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 ARHGAP9 64333 broad.mit.edu 37 12 57869582 57869582 + Missense_Mutation SNP T T C rs2277315 by1000genomes TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr12:57869582T>C ENST00000393797.2 - 13 1750 c.1558A>G c.(1558-1560)Acc>Gcc p.T520A ARHGAP9_ENST00000393791.3_Intron|ARHGAP9_ENST00000430041.2_Intron|ARHGAP9_ENST00000424809.2_Intron|ARHGAP9_ENST00000356411.2_Missense_Mutation_p.T449A|ARHGAP9_ENST00000550288.1_Intron Q9BRR9 RHG09_HUMAN Rho GTPase activating protein 9 449 regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction cytosol GTPase activator activity|protein binding endometrium(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(1) 30 GBM - Glioblastoma multiforme(3;3.37e-34) TCCCGGCCGGTCGGAGCCTCC 0.687000 5 134 0 0 1 0 0 KRAS 3845 broad.mit.edu 37 12 25398285 25398285 + Missense_Mutation SNP C C G rs121913530 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr12:25398285C>G ENST00000311936.3 - 2 225 c.34G>C c.(34-36)Ggt>Cgt p.G12R KRAS_ENST00000256078.4_Missense_Mutation_p.G12R|KRAS_ENST00000556131.1_Missense_Mutation_p.G12R|KRAS_ENST00000557334.1_Missense_Mutation_p.G12R NM_004985.3 NP_004976.2 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog 12 G -> A (in a colorectal cancer sample; somatic mutation).|G -> C (in lung carcinoma; somatic mutation).|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation).|G -> R (in lung cancer and bladder cancer; somatic mutation).|G -> S (in lung carcinoma and GASC; somatic mutation).|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation). activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction plasma membrane GTP binding|GTPase activity|protein binding p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12N(1) UBE2L3/KRAS(2) NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) CCTACGCCACCAGCTCCAACT 0.348000 G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE) 119 Mis """pancreatic, colorectal, lung, thyroid, AML, others""" Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) 20 131 0 0 1 0 0 OR10K2 391107 broad.mit.edu 37 1 158390039 158390039 + Silent SNP G G A TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:158390039G>A ENST00000314902.2 - 1 617 c.618C>T c.(616-618)gtC>gtT p.V206V NM_001004476.1 NP_001004476.1 Q6IF99 O10K2_HUMAN olfactory receptor, family 10, subfamily K, member 2 206 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity NS(1)|breast(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(19)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 36 all_hematologic(112;0.0378) GGATAGCCAGGACCAATGTAC 0.443000 45 388 0 0 1 0 0 IGSF1 3547 broad.mit.edu 37 X 130408064 130408064 + Nonsense_Mutation SNP G G A TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chrX:130408064G>A ENST00000370904.1 - 25 4751 c.3841C>T c.(3841-3843)Cga>Tga p.R1281* IGSF1_ENST00000361420.3_Nonsense_Mutation_p.R1290*|IGSF1_ENST00000370903.3_Nonsense_Mutation_p.R1295*|IGSF1_ENST00000370910.1_Nonsense_Mutation_p.R1281* Q8N6C5 IGSF1_HUMAN immunoglobulin superfamily, member 1 1290 regulation of transcription, DNA-dependent extracellular region|integral to membrane inhibin beta-A binding|inhibin beta-B binding breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|liver(1)|lung(37)|ovary(4)|skin(3)|upper_aerodigestive_tract(2) 78 TACCTGGTTCGCAGTCGAGGC 0.502000 261 1486 0 0 1 0 0 SEMG2 6407 broad.mit.edu 37 20 43851593 43851593 + Missense_Mutation SNP G G C TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr20:43851593G>C ENST00000372769.3 + 2 1410 c.1320G>C c.(1318-1320)gaG>gaC p.E440D NM_003008.2 NP_002999.1 Q02383 SEMG2_HUMAN semenogelin II 440 4 X 60 AA tandem repeats, type I.|Repeat-rich region. sexual reproduction extracellular space|stored secretory granule structural molecule activity autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2) 36 Myeloproliferative disorder(115;0.0122) AAACTGAAGAGAAAATACATG 0.383000 86 522 0 0 1 0 0 SACS 26278 broad.mit.edu 37 13 23906194 23906194 + Nonsense_Mutation SNP G G A TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr13:23906194G>A ENST00000382298.3 - 10 12409 c.11821C>T c.(11821-11823)Caa>Taa p.Q3941* SACS_ENST00000402364.1_Nonsense_Mutation_p.Q3191*|SACS_ENST00000382292.3_Nonsense_Mutation_p.Q3941* NM_014363.4 NP_055178.3 Q9NZJ4 SACS_HUMAN spastic ataxia of Charlevoix-Saguenay (sacsin) 3941 cell death|negative regulation of inclusion body assembly|protein folding axon|cell body fiber|dendrite|mitochondrion|nucleus ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11) 189 all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128) all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189) ACTAACATTTGCACACCAATA 0.403000 85 681 0 0 1 0 0 TTC3 7267 broad.mit.edu 37 21 38572533 38572533 + Splice_Site SNP G G A TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr21:38572533G>A ENST00000399017.2 + 45 8598 c.5850_splice c.e45-1 p.A1951_splice TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000354749.2_Splice_Site_p.A1951_splice|TTC3_ENST00000355666.1_Splice_Site_p.A1951_splice NM_003316.3 NP_003307.3 P53804 TTC3_HUMAN tetratricopeptide repeat domain 3 1951 protein K48-linked ubiquitination|ubiquitin-dependent protein catabolic process nucleus protein binding|ubiquitin-protein ligase activity|zinc ion binding breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5) 75 Myeloproliferative disorder(46;0.0412) GTTTCCACAGGCACTGGGTGC 0.428000 23 213 0 0 1 0 0 FBN3 84467 broad.mit.edu 37 19 8130859 8130859 + Nonsense_Mutation SNP G G A TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr19:8130859G>A ENST00000600128.1 - 64 8788 c.8374C>T c.(8374-8376)Cag>Tag p.Q2792* FBN3_ENST00000601739.1_Nonsense_Mutation_p.Q2792*|FBN3_ENST00000270509.2_Nonsense_Mutation_p.Q2792* Q75N90 FBN3_HUMAN fibrillin 3 2792 proteinaceous extracellular matrix calcium ion binding|extracellular matrix structural constituent NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2) 132 GGCCCTGGCTGCCCCTCTGGC 0.687000 42 309 0 0 1 0 0 KRT31 3881 broad.mit.edu 37 17 39551782 39551782 + Missense_Mutation SNP T T C TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr17:39551782T>C ENST00000251645.2 - 4 734 c.682A>G c.(682-684)Acc>Gcc p.T228A NM_002277.2 NP_002268.2 Q15323 K1H1_HUMAN keratin 31 228 Coil 2.|Rod. epidermis development intermediate filament protein binding|structural constituent of cytoskeleton breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1) 31 Breast(137;0.000496) TGACTCCTGGTCTCGTTCAGC 0.597000 83 520 0 0 1 0 0 RPF2 84154 broad.mit.edu 37 6 111346773 111346773 + Silent SNP T T A TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr6:111346773T>A ENST00000441448.2 + 10 1001 c.909T>A c.(907-909)atT>atA p.I303I NM_032194.1 NP_115570.1 Q9H7B2 RPF2_HUMAN ribosome production factor 2 homolog (S. cerevisiae) 303 nucleolus protein binding p.I303I(1) central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|ovary(2) 7 CAAAAAGAATTAAAAAAAATT 0.368000 17 124 0 0 1 0 0 DGKB 1607 broad.mit.edu 37 7 14724956 14724956 + Missense_Mutation SNP C C T TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr7:14724956C>T ENST00000403951.2 - 10 1162 c.743G>A c.(742-744)cGa>cAa p.R248Q DGKB_ENST00000403963.1_5'UTR|DGKB_ENST00000406247.3_Missense_Mutation_p.R248Q|DGKB_ENST00000407950.1_Missense_Mutation_p.R241Q|DGKB_ENST00000402815.1_Missense_Mutation_p.R248Q|DGKB_ENST00000399322.3_Missense_Mutation_p.R248Q|DGKB_ENST00000444700.2_Missense_Mutation_p.R241Q|DGKB_ENST00000258767.5_Missense_Mutation_p.R248Q Q9Y6T7 DGKB_HUMAN diacylglycerol kinase, beta 90kDa 248 activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation cytoplasm|plasma membrane ATP binding|calcium ion binding|diacylglycerol kinase activity|protein binding NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(34)|ovary(4)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 72 Phosphatidylserine(DB00144) GTGCTTCAGTCGCCACACGTG 0.463000 65 326 0 0 1 0 0 GLI3 2737 broad.mit.edu 37 7 42004926 42004926 + Missense_Mutation SNP A A C TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr7:42004926A>C ENST00000395925.3 - 15 3829 c.3745T>G c.(3745-3747)Tgt>Ggt p.C1249G GLI3_ENST00000479210.1_5'UTR NM_000168.5 NP_000159.3 P10071 GLI3_HUMAN GLI family zinc finger 3 1249 negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis cilium|cytosol|nucleolus beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 112 GGGGCCTTACAGGGCTGTTCA 0.612000 Pallister-Hall syndrome;Greig Cephalopolysyndactyly 65 509 0 0 1 0 0 EP400 57634 broad.mit.edu 37 12 132547087 132547087 + Silent SNP G G A rs12366766 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr12:132547087G>A ENST00000333577.4 + 48 8392 c.8283G>A c.(8281-8283)caG>caA p.Q2761Q EP400_ENST00000389561.2_Silent_p.Q2725Q|EP400_ENST00000332482.4_Silent_p.Q2688Q|EP400_ENST00000330386.6_Silent_p.Q2644Q|EP400_ENST00000389562.2_Silent_p.Q2724Q Q96L91 EP400_HUMAN E1A binding protein p400 2761 Interaction with ZNF42 (By similarity).|Poly-Gln. histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent NuA4 histone acetyltransferase complex|nuclear speck ATP binding|DNA binding|helicase activity p.Q2724Q(16)|p.Q2725Q(1) NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3) 161 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06) agcagcagcagcaacaacagc 0.562000 11 294 0 0 1 0 0 NRG1 3084 broad.mit.edu 37 8 32505402 32505402 + Missense_Mutation SNP G G A rs148668339 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr8:32505402G>A ENST00000520502.2 + 1 166 c.166G>A c.(166-168)Gtg>Atg p.V56M NRG1_ENST00000521670.1_Intron|NRG1_ENST00000341377.5_Intron|NRG1_ENST00000356819.4_Intron|NRG1_ENST00000520407.1_Intron|NRG1_ENST00000519301.1_Intron|NRG1_ENST00000287845.5_Intron|NRG1_ENST00000523079.1_Intron|NRG1_ENST00000338921.4_Intron|NRG1_ENST00000405005.2_Intron|NRG1_ENST00000287842.3_Intron|NRG1_ENST00000287840.5_Intron NM_013959.3 NP_039253.1 Q02297 NRG1_HUMAN neuregulin 1 0 Ig-like C2-type. activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane cytokine activity|ErbB-3 class receptor binding|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1) 39 Breast(100;0.203) KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943) GGGCCTGGCCGTGCCCTGCTG 0.602000 49 326 0 0 1 0 0 CLVS1 157807 broad.mit.edu 37 8 62212794 62212794 + Silent SNP C C T TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr8:62212794C>T ENST00000519846.1 + 3 880 c.408C>T c.(406-408)taC>taT p.Y136Y RP11-787D18.1_ENST00000518064.1_RNA|CLVS1_ENST00000518592.1_Intron|CLVS1_ENST00000325897.4_Silent_p.Y136Y Q8IUQ0 CLVS1_HUMAN clavesin 1 136 CRAL-TRIO. lysosome organization clathrin-coated vesicle|early endosome membrane|trans-Golgi network phosphatidylinositol-3,5-bisphosphate binding|transporter activity p.Y136*(1) endometrium(3)|kidney(4)|large_intestine(4)|lung(21)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1) 41 GAGACCATTACGGCAGGAAGA 0.443000 43 287 0 0 1 0 0 DLGAP4 22839 broad.mit.edu 37 20 35060133 35060133 + Missense_Mutation SNP G G A TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr20:35060133G>A ENST00000373913.3 + 3 493 c.13G>A c.(13-15)Ggt>Agt p.G5S DLGAP4_ENST00000373907.2_Missense_Mutation_p.G5S|DLGAP4_ENST00000339266.5_Missense_Mutation_p.G5S|DLGAP4_ENST00000401952.2_Missense_Mutation_p.G5S Q9Y2H0 DLGP4_HUMAN discs, large (Drosophila) homolog-associated protein 4 5 cell-cell signaling membrane protein binding breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(20)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1) 37 Breast(12;0.0192) Myeloproliferative disorder(115;0.00878) GAAAGGCCTCGGTGACAGCCG 0.692000 43 297 0 0 1 0 0 TAF5L 27097 broad.mit.edu 37 1 229730411 229730411 + Missense_Mutation SNP C C T TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:229730411C>T ENST00000258281.2 - 5 1568 c.1403G>A c.(1402-1404)cGt>cAt p.R468H TAF5L_ENST00000366676.1_Missense_Mutation_p.R468H NM_014409.3 NP_055224.1 O75529 TAF5L_HUMAN TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa 468 histone H3 acetylation|transcription from RNA polymerase II promoter STAGA complex|transcription factor TFTC complex sequence-specific DNA binding transcription factor activity|transcription coactivator activity p.R468P(1) breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1) 11 Breast(184;0.193)|Ovarian(103;0.249) Prostate(94;0.167) CACGGGGCCACGGTGGCCTGT 0.607000 52 752 0 0 1 0 0 CCT6P1 0 broad.mit.edu 37 7 65222986 65222986 + RNA SNP G G T TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr7:65222986G>T ENST00000442266.1 + 0 578 GAATTCTGGCGTTTTTTACAA 0.289000 6 106 1.49906e-05 1.49906e-05 1 1 0 TP53 7157 broad.mit.edu 37 17 7578206 7578206 + Missense_Mutation SNP T T C TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr17:7578206T>C ENST00000420246.2 - 6 775 c.643A>G c.(643-645)Agt>Ggt p.S215G TP53_ENST00000445888.2_Missense_Mutation_p.S215G|TP53_ENST00000574684.1_Intron|TP53_ENST00000455263.2_Missense_Mutation_p.S215G|TP53_ENST00000269305.4_Missense_Mutation_p.S215G|TP53_ENST00000359597.4_Missense_Mutation_p.S215G|TP53_ENST00000413465.2_Missense_Mutation_p.S215G NM_001126114.2|NM_001276696.1 NP_001119586.1|NP_001263625.1 P04637 P53_HUMAN tumor protein p53 215 Interaction with AXIN1 (By similarity).|Interaction with HIPK1 (By similarity).|Required for interaction with FBXO42. S -> C (in sporadic cancers; somatic mutation).|S -> G (in sporadic cancers; somatic mutation).|S -> I (in sporadic cancers; somatic mutation).|S -> K (in sporadic cancers; somatic mutation; requires 2 nucleotide substitutions).|S -> N (in sporadic cancers; somatic mutation).|S -> R (in sporadic cancers; somatic mutation).|S -> T (in sporadic cancers; somatic mutation). activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding p.0?(8)|p.S215G(6)|p.?(5)|p.S215C(5)|p.H214fs*5(2)|p.S215R(2)|p.D208fs*1(1)|p.R213_S215>X(1)|p.S215fs*32(1)|p.R209fs*6(1)|p.T211fs*28(1)|p.S215fs*31(1)|p.D207_V216del10(1)|p.S215fs*27(1)|p.H214fs*7(1)|p.R213fs*32(1)|p.T211_S215delTFRHS(1)|p.H214_S215insX(1)|p.S215del(1)|p.S215fs*29(1)|p.D208_V216delDRNTFRHSV(1) NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174) ACCACCACACTATGTCGAAAA 0.537000 111 """Mis, N, F""" """breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types""" """breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types""" Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) 36 217 0 0 1 0 0 SSMEM1 136263 broad.mit.edu 37 7 129856144 129856144 + Missense_Mutation SNP G G T TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr7:129856144G>T ENST00000297819.3 + 3 620 c.569G>T c.(568-570)aGt>aTt p.S190I NM_145268.3 NP_660311.1 serine-rich single-pass membrane protein 1 AATCTGGGAAGTTACCAAATG 0.507000 89 701 1.46381e-53 1.60104e-53 1 1 0 C5AR2 27202 broad.mit.edu 37 19 47844495 47844495 + Missense_Mutation SNP C C T rs149871591 byFrequency TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr19:47844495C>T ENST00000595464.1 + 2 657 c.439C>T c.(439-441)Cgg>Tgg p.R147W C5AR2_ENST00000257267.2_Missense_Mutation_p.R147W|C5AR2_ENST00000600626.1_Missense_Mutation_p.R147W NM_001271749.1 NP_001258678.1 complement component 5a receptor 2 TACGGTTCAGCGGGCGTGCGG 0.672000 69 550 0 0 1 0 0 DCHS1 8642 broad.mit.edu 37 11 6662161 6662161 + Nonsense_Mutation SNP A A C TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr11:6662161A>C ENST00000299441.3 - 2 1095 c.684T>G c.(682-684)taT>taG p.Y228* NM_003737.2 NP_003728.1 Q96JQ0 PCD16_HUMAN dachsous cadherin-related 1 228 Cadherin 2. calcium-dependent cell-cell adhesion|homophilic cell adhesion integral to membrane|plasma membrane calcium ion binding breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4) 103 Medulloblastoma(188;0.00263)|all_neural(188;0.026) Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135) AACCACCATCATAGGCCTCCA 0.602000 111 557 0 0 1 0 0 SLC6A10P 0 broad.mit.edu 37 16 32890622 32890622 + RNA SNP T T G TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr16:32890622T>G ENST00000330048.5 - 0 3176 NR_003083.2 CGTTGGTGTTTTTGTAGACCA 0.617000 5 108 0 0 1 0 0 PES1 23481 broad.mit.edu 37 22 30983324 30983324 + Missense_Mutation SNP C C T TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr22:30983324C>T ENST00000354694.6 - 4 423 c.317G>A c.(316-318)cGt>cAt p.R106H PES1_ENST00000335214.6_Missense_Mutation_p.R106H|PES1_ENST00000402281.1_5'UTR|PES1_ENST00000405677.1_5'UTR|PES1_ENST00000402284.3_Missense_Mutation_p.R106H NM_001243225.1|NM_014303.3 NP_001230154.1|NP_055118.1 O00541 PESC_HUMAN pescadillo ribosomal biogenesis factor 1 106 Sufficient for nucleolar localization. cell proliferation|maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|regulation of cell cycle chromosome|nucleoplasm|PeBoW complex|preribosome, large subunit precursor protein binding breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3) 29 GTCCTTTAAACGCTCTACAGT 0.498000 65 406 0 0 1 0 0 CTD-2139B15.2 0 broad.mit.edu 37 5 17354041 17354041 + RNA SNP T T C rs7715898 by1000genomes TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr5:17354041T>C ENST00000511821.1 + 0 23 FTH1P10_ENST00000401830.3_RNA TCCGCCAAGCTAGATTCGGGT 0.488000 8 298 0 0 1 0 0 RRAGC 64121 broad.mit.edu 37 1 39305328 39305328 + Missense_Mutation SNP A A C TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:39305328A>C ENST00000373001.3 - 7 1273 c.1097T>G c.(1096-1098)gTt>gGt p.V366G RRAGC_ENST00000474456.1_5'UTR NM_022157.2 NP_071440.1 Q9HB90 RRAGC_HUMAN Ras-related GTP binding C 366 apoptosis|cell growth|cellular protein localization|cellular response to amino acid stimulus|positive regulation of TOR signaling cascade|RNA splicing|small GTPase mediated signal transduction|transcription, DNA-dependent lysosome|nucleus GDP binding|GTP binding|GTPase activity|magnesium ion binding|protein heterodimerization activity endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1) 10 Acute lymphoblastic leukemia(166;0.074) Myeloproliferative disorder(586;0.0393) CACCTCAAAAACCTCATGAAT 0.458000 15 403 0 0 1 0 0 MBOAT7 79143 broad.mit.edu 37 19 54691118 54691118 + Silent SNP G G A TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr19:54691118G>A ENST00000245615.1 - 4 738 c.258C>T c.(256-258)ttC>ttT p.F86F MBOAT7_ENST00000338624.6_Intron|MBOAT7_ENST00000474910.1_5'UTR|MBOAT7_ENST00000431666.2_Intron|MBOAT7_ENST00000391754.1_Silent_p.F86F NM_024298.3 NP_077274.3 Q96N66 MBOA7_HUMAN membrane bound O-acyltransferase domain containing 7 86 phospholipid biosynthetic process integral to membrane acyltransferase activity endometrium(4)|large_intestine(1)|lung(3)|prostate(1)|skin(1) 10 all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19) TGAGGGCTCGGAAGAACAGGA 0.642000 13 74 0 0 1 0 0 GLI3 2737 broad.mit.edu 37 7 42004927 42004927 + Silent SNP G G A TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr7:42004927G>A ENST00000395925.3 - 15 3828 c.3744C>T c.(3742-3744)ccC>ccT p.P1248P GLI3_ENST00000479210.1_5'UTR NM_000168.5 NP_000159.3 P10071 GLI3_HUMAN GLI family zinc finger 3 1248 negative regulation of alpha-beta T cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of smoothened signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative thymic T cell selection|positive regulation of alpha-beta T cell differentiation|positive regulation of transcription from RNA polymerase II promoter|thymocyte apoptosis cilium|cytosol|nucleolus beta-catenin binding|histone acetyltransferase binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|zinc ion binding NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 112 GGGCCTTACAGGGCTGTTCAT 0.617000 Pallister-Hall syndrome;Greig Cephalopolysyndactyly 65 514 0 0 1 0 0 NFIX 4784 broad.mit.edu 37 19 13135824 13135824 + Missense_Mutation SNP G G T TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr19:13135824G>T ENST00000358552.3 + 1 14 c.14G>T c.(13-15)tGc>tTc p.C5F NFIX_ENST00000592199.1_Intron|NFIX_ENST00000585575.1_Intron|NFIX_ENST00000587760.1_Intron|NFIX_ENST00000360105.4_Intron|NFIX_ENST00000588228.1_Intron|NFIX_ENST00000587260.1_Missense_Mutation_p.C5F|NFIX_ENST00000397661.2_Intron Q14938 NFIX_HUMAN nuclear factor I/X (CCAAT-binding transcription factor) 6 DNA replication|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter nucleus DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(1) 11 OV - Ovarian serous cystadenocarcinoma(19;8.2e-22) CTCCCGGCTTGCCGCCTGCAG 0.632000 11 55 1.49906e-05 1.49906e-05 1 1 0 FLG 2312 broad.mit.edu 37 1 152277769 152277769 + Missense_Mutation SNP A A C rs143183339 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:152277769A>C ENST00000368799.1 - 3 9628 c.9593T>G c.(9592-9594)gTc>gGc p.V3198G FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA NM_002016.1 NP_002007.1 P20930 FILA_HUMAN filaggrin 3198 Ser-rich. keratinocyte differentiation cytoplasmic membrane-bounded vesicle|intermediate filament calcium ion binding|structural molecule activity autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12) 424 Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127) LUSC - Lung squamous cell carcinoma(543;0.206) TTGTCCCTGGACTGCCTGTGA 0.552000 Ichthyosis 207 1371 0 0 1 0 0 FOXJ2 55810 broad.mit.edu 37 12 8205432 8205432 + Missense_Mutation SNP G G C TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr12:8205432G>C ENST00000162391.3 + 11 2856 c.1711G>C c.(1711-1713)Gac>Cac p.D571H FOXJ2_ENST00000539192.1_3'UTR NM_018416.2 NP_060886.1 Q9P0K8 FOXJ2_HUMAN forkhead box J2 571 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) CTTCGACTGGGACTTGATCAC 0.552000 6 104 0 0 1 0 0 TFB2M 64216 broad.mit.edu 37 1 246704361 246704361 + Missense_Mutation SNP A A T TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:246704361A>T ENST00000366514.4 - 8 1348 c.1163T>A c.(1162-1164)cTg>cAg p.L388Q NM_022366.2 NP_071761.1 Q9H5Q4 TFB2M_HUMAN transcription factor B2, mitochondrial 388 positive regulation of transcription, DNA-dependent|transcription initiation from mitochondrial promoter mitochondrial nucleoid protein binding|rRNA (adenine-N6,N6-)-dimethyltransferase activity|transcription cofactor activity breast(1)|endometrium(1)|kidney(12)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1) 28 all_cancers(71;4.25e-05)|all_epithelial(71;4.92e-06)|Ovarian(71;0.0254)|all_lung(81;0.0272)|Breast(184;0.0318)|Lung NSC(105;0.0376) OV - Ovarian serous cystadenocarcinoma(106;0.00358) TTCATCATACAGCCATTTATA 0.373000 50 379 0 0 1 0 0 UNC13A 23025 broad.mit.edu 37 19 17760372 17760372 + Silent SNP G G A TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr19:17760372G>A ENST00000428389.2 - 14 1727 c.1728C>T c.(1726-1728)atC>atT p.I576I UNC13A_ENST00000519716.2_Silent_p.I488I|UNC13A_ENST00000252773.7_Silent_p.I488I|UNC13A_ENST00000552293.1_Silent_p.I488I|UNC13A_ENST00000551649.1_Silent_p.I488I|UNC13A_ENST00000550896.1_Silent_p.I488I Q9UPW8 UN13A_HUMAN unc-13 homolog A (C. elegans) 488 exocytosis|intracellular signal transduction cell junction|cytoplasm|presynaptic membrane metal ion binding p.I488I(1)|p.I576I(1) breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2) 61 GCATGCTGTCGATGATGATGA 0.567000 82 581 0 0 1 0 0 FAM179B 23116 broad.mit.edu 37 14 45473306 45473306 + Missense_Mutation SNP T T C TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr14:45473306T>C ENST00000361462.2 + 4 2564 c.2381T>C c.(2380-2382)tTt>tCt p.F794S FAM179B_ENST00000382233.2_Missense_Mutation_p.F794S|FAM179B_ENST00000361577.3_Missense_Mutation_p.F794S|KLHL28_ENST00000553817.1_Intron Q9Y4F4 F179B_HUMAN family with sequence similarity 179, member B 794 binding endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2) 45 CAGCAAACATTTGGTAGTCAA 0.363000 51 260 0 0 1 0 0 VAC14 55697 broad.mit.edu 37 16 70726807 70726807 + Silent SNP G G A TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr16:70726807G>A ENST00000261776.5 - 18 2363 c.2103C>T c.(2101-2103)ctC>ctT p.L701L VAC14_ENST00000536184.2_Silent_p.L133L NM_018052.3 NP_060522.3 Q08AM6 VAC14_HUMAN Vac14 homolog (S. cerevisiae) 701 interspecies interaction between organisms endoplasmic reticulum|endosome membrane|microsome protein binding|receptor activity breast(2)|endometrium(2)|kidney(10)|large_intestine(1)|lung(10)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 33 Ovarian(137;0.0699) GCAGGAGCATGAGCAGGCCGT 0.662000 16 97 0 0 1 0 0 ZYG11B 79699 broad.mit.edu 37 1 53287249 53287249 + Missense_Mutation SNP G G A rs151077871 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:53287249G>A ENST00000294353.6 + 14 2328 c.2183G>A c.(2182-2184)cGc>cAc p.R728H ZYG11B_ENST00000443756.2_Missense_Mutation_p.R658H NM_024646.2 NP_078922.1 Q9C0D3 ZY11B_HUMAN zyg-11 family member B, cell cycle regulator 728 protein binding breast(1)|endometrium(1)|kidney(6)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2) 30 CACATTGTGCGCCATGGGAGG 0.418000 45 322 0 0 1 0 0 POM121L9P 0 broad.mit.edu 37 22 24659805 24659805 + RNA SNP C C G TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr22:24659805C>G ENST00000414583.2 + 0 3330 NR_003714.1 TGCTCCCTATCTGCGCACCCG 0.607000 5 43 0 0 1 0 0 LRCH3 84859 broad.mit.edu 37 3 197553808 197553808 + Missense_Mutation SNP C C T TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr3:197553808C>T ENST00000438796.2 + 5 744 c.700C>T c.(700-702)Cct>Tct p.P234S LRCH3_ENST00000425562.2_Missense_Mutation_p.P234S|LRCH3_ENST00000414675.2_Missense_Mutation_p.P234S|LRCH3_ENST00000334859.4_Missense_Mutation_p.P234S|LRCH3_ENST00000441090.2_Missense_Mutation_p.P108S Q96II8 LRCH3_HUMAN leucine-rich repeats and calponin homology (CH) domain containing 3 234 extracellular region breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 29 all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976) Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07) GBM - Glioblastoma multiforme(93;0.119) TACCACAATCCCTGTTTGTTA 0.423000 28 471 0 0 1 0 0 POTEG 404785 broad.mit.edu 37 14 19553582 19553582 + Missense_Mutation SNP A A T TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr14:19553582A>T ENST00000409832.3 + 1 218 c.166A>T c.(166-168)Aca>Tca p.T56S NM_001005356.2 NP_001005356.1 Q6S5H5 POTEG_HUMAN POTE ankyrin domain family, member G 56 cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1) 47 TGCTATGAAGACACTCAGGAG 0.617000 95 3106 0 0 1 0 0 PHF13 148479 broad.mit.edu 37 1 6680069 6680071 + In_Frame_Del DEL GAA GAA - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:6680069_6680071delGAA ENST00000377648.4 + 3 730_732 c.348_350delGAA c.(346-351)ctg>ct p.LK116del PHF13_ENST00000495385.1_Intron NM_153812.2 NP_722519.2 Q86YI8 PHF13_HUMAN PHD finger protein 13 116 cell division|chromatin modification|mitotic chromosome condensation nucleoplasm chromatin binding|methylated histone residue binding|zinc ion binding endometrium(3)|large_intestine(1)|lung(3) 7 Ovarian(185;0.0212)|all_lung(157;0.154) all_cancers(23;1.46e-33)|all_epithelial(116;9.26e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Breast(487;0.000353)|Renal(390;0.0007)|Colorectal(325;0.00104)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443) Colorectal(212;1.19e-07)|COAD - Colon adenocarcinoma(227;1.3e-05)|Kidney(185;4.88e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000501)|KIRC - Kidney renal clear cell carcinoma(229;0.000871)|STAD - Stomach adenocarcinoma(132;0.0165)|READ - Rectum adenocarcinoma(331;0.0642) cggacaagctgaagaagaagaag 0.576 11 487 --- --- --- --- VAMP3 9341 broad.mit.edu 37 1 7838212 7838214 + In_Frame_Del DEL TCA TCA - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:7838212_7838214delTCA ENST00000054666.6 + 4 381_383 c.266_268delTCA c.(265-270)ttc>t p.FI89del VAMP3_ENST00000470357.1_In_Frame_Del_p.FI61del NM_004781.3 NP_004772.1 Q15836 VAMP3_HUMAN vesicle-associated membrane protein 3 89 cellular membrane fusion|positive regulation of receptor recycling|protein complex assembly|protein transport|retrograde transport, endosome to Golgi|substrate adhesion-dependent cell spreading|vesicle docking involved in exocytosis cell junction|clathrin-coated vesicle|integral to membrane|recycling endosome|synapse|synaptosome protein binding breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3) 6 Ovarian(185;0.0634)|all_lung(157;0.178) all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;6.33e-69)|GBM - Glioblastoma multiforme(8;2.07e-34)|Colorectal(212;1.36e-07)|COAD - Colon adenocarcinoma(227;1.38e-05)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000805)|KIRC - Kidney renal clear cell carcinoma(229;0.000917)|STAD - Stomach adenocarcinoma(132;0.000985)|READ - Rectum adenocarcinoma(331;0.0642) CTGGTTATCTTCATCATCATCAT 0.365 8 1347 --- --- --- --- CROCCP2 0 broad.mit.edu 37 1 16953827 16953828 + RNA INS - - C rs57007114 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:16953827_16953828insC ENST00000412962.1 - 0 477 TCACTTTCCTGCCCGAACCTCC 0.609 7 261 --- --- --- --- ZBTB40 9923 broad.mit.edu 37 1 22838561 22838563 + In_Frame_Del DEL AAG AAG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:22838561_22838563delAAG ENST00000404138.1 + 12 2906_2908 c.2395_2397delAAG c.(2395-2397)del p.K803del ZBTB40_ENST00000374651.4_In_Frame_Del_p.K691del|ZBTB40_ENST00000375647.4_In_Frame_Del_p.K803del NM_001083621.1 NP_001077090.1 Q9NUA8 ZBT40_HUMAN zinc finger and BTB domain containing 40 803 bone mineralization|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent nucleus DNA binding|zinc ion binding endometrium(4)|kidney(4)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 26 Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255) UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.86e-26)|Colorectal(126;8.55e-08)|COAD - Colon adenocarcinoma(152;4.1e-06)|GBM - Glioblastoma multiforme(114;1.39e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000712)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.216) CGATGCCCCCAAGAAGAAGAAGA 0.517 18 573 --- --- --- --- SYF2 25949 broad.mit.edu 37 1 25555531 25555531 + Frame_Shift_Del DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:25555531delT ENST00000236273.4 - 3 241 c.216delA c.(214-216)aafs p.K72fs SYF2_ENST00000354361.3_Intron NM_015484.4 NP_056299.1 O95926 SYF2_HUMAN SYF2 pre-mRNA-splicing factor 72 catalytic step 2 spliceosome kidney(1)|large_intestine(1)|lung(4) 6 Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936) UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.5e-26)|Colorectal(126;2.54e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000455)|STAD - Stomach adenocarcinoma(196;0.000766)|KIRC - Kidney renal clear cell carcinoma(1967;0.00145)|GBM - Glioblastoma multiforme(114;0.00443)|READ - Rectum adenocarcinoma(331;0.0936)|Lung(427;0.201) CCAAACGAGCTTTTTTGGCTT 0.348 7 880 --- --- --- --- TMCO2 127391 broad.mit.edu 37 1 40713708 40713709 + Frame_Shift_Del DEL TC TC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:40713708_40713709delTC ENST00000372766.3 + 1 136_137 c.43_44delTC c.(43-45)tfs p.S15fs TMCO2_ENST00000468258.1_Intron NM_001008740.3 NP_001008740.1 Q7Z6W1 TMCO2_HUMAN transmembrane and coiled-coil domains 2 15 integral to membrane kidney(1)|large_intestine(3)|lung(1)|ovary(1) 6 Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074) Myeloproliferative disorder(586;0.0255) OV - Ovarian serous cystadenocarcinoma(33;6.3e-18) CCTCTTAGAGTCTCTCTCTCTC 0.406 13 1309 --- --- --- --- ZMPSTE24 10269 broad.mit.edu 37 1 40756542 40756543 + Frame_Shift_Ins INS - - T rs137854889 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:40756542_40756543insT ENST00000372759.3 + 9 1241_1242 c.1076_1077insT c.(1075-1077)tttfs p.F359fs NM_005857.4 NP_005848.2 O75844 FACE1_HUMAN zinc metallopeptidase STE24 359 endoplasmic reticulum membrane|Golgi membrane|integral to membrane metal ion binding|metalloexopeptidase activity endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|prostate(1)|skin(1) 16 Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074) Myeloproliferative disorder(586;0.0255) OV - Ovarian serous cystadenocarcinoma(33;6.3e-18) TCTTTCCTGTGTTTTTTTTTAT 0.332 9 450 --- --- --- --- MAST2 23139 broad.mit.edu 37 1 46494559 46494559 + Frame_Shift_Del DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:46494559delT ENST00000361297.2 + 18 2455 c.2172delT c.(2170-2172)ccfs p.P724fs MAST2_ENST00000372009.2_Frame_Shift_Del_p.P654fs|MAST2_ENST00000372008.1_Frame_Shift_Del_p.P609fs NM_015112.2 NP_055927.2 Q6P0Q8 MAST2_HUMAN microtubule associated serine/threonine kinase 2 724 Protein kinase. regulation of interleukin-12 biosynthetic process|spermatid differentiation cytoplasm|cytoskeleton|plasma membrane ATP binding|magnesium ion binding|phosphatase binding|protein serine/threonine kinase activity breast(1)|lung(3)|ovary(5)|stomach(2) 11 Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184) GCTGCGTCCCTTTTTTTGGAG 0.552 8 1560 --- --- --- --- FAAH 2166 broad.mit.edu 37 1 46871370 46871370 + Frame_Shift_Del DEL C C - rs146965747 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:46871370delC ENST00000243167.8 + 5 773 c.689delC c.(688-690)tcfs p.S230fs FAAH_ENST00000493735.1_3'UTR NM_001441.2 NP_001432.2 O00519 FAAH1_HUMAN fatty acid amide hydrolase 230 fatty acid catabolic process cytoplasm|cytoskeleton|endomembrane system|integral to membrane|organelle membrane carbon-nitrogen ligase activity, with glutamine as amido-N-donor|fatty acid amide hydrolase activity breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1) 22 Acute lymphoblastic leukemia(166;0.155) Propofol(DB00818)|Thiopental(DB00599) TCTGGAGGCTCCCCCCTGGGC 0.637 8 814 --- --- --- --- NDC1 55706 broad.mit.edu 37 1 54298190 54298192 + In_Frame_Del DEL TTA TTA - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:54298190_54298192delTTA ENST00000371429.3 - 3 849_851 c.251_253delTAA c.(250-255)agt>a p.IS84del NDC1_ENST00000540001.1_In_Frame_Del_p.IS84del|NDC1_ENST00000537333.1_5'UTR|NDC1_ENST00000480952.1_5'UTR|NDC1_ENST00000234725.8_5'UTR NM_001168551.1|NM_018087.4 NP_001162023.1|NP_060557.3 NDC1 transmembrane nucleoporin TTGAAAATACTTATTATTATTAT 0.305 8 319 --- --- --- --- ST6GALNAC5 81849 broad.mit.edu 37 1 77334277 77334279 + In_Frame_Del DEL GCA GCA - rs113832855 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:77334277_77334279delGCA ENST00000477717.1 + 2 346_348 c.111_113delGCA c.(109-114)ccg>cc p.PQ37del ST6GALNAC5_ENST00000496845.1_3'UTR NM_030965.1 NP_112227.1 Q9BVH7 SIA7E_HUMAN ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5 37 protein glycosylation integral to Golgi membrane sialyltransferase activity endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1) 18 AGCGGCCCCCgcagcagcagcag 0.700 8 282 --- --- --- --- FNDC7 163479 broad.mit.edu 37 1 109276138 109276138 + Frame_Shift_Del DEL A A - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:109276138delA ENST00000370017.3 + 10 2401 c.2124delA c.(2122-2124)ccfs p.P708fs FNDC7_ENST00000271311.2_Frame_Shift_Del_p.P709fs NM_001144937.1 NP_001138409.1 Q5VTL7 FNDC7_HUMAN fibronectin type III domain containing 7 709 Fibronectin type-III 8. extracellular region p.I478fs*4(1) breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|skin(4)|stomach(1)|urinary_tract(1) 20 all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728) Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244) CTTTCTGTCCAAAAAAAATAT 0.363 8 508 --- --- --- --- KCND3 3752 broad.mit.edu 37 1 112524444 112524445 + Frame_Shift_Ins INS - - G TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:112524444_112524445insG ENST00000369697.1 - 1 973_974 c.904_905insC c.(904-906)ccafs p.P302fs KCND3_ENST00000315987.2_Frame_Shift_Ins_p.P302fs|KCND3_ENST00000302127.4_Frame_Shift_Ins_p.P302fs Q9UK17 KCND3_HUMAN potassium voltage-gated channel, Shal-related subfamily, member 3 302 sarcolemma|voltage-gated potassium channel complex A-type (transient outward) potassium channel activity|metal ion binding NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2) 49 all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05) all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231) CTGGGAGTGGCGGGAAAACTTG 0.579 7 565 --- --- --- --- SRGAP2B 0 broad.mit.edu 37 1 144043905 144043906 + RNA INS - - G TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:144043905_144043906insG ENST00000467933.1 + 0 1108 tcgctcacgctggagctgtaga 0.535 8 98 --- --- --- --- TCHH 7062 broad.mit.edu 37 1 152083818 152083820 + In_Frame_Del DEL CGG CGG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:152083818_152083820delCGG ENST00000368804.1 - 2 1872_1874 c.1873_1875delCCG c.(1873-1875)del p.P625del NM_007113.2 NP_009044.2 Q07283 TRHY_HUMAN trichohyalin 625 9 X 28 AA approximate tandem repeats. keratinization cytoskeleton calcium ion binding NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4) 105 Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127) LUSC - Lung squamous cell carcinoma(543;0.206) TCTCTTCCTCCGGCTCCTCGCGC 0.680 7 886 --- --- --- --- FLAD1 80308 broad.mit.edu 37 1 154962050 154962050 + Frame_Shift_Del DEL A A - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:154962050delA ENST00000368433.1 + 3 1475 c.1132delA c.(1132-1134)aafs p.K379fs FLAD1_ENST00000405236.2_Intron|FLAD1_ENST00000292180.3_Frame_Shift_Del_p.K379fs|FLAD1_ENST00000368428.1_5'UTR|FLAD1_ENST00000368432.1_Frame_Shift_Del_p.K282fs|FLAD1_ENST00000315144.10_Frame_Shift_Del_p.K282fs|FLAD1_ENST00000295530.2_Intron Q8NFF5 FAD1_HUMAN flavin adenine dinucleotide synthetase 1 379 FAD biosynthetic process|Mo-molybdopterin cofactor biosynthetic process|water-soluble vitamin metabolic process cytosol ATP binding|FMN adenylyltransferase activity p.K378E(3) endometrium(3)|kidney(4)|large_intestine(2)|lung(7)|ovary(3)|skin(3) 22 all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877) BRCA - Breast invasive adenocarcinoma(34;0.00034) TTCTTTGGGGAAAAAGGTGGC 0.567 7 783 --- --- --- --- GPATCH4 54865 broad.mit.edu 37 1 156565503 156565504 + Frame_Shift_Ins INS - - T TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:156565503_156565504insT ENST00000368232.4 - 8 746_747 c.614_615insA c.(613-615)aaafs p.K205fs GPATCH4_ENST00000438976.2_Frame_Shift_Ins_p.K210fs|GPATCH4_ENST00000497287.1_5'UTR NM_015590.3|NM_182679.2 NP_056405.2|NP_872620.1 Q5T3I0 GPTC4_HUMAN G patch domain containing 4 205 intracellular nucleic acid binding autonomic_ganglia(1)|breast(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(3)|stomach(1) 17 all_hematologic(923;0.088)|Hepatocellular(266;0.158) TTTTCTTTTTCTTTTTTTTGGG 0.535 7 851 --- --- --- --- PRCC 5546 broad.mit.edu 37 1 156761535 156761536 + Frame_Shift_Ins INS - - C TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:156761535_156761536insC ENST00000271526.4 + 4 1402_1403 c.1130_1131insC c.(1129-1131)gccfs p.A377fs PRCC_ENST00000491853.1_3'UTR|PRCC_ENST00000353233.3_Intron NM_005973.4 NP_005964.3 Q92733 PRCC_HUMAN papillary renal cell carcinoma (translocation-associated) 377 cell cycle|mitotic cell cycle checkpoint nucleus protein binding p.Q380fs*12(1) PRCC/TFE3(25) breast(1)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(5)|upper_aerodigestive_tract(1) 15 all_hematologic(923;0.0839)|Hepatocellular(266;0.158) CCGGCCCTGGTCCCCCCCCAGG 0.530 T TFE3 papillary renal 70 468 --- --- --- --- TMCO1 54499 broad.mit.edu 37 1 165712550 165712551 + Splice_Site INS - - A TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:165712550_165712551insA ENST00000367881.5 - 6 752 c.e6-2 TMCO1_ENST00000464650.1_Splice_Site|TMCO1_ENST00000580248.1_Splice_Site|TMCO1_ENST00000392129.6_Splice_Site Q9UM00 TMCO1_HUMAN transmembrane and coiled-coil domains 1 endoplasmic reticulum membrane|Golgi membrane|integral to membrane central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5) 9 all_hematologic(923;0.048)|Acute lymphoblastic leukemia(8;0.155) CCATCAAATCTAAAAGAAAAAA 0.381 7 369 --- --- --- --- SCYL3 57147 broad.mit.edu 37 1 169833511 169833511 + Splice_Site DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:169833511delT ENST00000367772.4 - 9 1151 c.955_splice c.e9+1 p.K318_splice SCYL3_ENST00000367770.1_Splice_Site_p.K318_splice|SCYL3_ENST00000367771.5_Splice_Site_p.K318_splice|SCYL3_ENST00000470238.1_5'UTR NM_181093.3 NP_851607.2 Q8IZE3 PACE1_HUMAN SCY1-like 3 (S. cerevisiae) 318 cell migration Golgi apparatus|lamellipodium ATP binding|protein binding|protein kinase activity breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 27 all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181) AGCATTCACCTTTTTTGGGGC 0.393 9 709 --- --- --- --- CAMSAP2 23271 broad.mit.edu 37 1 200822548 200822549 + Frame_Shift_Ins INS - - A rs11553541 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:200822548_200822549insA ENST00000358823.2 + 13 4018_4019 c.3748_3749insA c.(3748-3750)aaafs p.K1250fs CAMSAP2_ENST00000413307.2_Frame_Shift_Ins_p.K1234fs|CAMSAP2_ENST00000236925.4_Frame_Shift_Ins_p.K1261fs NM_203459.1 NP_982284.1 Q08AD1 CAMP2_HUMAN calmodulin regulated spectrin-associated protein family, member 2 1261 cytoplasm|microtubule protein binding AGTAGTAAAACAAAAAAAACAG 0.366 8 597 --- --- --- --- IPO9 55705 broad.mit.edu 37 1 201843998 201844000 + In_Frame_Del DEL GAG GAG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:201843998_201844000delGAG ENST00000361565.4 + 22 2941_2943 c.2872_2874delGAG c.(2872-2874)del p.E962del NM_018085.4 NP_060555.2 Q96P70 IPO9_HUMAN importin 9 962 protein import into nucleus cytoplasm|nucleus histone binding|protein transporter activity cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1) 38 ggaggaggaagaggaggaggagg 0.443 8 687 --- --- --- --- TMEM63A 9725 broad.mit.edu 37 1 226034840 226034842 + In_Frame_Del DEL CTG CTG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:226034840_226034842delCTG ENST00000366835.3 - 24 2593_2595 c.2323_2325delCAG c.(2323-2325)del p.Q775del NM_014698.2 NP_055513.2 O94886 TM63A_HUMAN transmembrane protein 63A 775 integral to membrane|lysosomal membrane nucleotide binding p.Q775delQ(1) breast(2)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1) 24 Breast(184;0.197) CACCATAGGTCTGCTGCTGCTGC 0.626 26 858 --- --- --- --- OR2T33 391195 broad.mit.edu 37 1 248437112 248437112 + Frame_Shift_Del DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr1:248437112delT ENST00000318021.2 - 1 26 c.5delA c.(4-6)ggfs p.E2fs NM_001004695.1 NP_001004695.1 Q8NG76 O2T33_HUMAN olfactory receptor, family 2, subfamily T, member 33 2 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity NS(2)|breast(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(41)|ovary(1)|prostate(1)|skin(4) 67 all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) OV - Ovarian serous cystadenocarcinoma(106;0.0245) ATTTCTCATCTCCATAATTTC 0.428 11 658 --- --- --- --- ATP6V1C2 245973 broad.mit.edu 37 2 10917819 10917820 + Frame_Shift_Del DEL AG AG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr2:10917819_10917820delAG ENST00000272238.4 + 11 1043_1044 c.934_935delAG c.(934-936)afs p.R312fs ATP6V1C2_ENST00000381661.3_Intron NM_001039362.1 NP_001034451.1 Q8NEY4 VATC2_HUMAN ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C2 312 ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport cytosol|proton-transporting V-type ATPase, V1 domain endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 19 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191) Epithelial(75;0.15)|OV - Ovarian serous cystadenocarcinoma(76;0.152) GCAGACCGACAGAGAGAGAGAG 0.604 19 593 --- --- --- --- SMC6 79677 broad.mit.edu 37 2 17898126 17898126 + Frame_Shift_Del DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr2:17898126delT ENST00000448223.2 - 14 1497 c.1228delA c.(1228-1230)tafs p.I410fs SMC6_ENST00000402989.1_Frame_Shift_Del_p.I410fs|SMC6_ENST00000381272.4_Frame_Shift_Del_p.I436fs|SMC6_ENST00000351948.4_Frame_Shift_Del_p.I410fs NM_001142286.1 NP_001135758.1 Q96SB8 SMC6_HUMAN structural maintenance of chromosomes 6 410 DNA recombination|DNA repair chromosome|nucleus ATP binding NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2) 43 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158) AACCAAGATATTTTTTTTTGT 0.343 10 293 --- --- --- --- OTOF 9381 broad.mit.edu 37 2 26693554 26693556 + In_Frame_Del DEL CTT CTT - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr2:26693554_26693556delCTT ENST00000272371.2 - 32 4054_4056 c.3928_3930delAAG c.(3928-3930)del p.K1310del OTOF_ENST00000338581.6_In_Frame_Del_p.K543del|OTOF_ENST00000402415.3_In_Frame_Del_p.K620del|OTOF_ENST00000339598.3_In_Frame_Del_p.K543del|OTOF_ENST00000403946.3_In_Frame_Del_p.K1310del NM_194248.2 NP_919224.1 Q9HC10 OTOF_HUMAN otoferlin 1310 Poly-Lys. cellular membrane fusion|sensory perception of sound|synaptic vesicle exocytosis basolateral plasma membrane|cell junction|cytosol|endoplasmic reticulum membrane|integral to membrane|membrane fraction|synaptic vesicle membrane calcium ion binding NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1) 106 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) CCGCAGTGCCcttcttcttcttc 0.576 7 469 --- --- --- --- FAM98A 25940 broad.mit.edu 37 2 33813402 33813402 + Splice_Site DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr2:33813402delT ENST00000403368.1 - 4 591 c.522_splice c.e4+1 p.K174_splice FAM98A_ENST00000498340.1_Intron|FAM98A_ENST00000441530.2_Intron|FAM98A_ENST00000238823.8_Splice_Site_p.K174_splice NM_015475.3 NP_056290.3 Q8NCA5 FA98A_HUMAN family with sequence similarity 98, member A 175 NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(1) 24 all_hematologic(175;0.115) AAGGTCTTACTTTTTTTTCAA 0.338 8 727 --- --- --- --- AC016995.3 0 broad.mit.edu 37 2 38710017 38710019 + RNA DEL AAT AAT - rs2005502 by1000genomes TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr2:38710017_38710019delAAT ENST00000417039.1 - 0 696 TTCTTtaaaaaataaataaataa 0.246 18 19 --- --- --- --- EPAS1 2034 broad.mit.edu 37 2 46609576 46609576 + Frame_Shift_Del DEL A A - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr2:46609576delA ENST00000263734.3 + 15 2810 c.2300delA c.(2299-2301)cafs p.Q767fs NM_001430.4 NP_001421.2 Q99814 EPAS1_HUMAN endothelial PAS domain protein 1 767 angiogenesis|myoblast cell fate commitment|positive regulation of transcription from RNA polymerase II promoter|response to hypoxia transcription factor complex histone acetyltransferase binding|protein heterodimerization activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|signal transducer activity|transcription coactivator activity|transcription factor binding NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 39 all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18) LUSC - Lung squamous cell carcinoma(58;0.151) AAGTTCACCCAAAACCCCATG 0.572 7 1113 --- --- --- --- FOXN2 3344 broad.mit.edu 37 2 48573666 48573667 + Frame_Shift_Ins INS - - A TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr2:48573666_48573667insA ENST00000340553.3 + 3 574_575 c.313_314insA c.(313-315)aaafs p.K105fs NM_002158.3 NP_002149.2 P32314 FOXN2_HUMAN forkhead box N2 105 embryo development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development transcription factor complex DNA bending activity|double-stranded DNA binding|promoter 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 activator activity|transcription factor binding endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|urinary_tract(1) 13 all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175) Lung(47;0.0272)|LUSC - Lung squamous cell carcinoma(58;0.036) CCAGAACCCAGAAAAAAAATCA 0.431 7 1084 --- --- --- --- IGKV1D-8 0 broad.mit.edu 37 2 90259860 90259861 + RNA INS - - C TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr2:90259860_90259861insC ENST00000471857.1 + 0 236 AATTTACTCAGCCAATGTGCTC 0.480 9 1032 --- --- --- --- AC027612.3 0 broad.mit.edu 37 2 91887905 91887906 + RNA INS - - T TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr2:91887905_91887906insT ENST00000436174.1 - 0 540 GCTATTTTCCATTTTTTTTTTT 0.292 18 288 --- --- --- --- TEKT4 150483 broad.mit.edu 37 2 95539831 95539832 + Frame_Shift_Ins INS - - C rs33966600 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr2:95539831_95539832insC ENST00000295201.4 + 3 828_829 c.691_692insC c.(691-693)ctcfs p.L231fs AC097374.2_ENST00000568768.1_RNA NM_144705.2 NP_653306.1 Q8WW24 TEKT4_HUMAN tektin 4 231 cell projection organization|microtubule cytoskeleton organization cilium axoneme|flagellar axoneme|microtubule NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1) 28 GGCTCATCCGTACTCCACCACC 0.663 9 613 --- --- --- --- ANKRD36 375248 broad.mit.edu 37 2 97808574 97808575 + Splice_Site INS - - A TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr2:97808574_97808575insA ENST00000420699.2 + 8 1145 c.e8+2 ANKRD36_ENST00000461153.2_Splice_Site NM_001164315.1 NP_001157787.1 A6QL64 AN36A_HUMAN ankyrin repeat domain 36 p.?(1) endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1) 23 CTGGGACAGGTATTTTGGAATA 0.366 33 58 --- --- --- --- FOXD4L1 200350 broad.mit.edu 37 2 114257058 114257059 + In_Frame_Ins INS - - GGC TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr2:114257058_114257059insGGC ENST00000306507.5 + 1 398_399 c.225_226insGGC c.(223-228)gagcgg>gaGGCgcgg p.75_76ER>EAR NM_012184.4 NP_036316.1 Q9NU39 FX4L1_HUMAN forkhead box D4-like 1 75 axon extension involved in axon guidance|cartilage development|dichotomous subdivision of terminal units involved in ureteric bud branching|embryo development|enteric nervous system development|iridophore differentiation|lateral line nerve glial cell development|melanocyte differentiation|neural crest cell migration|pattern specification process|peripheral nervous system development|positive regulation of BMP signaling pathway|positive regulation of kidney development|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|sympathetic nervous system development transcription factor complex DNA bending activity|double-stranded DNA binding|promoter 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 activator activity|transcription factor binding p.G76C(1) NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(2) 26 AGCACATCGAGGGCGGCGGCCC 0.708 8 527 --- --- --- --- PLA2R1 0 broad.mit.edu 37 2 160801442 160801442 + Frame_Shift_Del DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr2:160801442delT ENST00000283243.7 - 28 4325 c.4119delA c.(4117-4119)aafs p.K1373fs PLA2R1_ENST00000460710.1_5'UTR NM_001195641.1|NM_007366.4 NP_001182570.1|NP_031392.3 Q13018 PLA2R_HUMAN phospholipase A2 receptor 1, 180kDa 1373 C-type lectin 8. endocytosis extracellular space|integral to plasma membrane receptor activity|sugar binding PLA2R1/RBMS1(2) central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1) 60 ATATAAAGCCTTTTTTTTCTT 0.403 8 1297 --- --- --- --- ITGB6 3694 broad.mit.edu 37 2 160968592 160968592 + Splice_Site DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr2:160968592delT ENST00000283249.2 - 13 2337 c.2101_splice c.e13+1 p.K700_splice ITGB6_ENST00000428609.2_Splice_Site_p.K658_splice|ITGB6_ENST00000409967.2_Splice_Site_p.K593_splice|ITGB6_ENST00000409872.1_Splice_Site_p.K700_splice P18564 ITB6_HUMAN integrin, beta 6 700 cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|multicellular organismal development integrin complex receptor activity breast(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1) 23 AACACCCACCTTTTTCATTGA 0.418 7 1315 --- --- --- --- SSB 6741 broad.mit.edu 37 2 170665008 170665008 + Frame_Shift_Del DEL A A - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr2:170665008delA ENST00000409333.1 + 7 818 c.571delA c.(571-573)aafs p.K192fs SSB_ENST00000260956.4_Frame_Shift_Del_p.K192fs P05455 LA_HUMAN Sjogren syndrome antigen B (autoantigen La) 192 histone mRNA metabolic process|tRNA modification nucleus|ribonucleoprotein complex mRNA binding|nucleotide binding|protein binding|tRNA binding endometrium(3)|large_intestine(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1) 12 TTACTTTGCCAAAAAAAATGA 0.323 7 481 --- --- --- --- ZDBF2 57683 broad.mit.edu 37 2 207174427 207174428 + Frame_Shift_Ins INS - - A TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr2:207174427_207174428insA ENST00000374423.3 + 5 5561_5562 c.5175_5176insA c.(5173-5178)gaaaaafs p.EK1725fs NM_020923.1 NP_065974.1 Q9HCK1 ZDBF2_HUMAN zinc finger, DBF-type containing 2 1725 nucleic acid binding|zinc ion binding endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 95 GAAGGGCTGATAAAAAAAAACG 0.450 12 260 --- --- --- --- IKZF2 22807 broad.mit.edu 37 2 214012402 214012405 + Frame_Shift_Del DEL ACAA ACAA - rs6738070 by1000genomes TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr2:214012402_214012405delACAA ENST00000442445.1 - 3 241_244 c.184_187delTTGT c.(184-189)gtfs p.LC62fs IKZF2_ENST00000457361.1_Intron|IKZF2_ENST00000342002.2_Intron|IKZF2_ENST00000421754.2_Intron|IKZF2_ENST00000413091.3_Intron|IKZF2_ENST00000374327.4_Intron|IKZF2_ENST00000434687.1_Intron|IKZF2_ENST00000451136.2_Intron|IKZF2_ENST00000374319.4_Intron Q9UKS7 IKZF2_HUMAN IKAROS family zinc finger 2 (Helios) 0 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(7)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 23 Esophageal squamous(248;0.0559)|Renal(323;0.218) UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;2.97e-07)|all cancers(144;1.53e-05)|LUSC - Lung squamous cell carcinoma(224;0.00599)|Lung(261;0.00792) ACACACACACACAAAAAAAAATCA 0.407 9 695 --- --- --- --- GIGYF2 26058 broad.mit.edu 37 2 233681704 233681704 + Frame_Shift_Del DEL A A - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr2:233681704delA ENST00000373566.3 + 21 2595 c.2398delA c.(2398-2400)aafs p.K800fs GIGYF2_ENST00000452341.2_Frame_Shift_Del_p.K609fs|GIGYF2_ENST00000409451.3_Frame_Shift_Del_p.K799fs|GIGYF2_ENST00000409547.1_Frame_Shift_Del_p.K778fs|GIGYF2_ENST00000409480.1_Frame_Shift_Del_p.K800fs|GIGYF2_ENST00000409196.3_Frame_Shift_Del_p.K772fs|GIGYF2_ENST00000373563.4_Frame_Shift_Del_p.K778fs Q6Y7W6 PERQ2_HUMAN GRB10 interacting GYF protein 2 778 Gln-rich.|Glu-rich. cell death protein binding NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1) 63 Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839) Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145) AGAAGAAAGGAAAAGGCGAGA 0.488 8 1422 --- --- --- --- GAL3ST2 64090 broad.mit.edu 37 2 242738494 242738496 + In_Frame_Del DEL TCC TCC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr2:242738494_242738496delTCC ENST00000192314.6 + 2 175_177 c.44_46delTCC c.(43-48)atc>a p.IL15del NM_022134.2 NP_071417.2 Q9H3Q3 G3ST2_HUMAN galactose-3-O-sulfotransferase 2 15 biosynthetic process Golgi cisterna membrane|integral to membrane galactosylceramide sulfotransferase activity p.L16I(1) endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|prostate(1)|skin(1) 14 all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244) Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833) TTCCGGGTCATCCTCCTCCTCCT 0.631 8 581 --- --- --- --- TATDN2 9797 broad.mit.edu 37 3 10291121 10291123 + In_Frame_Del DEL CTC CTC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr3:10291121_10291123delCTC ENST00000287652.4 + 2 1288_1290 c.237_239delCTC c.(235-240)aac>aa p.NS79del TATDN2_ENST00000448281.2_In_Frame_Del_p.NS79del|RP11-438J1.1_ENST00000450534.1_In_Frame_Del_p.NS22del NM_014760.3 NP_055575.3 Q93075 TATD2_HUMAN TatD DNase domain containing 2 79 nucleus endodeoxyribonuclease activity, producing 5'-phosphomonoesters|metal ion binding autonomic_ganglia(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(9)|pancreas(2)|prostate(1)|stomach(2) 28 GCAGAAATAACTCCTCCTCCTCC 0.635 7 1431 --- --- --- --- USP4 7375 broad.mit.edu 37 3 49321969 49321971 + In_Frame_Del DEL TCT TCT - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr3:49321969_49321971delTCT ENST00000351842.4 - 17 2185_2187 c.2177_2179delAGA c.(2176-2181)acc>a p.KT726del USP4_ENST00000265560.4_In_Frame_Del_p.KT773del NM_199443.2 NP_955475.1 Q13107 UBP4_HUMAN ubiquitin specific peptidase 4 (proto-oncogene) 773 negative regulation of protein ubiquitination|protein deubiquitination|protein localization at cell surface|regulation of protein stability|ubiquitin-dependent protein catabolic process lysosome|nucleus adenosine receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1) 33 Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121) OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05) GCCACTGTGGTCTTCTTCTTCTT 0.532 7 732 --- --- --- --- STAB1 23166 broad.mit.edu 37 3 52546401 52546401 + Frame_Shift_Del DEL C C - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr3:52546401delC ENST00000321725.6 + 27 3004 c.2928delC c.(2926-2928)tgfs p.C976fs NM_015136.2 NP_055951.2 Q9NY15 STAB1_HUMAN stabilin 1 976 EGF-like 9. cell adhesion|cell-cell signaling|defense response to bacterium|inflammatory response|negative regulation of angiogenesis|receptor-mediated endocytosis integral to plasma membrane bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3) 76 BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482) TCTGCACGTGCCCCCCTGGCT 0.627 9 786 --- --- --- --- ERC2 26059 broad.mit.edu 37 3 55733470 55733472 + In_Frame_Del DEL TGG TGG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa 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 1189 --- --- --- --- MAGI1 9223 broad.mit.edu 37 3 65372850 65372851 + Frame_Shift_Del DEL TC TC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr3:65372850_65372851delTC ENST00000330909.8 - 15 2466_2467 c.2467_2468delGA c.(2467-2469)afs p.E823fs MAGI1_ENST00000497477.2_Intron|MAGI1_ENST00000402939.2_Intron|MAGI1_ENST00000483466.1_Frame_Shift_Del_p.E823fs NM_015520.1 NP_056335.1 Q96QZ7 MAGI1_HUMAN membrane associated guanylate kinase, WW and PDZ domain containing 1 823 PDZ 4. cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly tight junction ATP binding|protein C-terminus binding breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5) 51 Lung NSC(201;0.0016) BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133) GGAATTGATTTCTCTCTCTCTC 0.401 18 367 --- --- --- --- VGLL3 389136 broad.mit.edu 37 3 87027857 87027859 + In_Frame_Del DEL CTC CTC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr3:87027857_87027859delCTC ENST00000398399.2 - 2 583_585 c.220_222delGAG c.(220-222)del p.E74del VGLL3_ENST00000383698.3_In_Frame_Del_p.E74del NM_016206.2 NP_057290.2 A8MV65 VGLL3_HUMAN vestigial like 3 (Drosophila) 74 regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(11) 19 all_cancers(8;0.109)|Lung SC(3;0.184) Lung NSC(201;0.0777) LUSC - Lung squamous cell carcinoma(29;0.00241)|Lung(72;0.00712) GCTGGtctttctcctcctcctcc 0.502 8 309 --- --- --- --- MORC1 27136 broad.mit.edu 37 3 108682419 108682419 + Frame_Shift_Del DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr3:108682419delT ENST00000232603.5 - 27 2723 c.2641delA c.(2641-2643)tafs p.I881fs MORC1_ENST00000483760.1_Frame_Shift_Del_p.I860fs NM_014429.3 NP_055244.3 Q86VD1 MORC1_HUMAN MORC family CW-type zinc finger 1 881 cell differentiation|multicellular organismal development|spermatogenesis nucleus ATP binding|zinc ion binding breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3) 105 TTCCTCTTTATTTTTTTTTCA 0.284 7 403 --- --- --- --- WWTR1 25937 broad.mit.edu 37 3 149260194 149260196 + In_Frame_Del DEL CTG CTG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr3:149260194_149260196delCTG ENST00000465804.1 - 5 953_955 c.697_699delCAG c.(697-699)del p.Q233del WWTR1_ENST00000467467.1_In_Frame_Del_p.Q233del|WWTR1_ENST00000360632.3_In_Frame_Del_p.Q233del NM_001168278.1 NP_001161750.1 Q9GZV5 WWTR1_HUMAN WW domain containing transcription regulator 1 233 Gln-rich. hippo signaling cascade|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of protein kinase activity|negative regulation of protein phosphorylation|positive regulation of cell proliferation|positive regulation of epithelial to mesenchymal transition|regulation of SMAD protein import into nucleus|stem cell division|transcription, DNA-dependent cytoplasm transcription coactivator activity breast(5)|cervix(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1) 23 LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048) GCCGCAGTTTCTGCTGCTGCTGC 0.581 T CAMTA1 epitheliod hemangioendothelioma 7 424 --- --- --- --- MED12L 116931 broad.mit.edu 37 3 150877786 150877786 + Frame_Shift_Del DEL C C - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr3:150877786delC ENST00000474524.1 + 7 1043 c.1005delC c.(1003-1005)ggfs p.G335fs MED12L_ENST00000422248.2_Frame_Shift_Del_p.G335fs|MED12L_ENST00000309237.4_Frame_Shift_Del_p.G335fs|MED12L_ENST00000273432.4_Intron 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 1357 --- --- --- --- MED12L 116931 broad.mit.edu 37 3 151148114 151148116 + In_Frame_Del DEL CAG CAG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr3:151148114_151148116delCAG ENST00000474524.1 + 42 6369_6371 c.6331_6333delCAG c.(6331-6333)del p.Q2115del MED12L_ENST00000273432.4_In_Frame_Del_p.Q1779del NM_053002.4 NP_443728.3 Q86YW9 MD12L_HUMAN mediator complex subunit 12-like 2115 Gln-rich. regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent mediator complex p.Q2111E(1) 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) GCAGCAGACCCAGCAGCAGCAGC 0.527 9 645 --- --- --- --- GOLIM4 27333 broad.mit.edu 37 3 167747642 167747644 + In_Frame_Del DEL CTG CTG - rs61743912 byFrequency TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr3:167747642_167747644delCTG ENST00000470487.1 - 10 2046_2048 c.1357_1359delCAG c.(1357-1359)del p.Q453del GOLIM4_ENST00000309027.4_In_Frame_Del_p.Q425del NM_014498.3 NP_055313.1 O00461 GOLI4_HUMAN golgi integral membrane protein 4 453 Gln-rich.|Glu-rich. transport cis-Golgi network|endocytic vesicle|endosome membrane|Golgi cisterna membrane|Golgi lumen|integral to membrane|nucleus breast(5)|endometrium(2)|large_intestine(8)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 47 CTCTTGCCACctgctgctgctgc 0.640 7 378 --- --- --- --- RNF168 165918 broad.mit.edu 37 3 196214338 196214338 + Frame_Shift_Del DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr3:196214338delT ENST00000318037.3 - 3 1084 c.490delA c.(490-492)ggfs p.R166fs NM_152617.3 NP_689830.2 Q8IYW5 RN168_HUMAN ring finger protein 168, E3 ubiquitin protein ligase 166 Glu-rich. double-strand break repair|histone H2A K63-linked ubiquitination|positive regulation of DNA repair|response to ionizing radiation nucleus|ubiquitin ligase complex chromatin binding|histone binding|ubiquitin binding|ubiquitin-protein ligase activity|zinc ion binding NS(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1) 20 all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206) Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06) GBM - Glioblastoma multiforme(46;0.00348) GCTCTTCGCCTTTTTTCTGCC 0.448 10 2274 --- --- --- --- ZNF876P 0 broad.mit.edu 37 4 217874 217874 + RNA DEL G G - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr4:217874delG ENST00000356347.3 + 0 172 NR_027481.1 ggctgcttcagggagcacagc 0.537 7 223 --- --- --- --- FGFR3 2261 broad.mit.edu 37 4 1806180 1806181 + Frame_Shift_Ins INS - - C TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr4:1806180_1806181insC ENST00000340107.4 + 9 1461_1462 c.1205_1206insC c.(1204-1206)accfs p.T402fs FGFR3_ENST00000481110.2_Frame_Shift_Ins_p.T400fs|FGFR3_ENST00000260795.2_Frame_Shift_Ins_p.T400fs|FGFR3_ENST00000440486.2_Frame_Shift_Ins_p.T400fs|FGFR3_ENST00000352904.1_Intron|FGFR3_ENST00000412135.2_Intron NM_001163213.1 NP_001156685.1 P22607 FGFR3_HUMAN fibroblast growth factor receptor 3 400 bone maturation|cell growth|insulin receptor signaling pathway|JAK-STAT cascade|MAPKKK cascade|negative regulation of developmental growth|positive regulation of cell proliferation integral to plasma membrane ATP binding|fibroblast growth factor binding|fibroblast growth factor receptor activity|identical protein binding NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607) 3091 Breast(71;0.212)|all_epithelial(65;0.241) all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234) Palifermin(DB00039) CGCCTGCGCAGCCCCCCCAAGA 0.629 1 """Mis, T""" """IGH@, ETV6""" """bladder, MM, T-cell lymphoma""" """Hypochondroplasia, Thanatophoric dysplasia""" Saethre-Chotzen syndrome;Muenke syndrome 7 2023 --- --- --- --- SLC34A2 10568 broad.mit.edu 37 4 25678148 25678150 + In_Frame_Del DEL GCT GCT - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr4:25678148_25678150delGCT ENST00000382051.3 + 13 1900_1902 c.1850_1852delGCT c.(1849-1854)cgc>c p.RC617del SLC34A2_ENST00000503434.1_In_Frame_Del_p.RC616del|SLC34A2_ENST00000504570.1_In_Frame_Del_p.RC616del NM_001177998.1|NM_006424.2 NP_001171469.1|NP_006415.2 O95436 NPT2B_HUMAN solute carrier family 34 (type II sodium/phosphate contransporter), member 2 617 Cys-rich. cellular phosphate ion homeostasis apical plasma membrane|brush border membrane|integral to plasma membrane phosphate binding|sodium ion binding|sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity SLC34A2/ROS1(14) breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(4) 41 Breast(46;0.0503) TTCCAGATGCgctgctgctgctg 0.640 T ROS1 NSCLC 8 347 --- --- --- --- FIP1L1 81608 broad.mit.edu 37 4 54319248 54319249 + Frame_Shift_Del DEL AG AG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr4:54319248_54319249delAG ENST00000337488.6 + 16 1641_1642 c.1447_1448delAG c.(1447-1449)afs p.R483fs FIP1L1_ENST00000306932.6_Frame_Shift_Del_p.R409fs|FIP1L1_ENST00000507166.1_Intron|FIP1L1_ENST00000358575.5_Frame_Shift_Del_p.R477fs NM_030917.3 NP_112179.2 Q6UN15 FIP1_HUMAN factor interacting with PAPOLA and CPSF1 483 Arg-rich.|Glu-rich.|Sufficient for interaction with CPSF1 and CSTF3. mRNA processing nucleus RNA binding p.R487fs*3(2) large_intestine(3)|liver(1)|ovary(1)|skin(1) 6 GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134) agaACGCACCAGAGAGAGAGAG 0.470 T PDGFRA idiopathic hypereosinophilic syndrome 18 433 --- --- --- --- PRDM8 56978 broad.mit.edu 37 4 81123250 81123252 + In_Frame_Del DEL CAG CAG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr4:81123250_81123252delCAG ENST00000339711.4 + 10 1865_1867 c.634_636delCAG c.(634-636)del p.Q217del PRDM8_ENST00000415738.2_In_Frame_Del_p.Q217del|PRDM8_ENST00000504452.1_In_Frame_Del_p.Q217del NM_020226.3 NP_064611.3 Q9NQV8 PRDM8_HUMAN PR domain containing 8 217 Gly-rich.|Poly-Gln. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding|zinc ion binding breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(2) 10 tggcaaagaccagcagcagcagc 0.655 OREG0016246 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 12 545 --- --- --- --- RASGEF1B 153020 broad.mit.edu 37 4 82363491 82363492 + Frame_Shift_Ins INS - - T TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr4:82363491_82363492insT ENST00000509081.1 - 9 1185_1186 c.964_965insA c.(964-966)ttgfs p.L322fs RASGEF1B_ENST00000335927.7_Frame_Shift_Ins_p.L281fs|RASGEF1B_ENST00000264400.2_Frame_Shift_Ins_p.L323fs Q0VAM2 RGF1B_HUMAN RasGEF domain family, member 1B 323 Ras-GEF. regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction intracellular Ras guanyl-nucleotide exchange factor activity endometrium(2)|kidney(5)|large_intestine(4)|lung(13)|prostate(1)|skin(1) 26 TTTGGCCCAAGTTTTTTTTAGT 0.381 7 520 --- --- --- --- PKD2 5311 broad.mit.edu 37 4 88986559 88986559 + Frame_Shift_Del DEL A A - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr4:88986559delA ENST00000237596.2 + 11 2218 c.2152delA c.(2152-2154)aafs p.K719fs PKD2_ENST00000502363.1_Frame_Shift_Del_p.K137fs|PKD2_ENST00000508588.1_Frame_Shift_Del_p.K137fs|PKD2_ENST00000511337.1_3'UTR NM_000297.3 NP_000288.1 Q13563 PKD2_HUMAN polycystic kidney disease 2 (autosomal dominant) 719 EF-hand domain. basal cortex|basal plasma membrane|endoplasmic reticulum|integral to membrane|lamellipodium|microtubule basal body calcium ion binding|cytoskeletal protein binding|voltage-gated chloride channel activity|voltage-gated sodium channel activity breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(2)|lung(15)|skin(4)|upper_aerodigestive_tract(1) 36 Hepatocellular(203;0.114)|Acute lymphoblastic leukemia(40;0.221) OV - Ovarian serous cystadenocarcinoma(123;9.98e-10)|COAD - Colon adenocarcinoma(81;0.0237) ACTAAAACTGAAAAAAAATAC 0.383 7 919 --- --- --- --- CLGN 1047 broad.mit.edu 37 4 141313402 141313402 + Frame_Shift_Del DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr4:141313402delT ENST00000325617.5 - 13 2062 c.1622delA c.(1621-1623)agfs p.K541fs CLGN_ENST00000414773.1_Frame_Shift_Del_p.K541fs|CLGN_ENST00000537281.1_Frame_Shift_Del_p.K541fs NM_004362.2 NP_004353.1 O14967 CLGN_HUMAN calmegin 541 protein folding endoplasmic reticulum membrane|integral to membrane calcium ion binding|unfolded protein binding breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(5)|ovary(2)|prostate(3)|skin(4)|urinary_tract(1) 25 all_hematologic(180;0.162) ATCATTTTGCTTTTTTTCCTC 0.378 7 1513 --- --- --- --- SORBS2 8470 broad.mit.edu 37 4 186544620 186544622 + In_Frame_Del DEL GGT GGT - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr4:186544620_186544622delGGT ENST00000431808.1 - 14 2512_2514 c.1949_1951delACC c.(1948-1953)cgc>c p.HR650del SORBS2_ENST00000437304.2_Intron|SORBS2_ENST00000355634.5_In_Frame_Del_p.HR750del|SORBS2_ENST00000448662.2_Intron|SORBS2_ENST00000449407.2_Intron|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000418609.1_In_Frame_Del_p.HR554del|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000284776.7_In_Frame_Del_p.HR650del|SORBS2_ENST00000498125.1_Intron O94875 SRBS2_HUMAN sorbin and SH3 domain containing 2 650 His-rich. actin cytoskeleton|nucleus|perinuclear region of cytoplasm|Z disc cytoskeletal adaptor activity|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1) 53 all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244) OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205) ATGAggtggcggtggtggtggtg 0.522 10 549 --- --- --- --- IRX4 50805 broad.mit.edu 37 5 1879669 1879671 + In_Frame_Del DEL CCT CCT - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr5:1879669_1879671delCCT ENST00000505790.1 - 5 1139_1141 c.683_685delAGG c.(682-687)ggg>g p.EG228del IRX4_ENST00000231357.2_In_Frame_Del_p.EG228del|IRX4_ENST00000505938.1_5'UTR|IRX4_ENST00000513692.1_In_Frame_Del_p.EG228del NM_001278634.1 NP_001265563.1 P78413 IRX4_HUMAN iroquois homeobox 4 228 Poly-Glu. heart development nucleus sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity endometrium(1)|lung(7)|ovary(1)|prostate(1) 10 GBM - Glioblastoma multiforme(108;0.242) tcctcgcccccctcctcctcctc 0.685 7 299 --- --- --- --- THBS4 7060 broad.mit.edu 37 5 79372774 79372776 + In_Frame_Del DEL TGA TGA - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr5:79372774_79372776delTGA ENST00000350881.2 + 16 2179_2181 c.1989_1991delTGA c.(1987-1992)tgt>tg p.CD663del THBS4_ENST00000511733.1_In_Frame_Del_p.CD572del|CTD-2201I18.1_ENST00000503007.1_RNA|CTD-2201I18.1_ENST00000514042.1_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 10 1607 --- --- --- --- RAPGEF6 51735 broad.mit.edu 37 5 130815368 130815369 + Frame_Shift_Ins INS - - T TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr5:130815368_130815369insT ENST00000509018.1 - 16 2123_2124 c.1918_1919insA c.(1918-1920)taafs p.*640fs RAPGEF6_ENST00000512052.1_Frame_Shift_Ins_p.*355fs|FNIP1_ENST00000514667.1_Frame_Shift_Ins_p.*690fs|RAPGEF6_ENST00000510071.1_Frame_Shift_Ins_p.*640fs|RAPGEF6_ENST00000296859.6_Frame_Shift_Ins_p.*640fs|RAPGEF6_ENST00000507093.1_Frame_Shift_Ins_p.*640fs|RAPGEF6_ENST00000307984.5_Frame_Shift_Ins_p.*640fs|RAPGEF6_ENST00000308008.6_Frame_Shift_Ins_p.*640fs NM_001164386.1|NM_016340.5 NP_001157858.1|NP_057424.3 Q8TEU7 RPGF6_HUMAN Rap guanine nucleotide exchange factor (GEF) 6 640 Ras protein signal transduction|regulation of GTPase activity|regulation of small GTPase mediated signal transduction cytoplasm|plasma membrane GTP-dependent protein binding|guanyl-nucleotide exchange factor activity|Ras GTPase binding breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1) 31 KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) Lung(113;0.0721) ATGGCGATTACTTTTTTTTTCA 0.366 11 847 --- --- --- --- IK 3550 broad.mit.edu 37 5 140032593 140032594 + Frame_Shift_Del DEL GA GA - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa 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 9 315 --- --- --- --- SPRY4 81848 broad.mit.edu 37 5 141694361 141694363 + In_Frame_Del DEL TGC TGC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr5:141694361_141694363delTGC ENST00000344120.4 - 3 566_568 c.380_382delGCA c.(379-384)aca>a p.ST127del SPRY4_ENST00000434127.2_In_Frame_Del_p.ST104del NM_030964.3 NP_112226.2 Q9C004 SPY4_HUMAN sprouty homolog 4 (Drosophila) 104 multicellular organismal development cytoplasm|ruffle membrane protein binding breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(1) 18 all_hematologic(541;0.118) KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) TCAGAGGATGTGCTGCTGCTGCT 0.660 Testicular Cancer, Familial Clustering of 7 747 --- --- --- --- PPARGC1B 133522 broad.mit.edu 37 5 149216457 149216459 + In_Frame_Del DEL GGA GGA - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa 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 7 658 --- --- --- --- HAVCR2 84868 broad.mit.edu 37 5 156535948 156535950 + In_Frame_Del DEL AGC AGC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr5:156535948_156535950delAGC ENST00000307851.4 - 1 775_777 c.45_47delGCT c.(43-48)cta>ct p.LL17del CTB-120L21.1_ENST00000517708.1_RNA|HAVCR2_ENST00000522593.1_In_Frame_Del_p.LL17del NM_032782.4 NP_116171.3 Q8TDQ0 HAVR2_HUMAN hepatitis A virus cellular receptor 2 17 integral to membrane p.L18delL(1)|p.L15L(1) cervix(1)|large_intestine(4)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(2) 22 Renal(175;0.00212) Medulloblastoma(196;0.0354)|all_neural(177;0.0999) Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785) TGTAAGTAGTAGCAGCAGCAGCA 0.438 7 464 --- --- --- --- MAS1L 116511 broad.mit.edu 37 6 29455156 29455157 + Frame_Shift_Del DEL AC AC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr6:29455156_29455157delAC ENST00000377127.3 - 1 581_582 c.523_524delGT c.(523-525)cfs p.V175fs NM_052967.1 NP_443199.1 P35410 MAS1L_HUMAN MAS1 oncogene-like 175 cytoplasm|integral to membrane|nucleus|plasma membrane G-protein coupled receptor activity NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(7)|pancreas(1)|prostate(2)|skin(2) 28 GGGGAAGAGGACACACACACAC 0.495 11 555 --- --- --- --- GABBR1 0 broad.mit.edu 37 6 29573436 29573438 + In_Frame_Del DEL CAG CAG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr6:29573436_29573438delCAG ENST00000377034.4 - 20 2682_2684 c.2347_2349delCTG c.(2347-2349)del p.L783del GABBR1_ENST00000377012.4_In_Frame_Del_p.L666del|GABBR1_ENST00000376977.3_3'UTR|GABBR1_ENST00000377016.4_In_Frame_Del_p.L721del|GABBR1_ENST00000355973.3_In_Frame_Del_p.L666del NM_001470.2 NP_001461.1 Q9UBS5 GABR1_HUMAN gamma-aminobutyric acid (GABA) B receptor, 1 783 gamma-aminobutyric acid signaling pathway|negative regulation of adenylate cyclase activity|synaptic transmission cell junction|extracellular region|integral to plasma membrane|postsynaptic membrane G-protein coupled receptor activity|GABA-B receptor activity p.L783M(1) endometrium(3)|kidney(1)|large_intestine(13)|liver(1)|lung(16)|ovary(5)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 47 Baclofen(DB00181)|Progabide(DB00837) GGAAGATTCCCAGCAGCAGCAGC 0.512 12 539 --- --- --- --- HLA-DRB6 0 broad.mit.edu 37 6 32522379 32522380 + RNA INS - - C rs112115106 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr6:32522379_32522380insC ENST00000411500.1 - 0 740 NR_001298.1 TGAAAATAGGATTGGGAGAGTA 0.475 9 374 --- --- --- --- DAXX 1616 broad.mit.edu 37 6 33289253 33289253 + Frame_Shift_Del DEL A A - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr6:33289253delA ENST00000374542.5 - 3 503 c.299delT c.(298-300)tgfs p.L100fs DAXX_ENST00000477162.1_Intron|DAXX_ENST00000414083.2_Frame_Shift_Del_p.L25fs|DAXX_ENST00000266000.6_Frame_Shift_Del_p.L100fs 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 100 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 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 CGCCGAGGCCAAAAACAGAGA 0.547 """Mis, F, N""" Pancreatic neuroendocrine tumors. Paediatric GBM 8 986 --- --- --- --- GLTSCR1L 23506 broad.mit.edu 37 6 42789764 42789766 + In_Frame_Del DEL GAT GAT - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr6:42789764_42789766delGAT ENST00000314073.5 + 3 180_182 c.4_6delGAT c.(4-6)del p.D6del GLTSCR1L_ENST00000394168.1_In_Frame_Del_p.D6del GLTSCR1-like AGTTGTCATGGATGATGATGATG 0.369 11 846 --- --- --- --- DST 667 broad.mit.edu 37 6 56476324 56476324 + Frame_Shift_Del DEL A A - rs35805169 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr6:56476324delA ENST00000370754.5 - 37 5029 c.5030delT c.(5029-5031)tgfs p.L1677fs DST_ENST00000370788.2_Frame_Shift_Del_p.L1499fs|DST_ENST00000361203.3_Frame_Shift_Del_p.L1499fs|DST_ENST00000421834.2_Frame_Shift_Del_p.L1499fs|DST_ENST00000312431.6_Frame_Shift_Del_p.L1499fs|DST_ENST00000370769.4_Frame_Shift_Del_p.L1499fs|DST_ENST00000244364.6_Frame_Shift_Del_p.L1173fs|DST_ENST00000446842.2_Frame_Shift_Del_p.L1173fs Q03001 DYST_HUMAN dystonin 1499 cell adhesion|cell cycle arrest|cell motility|hemidesmosome assembly|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization|maintenance of cell polarity|microtubule cytoskeleton organization|response to wounding actin cytoskeleton|axon|axon part|basement membrane|cell cortex|cell leading edge|cytoplasmic membrane-bounded vesicle|endoplasmic reticulum membrane|hemidesmosome|integral to membrane|intermediate filament|intermediate filament cytoskeleton|microtubule cytoskeleton|microtubule plus end|nuclear envelope|sarcomere|Z disc actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein binding|protein C-terminus binding|protein homodimerization activity NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3) 105 Lung NSC(77;0.103) LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956) ATGTTTTGCCAAAAAAAGCTG 0.353 7 314 --- --- --- --- CYB5R4 51167 broad.mit.edu 37 6 84634230 84634231 + Frame_Shift_Ins INS - - A TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr6:84634230_84634231insA ENST00000369681.4 + 10 873_874 c.733_734insA c.(733-735)aaafs p.K245fs NM_016230.3 NP_057314.2 Q7L1T6 NB5R4_HUMAN cytochrome b5 reductase 4 245 CS. cell development|detection of oxygen|generation of precursor metabolites and energy|glucose homeostasis|insulin secretion|response to antibiotic|superoxide metabolic process endoplasmic reticulum|perinuclear region of cytoplasm cytochrome-b5 reductase activity|heme binding|NAD(P)H oxidase activity breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|prostate(1)|upper_aerodigestive_tract(1) 23 all_cancers(76;7e-07)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00128) BRCA - Breast invasive adenocarcinoma(397;0.0871) GATTGTTCTACAAAAAAAAGAG 0.337 8 514 --- --- --- --- SYNCRIP 10492 broad.mit.edu 37 6 86332353 86332354 + Frame_Shift_Ins INS - - T TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr6:86332353_86332354insT ENST00000355238.6 - 8 1060_1061 c.854_855insA c.(853-855)aagfs p.K285fs SYNCRIP_ENST00000369622.3_Frame_Shift_Ins_p.K285fs NM_001159673.1|NM_001159674.1|NM_001159676.1|NM_001159677.1|NM_001253771.1 NP_001153145.1|NP_001153146.1|NP_001153148.1|NP_001153149.1|NP_001240700.1 O60506 HNRPQ_HUMAN synaptotagmin binding, cytoplasmic RNA interacting protein 285 RRM 2. CRD-mediated mRNA stabilization|interspecies interaction between organisms catalytic step 2 spliceosome|CRD-mediated mRNA stability complex|endoplasmic reticulum|histone pre-mRNA 3'end processing complex|microsome|nucleoplasm nucleotide binding|protein binding autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(2)|skin(2)|upper_aerodigestive_tract(1) 33 all_cancers(76;0.000137)|Acute lymphoblastic leukemia(125;3.66e-08)|Prostate(29;8.2e-07)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0297) BRCA - Breast invasive adenocarcinoma(108;0.0389) AAAAGCCTCTGTTTTTTTTCTT 0.411 11 1054 --- --- --- --- MANEA 79694 broad.mit.edu 37 6 96034870 96034871 + Frame_Shift_Del DEL TA TA - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr6:96034870_96034871delTA ENST00000369293.1 + 2 689_690 c.555_556delTA c.(553-558)tgtafs p.CI185fs MANEA_ENST00000358812.4_Intron Q5SRI9 MANEA_HUMAN mannosidase, endo-alpha 0 Catalytic (Probable). post-translational protein modification|protein N-linked glycosylation via asparagine Golgi membrane|integral to membrane glycoprotein endo-alpha-1,2-mannosidase activity breast(2)|endometrium(3)|kidney(2)|liver(2)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1) 26 all_cancers(76;1.01e-06)|Acute lymphoblastic leukemia(125;3.58e-09)|all_hematologic(75;1.22e-06)|all_epithelial(107;0.00433)|Colorectal(196;0.0341) BRCA - Breast invasive adenocarcinoma(108;0.148) GTAATTATtgtatatatatata 0.292 7 372 --- --- --- --- UTRN 7402 broad.mit.edu 37 6 144769847 144769849 + In_Frame_Del DEL CCT CCT - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr6:144769847_144769849delCCT ENST00000367545.3 + 16 2014_2016 c.2014_2016delCCT c.(2014-2016)del p.P677del NM_007124.2 NP_009055.2 P46939 UTRO_HUMAN utrophin 677 Interaction with SYNM. muscle contraction|muscle organ development|positive regulation of cell-matrix adhesion cell junction|cytoplasm|cytoskeleton|membrane fraction|nucleus|postsynaptic membrane actin binding|calcium ion binding|zinc ion binding p.P672H(1) NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2) 148 Ovarian(120;0.218) OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213) GCAGGAACTGCCTCCTCCTCCTC 0.409 9 525 --- --- --- --- CARD11 84433 broad.mit.edu 37 7 2963941 2963943 + In_Frame_Del DEL GGA GGA - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr7:2963941_2963943delGGA ENST00000396946.4 - 15 2267_2269 c.1864_1866delTCC c.(1864-1866)del p.S622del NM_032415.4 NP_115791.3 Q9BXL7 CAR11_HUMAN caspase recruitment domain family, member 11 622 positive regulation of cytokine production|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis|T cell costimulation|T cell receptor signaling pathway cytosol|membrane raft|plasma membrane CARD domain binding|guanylate kinase activity NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2) 150 Ovarian(82;0.0115) OV - Ovarian serous cystadenocarcinoma(56;8.44e-14) CGGATTGGTGGGAGGAGGAGGAG 0.616 Mis DLBCL 8 403 --- --- --- --- INTS4L2 0 broad.mit.edu 37 7 65150713 65150714 + RNA INS - - A TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr7:65150713_65150714insA ENST00000430126.2 + 0 694_695 CATACCATGAGAAAATCTCTAA 0.436 10 208 --- --- --- --- GTF2IRD1P1 0 broad.mit.edu 37 7 66304731 66304731 + RNA DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr7:66304731delT ENST00000457166.1 - 0 189 NR_003934.1 TTTCTTTCCCttttttttttt 0.512 9 47 --- --- --- --- TYW1B 441250 broad.mit.edu 37 7 72040750 72040751 + RNA INS - - A rs72347331 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr7:72040750_72040751insA ENST00000438125.1 - 0 1399 Q6NUM6 TYW1B_HUMAN tRNA-yW synthesizing protein 1 homolog B (S. cerevisiae) tRNA processing 4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity AACATCCCTAGAAAAAAAAAAT 0.332 12 215 --- --- --- --- PCLO 27445 broad.mit.edu 37 7 82585469 82585469 + Frame_Shift_Del DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr7:82585469delT ENST00000423517.2 - 5 5137 c.4800delA c.(4798-4800)aafs p.K1600fs PCLO_ENST00000333891.8_Frame_Shift_Del_p.K1600fs NM_014510.2 NP_055325.2 Q9Y6V0 PCLO_HUMAN piccolo presynaptic cytomatrix protein 1531 cytoskeleton organization|synaptic vesicle exocytosis cell junction|cytoskeleton|synaptic vesicle calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2) 259 TTATTTTGCCTTTTCCCTTTG 0.433 7 1152 --- --- --- --- PEX1 5189 broad.mit.edu 37 7 92146721 92146721 + Frame_Shift_Del DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr7:92146721delT ENST00000248633.4 - 5 1203 c.1108delA c.(1108-1110)ttfs p.I370fs PEX1_ENST00000428214.1_Frame_Shift_Del_p.I370fs|PEX1_ENST00000438045.1_Intron|PEX1_ENST00000541751.1_5'UTR NM_000466.2 NP_000457.1 O43933 PEX1_HUMAN peroxisomal biogenesis factor 1 370 microtubule-based peroxisome localization|protein import into peroxisome matrix cytosol|nucleus|peroxisomal membrane ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1) 41 all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592) Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123) GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23) TCTGACCTAATTTTTTTTTGA 0.353 21 940 --- --- --- --- SRRT 51593 broad.mit.edu 37 7 100482040 100482042 + In_Frame_Del DEL AGG AGG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr7:100482040_100482042delAGG ENST00000388793.4 + 7 1029_1031 c.809_811delAGG c.(808-813)cag>c p.QE270del SRRT_ENST00000347433.4_In_Frame_Del_p.QE270del|SRRT_ENST00000457580.2_In_Frame_Del_p.QE270del|SRRT_ENST00000432932.1_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 7 201 --- --- --- --- TRBV7-8 0 broad.mit.edu 37 7 142099832 142099833 + RNA DEL CA CA - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr7:142099832_142099833delCA ENST00000390359.3 - 0 88 accactctctcacacacacaca 0.455 7 476 --- --- --- --- CTSB 1508 broad.mit.edu 37 8 11705590 11705591 + Frame_Shift_Ins INS - - A TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr8:11705590_11705591insA ENST00000353047.6 - 6 770_771 c.517_518insT c.(517-519)tgafs p.*173fs CTSB_ENST00000531089.1_Frame_Shift_Ins_p.*173fs|CTSB_ENST00000415599.2_3'UTR|CTSB_ENST00000453527.2_Frame_Shift_Ins_p.*173fs|CTSB_ENST00000534510.1_Frame_Shift_Ins_p.*173fs|CTSB_ENST00000345125.3_Frame_Shift_Ins_p.*173fs|CTSB_ENST00000530640.2_Frame_Shift_Ins_p.*173fs|CTSB_ENST00000434271.1_Frame_Shift_Ins_p.*173fs|CTSB_ENST00000533455.1_Frame_Shift_Ins_p.*173fs NM_001908.3 NP_001899.1 P07858 CATB_HUMAN cathepsin B 173 proteolysis|regulation of apoptosis|regulation of catalytic activity lysosome|melanosome cysteine-type endopeptidase activity breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(1) 16 all_epithelial(15;0.205) STAD - Stomach adenocarcinoma(15;0.00546) COAD - Colon adenocarcinoma(149;0.184) ATGGGATTCATAGAGGCCACCA 0.450 76 448 --- --- --- --- GOT1L1 137362 broad.mit.edu 37 8 37791833 37791834 + Frame_Shift_Ins INS - - T TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr8:37791833_37791834insT ENST00000307599.4 - 9 1342_1343 c.1243_1244insA c.(1243-1245)actfs p.T415fs NM_152413.2 NP_689626.2 Q8NHS2 AATC2_HUMAN glutamic-oxaloacetic transaminase 1-like 1 415 biosynthetic process|cellular amino acid metabolic process cytoplasm pyridoxal phosphate binding|transaminase activity central_nervous_system(1)|endometrium(3)|lung(8)|ovary(1)|prostate(1) 14 Colorectal(12;0.00627) Lung NSC(58;0.118)|all_lung(54;0.195) LUSC - Lung squamous cell carcinoma(8;1.37e-11) TCCAATCAGTGTTTTTTTTTCC 0.371 17 625 --- --- --- --- KAT6A 7994 broad.mit.edu 37 8 41798420 41798422 + In_Frame_Del DEL CTC CTC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa 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 16 1048 --- --- --- --- TOX 9760 broad.mit.edu 37 8 59750796 59750798 + In_Frame_Del DEL CTT CTT - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr8:59750796_59750798delCTT ENST00000361421.1 - 5 986_988 c.766_768delAAG c.(766-768)del p.K256del NM_014729.2 NP_055544.1 O94900 TOX_HUMAN thymocyte selection-associated high mobility group box 256 nucleus DNA binding endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(13)|prostate(1)|skin(2)|stomach(1) 33 all_cancers(86;0.165)|Myeloproliferative disorder(644;0.00452)|all_lung(136;0.036)|Lung NSC(129;0.0464)|all_epithelial(80;0.0607) CATTGGGATCCTTCTTCTTCTTC 0.453 15 1070 --- --- --- --- KCNB2 9312 broad.mit.edu 37 8 73480396 73480397 + Frame_Shift_Ins INS - - A TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr8:73480396_73480397insA ENST00000523207.1 + 2 1015_1016 c.427_428insA c.(427-429)aaafs p.K143fs NM_004770.2 NP_004761.2 Q92953 KCNB2_HUMAN potassium voltage-gated channel, Shab-related subfamily, member 2 143 regulation of smooth muscle contraction voltage-gated potassium channel complex delayed rectifier potassium channel activity|protein binding p.Q143K(1)|p.E146fs*3(1) NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1) 85 Breast(64;0.137) Epithelial(68;0.105) CAGATATCATCAAAAAAAAGAA 0.446 11 865 --- --- --- --- VPS13B 157680 broad.mit.edu 37 8 100654474 100654474 + Frame_Shift_Del DEL A A - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr8:100654474delA ENST00000358544.2 + 34 5842 c.5731delA c.(5731-5733)aafs p.K1912fs VPS13B_ENST00000357162.2_Frame_Shift_Del_p.K1887fs|VPS13B_ENST00000395996.1_3'UTR NM_017890.4 NP_060360.3 Q7Z7G8 VP13B_HUMAN vacuolar protein sorting 13 homolog B (yeast) 1912 protein transport NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9) 193 Breast(36;3.73e-07) OV - Ovarian serous cystadenocarcinoma(57;0.00636) TCCTTCAGGGAAAAAAATAGG 0.458 7 975 --- --- --- --- PABPC1 26986 broad.mit.edu 37 8 101724994 101724995 + Frame_Shift_Ins INS - - A rs140822921 by1000genomes TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr8:101724994_101724995insA ENST00000318607.5 - 6 1889_1890 c.761_762insT c.(760-762)agafs p.R254fs PABPC1_ENST00000519004.1_Frame_Shift_Ins_p.R209fs|PABPC1_ENST00000519596.1_5'UTR|PABPC1_ENST00000522387.1_Frame_Shift_Ins_p.R222fs NM_002568.3 NP_002559.2 P11940 PABP1_HUMAN poly(A) binding protein, cytoplasmic 1 254 CSDE1-binding.|RRM 3. mRNA polyadenylation|mRNA stabilization|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|translation catalytic step 2 spliceosome|cytosol nucleotide binding|poly(A) RNA binding|protein C-terminus binding|translation activator activity breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1) 40 all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125) Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206) CATTGAGCTCCTTTCCGTTCAT 0.371 8 414 --- --- --- --- UBR5 51366 broad.mit.edu 37 8 103289348 103289349 + Frame_Shift_Ins INS - - T TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr8:103289348_103289349insT ENST00000520539.1 - 45 6966_6967 c.6360_6361insA c.(6358-6363)aaaaggfs p.R2121fs UBR5_ENST00000521922.1_Frame_Shift_Ins_p.R2115fs|UBR5_ENST00000220959.4_Frame_Shift_Ins_p.R2121fs NM_015902.5 NP_056986.2 O95071 UBR5_HUMAN ubiquitin protein ligase E3 component n-recognin 5 2121 cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus nucleus|soluble fraction protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding p.E2121fs*28(2) NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2) 124 all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05) OV - Ovarian serous cystadenocarcinoma(57;0.000442) TCTTCCCCTTCTTTTTTTTGCC 0.381 10 803 --- --- --- --- OXR1 55074 broad.mit.edu 37 8 107704955 107704955 + Splice_Site DEL G G - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr8:107704955delG ENST00000445937.1 + 7 786 c.e7-1 OXR1_ENST00000312046.6_Splice_Site|OXR1_ENST00000442977.2_Splice_Site|OXR1_ENST00000497705.1_Splice_Site|OXR1_ENST00000531443.1_Splice_Site|OXR1_ENST00000452423.2_Splice_Site|OXR1_ENST00000517566.2_Splice_Site NM_018002.3 NP_060472.2 Q8N573 OXR1_HUMAN oxidation resistance 1 cell wall macromolecule catabolic process|response to oxidative stress mitochondrion NS(2)|breast(2)|endometrium(2)|large_intestine(9)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4) 31 OV - Ovarian serous cystadenocarcinoma(57;1.81e-09) AAAAAAAAAAGAATCCTGATG 0.348 10 279 --- --- --- --- RP11-262H14.3 0 broad.mit.edu 37 9 66545695 66545695 + RNA DEL A A - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr9:66545695delA ENST00000445604.2 - 0 669 CTGTAAGAGGAAAAAAAAACA 0.373 7 32 --- --- --- --- ROR2 4920 broad.mit.edu 37 9 94486026 94486028 + In_Frame_Del DEL TCC TCC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr9:94486026_94486028delTCC ENST00000375708.3 - 9 2946_2948 c.2748_2750delGGA c.(2746-2751)gaa>ga p.EE916del ROR2_ENST00000375715.1_Intron|ROR2_ENST00000550066.1_5'UTR NM_004560.3 NP_004551.2 Q01974 ROR2_HUMAN receptor tyrosine kinase-like orphan receptor 2 916 negative regulation of cell proliferation|positive regulation of cell migration|transmembrane receptor protein tyrosine kinase signaling pathway integral to plasma membrane ATP binding|transmembrane receptor protein tyrosine kinase activity|Wnt-protein binding autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1) 71 GACAGAGCCTTCCTCCTCCTCCT 0.645 12 781 --- --- --- --- ASTN2 23245 broad.mit.edu 37 9 119976989 119976991 + In_Frame_Del DEL CAG CAG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr9:119976989_119976991delCAG ENST00000313400.4 - 3 761_763 c.661_663delCTG c.(661-663)del p.L221del ASTN2_ENST00000361477.3_5'UTR|ASTN2_ENST00000361209.2_In_Frame_Del_p.L221del|ASTN2_ENST00000373996.3_In_Frame_Del_p.L221del O75129 ASTN2_HUMAN astrotactin 2 221 integral to membrane breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1) 102 CGGTGAACACCAGCAGCAGCAGC 0.601 14 398 --- --- --- --- DAB2IP 153090 broad.mit.edu 37 9 124522389 124522391 + In_Frame_Del DEL AAG AAG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr9:124522389_124522391delAAG ENST00000408936.3 + 6 1023_1025 c.841_843delAAG c.(841-843)del p.K285del DAB2IP_ENST00000259371.2_In_Frame_Del_p.K257del|DAB2IP_ENST00000309989.1_In_Frame_Del_p.K161del Q5VWQ8 DAB2P_HUMAN DAB2 interacting protein 285 C2. activation of JUN kinase activity|apoptosis in response to endoplasmic reticulum stress|cellular response to epidermal growth factor stimulus|cellular response to tumor necrosis factor|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of catenin import into nucleus|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|negative regulation of epithelial to mesenchymal transition|negative regulation of fibroblast proliferation|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of MAP kinase activity|negative regulation of NF-kappaB transcription factor activity|negative regulation of Ras GTPase activity|negative regulation of transcription from RNA polymerase II promoter|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter cytoplasm|intrinsic to internal side of plasma membrane 14-3-3 protein binding|death receptor binding|mitogen-activated protein kinase kinase kinase binding|protein homodimerization activity|protein phosphatase 2A binding|Ras GTPase activator activity|signaling adaptor activity breast(3)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(8)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1) 27 GGAGACCGACAAGAAGAAGAAGA 0.601 8 446 --- --- --- --- ABL1 25 broad.mit.edu 37 9 133759490 133759492 + In_Frame_Del DEL AAG AAG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr9:133759490_133759492delAAG ENST00000318560.5 + 11 2194_2196 c.1813_1815delAAG c.(1813-1815)del p.K609del NM_005157.4 NP_005148.2 P00519 ABL1_HUMAN c-abl oncogene 1, non-receptor tyrosine kinase 609 Poly-Lys. actin cytoskeleton organization|axon guidance|blood coagulation|cell adhesion|DNA damage induced protein phosphorylation|DNA damage response, signal transduction resulting in induction of apoptosis|mismatch repair|muscle cell differentiation|negative regulation of protein serine/threonine kinase activity|peptidyl-tyrosine phosphorylation|positive regulation of muscle cell differentiation|positive regulation of oxidoreductase activity|regulation of transcription involved in S phase of mitotic cell cycle cytoskeleton|cytosol|nuclear membrane|nucleolus|perinuclear region of cytoplasm ATP binding|DNA binding|magnesium ion binding|manganese ion binding|mitogen-activated protein kinase binding|non-membrane spanning protein tyrosine kinase activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 1195 all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204) OV - Ovarian serous cystadenocarcinoma(145;5.4e-05) Adenosine triphosphate(DB00171)|Dasatinib(DB01254)|Imatinib(DB00619) CGCCTTGATCAAGAAGAAGAAGA 0.616 """T, Mis""" """BCR, ETV6, NUP214""" """CML, ALL, T-ALL""" 31 1173 --- --- --- --- WDR5 11091 broad.mit.edu 37 9 137019598 137019598 + Frame_Shift_Del DEL C C - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr9:137019598delC ENST00000358625.3 + 10 813 c.642delC c.(640-642)aafs p.N214fs WDR5_ENST00000425041.1_Frame_Shift_Del_p.N214fs NM_017588.2 NP_060058.1 P61964 WDR5_HUMAN WD repeat domain 5 214 histone H3 acetylation|histone H3-K4 methylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent Ada2/Gcn5/Ada3 transcription activator complex|MLL1 complex|Set1C/COMPASS complex protein binding endometrium(1)|kidney(1)|large_intestine(2)|lung(5) 9 Myeloproliferative disorder(178;0.0255)|Medulloblastoma(224;0.123) Epithelial(140;6.61e-13)|all cancers(34;5.66e-12)|OV - Ovarian serous cystadenocarcinoma(145;3.93e-08)|GBM - Glioblastoma multiforme(294;0.00326)|READ - Rectum adenocarcinoma(205;0.154) ATGACGACAACCCCCCCGTGT 0.627 8 2165 --- --- --- --- SNAPC4 6621 broad.mit.edu 37 9 139277995 139277997 + In_Frame_Del DEL GCT GCT - rs34222232 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr9:139277995_139277997delGCT ENST00000298532.2 - 15 1992_1994 c.1624_1626delAGC c.(1624-1626)del p.S542del NM_003086.2 NP_003077.2 Q5SXM2 SNPC4_HUMAN small nuclear RNA activating complex, polypeptide 4, 190kDa 542 snRNA transcription from RNA polymerase II promoter|snRNA transcription from RNA polymerase III promoter snRNA-activating protein complex DNA binding|sequence-specific DNA binding transcription factor activity p.S542delS(2) biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1) 33 Myeloproliferative disorder(178;0.0511) OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06) CGTCCTCCTCgctgctgctgctg 0.690 8 107 --- --- --- --- TUBBP5 0 broad.mit.edu 37 9 141070013 141070014 + RNA INS - - GCG rs76591329 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr9:141070013_141070014insGCG ENST00000503395.1 + 0 1132 CTCCTGGGAACGCGGCCCTCCC 0.728 10 211 --- --- --- --- CUBN 8029 broad.mit.edu 37 10 17113554 17113554 + Frame_Shift_Del DEL A A - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr10:17113554delA ENST00000377833.4 - 19 2561 c.2496delT c.(2494-2496)ttfs p.F832fs NM_001081.3 NP_001072.2 O60494 CUBN_HUMAN cubilin (intrinsic factor-cobalamin receptor) 832 CUB 4. cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8) 241 Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200) ACACGTTAGGAAAAAAAGGCG 0.413 8 511 --- --- --- --- C10orf68 79741 broad.mit.edu 37 10 33018277 33018277 + Frame_Shift_Del DEL A A - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr10:33018277delA ENST00000375030.2 + 13 1360 c.742delA c.(742-744)aafs p.K250fs C10orf68_ENST00000375025.4_Frame_Shift_Del_p.K242fs|C10orf68_ENST00000375028.3_Frame_Shift_Del_p.K218fs Q9H943 CJ068_HUMAN chromosome 10 open reading frame 68 242 breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(4) 29 TTTAGAAATCAAAAAAAAGGA 0.323 7 477 --- --- --- --- ZSWIM8 23053 broad.mit.edu 37 10 75560463 75560464 + Frame_Shift_Ins INS - - C TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr10:75560463_75560464insC ENST00000604729.1 + 24 5365_5366 c.5068_5069insC c.(5068-5070)cccfs p.P1690fs ZSWIM8_ENST00000603114.1_Frame_Shift_Ins_p.P1652fs|NDST2_ENST00000456638.1_Intron|ZSWIM8_ENST00000604524.1_Frame_Shift_Ins_p.P1511fs|ZSWIM8_ENST00000398706.2_Frame_Shift_Ins_p.P1698fs|ZSWIM8_ENST00000605216.1_Frame_Shift_Ins_p.P1693fs zinc finger, SWIM-type containing 8 CTTCTCCCGCTCCCCCCCCTAC 0.604 8 624 --- --- --- --- RP11-399K21.11 0 broad.mit.edu 37 10 77054516 77054517 + RNA INS - - AGAA rs143565080 by1000genomes TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr10:77054516_77054517insAGAA ENST00000418818.2 - 0 142 ggagcccggagagaaagaaggg 0.718 4 8 --- --- --- --- LINC00502 0 broad.mit.edu 37 10 92813180 92813180 + RNA DEL A A - rs111380766 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr10:92813180delA ENST00000423621.1 + 0 264 TGGGCCTGATAAAAAAAAAGC 0.343 7 161 --- --- --- --- LZTS2 84445 broad.mit.edu 37 10 102763415 102763417 + In_Frame_Del DEL CCT CCT - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr10:102763415_102763417delCCT ENST00000370220.1 + 2 3623_3625 c.560_562delCCT c.(559-564)gcc>g p.AS187del LZTS2_ENST00000370223.3_In_Frame_Del_p.AS187del Q9BRK4 LZTS2_HUMAN leucine zipper, putative tumor suppressor 2 187 Required for centrosomal localization (By similarity). cell division|mitosis|Wnt receptor signaling pathway membrane|microtubule|microtubule organizing center breast(1)|large_intestine(6)|lung(7)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1) 22 Epithelial(162;7.3e-09)|all cancers(201;3.72e-07) GGGGGCCCTGcctcctcctcctc 0.650 8 1196 --- --- --- --- PDZD7 79955 broad.mit.edu 37 10 102789811 102789811 + Frame_Shift_Del DEL G G - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr10:102789811delG ENST00000370215.3 - 2 391 c.166delC c.(166-168)gcfs p.R56fs PDZD7_ENST00000470414.1_Frame_Shift_Del_p.R56fs NM_024895.4 NP_079171.1 Q9H5P4 PDZD7_HUMAN PDZ domain containing 7 56 cilium|nucleus protein binding p.R56C(1) breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 22 Epithelial(162;6.98e-09)|all cancers(201;3.55e-07) CGGATTCCGCGGGGGGGCCCG 0.667 8 613 --- --- --- --- NLRP6 171389 broad.mit.edu 37 11 281553 281555 + In_Frame_Del DEL GAG GAG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr11:281553_281555delGAG ENST00000534750.1 + 4 2024_2026 c.1819_1821delGAG c.(1819-1821)del p.E611del NLRP6_ENST00000312165.5_In_Frame_Del_p.E611del NM_001276700.1 NP_001263629.1 P59044 NALP6_HUMAN NLR family, pyrin domain containing 6 611 Poly-Glu. cytoplasm ATP binding breast(1)|skin(1)|upper_aerodigestive_tract(2) 4 all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762) all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122) CGAAGAGCCAGAGGAGGAGGAGG 0.670 13 775 --- --- --- --- SPON1 10418 broad.mit.edu 37 11 14276276 14276277 + RNA DEL GT GT - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr11:14276276_14276277delGT ENST00000310358.7 + 0 1627 Q9HCB6 SPON1_HUMAN spondin 1, extracellular matrix protein cell adhesion extracellular space|proteinaceous extracellular matrix protein binding NS(1)|endometrium(1)|large_intestine(5)|lung(11)|prostate(2)|upper_aerodigestive_tract(1) 21 Epithelial(150;0.00898) GACCTATGAGGTGTGTGTGTGT 0.594 9 328 --- --- --- --- PLEKHA7 144100 broad.mit.edu 37 11 16822525 16822525 + Frame_Shift_Del DEL A A - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr11:16822525delA ENST00000355661.3 - 17 2415 c.2405delT c.(2404-2406)tcfs p.F802fs PLEKHA7_ENST00000532079.1_Intron|PLEKHA7_ENST00000448080.2_Frame_Shift_Del_p.F802fs|PLEKHA7_ENST00000531066.1_Frame_Shift_Del_p.F802fs Q6IQ23 PKHA7_HUMAN pleckstrin homology domain containing, family A member 7 802 epithelial cell-cell adhesion|zonula adherens maintenance centrosome|zonula adherens delta-catenin binding breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1) 37 GGTCACCTGGAAAAAAAAGGC 0.443 13 1172 --- --- --- --- NAV2 89797 broad.mit.edu 37 11 19901475 19901477 + In_Frame_Del DEL AGC AGC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr11:19901475_19901477delAGC ENST00000396085.1 + 5 933_935 c.572_574delAGC c.(571-576)aag>a p.KQ191del NAV2_ENST00000360655.4_In_Frame_Del_p.KQ127del|NAV2_ENST00000349880.4_In_Frame_Del_p.KQ191del|NAV2_ENST00000534229.1_3'UTR|NAV2_ENST00000540292.1_In_Frame_Del_p.KQ122del|NAV2_ENST00000527559.2_In_Frame_Del_p.KQ120del|NAV2_ENST00000396087.3_In_Frame_Del_p.KQ191del NM_182964.5 NP_892009.3 Q8IVL1 NAV2_HUMAN neuron navigator 2 191 CH. nucleus ATP binding|helicase activity NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2) 116 TCCCGATACAagcagcagcagca 0.611 13 850 --- --- --- --- CKAP5 9793 broad.mit.edu 37 11 46829683 46829683 + Frame_Shift_Del DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr11:46829683delT ENST00000529230.1 - 8 922 c.876delA c.(874-876)aafs p.K292fs CKAP5_ENST00000415402.1_Frame_Shift_Del_p.K292fs|CKAP5_ENST00000312055.5_Frame_Shift_Del_p.K292fs|CKAP5_ENST00000354558.3_Frame_Shift_Del_p.K292fs Q14008 CKAP5_HUMAN cytoskeleton associated protein 5 292 cell division|centrosome organization|establishment or maintenance of microtubule cytoskeleton polarity|G2/M transition of mitotic cell cycle|mitotic prometaphase|RNA transport|spindle organization centrosome|cytosol protein binding breast(1)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1) 43 TCTCTTGCCATTTTTTTGCCT 0.363 9 1344 --- --- --- --- KBTBD4 55709 broad.mit.edu 37 11 47599139 47599139 + Frame_Shift_Del DEL A A - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr11:47599139delA ENST00000533290.1 - 1 1202 c.488delT c.(487-489)tgfs p.L163fs KBTBD4_ENST00000395288.2_Frame_Shift_Del_p.L138fs|KBTBD4_ENST00000430070.2_Frame_Shift_Del_p.L154fs|KBTBD4_ENST00000526005.1_Frame_Shift_Del_p.L138fs|KBTBD4_ENST00000525720.1_Frame_Shift_Del_p.L187fs|NDUFS3_ENST00000533507.1_Intron Q9NVX7 KBTB4_HUMAN kelch repeat and BTB (POZ) domain containing 4 138 BACK. NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4) 24 TGTGCGGGCCAAAAACCGAGA 0.517 7 1246 --- --- --- --- OR8I2 120586 broad.mit.edu 37 11 55861308 55861308 + Frame_Shift_Del DEL T T - rs112181516 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr11:55861308delT ENST00000302124.2 + 1 556 c.525delT c.(523-525)cafs p.H175fs OR8I2_ENST00000560768.1_Frame_Shift_Del_p.H175fs Q8N0Y5 OR8I2_HUMAN olfactory receptor, family 8, subfamily I, member 2 175 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity p.C178fs*2(1) NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1) 53 Esophageal squamous(21;0.00693) GCATCAATCATTTTTTTTGTG 0.443 10 1030 --- --- --- --- NOX4 50507 broad.mit.edu 37 11 89106662 89106663 + Splice_Site INS - - A rs56022003 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr11:89106662_89106663insA ENST00000535633.1 - 12 1313 c.e12-2 NOX4_ENST00000263317.4_Splice_Site|NOX4_ENST00000527626.1_Splice_Site|NOX4_ENST00000531342.1_Splice_Site|NOX4_ENST00000424319.1_Splice_Site|NOX4_ENST00000528341.1_Splice_Site|NOX4_ENST00000525196.1_Intron|NOX4_ENST00000542487.1_Splice_Site|NOX4_ENST00000343727.5_Splice_Site|NOX4_ENST00000534731.1_Splice_Site|NOX4_ENST00000527956.1_Splice_Site|NOX4_ENST00000413594.2_Splice_Site|NOX4_ENST00000375979.3_Splice_Site|NOX4_ENST00000532825.1_Splice_Site NM_001143836.1|NM_016931.3 NP_001137308.1|NP_058627.1 Q9NPH5 NOX4_HUMAN NADPH oxidase 4 cell aging|cell morphogenesis|inflammatory response|negative regulation of cell proliferation|superoxide anion generation endoplasmic reticulum membrane|focal adhesion|integral to membrane|nucleus electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|nucleotide binding|oxygen sensor activity p.?(1) NS(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(20)|ovary(2)|prostate(3)|skin(2) 44 Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011) AGTTGGACACTAAAAAAAAATA 0.292 11 769 --- --- --- --- SLC37A2 219855 broad.mit.edu 37 11 124949013 124949013 + Frame_Shift_Del DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr11:124949013delT ENST00000403796.2 + 5 621 c.320delT c.(319-321)gtfs p.V107fs SLC37A2_ENST00000407458.1_Frame_Shift_Del_p.V107fs|SLC37A2_ENST00000308074.4_Frame_Shift_Del_p.V107fs|SLC37A2_ENST00000298280.5_Frame_Shift_Del_p.V107fs NM_001145290.1 NP_001138762.1 Q8TED4 SPX2_HUMAN solute carrier family 37 (glucose-6-phosphate transporter), member 2 107 carbohydrate transport|transmembrane transport integral to membrane NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1) 27 all_hematologic(175;0.215) Breast(109;0.012)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.152)|all_lung(97;0.159)|all_neural(223;0.224) BRCA - Breast invasive adenocarcinoma(274;1.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0384) CCCAGTGGGGTTTTTGGGGAG 0.552 7 1450 --- --- --- --- SCAF11 9169 broad.mit.edu 37 12 46320707 46320708 + Frame_Shift_Del DEL TC TC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr12:46320707_46320708delTC ENST00000465950.1 - 1 3040_3041 c.1831_1832delGA c.(1831-1833)afs p.E611fs SCAF11_ENST00000369367.3_Frame_Shift_Del_p.E926fs|SCAF11_ENST00000419565.2_Frame_Shift_Del_p.E926fs|SCAF11_ENST00000549162.1_Frame_Shift_Del_p.E734fs Q99590 SCAFB_HUMAN SR-related CTD-associated factor 11 926 spliceosome assembly nucleus protein binding|zinc ion binding breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(17)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3) 69 GGTTCTCCTTTCTCTCTCTCTC 0.446 15 1063 --- --- --- --- CBX5 23468 broad.mit.edu 37 12 54645832 54645832 + Frame_Shift_Del DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr12:54645832delT ENST00000209875.4 - 3 453 c.317delA c.(316-318)agfs p.K106fs CBX5_ENST00000439541.2_Frame_Shift_Del_p.K106fs|CBX5_ENST00000550411.1_Frame_Shift_Del_p.K106fs NM_012117.2 NP_036249.1 P45973 CBX5_HUMAN chromobox homolog 5 106 blood coagulation|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent cytoplasm|histone deacetylase complex|histone methyltransferase complex|nuclear centromeric heterochromatin|nuclear envelope|nucleolus|transcriptional repressor complex methylated histone residue binding|protein binding, bridging|repressing transcription factor binding endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2) 8 TACCTCTCTCTTTTTTTTAGA 0.323 9 981 --- --- --- --- OR10A7 121364 broad.mit.edu 37 12 55615114 55615116 + In_Frame_Del DEL CTT CTT - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr12:55615114_55615116delCTT ENST00000326258.1 + 1 306_308 c.306_308delCTT c.(304-309)tac>ta p.YF102del NM_001005280.1 NP_001005280.1 Q8NGE5 O10A7_HUMAN olfactory receptor, family 10, subfamily A, member 7 102 sensory perception of smell integral to membrane|plasma membrane olfactory receptor activity endometrium(3)|kidney(1)|lung(11)|ovary(4)|prostate(2)|skin(3) 24 CCCAGATGTACTTCTTCTTCTTC 0.414 7 1081 --- --- --- --- MYO1A 4640 broad.mit.edu 37 12 57422572 57422573 + Frame_Shift_Ins INS - - T TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr12:57422572_57422573insT ENST00000442789.2 - 29 3385_3386 c.3098_3099insA c.(3097-3099)aggfs p.R1033fs TAC3_ENST00000415231.1_5'UTR|MYO1A_ENST00000300119.3_Frame_Shift_Ins_p.R1033fs|MYO1A_ENST00000544473.1_Frame_Shift_Ins_p.R871fs 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 8 635 --- --- --- --- TPCN1 53373 broad.mit.edu 37 12 113707611 113707613 + In_Frame_Del DEL CTG CTG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr12:113707611_113707613delCTG ENST00000550785.1 + 8 1094_1096 c.925_927delCTG c.(925-927)del p.L312del TPCN1_ENST00000335509.6_In_Frame_Del_p.L240del|TPCN1_ENST00000392569.4_In_Frame_Del_p.L172del|TPCN1_ENST00000541517.1_In_Frame_Del_p.L312del NM_001143819.1 NP_001137291.1 Q9ULQ1 TPC1_HUMAN two pore segment channel 1 240 endosome membrane|integral to membrane|lysosomal membrane NAADP-sensitive calcium-release channel activity|voltage-gated ion channel activity p.L237L(1) cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(1) 40 GGACATCCTCCTGCTGCTGCTGT 0.601 7 892 --- --- --- --- TPTE2P1 0 broad.mit.edu 37 13 25517701 25517702 + RNA INS - - T TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr13:25517701_25517702insT ENST00000429698.1 - 0 374 ACCATTTGCTATTTTTTTTTCT 0.426 10 565 --- --- --- --- EEF1DP3 0 broad.mit.edu 37 13 32527507 32527508 + RNA DEL GT GT - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr13:32527507_32527508delGT ENST00000428783.1 + 0 1207_1208 TCTGGCCTGAGTGTGTGTGTGT 0.460 8 479 --- --- --- --- KIAA1704 0 broad.mit.edu 37 13 45580365 45580367 + In_Frame_Del DEL GAT GAT - rs138421508 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr13:45580365_45580367delGAT ENST00000361121.2 + 3 285_287 c.250_252delGAT c.(250-252)del p.D88del KIAA1704_ENST00000379151.4_In_Frame_Del_p.D88del|KIAA1704_ENST00000357537.3_De_novo_Start_InFrame|RP11-321C24.1_ENST00000437748.2_lincRNA Q8IXQ4 K1704_HUMAN 88 Poly-Asp. breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|prostate(2)|skin(1) 12 Lung NSC(96;0.00143)|Prostate(109;0.0137)|Breast(139;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.133) KIRC - Kidney renal clear cell carcinoma(16;0.234) GBM - Glioblastoma multiforme(144;0.000313)|BRCA - Breast invasive adenocarcinoma(63;0.126) Ggatgatgacgatgatgatgatg 0.335 15 1431 --- --- --- --- ERCC5 2073 broad.mit.edu 37 13 103524612 103524612 + Frame_Shift_Del DEL A A - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr13:103524612delA ENST00000355739.4 + 13 4166 c.2743delA c.(2743-2745)aafs p.K917fs ERCC5_ENST00000375954.1_Frame_Shift_Del_p.K150fs|BIVM-ERCC5_ENST00000602836.1_Frame_Shift_Del_p.1340fs NM_000123.3 NP_000114.2 excision repair cross-complementing rodent repair deficiency, complementation group 5 breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2) 51 all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211) CACCAAAGTGAAAAAAAAATT 0.428 """Mis, N, F""" """skin basal cell, skin squamous cell, melanoma""" Nucleotide excision repair (NER) Xeroderma Pigmentosum 11 385 --- --- --- --- ACIN1 22985 broad.mit.edu 37 14 23528502 23528503 + Frame_Shift_Del DEL TC TC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr14:23528502_23528503delTC ENST00000262710.1 - 19 4207_4208 c.3880_3881delGA c.(3880-3882)afs p.E1294fs ACIN1_ENST00000338631.6_Frame_Shift_Del_p.E567fs|ACIN1_ENST00000605057.1_Frame_Shift_Del_p.E1236fs|ACIN1_ENST00000397341.3_Frame_Shift_Del_p.E536fs|ACIN1_ENST00000457657.1_Frame_Shift_Del_p.E1254fs|ACIN1_ENST00000557515.1_Frame_Shift_Del_p.E535fs|ACIN1_ENST00000555053.1_Frame_Shift_Del_p.E1281fs|ACIN1_ENST00000357481.2_Frame_Shift_Del_p.E536fs NM_001164814.1|NM_014977.3 NP_001158286.1|NP_055792.1 Q9UKV3 ACINU_HUMAN apoptotic chromatin condensation inducer 1 1294 Arg/Asp/Glu/Lys-rich. apoptotic chromosome condensation|erythrocyte differentiation|positive regulation of monocyte differentiation cytosol ATPase activity|enzyme binding|nucleic acid binding|nucleotide binding breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1) 37 all_cancers(95;1.36e-05) GBM - Glioblastoma multiforme(265;0.00816) ccgctccctttctctctctctc 0.629 OREG0022595 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 8 403 --- --- --- --- FBXO34 55030 broad.mit.edu 37 14 55818554 55818555 + Frame_Shift_Ins INS - - T TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr14:55818554_55818555insT ENST00000313833.4 + 2 1691_1692 c.1446_1447insT c.(1444-1449)ttttttfs p.FF482fs FBXO34_ENST00000440021.1_Frame_Shift_Ins_p.FF482fs NM_017943.3 NP_060413.2 Q9NWN3 FBX34_HUMAN F-box protein 34 482 breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3) 22 CAGGGATGTTGTTTTTTTTGCC 0.441 9 836 --- --- --- --- SYNE3 161176 broad.mit.edu 37 14 95921888 95921890 + In_Frame_Del DEL CTC CTC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr14:95921888_95921890delCTC ENST00000334258.5 - 5 975_977 c.961_963delGAG c.(961-963)del p.E321del SYNE3_ENST00000553340.1_In_Frame_Del_p.E321del|SYNE3_ENST00000554873.1_In_Frame_Del_p.E78del|SYNE3_ENST00000557275.1_In_Frame_Del_p.E321del NM_152592.3 NP_689805.3 spectrin repeat containing, nuclear envelope family member 3 breast(1)|endometrium(2)|lung(25) 28 CCCGCAGCCGCTCCTCCTCCTCC 0.616 8 832 --- --- --- --- IGHV3-20 0 broad.mit.edu 37 14 106667902 106667902 + RNA DEL A A - rs148276173 by1000genomes TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr14:106667902delA ENST00000390606.2 - 0 108 ACACAGAGACACCTGGTCAGA 0.517 7 229 --- --- --- --- IGHV3-43 0 broad.mit.edu 37 14 106926652 106926653 + RNA DEL TC TC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr14:106926652_106926653delTC ENST00000434710.1 - 0 71_72 CATGGTGCGTTCTCTGTGTTCA 0.495 23 1154 --- --- --- --- SRP14 6727 broad.mit.edu 37 15 40328597 40328599 + In_Frame_Del DEL TGC TGC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr15:40328597_40328599delTGC ENST00000267884.6 - 5 417_419 c.346_348delGCA c.(346-348)del p.A116del SRP14_ENST00000560773.1_In_Frame_Del_p.A36del|SRP14_ENST00000558527.1_5'UTR|SRP14_ENST00000558720.1_In_Frame_Del_p.A36del NM_003134.4 NP_003125.3 P37108 SRP14_HUMAN signal recognition particle 14kDa (homologous Alu RNA binding protein) 116 Ala/Thr-rich. negative regulation of translational elongation|response to drug|SRP-dependent cotranslational protein targeting to membrane cytosol|signal recognition particle, endoplasmic reticulum targeting 7S RNA binding|endoplasmic reticulum signal peptide binding|protein binding endometrium(1)|skin(1)|upper_aerodigestive_tract(1) 3 all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117) GBM - Glioblastoma multiforme(113;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505) ctgcggcaggtgctgctgctgct 0.478 7 507 --- --- --- --- ZNF106 64397 broad.mit.edu 37 15 42742957 42742957 + Frame_Shift_Del DEL A A - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr15:42742957delA ENST00000263805.4 - 2 1770 c.1444delT c.(1444-1446)ccfs p.S482fs ZNF106_ENST00000565380.1_Intron|ZNF106_ENST00000565611.1_Intron NM_022473.1 NP_071918.1 zinc finger protein 106 TCTCCAGGGGAAAAAAAATTT 0.393 9 1544 --- --- --- --- SLTM 79811 broad.mit.edu 37 15 59182525 59182526 + Frame_Shift_Del DEL TC TC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr15:59182525_59182526delTC ENST00000380516.2 - 15 2120_2121 c.2033_2034delGA c.(2032-2034)afs p.R678fs AC025918.2_ENST00000452467.1_RNA|SLTM_ENST00000536328.1_Frame_Shift_Del_p.R247fs NM_001013843.1|NM_024755.2 NP_001013865.1|NP_079031.2 Q9NWH9 SLTM_HUMAN SAFB-like, transcription modulator 678 Arg/Glu-rich. apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus nucleotide binding|RNA binding breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 28 CGCGTTCCATTCTCTCTCTCTC 0.431 7 1185 --- --- --- --- NARG2 79664 broad.mit.edu 37 15 60745782 60745782 + Frame_Shift_Del DEL A A - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr15:60745782delA ENST00000561114.1 - 9 1307 c.1145delT c.(1144-1146)tcfs p.F382fs NARG2_ENST00000439632.1_Intron|NARG2_ENST00000261520.4_Intron NM_001276385.1 NP_001263314.1 Q659A1 NARG2_HUMAN NMDA receptor regulated 2 0 nucleus breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2) 32 CCCTTAGGGGAAAAAAAAAGC 0.338 8 279 --- --- --- --- ARID3B 10620 broad.mit.edu 37 15 74888025 74888027 + In_Frame_Del DEL CAG CAG - rs141710149 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr15:74888025_74888027delCAG ENST00000346246.5 + 9 1824_1826 c.1593_1595delCAG c.(1591-1596)gcc>gc p.AS531del NM_006465.2 NP_006456.1 Q8IVW6 ARI3B_HUMAN AT rich interactive domain 3B (BRIGHT-like) 532 Ser-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus DNA binding NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(2) 14 gcagcagcgccagcagcagcagc 0.640 7 277 --- --- --- --- RP11-24M17.5 0 broad.mit.edu 37 15 76074745 76074746 + RNA INS - - A TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr15:76074745_76074746insA ENST00000395215.3 + 0 800 TCTGACCCTTCAGCCCCCactt 0.520 7 507 --- --- --- --- C15orf40 123207 broad.mit.edu 37 15 83674353 83674354 + Frame_Shift_Ins INS - - T TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr15:83674353_83674354insT ENST00000304177.5 - 4 490_491 c.376_377insA c.(376-378)atafs p.I126fs C15orf40_ENST00000451195.3_Intron|C15orf40_ENST00000565712.1_Frame_Shift_Ins_p.I68fs|RP11-382A20.5_ENST00000566841.1_RNA|C15orf40_ENST00000538348.2_Intron|C15orf40_ENST00000513601.2_Frame_Shift_Ins_p.I153fs NM_001160114.1|NM_144597.2 NP_001153586.1|NP_653198.2 Q8WUR7 CO040_HUMAN chromosome 15 open reading frame 40 126 large_intestine(3)|lung(2)|skin(1) 6 TTGCTTTTATGTTTTTTTGGCT 0.490 7 1088 --- --- --- --- POLG 5428 broad.mit.edu 37 15 89876828 89876830 + In_Frame_Del DEL TGC TGC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr15:89876828_89876830delTGC ENST00000268124.5 - 2 489_491 c.156_158delGCA c.(154-159)caa>ca p.QQ54del POLG_ENST00000442287.2_In_Frame_Del_p.QQ54del NM_001126131.1|NM_002693.2 NP_001119603.1|NP_002684.1 P54098 DPOG1_HUMAN polymerase (DNA directed), gamma 54 Poly-Gln. base-excision repair, gap-filling|cell death|DNA-dependent DNA replication mitochondrial nucleoid DNA binding|DNA-directed DNA polymerase activity|protease binding breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(3)|urinary_tract(2) 33 Lung NSC(78;0.0472)|all_lung(78;0.089) STAD - Stomach adenocarcinoma(125;0.165) aggctgctgttgctgctgctgct 0.690 DNA polymerases (catalytic subunits) 14 159 --- --- --- --- NAGPA 51172 broad.mit.edu 37 16 5083678 5083679 + Frame_Shift_Del DEL GC GC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr16:5083678_5083679delGC ENST00000312251.3 - 2 156_157 c.137_138delGC c.(136-138)cfs p.R46fs NAGPA_ENST00000381955.3_Frame_Shift_Del_p.R46fs|NAGPA_ENST00000564922.1_5'UTR|RP11-165E7.1_ENST00000588778.1_RNA NM_016256.3 NP_057340.2 Q9UK23 NAGPA_HUMAN N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase 46 carbohydrate metabolic process|lysosome organization|protein modification process|protein targeting to lysosome Golgi cisterna membrane|integral to membrane N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase activity endometrium(4)|large_intestine(4)|lung(3)|urinary_tract(1) 12 N-Acetyl-D-glucosamine(DB00141) CCCGGGGGAGGCGCGCGCGCGC 0.767 8 161 --- --- --- --- KIAA0430 9665 broad.mit.edu 37 16 15729982 15729984 + In_Frame_Del DEL CCA CCA - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr16:15729982_15729984delCCA ENST00000396368.3 - 3 566_568 c.360_362delTGG c.(358-363)ggc>gg p.GG120del KIAA0430_ENST00000602337.1_In_Frame_Del_p.GG120del|KIAA0430_ENST00000548025.1_In_Frame_Del_p.GG120del|KIAA0430_ENST00000551742.1_In_Frame_Del_p.GG120del|KIAA0430_ENST00000344181.3_5'UTR|KIAA0430_ENST00000540441.2_In_Frame_Del_p.GG120del NM_001184998.1|NM_001184999.1|NM_014647.3 NP_001171927.1|NP_001171928.1|NP_055462.2 Q9Y4F3 LKAP_HUMAN KIAA0430 119 Poly-Gly. peroxisome nucleotide binding|RNA binding breast(4)|endometrium(8)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(5)|skin(1) 40 TCCGCTACCGCCACCACCACCAC 0.532 7 1006 --- --- --- --- C16orf62 57020 broad.mit.edu 37 16 19580800 19580802 + In_Frame_Del DEL TCC TCC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr16:19580800_19580802delTCC ENST00000438132.3 + 3 487_489 c.439_441delTCC c.(439-441)del p.S153del C16orf62_ENST00000251143.5_In_Frame_Del_p.S64del|C16orf62_ENST00000542263.1_In_Frame_Del_p.S153del|C16orf62_ENST00000417362.2_In_Frame_Del_p.S64del|C16orf62_ENST00000538853.1_In_Frame_Del_p.S153del NM_020314.5 NP_064710.4 Q7Z3J2 CP062_HUMAN chromosome 16 open reading frame 62 64 integral to membrane breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2) 36 TTCTTCCACGTCCTCCTCCTCCT 0.562 8 480 --- --- --- --- KNOP1 400506 broad.mit.edu 37 16 19722724 19722724 + Frame_Shift_Del DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr16:19722724delT ENST00000219837.7 - 3 1035 c.957delA c.(955-957)aafs p.K319fs KNOP1_ENST00000568230.1_5'UTR|AC002550.5_ENST00000565916.1_RNA NM_001012991.2 NP_001013009.2 lysine-rich nucleolar protein 1 p.G320fs*5(1)|p.K319N(1) CCATGTTGCCTTTTTTTTCCA 0.562 11 739 --- --- --- --- RRN3P1 0 broad.mit.edu 37 16 21814060 21814060 + RNA DEL G G - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr16:21814060delG ENST00000546471.1 - 0 1607 CTATAACAAAGGGGGGGGAAA 0.383 7 333 --- --- --- --- SLC5A11 115584 broad.mit.edu 37 16 24921737 24921739 + In_Frame_Del DEL CAG CAG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr16:24921737_24921739delCAG ENST00000347898.3 + 15 2383_2385 c.1761_1763delCAG c.(1759-1764)gcc>gc p.AS587del SLC5A11_ENST00000565769.1_In_Frame_Del_p.AS523del|SLC5A11_ENST00000539472.1_In_Frame_Del_p.AS523del|SLC5A11_ENST00000449109.2_In_Frame_Del_p.AS431del|SLC5A11_ENST00000424767.2_In_Frame_Del_p.AS552del|SLC5A11_ENST00000569071.1_In_Frame_Del_p.AS431del|SLC5A11_ENST00000567758.1_In_Frame_Del_p.AS552del|SLC5A11_ENST00000545376.1_In_Frame_Del_p.AS517del|SLC5A11_ENST00000568579.1_In_Frame_Del_p.AS517del NM_052944.3 NP_443176.2 Q8WWX8 SC5AB_HUMAN solute carrier family 5 (sodium/inositol cotransporter), member 11 587 apoptosis|carbohydrate transport|sodium ion transport integral to membrane|plasma membrane polyol transmembrane transporter activity|symporter activity endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(30)|ovary(2)|prostate(2)|urinary_tract(1) 49 GBM - Glioblastoma multiforme(48;0.0365) TGCCAGAGGCCAGCAGCAGCAGC 0.542 16 514 --- --- --- --- RRN3P2 0 broad.mit.edu 37 16 29110406 29110406 + RNA DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr16:29110406delT ENST00000564580.1 + 0 1098 TTAAAAAATCTTTTTTTTTTT 0.299 13 175 --- --- --- --- SETD1A 9739 broad.mit.edu 37 16 30982809 30982811 + In_Frame_Del DEL TCC TCC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr16:30982809_30982811delTCC ENST00000262519.8 + 13 3813_3815 c.3127_3129delTCC c.(3127-3129)del p.S1058del NM_014712.1 NP_055527.1 O15047 SET1A_HUMAN SET domain containing 1A 1058 Ser-rich. regulation of transcription, DNA-dependent|transcription, DNA-dependent chromosome|nuclear speck|Set1C/COMPASS complex histone-lysine N-methyltransferase activity|nucleotide binding|protein binding|RNA binding NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1) 59 CAGctcctcatcctcctcctcct 0.547 9 536 --- --- --- --- RP11-23E10.4 0 broad.mit.edu 37 16 33365420 33365420 + RNA DEL A A - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr16:33365420delA ENST00000568520.1 - 0 249 TACAAACTATAAAAAAACAGA 0.358 7 103 --- --- --- --- NPIPB15 440348 broad.mit.edu 37 16 74425400 74425402 + In_Frame_Del DEL CAA CAA - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa 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 10 1034 --- --- --- --- ZZEF1 23140 broad.mit.edu 37 17 4020268 4020268 + Frame_Shift_Del DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr17:4020268delT ENST00000381638.2 - 3 816 c.692delA c.(691-693)agfs p.K231fs ZZEF1_ENST00000574474.1_5'UTR NM_015113.3 NP_055928.3 O43149 ZZEF1_HUMAN zinc finger, ZZ-type with EF-hand domain 1 231 DOC. calcium ion binding|zinc ion binding central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3) 84 ACACATACCCTTTTCCTTTTG 0.473 7 1667 --- --- --- --- MYH10 4628 broad.mit.edu 37 17 8415820 8415822 + In_Frame_Del DEL TTC TTC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr17:8415820_8415822delTTC ENST00000360416.3 - 24 3037_3039 c.2899_2901delGAA c.(2899-2901)del p.E967del MYH10_ENST00000379980.4_In_Frame_Del_p.E952del|MYH10_ENST00000269243.4_In_Frame_Del_p.E936del|MYH10_ENST00000396239.1_In_Frame_Del_p.E957del 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 7 360 --- --- --- --- MYOCD 93649 broad.mit.edu 37 17 12647692 12647694 + In_Frame_Del DEL CAG CAG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr17:12647692_12647694delCAG ENST00000425538.1 + 8 1110_1112 c.910_912delCAG c.(910-912)del p.Q310del MYOCD_ENST00000395988.1_In_Frame_Del_p.Q214del|MYOCD_ENST00000343344.4_In_Frame_Del_p.Q310del NM_001146312.1|NM_153604.2 NP_001139784.1|NP_705832.1 Q8IZQ8 MYCD_HUMAN myocardin 310 Gln-rich. cardiac muscle cell differentiation|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|positive regulation of smooth muscle cell differentiation|positive regulation of smooth muscle contraction|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation|regulation of histone acetylation|smooth muscle cell differentiation nucleus nucleic acid binding|RNA polymerase II transcription factor binding transcription factor activity|transcription factor binding breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(2)|lung(33)|ovary(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1) 70 UCEC - Uterine corpus endometrioid carcinoma (92;0.0969) AATCCTCAGCcagcagcagcagc 0.596 8 262 --- --- --- --- SMCR7 0 broad.mit.edu 37 17 18167778 18167780 + In_Frame_Del DEL GCT GCT - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa 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 7 457 --- --- --- --- POLDIP2 26073 broad.mit.edu 37 17 26684394 26684395 + Splice_Site INS - - G rs113730440 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa 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 36 --- --- --- --- SUPT6H 6830 broad.mit.edu 37 17 27027202 27027204 + In_Frame_Del DEL AGC AGC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr17:27027202_27027204delAGC ENST00000314616.6 + 34 4856_4858 c.4573_4575delAGC c.(4573-4575)del p.S1528del SUPT6H_ENST00000347486.4_In_Frame_Del_p.S1528del NM_003170.3 NP_003161.2 Q7KZ85 SPT6H_HUMAN suppressor of Ty 6 homolog (S. cerevisiae) 1528 Poly-Ser. chromatin remodeling|regulation of transcription elongation, DNA-dependent|regulation of transcription from RNA polymerase II promoter nucleus hydrolase activity, acting on ester bonds|RNA binding|sequence-specific DNA binding transcription factor activity NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1) 64 Lung NSC(42;0.00431) CATCACCCCTAGCAGCAGCAGCA 0.537 8 1763 --- --- --- --- NUFIP2 57532 broad.mit.edu 37 17 27620990 27620992 + In_Frame_Del DEL GCT GCT - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr17:27620990_27620992delGCT ENST00000225388.4 - 1 144_146 c.86_88delAGC c.(85-90)ccg>c p.QP29del NUFIP2_ENST00000579665.1_In_Frame_Del_p.QP29del NM_020772.2 NP_065823.1 Q7Z417 NUFP2_HUMAN nuclear fragile X mental retardation protein interacting protein 2 29 His-rich. nucleus|polysomal ribosome protein binding|RNA binding breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1) 24 BRCA - Breast invasive adenocarcinoma(11;0.000457)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551) tggtggtgcggctgctgctgctg 0.591 11 553 --- --- --- --- RP11-115K3.2 0 broad.mit.edu 37 17 36214141 36214141 + RNA DEL A A - rs76035088 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr17:36214141delA ENST00000590732.1 - 0 325 NR_024178.1 CAGCaaaattaaaaaaaaaaa 0.328 8 140 --- --- --- --- RP11-156P1.3 0 broad.mit.edu 37 17 45128629 45128629 + RNA DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr17:45128629delT ENST00000575173.1 - 0 418 TTCTGGTGTGtttttttttgt 0.333 8 362 --- --- --- --- SPAG9 9043 broad.mit.edu 37 17 49077041 49077041 + Frame_Shift_Del DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr17:49077041delT ENST00000262013.7 - 14 1853 c.1645delA c.(1645-1647)ggfs p.R549fs SPAG9_ENST00000505279.1_Frame_Shift_Del_p.R535fs|SPAG9_ENST00000357122.4_Frame_Shift_Del_p.R535fs|SPAG9_ENST00000510283.1_Frame_Shift_Del_p.R392fs NM_001130528.2 NP_001124000.1 O60271 JIP4_HUMAN sperm associated antigen 9 549 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 p.R535fs*28(1) 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) ATGCTTGACCTTTTTTTTTCC 0.323 17 320 --- --- --- --- AMZ2P1 0 broad.mit.edu 37 17 62968575 62968575 + RNA DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr17:62968575delT ENST00000430983.1 - 0 1593 NR_026903.1 TTGGTTGGAATTTTTTTCCCT 0.333 8 348 --- --- --- --- BPTF 2186 broad.mit.edu 37 17 65940454 65940456 + In_Frame_Del DEL CAC CAC - rs143937013 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr17:65940454_65940456delCAC ENST00000321892.4 + 22 7105_7107 c.7044_7046delCAC c.(7042-7047)agc>ag p.ST2348del BPTF_ENST00000335221.5_In_Frame_Del_p.ST2348del|BPTF_ENST00000306378.6_In_Frame_Del_p.ST2222del|BPTF_ENST00000424123.3_In_Frame_Del_p.ST2209del Q12830 BPTF_HUMAN bromodomain PHD finger transcription factor 2348 Thr-rich. brain development|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent cytoplasm|NURF complex sequence-specific DNA binding|transcription factor binding|zinc ion binding NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2) 78 all_cancers(12;6e-11) BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24) CCACAGCCAGCACCACCACCACC 0.542 7 622 --- --- --- --- SRP68 6730 broad.mit.edu 37 17 74068528 74068530 + In_Frame_Del DEL GCC GCC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr17:74068528_74068530delGCC ENST00000307877.2 - 1 204_206 c.43_45delGGC c.(43-45)del p.G15del SRP68_ENST00000355113.5_5'UTR|SRP68_ENST00000539137.1_In_Frame_Del_p.G15del NM_014230.3 NP_055045.2 Q9UHB9 SRP68_HUMAN signal recognition particle 68kDa 15 Poly-Gly. Missing (in Ref. 1). response to drug cytosol|endoplasmic reticulum|nucleolus|ribosome|signal recognition particle, endoplasmic reticulum targeting RNA binding|signal recognition particle binding NS(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|lung(4)|ovary(2)|prostate(3) 23 cgccgccactgccgccgccgccg 0.709 8 312 --- --- --- --- HAMP 57817 broad.mit.edu 37 19 35773520 35773522 + In_Frame_Del DEL CTC CTC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr19:35773520_35773522delCTC ENST00000598398.1 + 2 336_338 c.40_42delCTC c.(40-42)del p.L18del HAMP_ENST00000222304.3_In_Frame_Del_p.L18del NM_021175.2 NP_066998.1 P81172 HEPC_HUMAN hepcidin antimicrobial peptide 18 defense response to bacterium|defense response to fungus|immune response|killing of cells of other organism extracellular region hormone activity breast(1)|central_nervous_system(1)|large_intestine(1)|lung(1) 4 all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162) Epithelial(14;7.4e-20)|OV - Ovarian serous cystadenocarcinoma(14;6.47e-19)|all cancers(14;4.17e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417) TTGCCTCCTGCTCCTCCTCCTCC 0.640 9 1247 --- --- --- --- C19orf55 148137 broad.mit.edu 37 19 36255947 36255949 + In_Frame_Del DEL CTC CTC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr19:36255947_36255949delCTC ENST00000544099.1 + 7 702_704 c.639_641delCTC c.(637-642)atc>at p.IS213del C19orf55_ENST00000396908.4_In_Frame_Del_p.IS213del Q2NL68 CS055_HUMAN chromosome 19 open reading frame 55 213 Ser-rich. cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1) 15 all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0515) AAGCCTCCATCTCCTCCTCCTCC 0.631 10 1571 --- --- --- --- ERF 2077 broad.mit.edu 37 19 42753149 42753151 + In_Frame_Del DEL GAA GAA - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr19:42753149_42753151delGAA ENST00000222329.4 - 4 1270_1272 c.1113_1115delTTC c.(1111-1116)tcc>tc p.SS371del ERF_ENST00000440177.2_In_Frame_Del_p.SS296del|AC006486.9_ENST00000594664.1_Intron NM_006494.2 NP_006485.2 P50548 ERF_HUMAN Ets2 repressor factor 371 Poly-Ser. cell proliferation|regulation of transcription from RNA polymerase II promoter nucleus ligand-regulated transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1) 17 Prostate(69;0.00682) GAATGGGGAGGAAGAAGAAGAAG 0.680 7 858 --- --- --- --- LIPE-AS1 0 broad.mit.edu 37 19 43136362 43136363 + RNA DEL TG TG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr19:43136362_43136363delTG ENST00000594688.1 + 0 1450 LIPE-AS1_ENST00000594624.2_RNA NR_073179.1 TGAGTATGTATGTGTGTGTGTG 0.505 10 234 --- --- --- --- LYPD3 27076 broad.mit.edu 37 19 43969653 43969655 + In_Frame_Del DEL AGC AGC - rs141441894 byFrequency TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa 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 18 958 --- --- --- --- PTH2 113091 broad.mit.edu 37 19 49926531 49926533 + In_Frame_Del DEL CAG CAG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr19:49926531_49926533delCAG ENST00000270631.1 - 1 165_167 c.64_66delCTG c.(64-66)del p.L22del NM_178449.3 NP_848544.1 Q96A98 TIP39_HUMAN parathyroid hormone 2 22 neuropeptide signaling pathway extracellular region p.L22V(2) endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|skin(1) 6 OV - Ovarian serous cystadenocarcinoma(262;0.0015)|GBM - Glioblastoma multiforme(486;0.044)|Lung(386;0.0785)|LUSC - Lung squamous cell carcinoma(496;0.0836) AGGGCACCACcagcagcagcagc 0.690 8 163 --- --- --- --- CTD-2616J11.14 0 broad.mit.edu 37 19 51906669 51906670 + RNA INS - - T TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr19:51906669_51906670insT ENST00000600765.1 + 0 324_325 GGTTGTTCTTGTTTTTTTTGCT 0.446 8 317 --- --- --- --- ZNF880 400713 broad.mit.edu 37 19 52877717 52877717 + Frame_Shift_Del DEL T T - rs77187934 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr19:52877717delT ENST00000597976.1 + 3 325 c.305delT c.(304-306)atfs p.I102fs ZNF880_ENST00000424032.2_Intron|ZNF880_ENST00000600321.1_Intron|ZNF880_ENST00000422689.2_Intron|ZNF880_ENST00000344085.5_Intron Q6PDB4 ZN880_HUMAN zinc finger protein 880 0 regulation of transcription, DNA-dependent intracellular nucleic acid binding|zinc ion binding breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1) 10 GGCCCCATAAttttttttttt 0.473 10 70 --- --- --- --- TMC4 147798 broad.mit.edu 37 19 54675747 54675749 + In_Frame_Del DEL TCC TCC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr19:54675747_54675749delTCC ENST00000376591.4 - 2 332_334 c.201_203delGGA c.(199-204)gat>ga p.ED67del TMC4_ENST00000301187.4_In_Frame_Del_p.ED61del NM_001145303.1|NM_144686.2 NP_001138775.1|NP_653287.1 Q7Z404 TMC4_HUMAN transmembrane channel-like 4 67 Poly-Glu. integral to membrane breast(2)|endometrium(7)|large_intestine(4)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1) 22 all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19) CCTTCCTCCATCCTCCTCCTCCT 0.645 12 594 --- --- --- --- LILRB1 0 broad.mit.edu 37 19 55146148 55146150 + In_Frame_Del DEL CTC CTC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr19:55146148_55146150delCTC ENST00000396331.1 + 11 1774_1776 c.1417_1419delCTC c.(1417-1419)del p.L479del LILRB1_ENST00000324602.7_In_Frame_Del_p.L480del|LILRB1_ENST00000396315.1_In_Frame_Del_p.L480del|LILRB1_ENST00000396317.1_In_Frame_Del_p.L463del|LILRB1_ENST00000396327.3_In_Frame_Del_p.L480del|LILRB1_ENST00000462628.1_3'UTR|LILRB1_ENST00000427581.2_In_Frame_Del_p.L529del|LILRB1_ENST00000448689.1_In_Frame_Del_p.L479del|LILRB1_ENST00000396332.4_In_Frame_Del_p.L479del|LILRB1_ENST00000434867.2_In_Frame_Del_p.L479del|LILRB1_ENST00000418536.2_In_Frame_Del_p.L463del|LILRB1_ENST00000396321.2_In_Frame_Del_p.L479del NM_006669.3 NP_006660.3 Q8NHL6 LIRB1_HUMAN leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1 479 regulation of immune response|response to virus integral to membrane|plasma membrane protein phosphatase 1 binding|receptor activity NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1) 74 GBM - Glioblastoma multiforme(193;0.0188) CAtcctactgctcctcctcctcc 0.581 HNSCC(37;0.09) 12 442 --- --- --- --- NLRP4 147945 broad.mit.edu 37 19 56370311 56370311 + Frame_Shift_Del DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr19:56370311delT ENST00000301295.6 + 3 1974 c.1552delT c.(1552-1554)ttfs p.F519fs NLRP4_ENST00000346986.5_Frame_Shift_Del_p.F519fs|NLRP4_ENST00000587891.1_Frame_Shift_Del_p.F444fs NM_134444.4 NP_604393.2 Q96MN2 NALP4_HUMAN NLR family, pyrin domain containing 4 519 ATP binding breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8) 42 Colorectal(82;0.0002)|Ovarian(87;0.221) GBM - Glioblastoma multiforme(193;0.0606) ACTGGATGCGTTTTTTGGCTT 0.428 7 655 --- --- --- --- PANK2 80025 broad.mit.edu 37 20 3893120 3893120 + Frame_Shift_Del DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr20:3893120delT ENST00000497424.1 + 4 689 c.378delT c.(376-378)acfs p.T126fs PANK2_ENST00000336066.3_3'UTR|PANK2_ENST00000316562.4_Frame_Shift_Del_p.T417fs NM_024960.4|NM_153640.2 NP_079236.3|NP_705904.1 Q9BZ23 PANK2_HUMAN pantothenate kinase 2 417 G -> A (in dbSNP:rs3737084). cell death|coenzyme A biosynthetic process|pantothenate metabolic process mitochondrial intermembrane space|nucleus ATP binding|pantothenate kinase activity|protein binding breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1) 15 GAGGAGGAACTTTTTTTGGTC 0.343 8 1148 --- --- --- --- GZF1 64412 broad.mit.edu 37 20 23345921 23345923 + In_Frame_Del DEL GAG GAG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr20:23345921_23345923delGAG ENST00000338121.5 + 2 978_980 c.901_903delGAG c.(901-903)del p.E306del GZF1_ENST00000544236.1_Intron|GZF1_ENST00000542987.1_Intron|GZF1_ENST00000461789.1_3'UTR|GZF1_ENST00000377051.2_In_Frame_Del_p.E306del Q9H116 GZF1_HUMAN GDNF-inducible zinc finger protein 1 306 transcription, DNA-dependent nucleolus|nucleoplasm sequence-specific DNA binding|zinc ion binding endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|urinary_tract(2) 24 Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135) ggaggaggaagaggaggaggagg 0.532 9 507 --- --- --- --- FRG1B 0 broad.mit.edu 37 20 29628310 29628312 + In_Frame_Del DEL AGG AGG - rs111939959 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr20:29628310_29628312delAGG ENST00000278882.3 + 6 692_694 c.312_314delAGG c.(310-315)gca>gc p.AG104del FRG1B_ENST00000358464.4_In_Frame_Del_p.AG104del|FRG1B_ENST00000439954.2_In_Frame_Del_p.AG109del endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9) 53 GTAAAACAGCAGGAGAAGAAGAA 0.355 11 879 --- --- --- --- CTCFL 140690 broad.mit.edu 37 20 56099187 56099187 + Frame_Shift_Del DEL T T - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr20:56099187delT ENST00000426658.2 - 1 736 c.75delA c.(73-75)aafs p.K25fs CTCFL_ENST00000539382.1_Intron|CTCFL_ENST00000422109.2_Frame_Shift_Del_p.K25fs|CTCFL_ENST00000502686.2_Intron|CTCFL_ENST00000371196.2_Frame_Shift_Del_p.K25fs|CTCFL_ENST00000433949.2_Frame_Shift_Del_p.K25fs|CTCFL_ENST00000432255.2_Frame_Shift_Del_p.K25fs|CTCFL_ENST00000429804.2_Frame_Shift_Del_p.K25fs|CTCFL_ENST00000423479.2_Frame_Shift_Del_p.K25fs|CTCFL_ENST00000422869.2_Frame_Shift_Del_p.K25fs|CTCFL_ENST00000243914.3_Frame_Shift_Del_p.K25fs Q8NI51 CTCFL_HUMAN CCCTC-binding factor (zinc finger protein)-like 25 cell cycle|DNA methylation involved in gamete generation|histone methylation|positive regulation of transcription, DNA-dependent|regulation of gene expression by genetic imprinting|regulation of histone H3-K4 methylation|transcription, DNA-dependent cytoplasm|nucleus histone binding|sequence-specific DNA binding|transcription regulatory region DNA binding|zinc ion binding NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1) 58 Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242) BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07) CCTTCAGGCCTTTTTCCGGCA 0.502 11 2702 --- --- --- --- TPTEP1 0 broad.mit.edu 37 22 17127506 17127507 + RNA INS - - A TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr22:17127506_17127507insA ENST00000426585.1 + 0 442 AGGGCCTAGAGAAAAAAAAAAT 0.421 16 502 --- --- --- --- LL22NC03-80A10.6 0 broad.mit.edu 37 22 22661172 22661173 + RNA INS - - C rs7410785 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr22:22661172_22661173insC ENST00000426066.1 + 0 264_265 NR_027293.1 CATACAGGTTTTCCCCCCCCAC 0.411 7 244 --- --- --- --- MN1 4330 broad.mit.edu 37 22 28194934 28194936 + In_Frame_Del DEL TGC TGC - rs45480998 TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr22:28194934_28194936delTGC ENST00000302326.4 - 1 2550_2552 c.1596_1598delGCA c.(1594-1599)caa>ca p.QQ548del NM_002430.2 NP_002421.3 Q10571 MN1_HUMAN meningioma (disrupted in balanced translocation) 1 548 Poly-Gln. binding p.Q532Q(1) NS(1)|breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(1) 45 ctgctgctgttgctgctgctgct 0.650 T ETV6 """AML, meningioma""" 8 62 --- --- --- --- ZNRF3 84133 broad.mit.edu 37 22 29445819 29445821 + In_Frame_Del DEL CAG CAG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr22:29445819_29445821delCAG ENST00000544604.2 + 8 1825_1827 c.1650_1652delCAG c.(1648-1653)gac>ga p.DS550del ZNRF3_ENST00000402174.1_In_Frame_Del_p.DS450del|ZNRF3_ENST00000332811.4_In_Frame_Del_p.DS450del|ZNRF3_ENST00000406323.3_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 7 292 --- --- --- --- SF3A1 10291 broad.mit.edu 37 22 30742328 30742330 + In_Frame_Del DEL CTG CTG - rs141985009 byFrequency TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr22:30742328_30742330delCTG ENST00000215793.7 - 3 518_520 c.364_366delCAG c.(364-366)del p.Q122del SF3A1_ENST00000439242.1_Intron NM_005877.4 NP_005868.1 Q15459 SF3A1_HUMAN splicing factor 3a, subunit 1, 120kDa 122 Poly-Gln. nuclear mRNA 3'-splice site recognition catalytic step 2 spliceosome|nucleoplasm|U2-type spliceosomal complex protein binding|RNA binding endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|urinary_tract(1) 29 GCTGGGTGGTCTGCTGCTGCTGC 0.606 8 753 --- --- --- --- MYH9 4627 broad.mit.edu 37 22 36696948 36696950 + In_Frame_Del DEL CTC CTC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr22:36696948_36696950delCTC ENST00000216181.5 - 22 3015_3017 c.2785_2787delGAG c.(2785-2787)del p.E929del NM_002473.4 NP_002464.1 P35579 MYH9_HUMAN myosin, heavy chain 9, non-muscle 929 actin cytoskeleton reorganization|actin filament-based movement|angiogenesis|axon guidance|blood vessel endothelial cell migration|cytokinesis|integrin-mediated signaling pathway|leukocyte migration|membrane protein ectodomain proteolysis|monocyte differentiation|platelet formation|protein transport|regulation of cell shape actomyosin contractile ring|cleavage furrow|cytosol|myosin complex|nucleus|ruffle|stress fiber|uropod actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity|protein anchor|protein homodimerization activity NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3) 86 GCTGGCAGCGCTCCTCCTCCTCC 0.665 T ALK ALCL """Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome""" Hereditary Macrothrombocytopenia, MYH9-associated 8 841 --- --- --- --- TRIOBP 11078 broad.mit.edu 37 22 38119882 38119884 + In_Frame_Del DEL CCT CCT - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr22:38119882_38119884delCCT ENST00000406386.3 + 7 1574_1576 c.1319_1321delCCT c.(1318-1323)gcc>g p.AS440del RP1-37E16.12_ENST00000455236.1_RNA NM_001039141.2 NP_001034230.1 Q9H2D6 TARA_HUMAN TRIO and F-actin binding protein 440 actin modification|barbed-end actin filament capping actin cytoskeleton|cytoplasm|nucleus actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1) 12 Melanoma(58;0.0574) AATCCCAGAGCCTCCTCTCCCAG 0.601 8 845 --- --- --- --- RANGAP1 5905 broad.mit.edu 37 22 41650469 41650471 + In_Frame_Del DEL TCC TCC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr22:41650469_41650471delTCC ENST00000455915.2 - 10 2570_2572 c.1101_1103delGGA c.(1099-1104)gaa>ga p.EE367del RANGAP1_ENST00000356244.3_In_Frame_Del_p.EE367del|RANGAP1_ENST00000405486.1_In_Frame_Del_p.EE367del|RANGAP1_ENST00000407260.4_In_Frame_Del_p.EE312del P46060 RAGP1_HUMAN Ran GTPase activating protein 1 367 Asp/Glu-rich (highly acidic). mitotic prometaphase|signal transduction condensed chromosome kinetochore|cytosol|nuclear membrane|nuclear pore|soluble fraction|spindle pole protein binding|Ran GTPase activator activity breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1) 19 ctcttctccttcctcctcctcct 0.562 19 841 --- --- --- --- TCF20 6942 broad.mit.edu 37 22 42610362 42610364 + In_Frame_Del DEL TGC TGC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa 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 7 660 --- --- --- --- TCF20 6942 broad.mit.edu 37 22 42610573 42610575 + In_Frame_Del DEL AGG AGG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa 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 11 570 --- --- --- --- TXLNG 55787 broad.mit.edu 37 X 16850849 16850850 + Frame_Shift_Del DEL AG AG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chrX:16850849_16850850delAG ENST00000380122.5 + 6 1029_1030 c.968_969delAG c.(967-969)cfs p.Q323fs TXLNG_ENST00000398155.4_Frame_Shift_Del_p.Q191fs NM_018360.2 NP_060830.2 Q9NUQ3 TXLNG_HUMAN taxilin gamma 323 cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent cytosol|nuclear membrane breast(2)|large_intestine(5)|lung(6)|prostate(1)|skin(1) 15 GAAAAACATCAGAGAGAGAGAG 0.386 7 645 --- --- --- --- PHF8 23133 broad.mit.edu 37 X 54011405 54011407 + In_Frame_Del DEL CTC CTC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chrX:54011405_54011407delCTC ENST00000338154.6 - 18 2887_2889 c.2383_2385delGAG c.(2383-2385)del p.E795del PHF8_ENST00000338946.6_In_Frame_Del_p.E694del|PHF8_ENST00000322659.8_In_Frame_Del_p.E778del|PHF8_ENST00000357988.5_In_Frame_Del_p.E831del NM_015107.2 NP_055922.1 Q9UPP1 PHF8_HUMAN PHD finger protein 8 831 Ser-rich. brain development|G1/S transition of mitotic cell cycle|negative regulation of chromatin silencing at rDNA|positive regulation of transcription from RNA polymerase I promoter|transcription, DNA-dependent nucleolus chromatin binding|histone demethylase activity (H3-K27 specific)|histone demethylase activity (H3-K36 specific)|histone demethylase activity (H3-K9 specific)|histone demethylase activity (H4-K20 specific)|iron ion binding|methylated histone residue binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1) 40 GACTGGCGTTCTCCTCCTCCTCC 0.591 20 1128 --- --- --- --- MED12 9968 broad.mit.edu 37 X 70360680 70360682 + In_Frame_Del DEL GCA GCA - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chrX:70360680_70360682delGCA ENST00000333646.6 + 42 6448_6450 c.6249_6251delGCA c.(6247-6252)cgg>cg p.RQ2083del MED12_ENST00000374102.1_In_Frame_Del_p.RQ2079del|MED12_ENST00000374080.3_In_Frame_Del_p.RQ2080del NM_005120.2 NP_005111.2 Q93074 MED12_HUMAN mediator complex subunit 12 2080 Gln-rich. androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter mediator complex ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3) 420 Renal(35;0.156) accacatccggcagcagcagcag 0.586 """M, S""" uterine leiomyoma Opitz-Kaveggia Syndrome 12 354 --- --- --- --- TSIX 0 broad.mit.edu 37 X 73047124 73047125 + RNA DEL AC AC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chrX:73047124_73047125delAC ENST00000604411.1 + 0 35085_35086 XIST_ENST00000429829.1_lincRNA NR_003255.2 GCCACACATGACACACACACAC 0.470 18 840 --- --- --- --- ZDHHC15 158866 broad.mit.edu 37 X 74649035 74649036 + Splice_Site INS - - A TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chrX:74649035_74649036insA ENST00000541184.1 - 6 933 c.e6-2 ZDHHC15_ENST00000373361.3_Intron|ZDHHC15_ENST00000373367.3_Splice_Site NM_001146256.1 NP_001139728.1 Q96MV8 ZDH15_HUMAN zinc finger, DHHC-type containing 15 integral to membrane zinc ion binding central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(1)|lung(11)|ovary(2)|skin(2) 26 TTATTAACCCTAAAAAAAAAGA 0.366 8 446 --- --- --- --- NAP1L3 4675 broad.mit.edu 37 X 92928153 92928155 + In_Frame_Del DEL TGC TGC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chrX:92928153_92928155delTGC ENST00000373079.3 - 1 412_414 c.149_151delGCA c.(148-153)act>a p.ST50del NAP1L3_ENST00000475430.1_5'UTR NM_004538.5 NP_004529.2 Q99457 NP1L3_HUMAN nucleosome assembly protein 1-like 3 50 Ser-rich. nucleosome assembly chromatin assembly complex haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1) 34 ctgccactagtgctgctgctgct 0.586 7 274 --- --- --- --- NKAP 79576 broad.mit.edu 37 X 119072752 119072753 + Frame_Shift_Del DEL TC TC - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chrX:119072752_119072753delTC ENST00000371410.3 - 2 573_574 c.407_408delGA c.(406-408)afs p.R136fs NM_024528.3 NP_078804.2 Q8N5F7 NKAP_HUMAN NFKB activating protein 136 negative regulation of transcription, DNA-dependent|Notch signaling pathway|positive regulation of alpha-beta T cell differentiation|transcription, DNA-dependent cytoplasm|nucleus chromatin binding|protein binding breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1) 20 ATTCTCCAATTCTCTCTCTCTC 0.322 11 906 --- --- --- --- MAMLD1 10046 broad.mit.edu 37 X 149639325 149639327 + In_Frame_Del DEL CAG CAG - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chrX:149639325_149639327delCAG ENST00000370401.2 + 4 1790_1792 c.1480_1482delCAG c.(1480-1482)del p.Q502del MAMLD1_ENST00000455522.2_5'UTR|MAMLD1_ENST00000262858.5_In_Frame_Del_p.Q502del|MAMLD1_ENST00000426613.2_In_Frame_Del_p.Q477del|MAMLD1_ENST00000432680.2_In_Frame_Del_p.Q477del Q13495 MAMD1_HUMAN mastermind-like domain containing 1 502 Poly-Gln. male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus p.Q469Q(1)|p.Q494Q(1)|p.Q421Q(1) breast(1)|endometrium(4)|kidney(3)|large_intestine(12)|lung(14)|ovary(1)|prostate(2) 37 Acute lymphoblastic leukemia(192;6.56e-05) AAGCcagcaacagcagcagcagc 0.532 24 513 --- --- --- --- MAMLD1 10046 broad.mit.edu 37 X 149639633 149639635 + In_Frame_Del DEL GCA GCA - TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chrX:149639633_149639635delGCA ENST00000370401.2 + 4 2098_2100 c.1788_1790delGCA c.(1786-1791)ctg>ct p.LQ596del MAMLD1_ENST00000455522.2_In_Frame_Del_p.LQ77del|MAMLD1_ENST00000262858.5_In_Frame_Del_p.LQ596del|MAMLD1_ENST00000426613.2_In_Frame_Del_p.LQ571del|MAMLD1_ENST00000432680.2_In_Frame_Del_p.LQ571del Q13495 MAMD1_HUMAN mastermind-like domain containing 1 596 Poly-Gln. male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent nucleus breast(1)|endometrium(4)|kidney(3)|large_intestine(12)|lung(14)|ovary(1)|prostate(2) 37 Acute lymphoblastic leukemia(192;6.56e-05) CCTTgcagctgcagcagcagcag 0.611 11 860 --- --- --- --- F8 2157 broad.mit.edu 37 X 154158427 154158428 + Frame_Shift_Ins INS - - T TCGA-IB-7887-01A-11D-2154-08 TCGA-IB-7887-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chrX:154158427_154158428insT ENST00000360256.4 - 14 3837_3838 c.3637_3638insA c.(3637-3639)tcafs p.S1213fs NM_000132.3 NP_000123.1 P00451 FA8_HUMAN coagulation factor VIII, procoagulant component 1213 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 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) TTCTTCCTGAATTTTTTTTTCT 0.327 10 327 --- --- --- ---