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 COSMIC_overlapping_mutations COSMIC_fusion_genes COSMIC_total_alterations_in_gene Tumorscape_Amplification_Peaks Tumorscape_Deletion_Peaks TCGAscape_Amplification_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 ACHILLES_Lineage_Results_Top_Genes CGC_CancerGermlineMut CGC_CancerMolecularGenetics CGC_CancerSomaticMut CGC_CancerSyndrome CGC_Chr CGC_ChrBand CGC_GeneID CGC_Name CGC_OtherGermlineMut CGC_TissueType COSMIC_n_overlapping_mutations COSMIC_overlapping_mutation_descriptions ClinVar_ASSEMBLY ClinVar_HGMD_ID ClinVar_SYM ClinVar_TYPE ClinVar_rs Ensembl_so_accession Ensembl_so_term Familial_Cancer_Genes_Reference Familial_Cancer_Genes_Synonym annotation_transcript bcgsc broad build ccds_id dbNSFP_1000Gp1_AC dbNSFP_1000Gp1_AF dbNSFP_1000Gp1_AFR_AC dbNSFP_1000Gp1_AFR_AF dbNSFP_1000Gp1_AMR_AC dbNSFP_1000Gp1_AMR_AF dbNSFP_1000Gp1_ASN_AC dbNSFP_1000Gp1_ASN_AF dbNSFP_1000Gp1_EUR_AC dbNSFP_1000Gp1_EUR_AF dbNSFP_Ancestral_allele dbNSFP_CADD_phred dbNSFP_CADD_raw dbNSFP_CADD_raw_rankscore dbNSFP_ESP6500_AA_AF dbNSFP_ESP6500_EA_AF dbNSFP_Ensembl_geneid dbNSFP_Ensembl_transcriptid dbNSFP_FATHMM_pred dbNSFP_FATHMM_rankscore dbNSFP_FATHMM_score dbNSFP_GERP_NR dbNSFP_GERP_RS dbNSFP_GERP_RS_rankscore dbNSFP_Interpro_domain dbNSFP_LRT_Omega dbNSFP_LRT_converted_rankscore dbNSFP_LRT_pred dbNSFP_LRT_score dbNSFP_LR_pred dbNSFP_LR_rankscore dbNSFP_LR_score dbNSFP_MutationAssessor_pred dbNSFP_MutationAssessor_rankscore dbNSFP_MutationAssessor_score dbNSFP_MutationTaster_converted_rankscore dbNSFP_MutationTaster_pred dbNSFP_MutationTaster_score dbNSFP_Polyphen2_HDIV_pred dbNSFP_Polyphen2_HDIV_rankscore dbNSFP_Polyphen2_HDIV_score dbNSFP_Polyphen2_HVAR_pred dbNSFP_Polyphen2_HVAR_rankscore dbNSFP_Polyphen2_HVAR_score dbNSFP_RadialSVM_pred dbNSFP_RadialSVM_rankscore dbNSFP_RadialSVM_score dbNSFP_Reliability_index dbNSFP_SIFT_converted_rankscore dbNSFP_SIFT_pred dbNSFP_SIFT_score dbNSFP_SLR_test_statistic dbNSFP_SiPhy_29way_logOdds dbNSFP_SiPhy_29way_logOdds_rankscore dbNSFP_SiPhy_29way_pi dbNSFP_UniSNP_ids dbNSFP_Uniprot_aapos dbNSFP_Uniprot_acc dbNSFP_Uniprot_id dbNSFP_aaalt dbNSFP_aapos dbNSFP_aapos_FATHMM dbNSFP_aapos_SIFT dbNSFP_aaref dbNSFP_cds_strand dbNSFP_codonpos dbNSFP_folddegenerate dbNSFP_genename dbNSFP_hg18_pos1coor dbNSFP_phastCons100way_vertebrate dbNSFP_phastCons100way_vertebrate_rankscore dbNSFP_phastCons46way_placental dbNSFP_phastCons46way_placental_rankscore dbNSFP_phastCons46way_primate dbNSFP_phastCons46way_primate_rankscore dbNSFP_phyloP100way_vertebrate dbNSFP_phyloP100way_vertebrate_rankscore dbNSFP_phyloP46way_placental dbNSFP_phyloP46way_placental_rankscore dbNSFP_phyloP46way_primate dbNSFP_phyloP46way_primate_rankscore dbNSFP_refcodon entrez_gene_id external_id_capture gencode_transcript_name gencode_transcript_status gencode_transcript_tags gencode_transcript_type gene_type havana_transcript hgsc igv_bad ucsc t_alt_count t_ref_count n_alt_count n_ref_count validation_judgement_rna validation_power_rna validation_tumor_alt_count_rna validation_tumor_ref_count_rna validation_normal_alt_count_rna validation_normal_ref_count_rna min_val_count_rna validation_judgement_targeted validation_power_targeted validation_tumor_alt_count_targeted validation_tumor_ref_count_targeted validation_normal_alt_count_targeted validation_normal_ref_count_targeted min_val_count_targeted validation_judgement_localAssembly validation_power_localAssembly t_alt_count_localAssembly t_ref_count_localAssembly n_alt_count_localAssembly n_ref_count_localAssembly min_val_count_localAssembly validation_judgement_KRAS validation_power_KRAS t_alt_count_KRAS t_ref_count_KRAS n_alt_count_KRAS n_ref_count_KRAS min_val_count_KRAS pon_loglike pon_pass_loglike localAssembly_detected ExAC_AN ExAC_AC ExAC_LQ passExAC SCNA_NA SCNA_NB SCNA_q_hat SCNA_tau IS_SCNA purity ploidy dna_fraction_in_tumor CCF_hat CCF_CI95_low CCF_CI95_high CCF_mode CCF_mean CCF_median clonal CCF_CI_low CCF_CI_high 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 - A - - Inconclusive Somatic Phase_I WXS RNA 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)tatfs p.Y173fs CTSB_ENST00000534510.1_Frame_Shift_Ins_p.Y173fs|CTSB_ENST00000453527.2_Frame_Shift_Ins_p.Y173fs|CTSB_ENST00000533455.1_Frame_Shift_Ins_p.Y173fs|CTSB_ENST00000530640.2_Frame_Shift_Ins_p.Y173fs|CTSB_ENST00000415599.2_3'UTR|RP11-589N15.2_ENST00000602711.1_RNA|CTSB_ENST00000525076.1_5'Flank|CTSB_ENST00000531089.1_Frame_Shift_Ins_p.Y173fs|CTSB_ENST00000345125.3_Frame_Shift_Ins_p.Y173fs|CTSB_ENST00000434271.1_Frame_Shift_Ins_p.Y173fs NM_001908.3 NP_001899.1 P07858 CATB_HUMAN cathepsin B 16 all_epithelial(15;0.205) STAD - Stomach adenocarcinoma(15;0.00546) ATGGGATTCATAGAGGCCACCA 0.450000 0 SO:0001589 frameshift_variant ENST00000353047.6 0 1 hg19 CCDS5986.1 TCGA-IB-7887-01A-11D-2154-08 CTSB-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207586.3 1 0 0 62 503 0 111 0 1 1 1387 0 111 2 0 0 0 0 0 0 1 1.000000 63 499 0 111 2 0 0 0 0 0 0 -19.974620 1 1 0 0 1 0 1 1 1.802685 1 0.270000 1.780000 0.156069 0.690000 0.540000 0.860000 0.700000 0.704933 0.690000 0 6.100000e-01 7.800000e-01 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 1 103 Medulloblastoma(188;0.00263)|all_neural(188;0.026) AACCACCATCATAGGCCTCCA 0.602000 0 SO:0001587 stop_gained ENST00000299441.3 0 1 hg19 CCDS7771.1 . . . . . . . . . . A 37 6.418677 0.97550 . . ENSG00000166341 ENST00000299441 . . . 4.18 -1.56 0.08532 . 0.000000 0.42294 D 0.000731 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 . 10.368 0.44035 0.6186:0.0:0.3814:0.0 . . . . X 228 . ENSP00000299441:Y228X Y - 3 2 DCHS1 6618737 0.966000 0.33281 0.995000 0.50966 0.991000 0.79684 0.258000 0.18387 -0.379000 0.07906 0.445000 0.29226 TAT TCGA-IB-7887-01A-11D-2154-08 DCHS1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257258.1 1 0 1 111 559 0 114 0 5.675710e-01 0 11 0 114 2 0 0 0 0 0 2 1 1.000000 109 552 0 114 2 0 0 0 0 114 2 -20.000000 1 1 0 0 1 0 1 1 1.779903 1 0.270000 1.780000 0.156069 0.950000 0.840000 1.000000 0.990000 0.950780 0.950000 1 9.000000e-01 9.900000e-01 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 C G C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr12:25398285C>G ENST00000256078.4 - 2 97 c.34G>C c.(34-36)Ggt>Cgt p.G12R KRAS_ENST00000556131.1_Missense_Mutation_p.G12R|KRAS_ENST00000557334.1_Missense_Mutation_p.G12R|KRAS_ENST00000311936.3_Missense_Mutation_p.G12R NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog 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) 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) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 5144 Substitution - Missense(5142)|Insertion - In frame(2) GRCh37 CM076251 KRAS M rs121913530 SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 0 1 hg19 CCDS8703.1 . . . . . . . . . . C 28.6 4.930538 0.92389 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78246 -1.16;-1.16;-1.16;-1.16 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.84893 0.5573 M 0.84082 2.675 0.80722 D 1 P;P 0.43287 0.802;0.741 B;P 0.47941 0.36;0.562 D 0.86658 0.1902 10 0.66056 D 0.02 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN R 12 ENSP00000308495:G12R;ENSP00000452512:G12R;ENSP00000256078:G12R;ENSP00000451856:G12R ENSP00000256078:G12R G - 1 0 KRAS 25289552 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-IB-7887-01A-11D-2154-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 0 20 132 1 23 1 1.691198e-01 9 18 1 23 6 1 1 62 365 0 447 2 1 0.659073 20 128 1 23 18 1 9.910251e-01 653 7363 1 23 627 -11.314890 1 1 0 0 1 2 2 4 2.192614 1 0.270000 1.780000 0.314425 0.990000 0.680000 1.000000 1.000000 0.952741 0.990000 1 8.600000e-01 1 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 16 CTTCGACTGGGACTTGATCAC 0.552000 0 SO:0001583 missense ENST00000162391.3 0 1 hg19 CCDS8587.1 . . . . . . . . . . G 25.4 4.637902 0.87760 . . ENSG00000065970 ENST00000162391 D 0.99311 -5.73 5.85 5.85 0.93711 . 0.244803 0.28724 N 0.014344 D 0.99254 0.9740 M 0.63843 1.955 0.80722 D 1 D 0.76494 0.999 D 0.81914 0.995 D 0.99819 1.1046 10 0.87932 D 0 . 17.6544 0.88174 0.0:0.0:1.0:0.0 . 571 Q9P0K8 FOXJ2_HUMAN H 571 ENSP00000162391:D571H ENSP00000162391:D571H D + 1 0 FOXJ2 8096699 1.000000 0.71417 1.000000 0.80357 0.975000 0.68041 6.918000 0.75788 2.772000 0.95346 0.650000 0.86243 GAC TCGA-IB-7887-01A-11D-2154-08 FOXJ2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000400088.1 1 0 0 6 107 0 20 1 4.390966e-01 7 18 0 20 2 0 0 0 0 0 2 1 0.957759 6 99 0 20 2 0 0 0 0 20 2 -9.940343 1 1 0 0 1 2 2 4 2.194364 1 0.270000 1.780000 0.316159 0.490000 0.190000 1.000000 0.410000 0.566397 0.490000 0 3.100000e-01 1 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 ENST00000382292.3 - 9 12094 c.11821C>T c.(11821-11823)Caa>Taa p.Q3941* SACS_ENST00000402364.1_Nonsense_Mutation_p.Q3191*|SACS_ENST00000382298.3_Nonsense_Mutation_p.Q3941* Q9NZJ4 SACS_HUMAN sacsin molecular chaperone 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) ACTAACATTTGCACACCAATA 0.403000 0 SO:0001587 stop_gained ENST00000382292.3 0 1 hg19 CCDS9300.2 . . . . . . . . . . G 58 33.524865 0.99981 . . ENSG00000151835 ENST00000382292;ENST00000402364;ENST00000382298 . . . 5.82 5.82 0.92795 . 0.053109 0.85682 D 0.000000 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.39692 T 0.17 . 20.1013 0.97878 0.0:0.0:1.0:0.0 . . . . X 3941;3191;3941 . ENSP00000371729:Q3941X Q - 1 0 SACS 22804194 1.000000 0.71417 0.990000 0.47175 0.948000 0.59901 9.865000 0.99609 2.748000 0.94277 0.655000 0.94253 CAA TCGA-IB-7887-01A-11D-2154-08 SACS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044148.3 1 0 0 85 683 0 102 1 5.443034e-01 2 14 0 102 2 0 0 0 0 0 2 1 1.000000 85 669 0 102 2 0 0 0 0 102 2 -20.000000 1 1 0 0 1 1 2 3 2.062589 0 0.270000 1.780000 0.270984 0.810000 0.660000 1.000000 0.820000 0.824706 0.810000 0 7.300000e-01 9.100000e-01 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 47 TGCTATGAAGACACTCAGGAG 0.617000 0 SO:0001583 missense ENST00000409832.3 1 1 hg19 CCDS32018.1 . . . . . . . . . . a 10.49 1.364135 0.24684 . . ENSG00000222036 ENST00000409832 T 0.29397 1.57 . . . . . . . . T 0.23727 0.0574 L 0.43152 1.355 0.09310 N 1 P 0.35745 0.518 B 0.36418 0.224 T 0.17745 -1.0359 7 0.56958 D 0.05 . . . . . 56 Q6S5H5 POTEG_HUMAN S 56 ENSP00000386971:T56S ENSP00000386971:T56S T + 1 0 POTEG 18623582 0.003000 0.15002 0.006000 0.13384 0.006000 0.05464 0.468000 0.22051 0.141000 0.18875 0.139000 0.15985 ACA TCGA-IB-7887-01A-11D-2154-08 POTEG-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000408579.1 0 0 0 97 3062 0 550 0 0 0 0 550 2 0 0 0 0 0 2 1 1.000000 53 1800 0 808 2 0 0 0 0 550 2 -3.191071 1 1 0 0 1 0.270000 1.780000 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 ENST00000361577.3 + 4 2595 c.2381T>C c.(2380-2382)tTt>tCt p.F794S FAM179B_ENST00000382233.2_Missense_Mutation_p.F794S|KLHL28_ENST00000553817.1_Intron|FAM179B_ENST00000361462.2_Missense_Mutation_p.F794S NM_015091.2 NP_055906.2 Q9Y4F4 F179B_HUMAN family with sequence similarity 179, member B 45 CAGCAAACATTTGGTAGTCAA 0.363000 0 SO:0001583 missense ENST00000361577.3 1 1 hg19 CCDS9681.1 . . . . . . . . . . T 19.28 3.798217 0.70567 . . ENSG00000198718 ENST00000429476;ENST00000361577;ENST00000361462;ENST00000382233;ENST00000555874 T;T;T;T 0.13538 2.58;2.58;4.05;4.05 5.56 4.4 0.53042 Armadillo-type fold (1); 0.352636 0.27253 N 0.020216 T 0.17916 0.0430 N 0.24115 0.695 0.27467 N 0.952969 P;D;D 0.62365 0.567;0.974;0.991 B;P;P 0.56563 0.175;0.57;0.801 T 0.02901 -1.1096 10 0.87932 D 0 -10.7199 11.2492 0.49015 0.0:0.0:0.1532:0.8468 . 794;794;794 G3XAE9;Q9Y4F4;Q9Y4F4-2 .;F179B_HUMAN;. S 794;794;794;794;113 ENSP00000355045:F794S;ENSP00000354917:F794S;ENSP00000371668:F794S;ENSP00000451141:F113S ENSP00000354917:F794S F + 2 0 FAM179B 44543056 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 3.528000 0.53524 0.916000 0.36871 0.460000 0.39030 TTT TCGA-IB-7887-01A-11D-2154-08 FAM179B-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000276791.1 1 0 1 51 260 0 27 1 8.931436e-01 8 14 0 27 2 0 0 0 0 0 2 1 1.000000 51 254 0 26 2 0 0 0 0 27 2 -20.000000 1 1 0 0 1 0 1 1 2.054966 0 0.270000 1.780000 0.268024 0.990000 0.920000 1.000000 1.000000 0.995573 0.990000 1 9.900000e-01 1 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 G A G G Valid Somatic Phase_I WXS RNA 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_ENST00000571759.1_5'Flank|VAC14_ENST00000536184.2_Silent_p.L133L NM_018052.3 NP_060522.3 Q08AM6 VAC14_HUMAN Vac14 homolog (S. cerevisiae) 33 Ovarian(137;0.0699) GCAGGAGCATGAGCAGGCCGT 0.662000 0 SO:0001819 synonymous_variant ENST00000261776.5 0 1 hg19 CCDS10896.1 TCGA-IB-7887-01A-11D-2154-08 VAC14-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268973.3 1 0 1 16 97 0 10 1 9.999064e-01 46 56 0 10 2 0 0 0 0 0 2 1 0.999941 16 93 0 9 2 0 0 0 0 10 2 -20.000000 1 1 120788 3 30 1 0 1 1 2.059000 0 0.270000 1.780000 0.269013 0.990000 0.640000 1.000000 1.000000 0.937106 0.990000 1 8.200000e-01 1 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 31 Breast(137;0.000496) TGACTCCTGGTCTCGTTCAGC 0.597000 0 SO:0001583 missense ENST00000251645.2 1 1 hg19 CCDS11391.1 . . . . . . . . . . t 13.06 2.125541 0.37533 . . ENSG00000094796 ENST00000251645 D 0.88586 -2.4 5.4 4.33 0.51752 Filament (1); 0.180058 0.39759 N 0.001269 D 0.86764 0.6011 L 0.50333 1.59 0.31092 N 0.710708 B 0.22604 0.072 B 0.32980 0.156 D 0.84831 0.0802 10 0.87932 D 0 . 10.2699 0.43477 0.0:0.0774:0.0:0.9226 . 228 Q15323 K1H1_HUMAN A 228 ENSP00000251645:T228A ENSP00000251645:T228A T - 1 0 KRT31 36805308 0.978000 0.34361 0.998000 0.56505 0.529000 0.34654 1.848000 0.39309 0.888000 0.36160 0.460000 0.39030 ACC TCGA-IB-7887-01A-11D-2154-08 KRT31-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257286.1 0 0 1 83 528 0 88 0 0 0 0 88 2 0 0 0 0 0 2 1 1.000000 82 514 0 88 2 0 0 0 0 88 2 -20.000000 1 1 0 0 1 0 0 0 2.045882 0 0.270000 1.780000 0.262030 0.990000 0.800000 1.000000 1.000000 0.959288 0.990000 1 8.900000e-01 1 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 T C T T Valid Somatic Phase_I WXS targeted Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr17:7578206T>C ENST00000269305.4 - 6 832 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_ENST00000420246.2_Missense_Mutation_p.S215G|TP53_ENST00000359597.4_Missense_Mutation_p.S215G|TP53_ENST00000413465.2_Missense_Mutation_p.S215G NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1 NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1 P04637 P53_HUMAN tumor protein p53 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) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) 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) Pancreas(47;798 1329 9957 10801) yes Rec yes Li-Fraumeni syndrome 17 17p13 7157 tumor protein p53 L, E, M, O 43 Substitution - Missense(13)|Deletion - Frameshift(11)|Whole gene deletion(8)|Unknown(5)|Deletion - In frame(4)|Insertion - In frame(1)|Complex - deletion inframe(1) SO:0001583 missense Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 1 1 hg19 CCDS11118.1 . . . . . . . . . . T 22.3 4.274381 0.80580 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315 D;D;D;D;D;D;D;D 0.99851 -7.17;-7.17;-7.17;-7.17;-7.17;-7.17;-7.17;-7.17 5.28 4.18 0.49190 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.000000 0.85682 D 0.000000 D 0.99851 0.9931 M 0.90705 3.14 0.58432 D 0.999999 D;D;D;D;D;D;D 0.89917 1.0;1.0;0.999;1.0;1.0;1.0;1.0 D;D;D;D;D;D;D 0.97110 0.995;1.0;0.98;0.996;1.0;1.0;0.999 D 0.97163 0.9839 10 0.87932 D 0 -18.3023 10.6958 0.45899 0.0:0.0:0.1605:0.8394 . 176;215;215;122;215;215;215 B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7 .;.;.;.;P53_HUMAN;.;. G 215;215;215;215;215;215;204;122;83;122;83 ENSP00000410739:S215G;ENSP00000352610:S215G;ENSP00000269305:S215G;ENSP00000398846:S215G;ENSP00000391127:S215G;ENSP00000391478:S215G;ENSP00000425104:S83G;ENSP00000423862:S122G ENSP00000269305:S215G S - 1 0 TP53 7518931 1.000000 0.71417 0.471000 0.27229 0.962000 0.63368 6.146000 0.71777 0.919000 0.36945 0.460000 0.39030 AGT TCGA-IB-7887-01A-11D-2154-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 36 217 0 42 1 9.999603e-01 64 32 0 42 2 1 1 134 654 0 1530 2 1 1.000000 35 208 0 42 2 0 0 0 0 42 2 -20.000000 1 1 0 0 1 0 1 1 1.788086 1 0.270000 1.780000 0.156069 0.850000 0.630000 0.990000 0.890000 0.851546 0.850000 1 7.400000e-01 9.500000e-01 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 ENST00000519716.2 - 13 1463 c.1464C>T c.(1462-1464)atC>atT p.I488I UNC13A_ENST00000551649.1_Silent_p.I488I|UNC13A_ENST00000252773.7_Silent_p.I488I|UNC13A_ENST00000552293.1_Silent_p.I488I|UNC13A_ENST00000550896.1_Silent_p.I488I|UNC13A_ENST00000428389.2_Silent_p.I576I NM_001080421.2 NP_001073890.2 Q9UPW8 UN13A_HUMAN unc-13 homolog A (C. elegans) p.I488I(1)|p.I576I(1) 61 GCATGCTGTCGATGATGATGA 0.567000 2 Substitution - coding silent(2) SO:0001819 synonymous_variant ENST00000519716.2 1 1 hg19 CCDS46013.2 TCGA-IB-7887-01A-11D-2154-08 UNC13A-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000376169.2 1 0 1 82 584 1 119 0 0 0 1 119 2 0 0 0 0 0 2 1 1.000000 81 575 1 118 19 0 0 0 1 119 2 -20.000000 1 1 0 0 1 0 0 0 2.033670 0 0.270000 1.780000 0.257979 0.890000 0.720000 1.000000 1.000000 0.894076 0.890000 1 8.000000e-01 9.900000e-01 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 G A G G Valid Somatic Phase_I WXS RNA 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_ENST00000391754.1_Silent_p.F86F|MBOAT7_ENST00000431666.2_Intron|MBOAT7_ENST00000474910.1_5'UTR NM_024298.3 NP_077274.3 Q96N66 MBOA7_HUMAN membrane bound O-acyltransferase domain containing 7 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 NSCLC(97;826 2151 10470 22540) 0 SO:0001819 synonymous_variant ENST00000245615.1 0 1 hg19 CCDS12883.1 TCGA-IB-7887-01A-11D-2154-08 MBOAT7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000142203.1 1 0 0 13 77 0 11 1 9.999996e-01 66 137 0 11 2 0 0 0 0 0 2 1 0.999339 12 69 0 11 2 0 0 0 0 11 2 -19.995520 1 1 0 0 1 0 1 1 2.058955 0 0.270000 1.780000 0.269013 0.990000 0.610000 1.000000 1.000000 0.936127 0.990000 1 8.200000e-01 1 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 3 132 GGCCCTGGCTGCCCCTCTGGC 0.687000 0 SO:0001587 stop_gained ENST00000600128.1 0 1 hg19 CCDS12196.1 . . . . . . . . . . G 48 14.127981 0.99781 . . ENSG00000142449 ENST00000270509;ENST00000341066 . . . 3.83 -4.06 0.03986 . 0.602780 0.16277 U 0.221518 . . . . . . 0.37599 D 0.920499 . . . . . . . . . . 0.49607 T 0.09 . 9.7216 0.40306 0.5538:0.0:0.4462:0.0 . . . . X 2792;855 . ENSP00000270509:Q2792X Q - 1 0 FBN3 8036859 0.000000 0.05858 0.000000 0.03702 0.002000 0.02628 0.106000 0.15354 -0.844000 0.04184 -0.768000 0.03414 CAG TCGA-IB-7887-01A-11D-2154-08 FBN3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000461428.2 1 0 1 44 313 0 61 0 0 0 0 61 2 0 0 0 0 0 2 1 1.000000 43 303 0 60 2 0 0 0 0 61 2 -20.000000 1 1 0 0 1 0 0 0 2.045320 0 0.270000 1.780000 0.262030 0.890000 0.670000 1.000000 1.000000 0.892067 0.890000 1 7.700000e-01 1 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 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 0 SO:0001583 missense Familial Cancer Database X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris ENST00000368799.1 1 1 hg19 CCDS30860.1 . . . . . . . . . . C 1.935 -0.444964 0.04604 4.54E-4 0.0 ENSG00000143631 ENST00000368799 T 0.01963 4.53 1.93 -1.78 0.07957 . . . . . T 0.00144 0.0004 N 0.00347 -1.61 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.32402 -0.9908 9 0.10636 T 0.68 . 0.4443 0.00491 0.198:0.336:0.196:0.27 . 3198 P20930 FILA_HUMAN G 3198 ENSP00000357789:V3198G ENSP00000357789:V3198G V - 2 0 FLG 150544393 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -0.291000 0.08343 -0.950000 0.03659 -0.383000 0.06682 GTC TCGA-IB-7887-01A-11D-2154-08 FLG-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000033742.1 1 0 0 209 1382 0 242 0 0 0 0 242 2 0 0 0 0 0 2 1 1.000000 194 1276 0 333 2 0 0 0 0 242 2 -20.000000 1 1 121402 17 46 1 0 0 0 2.052197 0 0.270000 1.780000 0.266037 0.960000 0.840000 1.000000 1.000000 0.956658 0.960000 1 9.000000e-01 1 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 36 all_hematologic(112;0.0378) GGATAGCCAGGACCAATGTAC 0.443000 0 SO:0001819 synonymous_variant ENST00000314902.2 1 1 hg19 CCDS30896.1 TCGA-IB-7887-01A-11D-2154-08 OR10K2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051854.1 1 0 1 45 391 0 75 0 0 0 0 75 2 0 0 0 0 0 2 1 1.000000 45 376 0 75 2 0 0 0 0 75 2 -20.000000 1 1 0 0 1 0 0 0 2.052197 0 0.270000 1.780000 0.266037 0.750000 0.560000 0.970000 0.760000 0.767868 0.750000 0 6.500000e-01 8.700000e-01 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 ENST00000366676.1 - 4 1402 c.1403G>A c.(1402-1404)cGt>cAt p.R468H TAF5L_ENST00000258281.2_Missense_Mutation_p.R468H O75529 TAF5L_HUMAN TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa p.R468P(1) 11 Breast(184;0.193)|Ovarian(103;0.249) Prostate(94;0.167) CACGGGGCCACGGTGGCCTGT 0.607000 1 Substitution - Missense(1) SO:0001583 missense ENST00000366676.1 1 1 hg19 CCDS1581.1 . . . . . . . . . . C 12.60 1.987862 0.35036 . . ENSG00000135801 ENST00000366676;ENST00000258281 T;T 0.60548 0.18;0.18 5.97 5.06 0.68205 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1); 0.047962 0.85682 D 0.000000 T 0.45935 0.1367 N 0.21097 0.63 0.80722 D 1 B 0.15473 0.013 B 0.10450 0.005 T 0.37407 -0.9707 10 0.54805 T 0.06 -7.1912 15.1546 0.72730 0.0:0.9326:0.0:0.0674 . 468 O75529 TAF5L_HUMAN H 468 ENSP00000355636:R468H;ENSP00000258281:R468H ENSP00000258281:R468H R - 2 0 TAF5L 227797034 1.000000 0.71417 0.921000 0.36526 0.013000 0.08279 7.785000 0.85724 1.537000 0.49254 0.655000 0.94253 CGT TCGA-IB-7887-01A-11D-2154-08 TAF5L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000095229.1 1 0 1 52 760 0 107 1 8.652265e-01 10 44 0 107 2 0 0 0 0 0 2 1 1.000000 52 752 0 106 2 0 0 0 0 107 2 -9.415912 1 1 0 0 1 0 1 1 2.057782 0 0.270000 1.780000 0.268024 0.470000 0.350000 0.600000 0.470000 0.479382 0.470000 0 4.100000e-01 5.400000e-01 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 A T A A Valid Somatic Phase_I WXS RNA 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 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 0 SO:0001583 missense ENST00000366514.4 1 1 hg19 CCDS1627.1 . . . . . . . . . . A 14.54 2.567021 0.45694 . . ENSG00000162851 ENST00000366514 T 0.40476 1.03 5.23 5.23 0.72850 . 0.173798 0.38837 N 0.001547 T 0.56411 0.1983 L 0.54323 1.7 0.80722 D 1 D 0.89917 1.0 D 0.63597 0.916 T 0.59883 -0.7370 10 0.87932 D 0 -0.8824 12.7768 0.57453 1.0:0.0:0.0:0.0 . 388 Q9H5Q4 TFB2M_HUMAN Q 388 ENSP00000355471:L388Q ENSP00000355471:L388Q L - 2 0 TFB2M 244770984 0.993000 0.37304 0.292000 0.24919 0.018000 0.09664 4.722000 0.61958 2.108000 0.64289 0.528000 0.53228 CTG TCGA-IB-7887-01A-11D-2154-08 TFB2M-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000096673.1 1 0 1 50 380 0 62 1 9.999654e-01 40 76 0 62 2 0 0 0 0 0 2 1 1.000000 50 375 0 62 2 0 0 0 0 62 2 -18.936130 1 1 0 0 1 0 1 1 2.056446 0 0.270000 1.780000 0.268024 0.850000 0.650000 1.000000 1.000000 0.858840 0.850000 1 7.400000e-01 9.800000e-01 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 Ras-related GTP binding C 10 Acute lymphoblastic leukemia(166;0.074) Myeloproliferative disorder(586;0.0393) CACCTCAAAAACCTCATGAAT 0.458000 0 SO:0001583 missense ENST00000373001.3 0 1 hg19 CCDS430.1 . . . . . . . . . . A 21.0 4.082251 0.76528 . . ENSG00000116954 ENST00000373001 . . . 5.85 5.85 0.93711 . 0.000000 0.85682 D 0.000000 D 0.85013 0.5600 M 0.90309 3.105 0.80722 D 1 D;D;D 0.89917 1.0;0.999;0.999 D;D;D 0.76071 0.987;0.944;0.979 D 0.87774 0.2607 9 0.62326 D 0.03 -33.3787 16.2355 0.82371 1.0:0.0:0.0:0.0 . 332;300;366 E7ENI3;D3DPT8;Q9HB90 .;.;RRAGC_HUMAN G 366 . ENSP00000362092:V366G V - 2 0 RRAGC 39077915 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 9.339000 0.96797 2.238000 0.73509 0.533000 0.62120 GTT TCGA-IB-7887-01A-11D-2154-08 RRAGC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000001222.2 0 0 0 15 405 1 49 0 3.517657e-02 0 123 1 49 10 0 0 0 0 0 2 0 0.063780 15 398 1 49 25 0 0 0 1 49 2 -15.126710 1 1 0 0 1 1 2 3 2.067602 0 0.270000 1.780000 0.271966 0.270000 0.150000 0.450000 0.260000 0.286871 0.270000 0 2.000000e-01 3.500000e-01 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 30 CACATTGTGCGCCATGGGAGG 0.418000 0 SO:0001583 missense ENST00000294353.6 1 1 hg19 CCDS30717.1 . . . . . . . . . . G 18.24 3.579177 0.65878 2.27E-4 0.0 ENSG00000162378 ENST00000443756;ENST00000294353 T 0.47177 0.85 5.48 5.48 0.80851 . 0.000000 0.85682 D 0.000000 T 0.37046 0.0989 L 0.51422 1.61 0.80722 D 1 P;B 0.39601 0.68;0.07 B;B 0.26094 0.066;0.019 T 0.35525 -0.9785 10 0.48119 T 0.1 . 12.6624 0.56822 0.0756:0.0:0.9244:0.0 . 658;728 B4DK95;Q9C0D3 .;ZY11B_HUMAN H 658;728 ENSP00000294353:R728H ENSP00000294353:R728H R + 2 0 ZYG11B 53059837 1.000000 0.71417 0.997000 0.53966 0.997000 0.91878 5.446000 0.66600 2.567000 0.86603 0.591000 0.81541 CGC TCGA-IB-7887-01A-11D-2154-08 ZYG11B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000024749.1 1 0 1 46 322 0 70 1 5.009208e-01 4 9 0 70 2 0 0 0 0 0 2 1 1.000000 45 318 0 70 2 0 0 0 0 70 2 -3.318834 1 1 121412 2 33 1 1 2 3 2.067602 0 0.270000 1.780000 0.271966 0.920000 0.690000 1.000000 1.000000 0.911345 0.920000 1 8.000000e-01 1 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 ENST00000373907.2 + 2 212 c.13G>A c.(13-15)Ggt>Agt p.G5S DLGAP4_ENST00000373913.3_Missense_Mutation_p.G5S|DLGAP4_ENST00000401952.2_Missense_Mutation_p.G5S|DLGAP4_ENST00000339266.5_Missense_Mutation_p.G5S Q9Y2H0 DLGP4_HUMAN discs, large (Drosophila) homolog-associated protein 4 37 Breast(12;0.0192) Myeloproliferative disorder(115;0.00878) GAAAGGCCTCGGTGACAGCCG 0.692000 0 SO:0001583 missense ENST00000373907.2 1 1 hg19 . . . . . . . . . . G 11.48 1.651735 0.29336 . . ENSG00000080845 ENST00000373913;ENST00000401952;ENST00000373907;ENST00000339266 T;T;T;T 0.48522 0.81;0.81;0.81;0.81 5.67 3.36 0.38483 . 0.151756 0.64402 D 0.000016 T 0.45438 0.1342 N 0.19112 0.55 0.44852 D 0.997862 D 0.89917 1.0 D 0.91635 0.999 T 0.39165 -0.9627 10 0.02654 T 1 . 11.4918 0.50385 0.0787:0.1303:0.7911:0.0 . 5 Q9Y2H0-1 . S 5 ENSP00000363023:G5S;ENSP00000384954:G5S;ENSP00000363014:G5S;ENSP00000341633:G5S ENSP00000341633:G5S G + 1 0 DLGAP4 34493547 1.000000 0.71417 0.994000 0.49952 0.997000 0.91878 5.453000 0.66645 1.377000 0.46286 0.561000 0.74099 GGT TCGA-IB-7887-01A-11D-2154-08 DLGAP4-007 KNOWN basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000079025.2 1 0 0 44 302 0 41 0 0 0 0 41 2 0 0 0 0 0 2 1 1.000000 41 288 0 39 2 0 0 0 0 41 2 -3.221981 1 1 120658 5 36 1 0 0 0 2.051649 0 0.270000 1.780000 0.266037 0.930000 0.690000 1.000000 1.000000 0.914925 0.930000 1 8.000000e-01 1 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 36 Myeloproliferative disorder(115;0.0122) AAACTGAAGAGAAAATACATG 0.383000 0 SO:0001583 missense ENST00000372769.3 1 1 hg19 CCDS13346.1 . . . . . . . . . . G 5.930 0.355577 0.11239 . . ENSG00000124157 ENST00000372769 T 0.10005 2.92 1.03 -1.67 0.08238 . . . . . T 0.14141 0.0342 L 0.27053 0.805 0.09310 N 1 P;B 0.51057 0.941;0.004 D;B 0.71414 0.973;0.012 T 0.18209 -1.0344 9 0.41790 T 0.15 . 3.074 0.06240 0.0:0.2992:0.3985:0.3023 . 440;440 A8K6Z6;Q02383 .;SEMG2_HUMAN D 440 ENSP00000361855:E440D ENSP00000361855:E440D E + 3 2 SEMG2 43285007 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 -0.388000 0.07352 -0.534000 0.06315 -1.468000 0.01013 GAG TCGA-IB-7887-01A-11D-2154-08 SEMG2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079417.1 1 0 1 87 525 0 87 0 0 0 0 87 2 0 0 0 0 0 2 1 1.000000 86 510 0 87 2 0 0 0 0 87 2 -20.000000 1 1 0 0 1 0 0 0 2.051649 0 0.270000 1.780000 0.266037 0.990000 0.850000 1.000000 1.000000 0.979746 0.990000 1 9.400000e-01 1 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 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr21:38572533G>A ENST00000399017.2 + 45 8598 c.5851G>A c.(5851-5853)Gca>Aca p.A1951T TTC3_ENST00000355666.1_Splice_Site_p.A1951T|TTC3_ENST00000354749.2_Splice_Site_p.A1951T|TTC3_ENST00000479930.1_3'UTR NM_003316.3 NP_003307.3 P53804 TTC3_HUMAN tetratricopeptide repeat domain 3 75 Myeloproliferative disorder(46;0.0412) GTTTCCACAGGCACTGGGTGC 0.428000 Ovarian(38;194 1649 35661) 0 SO:0001630 splice_region_variant ENST00000399017.2 1 0 hg19 CCDS13651.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 3.961|3.961 -0.010251|-0.010251 0.07727|0.07727 .|. .|. ENSG00000182670|ENSG00000182670 ENST00000355666;ENST00000399017;ENST00000354749|ENST00000428693 T;T;T|. 0.08807|. 3.05;3.05;3.05|. 5.58|5.58 1.74|1.74 0.24563|0.24563 .|. 0.905217|. 0.09312|. N|. 0.819490|. T|T 0.45776|0.45776 0.1359|0.1359 L|L 0.46157|0.46157 1.445|1.445 0.58432|0.58432 D|D 0.999999|0.999999 B|. 0.18461|. 0.028|. B|. 0.12837|. 0.008|. T|T 0.25398|0.25398 -1.0133|-1.0133 9|5 .|. .|. .|. -0.7948|-0.7948 3.6024|3.6024 0.08030|0.08030 0.2713:0.0:0.553:0.1756|0.2713:0.0:0.553:0.1756 .|. 1951|. P53804|. TTC3_HUMAN|. T|Y 1951|242 ENSP00000347889:A1951T;ENSP00000381981:A1951T;ENSP00000346791:A1951T|. .|. A|C +|+ 1|2 0|0 TTC3|TTC3 37494403|37494403 0.258000|0.258000 0.24033|0.24033 0.448000|0.448000 0.26945|0.26945 0.031000|0.031000 0.12232|0.12232 0.312000|0.312000 0.19397|0.19397 0.303000|0.303000 0.22785|0.22785 -0.182000|-0.182000 0.12963|0.12963 GCA|TGC TCGA-IB-7887-01A-11D-2154-08 TTC3-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000194776.1 1 0 1 24 215 0 29 1 9.999399e-01 39 103 0 29 2 0 0 0 0 0 2 1 1.000000 23 210 0 29 2 0 0 0 0 29 2 -20.000000 1 1 0 0 1 0 1 1 1.781476 1 0.270000 1.780000 0.157384 0.630000 0.420000 0.880000 0.630000 0.649148 0.630000 0 5.200000e-01 7.700000e-01 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 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 35c4c115-e867-4ae4-987f-9ff02003be62 73139364-4a90-4b65-82fb-efa77a95b3fa g.chr22:30983324C>T ENST00000354694.7 - 4 423 c.317G>A c.(316-318)cGt>cAt p.R106H PES1_ENST00000405677.1_5'UTR|PES1_ENST00000335214.6_Missense_Mutation_p.R106H|PES1_ENST00000402284.3_Missense_Mutation_p.R106H|PES1_ENST00000402281.1_5'UTR NM_001243225.1|NM_014303.3 NP_001230154.1|NP_055118.1 pescadillo ribosomal biogenesis factor 1 29 GTCCTTTAAACGCTCTACAGT 0.498000 0 SO:0001583 missense ENST00000354694.7 1 1 hg19 CCDS13880.1 . . . . . . . . . . C 22.3 4.272796 0.80580 . . ENSG00000100029 ENST00000354694;ENST00000402284;ENST00000335214;ENST00000433575 T;T;T;T 0.48201 0.82;0.82;0.82;0.82 5.6 5.6 0.85130 . 0.000000 0.85682 D 0.000000 T 0.51736 0.1692 M 0.75085 2.285 0.80722 D 1 B;B;B;B 0.32245 0.361;0.25;0.14;0.361 B;B;B;B 0.28232 0.041;0.087;0.024;0.041 T 0.55147 -0.8186 10 0.54805 T 0.06 -9.5911 19.2042 0.93723 0.0:1.0:0.0:0.0 . 106;106;106;106 B2RDF2;B5MCF9;O00541-2;O00541 .;.;.;PESC_HUMAN H 106 ENSP00000346725:R106H;ENSP00000384252:R106H;ENSP00000334612:R106H;ENSP00000388071:R106H ENSP00000334612:R106H R - 2 0 PES1 29313324 1.000000 0.71417 0.990000 0.47175 0.937000 0.57800 7.192000 0.77771 2.650000 0.89964 0.655000 0.94253 CGT TCGA-IB-7887-01A-11D-2154-08 PES1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000321188.3 1 0 1 65 406 0 62 1 1 56 115 0 62 2 0 0 0 0 0 2 1 1.000000 65 393 0 62 2 0 0 0 0 62 2 -20.000000 1 1 121412 2 35 1 1 2 3 2.066540 0 0.270000 1.780000 0.271966 0.990000 0.800000 1.000000 1.000000 0.967455 0.990000 1 9.000000e-01 1 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 ENST00000425562.2 + 5 700 c.700C>T c.(700-702)Cct>Tct p.P234S LRCH3_ENST00000536618.1_5'Flank|LRCH3_ENST00000334859.4_Missense_Mutation_p.P234S|LRCH3_ENST00000438796.2_Missense_Mutation_p.P234S|LRCH3_ENST00000414675.2_Missense_Mutation_p.P234S|LRCH3_ENST00000441090.2_Missense_Mutation_p.P108S Q96II8 LRCH3_HUMAN leucine-rich repeats and calponin homology (CH) domain containing 3 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) TACCACAATCCCTGTTTGTTA 0.423000 0 SO:0001583 missense ENST00000425562.2 0 1 hg19 . . . . . . . . . . C 33 5.261561 0.95368 . . ENSG00000186001 ENST00000438796;ENST00000441090;ENST00000414675;ENST00000334859;ENST00000425562 T;T;T;T;T 0.59502 1.85;0.26;1.85;1.85;1.85 5.31 5.31 0.75309 . 0.000000 0.85682 D 0.000000 T 0.78773 0.4336 M 0.81614 2.55 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;0.997 D;D;D;D 0.97110 1.0;1.0;1.0;0.966 T 0.81291 -0.0999 10 0.87932 D 0 -15.0214 19.3993 0.94621 0.0:1.0:0.0:0.0 . 108;234;234;234 E9PD99;B4E0T7;Q96II8-2;Q96II8-3 .;.;.;. S 234;108;234;234;234 ENSP00000399751:P234S;ENSP00000394609:P108S;ENSP00000394965:P234S;ENSP00000334375:P234S;ENSP00000393579:P234S ENSP00000334375:P234S P + 1 0 LRCH3 199038205 1.000000 0.71417 1.000000 0.80357 0.985000 0.73830 7.421000 0.80204 2.654000 0.90174 0.650000 0.86243 CCT TCGA-IB-7887-01A-11D-2154-08 LRCH3-006 KNOWN basic protein_coding protein_coding OTTHUMT00000339965.1 0 0 1 28 475 1 70 1 2.043922e-01 9 45 1 70 5 0 0 0 0 0 2 1 0.817563 28 462 1 69 22 0 0 0 1 70 2 -2.619927 1 1 0 0 1 1 2 3 2.341094 1 0.270000 1.780000 0.356828 0.470000 0.310000 0.650000 0.460000 0.481075 0.470000 0 3.800000e-01 5.600000e-01 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_ENST00000258767.5_Missense_Mutation_p.R248Q|DGKB_ENST00000403963.1_5'UTR|DGKB_ENST00000402815.1_Missense_Mutation_p.R248Q|DGKB_ENST00000406247.3_Missense_Mutation_p.R248Q|DGKB_ENST00000407950.1_Missense_Mutation_p.R241Q|DGKB_ENST00000444700.2_Missense_Mutation_p.R241Q|DGKB_ENST00000399322.3_Missense_Mutation_p.R248Q Q9Y6T7 DGKB_HUMAN diacylglycerol kinase, beta 90kDa 72 GTGCTTCAGTCGCCACACGTG 0.463000 0 SO:0001583 missense ENST00000403951.2 1 1 hg19 CCDS47547.1 . . . . . . . . . . C 36 5.902986 0.97087 . . ENSG00000136267 ENST00000403951;ENST00000399322;ENST00000258767;ENST00000402815;ENST00000407950;ENST00000444700;ENST00000406247 D;D;D;D;D;D;D 0.92647 -3.08;-3.08;-3.08;-3.08;-3.08;-3.08;-3.08 6.16 6.16 0.99307 Protein kinase C-like, phorbol ester/diacylglycerol binding (4); 0.052374 0.64402 D 0.000001 D 0.94683 0.8285 L 0.43701 1.375 0.58432 D 0.999999 D;D;D;D 0.89917 0.999;0.995;0.995;1.0 D;P;P;D 0.70227 0.943;0.876;0.876;0.968 D 0.93847 0.7142 10 0.52906 T 0.07 . 20.8598 0.99761 0.0:1.0:0.0:0.0 . 248;241;248;248 B7ZL83;C9JTC0;Q9Y6T7-2;Q9Y6T7 .;.;.;DGKB_HUMAN Q 248;248;248;248;241;241;248 ENSP00000385780:R248Q;ENSP00000382260:R248Q;ENSP00000258767:R248Q;ENSP00000384909:R248Q;ENSP00000385031:R241Q;ENSP00000388451:R241Q;ENSP00000386066:R248Q ENSP00000258767:R248Q R - 2 0 DGKB 14691481 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 7.818000 0.86416 2.937000 0.99478 0.650000 0.86243 CGA TCGA-IB-7887-01A-11D-2154-08 DGKB-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000326356.2 1 0 1 65 326 0 48 0 0 0 0 48 2 0 0 0 0 0 2 1 1.000000 64 322 0 48 2 0 0 0 0 48 2 -3.039706 1 1 0 0 1 0 1 1 2.055534 0 0.270000 1.780000 0.268024 0.990000 0.960000 1.000000 1.000000 0.998013 0.990000 1 9.900000e-01 1 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 3 112 GGGGCCTTACAGGGCTGTTCA 0.612000 Pallister-Hall syndrome;Greig Cephalopolysyndactyly 0 SO:0001583 missense Familial Cancer Database ; ENST00000395925.3 1 1 hg19 CCDS5465.1 . . . . . . . . . . A 8.711 0.912013 0.17907 . . ENSG00000106571 ENST00000395925 T 0.12465 2.68 5.8 3.26 0.37387 . 0.934476 0.09053 N 0.855569 T 0.12475 0.0303 L 0.49126 1.545 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.19451 -1.0305 10 0.26408 T 0.33 . 5.4414 0.16511 0.4156:0.3209:0.0:0.2635 . 1249 P10071 GLI3_HUMAN G 1249 ENSP00000379258:C1249G ENSP00000379258:C1249G C - 1 0 GLI3 41971451 0.095000 0.21747 0.036000 0.18154 0.117000 0.20001 1.910000 0.39927 2.209000 0.71365 0.533000 0.62120 TGT TCGA-IB-7887-01A-11D-2154-08 GLI3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250806.3 1 0 1 65 513 0 99 0 6.186468e-01 0 18 0 99 2 0 0 0 0 0 2 1 1.000000 64 504 0 99 2 0 0 0 0 99 2 -20.000000 1 1 0 0 1 0 1 1 2.055534 0 0.270000 1.780000 0.268024 0.820000 0.650000 1.000000 1.000000 0.834291 0.820000 0 7.300000e-01 9.300000e-01 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 3 112 GGGCCTTACAGGGCTGTTCAT 0.617000 Pallister-Hall syndrome;Greig Cephalopolysyndactyly 0 SO:0001819 synonymous_variant Familial Cancer Database ; ENST00000395925.3 1 1 hg19 CCDS5465.1 TCGA-IB-7887-01A-11D-2154-08 GLI3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250806.3 0 0 1 65 518 0 98 0 6.718914e-01 0 20 0 98 2 0 0 0 0 0 2 1 1.000000 65 508 0 98 2 0 0 0 0 98 2 -2.598634 1 1 121412 1 31 1 0 1 1 2.055534 0 0.270000 1.780000 0.268024 0.820000 0.640000 1.000000 1.000000 0.827592 0.820000 0 7.200000e-01 9.200000e-01 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 CLVS1_ENST00000518592.1_Intron|RP11-787D18.1_ENST00000518064.1_RNA|CLVS1_ENST00000325897.4_Silent_p.Y136Y|RP11-787D18.1_ENST00000521801.1_RNA Q8IUQ0 CLVS1_HUMAN clavesin 1 p.Y136*(1) 41 GAGACCATTACGGCAGGAAGA 0.443000 1 Substitution - Nonsense(1) SO:0001819 synonymous_variant ENST00000519846.1 1 1 hg19 CCDS6176.1 TCGA-IB-7887-01A-11D-2154-08 CLVS1-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000378323.1 1 0 1 45 300 0 50 0 0 0 1 0 50 2 0 0 0 0 0 2 1 1.000000 44 290 0 49 2 0 0 0 0 50 2 -20.000000 1 1 121400 4 35 1 0 1 1 2.056610 0 0.270000 1.780000 0.268024 0.950000 0.710000 1.000000 1.000000 0.931040 0.950000 1 8.300000e-01 1 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 ENST00000361420.3 - 19 3947 c.3868C>T c.(3868-3870)Cga>Tga p.R1290* IGSF1_ENST00000370903.3_Nonsense_Mutation_p.R1295*|IGSF1_ENST00000370904.1_Nonsense_Mutation_p.R1281*|IGSF1_ENST00000467244.1_5'Flank|IGSF1_ENST00000370910.1_Nonsense_Mutation_p.R1281* Q8N6C5 IGSF1_HUMAN immunoglobulin superfamily, member 1 78 TACCTGGTTCGCAGTCGAGGC 0.502000 0 SO:0001587 stop_gained ENST00000361420.3 0 1 hg19 CCDS14629.1 . . . . . . . . . . G 42 9.400588 0.99159 . . ENSG00000147255 ENST00000370910;ENST00000361420;ENST00000370904;ENST00000370903 . . . 4.48 4.48 0.54585 . 0.350736 0.21139 N 0.079510 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 . 11.4099 0.49919 0.0:0.0:1.0:0.0 . . . . X 1281;1290;1281;1295 . ENSP00000355010:R1290X R - 1 2 IGSF1 130235745 1.000000 0.71417 1.000000 0.80357 0.974000 0.67602 1.588000 0.36633 2.465000 0.83290 0.544000 0.68410 CGA TCGA-IB-7887-01A-11D-2154-08 IGSF1-003 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000058288.1 1 0 1 263 1495 0 242 1 7.144762e-01 15 1 0 242 2 0 0 0 0 0 2 1 1.000000 250 1450 0 241 2 0 0 0 0 242 2 -20.000000 1 1 121410 2 29 1 0 1 1 0.270000 1.780000 0.270000 0.990000 0.980000 1.000000 1.000000 0.999062 0.990000 1 9.900000e-01 1