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 SEC31B 25956 broad.mit.edu 37 10 102262171 102262171 + Missense_Mutation SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr10:102262171C>T ENST00000370345.3 - 11 1347 c.1250G>A c.(1249-1251)cGc>cAc p.R417H SEC31B_ENST00000494350.1_5'Flank|SEC31B_ENST00000451524.1_Missense_Mutation_p.R417H NM_015490.3 NP_056305.1 Q9NQW1 SC31B_HUMAN SEC31 homolog B (S. cerevisiae) 36 Colorectal(252;0.117) GAAGACTAGGCGGGGGCAAGG 0.527000 0 SO:0001583 missense ENST00000370345.3 1 1 hg19 CCDS7495.1 . . . . . . . . . . c 7.417 0.635990 0.14386 2.27E-4 0.0 ENSG00000075826 ENST00000370345;ENST00000451524 T;T 0.59083 0.66;0.29 5.38 -1.01 0.10169 . 0.242628 0.49305 N 0.000156 T 0.39627 0.1085 L 0.31926 0.97 0.80722 D 1 B;B 0.06786 0.001;0.0 B;B 0.10450 0.005;0.002 T 0.16778 -1.0391 10 0.14656 T 0.56 -0.3817 11.439 0.50086 0.0:0.5274:0.0:0.4726 . 416;417 Q9NQW1-5;Q9NQW1 .;SC31B_HUMAN H 417 ENSP00000359370:R417H;ENSP00000391178:R417H ENSP00000359370:R417H R - 2 0 SEC31B 102252161 0.334000 0.24739 0.219000 0.23793 0.509000 0.34042 -0.023000 0.12456 -0.190000 0.10465 -0.227000 0.12334 CGC TCGA-IB-7647-01A-11D-2154-08 SEC31B-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051198.1 1 0 1 49 328 0 65 0 0 0 0 65 2 0 0 0 0 0 2 1 1.000000 49 327 0 65 2 -2.879556 1 1 121412 3 36 1 1 2 3 2.033932 0 0.240000 1.920000 0.244533 0.990000 0.820000 1.000000 1.000000 0.980343 0.990000 1 0.950000 1.000000 CUBN 8029 broad.mit.edu 37 10 16970247 16970247 + Silent SNP C C A TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr10:16970247C>A ENST00000377833.4 - 41 6245 c.6180G>T c.(6178-6180)ggG>ggT p.G2060G NM_001081.3 NP_001072.2 O60494 CUBN_HUMAN cubilin (intrinsic factor-cobalamin receptor) 241 Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200) ACCGGATGGGCCCAGGGATCT 0.478000 0 SO:0001819 synonymous_variant ENST00000377833.4 1 1 hg19 CCDS7113.1 TCGA-IB-7647-01A-11D-2154-08 CUBN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047009.1 0 0 0 9 289 0 81 0 0 0 1 0 81 2 0 0 0 0 0 2 1 0.994409 9 289 0 79 2 -3.318793 1 1 0 0 1 1 2 3 2.033932 0 0.240000 1.920000 0.244533 0.260000 0.120000 1.000000 0.250000 0.304030 0.260000 0 0.180000 0.380000 ST8SIA6 338596 broad.mit.edu 37 10 17363212 17363212 + Missense_Mutation SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr10:17363212C>T ENST00000377602.4 - 8 936 c.862G>A c.(862-864)Gaa>Aaa p.E288K NM_001004470.1 NP_001004470.1 P61647 SIA8F_HUMAN ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6 37 TTAGACTCTTCGAGCGTGTAG 0.443000 0 SO:0001583 missense ENST00000377602.4 1 1 hg19 CCDS31158.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 0.010|0.010 -1.793994|-1.793994 0.00617|0.00617 .|. .|. ENSG00000148488|ENSG00000148488 ENST00000377610;ENST00000377602|ENST00000440449 T|. 0.28454|. 1.61|. 5.18|5.18 1.42|1.42 0.22433|0.22433 .|. 0.613081|. 0.19292|. N|. 0.117871|. T|T 0.09423|0.09423 0.0232|0.0232 N|N 0.01874|0.01874 -0.695|-0.695 0.09310|0.09310 N|N 1|1 B|. 0.11235|. 0.004|. B|. 0.04013|. 0.001|. T|T 0.32025|0.32025 -0.9922|-0.9922 10|5 0.02654|. T|. 1|. -14.1943|-14.1943 5.6706|5.6706 0.17721|0.17721 0.0:0.2239:0.2137:0.5624|0.0:0.2239:0.2137:0.5624 .|. 288|. P61647|. SIA8F_HUMAN|. K|Q 118;288|108 ENSP00000366827:E288K|. ENSP00000366827:E288K|. E|R -|- 1|2 0|0 ST8SIA6|ST8SIA6 17403218|17403218 0.060000|0.060000 0.20803|0.20803 0.011000|0.011000 0.14972|0.14972 0.107000|0.107000 0.19398|0.19398 1.102000|1.102000 0.31050|0.31050 0.533000|0.533000 0.28675|0.28675 -0.312000|-0.312000 0.09012|0.09012 GAA|CGA TCGA-IB-7647-01A-11D-2154-08 ST8SIA6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047036.1 0 0 0 28 1142 0 176 0 6.317615e-04 0 2 0 176 2 0 0 0 0 0 2 1 1.000000 29 1130 0 175 2 -2.564368 1 1 121412 8 45 1 1 2 3 2.033932 0 0.240000 1.920000 0.244533 0.200000 0.130000 1.000000 0.200000 0.237006 0.200000 0 0.160000 0.250000 ANK3 288 broad.mit.edu 37 10 61847990 61847990 + Missense_Mutation SNP C C G TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr10:61847990C>G ENST00000280772.2 - 29 3646 c.3455G>C c.(3454-3456)gGa>gCa p.G1152A ANK3_ENST00000355288.2_Missense_Mutation_p.G286A|ANK3_ENST00000373827.2_Missense_Mutation_p.G1146A|ANK3_ENST00000503366.1_Missense_Mutation_p.G1153A NM_020987.3 NP_066267.2 Q12955 ANK3_HUMAN ankyrin 3, node of Ranvier (ankyrin G) 196 GCTCAGAATTCCACCTTCAGG 0.468000 0 SO:0001583 missense ENST00000280772.2 1 1 hg19 CCDS7258.1 . . . . . . . . . . C 34 5.306184 0.95629 . . ENSG00000151150 ENST00000280772;ENST00000373827;ENST00000355288;ENST00000423532;ENST00000503366;ENST00000395299;ENST00000373817;ENST00000395293;ENST00000395304;ENST00000544789;ENST00000536348 T;T;T;T 0.26223 1.75;1.75;1.75;1.75 6.17 6.17 0.99709 . 0.000000 0.41500 D 0.000864 T 0.62756 0.2454 M 0.90542 3.125 0.80722 D 1 P;D;D;D;D;D;D 0.89917 0.947;1.0;1.0;1.0;0.999;1.0;0.999 P;D;D;D;D;D;D 0.91635 0.878;0.998;0.999;0.999;0.997;0.997;0.996 T 0.67317 -0.5701 10 0.87932 D 0 . 20.8794 0.99867 0.0:1.0:0.0:0.0 . 1153;286;685;1146;1152;387;286 E9PE32;A8KA62;Q59G01;Q5CZH9;Q12955;F5GXK0;B1AQT2 .;.;.;.;ANK3_HUMAN;.;. A 1152;1146;286;286;1153;1132;387;787;787;285;685 ENSP00000280772:G1152A;ENSP00000362933:G1146A;ENSP00000347436:G286A;ENSP00000425236:G1153A ENSP00000280772:G1152A G - 2 0 ANK3 61517996 1.000000 0.71417 1.000000 0.80357 0.932000 0.56968 7.466000 0.80914 2.941000 0.99782 0.655000 0.94253 GGA TCGA-IB-7647-01A-11D-2154-08 ANK3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000048201.4 1 0 1 69 507 0 136 1 9.863805e-01 20 31 0 136 2 0 0 0 0 0 2 1 1.000000 68 504 0 135 2 -19.999990 1 1 0 0 1 1 2 3 2.033932 0 0.240000 1.920000 0.244533 0.990000 0.790000 1.000000 1.000000 0.961262 0.990000 1 0.890000 1.000000 MUC6 4588 broad.mit.edu 37 11 1031906 1031906 + Missense_Mutation SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr11:1031906C>T ENST00000421673.2 - 3 313 c.263G>A c.(262-264)cGa>cAa p.R88Q NM_005961.2 NP_005952.2 Q6W4X9 MUC6_HUMAN mucin 6, oligomeric mucus/gel-forming 80 all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229) GTCTGGGCCTCGCCGCAGCTG 0.622000 0 SO:0001583 missense ENST00000421673.2 1 1 hg19 CCDS44513.1 . . . . . . . . . . C 20.2 3.941759 0.73557 . . ENSG00000184956 ENST00000421673;ENST00000525923 T;T 0.59638 0.25;0.25 4.03 4.03 0.46877 von Willebrand factor, type D domain (3); 0.000000 0.28016 U 0.016921 T 0.75443 0.3850 M 0.76002 2.32 0.34055 D 0.656646 D 0.89917 1.0 D 0.91635 0.999 D 0.84681 0.0717 10 0.72032 D 0.01 . 16.1414 0.81528 0.0:1.0:0.0:0.0 . 88 Q6W4X9 MUC6_HUMAN Q 88;112 ENSP00000406861:R88Q;ENSP00000433790:R112Q ENSP00000406861:R88Q R - 2 0 MUC6 1021906 0.828000 0.29307 0.981000 0.43875 0.586000 0.36452 3.799000 0.55529 1.968000 0.57251 0.462000 0.41574 CGA TCGA-IB-7647-01A-11D-2154-08 MUC6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000382120.2 1 0 0 11 193 0 68 0 0 0 1 0 68 2 0 0 0 0 0 2 1 0.998386 11 191 0 65 2 -3.231474 1 1 121076 3 38 1 1 2 3 2.282413 1 0.240000 1.920000 0.319971 0.520000 0.270000 0.910000 0.500000 0.541109 0.520000 0 0.380000 0.690000 LDLRAD3 143458 broad.mit.edu 37 11 36250849 36250849 + Missense_Mutation SNP G G A TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr11:36250849G>A ENST00000315571.5 + 6 961 c.940G>A c.(940-942)Gtg>Atg p.V314M LDLRAD3_ENST00000524419.1_Missense_Mutation_p.V304M|LDLRAD3_ENST00000528989.1_Missense_Mutation_p.V265M NM_174902.2 NP_777562.1 Q86YD5 LRAD3_HUMAN low density lipoprotein receptor class A domain containing 3 28 all_lung(20;0.089)|Lung NSC(22;0.175)|all_epithelial(35;0.177) all_hematologic(20;0.124) CCTCCTGAGCGTGGAAGACAC 0.662000 0 SO:0001583 missense ENST00000315571.5 0 1 hg19 CCDS31462.1 . . . . . . . . . . G 9.730 1.161967 0.21538 0.0 1.16E-4 ENSG00000179241 ENST00000528989;ENST00000524419;ENST00000315571 D;D;D 0.94576 -3.46;-3.33;-3.22 5.22 -1.14 0.09741 . 1.345450 0.04918 N 0.454465 D 0.86151 0.5864 N 0.14661 0.345 0.09310 N 1 B;B;B 0.15473 0.013;0.003;0.003 B;B;B 0.08055 0.003;0.0;0.0 T 0.73984 -0.3810 10 0.38643 T 0.18 . 2.0251 0.03517 0.5317:0.1415:0.1838:0.1429 . 304;265;314 E9PR86;B7Z1U3;Q86YD5 .;.;LRAD3_HUMAN M 265;304;314 ENSP00000433954:V265M;ENSP00000434313:V304M;ENSP00000318607:V314M ENSP00000318607:V314M V + 1 0 LDLRAD3 36207425 0.000000 0.05858 0.031000 0.17742 0.580000 0.36256 -0.821000 0.04452 -0.105000 0.12132 0.563000 0.77884 GTG TCGA-IB-7647-01A-11D-2154-08 LDLRAD3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000389085.1 0 0 0 16 941 0 167 0 9.819553e-04 0 3 0 167 2 0 0 0 0 0 2 1 0.999917 16 919 0 159 2 -3.078595 1 1 121390 9 42 1 1 2 3 2.282413 1 0.240000 1.920000 0.319971 0.150000 0.080000 0.260000 0.150000 0.172912 0.150000 0 0.110000 0.210000 LRRC4C 57689 broad.mit.edu 37 11 40137319 40137319 + Missense_Mutation SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr11:40137319C>T ENST00000278198.2 - 2 2487 c.524G>A c.(523-525)cGc>cAc p.R175H LRRC4C_ENST00000530763.1_Missense_Mutation_p.R175H|LRRC4C_ENST00000527150.1_Missense_Mutation_p.R175H|LRRC4C_ENST00000528697.1_Missense_Mutation_p.R175H Q9HCJ2 LRC4C_HUMAN leucine rich repeat containing 4C 86 all_lung(304;0.0575)|Lung NSC(402;0.138) GTCTAGTCGGCGCAAAGAAGG 0.428000 0 SO:0001583 missense ENST00000278198.2 0 1 hg19 CCDS31464.1 . . . . . . . . . . C 17.11 3.305659 0.60305 . . ENSG00000148948 ENST00000278198;ENST00000527150;ENST00000528697;ENST00000530763 T;T;T;T 0.05081 3.5;3.5;3.5;3.5 5.82 5.82 0.92795 . 0.000000 0.85682 D 0.000000 T 0.25344 0.0616 M 0.67517 2.055 0.58432 D 0.999998 D 0.89917 1.0 D 0.80764 0.994 T 0.00029 -1.2295 10 0.49607 T 0.09 . 19.0894 0.93221 0.0:1.0:0.0:0.0 . 175 Q9HCJ2 LRC4C_HUMAN H 175 ENSP00000278198:R175H;ENSP00000436976:R175H;ENSP00000437132:R175H;ENSP00000434761:R175H ENSP00000278198:R175H R - 2 0 LRRC4C 40093895 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 6.050000 0.71063 2.754000 0.94517 0.650000 0.86243 CGC TCGA-IB-7647-01A-11D-2154-08 LRRC4C-001 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000389499.1 0 0 0 30 551 1 74 0 1.120463e-01 0 22 1 74 3 0 0 0 0 0 2 1 0.830445 30 550 1 73 24 -5.881021 1 1 121412 3 34 1 1 2 3 2.282413 1 0.240000 1.920000 0.319971 0.480000 0.330000 0.700000 0.480000 0.498374 0.480000 0 0.400000 0.580000 TAS2R31 259290 broad.mit.edu 37 12 11183165 11183165 + Missense_Mutation SNP T T C TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr12:11183165T>C ENST00000390675.2 - 1 841 c.770A>G c.(769-771)aAc>aGc p.N257S TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron NM_176885.2 NP_795366.2 P59538 T2R31_HUMAN taste receptor, type 2, member 31 7 GACAGGTTTGTTTTCCAGACT 0.383000 0 SO:0001583 missense ENST00000390675.2 0 1 hg19 CCDS53747.1 . . . . . . . . . . . 5.489 0.275150 0.10403 . . ENSG00000256436 ENST00000390675 T 0.00760 5.73 2.45 -0.013 0.13986 . . . . . T 0.00906 0.0030 L 0.42487 1.325 0.09310 N 1 B 0.26672 0.156 B 0.33799 0.17 T 0.46148 -0.9212 9 0.26408 T 0.33 . 4.233 0.10613 0.0:0.3766:0.0:0.6234 . 257 P59538 T2R31_HUMAN S 257 ENSP00000375093:N257S ENSP00000375093:N257S N - 2 0 TAS2R31 11074432 0.000000 0.05858 0.003000 0.11579 0.023000 0.10783 0.106000 0.15354 0.198000 0.20407 0.163000 0.16589 AAC TCGA-IB-7647-01A-11D-2154-08 TAS2R31-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000400233.1 0 0 0 21 1452 0 223 0 0 0 1 0 223 2 0 0 0 0 0 2 1 0.999996 18 1399 0 227 2 -2.774755 1 1 0 0 1 0 0 0 2.006602 0 0.240000 1.920000 0.232633 0.110000 0.060000 0.180000 0.120000 0.122824 0.110000 0 0.090000 0.150000 TBX5 6910 broad.mit.edu 37 12 114836449 114836449 + Missense_Mutation SNP G G T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr12:114836449G>T ENST00000310346.4 - 5 1105 c.439C>A c.(439-441)Cat>Aat p.H147N TBX5_ENST00000552726.1_5'UTR|TBX5_ENST00000405440.2_Missense_Mutation_p.H147N|TBX5_ENST00000349716.5_Missense_Mutation_p.H97N|TBX5_ENST00000526441.1_Missense_Mutation_p.H147N NM_000192.3 NP_000183.2 Q99593 TBX5_HUMAN T-box 5 56 Medulloblastoma(191;0.163)|all_neural(191;0.178) CTCATCCAATGCGCCCCGGTG 0.612000 NSCLC(152;1358 1980 4050 23898 40356) 0 SO:0001583 missense ENST00000310346.4 0 1 hg19 CCDS9173.1 . . . . . . . . . . G 21.4 4.143320 0.77888 . . ENSG00000089225 ENST00000349716;ENST00000310346;ENST00000448888;ENST00000405440;ENST00000526441 D;D;D;D 0.87887 -2.31;-2.31;-2.31;-2.31 4.35 4.35 0.52113 Transcription factor, T-box, conserved site (1);p53-like transcription factor, DNA-binding (1); 0.000000 0.85682 D 0.000000 D 0.92971 0.7763 M 0.77103 2.36 0.80722 D 1 D;D 0.65815 0.995;0.988 D;D 0.66979 0.948;0.947 D 0.93955 0.7235 10 0.72032 D 0.01 . 17.429 0.87534 0.0:0.0:1.0:0.0 . 147;147 Q99593-2;Q99593 .;TBX5_HUMAN N 97;147;44;147;147 ENSP00000337723:H97N;ENSP00000309913:H147N;ENSP00000384152:H147N;ENSP00000433292:H147N ENSP00000309913:H147N H - 1 0 TBX5 113320832 1.000000 0.71417 0.733000 0.30861 0.486000 0.33341 9.581000 0.98210 2.392000 0.81423 0.655000 0.94253 CAT TCGA-IB-7647-01A-11D-2154-08 TBX5-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000388297.1 1 0 1 15 85 0 22 0 0 0 0 22 2 0 0 0 0 0 2 1 0.999893 13 85 0 22 2 -19.999990 1 1 0 0 1 0 1 1 2.015391 0 0.240000 1.920000 0.238172 0.990000 0.740000 1.000000 1.000000 0.976400 0.990000 1 0.970000 1.000000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C A rs121913529 TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 C A C C Valid Somatic Phase_I WXS targeted Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr12:25398284C>A ENST00000256078.4 - 2 98 c.35G>T c.(34-36)gGt>gTt p.G12V KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) 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 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) 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 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 27.2 4.808637 0.90707 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78707 -1.2;-1.2;-1.2;-1.2 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.90373 0.6987 M 0.90650 3.135 0.80722 D 1 D;D 0.76494 0.997;0.999 D;D 0.72625 0.969;0.978 D 0.91773 0.5429 10 0.72032 D 0.01 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN V 12 ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V ENSP00000256078:G12V G - 2 0 KRAS 25289551 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-7647-01A-11D-2154-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 0 9 94 0 25 1 9.830912e-01 25 53 0 25 2 1 1 57 534 0 389 2 1 0.994669 9 93 0 25 2 -6.245686 1 1 0 0 1 0 0 0 2.006602 0 0.240000 1.920000 0.232633 0.730000 0.370000 1.000000 1.000000 0.739733 0.730000 0 0.530000 0.980000 NELL2 4753 broad.mit.edu 37 12 44917143 44917143 + Missense_Mutation SNP A A T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr12:44917143A>T ENST00000429094.2 - 17 2433 c.1929T>A c.(1927-1929)gaT>gaA p.D643E NELL2_ENST00000437801.2_Missense_Mutation_p.D693E|NELL2_ENST00000549027.1_Missense_Mutation_p.D642E|NELL2_ENST00000452445.2_Missense_Mutation_p.D643E|NELL2_ENST00000395487.2_Missense_Mutation_p.D642E|NELL2_ENST00000333837.4_Missense_Mutation_p.D666E|NELL2_ENST00000551601.1_Missense_Mutation_p.D595E NM_001145108.1 NP_001138580.1 Q99435 NELL2_HUMAN NEL-like 2 (chicken) 65 Lung SC(27;0.192) Lung NSC(34;0.144) TAACTTTTCCATCATGGATGC 0.413000 0 SO:0001583 missense ENST00000429094.2 1 1 hg19 CCDS8746.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. A|A 6.402|6.402 0.442294|0.442294 0.12164|0.12164 .|. .|. ENSG00000184613|ENSG00000184613 ENST00000395487;ENST00000429094;ENST00000551601;ENST00000452445;ENST00000549027;ENST00000333837;ENST00000437801|ENST00000550139 T;T;T;T;T;T;D|. 0.81739|. -1.47;-1.46;-1.13;-1.46;-1.47;-1.4;-1.53|. 5.82|5.82 -1.94|-1.94 0.07571|0.07571 von Willebrand factor, type C (2);|. 0.336601|. 0.33753|. N|. 0.004596|. T|T 0.12902|0.12902 0.0313|0.0313 N|N 0.10629|0.10629 0.01|0.01 0.29822|0.29822 N|N 0.830744|0.830744 B;B;B;B;B|. 0.06786|. 0.0;0.0;0.001;0.0;0.0|. B;B;B;B;B|. 0.08055|. 0.001;0.001;0.003;0.001;0.001|. T|T 0.26780|0.26780 -1.0093|-1.0093 10|5 0.02654|. T|. 1|. -8.98|-8.98 0.8838|0.8838 0.01240|0.01240 0.3152:0.0985:0.2528:0.3335|0.3152:0.0985:0.2528:0.3335 .|. 666;693;595;643;642|. B7Z2U7;B7Z9U3;F8VVB6;Q99435;Q96JS2|. .;.;.;NELL2_HUMAN;.|. E|R 642;643;595;643;642;666;693|56 ENSP00000378866:D642E;ENSP00000390680:D643E;ENSP00000449332:D595E;ENSP00000394612:D643E;ENSP00000447927:D642E;ENSP00000327988:D666E;ENSP00000416341:D693E|. ENSP00000327988:D666E|. D|W -|- 3|1 2|0 NELL2|NELL2 43203410|43203410 0.983000|0.983000 0.35010|0.35010 0.406000|0.406000 0.26421|0.26421 0.961000|0.961000 0.63080|0.63080 0.473000|0.473000 0.22132|0.22132 -0.594000|-0.594000 0.05836|0.05836 0.523000|0.523000 0.50628|0.50628 GAT|TGG TCGA-IB-7647-01A-11D-2154-08 NELL2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000404180.1 1 0 1 83 701 0 114 0 8.391413e-01 0 30 0 114 2 0 0 0 0 0 2 1 1.000000 83 696 0 112 2 -20.000000 1 1 0 0 1 0 1 1 2.015391 0 0.240000 1.920000 0.238172 0.870000 0.700000 1.000000 1.000000 0.879691 0.870000 1 0.780000 0.970000 TUBA1A 7846 broad.mit.edu 37 12 49580155 49580155 + Nonsense_Mutation SNP G G A TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr12:49580155G>A ENST00000295766.5 - 3 792 c.313C>T c.(313-315)Cga>Tga p.R105* TUBA1A_ENST00000550767.1_Nonsense_Mutation_p.R70*|TUBA1A_ENST00000546918.1_Silent_p.P155P|TUBA1A_ENST00000301071.7_Nonsense_Mutation_p.R105* NM_001270399.1 NP_001257328.1 Q71U36 TBA1A_HUMAN tubulin, alpha 1a 2 Albendazole(DB00518)|Mebendazole(DB00643)|Vinblastine(DB00570) TAGTGCCCTCGGGCATAGTTA 0.468000 Pancreas(111;782 2307 24613 44561)|NSCLC(165;1667 2752 9496 39006)|Ovarian(19;24 776 10875 37451) 0 SO:0001587 stop_gained ENST00000295766.5 0 1 hg19 CCDS58227.1 . . . . . . . . . . G 26.2 4.716103 0.89205 . . ENSG00000167552 ENST00000301071;ENST00000295766;ENST00000550767;ENST00000547939;ENST00000552924 . . . 5.22 5.22 0.72569 . 0.000000 0.64402 D 0.000001 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 . 13.5677 0.61828 0.0:0.0:0.8438:0.1562 . . . . X 105;105;70;70;70 . ENSP00000439020:R105X R - 1 2 TUBA1A 47866422 1.000000 0.71417 0.997000 0.53966 0.996000 0.88848 7.541000 0.82084 2.605000 0.88082 0.561000 0.74099 CGA TCGA-IB-7647-01A-11D-2154-08 TUBA1A-002 PUTATIVE basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000404547.2 0 0 0 34 956 0 180 0 1 1 1406 0 180 2 0 0 0 0 0 2 1 1.000000 34 946 0 183 2 -2.222362 0 1 0 0 1 0 1 1 2.015391 0 0.240000 1.920000 0.238172 0.280000 0.190000 0.390000 0.280000 0.292366 0.280000 0 0.230000 0.340000 KCNA5 3741 broad.mit.edu 37 12 5153781 5153781 + Missense_Mutation SNP C C A TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr12:5153781C>A ENST00000252321.3 + 1 697 c.468C>A c.(466-468)ttC>ttA p.F156L NM_002234.3 NP_002225.2 P22460 KCNA5_HUMAN potassium voltage-gated channel, shaker-related subfamily, member 5 52 Dalfampridine(DB06637) TGCGCTACTTCGACCCCCTGA 0.652000 0 SO:0001583 missense ENST00000252321.3 0 1 hg19 CCDS8536.1 . . . . . . . . . . C 16.79 3.219176 0.58560 . . ENSG00000130037 ENST00000252321 T 0.75821 -0.97 4.7 1.64 0.23874 BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1); 0.000000 0.85682 U 0.000000 D 0.82342 0.5016 M 0.71036 2.16 0.50632 D 0.999888 D 0.76494 0.999 D 0.79784 0.993 T 0.82074 -0.0637 10 0.87932 D 0 . 9.7379 0.40399 0.0:0.676:0.0:0.324 . 156 P22460 KCNA5_HUMAN L 156 ENSP00000252321:F156L ENSP00000252321:F156L F + 3 2 KCNA5 5024042 0.971000 0.33674 1.000000 0.80357 0.994000 0.84299 0.197000 0.17197 0.598000 0.29829 0.511000 0.50034 TTC TCGA-IB-7647-01A-11D-2154-08 KCNA5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000398925.2 0 0 0 7 305 0 84 0 4.185718e-03 0 4 0 84 2 0 0 0 0 0 2 1 0.980472 7 303 0 83 2 -7.322644 1 1 0 0 1 1 2 3 2.022387 0 0.240000 1.920000 0.241820 0.190000 0.080000 0.400000 0.180000 0.218423 0.190000 0 0.130000 0.290000 CAPS2 84698 broad.mit.edu 37 12 75687069 75687069 + Nonsense_Mutation SNP G G A TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr12:75687069G>A ENST00000409445.3 - 13 1376 c.1180C>T c.(1180-1182)Cga>Tga p.R394* CAPS2_ENST00000393284.3_Nonsense_Mutation_p.R162*|RP11-560G2.1_ENST00000534648.2_RNA|CAPS2_ENST00000409799.1_Nonsense_Mutation_p.R312*|CAPS2_ENST00000409004.1_5'UTR|RP11-560G2.1_ENST00000549953.1_RNA|CAPS2_ENST00000442339.2_5'UTR NM_032606.3 NP_115995.2 Q9BXY5 CAYP2_HUMAN calcyphosine 2 10 TTTGTGATTCGGAGTTTAAGT 0.318000 0 SO:0001587 stop_gained ENST00000409445.3 0 1 hg19 CCDS9008.2 1 4.578754578754579E-4 1 0.0020325203252032522 0 0.0 0 0.0 0 0.0 G 21.2 4.110650 0.77210 . . ENSG00000180881 ENST00000409799;ENST00000409445;ENST00000378703;ENST00000393284 . . . 4.6 4.6 0.57074 . 0.130292 0.34245 N 0.004139 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 -8.0574 8.339 0.32232 0.0819:0.0:0.7645:0.1536 . . . . X 312;394;130;162 . ENSP00000367975:R130X R - 1 2 CAPS2 73973336 1.000000 0.71417 0.988000 0.46212 0.091000 0.18340 3.286000 0.51724 2.282000 0.76494 0.446000 0.29264 CGA TCGA-IB-7647-01A-11D-2154-08 CAPS2-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000327880.2 1 0 0 11 250 0 45 0 2.246803e-03 1 1 0 45 2 0 0 0 0 0 2 1 0.998329 11 247 0 45 2 -2.557264 1 1 121410 9 41 1 0 1 1 2.015391 0 0.240000 1.920000 0.238172 0.350000 0.190000 0.590000 0.340000 0.374684 0.350000 0 0.260000 0.470000 EXOSC8 11340 broad.mit.edu 37 13 37576427 37576427 + Missense_Mutation SNP A A G TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr13:37576427A>G ENST00000389704.3 + 2 300 c.35A>G c.(34-36)gAg>gGg p.E12G ALG5_ENST00000443765.1_5'Flank|EXOSC8_ENST00000489088.1_3'UTR|ALG5_ENST00000413537.2_5'Flank|ALG5_ENST00000496689.1_5'Flank|ALG5_ENST00000239891.3_5'Flank NM_181503.2 NP_852480.1 Q96B26 EXOS8_HUMAN exosome component 8 7 Lung NSC(96;6.57e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184) GAACCTCTGGAGTATTACAGG 0.323000 0 SO:0001583 missense ENST00000389704.3 1 1 hg19 CCDS31958.1 . . . . . . . . . . A 20.2 3.943943 0.73672 . . ENSG00000120699 ENST00000389704;ENST00000379809 T 0.45276 0.9 5.47 5.47 0.80525 . 0.000000 0.85682 D 0.000000 T 0.43743 0.1261 M 0.75615 2.305 0.80722 D 1 B;P 0.35139 0.219;0.486 B;B 0.28465 0.072;0.09 T 0.48468 -0.9033 10 0.52906 T 0.07 -14.8925 15.5547 0.76184 1.0:0.0:0.0:0.0 . 12;12 Q5JXM0;Q96B26 .;EXOS8_HUMAN G 12 ENSP00000374354:E12G ENSP00000369137:E12G E + 2 0 EXOSC8 36474427 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 6.767000 0.74975 2.088000 0.63022 0.528000 0.53228 GAG TCGA-IB-7647-01A-11D-2154-08 EXOSC8-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044535.2 0 0 0 14 486 0 73 0 9.285532e-01 1 158 0 73 2 0 0 0 0 0 2 1 0.999742 14 481 0 71 2 -3.490276 1 1 0 0 1 1 2 3 2.183870 1 0.240000 1.920000 0.294991 0.280000 0.140000 1.000000 0.250000 0.428207 0.280000 0 0.200000 1.000000 AKAP11 11215 broad.mit.edu 37 13 42873717 42873717 + Missense_Mutation SNP A A T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr13:42873717A>T ENST00000025301.2 + 8 1010 c.835A>T c.(835-837)Agg>Tgg p.R279W NM_016248.3 NP_057332.1 Q9UKA4 AKA11_HUMAN A kinase (PRKA) anchor protein 11 56 Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114) TTGGACCCAAAGGAGTTTCTA 0.393000 0 SO:0001583 missense ENST00000025301.2 1 1 hg19 CCDS9383.1 . . . . . . . . . . A 17.48 3.399892 0.62177 . . ENSG00000023516 ENST00000025301 T 0.54675 0.56 5.43 5.43 0.79202 . 0.257696 0.42548 D 0.000687 T 0.49575 0.1565 L 0.51422 1.61 0.29627 N 0.845705 B 0.24426 0.103 B 0.21917 0.037 T 0.53229 -0.8468 10 0.54805 T 0.06 . 15.787 0.78315 1.0:0.0:0.0:0.0 . 279 Q9UKA4 AKA11_HUMAN W 279 ENSP00000025301:R279W ENSP00000025301:R279W R + 1 2 AKAP11 41771717 1.000000 0.71417 0.999000 0.59377 0.991000 0.79684 4.323000 0.59221 2.197000 0.70478 0.533000 0.62120 AGG TCGA-IB-7647-01A-11D-2154-08 AKAP11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044700.2 0 0 0 16 672 0 101 1 6.627483e-01 4 91 0 101 2 0 0 0 0 0 2 1 0.999931 16 670 0 100 2 -12.642810 1 1 0 0 1 1 2 3 2.183870 1 0.240000 1.920000 0.294991 0.230000 0.120000 1.000000 0.210000 0.391861 0.230000 0 0.170000 1.000000 KLHL1 57626 broad.mit.edu 37 13 70281775 70281775 + Silent SNP T T C TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr13:70281775T>C ENST00000377844.4 - 10 2928 c.2169A>G c.(2167-2169)caA>caG p.Q723Q KLHL1_ENST00000545028.1_Silent_p.Q530Q NM_020866.2 NP_065917.1 Q9NR64 KLHL1_HUMAN kelch-like family member 1 84 Breast(118;0.000162) ACTCATTAGTTTGTGGGTCAT 0.413000 0 SO:0001819 synonymous_variant ENST00000377844.4 0 1 hg19 CCDS9445.1 TCGA-IB-7647-01A-11D-2154-08 KLHL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045231.3 0 0 0 8 356 0 69 0 0 0 0 69 2 0 0 0 0 0 2 1 0.989198 8 353 0 69 2 -8.438654 1 1 0 0 1 1 2 3 2.050432 0 0.240000 1.920000 0.248120 0.190000 0.080000 1.000000 0.190000 0.263195 0.190000 0 0.130000 0.300000 LRFN5 145581 broad.mit.edu 37 14 42356419 42356419 + Missense_Mutation SNP G G A TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr14:42356419G>A ENST00000298119.4 + 3 1780 c.591G>A c.(589-591)atG>atA p.M197I LRFN5_ENST00000554171.1_Missense_Mutation_p.M197I|LRFN5_ENST00000554120.1_Missense_Mutation_p.M197I NM_152447.3 NP_689660.2 Q96NI6 LRFN5_HUMAN leucine rich repeat and fibronectin type III domain containing 5 120 LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728) TGCACAAGATGACTCGGTTAG 0.443000 HNSCC(30;0.082) 0 SO:0001583 missense ENST00000298119.4 1 1 hg19 CCDS9678.1 . . . . . . . . . . G 12.01 1.809997 0.31961 . . ENSG00000165379 ENST00000298119;ENST00000554120;ENST00000554171 T;T;T 0.49139 0.79;0.79;0.79 5.56 5.56 0.83823 . 0.000000 0.64402 D 0.000002 T 0.23289 0.0563 N 0.01771 -0.73 0.42698 D 0.993608 B;B 0.16396 0.001;0.017 B;B 0.19666 0.009;0.026 T 0.11916 -1.0568 10 0.66056 D 0.02 . 10.4503 0.44518 0.0879:0.0:0.9121:0.0 . 197;197 G3V364;Q96NI6 .;LRFN5_HUMAN I 197 ENSP00000298119:M197I;ENSP00000451897:M197I;ENSP00000451067:M197I ENSP00000298119:M197I M + 3 0 LRFN5 41426169 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 2.040000 0.41203 2.595000 0.87683 0.650000 0.86243 ATG TCGA-IB-7647-01A-11D-2154-08 LRFN5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000276786.1 1 0 1 41 258 0 57 0 0 0 1 0 57 2 0 0 0 0 0 2 1 1.000000 40 254 0 55 2 -20.000000 1 1 0 0 1 0 0 0 1.926440 0 0.240000 1.920000 0.201681 0.990000 0.790000 1.000000 1.000000 0.974723 0.990000 1 0.930000 1.000000 MAGEL2 54551 broad.mit.edu 37 15 23890566 23890566 + Missense_Mutation SNP T T C TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr15:23890566T>C ENST00000532292.1 - 1 609 c.515A>G c.(514-516)aAc>aGc p.N172S NM_019066.4 NP_061939.3 Q9UJ55 MAGL2_HUMAN MAGE-like 2 7 all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14) GGCAGGCAGGTTTTTCCAGGC 0.587000 0 SO:0001583 missense ENST00000532292.1 0 1 hg19 . . . . . . . . . . T 1.611 -0.523921 0.04141 . . ENSG00000254585 ENST00000532292 . . . 4.08 -6.12 0.02124 . . . . . T 0.23649 0.0572 N 0.24115 0.695 0.09310 N 1 . . . . . . T 0.28776 -1.0033 5 . . . . 6.4455 0.21873 0.0:0.3177:0.3652:0.317 . . . . A 204 . . T - 1 0 MAGEL2 21441659 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 -0.962000 0.03841 -1.381000 0.02112 -1.151000 0.01829 ACC TCGA-IB-7647-01A-11D-2154-08 MAGEL2-001 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000395182.2 0 0 0 7 218 0 60 0 1.252798e-02 0 5 0 60 2 0 0 0 0 0 2 1 0.979509 6 214 0 54 2 -1.629323 0 1 0 0 1 0 0 0 1.976255 0 0.240000 1.920000 0.221311 0.260000 0.110000 0.480000 0.250000 0.282175 0.260000 0 0.180000 0.370000 GDE1 51573 broad.mit.edu 37 16 19528371 19528371 + Silent SNP A A T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 A T A A Valid Somatic Phase_I WXS RNA Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr16:19528371A>T ENST00000353258.3 - 2 582 c.402T>A c.(400-402)atT>atA p.I134I NM_016641.3 NP_057725.1 Q9NZC3 GDE1_HUMAN glycerophosphodiester phosphodiesterase 1 13 TCAGCTTCCTAATTTGTTCAA 0.408000 0 SO:0001819 synonymous_variant ENST00000353258.3 1 1 hg19 CCDS10578.1 TCGA-IB-7647-01A-11D-2154-08 GDE1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254274.2 1 0 1 70 578 0 99 1 1 82 228 0 99 2 0 0 0 0 0 2 1 1.000000 70 575 0 96 2 -19.999400 1 1 0 0 1 1 2 3 2.033166 0 0.240000 1.920000 0.244533 0.900000 0.710000 1.000000 1.000000 0.903514 0.900000 1 0.800000 1.000000 GDE1 51573 broad.mit.edu 37 16 19528372 19528372 + Missense_Mutation SNP A A T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 A T A A Valid Somatic Phase_I WXS RNA Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr16:19528372A>T ENST00000353258.3 - 2 581 c.401T>A c.(400-402)aTt>aAt p.I134N NM_016641.3 NP_057725.1 Q9NZC3 GDE1_HUMAN glycerophosphodiester phosphodiesterase 1 13 CAGCTTCCTAATTTGTTCAAA 0.408000 0 SO:0001583 missense ENST00000353258.3 1 1 hg19 CCDS10578.1 . . . . . . . . . . A 23.7 4.443829 0.83993 . . ENSG00000006007 ENST00000353258 T 0.14893 2.47 5.56 5.56 0.83823 PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2); 0.404440 0.27189 N 0.020509 T 0.43389 0.1245 M 0.84683 2.71 0.42041 D 0.991079 P 0.46457 0.878 P 0.57204 0.815 T 0.49011 -0.8983 10 0.87932 D 0 -2.948 15.7008 0.77541 1.0:0.0:0.0:0.0 . 134 Q9NZC3 GDE1_HUMAN N 134 ENSP00000261386:I134N ENSP00000261386:I134N I - 2 0 GDE1 19435873 0.993000 0.37304 1.000000 0.80357 0.995000 0.86356 8.900000 0.92551 2.124000 0.65301 0.460000 0.39030 ATT TCGA-IB-7647-01A-11D-2154-08 GDE1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254274.2 1 0 1 71 576 0 100 1 1 82 226 0 100 2 0 0 0 0 0 2 1 1.000000 71 573 0 97 2 -20.000000 1 1 0 0 1 1 2 3 2.033166 0 0.240000 1.920000 0.244533 0.920000 0.720000 1.000000 1.000000 0.914132 0.920000 1 0.820000 1.000000 UQCRC2 7385 broad.mit.edu 37 16 21974207 21974207 + Splice_Site SNP G G T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr16:21974207G>T ENST00000268379.4 + 6 1278 c.e6+1 UQCRC2_ENST00000561553.1_Splice_Site NM_003366.2 NP_003357.2 P22695 QCR2_HUMAN ubiquinol-cytochrome c reductase core protein II 15 CCGCAGACTCGTAAGTACATT 0.363000 Colon(123;450 1645 12841 25393 45623) 0 SO:0001630 splice_region_variant ENST00000268379.4 1 1 hg19 CCDS10601.1 . . . . . . . . . . G 21.8 4.208992 0.79240 . . ENSG00000140740 ENST00000268379 . . . 4.88 4.88 0.63580 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 16.9872 0.86342 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . UQCRC2 21881708 1.000000 0.71417 1.000000 0.80357 0.976000 0.68499 9.328000 0.96403 2.411000 0.81874 0.563000 0.77884 . TCGA-IB-7647-01A-11D-2154-08 UQCRC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254466.1 1 0 0 32 283 0 56 1 3.076204e-02 3 0 0 56 2 0 0 0 0 0 2 1 1.000000 32 281 0 56 2 -20.000000 1 1 0 0 1 1 2 3 2.033166 0 0.240000 1.920000 0.244533 0.850000 0.600000 1.000000 1.000000 0.855447 0.850000 1 0.720000 1.000000 ABCC11 85320 broad.mit.edu 37 16 48209224 48209224 + Missense_Mutation SNP G G A TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr16:48209224G>A ENST00000394747.1 - 25 3992 c.3643C>T c.(3643-3645)Cgg>Tgg p.R1215W ABCC11_ENST00000353782.5_Missense_Mutation_p.R1215W|ABCC11_ENST00000394748.1_Missense_Mutation_p.R1215W|ABCC11_ENST00000356608.2_Missense_Mutation_p.R1215W|ABCC11_ENST00000565329.1_5'UTR NM_033151.3 NP_149163.2 Q96J66 ABCCB_HUMAN ATP-binding cassette, sub-family C (CFTR/MRP), member 11 83 all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166) Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032) AGCTTGGACCGCAAGTCCTCC 0.622000 0 SO:0001583 missense ENST00000394747.1 0 1 hg19 CCDS10732.1 . . . . . . . . . . G 20.5 3.998707 0.74818 . . ENSG00000121270 ENST00000353782;ENST00000356608;ENST00000394748;ENST00000394747 D;D;D;D 0.94966 -3.57;-3.57;-3.57;-3.57 4.99 2.72 0.32119 ATPase, AAA+ type, core (1);ABC transporter-like (2); 0.000000 0.85682 D 0.000000 D 0.96904 0.8989 M 0.91196 3.185 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 0.977;1.0 D 0.94753 0.7929 10 0.87932 D 0 -11.4901 4.5859 0.12282 0.1267:0.0:0.5176:0.3557 . 1215;1215 Q96J66-2;Q96J66 .;ABCCB_HUMAN W 1215 ENSP00000311326:R1215W;ENSP00000349017:R1215W;ENSP00000378231:R1215W;ENSP00000378230:R1215W ENSP00000311326:R1215W R - 1 2 ABCC11 46766725 1.000000 0.71417 0.310000 0.25168 0.990000 0.78478 2.368000 0.44222 0.342000 0.23796 0.591000 0.81541 CGG TCGA-IB-7647-01A-11D-2154-08 ABCC11-004 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000429984.1 0 0 0 5 189 0 56 0 0 0 1 0 56 2 0 0 0 0 0 2 1 0.937509 5 188 0 56 2 -2.791385 1 1 0 0 1 1 2 3 2.033166 0 0.240000 1.920000 0.244533 0.230000 0.080000 1.000000 0.210000 0.280950 0.230000 0 0.150000 0.370000 NLRC5 84166 broad.mit.edu 37 16 57060803 57060803 + Missense_Mutation SNP G G A TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr16:57060803G>A ENST00000262510.6 + 6 2173 c.1948G>A c.(1948-1950)Gac>Aac p.D650N NLRC5_ENST00000539144.1_Missense_Mutation_p.D650N|NLRC5_ENST00000308149.7_Missense_Mutation_p.D650N|NLRC5_ENST00000436936.1_Missense_Mutation_p.D650N NM_032206.4 NP_115582.4 Q86WI3 NLRC5_HUMAN NLR family, CARD domain containing 5 75 all_neural(199;0.225) GACCTGCACCGACCTGGCCAC 0.602000 0 SO:0001583 missense ENST00000262510.6 1 1 hg19 CCDS10773.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 16.20|16.20 3.055616|3.055616 0.55325|0.55325 .|. .|. ENSG00000140853|ENSG00000140853 ENST00000262510;ENST00000308149;ENST00000436936;ENST00000327982;ENST00000539144;ENST00000538110;ENST00000543030|ENST00000538805 T;T;T;T;T;T|. 0.54675|. 0.56;0.56;0.56;0.56;0.56;0.56|. 5.52|5.52 4.57|4.57 0.56435|0.56435 .|. 0.000000|. 0.36591|. N|. 0.002501|. T|T 0.70011|0.70011 0.3175|0.3175 M|M 0.79475|0.79475 2.455|2.455 0.33435|0.33435 D|D 0.581619|0.581619 D;D;D;D|. 0.89917|. 1.0;1.0;0.993;0.992|. D;D;P;D|. 0.97110|. 1.0;1.0;0.88;0.915|. T|T 0.79398|0.79398 -0.1820|-0.1820 10|5 0.41790|. T|. 0.15|. .|. 13.374|13.374 0.60728|0.60728 0.0759:0.0:0.9241:0.0|0.0759:0.0:0.9241:0.0 .|. 650;650;650;650|. Q86WI3-5;Q86WI3-4;Q86WI3-6;Q86WI3|. .;.;.;NLRC5_HUMAN|. N|Q 650;650;650;124;650;157;5|402 ENSP00000262510:D650N;ENSP00000308886:D650N;ENSP00000389739:D650N;ENSP00000441727:D650N;ENSP00000441597:D157N;ENSP00000440153:D5N|. ENSP00000262510:D650N|. D|R +|+ 1|2 0|0 NLRC5|NLRC5 55618304|55618304 1.000000|1.000000 0.71417|0.71417 0.861000|0.861000 0.33841|0.33841 0.050000|0.050000 0.14768|0.14768 6.066000|6.066000 0.71185|0.71185 1.338000|1.338000 0.45544|0.45544 0.561000|0.561000 0.74099|0.74099 GAC|CGA TCGA-IB-7647-01A-11D-2154-08 NLRC5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257346.1 1 0 0 20 416 0 129 1 8.538147e-01 6 68 0 129 2 0 0 0 0 0 2 1 0.999995 19 412 0 126 2 -4.442301 1 1 0 0 1 1 2 3 2.033166 0 0.240000 1.920000 0.244533 0.390000 0.240000 1.000000 0.380000 0.421919 0.390000 0 0.310000 0.500000 RTN4RL1 146760 broad.mit.edu 37 17 1840990 1840990 + Silent SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr17:1840990C>T ENST00000331238.6 - 2 605 c.126G>A c.(124-126)gcG>gcA p.A42A NM_178568.2 NP_848663.1 reticulon 4 receptor-like 1 11 CAAAGTTGTGCGCCTGGCAGC 0.672000 GBM(68;949 1139 14865 32798 38342) 0 SO:0001819 synonymous_variant ENST00000331238.6 1 1 hg19 CCDS45569.1 TCGA-IB-7647-01A-11D-2154-08 RTN4RL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000450155.2 1 0 1 18 88 0 32 0 3.227999e-02 1 1 0 32 2 0 0 0 0 0 2 1 0.999990 18 88 0 31 2 -20.000000 1 1 121148 15 39 1 0 1 1 1.815224 1 0.240000 1.920000 0.144529 0.950000 0.670000 1.000000 1.000000 0.924934 0.950000 1 0.820000 1.000000 CDK12 51755 broad.mit.edu 37 17 37687333 37687333 + Missense_Mutation SNP C C G TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr17:37687333C>G ENST00000447079.4 + 14 4270 c.4237C>G c.(4237-4239)Cac>Gac p.H1413D CDK12_ENST00000430627.2_Missense_Mutation_p.H1404D NM_015083.1|NM_016507.2 NP_055898.1|NP_057591.2 Q9NYV4 CDK12_HUMAN cyclin-dependent kinase 12 70 CTTAGCGTTACACCCGGTGGT 0.582000 Mis, N, F serous ovarian TCGA Ovarian(9;0.13) Rec yes 17 17q12 51755 cyclin-dependent kinase 12 E 0 SO:0001583 missense ENST00000447079.4 0 1 hg19 CCDS11337.1 . . . . . . . . . . C 13.10 2.136315 0.37728 . . ENSG00000167258 ENST00000430627;ENST00000447079 T;T 0.69435 -0.37;-0.4 5.34 5.34 0.76211 . 0.124406 0.36665 N 0.002461 T 0.50922 0.1644 N 0.08118 0 0.42641 D 0.99341 P;P 0.40476 0.596;0.718 B;B 0.38803 0.146;0.282 T 0.61143 -0.7122 10 0.62326 D 0.03 -4.3884 18.8418 0.92188 0.0:1.0:0.0:0.0 . 1413;1404 Q9NYV4;Q9NYV4-2 CDK12_HUMAN;. D 1404;1413 ENSP00000407720:H1404D;ENSP00000398880:H1413D ENSP00000407720:H1404D H + 1 0 CDK12 34940859 1.000000 0.71417 1.000000 0.80357 0.991000 0.79684 2.938000 0.48987 2.775000 0.95449 0.650000 0.86243 CAC TCGA-IB-7647-01A-11D-2154-08 CDK12-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000256941.4 0 0 0 8 351 0 78 1 6.865565e-01 4 98 0 78 2 0 0 0 0 0 2 1 0.989198 8 348 0 77 2 -8.065260 1 1 0 0 1 1 2 3 2.046166 0 0.240000 1.920000 0.247227 0.200000 0.090000 1.000000 0.190000 0.258934 0.200000 0 0.130000 0.300000 KIF18B 146909 broad.mit.edu 37 17 43011628 43011628 + Silent SNP G G A TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr17:43011628G>A ENST00000593135.1 - 6 955 c.858C>T c.(856-858)aaC>aaT p.N286N KIF18B_ENST00000590129.1_Silent_p.N295N|KIF18B_ENST00000438933.2_Silent_p.N286N|KIF18B_ENST00000587309.1_Silent_p.N286N|KIF18B_ENST00000339151.4_Silent_p.N286N NM_001265577.1 NP_001252506.1 Q86Y91 KI18B_HUMAN kinesin family member 18B 21 Prostate(33;0.155) CATTGAGGACGTTGATGAGCG 0.617000 0 SO:0001819 synonymous_variant ENST00000593135.1 1 1 hg19 CCDS45709.2 TCGA-IB-7647-01A-11D-2154-08 KIF18B-001 PUTATIVE basic|appris_candidate|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000448724.1 0 0 0 4 101 0 29 0 2.903272e-01 1 22 0 29 2 0 0 0 0 0 2 1 0.891773 4 101 0 29 2 -7.196137 1 1 121048 2 29 1 1 2 3 2.046166 0 0.240000 1.920000 0.247227 0.360000 0.120000 1.000000 0.310000 0.421424 0.360000 0 0.220000 0.600000 CACNA1G 8913 broad.mit.edu 37 17 48650006 48650006 + Missense_Mutation SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr17:48650006C>T ENST00000359106.5 + 6 838 c.838C>T c.(838-840)Cgg>Tgg p.R280W CACNA1G_ENST00000515411.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000354983.4_Missense_Mutation_p.R280W|CACNA1G_ENST00000507896.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000513689.2_Missense_Mutation_p.R280W|CACNA1G_ENST00000352832.5_Missense_Mutation_p.R280W|CACNA1G_ENST00000515765.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000514717.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000429973.2_Missense_Mutation_p.R280W|CACNA1G_ENST00000507336.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000505165.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000510115.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000514079.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000512389.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000514181.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000507609.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000360761.4_Missense_Mutation_p.R280W|CACNA1G_ENST00000515165.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000416767.4_Missense_Mutation_p.R280W|CACNA1G_ENST00000510366.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000502264.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000507510.2_Missense_Mutation_p.R280W|CACNA1G_ENST00000358244.5_Missense_Mutation_p.R280W|CACNA1G_ENST00000503485.1_Missense_Mutation_p.R280W|CACNA1G_ENST00000442258.2_Missense_Mutation_p.R280W|CACNA1G_ENST00000513964.1_Missense_Mutation_p.R280W NM_018896.4 NP_061496.2 O43497 CAC1G_HUMAN calcium channel, voltage-dependent, T type, alpha 1G subunit 47 Breast(11;6.7e-17) BRCA - Breast invasive adenocarcinoma(22;7.52e-09) Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909) GAACGGCATGCGGTCCTGCAG 0.647000 0 SO:0001583 missense ENST00000359106.5 0 1 hg19 CCDS45730.1 . . . . . . . . . . c 21.5 4.154466 0.78114 . . ENSG00000006283 ENST00000360761;ENST00000352832;ENST00000416767;ENST00000354983;ENST00000442258;ENST00000502264;ENST00000512389;ENST00000513964;ENST00000514717;ENST00000510366;ENST00000503485;ENST00000507510;ENST00000507336;ENST00000513689;ENST00000507609;ENST00000510115;ENST00000515165;ENST00000514181;ENST00000515765;ENST00000514079;ENST00000358244;ENST00000359106;ENST00000429973;ENST00000515411;ENST00000505165;ENST00000507896 D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D 0.97066 -4.09;-4.09;-4.23;-4.04;-4.09;-4.08;-4.11;-4.18;-4.15;-4.16;-4.17;-4.04;-4.06;-4.12;-4.07;-4.03;-4.11;-4.07;-4.05;-4.11;-4.09;-4.06;-4.1;-4.05;-4.11;-4.11 5.36 4.38 0.52667 Ion transport (1); 0.332930 0.22063 N 0.065148 D 0.98021 0.9348 M 0.65498 2.005 0.54753 D 0.99998 D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0 D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D 0.97110 0.998;0.993;0.997;0.997;0.999;0.986;0.999;1.0;0.999;0.981;1.0;0.975;0.993;0.998;0.999;0.993;0.991;0.984;1.0;0.987;0.993;0.993;0.999;0.99;0.981;0.985 D 0.98545 1.0634 10 0.66056 D 0.02 . 15.6493 0.77078 0.138:0.862:0.0:0.0 . 280;280;280;280;280;280;280;280;280;280;280;280;280;280;280;280;280;280;280;280;280;280;280;280;280;280 Q19QZ5;Q19QZ1;Q19QZ4;Q19R07;Q19QY8;Q19R10;Q19QZ6;Q19QZ3;Q19R06;Q19R00;Q19R04;O43497-10;Q19QZ9;Q19QZ7;Q19R08;Q19QZ8;Q19R03;O43497-4;Q19R02;Q19R12;Q19R17;Q19R11;Q2TAC4;O43497;Q19R13;O43497-11 .;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;CAC1G_HUMAN;.;. W 280 ENSP00000353990:R280W;ENSP00000339302:R280W;ENSP00000392390:R280W;ENSP00000347078:R280W;ENSP00000409759:R280W;ENSP00000425522:R280W;ENSP00000426261:R280W;ENSP00000425451:R280W;ENSP00000422407:R280W;ENSP00000426814:R280W;ENSP00000427238:R280W;ENSP00000423112:R280W;ENSP00000420918:R280W;ENSP00000426172:R280W;ENSP00000423045:R280W;ENSP00000427173:R280W;ENSP00000426098:R280W;ENSP00000425698:R280W;ENSP00000426232:R280W;ENSP00000423317:R280W;ENSP00000350979:R280W;ENSP00000352011:R280W;ENSP00000414388:R280W;ENSP00000423155:R280W;ENSP00000422268:R280W;ENSP00000421518:R280W ENSP00000339302:R280W R + 1 2 CACNA1G 46005005 1.000000 0.71417 1.000000 0.80357 0.970000 0.65996 2.314000 0.43743 1.259000 0.44117 0.505000 0.49811 CGG TCGA-IB-7647-01A-11D-2154-08 CACNA1G-013 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000367895.1 0 0 0 3 53 0 23 0 0 0 0 23 2 0 0 0 0 0 2 1 0.801111 3 51 0 21 2 -6.777303 1 0 0 0 1 1 2 3 2.076965 0 0.240000 1.920000 0.252557 0.550000 0.150000 1.000000 1.000000 0.594085 0.550000 0 0.300000 1.000000 LUC7L3 51747 broad.mit.edu 37 17 48821167 48821167 + Missense_Mutation SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr17:48821167C>T ENST00000505658.1 + 6 716 c.527C>T c.(526-528)aCg>aTg p.T176M LUC7L3_ENST00000393227.2_Missense_Mutation_p.T176M|LUC7L3_ENST00000240304.1_Missense_Mutation_p.T176M|LUC7L3_ENST00000544170.1_Missense_Mutation_p.T100M O95232 LC7L3_HUMAN LUC7-like 3 (S. cerevisiae) 12 AGGTCCACAACGTCGGTGAGT 0.368000 0 SO:0001583 missense ENST00000505658.1 1 1 hg19 CCDS11573.1 . . . . . . . . . . C 12.55 1.970220 0.34754 . . ENSG00000108848 ENST00000505658;ENST00000393227;ENST00000240304;ENST00000542316;ENST00000544170 T;T;T;T 0.30448 1.53;1.53;1.53;1.53 5.48 5.48 0.80851 . 0.097706 0.64402 D 0.000001 T 0.37489 0.1005 N 0.16478 0.41 0.53005 D 0.99996 P;D;D 0.67145 0.629;0.988;0.996 B;P;P 0.58928 0.091;0.761;0.848 T 0.13282 -1.0515 10 0.38643 T 0.18 -7.8056 19.7073 0.96079 0.0:1.0:0.0:0.0 . 100;176;176 B4DJ96;O95232;A8K3C5 .;LC7L3_HUMAN;. M 176;176;176;176;100 ENSP00000425092:T176M;ENSP00000376919:T176M;ENSP00000240304:T176M;ENSP00000444253:T100M ENSP00000240304:T176M T + 2 0 LUC7L3 46176166 1.000000 0.71417 0.963000 0.40424 0.042000 0.13812 5.910000 0.69931 2.722000 0.93159 0.557000 0.71058 ACG TCGA-IB-7647-01A-11D-2154-08 LUC7L3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000368205.2 1 0 1 36 246 0 64 1 1 85 188 0 64 2 0 0 0 0 0 2 1 1.000000 36 245 0 63 2 -16.138760 1 1 0 0 1 1 2 3 2.088520 0 0.240000 1.920000 0.254317 0.990000 0.790000 1.000000 1.000000 0.975263 0.990000 1 0.930000 1.000000 TP53 7157 broad.mit.edu 37 17 7577539 7577539 + Missense_Mutation SNP G G A rs121912651 TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr17:7577539G>A ENST00000269305.4 - 7 931 c.742C>T c.(742-744)Cgg>Tgg p.R248W TP53_ENST00000445888.2_Missense_Mutation_p.R248W|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R248W|TP53_ENST00000420246.2_Missense_Mutation_p.R248W|TP53_ENST00000359597.4_Missense_Mutation_p.R248W|TP53_ENST00000413465.2_Missense_Mutation_p.R248W 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.R248W(544)|p.R155W(28)|p.R248G(12)|p.0?(8)|p.?(5)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.N247_R248>KW(2)|p.M246_P250delMNRRP(2)|p.R248fs*97(2)|p.R248R(2)|p.R248fs*>39(1)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) ATGGGCCTCCGGTTCATGCCG 0.577000 R248W(786O_KIDNEY)|R248W(CAS1_CENTRAL_NERVOUS_SYSTEM)|R248W(COLO320_LARGE_INTESTINE)|R248W(COLO680N_OESOPHAGUS)|R248W(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(GCT_SOFT_TISSUE)|R248W(HCC2157_BREAST)|R248W(JIMT1_BREAST)|R248W(KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(LUDLU1_LUNG)|R248W(LXF289_LUNG)|R248W(MIAPACA2_PANCREAS)|R248W(RD_SOFT_TISSUE)|R248W(SW837_LARGE_INTESTINE)|R248W(VCAP_PROSTATE) 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 617 Substitution - Missense(585)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(3)|Complex - compound substitution(3)|Substitution - coding silent(2) GRCh37 CM010465|CM900211 TP53 M rs121912651 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 . . . . . . . . . . G 18.84 3.710019 0.68730 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944 D;D;D;D;D;D;D;D 0.99869 -7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34 4.62 2.56 0.30785 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 0.99843 0.9928 M 0.92507 3.315 0.58432 A 0.999997 D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0;1.0 D;D;D;D;D;D 0.97110 1.0;1.0;1.0;1.0;1.0;1.0 D 0.97208 0.9869 9 0.87932 D 0 -9.5643 7.568 0.27890 0.0893:0.0:0.7471:0.1636 . 248;248;155;248;248;248 P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7 .;.;.;P53_HUMAN;.;. W 248;248;248;248;248;248;237;155;116;155 ENSP00000410739:R248W;ENSP00000352610:R248W;ENSP00000269305:R248W;ENSP00000398846:R248W;ENSP00000391127:R248W;ENSP00000391478:R248W;ENSP00000425104:R116W;ENSP00000423862:R155W ENSP00000269305:R248W R - 1 2 TP53 7518264 1.000000 0.71417 1.000000 0.80357 0.910000 0.53928 1.447000 0.35101 0.644000 0.30656 0.462000 0.41574 CGG TCGA-IB-7647-01A-11D-2154-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 37 216 0 71 1 1 95 99 0 71 2 1 1 107 905 0 942 2 1 1.000000 36 214 0 71 2 -2.605585 1 1 121412 1 37 1 0 1 1 1.820921 1 0.240000 1.920000 0.136364 0.910000 0.710000 1.000000 0.990000 0.904389 0.910000 1 0.820000 0.980000 RAB40B 10966 broad.mit.edu 37 17 80615798 80615798 + Missense_Mutation SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr17:80615798C>T ENST00000571995.1 - 6 909 c.778G>A c.(778-780)Gtc>Atc p.V260I RAB40B_ENST00000571880.1_5'Flank|RAB40B_ENST00000269347.6_Missense_Mutation_p.V81I|RAB40B_ENST00000538809.2_3'UTR NM_006822.2 NP_006813.1 Q12829 RB40B_HUMAN RAB40B, member RAS oncogene family 10 Breast(20;0.00132)|all_neural(118;0.0952) all_cancers(8;0.072)|all_epithelial(8;0.139) BRCA - Breast invasive adenocarcinoma(99;0.0262)|OV - Ovarian serous cystadenocarcinoma(97;0.061) GGGGGGCGGACGAGCTTCACT 0.572000 0 SO:0001583 missense ENST00000571995.1 0 1 hg19 CCDS11816.1 . . . . . . . . . . C 2.276 -0.365935 0.05069 . . ENSG00000141542 ENST00000269347;ENST00000538809 . . . 4.79 -9.58 0.00559 . 2.176640 0.02755 N 0.117936 T 0.05868 0.0153 N 0.00308 -1.67 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.13683 -1.0500 9 0.02654 T 1 . 7.8491 0.29444 0.0702:0.0823:0.1585:0.6889 . 260 Q12829 RB40B_HUMAN I 260;294 . ENSP00000269347:V260I V - 1 0 RAB40B 78209087 0.000000 0.05858 0.000000 0.03702 0.025000 0.11179 -0.991000 0.03728 -3.220000 0.00212 -0.244000 0.11960 GTC TCGA-IB-7647-01A-11D-2154-08 RAB40B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000439007.1 0 0 0 16 847 1 184 1 1.813240e-01 12 135 1 184 5 0 0 0 0 0 2 0 0.309789 14 712 1 153 17 -2.386141 0 0 0 0 1 0 1 1 1.963353 0 0.240000 1.920000 0.214551 0.140000 0.080000 0.230000 0.150000 0.157809 0.140000 0 0.110000 0.190000 TECR 9524 broad.mit.edu 37 19 14674472 14674472 + Missense_Mutation SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr19:14674472C>T ENST00000215567.5 + 4 258 c.121C>T c.(121-123)Ccg>Tcg p.P41S TECR_ENST00000600083.1_5'UTR|TECR_ENST00000596164.1_3'UTR|TECR_ENST00000436007.2_Missense_Mutation_p.P56S|TECR_ENST00000596073.1_5'UTR NM_138501.5 NP_612510.1 Q9NZ01 TECR_HUMAN trans-2,3-enoyl-CoA reductase 3 CCCCGCAGATCCGCAGTGGTA 0.697000 0 SO:0001583 missense ENST00000215567.5 1 1 hg19 CCDS12313.1 . . . . . . . . . . C 17.52 3.409144 0.62399 . . ENSG00000099797 ENST00000215567;ENST00000436007 T;T 0.46451 0.87;0.87 5.25 5.25 0.73442 . 0.000000 0.85682 D 0.000000 T 0.58206 0.2106 L 0.48218 1.51 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.87578 0.998;0.998;0.998 T 0.56335 -0.7996 10 0.45353 T 0.12 -10.426 16.3276 0.82990 0.0:1.0:0.0:0.0 . 41;56;41 B3KM97;B3KSQ1;Q9NZ01 .;.;TECR_HUMAN S 41;56 ENSP00000215567:P41S;ENSP00000397206:P56S ENSP00000215567:P41S P + 1 0 TECR 14535472 1.000000 0.71417 0.989000 0.46669 0.027000 0.11550 4.298000 0.59067 2.462000 0.83206 0.561000 0.74099 CCG TCGA-IB-7647-01A-11D-2154-08 TECR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000466000.1 1 0 0 12 203 0 48 1 9.999992e-01 90 442 0 48 2 0 0 0 0 0 2 1 0.999045 12 197 0 47 2 -15.968060 1 0 121354 3 34 1 0 1 1 1.952177 0 0.240000 1.920000 0.204688 0.450000 0.240000 0.720000 0.440000 0.468466 0.450000 0 0.330000 0.590000 NOTCH3 4854 broad.mit.edu 37 19 15271507 15271507 + Missense_Mutation SNP G G A TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr19:15271507G>A ENST00000263388.2 - 33 7007 c.6932C>T c.(6931-6933)cCg>cTg p.P2311L NM_000435.2 NP_000426.2 Q9UM47 NOTC3_HUMAN notch 3 93 OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15) GGTAACTTCCGGCTGGGGCCC 0.627000 0 SO:0001583 missense ENST00000263388.2 1 1 hg19 CCDS12326.1 . . . . . . . . . . G 10.58 1.390466 0.25118 . . ENSG00000074181 ENST00000263388 T 0.81247 -1.47 3.99 3.99 0.46301 . . . . . T 0.59390 0.2190 N 0.08118 0 0.21105 N 0.999789 P 0.34587 0.458 B 0.19391 0.025 T 0.55685 -0.8102 9 0.87932 D 0 . 9.199 0.37246 0.1056:0.0:0.8944:0.0 . 2311 Q9UM47 NOTC3_HUMAN L 2311 ENSP00000263388:P2311L ENSP00000263388:P2311L P - 2 0 NOTCH3 15132507 0.858000 0.29795 0.387000 0.26183 0.565000 0.35776 2.105000 0.41825 1.948000 0.56530 0.591000 0.81541 CCG TCGA-IB-7647-01A-11D-2154-08 NOTCH3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000465714.1 1 0 1 48 371 0 89 1 1 56 481 0 89 2 0 0 0 0 0 2 1 1.000000 47 366 0 88 2 -3.075756 1 1 121400 1 26 1 0 1 1 1.952177 0 0.240000 1.920000 0.204688 0.900000 0.680000 1.000000 1.000000 0.898655 0.900000 1 0.790000 1.000000 RYR1 6261 broad.mit.edu 37 19 38976522 38976522 + Missense_Mutation SNP G G A TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr19:38976522G>A ENST00000359596.3 + 34 5227 c.5227G>A c.(5227-5229)Gcc>Acc p.A1743T RYR1_ENST00000360985.3_Missense_Mutation_p.A1743T|RYR1_ENST00000355481.4_Missense_Mutation_p.A1743T P21817 RYR1_HUMAN ryanodine receptor 1 (skeletal) 285 all_cancers(60;7.91e-06) Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272) Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786) TGAGACCCGCGCCATCACGCT 0.622000 0 SO:0001583 missense ENST00000359596.3 1 1 hg19 CCDS33011.1 . . . . . . . . . . G 13.64 2.297479 0.40694 . . ENSG00000196218 ENST00000359596;ENST00000355481;ENST00000360985 T;T;T 0.72615 -0.67;-0.67;-0.67 3.77 1.49 0.22878 . 0.137822 0.45126 U 0.000388 T 0.41581 0.1165 N 0.14661 0.345 0.29121 N 0.880273 B;B 0.33940 0.433;0.274 B;B 0.26614 0.071;0.056 T 0.23368 -1.0190 10 0.19590 T 0.45 . 4.2144 0.10528 0.5402:0.0:0.4598:0.0 . 1743;1743 P21817-2;P21817 .;RYR1_HUMAN T 1743 ENSP00000352608:A1743T;ENSP00000347667:A1743T;ENSP00000354254:A1743T ENSP00000347667:A1743T A + 1 0 RYR1 43668362 0.108000 0.22018 1.000000 0.80357 0.613000 0.37349 0.876000 0.28092 0.796000 0.33947 -0.225000 0.12378 GCC TCGA-IB-7647-01A-11D-2154-08 RYR1-010 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000462137.1 1 0 1 50 366 0 120 0 0 0 0 120 2 0 0 0 0 0 2 1 1.000000 50 360 0 117 2 -19.044860 1 1 0 0 1 1 2 3 2.062989 0 0.240000 1.920000 0.249901 0.990000 0.770000 1.000000 1.000000 0.961260 0.990000 1 0.890000 1.000000 BCKDHA 593 broad.mit.edu 37 19 41928085 41928085 + Silent SNP C C T rs151227241 TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr19:41928085C>T ENST00000269980.2 + 6 1031 c.663C>T c.(661-663)taC>taT p.Y221Y BCKDHA_ENST00000457836.2_Silent_p.Y199Y|CTC-435M10.3_ENST00000540732.1_Silent_p.Y255Y|BCKDHA_ENST00000595085.1_Silent_p.Y255Y|BCKDHA_ENST00000535632.1_3'UTR NM_000709.3|NM_001164783.1 NP_000700.1|NP_001158255.1 P12694 ODBA_HUMAN branched chain keto acid dehydrogenase E1, alpha polypeptide 10 GGGCGGCGTACGCAGCCAAGC 0.637000 0 SO:0001819 synonymous_variant ENST00000269980.2 1 1 hg19 CCDS12581.1 . . . . . . . . . . C 1.529 -0.544937 0.04024 0.0 1.16E-4 ENSG00000248098 ENST00000541315 . . . 4.85 -8.87 0.00792 . . . . . T 0.64461 0.2600 . . . 0.80722 D 1 . . . . . . T 0.72304 -0.4333 4 . . . -19.325 17.7578 0.88455 0.0:0.1167:0.0:0.8833 . . . . M 188 . . T + 2 0 BCKDHA 46619925 0.000000 0.05858 0.295000 0.24960 0.242000 0.25591 -2.269000 0.01168 -1.955000 0.01023 -1.202000 0.01658 ACG TCGA-IB-7647-01A-11D-2154-08 BCKDHA-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000398313.3 0 0 0 7 183 0 38 1 9.727769e-01 11 160 0 38 2 0 0 0 0 0 2 1 0.980097 7 180 0 37 2 -9.434995 1 1 121412 9 40 1 2 3 5 2.327642 1 0.240000 1.920000 0.343923 0.430000 0.170000 1.000000 0.360000 0.541928 0.430000 0 0.270000 1.000000 KLC3 147700 broad.mit.edu 37 19 45853603 45853603 + Nonsense_Mutation SNP C C G TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr19:45853603C>G ENST00000391946.2 + 9 1250 c.1148C>G c.(1147-1149)tCa>tGa p.S383* ERCC2_ENST00000391945.4_3'UTR|KLC3_ENST00000585434.1_Nonsense_Mutation_p.S382*|KLC3_ENST00000470402.1_Nonsense_Mutation_p.S397* NM_177417.2 NP_803136.2 Q6P597 KLC3_HUMAN kinesin light chain 3 8 Ovarian(192;0.0728)|all_neural(266;0.112) CCGCAGGCCTCAGCCTACCTG 0.532000 0 SO:0001587 stop_gained ENST00000391946.2 0 1 hg19 CCDS12660.2 . . . . . . . . . . C 33 5.269984 0.95429 . . ENSG00000104892 ENST00000391946;ENST00000470402 . . . 3.74 3.74 0.42951 . 0.094375 0.44285 D 0.000478 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.56958 D 0.05 1.0098 13.0785 0.59100 0.0:1.0:0.0:0.0 . . . . X 383;397 . ENSP00000375810:S383X S + 2 0 KLC3 50545443 1.000000 0.71417 0.980000 0.43619 0.644000 0.38419 7.541000 0.82084 1.913000 0.55393 0.462000 0.41574 TCA TCGA-IB-7647-01A-11D-2154-08 KLC3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000289776.1 1 0 1 21 272 0 65 1 5.967317e-01 5 22 0 65 2 0 0 0 0 0 2 1 0.999998 21 270 0 65 2 -20.000000 1 0 0 0 1 1 2 3 2.335259 1 0.240000 1.920000 0.321429 0.670000 0.430000 0.970000 0.660000 0.689497 0.670000 0 0.540000 0.830000 KLC3 147700 broad.mit.edu 37 19 45853629 45853629 + Nonsense_Mutation SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr19:45853629C>T ENST00000391946.2 + 9 1276 c.1174C>T c.(1174-1176)Caa>Taa p.Q392* ERCC2_ENST00000391945.4_3'UTR|KLC3_ENST00000585434.1_Nonsense_Mutation_p.Q391*|KLC3_ENST00000470402.1_Nonsense_Mutation_p.Q406* NM_177417.2 NP_803136.2 Q6P597 KLC3_HUMAN kinesin light chain 3 8 Ovarian(192;0.0728)|all_neural(266;0.112) GAACAAGTATCAACAAGCGGA 0.567000 0 SO:0001587 stop_gained ENST00000391946.2 0 1 hg19 CCDS12660.2 . . . . . . . . . . C 27.3 4.816862 0.90790 . . ENSG00000104892 ENST00000391946;ENST00000470402 . . . 3.93 -1.34 0.09143 . 0.172476 0.38436 N 0.001693 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 12.5559 7.0831 0.25241 0.2875:0.2665:0.446:0.0 . . . . X 392;406 . ENSP00000375810:Q392X Q + 1 0 KLC3 50545469 0.571000 0.26659 0.999000 0.59377 0.813000 0.45954 0.192000 0.17096 0.256000 0.21614 0.462000 0.41574 CAA TCGA-IB-7647-01A-11D-2154-08 KLC3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000289776.1 1 0 0 32 302 0 79 1 5.890675e-01 4 16 0 79 2 0 0 0 0 0 2 1 1.000000 32 301 0 79 2 -20.000000 1 0 0 0 1 1 2 3 2.335259 1 0.240000 1.920000 0.321429 0.890000 0.630000 1.000000 1.000000 0.883752 0.890000 1 0.750000 1.000000 ERCC2 2068 broad.mit.edu 37 19 45854888 45854888 + Nonstop_Mutation SNP C C G TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr19:45854888C>G ENST00000391945.4 - 23 2359 c.2282G>C c.(2281-2283)tGa>tCa p.*761S ERCC2_ENST00000391944.3_Nonstop_Mutation_p.*683S NM_000400.3 NP_000391.1 P18074 ERCC2_HUMAN excision repair cross-complementation group 2 9 Ovarian(192;0.0728)|all_neural(266;0.112) CCGCCCCACTCAGAGCTGCTG 0.592000 Mis, N, F, S skin basal cell, skin squamous cell, melanoma Nucleotide excision repair (NER) Xeroderma Pigmentosum yes Rec Xeroderma pigmentosum (D) 19 19q13.2-q13.3 2068 excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D) E 0 SO:0001578 stop_lost Familial Cancer Database incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV ENST00000391945.4 0 1 hg19 CCDS33049.1 . . . . . . . . . . C 9.890 1.203909 0.22121 . . ENSG00000104884 ENST00000391941;ENST00000391942;ENST00000391945;ENST00000391944 . . . 4.29 3.26 0.37387 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 6.3154 0.21188 0.0:0.8316:0.0:0.1684 . . . . S 711;737;761;683 . . X - 2 2 ERCC2 50546728 1.000000 0.71417 0.948000 0.38648 0.024000 0.10985 3.262000 0.51538 0.932000 0.37266 0.561000 0.74099 TGA TCGA-IB-7647-01A-11D-2154-08 ERCC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000109626.2 0 0 0 98 1089 0 291 1 8.424976e-01 7 32 0 291 2 0 0 0 0 0 2 1 1.000000 97 1070 0 286 2 -19.928260 1 0 0 0 1 1 2 3 2.335259 1 0.240000 1.920000 0.321429 0.760000 0.620000 0.920000 0.780000 0.775677 0.760000 0 0.690000 0.850000 ERCC2 2068 broad.mit.edu 37 19 45854979 45854979 + Splice_Site SNP C C G TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr19:45854979C>G ENST00000391945.4 - 23 2268 c.2191G>C c.(2191-2193)Gag>Cag p.E731Q ERCC2_ENST00000391944.3_Splice_Site_p.E653Q NM_000400.3 NP_000391.1 P18074 ERCC2_HUMAN excision repair cross-complementation group 2 9 Ovarian(192;0.0728)|all_neural(266;0.112) AGCTGATCCTCCTGCAGAGAA 0.627000 Mis, N, F, S skin basal cell, skin squamous cell, melanoma Nucleotide excision repair (NER) Xeroderma Pigmentosum yes Rec Xeroderma pigmentosum (D) 19 19q13.2-q13.3 2068 excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D) E 0 SO:0001630 splice_region_variant Familial Cancer Database incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV ENST00000391945.4 1 0 hg19 CCDS33049.1 . . . . . . . . . . C 20.8 4.056286 0.76074 . . ENSG00000104884 ENST00000391941;ENST00000391942;ENST00000391945;ENST00000391944 T;D 0.82893 -1.44;-1.66 4.13 4.13 0.48395 . 0.058002 0.64402 D 0.000002 D 0.90205 0.6938 M 0.79805 2.47 0.80722 D 1 B;B;D 0.63880 0.066;0.114;0.993 B;B;D 0.72982 0.109;0.04;0.979 D 0.90111 0.4192 10 0.41790 T 0.15 -29.0483 13.9463 0.64086 0.0:1.0:0.0:0.0 . 653;731;424 E7EVE9;P18074;Q6ZNQ5 .;ERCC2_HUMAN;. Q 681;707;731;653 ENSP00000375809:E731Q;ENSP00000375808:E653Q ENSP00000375805:E681Q E - 1 0 ERCC2 50546819 1.000000 0.71417 1.000000 0.80357 0.869000 0.49853 6.925000 0.75829 2.153000 0.67306 0.561000 0.74099 GAG TCGA-IB-7647-01A-11D-2154-08 ERCC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000109626.2 1 0 0 51 504 0 131 1 9.181251e-01 3 41 0 131 2 0 0 0 0 0 2 1 1.000000 50 501 0 131 2 -3.017764 1 0 0 0 1 1 2 3 2.335259 1 0.240000 1.920000 0.321429 0.850000 0.640000 1.000000 1.000000 0.859816 0.850000 1 0.740000 0.980000 ZNF671 79891 broad.mit.edu 37 19 58232832 58232832 + Missense_Mutation SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr19:58232832C>T ENST00000317398.6 - 4 717 c.622G>A c.(622-624)Gac>Aac p.D208N ZNF671_ENST00000594803.1_5'Flank|ZNF671_ENST00000335820.3_Missense_Mutation_p.D110N|AC003006.7_ENST00000599221.1_Intron|AC003006.7_ENST00000594684.1_Intron NM_024833.2 NP_079109.2 Q8TAW3 ZN671_HUMAN zinc finger protein 671 22 Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156) TGGTGCTGGTCAAAGTCTGTA 0.502000 0 SO:0001583 missense ENST00000317398.6 1 1 hg19 CCDS12961.1 . . . . . . . . . . C 13.37 2.218275 0.39201 . . ENSG00000083814 ENST00000317398;ENST00000335820 T;T 0.27402 1.67;1.67 2.45 -2.07 0.07276 Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.10895 0.0266 N 0.04297 -0.235 0.09310 N 1 B 0.17038 0.02 B 0.19391 0.025 T 0.37314 -0.9711 9 0.13108 T 0.6 . 4.9308 0.13916 0.0:0.5176:0.2982:0.1842 . 208 Q8TAW3 ZN671_HUMAN N 208;110 ENSP00000321848:D208N;ENSP00000338670:D110N ENSP00000321848:D208N D - 1 0 ZNF671 62924644 0.000000 0.05858 0.006000 0.13384 0.365000 0.29674 -2.416000 0.01035 -0.084000 0.12595 0.467000 0.42956 GAC TCGA-IB-7647-01A-11D-2154-08 ZNF671-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000466817.1 1 0 0 31 540 0 131 0 4.824536e-01 0 29 0 131 2 0 0 0 0 0 2 1 1.000000 31 536 0 130 2 -6.069153 1 1 0 0 1 0 3 3 2.098921 1 0.240000 1.920000 0.301984 0.520000 0.340000 1.000000 0.490000 0.595968 0.520000 0 0.420000 1.000000 MUC16 94025 broad.mit.edu 37 19 9074001 9074001 + Missense_Mutation SNP G G A TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr19:9074001G>A ENST00000397910.4 - 3 13648 c.13445C>T c.(13444-13446)gCg>gTg p.A4482V NM_024690.2 NP_078966.2 Q8WXI7 MUC16_HUMAN mucin 16, cell surface associated 590 AACTGAAGTCGCAGAAACAGG 0.463000 0 SO:0001583 missense ENST00000397910.4 1 1 hg19 CCDS54212.1 . . . . . . . . . . a 1.841 -0.467526 0.04476 4.95E-4 1.2E-4 ENSG00000181143 ENST00000397910 T 0.15603 2.41 2.22 -4.44 0.03557 . . . . . T 0.03564 0.0102 N 0.00368 -1.59 . . . B 0.02656 0.0 B 0.04013 0.001 T 0.44667 -0.9313 8 0.87932 D 0 . 5.0828 0.14666 0.4495:0.0:0.4123:0.1382 . 4482 B5ME49 . V 4482 ENSP00000381008:A4482V ENSP00000381008:A4482V A - 2 0 MUC16 8935001 0.000000 0.05858 0.000000 0.03702 0.004000 0.04260 -2.514000 0.00956 -2.395000 0.00582 -2.024000 0.00429 GCG TCGA-IB-7647-01A-11D-2154-08 MUC16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000402806.1 1 0 0 34 465 0 110 0 5.009901e-03 0 2 0 110 2 0 0 0 1 0 0 2 1 1.000000 34 458 0 109 2 -7.773385 1 1 120972 3 41 1 0 1 1 1.952177 0 0.240000 1.920000 0.204688 0.540000 0.380000 0.730000 0.540000 0.551997 0.540000 0 0.450000 0.640000 EPHA2 1969 broad.mit.edu 37 1 16455955 16455955 + Silent SNP G G A TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr1:16455955G>A ENST00000358432.5 - 16 2953 c.2799C>T c.(2797-2799)atC>atT p.I933I NM_004431.3 NP_004422.2 P29317 EPHA2_HUMAN EPH receptor A2 42 Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255) Dasatinib(DB01254)|Regorafenib(DB08896) CCACCTTCTCGATGGCAGTGT 0.652000 0 SO:0001819 synonymous_variant ENST00000358432.5 1 1 hg19 CCDS169.1 TCGA-IB-7647-01A-11D-2154-08 EPHA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000026322.1 0 0 0 14 398 0 107 1 9.973017e-01 17 262 0 107 2 0 0 0 0 0 2 1 0.999725 13 390 0 106 2 -13.482850 1 1 121412 9 44 1 1 2 3 2.028492 0 0.240000 1.920000 0.243631 0.290000 0.160000 1.000000 0.280000 0.321218 0.290000 0 0.220000 0.390000 CACNA1E 777 broad.mit.edu 37 1 181732595 181732595 + Silent SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr1:181732595C>T ENST00000367573.2 + 34 4743 c.4743C>T c.(4741-4743)gcC>gcT p.A1581A CACNA1E_ENST00000367567.4_Silent_p.A1188A|CACNA1E_ENST00000526775.1_Silent_p.A1562A|CACNA1E_ENST00000360108.3_Silent_p.A1562A|CACNA1E_ENST00000358338.5_Silent_p.A1513A|CACNA1E_ENST00000357570.5_Silent_p.A1532A|CACNA1E_ENST00000367570.1_Silent_p.A1581A NM_001205293.1 NP_001192222.1 Q15878 CAC1E_HUMAN calcium channel, voltage-dependent, R type, alpha 1E subunit 204 TCCGAGCTGCCCGCCTCATAA 0.463000 0 SO:0001819 synonymous_variant ENST00000367573.2 1 1 hg19 CCDS55664.1 TCGA-IB-7647-01A-11D-2154-08 CACNA1E-003 KNOWN non_canonical_U12|basic|CCDS protein_coding protein_coding OTTHUMT00000090793.2 0 0 0 8 281 0 38 0 1.962366e-02 0 7 0 38 2 0 0 0 0 0 2 1 0.989183 8 278 0 37 2 -3.614931 1 1 0 0 1 0 1 1 2.016410 0 0.240000 1.920000 0.235412 0.230000 0.110000 0.420000 0.230000 0.253315 0.230000 0 0.160000 0.330000 TMCC2 9911 broad.mit.edu 37 1 205241064 205241064 + Missense_Mutation SNP A A G TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr1:205241064A>G ENST00000358024.3 + 5 2331 c.1942A>G c.(1942-1944)Aac>Gac p.N648D TMCC2_ENST00000329800.7_Missense_Mutation_p.N408D|TMCC2_ENST00000330675.7_Missense_Mutation_p.N423D|TMCC2_ENST00000495538.1_3'UTR|TMCC2_ENST00000545499.1_Missense_Mutation_p.N570D NM_014858.3 NP_055673.2 O75069 TMCC2_HUMAN transmembrane and coiled-coil domain family 2 20 Breast(84;0.0871) BRCA - Breast invasive adenocarcinoma(75;0.117) CAAGTTCATCAACGTGATCCT 0.627000 0 SO:0001583 missense ENST00000358024.3 1 1 hg19 CCDS30984.1 . . . . . . . . . . A 32 5.136024 0.94517 . . ENSG00000133069 ENST00000358024;ENST00000545499;ENST00000330675;ENST00000329800 T;T;T;T 0.56444 0.46;0.46;0.46;0.46 5.32 5.32 0.75619 . 0.000000 0.85682 D 0.000000 T 0.75831 0.3903 M 0.88181 2.935 0.80722 D 1 D;D;D 0.76494 0.998;0.999;0.999 D;D;D 0.69479 0.94;0.964;0.964 T 0.81191 -0.1045 10 0.72032 D 0.01 . 15.1067 0.72326 1.0:0.0:0.0:0.0 . 408;423;648 G5E963;B2RAX5;O75069 .;.;TMCC2_HUMAN D 648;570;423;408 ENSP00000350718:N648D;ENSP00000437943:N570D;ENSP00000331842:N423D;ENSP00000329436:N408D ENSP00000329436:N408D N + 1 0 TMCC2 203507687 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 9.139000 0.94554 2.233000 0.73108 0.533000 0.62120 AAC TCGA-IB-7647-01A-11D-2154-08 TMCC2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000090383.1 1 0 1 70 516 0 162 0 2.971353e-01 1 8 0 162 2 0 0 0 0 0 2 1 1.000000 70 509 0 160 2 -20.000000 1 1 0 0 1 1 2 3 2.024286 0 0.240000 1.920000 0.248120 0.990000 0.790000 1.000000 1.000000 0.963737 0.990000 1 0.900000 1.000000 OBSCN 84033 broad.mit.edu 37 1 228494661 228494661 + Missense_Mutation SNP G G A TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr1:228494661G>A ENST00000422127.1 + 45 12030 c.11986G>A c.(11986-11988)Gca>Aca p.A3996T OBSCN_ENST00000284548.11_Missense_Mutation_p.A3996T|OBSCN_ENST00000366707.4_Missense_Mutation_p.A1630T|OBSCN_ENST00000570156.2_Missense_Mutation_p.A4953T|OBSCN_ENST00000366709.4_Missense_Mutation_p.A1115T NM_001098623.2 NP_001092093.2 Q5VST9 OBSCN_HUMAN obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF 223 Prostate(94;0.0405) GGGAGGCACCGCACACTTATG 0.662000 0 SO:0001583 missense ENST00000422127.1 0 1 hg19 CCDS58065.1 . . . . . . . . . . G 16.84 3.234904 0.58886 . . ENSG00000154358 ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709 T;T;T;T 0.05996 3.36;3.36;3.36;3.36 5.75 4.83 0.62350 Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.080615 0.51477 D 0.000084 T 0.23806 0.0576 M 0.76433 2.335 0.09310 N 1 D;P 0.89917 1.0;0.945 D;P 0.91635 0.999;0.465 T 0.02450 -1.1157 10 0.35671 T 0.21 . 15.1731 0.72891 0.069:0.0:0.931:0.0 . 3996;3996 Q5VST9;Q5VST9-3 OBSCN_HUMAN;. T 3996;3996;1630;1115 ENSP00000284548:A3996T;ENSP00000409493:A3996T;ENSP00000355668:A1630T;ENSP00000355670:A1115T ENSP00000284548:A3996T A + 1 0 OBSCN 226561284 0.393000 0.25237 0.150000 0.22450 0.002000 0.02628 3.437000 0.52863 2.722000 0.93159 0.462000 0.41574 GCA TCGA-IB-7647-01A-11D-2154-08 OBSCN-204 KNOWN basic|CCDS protein_coding protein_coding 0 0 0 3 44 0 13 0 0 0 0 13 2 0 0 0 0 0 2 1 0.812608 3 44 0 13 2 -7.313587 1 1 0 0 1 1 2 3 2.024286 0 0.240000 1.920000 0.248120 0.620000 0.180000 1.000000 1.000000 0.645483 0.620000 0 0.350000 1.000000 ACTA1 58 broad.mit.edu 37 1 229568336 229568336 + Missense_Mutation SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr1:229568336C>T ENST00000366684.3 - 3 523 c.421G>A c.(421-423)Gtg>Atg p.V141M ACTA1_ENST00000366683.2_Intron NM_001100.3 NP_001091.1 P68133 ACTS_HUMAN actin, alpha 1, skeletal muscle 28 Breast(184;0.0858)|Ovarian(103;0.103) Prostate(94;0.167) AGGGACAGCACGGCCTGGATG 0.706000 0 SO:0001583 missense ENST00000366684.3 1 1 hg19 CCDS1578.1 . . . . . . . . . . C 14.13 2.444060 0.43429 . . ENSG00000143632 ENST00000366684;ENST00000366682;ENST00000342787 D 0.96136 -3.92 4.54 4.54 0.55810 . 0.000000 0.64402 D 0.000001 D 0.97838 0.9290 H 0.96111 3.77 0.80722 D 1 P 0.41475 0.751 P 0.49332 0.607 D 0.99867 1.1091 10 0.87932 D 0 . 17.4768 0.87661 0.0:1.0:0.0:0.0 . 141 P68133 ACTS_HUMAN M 141;106;141 ENSP00000355645:V141M ENSP00000344142:V141M V - 1 0 ACTA1 227634959 1.000000 0.71417 0.998000 0.56505 0.419000 0.31324 7.620000 0.83070 2.360000 0.80028 0.655000 0.94253 GTG TCGA-IB-7647-01A-11D-2154-08 ACTA1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000092781.1 1 0 0 75 367 0 103 0 0 0 0 103 2 0 0 0 0 0 2 1 1.000000 74 360 0 100 2 -20.000000 1 1 0 0 1 1 2 3 2.024286 0 0.240000 1.920000 0.248120 0.990000 0.990000 1.000000 1.000000 0.999975 0.990000 1 0.990000 1.000000 OR2W5 441932 broad.mit.edu 37 1 247655201 247655201 + RNA SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr1:247655201C>T ENST00000522351.1 + 0 832 A6NFC9 OR2W5_HUMAN olfactory receptor, family 2, subfamily W, member 5 39 all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724) all_cancers(173;0.222) OV - Ovarian serous cystadenocarcinoma(106;0.0188) CCATCATCTACGTGTACCTGA 0.532000 0 ENST00000522351.1 1 1 hg19 TCGA-IB-7647-01A-11D-2154-08 OR2W5-002 KNOWN basic processed_transcript pseudogene OTTHUMT00000375789.1 0 0 0 25 603 0 123 0 0 0 0 123 2 0 0 0 0 0 2 1 1.000000 24 601 0 121 2 -4.257193 1 1 0 0 1 1 2 3 2.024286 0 0.240000 1.920000 0.248120 0.340000 0.220000 1.000000 0.330000 0.393516 0.340000 0 0.270000 0.440000 OR2L13 284521 broad.mit.edu 37 1 248262826 248262826 + Missense_Mutation SNP T T G TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr1:248262826T>G ENST00000358120.2 + 2 294 c.149T>G c.(148-150)gTg>gGg p.V50G OR2L13_ENST00000366478.2_Missense_Mutation_p.V50G Q8N349 OR2LD_HUMAN olfactory receptor, family 2, subfamily L, member 13 59 all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) OV - Ovarian serous cystadenocarcinoma(106;0.0132) CTCATCCACGTGGATCCTCGT 0.502000 0 SO:0001583 missense ENST00000358120.2 1 1 hg19 CCDS1637.1 . . . . . . . . . . T 8.900 0.956010 0.18507 . . ENSG00000196071 ENST00000366478;ENST00000358120 T;T 0.03004 4.08;4.08 4.07 2.92 0.33932 GPCR, rhodopsin-like superfamily (1); 0.615698 0.13314 N 0.397234 T 0.02807 0.0084 L 0.28014 0.82 0.09310 N 1 B 0.24258 0.1 B 0.21708 0.036 T 0.44697 -0.9311 10 0.54805 T 0.06 . 2.5302 0.04701 0.2215:0.1561:0.0:0.6224 . 50 Q8N349 OR2LD_HUMAN G 50 ENSP00000355434:V50G;ENSP00000350836:V50G ENSP00000350836:V50G V + 2 0 OR2L13 246329449 0.000000 0.05858 0.003000 0.11579 0.019000 0.09904 -3.499000 0.00450 0.580000 0.29522 0.528000 0.53228 GTG TCGA-IB-7647-01A-11D-2154-08 OR2L13-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000097342.1 0 0 0 29 734 0 169 0 0 0 0 169 2 0 0 0 0 0 2 1 1.000000 29 723 0 167 2 -20.000000 1 1 0 0 1 1 2 3 2.024286 0 0.240000 1.920000 0.248120 0.320000 0.210000 1.000000 0.320000 0.377809 0.320000 0 0.260000 0.410000 ACOT11 26027 broad.mit.edu 37 1 55062956 55062956 + Missense_Mutation SNP G G A TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr1:55062956G>A ENST00000371316.3 + 7 714 c.632G>A c.(631-633)cGc>cAc p.R211H ACOT11_ENST00000343744.2_Missense_Mutation_p.R211H|ACOT11_ENST00000481208.1_3'UTR NM_015547.3 NP_056362.1 Q8WXI4 ACO11_HUMAN acyl-CoA thioesterase 11 p.R211H(2) 17 GACTGTAGCCGCATGGTGCCG 0.627000 Ovarian(148;1440 1861 22015 32453 51933) 2 Substitution - Missense(2) SO:0001583 missense ENST00000371316.3 1 1 hg19 CCDS592.1 . . . . . . . . . . G 10.16 1.273318 0.23221 . . ENSG00000162390 ENST00000343744;ENST00000371316 T;T 0.10573 2.88;2.86 4.93 -7.81 0.01210 . 1.969230 0.02401 N 0.080685 T 0.06872 0.0175 L 0.34521 1.04 0.09310 N 1 B;B 0.09022 0.002;0.0 B;B 0.09377 0.004;0.003 T 0.27606 -1.0069 10 0.44086 T 0.13 -24.5333 2.1472 0.03790 0.4433:0.0829:0.2566:0.2172 . 211;211 Q8WXI4;Q8WXI4-2 ACO11_HUMAN;. H 211 ENSP00000340260:R211H;ENSP00000360366:R211H ENSP00000340260:R211H R + 2 0 ACOT11 54835544 0.000000 0.05858 0.016000 0.15963 0.557000 0.35523 -2.496000 0.00970 -1.568000 0.01670 -1.808000 0.00615 CGC TCGA-IB-7647-01A-11D-2154-08 ACOT11-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000027356.1 0 0 0 6 173 0 53 0 2.935509e-01 0 28 0 53 2 0 0 0 0 0 2 1 0.965767 6 173 0 52 2 -3.471743 1 1 0 0 1 0 0 0 2.004852 0 0.240000 1.920000 0.232633 0.290000 0.120000 0.550000 0.270000 0.313339 0.290000 0 0.190000 0.420000 HOOK1 51361 broad.mit.edu 37 1 60330911 60330911 + Missense_Mutation SNP C C A TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr1:60330911C>A ENST00000371208.3 + 18 1995 c.1738C>A c.(1738-1740)Caa>Aaa p.Q580K HOOK1_ENST00000395561.2_Missense_Mutation_p.Q538K|HOOK1_ENST00000465876.1_Intron NM_015888.4 NP_056972.1 Q9UJC3 HOOK1_HUMAN hook microtubule-tethering protein 1 29 all_cancers(7;0.000129) AGATATAAATCAAAATGGTAG 0.363000 0 SO:0001583 missense ENST00000371208.3 0 1 hg19 CCDS612.1 . . . . . . . . . . C 12.53 1.965749 0.34659 . . ENSG00000134709 ENST00000371208;ENST00000395561 T;T 0.17213 2.29;2.29 6.03 6.03 0.97812 . 0.156942 0.56097 D 0.000022 T 0.19005 0.0456 L 0.45581 1.43 0.58432 D 0.999999 B 0.11235 0.004 B 0.16722 0.016 T 0.13202 -1.0518 10 0.10377 T 0.69 . 20.6398 0.99548 0.0:1.0:0.0:0.0 . 580 Q9UJC3 HOOK1_HUMAN K 580;538 ENSP00000360252:Q580K;ENSP00000378928:Q538K ENSP00000360252:Q580K Q + 1 0 HOOK1 60103499 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 6.497000 0.73674 2.881000 0.98747 0.650000 0.86243 CAA TCGA-IB-7647-01A-11D-2154-08 HOOK1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000024934.1 0 0 0 9 237 0 47 1 6.083853e-01 9 44 0 47 2 0 0 0 0 0 2 1 0.994360 9 236 0 47 2 -3.995250 1 1 0 0 1 0 0 0 2.004852 0 0.240000 1.920000 0.232633 0.310000 0.150000 0.530000 0.300000 0.328351 0.310000 0 0.220000 0.420000 NKX2-2 4821 broad.mit.edu 37 20 21492879 21492879 + Silent SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr20:21492879C>T ENST00000377142.4 - 2 860 c.504G>A c.(502-504)acG>acA p.T168T NKX2-2-AS1_ENST00000549659.1_RNA NM_002509.3 NP_002500.1 O95096 NKX22_HUMAN NK2 homeobox 2 21 CCTGCGTGGGCGTGAGGCGGA 0.677000 0 SO:0001819 synonymous_variant ENST00000377142.4 1 1 hg19 CCDS13145.1 TCGA-IB-7647-01A-11D-2154-08 NKX2-2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000078278.9 1 0 1 23 167 0 50 0 1.685971e-01 0 6 0 50 2 0 0 0 0 0 2 1 1.000000 22 165 0 49 2 -20.000000 1 1 0 0 1 0 1 1 1.927046 0 0.240000 1.920000 0.194574 0.940000 0.620000 1.000000 1.000000 0.905623 0.940000 1 0.770000 1.000000 NFATC2 4773 broad.mit.edu 37 20 50140613 50140613 + Missense_Mutation SNP G G A TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr20:50140613G>A ENST00000396009.3 - 2 386 c.167C>T c.(166-168)tCc>tTc p.S56F NFATC2_ENST00000414705.1_Missense_Mutation_p.S36F|NFATC2_ENST00000609943.1_Missense_Mutation_p.S36F|NFATC2_ENST00000610033.1_Intron|NFATC2_ENST00000609507.1_Intron|NFATC2_ENST00000371564.3_Missense_Mutation_p.S56F NM_001258297.1|NM_173091.3 NP_001245226.1|NP_775114.1 Q13469 NFAC2_HUMAN nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2 EWSR1/NFATC2(9) 53 Hepatocellular(150;0.248) TGCGGGTCCGGAGGGTGGGCT 0.597000 0 SO:0001583 missense ENST00000396009.3 1 1 hg19 CCDS13437.1 . . . . . . . . . . G 18.23 3.577607 0.65878 . . ENSG00000101096 ENST00000371564;ENST00000396009;ENST00000414705 T;T;T 0.18016 2.26;2.26;2.24 5.13 5.13 0.70059 . 0.428509 0.25903 N 0.027548 T 0.30479 0.0766 N 0.22421 0.69 0.50039 D 0.999842 D;D;D;D 0.71674 0.997;0.998;0.998;0.998 P;D;D;D 0.78314 0.897;0.991;0.943;0.987 T 0.07501 -1.0769 10 0.54805 T 0.06 -28.7684 18.9234 0.92536 0.0:0.0:1.0:0.0 . 36;36;56;56 B5B2N9;B5B2P2;Q13469;B5B2N8 .;.;NFAC2_HUMAN;. F 56;56;36 ENSP00000360619:S56F;ENSP00000379330:S56F;ENSP00000396471:S36F ENSP00000360619:S56F S - 2 0 NFATC2 49574020 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 8.705000 0.91357 2.550000 0.86006 0.313000 0.20887 TCC TCGA-IB-7647-01A-11D-2154-08 NFATC2-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000079730.2 1 0 0 20 393 0 93 0 3.061662e-01 0 22 0 93 2 0 0 0 0 0 2 1 0.999995 20 385 0 91 2 -5.147189 1 1 0 0 1 1 2 3 2.049961 0 0.240000 1.920000 0.247227 0.410000 0.260000 1.000000 0.410000 0.459752 0.410000 0 0.330000 0.540000 MYT1 4661 broad.mit.edu 37 20 62851191 62851191 + Silent SNP C C T rs117853857 by1000genomes TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr20:62851191C>T ENST00000328439.1 + 13 2461 c.2097C>T c.(2095-2097)gaC>gaT p.D699D MYT1_ENST00000536311.1_Silent_p.D726D|MYT1_ENST00000360149.4_Silent_p.D401D NM_004535.2 NP_004526.1 Q99640 PMYT1_HUMAN myelin transcription factor 1 55 all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09) AGTCTCCCGACGCCTCCCAGC 0.657000 GBM(59;481 1041 20555 21139 33705) 0 SO:0001819 synonymous_variant ENST00000328439.1 1 1 hg19 CCDS13558.1 TCGA-IB-7647-01A-11D-2154-08 MYT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000080297.1 1 0 0 8 83 0 32 0 0 0 1 0 32 2 0 0 0 0 0 2 1 0.989531 8 81 0 32 2 -5.894015 1 1 121286 33 41 1 0 1 1 1.770176 1 0.240000 1.920000 0.136364 0.620000 0.300000 0.950000 0.610000 0.632616 0.620000 0 0.440000 0.810000 SLC37A1 54020 broad.mit.edu 37 21 43999848 43999848 + Silent SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr21:43999848C>T ENST00000352133.2 + 19 2506 c.1524C>T c.(1522-1524)ttC>ttT p.F508F SLC37A1_ENST00000398341.3_Silent_p.F508F P57057 GLPT_HUMAN solute carrier family 37 (glucose-6-phosphate transporter), member 1 15 TGGTGCAGTTCCTGATCCGCC 0.647000 0 SO:0001819 synonymous_variant ENST00000352133.2 1 1 hg19 CCDS13689.1 TCGA-IB-7647-01A-11D-2154-08 SLC37A1-004 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000195377.1 1 0 0 17 144 0 35 1 9.998573e-01 44 86 0 35 2 0 0 0 0 0 2 1 0.999973 17 143 0 35 2 -19.999980 1 1 0 0 1 0 0 0 1.959383 0 0.240000 1.920000 0.215524 0.850000 0.520000 1.000000 1.000000 0.840128 0.850000 1 0.670000 1.000000 OR11H1 81061 broad.mit.edu 37 22 16449649 16449649 + Silent SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr22:16449649C>T ENST00000252835.4 - 1 156 c.156G>A c.(154-156)ctG>ctA p.L52L NM_001005239.1 NP_001005239.1 Q8NG94 O11H1_HUMAN olfactory receptor, family 11, subfamily H, member 1 11 all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977) all_epithelial(15;0.208) CTGTTATAGTCAGTGCATATG 0.418000 0 SO:0001819 synonymous_variant ENST00000252835.4 1 1 hg19 CCDS33594.1 TCGA-IB-7647-01A-11D-2154-08 OR11H1-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000074923.2 0 0 0 42 1003 0 189 0 0 0 0 189 2 0 0 0 0 0 2 1 1.000000 23 570 0 333 2 -4.182016 1 1 0 0 1 1 2 3 2.027205 0 0.240000 1.920000 0.243631 0.330000 0.240000 1.000000 0.340000 0.361786 0.330000 0 0.280000 0.400000 GPR45 11250 broad.mit.edu 37 2 105858390 105858390 + Silent SNP G G A TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr2:105858390G>A ENST00000258456.1 + 1 191 c.75G>A c.(73-75)ggG>ggA p.G25G NM_007227.3 NP_009158.3 Q9Y5Y3 GPR45_HUMAN G protein-coupled receptor 45 28 CAGACTCGGGGTCCACCCAGT 0.602000 0 SO:0001819 synonymous_variant ENST00000258456.1 1 1 hg19 CCDS2066.1 TCGA-IB-7647-01A-11D-2154-08 GPR45-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253348.1 1 0 0 26 407 0 111 0 0 0 0 111 2 0 0 0 0 0 2 1 1.000000 26 404 0 109 2 -6.753744 1 1 0 0 1 1 2 3 2.055490 0 0.240000 1.920000 0.249012 0.520000 0.340000 1.000000 0.500000 0.558657 0.520000 0 0.420000 0.660000 TTN 7273 broad.mit.edu 37 2 179464316 179464316 + Missense_Mutation SNP C C A TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr2:179464316C>A ENST00000591111.1 - 239 51613 c.51389G>T c.(51388-51390)gGa>gTa p.G17130V TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.G16203V|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.G9706V|TTN_ENST00000589042.1_Missense_Mutation_p.G18771V|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.G9898V|TTN_ENST00000359218.5_Missense_Mutation_p.G9831V|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA Q8WZ42 TITIN_HUMAN titin 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TGATGCTGTTCCCAGATTATT 0.388000 0 SO:0001583 missense ENST00000591111.1 1 1 hg19 . . . . . . . . . . C 14.85 2.657649 0.47467 . . ENSG00000155657 ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127 T;T;T;T 0.75050 -0.9;-0.9;-0.9;-0.9 5.55 5.55 0.83447 Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1); . . . . D 0.91219 0.7233 H 0.96175 3.78 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.97110 1.0;1.0;1.0;1.0 D 0.93592 0.6922 9 0.87932 D 0 . 19.5067 0.95121 0.0:1.0:0.0:0.0 . 9706;9831;9898;17130 D3DPF9;E7EQE6;E7ET18;Q8WZ42 .;.;.;TITIN_HUMAN V 16203;9706;9898;9831;9704 ENSP00000343764:G16203V;ENSP00000434586:G9706V;ENSP00000340554:G9898V;ENSP00000352154:G9831V ENSP00000340554:G9898V G - 2 0 TTN 179172561 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 7.760000 0.85248 2.609000 0.88269 0.650000 0.86243 GGA TCGA-IB-7647-01A-11D-2154-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 1 0 0 74 1376 0 254 0 0 0 0 254 2 0 0 0 0 0 2 1 1.000000 73 1365 0 254 2 -7.614373 1 1 0 0 1 1 2 3 2.037028 0 0.240000 1.920000 0.245433 0.420000 0.330000 1.000000 0.430000 0.459265 0.420000 0 0.380000 0.490000 TTN 7273 broad.mit.edu 37 2 179641506 179641506 + Silent SNP A A G TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr2:179641506A>G ENST00000591111.1 - 28 5309 c.5085T>C c.(5083-5085)taT>taC p.Y1695Y TTN_ENST00000360870.5_Silent_p.Y1695Y|RP11-88L24.4_ENST00000582038.2_RNA|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000342992.6_Silent_p.Y1695Y|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Silent_p.Y1649Y|TTN_ENST00000589042.1_Silent_p.Y1695Y|TTN_ENST00000342175.6_Silent_p.Y1649Y|TTN_ENST00000359218.5_Silent_p.Y1649Y|TTN-AS1_ENST00000584485.1_RNA Q8WZ42 TITIN_HUMAN titin 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TCTCTTTGTCATAGAGATCAC 0.473000 0 SO:0001819 synonymous_variant ENST00000591111.1 1 1 hg19 TCGA-IB-7647-01A-11D-2154-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 1 0 1 54 331 0 53 0 0 0 0 53 2 0 0 0 0 0 2 1 1.000000 54 330 0 52 2 -19.999890 1 1 0 0 1 1 2 3 2.037028 0 0.240000 1.920000 0.245433 0.990000 0.900000 1.000000 1.000000 0.993917 0.990000 1 0.990000 1.000000 OTOF 9381 broad.mit.edu 37 2 26702178 26702178 + Missense_Mutation SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr2:26702178C>T ENST00000272371.2 - 18 2294 c.2168G>A c.(2167-2169)cGc>cAc p.R723H OTOF_ENST00000402415.3_5'Flank|OTOF_ENST00000339598.3_5'Flank|OTOF_ENST00000338581.6_5'Flank|OTOF_ENST00000403946.3_Missense_Mutation_p.R723H NM_194248.2 NP_919224.1 Q9HC10 OTOF_HUMAN otoferlin 106 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) GTAGAGGCGGCGGCGCTGGTC 0.652000 GBM(102;732 1451 20652 24062 31372) 0 SO:0001583 missense ENST00000272371.2 0 1 hg19 CCDS1725.1 . . . . . . . . . . C 28.1 4.888835 0.91814 . . ENSG00000115155 ENST00000272371;ENST00000403946 T;T 0.80123 -1.34;-1.34 4.54 4.54 0.55810 . 0.051541 0.64402 D 0.000001 D 0.84215 0.5423 M 0.82056 2.57 0.54753 D 0.999985 D 0.54397 0.966 P 0.50231 0.635 T 0.82952 -0.0202 10 0.15066 T 0.55 -18.8365 15.9074 0.79442 0.0:1.0:0.0:0.0 . 723 Q9HC10 OTOF_HUMAN H 723 ENSP00000272371:R723H;ENSP00000385255:R723H ENSP00000272371:R723H R - 2 0 OTOF 26555682 0.983000 0.35010 0.997000 0.53966 0.970000 0.65996 5.961000 0.70356 2.074000 0.62210 0.555000 0.69702 CGC TCGA-IB-7647-01A-11D-2154-08 OTOF-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000214047.3 1 0 1 14 93 0 20 0 0 0 0 20 2 0 0 0 0 0 2 1 0.999799 14 91 0 19 2 -2.659288 1 1 120760 12 37 1 1 2 3 2.055490 0 0.240000 1.920000 0.249012 0.990000 0.650000 1.000000 1.000000 0.952634 0.990000 1 0.870000 1.000000 TCF7L1 83439 broad.mit.edu 37 2 85533483 85533483 + Nonsense_Mutation SNP A A T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr2:85533483A>T ENST00000282111.3 + 9 1419 c.1144A>T c.(1144-1146)Aga>Tga p.R382* NM_031283.2 NP_112573.1 Q9HCS4 TF7L1_HUMAN transcription factor 7-like 1 (T-cell specific, HMG-box) 18 GATCCTTGGAAGAAAGGTAAG 0.567000 0 SO:0001587 stop_gained ENST00000282111.3 0 1 hg19 CCDS1971.1 . . . . . . . . . . A 25.5 4.644390 0.87859 . . ENSG00000152284 ENST00000282111 . . . 5.17 2.67 0.31697 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 . 10.7191 0.46030 0.5148:0.4852:0.0:0.0 . . . . X 382 . ENSP00000282111:R382X R + 1 2 TCF7L1 85386994 0.082000 0.21442 0.979000 0.43373 0.034000 0.12701 0.726000 0.25984 0.257000 0.21650 -0.435000 0.05868 AGA TCGA-IB-7647-01A-11D-2154-08 TCF7L1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252301.2 0 0 0 11 273 0 64 0 2.809593e-01 0 25 0 64 2 0 0 0 0 0 2 1 0.998326 11 270 0 65 2 -3.959755 1 1 0 0 1 1 2 3 2.055490 0 0.240000 1.920000 0.249012 0.340000 0.170000 1.000000 0.320000 0.402678 0.340000 0 0.250000 0.490000 PARP14 54625 broad.mit.edu 37 3 122422822 122422822 + Silent SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr3:122422822C>T ENST00000474629.2 + 7 3581 c.3315C>T c.(3313-3315)ctC>ctT p.L1105L NM_017554.2 NP_060024.2 Q460N5 PAR14_HUMAN poly (ADP-ribose) polymerase family, member 14 50 CATCTTCACTCAAGGTTGGGC 0.483000 0 SO:0001819 synonymous_variant ENST00000474629.2 0 1 hg19 CCDS46894.1 TCGA-IB-7647-01A-11D-2154-08 PARP14-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000356173.2 0 0 0 8 444 0 73 1 8.402633e-01 3 184 0 73 2 0 0 0 0 0 2 1 0.988910 8 438 0 73 2 -2.854990 1 1 0 0 1 1 2 3 2.200593 1 0.240000 1.920000 0.294991 0.180000 0.070000 1.000000 0.160000 0.357987 0.180000 0 0.120000 1.000000 IGSF10 285313 broad.mit.edu 37 3 151155325 151155325 + Missense_Mutation SNP G G C TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr3:151155325G>C ENST00000282466.3 - 6 7023 c.7024C>G c.(7024-7026)Cca>Gca p.P2342A IGSF10_ENST00000495443.1_5'UTR NM_001178145.1|NM_001178146.1|NM_178822.4 NP_001171616.1|NP_001171617.1|NP_849144.2 Q6WRI0 IGS10_HUMAN immunoglobulin superfamily, member 10 116 LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517) TCATTAAATGGATTTCTAAAT 0.423000 0 SO:0001583 missense ENST00000282466.3 1 1 hg19 CCDS3160.1 . . . . . . . . . . G 21.6 4.173936 0.78452 . . ENSG00000152580 ENST00000282466 T 0.66815 -0.23 5.77 5.77 0.91146 Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.000000 0.46442 D 0.000299 T 0.82254 0.4997 M 0.73217 2.22 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;0.999 T 0.82118 -0.0615 10 0.56958 D 0.05 . 19.9792 0.97320 0.0:0.0:1.0:0.0 . 2342;369 Q6WRI0;Q6WRI0-2 IGS10_HUMAN;. A 2342 ENSP00000282466:P2342A ENSP00000282466:P2342A P - 1 0 IGSF10 152638015 1.000000 0.71417 0.549000 0.28204 0.904000 0.53231 9.414000 0.97362 2.727000 0.93392 0.591000 0.81541 CCA TCGA-IB-7647-01A-11D-2154-08 IGSF10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000357782.1 0 0 0 30 883 0 108 0 1.178419e-03 0 2 0 108 2 0 0 0 0 0 2 1 1.000000 30 879 0 107 2 -3.588511 1 1 0 0 1 1 2 3 2.200593 1 0.240000 1.920000 0.294991 0.310000 0.200000 1.000000 0.290000 0.456618 0.310000 0 0.250000 1.000000 PIK3CA 5290 broad.mit.edu 37 3 178948163 178948163 + Splice_Site SNP A A G TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr3:178948163A>G ENST00000263967.3 + 20 3092 c.2935A>G c.(2935-2937)Agg>Ggg p.R979G NM_006218.2 NP_006209.2 P42336 PK3CA_HUMAN phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha 5269 all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155) OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282) Caffeine(DB00201) AGAATTTGAGAGGTGAGCTCG 0.338000 57 Mis colorectal, gastric, gliobastoma, breast HNSCC(19;0.045)|TSP Lung(28;0.18) Colon(199;1504 1750 3362 26421 31210 32040) Dom yes 3 3q26.3 5290 phosphoinositide-3-kinase, catalytic, alpha polypeptide E, O 0 SO:0001630 splice_region_variant ENST00000263967.3 1 0 hg19 CCDS43171.1 . . . . . . . . . . A 18.36 3.606615 0.66558 . . ENSG00000121879 ENST00000263967 T 0.75938 -0.98 4.99 4.99 0.66335 Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4); 0.000000 0.85682 D 0.000000 T 0.73590 0.3606 L 0.55213 1.73 0.80722 D 1 P 0.45827 0.867 P 0.45071 0.468 T 0.75297 -0.3367 10 0.44086 T 0.13 -11.9936 14.9656 0.71188 1.0:0.0:0.0:0.0 . 979 P42336 PK3CA_HUMAN G 979 ENSP00000263967:R979G ENSP00000263967:R979G R + 1 2 PIK3CA 180430857 1.000000 0.71417 1.000000 0.80357 0.961000 0.63080 6.842000 0.75379 1.990000 0.58119 0.477000 0.44152 AGG TCGA-IB-7647-01A-11D-2154-08 PIK3CA-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000348409.2 1 0 1 63 427 0 68 1 9.999911e-01 4 111 0 68 2 0 0 0 0 0 2 1 1.000000 62 423 0 66 2 -19.999990 1 1 0 0 1 1 2 3 2.200593 1 0.240000 1.920000 0.294991 0.990000 0.910000 1.000000 1.000000 0.994887 0.990000 1 0.990000 1.000000 LMLN 89782 broad.mit.edu 37 3 197707289 197707289 + Silent SNP C C T rs146220433 TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr3:197707289C>T ENST00000330198.4 + 6 664 c.642C>T c.(640-642)taC>taT p.Y214Y LMLN_ENST00000420910.2_Silent_p.Y214Y|LMLN_ENST00000482695.1_Silent_p.Y162Y|LMLN_ENST00000332636.5_Silent_p.Y162Y NM_033029.3 NP_149018.2 Q96KR4 LMLN_HUMAN leishmanolysin-like (metallopeptidase M8 family) 25 all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976) Lung NSC(153;0.132) Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07) TTGTTCTTTACGTTGGTGCTC 0.527000 0 SO:0001819 synonymous_variant ENST00000330198.4 1 1 hg19 CCDS3332.1 TCGA-IB-7647-01A-11D-2154-08 LMLN-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000339701.1 0 0 0 25 785 1 120 0 6.458159e-02 1 12 1 120 2 0 0 0 0 0 2 1 0.706700 24 776 1 120 22 -3.247122 1 1 121412 4 41 1 1 2 3 2.316141 1 0.240000 1.920000 0.319971 0.280000 0.180000 0.440000 0.290000 0.304312 0.280000 0 0.230000 0.360000 CELSR3 1951 broad.mit.edu 37 3 48677669 48677669 + Missense_Mutation SNP G G A TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr3:48677669G>A ENST00000164024.4 - 34 9629 c.9349C>T c.(9349-9351)Cgg>Tgg p.R3117W CELSR3_ENST00000544264.1_Missense_Mutation_p.R3122W NM_001407.2 NP_001398.2 Q9NYQ7 CELR3_HUMAN cadherin, EGF LAG seven-pass G-type receptor 3 83 GTGCTGCCCCGATCTTTGGGC 0.682000 0 SO:0001583 missense ENST00000164024.4 1 1 hg19 CCDS2775.1 . . . . . . . . . . G 16.74 3.207667 0.58343 . . ENSG00000008300 ENST00000164024;ENST00000544264 T;T 0.72167 -0.63;-0.62 4.72 2.78 0.32641 . . . . . T 0.71065 0.3296 N 0.19112 0.55 0.29159 N 0.877919 D;D;D 0.89917 0.999;0.999;1.0 P;P;P 0.62885 0.9;0.798;0.908 T 0.67534 -0.5646 9 0.72032 D 0.01 . 12.7798 0.57471 0.0:0.0:0.6916:0.3084 . 3122;3117;3215 Q9NYQ7-2;Q9NYQ7;Q5Y190 .;CELR3_HUMAN;. W 3117;3122 ENSP00000164024:R3117W;ENSP00000445694:R3122W ENSP00000164024:R3117W R - 1 2 CELSR3 48652673 0.936000 0.31750 0.981000 0.43875 0.483000 0.33249 1.494000 0.35616 0.333000 0.23563 0.484000 0.47621 CGG TCGA-IB-7647-01A-11D-2154-08 CELSR3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257523.1 1 0 1 37 228 0 81 1 5.218463e-01 6 6 0 81 2 1 1 137 795 0 865 2 1 1.000000 36 226 0 80 2 -17.797470 1 1 0 0 1 0 1 1 1.793368 1 0.240000 1.920000 0.136364 0.900000 0.690000 1.000000 0.990000 0.892557 0.900000 1 0.800000 0.970000 ADH1A 124 broad.mit.edu 37 4 100205883 100205883 + Silent SNP A A G TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr4:100205883A>G ENST00000209668.2 - 4 450 c.337T>C c.(337-339)Ttg>Ctg p.L113L RP11-696N14.1_ENST00000500358.2_RNA|ADH1A_ENST00000511656.1_5'Flank NM_000667.3 NP_000658.1 P07327 ADH1A_HUMAN alcohol dehydrogenase 1A (class I), alpha polypeptide 25 Ethanol(DB00898)|Fomepizole(DB01213) TCGTTTTTCAAGCAGTAGTTG 0.433000 0 SO:0001819 synonymous_variant ENST00000209668.2 1 1 hg19 CCDS3648.1 TCGA-IB-7647-01A-11D-2154-08 ADH1A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253669.1 1 0 1 52 293 0 49 0 0 0 0 49 2 0 0 0 0 0 2 1 1.000000 52 289 0 49 2 -20.000000 1 1 0 0 1 1 2 3 2.040586 0 0.240000 1.920000 0.246331 0.990000 0.970000 1.000000 1.000000 0.998027 0.990000 1 0.990000 1.000000 COX7B2 170712 broad.mit.edu 37 4 46736995 46736995 + Missense_Mutation SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr4:46736995C>T ENST00000396533.1 - 4 465 c.215G>A c.(214-216)aGa>aAa p.R72K COX7B2_ENST00000355591.3_Missense_Mutation_p.R72K|COX7B2_ENST00000543208.1_Missense_Mutation_p.R71K|COX7B2_ENST00000302930.5_Missense_Mutation_p.R72K Q8TF08 CX7B2_HUMAN cytochrome c oxidase subunit VIIb2 p.R71I(1) 5 TGGGGTAACTCTGCCAACAGG 0.428000 1 Substitution - Missense(1) SO:0001583 missense ENST00000396533.1 0 1 hg19 CCDS3472.2 . . . . . . . . . . C 18.21 3.574133 0.65765 . . ENSG00000170516 ENST00000355591;ENST00000396533;ENST00000302930;ENST00000543208 T;T;T;T 0.45276 0.9;0.9;0.9;0.9 4.57 4.57 0.56435 Cytochrome C oxidase, subunit VIIB, domain (2); 0.057494 0.64402 D 0.000001 T 0.56031 0.1958 . . . 0.28946 N 0.890717 D 0.76494 0.999 D 0.85130 0.997 T 0.46555 -0.9183 9 0.24483 T 0.36 -8.9049 13.1628 0.59554 0.0:1.0:0.0:0.0 . 72 Q8TF08 CX7B2_HUMAN K 72;72;72;71 ENSP00000347799:R72K;ENSP00000379784:R72K;ENSP00000305964:R72K;ENSP00000437439:R71K ENSP00000305964:R72K R - 2 0 COX7B2 46431752 1.000000 0.71417 1.000000 0.80357 0.986000 0.74619 0.933000 0.28897 2.830000 0.97506 0.585000 0.79938 AGA TCGA-IB-7647-01A-11D-2154-08 COX7B2-002 KNOWN alternative_5_UTR|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000313899.1 0 0 0 9 395 0 76 0 0 0 0 76 2 0 0 0 0 0 2 1 0.994208 9 393 0 75 2 -3.868727 1 1 0 0 1 1 2 3 2.040586 0 0.240000 1.920000 0.246331 0.190000 0.090000 1.000000 0.190000 0.249716 0.190000 0 0.130000 0.290000 PCDHA2 56146 broad.mit.edu 37 5 140176361 140176361 + Silent SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr5:140176361C>T ENST00000526136.1 + 1 1812 c.1812C>T c.(1810-1812)aaC>aaT p.N604N PCDHA2_ENST00000520672.2_Silent_p.N604N|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000378132.1_Silent_p.N604N|PCDHA1_ENST00000394633.3_Intron NM_018905.2 NP_061728.1 Q9Y5H9 PCDA2_HUMAN protocadherin alpha 2 p.N604N(2) 71 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) CAGGCTACAACGCGTGGCTTT 0.657000 2 Substitution - coding silent(2) SO:0001819 synonymous_variant ENST00000526136.1 1 1 hg19 CCDS54914.1 TCGA-IB-7647-01A-11D-2154-08 PCDHA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000372877.3 1 0 0 27 384 0 130 0 2.582454e-02 0 4 0 130 2 0 0 0 0 0 2 1 1.000000 27 382 0 129 2 -7.190530 1 1 0 0 1 0 0 0 1.994106 0 0.240000 1.920000 0.228896 0.540000 0.360000 0.750000 0.530000 0.552279 0.540000 0 0.440000 0.650000 LMBRD1 55788 broad.mit.edu 37 6 70428941 70428941 + Silent SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr6:70428941C>T ENST00000370577.3 - 8 898 c.669G>A c.(667-669)ctG>ctA p.L223L LMBRD1_ENST00000370570.1_Silent_p.L150L NM_018368.3 NP_060838.3 Q9NUN5 LMBD1_HUMAN LMBR1 domain containing 1 31 TGCCTTTTATCAGATTTAAAG 0.313000 0 SO:0001819 synonymous_variant ENST00000370577.3 0 1 hg19 CCDS4969.1 TCGA-IB-7647-01A-11D-2154-08 LMBRD1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041124.1 1 0 0 8 188 0 27 0 9.989937e-01 0 320 0 27 2 0 0 0 0 0 2 1 0.988433 4 186 0 26 2 -4.171414 1 0 0 0 1 0 1 1 1.794209 1 0.240000 1.920000 0.136364 0.300000 0.140000 0.530000 0.290000 0.322612 0.300000 0 0.210000 0.420000 ZNF777 27153 broad.mit.edu 37 7 149129516 149129516 + Missense_Mutation SNP G G A TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr7:149129516G>A ENST00000247930.4 - 6 2170 c.1847C>T c.(1846-1848)gCg>gTg p.A616V NM_015694.2 NP_056509.2 Q9ULD5 ZN777_HUMAN zinc finger protein 777 26 Melanoma(164;0.165) OV - Ovarian serous cystadenocarcinoma(82;0.00358) CGGCTTGAGCGCGTGCTTGGG 0.672000 0 SO:0001583 missense ENST00000247930.4 1 1 hg19 CCDS43675.1 . . . . . . . . . . G 13.37 2.216935 0.39201 . . ENSG00000196453 ENST00000247930;ENST00000314683 T 0.05319 3.46 5.02 5.02 0.67125 . 1.524830 0.03983 N 0.293589 T 0.07458 0.0188 N 0.25144 0.715 0.30708 N 0.749545 B 0.28971 0.229 B 0.24269 0.052 T 0.30621 -0.9972 10 0.24483 T 0.36 -3.7701 15.8456 0.78887 0.0:0.0:1.0:0.0 . 616 Q9ULD5-2 . V 616;359 ENSP00000247930:A616V ENSP00000247930:A616V A - 2 0 ZNF777 148760449 0.825000 0.29262 0.934000 0.37439 0.724000 0.41520 3.866000 0.56040 2.328000 0.79073 0.460000 0.39030 GCG TCGA-IB-7647-01A-11D-2154-08 ZNF777-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000352708.1 1 0 1 92 604 0 141 1 8.882131e-02 2 2 0 141 2 0 0 0 0 0 2 1 1.000000 93 590 0 138 2 -20.000000 1 1 121190 2 36 1 1 2 3 2.022996 0 0.240000 1.920000 0.241820 0.990000 0.900000 1.000000 1.000000 0.992020 0.990000 1 0.990000 1.000000 PPP1R9A 55607 broad.mit.edu 37 7 94740662 94740662 + Missense_Mutation SNP G G A TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr7:94740662G>A ENST00000433881.1 + 3 2019 c.1487G>A c.(1486-1488)cGt>cAt p.R496H PPP1R9A_ENST00000456331.2_Missense_Mutation_p.R496H|PPP1R9A_ENST00000424654.1_Missense_Mutation_p.R496H|PPP1R9A_ENST00000289495.5_Missense_Mutation_p.R496H|PPP1R9A_ENST00000340694.4_Missense_Mutation_p.R496H|PPP1R9A_ENST00000433360.1_Missense_Mutation_p.R496H Q9ULJ8 NEB1_HUMAN protein phosphatase 1, regulatory subunit 9A 71 all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09) STAD - Stomach adenocarcinoma(171;0.0031) CTTGAAAAACGTGTAGAAAAG 0.383000 HNSCC(28;0.073) 0 SO:0001583 missense ENST00000433881.1 1 1 hg19 CCDS34683.1 1 4.578754578754579E-4 0 0.0 0 0.0 0 0.0 1 0.0013192612137203166 G 19.83 3.899587 0.72754 . . ENSG00000158528 ENST00000433360;ENST00000340694;ENST00000424654;ENST00000433881;ENST00000289495;ENST00000456331 T;T;T;T;T;T 0.39229 1.09;1.09;1.09;1.09;1.09;1.09 4.98 4.98 0.66077 PDZ/DHR/GLGF (1); 0.000000 0.85682 D 0.000000 T 0.67951 0.2948 M 0.80616 2.505 0.80722 D 1 D;D;D;D;D 0.89917 0.981;0.987;0.989;1.0;1.0 P;P;P;D;D 0.79784 0.59;0.767;0.819;0.988;0.993 T 0.72268 -0.4343 10 0.87932 D 0 . 18.8349 0.92157 0.0:0.0:1.0:0.0 . 496;496;496;496;496 B7ZLX4;F8W7J9;E9PDX1;E9PCK6;Q9ULJ8 .;.;.;.;NEB1_HUMAN H 496 ENSP00000405514:R496H;ENSP00000344524:R496H;ENSP00000411342:R496H;ENSP00000398870:R496H;ENSP00000289495:R496H;ENSP00000402893:R496H ENSP00000289495:R496H R + 2 0 PPP1R9A 94578598 1.000000 0.71417 1.000000 0.80357 0.083000 0.17756 9.587000 0.98229 2.755000 0.94549 0.650000 0.86243 CGT TCGA-IB-7647-01A-11D-2154-08 PPP1R9A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000340662.1 1 0 0 16 294 0 45 0 2.771978e-02 0 5 0 45 2 0 0 0 0 0 2 1 0.999936 16 292 0 45 2 -17.873090 1 1 121402 1 31 1 1 2 3 2.022996 0 0.240000 1.920000 0.241820 0.430000 0.260000 0.710000 0.420000 0.455942 0.430000 0 0.340000 0.560000 ADCY8 114 broad.mit.edu 37 8 132051844 132051844 + Missense_Mutation SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr8:132051844C>T ENST00000286355.5 - 1 2828 c.736G>A c.(736-738)Ggc>Agc p.G246S ADCY8_ENST00000377928.3_Missense_Mutation_p.G246S NM_001115.2 NP_001106.1 P40145 ADCY8_HUMAN adenylate cyclase 8 (brain) 134 Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155) BRCA - Breast invasive adenocarcinoma(115;0.000538) GTGACCACGCCGCTGTACTGC 0.637000 HNSCC(32;0.087) 0 SO:0001583 missense ENST00000286355.5 1 1 hg19 CCDS6363.1 . . . . . . . . . . C 16.19 3.052698 0.55218 . . ENSG00000155897 ENST00000286355;ENST00000377928 T;T 0.39406 1.08;1.08 5.46 5.46 0.80206 . 0.131197 0.52532 D 0.000067 T 0.29652 0.0740 N 0.21545 0.675 0.41736 D 0.989582 B;B 0.19817 0.011;0.039 B;B 0.12156 0.004;0.007 T 0.12451 -1.0547 10 0.08179 T 0.78 . 18.2863 0.90115 0.0:1.0:0.0:0.0 . 246;246 E7EVL1;P40145 .;ADCY8_HUMAN S 246 ENSP00000286355:G246S;ENSP00000367161:G246S ENSP00000286355:G246S G - 1 0 ADCY8 132121026 1.000000 0.71417 0.889000 0.34880 0.907000 0.53573 5.747000 0.68689 2.580000 0.87095 0.455000 0.32223 GGC TCGA-IB-7647-01A-11D-2154-08 ADCY8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000380080.1 1 0 0 13 216 0 36 0 0 0 0 36 2 0 0 0 0 0 2 1 0.999553 13 214 0 35 2 -16.078160 1 1 0 0 1 1 4 5 2.610665 1 0.240000 1.920000 0.404948 0.660000 0.350000 1.000000 1.000000 0.699734 0.660000 0 0.480000 1.000000 TSTA3 7264 broad.mit.edu 37 8 144698284 144698284 + Missense_Mutation SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr8:144698284C>T ENST00000425753.2 - 3 356 c.253G>A c.(253-255)Gac>Aac p.D85N TSTA3_ENST00000529064.1_Missense_Mutation_p.D85N NM_003313.3 NP_003304.1 Q13630 FCL_HUMAN tissue specific transplantation antigen P35B 9 all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;1.17e-38)|Epithelial(56;7.17e-37)|all cancers(56;2.46e-32)|Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239) ACCCAGAAGTCCAAATTGTAT 0.562000 0 SO:0001583 missense ENST00000425753.2 1 1 hg19 CCDS6408.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 35|35 5.477638|5.477638 0.96291|0.96291 .|. .|. ENSG00000104522|ENSG00000104522 ENST00000529064;ENST00000425753;ENST00000529048;ENST00000533817;ENST00000526290|ENST00000527006 D;D;D;D;D|. 0.94138|. -3.36;-3.36;-3.36;-3.36;-3.36|. 4.75|4.75 4.75|4.75 0.60458|0.60458 NAD-dependent epimerase/dehydratase (1);NAD(P)-binding domain (1);|. 0.266244|. 0.39759|. N|. 0.001266|. D|. 0.85173|. 0.5636|. M|M 0.93283|0.93283 3.4|3.4 0.80722|0.80722 D|D 1|1 D;D|. 0.56035|. 0.974;0.958|. P;P|. 0.62382|. 0.901;0.77|. D|. 0.89272|. 0.3605|. 10|. 0.87932|. D|. 0|. -33.5833|-33.5833 14.467|14.467 0.67490|0.67490 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. 85;85|. B4DZW9;Q13630|. .;FCL_HUMAN|. N|X 85|117 ENSP00000435386:D85N;ENSP00000398803:D85N;ENSP00000431587:D85N;ENSP00000437012:D85N;ENSP00000433331:D85N|. ENSP00000398803:D85N|. D|W -|- 1|3 0|0 TSTA3|TSTA3 144769427|144769427 1.000000|1.000000 0.71417|0.71417 0.998000|0.998000 0.56505|0.56505 0.997000|0.997000 0.91878|0.91878 5.485000|5.485000 0.66850|0.66850 2.158000|2.158000 0.67659|0.67659 0.655000|0.655000 0.94253|0.94253 GAC|TGG TCGA-IB-7647-01A-11D-2154-08 TSTA3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000382263.1 1 0 1 90 494 0 90 1 1 467 909 0 90 2 0 0 0 0 0 2 1 1.000000 88 488 0 90 2 -20.000000 1 1 0 0 1 1 4 5 2.610665 1 0.240000 1.920000 0.404948 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 LRRCC1 85444 broad.mit.edu 37 8 86027446 86027446 + Missense_Mutation SNP G G A TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr8:86027446G>A ENST00000360375.3 + 5 805 c.656G>A c.(655-657)tGc>tAc p.C219Y LRRCC1_ENST00000414626.2_Missense_Mutation_p.C199Y NM_033402.4 NP_208325.3 Q9C099 LRCC1_HUMAN leucine rich repeat and coiled-coil centrosomal protein 1 43 CAGCTGCAGTGCCTAGAAGGT 0.323000 0 SO:0001583 missense ENST00000360375.3 1 1 hg19 CCDS43750.1 . . . . . . . . . . G 11.80 1.747158 0.30955 . . ENSG00000133739 ENST00000426019;ENST00000360375;ENST00000414626 T;T 0.32272 1.46;1.47 5.52 4.63 0.57726 . 0.000000 0.42420 D 0.000701 T 0.31575 0.0801 L 0.59436 1.845 0.38194 D 0.940008 B;B;B 0.18610 0.016;0.029;0.005 B;B;B 0.25614 0.062;0.037;0.014 T 0.18023 -1.0350 10 0.42905 T 0.14 -1.709 12.0541 0.53524 0.0795:0.0:0.9205:0.0 . 199;126;219 Q9C099-2;E9PE41;Q9C099 .;.;LRCC1_HUMAN Y 126;219;199 ENSP00000353538:C219Y;ENSP00000394695:C199Y ENSP00000353538:C219Y C + 2 0 LRRCC1 86214698 1.000000 0.71417 0.998000 0.56505 0.666000 0.39218 6.269000 0.72558 2.585000 0.87301 0.460000 0.39030 TGC TCGA-IB-7647-01A-11D-2154-08 LRRCC1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000380267.1 1 0 1 82 579 0 75 1 9.846473e-01 11 37 0 75 2 0 0 0 0 0 2 1 1.000000 82 577 0 74 2 -20.000000 1 1 0 0 1 1 2 3 2.244964 1 0.240000 1.920000 0.316301 0.990000 0.920000 1.000000 1.000000 0.995710 0.990000 1 0.990000 1.000000 FPGS 2356 broad.mit.edu 37 9 130575756 130575756 + Missense_Mutation SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr9:130575756C>T ENST00000373247.2 + 15 1687 c.1637C>T c.(1636-1638)aCc>aTc p.T546I FPGS_ENST00000373245.1_3'UTR|FPGS_ENST00000460181.1_3'UTR|FPGS_ENST00000393706.2_Missense_Mutation_p.T520I|RP11-228B15.4_ENST00000439298.1_RNA|FPGS_ENST00000373225.3_Missense_Mutation_p.T496I NM_004957.4 NP_004948.4 Q05932 FOLC_HUMAN folylpolyglutamate synthase 7 Methotrexate(DB00563)|Pralatrexate(DB06813)|Raltitrexed(DB00293) GGCCTCCTCACCCACCCTGTG 0.607000 0 SO:0001583 missense ENST00000373247.2 1 1 hg19 CCDS35148.1 . . . . . . . . . . C 5.750 0.322762 0.10900 . . ENSG00000136877 ENST00000373247;ENST00000393706;ENST00000373225 T;T;T 0.14144 2.94;2.94;2.53 5.16 3.12 0.35913 . 0.920751 0.09423 N 0.804181 T 0.09598 0.0236 N 0.14661 0.345 0.80722 D 1 B;B 0.22003 0.063;0.063 B;B 0.20577 0.03;0.03 T 0.13764 -1.0497 10 0.33940 T 0.23 -4.02 11.7357 0.51763 0.4523:0.5477:0.0:0.0 . 520;546 Q05932-4;Q05932 .;FOLC_HUMAN I 546;520;496 ENSP00000362344:T546I;ENSP00000377309:T520I;ENSP00000362322:T496I ENSP00000362322:T496I T + 2 0 FPGS 129615577 0.211000 0.23529 0.692000 0.30179 0.023000 0.10783 0.343000 0.19944 1.103000 0.41568 0.650000 0.86243 ACC TCGA-IB-7647-01A-11D-2154-08 FPGS-011 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054251.1 1 0 1 61 540 0 181 1 1 71 161 0 181 2 0 0 0 0 0 2 1 1.000000 61 533 0 178 2 -20.000000 1 1 0 0 1 1 2 3 2.053842 0 0.240000 1.920000 0.248120 0.860000 0.660000 1.000000 1.000000 0.866966 0.860000 1 0.750000 1.000000 DDX31 64794 broad.mit.edu 37 9 135537950 135537950 + Missense_Mutation SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr9:135537950C>T ENST00000372159.3 - 2 674 c.523G>A c.(523-525)Gca>Aca p.A175T DDX31_ENST00000480876.1_5'UTR|DDX31_ENST00000438527.3_Missense_Mutation_p.A46T|DDX31_ENST00000544003.1_Missense_Mutation_p.A79T|DDX31_ENST00000372153.1_Missense_Mutation_p.A175T|DDX31_ENST00000310532.2_Missense_Mutation_p.A175T NM_022779.7 NP_073616.6 Q9H8H2 DDX31_HUMAN DEAD (Asp-Glu-Ala-Asp) box polypeptide 31 27 ATTTTTTGTGCGTTCCCCTTA 0.428000 0 SO:0001583 missense ENST00000372159.3 1 1 hg19 CCDS6951.1 . . . . . . . . . . c 3.149 -0.174630 0.06421 0.0 1.16E-4 ENSG00000125485 ENST00000372159;ENST00000372155;ENST00000372153;ENST00000438527;ENST00000310532;ENST00000544003 T;T;T;T;T 0.47869 4.37;3.92;4.34;3.5;0.83 5.6 -7.73 0.01245 . 1.174590 0.05861 N 0.622977 T 0.15998 0.0385 N 0.08118 0 0.09310 N 1 B;B;B 0.23891 0.093;0.003;0.002 B;B;B 0.14578 0.011;0.003;0.0 T 0.18871 -1.0323 10 0.09843 T 0.71 0.329 0.3822 0.00396 0.2246:0.2316:0.2547:0.2891 . 175;175;175 Q9H8H2-2;Q9H8H2-3;Q9H8H2 .;.;DDX31_HUMAN T 175;175;175;46;175;79 ENSP00000361232:A175T;ENSP00000361226:A175T;ENSP00000387730:A46T;ENSP00000310539:A175T;ENSP00000442425:A79T ENSP00000310539:A175T A - 1 0 DDX31 134527771 0.000000 0.05858 0.000000 0.03702 0.024000 0.10985 -0.965000 0.03829 -0.997000 0.03450 -0.285000 0.09966 GCA TCGA-IB-7647-01A-11D-2154-08 DDX31-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000054794.1 1 0 1 85 660 0 95 1 9.686397e-01 8 37 0 95 2 0 0 0 0 0 2 1 1.000000 85 650 0 94 2 -20.000000 1 1 121412 3 39 1 1 2 3 2.049767 0 0.240000 1.920000 0.247227 0.960000 0.770000 1.000000 1.000000 0.944172 0.960000 1 0.860000 1.000000 ADAMTSL1 92949 broad.mit.edu 37 9 18777015 18777015 + Missense_Mutation SNP G G A TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chr9:18777015G>A ENST00000380548.4 + 19 3127 c.2788G>A c.(2788-2790)Ggc>Agc p.G930S NM_001040272.5 NP_001035362.3 Q8N6G6 ATL1_HUMAN ADAMTS-like 1 42 GGCCCCCTTCGGCTATCTCAA 0.667000 0 SO:0001583 missense ENST00000380548.4 1 1 hg19 CCDS47954.1 . . . . . . . . . . g 17.01 3.279858 0.59758 . . ENSG00000178031 ENST00000380548 T 0.73469 -0.75 5.53 4.64 0.57946 Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 1.719030 0.08080 U 1.000000 D 0.85630 0.5741 M 0.73319 2.225 0.80722 D 1 D 0.89917 1.0 D 0.64877 0.93 T 0.79303 -0.1859 10 0.62326 D 0.03 . 14.6057 0.68478 0.0701:0.0:0.9299:0.0 . 930 Q8N6G6 ATL1_HUMAN S 930 ENSP00000369921:G930S ENSP00000369921:G930S G + 1 0 ADAMTSL1 18767015 1.000000 0.71417 0.881000 0.34555 0.031000 0.12232 9.551000 0.98112 1.350000 0.45770 -0.355000 0.07637 GGC TCGA-IB-7647-01A-11D-2154-08 ADAMTSL1-012 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000401206.1 1 0 1 43 276 0 89 0 9.429832e-02 0 4 0 89 2 0 0 0 0 0 2 1 1.000000 42 271 0 89 2 -2.775340 1 1 120966 6 37 1 0 1 1 1.797798 1 0.240000 1.920000 0.136364 0.890000 0.700000 1.000000 0.970000 0.889925 0.890000 1 0.800000 0.970000 GPR112 139378 broad.mit.edu 37 X 135432097 135432097 + Missense_Mutation SNP G G C TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chrX:135432097G>C ENST00000394143.1 + 6 6523 c.6232G>C c.(6232-6234)Ggt>Cgt p.G2078R GPR112_ENST00000412101.1_Missense_Mutation_p.G1873R|GPR112_ENST00000370652.1_Missense_Mutation_p.G2078R|GPR112_ENST00000394141.1_Missense_Mutation_p.G1873R|GPR112_ENST00000287534.4_Missense_Mutation_p.G2015R NM_153834.3 NP_722576.3 Q8IZF6 GP112_HUMAN G protein-coupled receptor 112 199 Acute lymphoblastic leukemia(192;0.000127) ACCTACACTGGGTGGTATCAC 0.468000 0 SO:0001583 missense ENST00000394143.1 1 1 hg19 CCDS35409.1 . . . . . . . . . . g 13.55 2.270870 0.40194 . . ENSG00000156920 ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141 T;T;T;T;T 0.30981 1.55;1.55;1.51;1.54;1.51 4.04 2.04 0.26737 . . . . . T 0.32346 0.0826 L 0.29908 0.895 0.09310 N 1 D;P;D 0.64830 0.982;0.926;0.994 P;P;P 0.59221 0.763;0.45;0.854 T 0.09907 -1.0653 9 0.59425 D 0.04 . 3.828 0.08863 0.1358:0.0:0.6268:0.2374 . 2015;1873;2078 Q8IZF6-2;Q8IZF6-3;Q8IZF6 .;.;GP112_HUMAN R 2078;2078;1873;2015;1873 ENSP00000377699:G2078R;ENSP00000359686:G2078R;ENSP00000416526:G1873R;ENSP00000287534:G2015R;ENSP00000377697:G1873R ENSP00000287534:G2015R G + 1 0 GPR112 135259763 0.000000 0.05858 0.001000 0.08648 0.135000 0.20990 -0.243000 0.08915 0.646000 0.30693 0.509000 0.49947 GGT TCGA-IB-7647-01A-11D-2154-08 GPR112-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000286639.1 1 0 0 26 396 0 60 0 0 0 0 60 2 0 0 0 0 0 2 1 1.000000 26 388 0 59 2 -2.598543 1 1 0 0 1 0 1 1 0.240000 1.920000 0.240000 0.250000 0.170000 0.360000 0.250000 0.263339 0.250000 0 0.200000 0.310000 MAGEB16 139604 broad.mit.edu 37 X 35820358 35820358 + Silent SNP C C T TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chrX:35820358C>T ENST00000399989.1 + 2 324 c.45C>T c.(43-45)caC>caT p.H15H MAGEB16_ENST00000399988.1_Silent_p.H15H|MAGEB16_ENST00000399985.1_Silent_p.H15H|MAGEB16_ENST00000399987.1_Silent_p.H15H|MAGEB16_ENST00000399992.1_Silent_p.H47H NM_001099921.1 NP_001093391.1 A2A368 MAGBG_HUMAN melanoma antigen family B, 16 31 ATGATCAGCACCTTCAGACCT 0.572000 0 SO:0001819 synonymous_variant ENST00000399989.1 1 1 hg19 CCDS43927.1 TCGA-IB-7647-01A-11D-2154-08 MAGEB16-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251034.1 1 0 1 23 116 0 24 0 0 0 0 24 2 0 0 0 0 0 2 1 1.000000 22 116 0 23 2 -20.000000 1 1 0 0 1 0 1 1 0.240000 1.920000 0.240000 0.670000 0.450000 0.920000 0.670000 0.688523 0.670000 0 0.550000 0.810000 CXorf22 170063 broad.mit.edu 37 X 35974224 35974224 + Missense_Mutation SNP G G A TCGA-IB-7647-01A-11D-2154-08 TCGA-IB-7647-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx d2579415-7e40-48ba-a59c-e5543b8097dc fae3bedd-75e3-4f2a-86fa-c7e2c4dd4880 g.chrX:35974224G>A ENST00000297866.5 + 8 1387 c.1321G>A c.(1321-1323)Gaa>Aaa p.E441K NM_152632.3 NP_689845.2 Q6ZTR5 CX022_HUMAN chromosome X open reading frame 22 p.E441K(2) 44 AAATCAATGCGAATTACTTCC 0.358000 2 Substitution - Missense(2) SO:0001583 missense ENST00000297866.5 1 1 hg19 CCDS14237.2 . . . . . . . . . . G 0.006 -2.057199 0.00390 . . ENSG00000165164 ENST00000297866 T 0.53640 0.61 5.2 -5.28 0.02755 . 1.251890 0.05007 N 0.470268 T 0.16257 0.0391 N 0.03324 -0.35 0.09310 N 1 B 0.13594 0.008 B 0.06405 0.002 T 0.21999 -1.0229 10 0.05959 T 0.93 -31.1423 3.3027 0.06989 0.2448:0.3051:0.3491:0.101 . 441 Q6ZTR5 CX022_HUMAN K 441 ENSP00000297866:E441K ENSP00000297866:E441K E + 1 0 CXorf22 35884145 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 -0.269000 0.08596 -0.677000 0.05231 -1.184000 0.01707 GAA TCGA-IB-7647-01A-11D-2154-08 CXorf22-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056216.2 1 0 0 21 227 0 47 0 0 0 0 47 2 0 0 0 0 0 2 1 0.999998 21 226 0 47 2 -8.067526 1 1 121408 4 33 1 0 1 1 0.240000 1.920000 0.240000 0.350000 0.220000 0.510000 0.350000 0.362001 0.350000 0 0.280000 0.430000