HUMAN SIK family kinase 3 954 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 ctgttgctgctgttgctgctgct 0.596 10 270 --- --- --- --- IFT46 56912 broad.mit.edu 37 11 118427683 118427685 + In_Frame_Del DEL ATC ATC - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr11:118427683_118427685delATC ENST00000264020.2 - 5 651_653 c.274_276delGAT c.(274-276)del p.D92del IFT46_ENST00000530872.1_In_Frame_Del_p.D92del|IFT46_ENST00000264021.3_In_Frame_Del_p.D41del NM_020153.3 NP_064538.3 Q9NQC8 IFT46_HUMAN intraflagellar transport 46 homolog (Chlamydomonas) 41 flagellum assembly|intraflagellar transport|protein stabilization microtubule basal body|microtubule-based flagellum|nucleus protein C-terminus binding central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4) 9 TTTCAGATGAatcatcatcatca 0.478 8 452 --- --- --- --- USP2-AS1 0 broad.mit.edu 37 11 119274142 119274142 + RNA DEL T T - rs66493459 TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr11:119274142delT ENST00000498979.2 + 0 273 USP2-AS1_ENST00000500970.1_RNA|USP2-AS1_ENST00000578923.1_RNA|USP2-AS1_ENST00000577297.1_RNA|USP2-AS1_ENST00000530002.1_RNA NR_034160.1 AGTGTTTAAGttttttttttt 0.343 9 42 --- --- --- --- NTF3 4908 broad.mit.edu 37 12 5603608 5603609 + Frame_Shift_Ins INS - - C TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr12:5603608_5603609insC ENST00000423158.3 + 2 479_480 c.267_268insC c.(265-270)ggccgcfs p.R90fs NTF3_ENST00000331010.6_Frame_Shift_Ins_p.R77fs|NTF3_ENST00000535299.1_Intron 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 9 557 --- --- --- --- CHD4 1108 broad.mit.edu 37 12 6711207 6711209 + In_Frame_Del DEL CTT CTT - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr12:6711207_6711209delCTT ENST00000309577.6 - 4 518_520 c.355_357delAAG c.(355-357)del p.K119del CHD4_ENST00000544484.1_In_Frame_Del_p.K116del|CHD4_ENST00000544040.1_In_Frame_Del_p.K112del|CHD4_ENST00000357008.2_In_Frame_Del_p.K119del Q14839 CHD4_HUMAN chromodomain helicase DNA binding protein 4 119 Poly-Lys. 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 p.K119delK(3) central_nervous_system(2) 2 TAGGTCCAAGCTTCTTCTTCTTC 0.537 8 345 --- --- --- --- FOXJ2 55810 broad.mit.edu 37 12 8200558 8200560 + In_Frame_Del DEL CAG CAG - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr12:8200558_8200560delCAG ENST00000162391.3 + 7 2043_2045 c.898_900delCAG c.(898-900)del p.Q306del FOXJ2_ENST00000428177.2_In_Frame_Del_p.Q306del NM_018416.2 NP_060886.1 Q9P0K8 FOXJ2_HUMAN forkhead box J2 306 Poly-Gln. embryo development|organ development|pattern specification process|positive regulation of transcription, DNA-dependent|regulation of sequence-specific DNA binding transcription factor activity|tissue development nucleolus|transcription factor complex DNA bending activity|double-stranded DNA binding|promoter binding|protein domain specific binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding autonomic_ganglia(1)|large_intestine(2)|lung(6)|ovary(2)|skin(3)|upper_aerodigestive_tract(2) 16 Kidney(36;0.0944) gccacctcaacagcagcagcagc 0.640 13 277 --- --- --- --- KRT73 319101 broad.mit.edu 37 12 53001991 53001991 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr12:53001991delT ENST00000305748.3 - 9 1646 c.1612delA c.(1612-1614)ccfs p.T538fs RP11-641A6.2_ENST00000551089.1_RNA NM_175068.2 NP_778238.1 Q86Y46 K2C73_HUMAN keratin 73 538 Tail. keratin filament structural molecule activity NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 44 BRCA - Breast invasive adenocarcinoma(357;0.189) TATCTCATGGTTTTTTTGGTG 0.532 9 1265 --- --- --- --- MYO1A 4640 broad.mit.edu 37 12 57422572 57422573 + Frame_Shift_Ins INS - - T TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr12:57422572_57422573insT ENST00000442789.2 - 29 3385_3386 c.3098_3099insA c.(3097-3099)aggfs p.R1033fs MYO1A_ENST00000300119.3_Frame_Shift_Ins_p.R1033fs|MYO1A_ENST00000544473.1_Frame_Shift_Ins_p.R871fs|TAC3_ENST00000415231.1_5'UTR NM_001256041.1 NP_001242970.1 Q9UBC5 MYO1A_HUMAN myosin IA 1033 sensory perception of sound|vesicle localization brush border|cortical actin cytoskeleton|filamentous actin|lateral plasma membrane|microvillus|myosin complex actin binding|ATP binding|calmodulin binding|motor activity p.?(1) breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(7)|urinary_tract(3) 50 AATGACTCCCCTTTTTTTTGTA 0.559 8 557 --- --- --- --- ZFC3H1 196441 broad.mit.edu 37 12 72057256 72057258 + In_Frame_Del DEL GCT GCT - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr12:72057256_72057258delGCT ENST00000378743.3 - 1 491_493 c.133_135delAGC c.(133-135)del p.S45del THAP2_ENST00000308086.2_5'UTR|ZFC3H1_ENST00000552037.1_In_Frame_Del_p.S45del|ZFC3H1_ENST00000548100.1_In_Frame_Del_p.S45del NM_144982.4 NP_659419.3 O60293 ZC3H1_HUMAN zinc finger, C3H1-type containing 45 Ser-rich. RNA processing intracellular metal ion binding NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2) 69 GCCCGCCGCCGCTGCTGCTGCTG 0.631 OREG0021993 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 12 970 --- --- --- --- TMEM19 55266 broad.mit.edu 37 12 72094757 72094757 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr12:72094757delT ENST00000266673.5 + 6 1587 c.993delT c.(991-993)ggfs p.G331fs NM_018279.3 NP_060749.2 Q96HH6 TMM19_HUMAN transmembrane protein 19 331 integral to membrane large_intestine(1)|lung(8) 9 Breast(359;0.0889) GBM - Glioblastoma multiforme(134;0.044) CTGCTTGGGGTTTTTGGCCCA 0.433 9 1112 --- --- --- --- UTP20 27340 broad.mit.edu 37 12 101680156 101680157 + Frame_Shift_Ins INS - - T TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr12:101680156_101680157insT ENST00000261637.4 + 5 558_559 c.384_385insT c.(382-387)gattttfs p.DF128fs NM_014503.2 NP_055318.2 O75691 UTP20_HUMAN UTP20, small subunit (SSU) processome component, homolog (yeast) 128 endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation 90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome protein binding NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2) 88 ACTTTCCAGAGTTTTTTTTGAC 0.396 8 1217 --- --- --- --- PDS5B 23047 broad.mit.edu 37 13 33344580 33344580 + Frame_Shift_Del DEL A A - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f 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 7 258 --- --- --- --- TSC22D1 8848 broad.mit.edu 37 13 45148706 45148708 + In_Frame_Del DEL TGC TGC - rs112613609 TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr13:45148706_45148708delTGC ENST00000458659.2 - 1 1993_1995 c.1503_1505delGCA c.(1501-1506)caa>ca p.QQ507del TSC22D1_ENST00000501704.2_In_Frame_Del_p.QQ507del NM_183422.3 NP_904358.2 Q15714 T22D1_HUMAN TSC22 domain family, member 1 507 Gln-rich. transcription from RNA polymerase II promoter cytoplasm|nucleus protein binding|sequence-specific DNA binding transcription factor activity breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 27 all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262) GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118) ttgttgttgttgctgctgctgct 0.507 14 657 --- --- --- --- ZC3H13 23091 broad.mit.edu 37 13 46549613 46549614 + Frame_Shift_Del DEL CT CT - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f 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 10 412 --- --- --- --- EBPL 84650 broad.mit.edu 37 13 50235208 50235209 + Frame_Shift_Ins INS - - A TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr13:50235208_50235209insA ENST00000242827.6 - 4 566_567 c.516_517insT c.(514-519)ttacggfs p.LR172fs EBPL_ENST00000378272.5_3'UTR|EBPL_ENST00000495963.2_5'UTR|EBPL_ENST00000378270.5_Stop_Codon_Ins|EBPL_ENST00000378284.2_3'UTR NM_032565.3 NP_115954.1 Q9BY08 EBPL_HUMAN emopamil binding protein-like 172 sterol metabolic process endoplasmic reticulum membrane|integral to membrane cholestenol delta-isomerase activity p.F172fs*7(1) endometrium(8)|kidney(6)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 21 Lung NSC(96;0.000468)|Breast(56;0.0011)|Prostate(109;0.00243)|Hepatocellular(98;0.0556)|Glioma(44;0.236) GBM - Glioblastoma multiforme(99;2.06e-09) CACACACCGTTAAAAAAAAACA 0.480 10 294 --- --- --- --- ABCC4 10257 broad.mit.edu 37 13 95696016 95696016 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr13:95696016delT ENST00000376887.4 - 29 3769 c.3655delA c.(3655-3657)tcfs p.I1219fs ABCC4_ENST00000412704.1_Frame_Shift_Del_p.I1172fs NM_005845.3 NP_005836.2 O15439 MRP4_HUMAN ATP-binding cassette, sub-family C (CFTR/MRP), member 4 1219 ABC transporter 2. platelet activation|platelet degranulation integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane 15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1) 43 all_neural(89;0.0878)|Medulloblastoma(90;0.163) Cefazolin(DB01327) TTCTCCCGGATTTTTTTTTGT 0.378 7 435 --- --- --- --- LRP10 26020 broad.mit.edu 37 14 23341527 23341529 + In_Frame_Del DEL CCT CCT - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f 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 12 494 --- --- --- --- IRF9 10379 broad.mit.edu 37 14 24633132 24633134 + In_Frame_Del DEL AGC AGC - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr14:24633132_24633134delAGC ENST00000396864.3 + 5 828_830 c.541_543delAGC c.(541-543)del p.S187del IRF9_ENST00000557894.1_In_Frame_Del_p.S85del|RP11-468E2.4_ENST00000558468.1_3'UTR NM_006084.4 NP_006075.3 Q00978 IRF9_HUMAN interferon regulatory factor 9 187 Poly-Ser. interferon-gamma-mediated signaling pathway|response to virus|transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway cytosol|nucleoplasm DNA binding|identical protein binding|sequence-specific DNA binding transcription factor activity NS(1)|breast(2)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|skin(2) 16 GBM - Glioblastoma multiforme(265;0.00853) AGACATTGGGagcagcagcagca 0.567 16 589 --- --- --- --- KIAA0391 9692 broad.mit.edu 37 14 35592700 35592700 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr14:35592700delT ENST00000557565.1 + 2 630 c.249delT c.(247-249)cafs p.H83fs KIAA0391_ENST00000603588.1_Intron|KIAA0391_ENST00000321130.10_Frame_Shift_Del_p.H83fs|KIAA0391_ENST00000250377.7_5'UTR|KIAA0391_ENST00000604948.1_Intron|KIAA0391_ENST00000534898.4_Frame_Shift_Del_p.H83fs|KIAA0391_ENST00000603544.1_Frame_Shift_Del_p.H83fs|KIAA0391_ENST00000605870.1_Intron O15091 MRRP3_HUMAN KIAA0391 83 tRNA processing mitochondrion central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1) 14 Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184) Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277) GBM - Glioblastoma multiforme(112;0.0593) CTGTTCCTCATTTTTTTTTAG 0.423 8 223 --- --- --- --- RALGAPA1 253959 broad.mit.edu 37 14 36194270 36194270 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr14:36194270delT ENST00000258840.6 - 14 2216 c.1826delA c.(1825-1827)atfs p.N609fs RALGAPA1_ENST00000554704.1_5'UTR|RALGAPA1_ENST00000307138.6_Frame_Shift_Del_p.N609fs|RALGAPA1_ENST00000382366.3_Frame_Shift_Del_p.N609fs|RALGAPA1_ENST00000389698.3_Frame_Shift_Del_p.N609fs Q6GYQ0 RGPA1_HUMAN Ral GTPase activating protein, alpha subunit 1 (catalytic) 609 activation of Ral GTPase activity cytosol|mitochondrion|nucleus protein heterodimerization activity|Ral GTPase activator activity breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 67 CAAGGTCATATTTTTTTTCCC 0.378 7 287 --- --- --- --- MIS18BP1 55320 broad.mit.edu 37 14 45693722 45693722 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr14:45693722delT ENST00000310806.4 - 11 2526 c.2068delA c.(2068-2070)gtfs p.S690fs NM_018353.4 NP_060823.3 Q6P0N0 M18BP_HUMAN MIS18 binding protein 1 690 cell division|CenH3-containing nucleosome assembly at centromere|mitosis chromosome, centromeric region|nucleoplasm DNA binding NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2) 39 CTGATGGGACTTTTTTTTTGA 0.373 16 591 --- --- --- --- ELMSAN1 91748 broad.mit.edu 37 14 74205926 74205928 + In_Frame_Del DEL CTG CTG - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr14:74205926_74205928delCTG ENST00000286523.5 - 2 1566_1568 c.784_786delCAG c.(784-786)del p.Q262del ELMSAN1_ENST00000394071.2_In_Frame_Del_p.Q262del NM_194278.3 NP_919254.2 ELM2 and Myb/SANT-like domain containing 1 GTAGGgctgcctgctgctgctgc 0.650 9 211 --- --- --- --- IGHV3-43 0 broad.mit.edu 37 14 106926652 106926653 + RNA DEL TC TC - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr14:106926652_106926653delTC ENST00000434710.1 - 0 71_72 CATGGTGCGTTCTCTGTGTTCA 0.495 18 747 --- --- --- --- HERC2P2 0 broad.mit.edu 37 15 23333801 23333802 + RNA INS - - A TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr15:23333801_23333802insA ENST00000560464.1 - 0 908 ACTTACAGTTCAAAAAAAAAAA 0.441 9 90 --- --- --- --- SNHG14 0 broad.mit.edu 37 15 25456925 25456925 + RNA DEL G G - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr15:25456925delG ENST00000424208.1 + 0 2516 SNHG14_ENST00000450809.1_RNA|SNHG14_ENST00000424333.1_RNA NR_003305.1 TGTGTGGGCAGGGGGGGTGCC 0.557 12 979 --- --- --- --- SPATA5L1 79029 broad.mit.edu 37 15 45710840 45710841 + Frame_Shift_Ins INS - - T TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr15:45710840_45710841insT ENST00000305560.6 + 7 2153_2154 c.2054_2055insT c.(2053-2055)tttfs p.F685fs SPATA5L1_ENST00000533841.1_3'UTR NM_024063.2 NP_076968.2 Q9BVQ7 SPA5L_HUMAN spermatogenesis associated 5-like 1 685 cytoplasm ATP binding|nucleoside-triphosphatase activity kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1) 14 Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417) all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07) GCAGAAACCTGTTTTTTTTCTG 0.361 7 366 --- --- --- --- FAM63B 54629 broad.mit.edu 37 15 59144132 59144134 + In_Frame_Del DEL GCT GCT - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr15:59144132_59144134delGCT ENST00000559228.1 + 8 1787_1789 c.1705_1707delGCT c.(1705-1707)del p.A574del FAM63B_ENST00000450403.2_In_Frame_Del_p.A574del Q8NBR6 FA63B_HUMAN family with sequence similarity 63, member B 574 Gln-rich. central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1) 15 ACAAGCAGCAGCTGCTGCTGCTG 0.468 7 447 --- --- --- --- CSPG4P5 0 broad.mit.edu 37 15 84957480 84957499 + RNA DEL GGCCCCACATCCATTGAGAA GGCCCCACATCCATTGAGAA - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr15:84957480_84957499delGGCCCCACATCCATTGAGAA ENST00000558801.1 - 0 7230_7249 TGTGTGCACTGGCCCCACATCCATTGAGAAGGCCCCACAT 0.586 8 49 --- --- --- --- IQGAP1 8826 broad.mit.edu 37 15 91019925 91019925 + Frame_Shift_Del DEL A A - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr15:91019925delA ENST00000268182.5 + 24 2939 c.2815delA c.(2815-2817)aafs p.K940fs IQGAP1_ENST00000560738.1_Frame_Shift_Del_p.K368fs NM_003870.3 NP_003861.1 P46940 IQGA1_HUMAN IQ motif containing GTPase activating protein 1 940 energy reserve metabolic process|regulation of insulin secretion|small GTPase mediated signal transduction actin filament|cytoplasm|midbody|nucleus|plasma membrane calmodulin binding|GTPase inhibitor activity|protein phosphatase binding|Ras GTPase activator activity breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 59 Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488) BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194) AAAACTTACCAAAAAAAATAA 0.363 11 685 --- --- --- --- VPS33B 26276 broad.mit.edu 37 15 91550236 91550238 + In_Frame_Del DEL TCC TCC - rs147271815 TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr15:91550236_91550238delTCC ENST00000333371.3 - 9 995_997 c.642_644delGGA c.(640-645)gat>ga p.ED214del VPS33B_ENST00000535843.1_In_Frame_Del_p.ED123del|VPS33B_ENST00000535906.1_In_Frame_Del_p.ED187del 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 10 692 --- --- --- --- RP11-266O8.1 0 broad.mit.edu 37 15 93974510 93974510 + RNA DEL C C - rs57286078 TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr15:93974510delC ENST00000543286.1 + 0 545 TGGCTGGGTTCtttttttttt 0.433 8 175 --- --- --- --- AXIN1 8312 broad.mit.edu 37 16 347089 347089 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr16:347089delT ENST00000262320.3 - 7 2293 c.1922delA c.(1921-1923)agfs p.K641fs AXIN1_ENST00000354866.3_Frame_Shift_Del_p.K641fs NM_003502.3 NP_003493.1 O15169 AXIN1_HUMAN axin 1 641 Interaction with PPP2CA.|Interaction with RNF111. activation of JUN kinase activity|activation of protein kinase activity|apoptosis|axial mesoderm formation|canonical Wnt receptor signaling pathway involved in neural plate anterior/posterior pattern formation|cellular protein complex assembly|cellular response to organic cyclic compound|cytoplasmic microtubule organization|determination of left/right symmetry|dorsal/ventral axis specification|embryonic eye morphogenesis|embryonic skeletal joint morphogenesis|forebrain anterior/posterior pattern formation|muscle cell development|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fat cell differentiation|olfactory placode formation|optic placode formation|positive regulation of JNK cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of transcription, DNA-dependent|positive regulation of ubiquitin-protein ligase activity|regulation of catenin import into nucleus|tail morphogenesis|Wnt receptor signaling pathway involved in forebrain neuron fate commitment|Wnt receptor signaling pathway involved in somitogenesis APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|cell cortex|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|cytosol|lateral plasma membrane|nucleus|perinuclear region of cytoplasm|postsynaptic density armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|I-SMAD binding|p53 binding|protein complex scaffold|protein homodimerization activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2) 221 all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187) GCTGATCTCCTTTTCCCCCTC 0.647 7 1624 --- --- --- --- EME2 197342 broad.mit.edu 37 16 1824298 1824300 + In_Frame_Del DEL TGC TGC - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr16:1824298_1824300delTGC ENST00000307394.7 + 3 422_424 c.422_424delTGC c.(421-426)ttg>t p.LL143del EME2_ENST00000568449.1_In_Frame_Del_p.LL143del A4GXA9 EME2_HUMAN essential meiotic structure-specific endonuclease subunit 2 143 DNA recombination|DNA repair nucleus DNA binding|endonuclease activity central_nervous_system(1)|kidney(2)|lung(5)|pancreas(1) 9 GAACAGGAATTGCTGCTGCTGCT 0.655 Direct reversal of damage;Homologous recombination 8 670 --- --- --- --- RRN3P3 0 broad.mit.edu 37 16 22448752 22448753 + RNA INS - - GCG TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr16:22448752_22448753insGCG ENST00000551766.1 - 0 283_284 NR_027460.1 GTCTCGGCTGAGCGGCGGCGGC 0.733 7 44 --- --- --- --- TNRC6A 27327 broad.mit.edu 37 16 24807240 24807240 + Frame_Shift_Del DEL A A - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f 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 12 948 --- --- --- --- RRN3P2 0 broad.mit.edu 37 16 29110406 29110406 + RNA DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr16:29110406delT ENST00000564580.1 + 0 1098 TTAAAAAATCTTTTTTTTTTT 0.299 10 100 --- --- --- --- RP11-23E10.4 0 broad.mit.edu 37 16 33365420 33365420 + RNA DEL A A - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr16:33365420delA ENST00000568520.1 - 0 249 TACAAACTATAAAAAAACAGA 0.358 11 63 --- --- --- --- COQ9 57017 broad.mit.edu 37 16 57486732 57486734 + In_Frame_Del DEL GAG GAG - rs149029279 TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr16:57486732_57486734delGAG ENST00000262507.6 + 3 331_333 c.262_264delGAG c.(262-264)del p.E91del COQ9_ENST00000567933.1_In_Frame_Del_p.E91del|COQ9_ENST00000567384.1_3'UTR|COQ9_ENST00000567072.1_In_Frame_Del_p.E91del NM_020312.3 NP_064708.1 O75208 COQ9_HUMAN coenzyme Q9 91 ubiquinone biosynthetic process mitochondrion breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(1) 16 CCAGGGCGGCGAGGAGGAGGAGG 0.576 11 708 --- --- --- --- RANBP10 57610 broad.mit.edu 37 16 67763279 67763281 + In_Frame_Del DEL GAG GAG - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr16:67763279_67763281delGAG ENST00000317506.3 - 10 1369_1371 c.1254_1256delCTC c.(1252-1257)tcg>tc p.SS420del RANBP10_ENST00000448631.2_In_Frame_Del_p.SS364del|RANBP10_ENST00000411657.2_In_Frame_Del_p.SS303del|RANBP10_ENST00000536251.1_In_Frame_Del_p.SS191del|RANBP10_ENST00000602677.1_In_Frame_Del_p.SS420del NM_020850.1 NP_065901.1 Q6VN20 RBP10_HUMAN RAN binding protein 10 420 Ser-rich. p.S418S(2) endometrium(5)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|skin(1) 23 Acute lymphoblastic leukemia(13;4.34e-06)|all_hematologic(13;0.000643)|Ovarian(137;0.192) OV - Ovarian serous cystadenocarcinoma(108;0.00522)|Epithelial(162;0.025)|all cancers(182;0.157) ggaagaggacgaggaggaggagg 0.567 9 268 --- --- --- --- ZFHX3 463 broad.mit.edu 37 16 72991713 72991715 + In_Frame_Del DEL CCA CCA - rs4788682 by1000genomes TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr16:72991713_72991715delCCA ENST00000268489.5 - 2 3002_3004 c.2330_2332delTGG c.(2329-2334)gct>g p.VA777del ZFHX3_ENST00000397992.5_Intron NM_006885.3 NP_008816.3 Q15911 ZFHX3_HUMAN zinc finger homeobox 3 777 Poly-Ala. V -> A (in dbSNP:rs4788682). muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation transcription factor complex enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding p.V777V(1) NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11) 153 Ovarian(137;0.13) gccgccgcagccaccgccgccgc 0.635 7 513 --- --- --- --- NPIPB15 440348 broad.mit.edu 37 16 74425400 74425402 + In_Frame_Del DEL CAA CAA - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f 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 8 427 --- --- --- --- TCF25 22980 broad.mit.edu 37 16 89951019 89951020 + Frame_Shift_Ins INS - - A TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr16:89951019_89951020insA ENST00000263346.8 + 3 440_441 c.384_385insA c.(382-387)aaaaaafs p.KK128fs TCF25_ENST00000563406.1_3'UTR NM_014972.2 NP_055787.1 Q9BQ70 TCF25_HUMAN transcription factor 25 (basic helix-loop-helix) 128 heart development|negative regulation of transcription from RNA polymerase II promoter nucleus DNA binding|protein binding|sequence-specific DNA binding transcription factor activity breast(1)|endometrium(2)|large_intestine(1)|lung(8)|ovary(3)|skin(1)|urinary_tract(2) 18 all_cancers(9;4.71e-08)|Lung NSC(15;0.000192)|all_lung(18;0.000319)|all_neural(9;0.0122)|all_hematologic(23;0.027) BRCA - Breast invasive adenocarcinoma(80;0.0288) TCCGGAAGAAGAAAAAAAAACA 0.446 8 204 --- --- --- --- C17orf85 55421 broad.mit.edu 37 17 3721809 3721811 + In_Frame_Del DEL TCC TCC - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr17:3721809_3721811delTCC ENST00000158149.3 - 11 1111_1113 c.216_218delGGA c.(214-219)gaa>ga p.EE78del C17orf85_ENST00000389005.4_In_Frame_Del_p.EE358del Q53F19 CQ085_HUMAN chromosome 17 open reading frame 85 358 nucleotide binding endometrium(2)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(1) 10 UCEC - Uterine corpus endometrioid carcinoma (3;0.0725) ctcttcctcttcctcctcctcct 0.507 13 650 --- --- --- --- MYH10 4628 broad.mit.edu 37 17 8415820 8415822 + In_Frame_Del DEL TTC TTC - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr17:8415820_8415822delTTC ENST00000360416.3 - 24 3037_3039 c.2899_2901delGAA c.(2899-2901)del p.E967del MYH10_ENST00000269243.4_In_Frame_Del_p.E936del|MYH10_ENST00000396239.1_In_Frame_Del_p.E957del|MYH10_ENST00000379980.4_In_Frame_Del_p.E952del NM_001256012.1 NP_001242941.1 P35580 MYH10_HUMAN myosin, heavy chain 10, non-muscle 936 actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape cell cortex|cleavage furrow|midbody|myosin complex|stress fiber actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1) 52 TTTGGTTTCTTTCTTCTTCTTCT 0.350 7 305 --- --- --- --- MED9 55090 broad.mit.edu 37 17 17394705 17394707 + In_Frame_Del DEL CAG CAG - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr17:17394705_17394707delCAG ENST00000268711.3 + 2 393_395 c.337_339delCAG c.(337-339)del p.Q117del NM_018019.2 NP_060489.1 Q9NWA0 MED9_HUMAN mediator complex subunit 9 117 regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent protein binding cervix(1)|endometrium(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 7 GAGCCCCGAACAGCAGCAGCAGC 0.581 8 660 --- --- --- --- SMCR7 0 broad.mit.edu 37 17 18167778 18167780 + In_Frame_Del DEL GCT GCT - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr17:18167778_18167780delGCT ENST00000323019.4 + 4 1276_1278 c.1065_1067delGCT c.(1063-1068)cgg>cg p.RL355del SMCR7_ENST00000395704.4_3'UTR|SMCR7_ENST00000395706.2_In_Frame_Del_p.RL366del NM_001144900.1|NM_139162.3 NP_001138372.1|NP_631901.2 Q96C03 SMCR7_HUMAN 355 integral to membrane protein binding p.L356R(1) breast(1)|central_nervous_system(1)|endometrium(3)|lung(4) 9 all_neural(463;0.228) CTCGCCGGCGGCTGCTGCTGCTG 0.685 7 560 --- --- --- --- POLDIP2 26073 broad.mit.edu 37 17 26684394 26684395 + Splice_Site INS - - G rs113730440 TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f 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 8 47 --- --- --- --- RP11-156P1.3 0 broad.mit.edu 37 17 45128628 45128629 + RNA INS - - T TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr17:45128628_45128629insT ENST00000575173.1 - 0 418 ATTCTGGTGTGtttttttttgt 0.337 7 245 --- --- --- --- SPAG9 9043 broad.mit.edu 37 17 49157025 49157025 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr17:49157025delT ENST00000262013.7 - 2 552 c.344delA c.(343-345)agfs p.K115fs SPAG9_ENST00000357122.4_Frame_Shift_Del_p.K115fs|RP11-481C4.1_ENST00000509833.1_RNA|SPAG9_ENST00000505279.1_Frame_Shift_Del_p.K115fs NM_001130528.2 NP_001124000.1 O60271 JIP4_HUMAN sperm associated antigen 9 115 positive regulation of cell migration|positive regulation of muscle cell differentiation|retrograde transport, endosome to Golgi|spermatogenesis acrosomal vesicle|integral to membrane|perinuclear region of cytoplasm NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1) 37 BRCA - Breast invasive adenocarcinoma(22;4.24e-07) CTGTAAGTCCTTTTTTTCCTG 0.313 8 569 --- --- --- --- FTSJ3 117246 broad.mit.edu 37 17 61899155 61899157 + In_Frame_Del DEL CTC CTC - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f 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 1076 --- --- --- --- SEH1L 81929 broad.mit.edu 37 18 12986927 12986929 + In_Frame_Del DEL TCC TCC - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr18:12986927_12986929delTCC ENST00000399892.2 + 9 1238_1240 c.1137_1139delTCC c.(1135-1140)ctt>ct p.LP379del SEH1L_ENST00000262124.11_3'UTR|RP11-773H22.4_ENST00000588211.1_RNA NM_001013437.1 NP_001013455.1 Q96EE3 SEH1_HUMAN SEH1-like (S. cerevisiae) 0 attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation|carbohydrate metabolic process|cell division|glucose transport|mitotic metaphase plate congression|mitotic prometaphase|mRNA transport|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction condensed chromosome kinetochore|cytosol|Nup107-160 complex central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1) 11 CCCAGCTCCTtcctcctcctcct 0.522 8 238 --- --- --- --- HAUS8 93323 broad.mit.edu 37 19 17160706 17160707 + Frame_Shift_Del DEL GA GA - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr19:17160706_17160707delGA ENST00000593360.1 - 10 3044_3045 c.1026_1027delTC c.(1024-1029)tcgtfs p.SR342fs HAUS8_ENST00000448593.2_Frame_Shift_Del_p.SR402fs|HAUS8_ENST00000253669.5_Frame_Shift_Del_p.SR403fs Q9BT25 HAUS8_HUMAN HAUS augmin-like complex, subunit 8 403 cell division|centrosome organization|mitosis|spindle assembly centrosome|HAUS complex|microtubule|spindle pole endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1) 12 CTCCCTGAACGAGAGAGAGAGG 0.495 8 1265 --- --- --- --- DMKN 93099 broad.mit.edu 37 19 36002362 36002412 + In_Frame_Del DEL CTGCTGCCACCACTGCTGCCGCCACTGCTGCCGCCACTGCTGCTGCCACTG CTGCTGCCACCACTGCTGCCGCCACTGCTGCCGCCACTGCTGCTGCCACTG - rs112672248 byFrequency TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr19:36002362_36002412delCTGCTGCCACCACTGCTGCCGCCACTGCTGCCGCCACTGCTGCTGCCACTG ENST00000339686.3 - 5 995_1045 c.819_869delCAGTGGCAGCAGCAGTGGCGGCAGCAGTGGCGGCAGCAGTGGTGGCAGCAG c.(817-870)agt>ag p.SSGSSSGGSSGGSSGGSS273del DMKN_ENST00000429837.1_Intron|DMKN_ENST00000447113.2_In_Frame_Del_p.SSGSSSGGSSGGSSGGSS273del|DMKN_ENST00000440396.1_In_Frame_Del_p.SSGSSSGGSSGGSSGGSS273del|DMKN_ENST00000424570.2_In_Frame_Del_p.SSGSSSGGSSGGSSGGSS273del|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000418261.1_In_Frame_Del_p.SSGSSSGGSSGGSSGGSS273del|DMKN_ENST00000451297.2_In_Frame_Del_p.SSGSSSGGSSGGSSGGSS273del NM_033317.4 NP_201574.3 Q6E0U4 DMKN_HUMAN dermokine 273 Gly-rich. extracellular region p.S274_S290del(1) NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2) 27 all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0724) actgttgccactgctgccaccactgctgccgccactgctgccgccactgctgctgccactgctgctgccac 0.641 29 114 --- --- --- --- PRX 57716 broad.mit.edu 37 19 40900180 40900182 + In_Frame_Del DEL TCC TCC - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr19:40900180_40900182delTCC ENST00000324001.7 - 7 4347_4349 c.4077_4079delGGA c.(4075-4080)gaa>ga p.EE1359del PRX_ENST00000291825.7_3'UTR NM_181882.2 NP_870998.2 Q9BXM0 PRAX_HUMAN periaxin 1359 Poly-Glu. Missing. axon ensheathment cytoplasm|nucleus|plasma membrane protein binding breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|urinary_tract(9) 47 Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384) ACTGCcctcttcctcctcctcct 0.695 9 170 --- --- --- --- LYPD3 27076 broad.mit.edu 37 19 43969653 43969655 + In_Frame_Del DEL AGC AGC - rs141441894 byFrequency TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr19:43969653_43969655delAGC ENST00000244333.3 - 1 157_159 c.69_71delGCT c.(67-72)ctt>ct p.LL23del NM_014400.2 NP_055215.2 O95274 LYPD3_HUMAN LY6/PLAUR domain containing 3 23 anchored to plasma membrane cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|upper_aerodigestive_tract(2) 11 Prostate(69;0.0153) ACCTCCGCGAAGCAGCAGCAGCA 0.675 22 887 --- --- --- --- CD3EAP 10849 broad.mit.edu 37 19 45911859 45911861 + In_Frame_Del DEL GAA GAA - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr19:45911859_45911861delGAA ENST00000309424.3 + 3 1121_1123 c.633_635delGAA c.(631-636)cgg>cg p.RK211del ERCC1_ENST00000423698.2_3'UTR|ERCC1_ENST00000300853.3_3'UTR|CD3EAP_ENST00000589804.1_In_Frame_Del_p.RK213del NM_012099.1 NP_036231.1 O15446 RPA34_HUMAN CD3e molecule, epsilon associated protein 211 rRNA transcription|transmembrane receptor protein tyrosine kinase signaling pathway chromosome|RNA polymerase I transcription factor complex DNA-directed RNA polymerase activity breast(2)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1) 11 all_neural(266;0.224)|Ovarian(192;0.231) OV - Ovarian serous cystadenocarcinoma(262;0.0251) TGGATGTGCGGAAGAAGAAGAAG 0.581 9 835 --- --- --- --- SIGLEC8 27181 broad.mit.edu 37 19 51961617 51961619 + In_Frame_Del DEL GCA GCA - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f 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 12 520 --- --- --- --- BRSK1 84446 broad.mit.edu 37 19 55815035 55815036 + Splice_Site INS - - C TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr19:55815035_55815036insC ENST00000309383.1 + 12 1404_1405 c.1126_splice c.e12-1 p.A376_splice BRSK1_ENST00000326848.7_Splice_Site_p.A71_splice|BRSK1_ENST00000590333.1_Splice_Site_p.A392_splice NM_032430.1 NP_115806.1 Q8TDC3 BRSK1_HUMAN BR serine/threonine kinase 1 376 establishment of cell polarity|G2/M transition DNA damage checkpoint|neuron differentiation|response to UV cell junction|cytoplasm|nucleus magnesium ion binding|protein serine/threonine kinase activity p.R379fs*9(2) NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(15)|ovary(2)|prostate(2)|skin(6)|stomach(1) 48 Renal(1328;0.245) BRCA - Breast invasive adenocarcinoma(297;0.209) GBM - Glioblastoma multiforme(193;0.0474) TGTCCCTCAGACCCCCCCCGGA 0.579 8 480 --- --- --- --- ZNF552 79818 broad.mit.edu 37 19 58319468 58319468 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr19:58319468delT ENST00000391701.1 - 3 1333 c.1164delA c.(1162-1164)aafs p.K388fs ZNF586_ENST00000598885.1_Intron|ZNF586_ENST00000599802.1_Intron NM_024762.3 NP_079038.2 Q9H707 ZN552_HUMAN zinc finger protein 552 388 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 11 Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157) UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0259) TTTGCCTAAATTTTTTTTCAC 0.413 9 651 --- --- --- --- DIDO1 11083 broad.mit.edu 37 20 61512380 61512381 + Frame_Shift_Ins INS - - G TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr20:61512380_61512381insG ENST00000266070.4 - 16 5252_5253 c.4927_4928insC c.(4927-4929)cccfs p.P1643fs DIDO1_ENST00000395343.1_Frame_Shift_Ins_p.P1643fs NM_033081.2 NP_149072.2 Q9BTC0 DIDO1_HUMAN death inducer-obliterator 1 1643 apoptosis|transcription, DNA-dependent cytoplasm|nucleus zinc ion binding NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1) 99 Breast(26;5.68e-08) CGTGGCGGGGCGGGTGCCCTCC 0.728 8 155 --- --- --- --- DIDO1 11083 broad.mit.edu 37 20 61537401 61537402 + Frame_Shift_Ins INS - - T rs140153728 TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr20:61537401_61537402insT ENST00000266070.4 - 6 1750_1751 c.1425_1426insA c.(1423-1428)aaagacfs p.D476fs DIDO1_ENST00000370371.4_Frame_Shift_Ins_p.D476fs|DIDO1_ENST00000395343.1_Frame_Shift_Ins_p.D476fs|DIDO1_ENST00000266071.5_Frame_Shift_Ins_p.D476fs|DIDO1_ENST00000370368.1_Frame_Shift_Ins_p.D476fs|DIDO1_ENST00000395340.1_Frame_Shift_Ins_p.D476fs|DIDO1_ENST00000370366.1_Frame_Shift_Ins_p.D476fs|DIDO1_ENST00000354665.4_Frame_Shift_Ins_p.D476fs|DIDO1_ENST00000395335.2_Frame_Shift_Ins_p.D476fs NM_033081.2 NP_149072.2 Q9BTC0 DIDO1_HUMAN death inducer-obliterator 1 476 apoptosis|transcription, DNA-dependent cytoplasm|nucleus zinc ion binding NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1) 99 Breast(26;5.68e-08) ACTGTGGTCTCTTTTTTTTCTG 0.490 8 743 --- --- --- --- ANKRD20A11P 0 broad.mit.edu 37 21 15343608 15343609 + RNA INS - - A TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr21:15343608_15343609insA ENST00000344693.5 - 0 736 NR_027270.1 TAAAACAGCAGAAAAAATTAAT 0.272 9 345 --- --- --- --- APP 351 broad.mit.edu 37 21 27394182 27394184 + In_Frame_Del DEL GTG GTG - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr21:27394182_27394184delGTG ENST00000358918.3 - 6 1036_1038 c.837_839delCAC c.(835-840)aca>ac p.TT279del APP_ENST00000448388.2_In_Frame_Del_p.TT244del|APP_ENST00000354192.3_In_Frame_Del_p.TT223del|APP_ENST00000357903.3_In_Frame_Del_p.TT279del|APP_ENST00000439274.2_In_Frame_Del_p.TT223del|APP_ENST00000359726.3_In_Frame_Del_p.TT279del|APP_ENST00000348990.5_In_Frame_Del_p.TT279del|APP_ENST00000346798.3_In_Frame_Del_p.TT279del|APP_ENST00000440126.3_In_Frame_Del_p.TT274del|APP_ENST00000474136.1_5'UTR 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 7 244 --- --- --- --- PWP2 5822 broad.mit.edu 37 21 45535623 45535623 + Frame_Shift_Del DEL C C - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr21:45535623delC ENST00000291576.7 + 7 785 c.658delC c.(658-660)ccfs p.P221fs NM_005049.2 NP_005040.2 Q15269 PWP2_HUMAN PWP2 periodic tryptophan protein homolog (yeast) 221 cytoplasm|nucleolus signal transducer activity cervix(1)|endometrium(6)|large_intestine(6)|lung(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1) 21 STAD - Stomach adenocarcinoma(101;0.172)|Colorectal(79;0.2) GTGTGACACGCCCCCCGAGGG 0.667 9 681 --- --- --- --- C22orf43 51233 broad.mit.edu 37 22 23959767 23959769 + In_Frame_Del DEL CAT CAT - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr22:23959767_23959769delCAT ENST00000317749.5 - 7 809_811 c.512_514delATG c.(511-516)gcc>g p.DA171del NM_016449.3 NP_057533.2 Q6PGQ1 CV043_HUMAN chromosome 22 open reading frame 43 171 Asp-rich. endometrium(1)|large_intestine(3)|lung(5)|pancreas(1)|skin(1) 11 CTTACCTGGGcatcatcatcatc 0.433 9 369 --- --- --- --- ZNRF3 84133 broad.mit.edu 37 22 29445819 29445821 + In_Frame_Del DEL CAG CAG - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr22:29445819_29445821delCAG ENST00000544604.2 + 8 1825_1827 c.1650_1652delCAG c.(1648-1653)gac>ga p.DS550del ZNRF3_ENST00000332811.4_In_Frame_Del_p.DS450del|ZNRF3_ENST00000406323.3_In_Frame_Del_p.DS450del|ZNRF3_ENST00000402174.1_In_Frame_Del_p.DS450del NM_001206998.1 NP_001193927.1 Q9ULT6 ZNRF3_HUMAN zinc and ring finger 3 550 integral to membrane zinc ion binding NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(4)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2) 28 CAGgcagcgacagcagcagcagc 0.660 8 335 --- --- --- --- SREBF2 6721 broad.mit.edu 37 22 42262949 42262951 + In_Frame_Del DEL GCA GCA - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr22:42262949_42262951delGCA ENST00000361204.4 + 2 369_371 c.203_205delGCA c.(202-207)ggc>g p.GS68del NM_004599.2 NP_004590.2 Q12772 SRBP2_HUMAN sterol regulatory element binding transcription factor 2 68 Gly/Pro/Ser-rich. cholesterol metabolic process ER to Golgi transport vesicle membrane|Golgi membrane|nucleus|SREBP-SCAP-Insig complex protein C-terminus binding NS(2)|breast(6)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1) 38 ggcagcagtggcagcagcagcag 0.567 24 634 --- --- --- --- SMDT1 91689 broad.mit.edu 37 22 42478046 42478048 + In_Frame_Del DEL GAT GAT - rs141840500 TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr22:42478046_42478048delGAT ENST00000331479.3 + 2 378_380 c.304_306delGAT c.(304-306)del p.D107del SMDT1_ENST00000547929.1_Intron NM_033318.4 NP_201575.3 single-pass membrane protein with aspartate-rich tail 1 TGTTCCAGAGGATGATGATGATG 0.478 9 423 --- --- --- --- TCF20 6942 broad.mit.edu 37 22 42610362 42610364 + In_Frame_Del DEL TGC TGC - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr22:42610362_42610364delTGC ENST00000359486.3 - 1 1084_1086 c.948_950delGCA c.(946-951)caa>ca p.QQ316del TCF20_ENST00000335626.4_In_Frame_Del_p.QQ316del NM_005650.1 NP_005641.1 Q9UGU0 TCF20_HUMAN transcription factor 20 (AR1) 316 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 ttgctgcggttgctgctgctgct 0.502 12 584 --- --- --- --- TCF20 6942 broad.mit.edu 37 22 42610573 42610575 + In_Frame_Del DEL AGG AGG - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chr22:42610573_42610575delAGG ENST00000359486.3 - 1 873_875 c.737_739delCCT c.(736-741)ttc>t p.SF246del TCF20_ENST00000335626.4_In_Frame_Del_p.SF246del NM_005650.1 NP_005641.1 Q9UGU0 TCF20_HUMAN transcription factor 20 (AR1) 246 Ser-rich. 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 GGTGAAGGGAaggaggaggagga 0.507 15 503 --- --- --- --- TFE3 7030 broad.mit.edu 37 X 48887952 48887952 + Frame_Shift_Del DEL C C - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f 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""" 7 453 --- --- --- --- NAP1L2 4674 broad.mit.edu 37 X 72433664 72433666 + In_Frame_Del DEL TCC TCC - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chrX:72433664_72433666delTCC ENST00000373517.3 - 1 1018_1020 c.663_665delGGA c.(661-666)gac>ga p.ED221del NAP1L2_ENST00000536638.1_In_Frame_Del_p.ED79del NM_021963.3 NP_068798.1 Q9ULW6 NP1L2_HUMAN nucleosome assembly protein 1-like 2 221 Glu-rich (acidic). nucleosome assembly chromatin assembly complex NS(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(12)|skin(3) 29 Renal(35;0.156) CTCAATGTCGtcctcctcctcct 0.424 11 166 --- --- --- --- TSIX 0 broad.mit.edu 37 X 73046080 73046080 + RNA DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chrX:73046080delT ENST00000604411.1 + 0 34041 XIST_ENST00000429829.1_lincRNA NR_003255.2 AGCCTGGCACTTTTTTTTCCC 0.423 8 342 --- --- --- --- USP26 83844 broad.mit.edu 37 X 132160788 132160788 + Frame_Shift_Del DEL A A - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chrX:132160788delA ENST00000511190.1 - 6 1930 c.1461delT c.(1459-1461)ttfs p.F487fs USP26_ENST00000406273.1_Frame_Shift_Del_p.F487fs|USP26_ENST00000370832.1_Frame_Shift_Del_p.F487fs NM_031907.1 NP_114113.1 Q9BXU7 UBP26_HUMAN ubiquitin specific peptidase 26 487 protein deubiquitination|ubiquitin-dependent protein catabolic process nucleus cysteine-type peptidase activity|protein binding|ubiquitin thiolesterase activity p.G488fs*6(2)|p.F487fs*7(1) breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3) 60 Acute lymphoblastic leukemia(192;0.000127) CTTCTGCTCCAAAAAAAAGAT 0.383 7 590 --- --- --- --- PASD1 139135 broad.mit.edu 37 X 150817142 150817144 + In_Frame_Del DEL GCT GCT - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chrX:150817142_150817144delGCT ENST00000370357.4 + 9 930_932 c.685_687delGCT c.(685-687)del p.A236del NM_173493.2 NP_775764.2 Q8IV76 PASD1_HUMAN PAS domain containing 1 236 Poly-Ala. nucleus signal transducer activity p.A229A(2) breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1) 48 Acute lymphoblastic leukemia(192;6.56e-05) CGTTGAACCCgctgctgctgctg 0.433 13 505 --- --- --- --- F8 2157 broad.mit.edu 37 X 154157686 154157686 + Frame_Shift_Del DEL T T - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chrX:154157686delT ENST00000360256.4 - 14 4579 c.4379delA c.(4378-4380)atfs p.N1461fs NM_000132.3 NP_000123.1 P00451 FA8_HUMAN coagulation factor VIII, procoagulant component 1461 B. acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation extracellular space|plasma membrane|platelet alpha granule lumen copper ion binding|oxidoreductase activity|protein binding p.N1460fs*5(2)|p.N1460fs*2(2) NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2) 120 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) AGAAAGGTTATTTTTTTTGGC 0.413 7 342 --- --- --- --- SLC9B1P1 0 broad.mit.edu 37 Y 13501672 13501674 + In_Frame_Del DEL AAT AAT - TCGA-FB-A4P6-01A-12D-A26I-08 TCGA-FB-A4P6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 45d20fcd-f456-4f39-a709-8fbf27cf73ff a4f4f26d-1538-428f-b856-9e7a9f7e0c7f g.chrY:13501672_13501674delAAT ENST00000331172.6 - 4 534_536 c.535_537delATT c.(535-537)del p.I179del TCTTACCAACAATATTTGATTCA 0.241 13 56 --- --- --- ---