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 DNMBP 23268 broad.mit.edu 37 10 101716827 101716827 + Missense_Mutation SNP G G T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr10:101716827G>T ENST00000324109.4 - 4 495 c.404C>A c.(403-405)tCc>tAc p.S135Y DNMBP-AS1_ENST00000434409.1_RNA|DNMBP_ENST00000342239.3_Missense_Mutation_p.S135Y NM_015221.2 NP_056036.1 Q6XZF7 DNMBP_HUMAN dynamin binding protein 61 Colorectal(252;0.234) GGCGCTCTGGGAGTGCCACTG 0.617000 0 SO:0001583 missense ENST00000324109.4 1 1 hg19 CCDS7485.1 . . . . . . . . . . G 19.22 3.785820 0.70337 . . ENSG00000107554 ENST00000342239;ENST00000324109 T;T 0.13778 2.61;2.56 5.47 5.47 0.80525 Src homology-3 domain (2); 0.160351 0.29791 N 0.011192 T 0.14141 0.0342 N 0.19112 0.55 0.80722 D 1 P 0.49559 0.925 P 0.47206 0.541 T 0.01212 -1.1417 10 0.66056 D 0.02 -8.7178 15.2145 0.73254 0.0:0.1401:0.8598:0.0 . 135 Q6XZF7 DNMBP_HUMAN Y 135 ENSP00000344914:S135Y;ENSP00000315659:S135Y ENSP00000315659:S135Y S - 2 0 DNMBP 101706817 1.000000 0.71417 0.995000 0.50966 0.977000 0.68977 4.044000 0.57361 2.724000 0.93272 0.561000 0.74099 TCC TCGA-IB-7890-01A-12D-2201-08 DNMBP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049832.2 1 0 1 20 159 0 54 1 4.104331e-01 4 8 0 54 2 0 0 0 0 0 2 1 0.999995 18 155 0 53 2 0 0 0 0 54 2 -20.000000 1 1 0 0 1 1 3 4 2.127873 1 0.360000 2.800000 0.468968 0.820000 0.490000 1.000000 1.000000 0.820667 0.820000 0 0.630000 1.000000 ANKRD30A 91074 broad.mit.edu 37 10 37430910 37430910 + Missense_Mutation SNP C C T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr10:37430910C>T ENST00000602533.1 + 7 1016 c.917C>T c.(916-918)aCg>aTg p.T306M ANKRD30A_ENST00000374660.1_Missense_Mutation_p.T306M|ANKRD30A_ENST00000361713.1_Missense_Mutation_p.T306M Q9BXX3 AN30A_HUMAN ankyrin repeat domain 30A 158 AGGGAAATTACGAGTCCTGCA 0.433000 0 SO:0001583 missense ENST00000602533.1 1 0 hg19 . . . . . . . . . . . 14.40 2.523711 0.44866 . . ENSG00000148513 ENST00000361713;ENST00000374660 T;T 0.05382 3.45;3.45 0.5 0.5 0.16919 . . . . . T 0.02571 0.0078 N 0.03608 -0.345 0.09310 N 1 B 0.25351 0.124 B 0.10450 0.005 T 0.45366 -0.9266 8 0.33940 T 0.23 . . . . . 362 Q9BXX3 AN30A_HUMAN M 306 ENSP00000354432:T306M;ENSP00000363792:T306M ENSP00000354432:T306M T + 2 0 ANKRD30A 37470916 0.012000 0.17670 0.007000 0.13788 0.009000 0.06853 -0.326000 0.07965 0.525000 0.28522 0.134000 0.15878 ACG TCGA-IB-7890-01A-12D-2201-08 ANKRD30A-001 KNOWN NMD_exception|basic|appris_principal protein_coding protein_coding OTTHUMT00000047588.2 1 0 1 67 291 2 105 0 0 0 2 105 2 0 0 0 0 0 2 1 1.000000 62 289 0 104 2 0 0 0 2 105 2 -2.144294 0 1 0 0 1 0 2 2 1.780639 1 0.360000 2.800000 0.360000 0.990000 0.820000 1.000000 1.000000 0.973685 0.990000 1 0.920000 1.000000 C10orf62 414157 broad.mit.edu 37 10 99350210 99350210 + Silent SNP C C A rs145450971 byFrequency TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr10:99350210C>A ENST00000370640.3 + 1 761 c.556C>A c.(556-558)Cgg>Agg p.R186R HOGA1_ENST00000370647.4_Intron|PI4K2A_ENST00000370649.3_Intron|PI4K2A_ENST00000555577.1_Intron|HOGA1_ENST00000370646.4_Intron NM_001009997.2 NP_001009997.2 Q5T681 CJ062_HUMAN chromosome 10 open reading frame 62 4 Colorectal(252;0.162) CCTCACCCAGCGGGAAAACAC 0.567000 0 SO:0001819 synonymous_variant ENST00000370640.3 1 1 hg19 CCDS31261.1 TCGA-IB-7890-01A-12D-2201-08 C10orf62-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049723.1 1 0 1 85 529 1 148 0 0 0 1 148 2 0 0 0 0 0 2 1 1.000000 84 520 1 147 15 0 0 0 1 148 2 -7.194516 1 1 121412 82 53 1 1 3 4 2.127873 1 0.360000 2.800000 0.468968 0.960000 0.760000 1.000000 1.000000 0.938489 0.960000 1 0.850000 1.000000 SIK3 23387 broad.mit.edu 37 11 116729339 116729339 + Missense_Mutation SNP G G A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr11:116729339G>A ENST00000292055.4 - 20 2559 c.2524C>T c.(2524-2526)Cgg>Tgg p.R842W SIK3_ENST00000375288.1_Intron|SIK3_ENST00000375300.1_Missense_Mutation_p.R900W|SIK3_ENST00000542607.1_Intron|SIK3_ENST00000446921.2_Intron|SIK3_ENST00000434315.2_Intron|AP006216.12_ENST00000444200.1_RNA|SIK3_ENST00000488337.1_Intron NM_025164.3 NP_079440.3 Q9Y2K2 SIK3_HUMAN SIK family kinase 3 57 GGGGAACCCCGGGACTGGTCC 0.567000 0 SO:0001583 missense ENST00000292055.4 1 1 hg19 CCDS8379.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 22.1|22.1 4.240336|4.240336 0.79912|0.79912 .|. .|. ENSG00000160584|ENSG00000160584 ENST00000445177|ENST00000375300;ENST00000292055 .|T;T .|0.73363 .|-0.7;-0.74 5.67|5.67 5.67|5.67 0.87782|0.87782 .|. .|0.000000 .|0.38217 .|U .|0.001766 T|T 0.71492|0.71492 0.3346|0.3346 L|L 0.29908|0.29908 0.895|0.895 0.80722|0.80722 D|D 1|1 .|D;D .|0.64830 .|0.994;0.99 .|P;B .|0.50049 .|0.629;0.306 T|T 0.75379|0.75379 -0.3338|-0.3338 5|10 .|0.87932 .|D .|0 .|. 14.5942|14.5942 0.68392|0.68392 0.0:0.0:0.8541:0.1459|0.0:0.0:0.8541:0.1459 .|. .|842;842 .|Q9Y2K2-3;Q9Y2K2 .|.;SIK3_HUMAN L|W 941|900;842 .|ENSP00000364449:R900W;ENSP00000292055:R842W .|ENSP00000292055:R842W P|R -|- 2|1 0|2 SIK3|SIK3 116234549|116234549 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.999000|0.999000 0.98932|0.98932 6.705000|6.705000 0.74644|0.74644 2.654000|2.654000 0.90174|0.90174 0.655000|0.655000 0.94253|0.94253 CCG|CGG TCGA-IB-7890-01A-12D-2201-08 SIK3-201 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding 1 0 1 100 606 0 168 1 7.160760e-01 5 12 0 168 2 0 0 0 0 0 2 1 1.000000 98 588 0 166 2 0 0 0 0 168 2 -2.744776 1 1 121400 1 33 1 0 3 3 2.101542 1 0.360000 2.800000 0.457627 0.920000 0.760000 1.000000 1.000000 0.922059 0.920000 1 0.840000 1.000000 ESAM 90952 broad.mit.edu 37 11 124623837 124623837 + Missense_Mutation SNP C C T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr11:124623837C>T ENST00000278927.5 - 7 1007 c.878G>A c.(877-879)cGg>cAg p.R293Q ESAM_ENST00000442070.2_Intron|VSIG2_ENST00000403470.1_5'Flank|VSIG2_ENST00000326621.5_5'Flank NM_138961.2 NP_620411.2 Q96AP7 ESAM_HUMAN endothelial cell adhesion molecule 16 all_hematologic(175;0.215) Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) GGGCAGGGTCCGGGGAGCAAT 0.567000 0 SO:0001583 missense ENST00000278927.5 1 1 hg19 CCDS8453.1 . . . . . . . . . . C 21.0 4.074636 0.76415 . . ENSG00000149564 ENST00000278927 T 0.31510 1.49 5.28 3.37 0.38596 . 0.354761 0.28730 N 0.014326 T 0.36936 0.0985 L 0.47716 1.5 0.80722 D 1 D 0.76494 0.999 P 0.59115 0.852 T 0.08330 -1.0727 10 0.21014 T 0.42 . 7.9712 0.30127 0.0:0.6063:0.3104:0.0832 . 293 Q96AP7 ESAM_HUMAN Q 293 ENSP00000278927:R293Q ENSP00000278927:R293Q R - 2 0 ESAM 124129047 1.000000 0.71417 0.998000 0.56505 0.851000 0.48451 1.757000 0.38400 0.683000 0.31428 -0.176000 0.13171 CGG TCGA-IB-7890-01A-12D-2201-08 ESAM-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000324686.1 1 0 1 39 105 0 40 1 1 7 157 0 40 2 0 0 0 0 0 2 1 1.000000 37 102 0 40 2 0 0 0 0 40 2 -4.781374 1 1 121408 3 34 1 0 3 3 2.101542 1 0.360000 2.800000 0.457627 0.990000 0.990000 1.000000 1.000000 0.999995 0.990000 1 0.990000 1.000000 OR52K2 119774 broad.mit.edu 37 11 4471098 4471098 + Missense_Mutation SNP G G A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr11:4471098G>A ENST00000325719.4 + 1 574 c.529G>A c.(529-531)Gct>Act p.A177T NM_001005172.2 NP_001005172.2 Q8NGK3 O52K2_HUMAN olfactory receptor, family 52, subfamily K, member 2 25 Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577) CCCAGTGATCGCTCACTGCTA 0.547000 0 SO:0001583 missense ENST00000325719.4 1 1 hg19 CCDS31351.1 . . . . . . . . . . G 15.42 2.828372 0.50845 . . ENSG00000181963 ENST00000325719 T 0.00107 8.72 4.0 3.05 0.35203 GPCR, rhodopsin-like superfamily (1); 0.154049 0.30085 N 0.010452 T 0.00178 0.0005 L 0.41415 1.275 0.09310 N 1 D 0.53151 0.958 P 0.52343 0.696 T 0.50250 -0.8850 10 0.72032 D 0.01 . 5.1676 0.15094 0.1064:0.0:0.5869:0.3067 . 177 Q8NGK3 O52K2_HUMAN T 177 ENSP00000318956:A177T ENSP00000318956:A177T A + 1 0 OR52K2 4427674 0.000000 0.05858 0.994000 0.49952 0.921000 0.55340 -0.481000 0.06552 2.054000 0.61138 0.485000 0.47835 GCT TCGA-IB-7890-01A-12D-2201-08 OR52K2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000385844.1 0 0 1 101 528 1 149 0 0 0 1 149 2 0 0 0 0 0 2 1 1.000000 101 518 1 147 15 0 0 0 1 149 2 -20.000000 1 1 0 0 1 1 2 3 2.073852 1 0.360000 2.800000 0.457627 0.990000 0.860000 1.000000 1.000000 0.984129 0.990000 1 0.950000 1.000000 RTN3 10313 broad.mit.edu 37 11 63472339 63472339 + Silent SNP C C T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr11:63472339C>T ENST00000377819.5 + 2 313 c.159C>T c.(157-159)tcC>tcT p.S53S RTN3_ENST00000354497.4_Intron|RTN3_ENST00000538995.1_Intron|RTN3_ENST00000540798.1_Intron|RTN3_ENST00000537981.1_Intron|RTN3_ENST00000356000.3_Silent_p.S53S|RTN3_ENST00000339997.4_Intron|RTN3_ENST00000341307.2_Intron NM_001265589.1 NP_001252518.1 O95197 RTN3_HUMAN reticulon 3 20 TTGTTTCTTCCTCTTCCTCTC 0.363000 0 SO:0001819 synonymous_variant ENST00000377819.5 1 1 hg19 CCDS58141.1 TCGA-IB-7890-01A-12D-2201-08 RTN3-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000397846.1 1 0 1 127 385 0 92 0 6.237770e-02 0 2 0 92 2 0 0 0 0 0 2 1 1.000000 114 361 0 87 2 0 0 0 0 92 2 -20.000000 1 1 120790 1 30 1 1 2 3 2.073852 1 0.360000 2.800000 0.457627 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 TMEM151A 256472 broad.mit.edu 37 11 66062807 66062807 + Missense_Mutation SNP G G A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr11:66062807G>A ENST00000327259.4 + 2 1234 c.1090G>A c.(1090-1092)Gtg>Atg p.V364M NM_153266.3 NP_694998.1 Q8N4L1 T151A_HUMAN transmembrane protein 151A 11 CTCGGAGGCCGTGGTCATGGG 0.731000 0 SO:0001583 missense ENST00000327259.4 0 1 hg19 CCDS8133.1 . . . . . . . . . . G 7.944 0.743434 0.15642 . . ENSG00000179292 ENST00000327259 . . . 4.14 2.04 0.26737 . 0.189097 0.36167 N 0.002755 T 0.14570 0.0352 N 0.10916 0.065 0.29651 N 0.843971 B 0.21905 0.062 B 0.14023 0.01 T 0.12553 -1.0543 9 0.17369 T 0.5 . 4.6644 0.12659 0.1644:0.0:0.6246:0.211 . 364 Q8N4L1 T151A_HUMAN M 364 . ENSP00000326244:V364M V + 1 0 TMEM151A 65819383 0.997000 0.39634 0.962000 0.40283 0.992000 0.81027 2.403000 0.44530 0.944000 0.37579 0.462000 0.41574 GTG TCGA-IB-7890-01A-12D-2201-08 TMEM151A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391897.1 0 0 0 4 32 0 10 0 0 0 0 10 2 0 0 0 0 0 2 1 0.887472 4 31 0 10 2 0 0 0 0 10 2 -9.808765 1 1 0 0 1 1 2 3 2.073852 1 0.360000 2.800000 0.457627 0.780000 0.280000 1.000000 1.000000 0.759273 0.780000 0 0.490000 1.000000 EED 8726 broad.mit.edu 37 11 85967469 85967469 + Missense_Mutation SNP G G C TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr11:85967469G>C ENST00000263360.6 + 5 1153 c.467G>C c.(466-468)aGc>aCc p.S156T EED_ENST00000528180.1_Missense_Mutation_p.S156T|EED_ENST00000327320.4_Missense_Mutation_p.S156T|EED_ENST00000351625.6_Missense_Mutation_p.S156T NM_003797.3 NP_003788.2 O75530 EED_HUMAN embryonic ectoderm development 21 Acute lymphoblastic leukemia(157;7.24e-07)|all_hematologic(158;0.00092) ACCTATGATAGCAATACGAGC 0.353000 0 SO:0001583 missense ENST00000263360.6 1 1 hg19 CCDS8273.1 . . . . . . . . . . G 11.25 1.582457 0.28180 . . ENSG00000074266 ENST00000263360;ENST00000528180;ENST00000351625;ENST00000327320 T;T;T;T 0.31247 1.5;1.5;1.5;1.5 5.59 5.59 0.84812 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1); 0.087878 0.85682 D 0.000000 T 0.15825 0.0381 N 0.02802 -0.49 0.80722 D 1 B;B;B;B 0.02656 0.0;0.0;0.0;0.0 B;B;B;B 0.04013 0.0;0.0;0.001;0.0 T 0.15235 -1.0444 9 . . . -11.6578 19.5799 0.95461 0.0:0.0:1.0:0.0 . 156;156;156;156 O75530-3;E9PJK2;O75530-2;O75530 .;.;.;EED_HUMAN T 156 ENSP00000263360:S156T;ENSP00000431778:S156T;ENSP00000338186:S156T;ENSP00000315587:S156T . S + 2 0 EED 85645117 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 6.041000 0.70988 2.606000 0.88127 0.585000 0.79938 AGC TCGA-IB-7890-01A-12D-2201-08 EED-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000393733.1 1 0 1 45 288 0 37 1 9.958223e-01 15 41 0 37 2 0 0 0 0 0 2 1 1.000000 43 279 0 37 2 0 0 0 0 37 2 -19.685700 1 1 0 0 1 0 3 3 2.101542 1 0.360000 2.800000 0.457627 0.880000 0.660000 1.000000 1.000000 0.882042 0.880000 1 0.760000 1.000000 GIT2 9815 broad.mit.edu 37 12 110390957 110390957 + Silent SNP G G A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr12:110390957G>A ENST00000355312.3 - 13 1181 c.1182C>T c.(1180-1182)agC>agT p.S394S GIT2_ENST00000551209.1_Silent_p.S393S|TCHP_ENST00000550780.1_Intron|GIT2_ENST00000356259.4_Silent_p.S394S|GIT2_ENST00000338373.5_Silent_p.S394S|GIT2_ENST00000360185.4_Silent_p.S394S|GIT2_ENST00000343646.5_Intron|GIT2_ENST00000354574.4_Silent_p.S396S|GIT2_ENST00000553118.1_Silent_p.S394S|GIT2_ENST00000547815.1_Silent_p.S394S|GIT2_ENST00000320063.9_Silent_p.S394S|GIT2_ENST00000361006.5_Silent_p.S394S|GIT2_ENST00000457474.2_Silent_p.S396S NM_057169.3 NP_476510.1 Q14161 GIT2_HUMAN G protein-coupled receptor kinase interacting ArfGAP 2 27 CTGATGCCACGCTGTCATAGT 0.488000 0 SO:0001819 synonymous_variant ENST00000355312.3 0 1 hg19 CCDS9138.1 TCGA-IB-7890-01A-12D-2201-08 GIT2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000403407.1 0 0 0 8 376 0 74 0 3.460154e-01 0 53 0 74 2 0 0 0 0 0 2 1 0.989317 8 374 0 74 2 0 0 0 0 74 2 -3.105365 1 1 121412 5 38 1 0 3 3 1.882622 1 0.360000 2.800000 0.434329 0.150000 0.060000 1.000000 0.130000 0.307514 0.150000 0 0.090000 1.000000 KRAS 3845 broad.mit.edu 37 12 25380276 25380276 + Missense_Mutation SNP T T C rs121913240 TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 T C T T Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr12:25380276T>C ENST00000256078.4 - 3 245 c.182A>G c.(181-183)cAa>cGa p.Q61R KRAS_ENST00000557334.1_Intron|AC087239.1_ENST00000594112.1_5'Flank|KRAS_ENST00000311936.3_Missense_Mutation_p.Q61R NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.Q61L(73)|p.Q61R(56)|p.Q61P(12) 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) GTACTCCTCTTGACCTGCTGT 0.418000 Q61L(NCIH650_LUNG)|Q61L(SW948_LARGE_INTESTINE)|Q61R(PANC0213_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 141 Substitution - Missense(141) 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 . . . . . . . . . . T 20.6 4.022613 0.75275 . . ENSG00000133703 ENST00000311936;ENST00000256078 D;D 0.83673 -1.75;-1.75 5.77 5.77 0.91146 Small GTP-binding protein domain (1); 0.049057 0.85682 D 0.000000 D 0.88358 0.6415 M 0.92367 3.3 0.80722 D 1 B;B 0.26744 0.158;0.026 B;B 0.32805 0.135;0.153 D 0.87885 0.2680 10 0.66056 D 0.02 . 15.5753 0.76373 0.0:0.0:0.0:1.0 . 61;61 P01116-2;P01116 .;RASK_HUMAN R 61 ENSP00000308495:Q61R;ENSP00000256078:Q61R ENSP00000256078:Q61R Q - 2 0 KRAS 25271543 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 7.983000 0.88140 2.326000 0.78906 0.533000 0.62120 CAA TCGA-IB-7890-01A-12D-2201-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 131 305 0 53 1 1 13 56 0 53 2 1 1 238 705 0 889 2 1 1.000000 130 300 0 53 2 1 1 2290 5741 0 53 2 -20.000000 1 1 0 0 1 3 4 7 2.408262 1 0.360000 2.800000 0.535559 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 PUS7L 83448 broad.mit.edu 37 12 44142334 44142334 + Missense_Mutation SNP G G A rs143739935 byFrequency TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr12:44142334G>A ENST00000416848.2 - 3 1477 c.989C>T c.(988-990)tCg>tTg p.S330L PUS7L_ENST00000553166.1_Missense_Mutation_p.S330L|PUS7L_ENST00000551923.1_Missense_Mutation_p.S330L|PUS7L_ENST00000431332.3_Missense_Mutation_p.S17L|PUS7L_ENST00000344862.5_Missense_Mutation_p.S330L NM_001098615.1|NM_001271826.1 NP_001092085.1|NP_001258755.1 Q9H0K6 PUS7L_HUMAN pseudouridylate synthase 7 homolog (S. cerevisiae)-like 32 all_cancers(12;0.00027) Lung NSC(34;0.114)|all_lung(34;0.24) ACTAAAATCCGAAGGAATAAC 0.348000 0 SO:0001583 missense ENST00000416848.2 1 0 hg19 CCDS8743.1 3 0.0013736263736263737 0 0.0 0 0.0 0 0.0 3 0.00395778364116095 G 25.6 4.658329 0.88154 0.0 0.002326 ENSG00000129317 ENST00000416848;ENST00000344862;ENST00000551923;ENST00000431332;ENST00000550784;ENST00000547156;ENST00000553166 T;T;T;T;T;T;T 0.44083 0.93;0.93;0.93;0.93;0.93;0.93;0.93 4.86 4.86 0.63082 Pseudouridine synthase, catalytic domain (1); 0.135257 0.52532 D 0.000074 T 0.66858 0.2832 M 0.79693 2.465 0.58432 D 0.999999 D 0.89917 1.0 D 0.69142 0.962 T 0.70051 -0.4978 10 0.52906 T 0.07 -1.7808 18.8708 0.92313 0.0:0.0:1.0:0.0 . 330 Q9H0K6 PUS7L_HUMAN L 330;330;330;17;17;17;330 ENSP00000415899:S330L;ENSP00000343081:S330L;ENSP00000447706:S330L;ENSP00000398497:S17L;ENSP00000449222:S17L;ENSP00000450341:S17L;ENSP00000446865:S330L ENSP00000343081:S330L S - 2 0 PUS7L 42428601 1.000000 0.71417 0.980000 0.43619 0.983000 0.72400 7.429000 0.80309 2.612000 0.88384 0.563000 0.77884 TCG TCGA-IB-7890-01A-12D-2201-08 PUS7L-004 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000403931.1 0 0 1 163 281 0 101 0 7.930302e-01 1 6 0 101 2 0 0 0 0 0 2 1 1.000000 162 278 0 101 2 0 0 0 0 101 2 -2.578431 1 1 121406 215 56 1 0 3 3 1.882622 1 0.360000 2.800000 0.434329 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 NTF3 4908 broad.mit.edu 37 12 5603687 5603687 + Missense_Mutation SNP C C T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr12:5603687C>T ENST00000331010.6 + 1 390 c.307C>T c.(307-309)Cgg>Tgg p.R103W NTF3_ENST00000535299.1_Intron|NTF3_ENST00000423158.3_Missense_Mutation_p.R116W NM_002527.4 NP_002518.1 P20783 NTF3_HUMAN neurotrophin 3 22 CAACTCACCGCGGGTCCTGCT 0.642000 GBM(194;1104 2182 8339 9578 18493) 0 SO:0001583 missense ENST00000331010.6 1 1 hg19 CCDS8538.1 . . . . . . . . . . C 17.49 3.403819 0.62288 . . ENSG00000185652 ENST00000423158;ENST00000331010 T;T 0.48201 0.82;0.82 5.52 3.64 0.41730 . 0.000000 0.85682 D 0.000000 T 0.72526 0.3471 M 0.89904 3.07 0.58432 D 0.999992 D;D 0.89917 1.0;1.0 D;D 0.83275 0.996;0.996 T 0.77156 -0.2691 10 0.72032 D 0.01 -12.4294 12.7492 0.57298 0.4323:0.5677:0.0:0.0 . 103;116 P20783;B7Z1T5 NTF3_HUMAN;. W 116;103 ENSP00000397297:R116W;ENSP00000328738:R103W ENSP00000328738:R103W R + 1 2 NTF3 5473948 0.915000 0.31059 1.000000 0.80357 0.992000 0.81027 1.904000 0.39868 0.660000 0.30964 0.591000 0.81541 CGG TCGA-IB-7890-01A-12D-2201-08 NTF3-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000400486.1 1 0 1 56 363 0 102 0 3.987962e-01 0 10 0 102 2 0 0 0 0 0 2 1 1.000000 54 359 0 100 2 0 0 0 0 102 2 -20.000000 1 1 0 0 1 2 6 8 2.212491 1 0.360000 2.800000 0.496063 0.970000 0.730000 1.000000 1.000000 0.938563 0.970000 1 0.840000 1.000000 LPCAT3 10162 broad.mit.edu 37 12 7091020 7091020 + Missense_Mutation SNP C C A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr12:7091020C>A ENST00000261407.4 - 4 497 c.412G>T c.(412-414)Gat>Tat p.D138Y U47924.30_ENST00000606112.1_lincRNA|LPCAT3_ENST00000535021.1_5'Flank NM_005768.5 NP_005759.4 Q6P1A2 MBOA5_HUMAN lysophosphatidylcholine acyltransferase 3 17 CACTTGATATCGTAGTTGCCG 0.473000 0 SO:0001583 missense ENST00000261407.4 0 1 hg19 CCDS8572.1 . . . . . . . . . . C 11.65 1.700633 0.30142 . . ENSG00000111684 ENST00000261407 T 0.73897 -0.79 5.32 5.32 0.75619 . 0.000000 0.85682 D 0.000000 D 0.86900 0.6044 M 0.79258 2.445 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.87121 0.2191 10 0.56958 D 0.05 -20.8345 19.1925 0.93672 0.0:1.0:0.0:0.0 . 138 Q6P1A2 MBOA5_HUMAN Y 138 ENSP00000261407:D138Y ENSP00000261407:D138Y D - 1 0 LPCAT3 6961281 1.000000 0.71417 0.998000 0.56505 0.895000 0.52256 7.320000 0.79064 2.767000 0.95098 0.655000 0.94253 GAT TCGA-IB-7890-01A-12D-2201-08 LPCAT3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000401812.1 0 0 0 10 405 1 68 0 1.882812e-02 4 86 1 68 7 0 0 0 0 0 2 0 0.041894 10 399 1 66 20 0 0 0 1 68 2 -3.304375 1 1 0 0 1 2 6 8 2.212491 1 0.360000 2.800000 0.496063 0.190000 0.080000 1.000000 0.170000 0.331733 0.190000 0 0.130000 1.000000 TMTC4 84899 broad.mit.edu 37 13 101289837 101289837 + Silent SNP G G A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr13:101289837G>A ENST00000376234.3 - 8 1086 c.897C>T c.(895-897)acC>acT p.T299T TMTC4_ENST00000462211.1_5'UTR|TMTC4_ENST00000328767.5_Silent_p.T188T|TMTC4_ENST00000342624.5_Silent_p.T318T NM_001079669.1 NP_001073137.1 Q5T4D3 TMTC4_HUMAN transmembrane and tetratricopeptide repeat containing 4 34 all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184) TGTCCACCTCGGTGAAGGCCG 0.642000 0 SO:0001819 synonymous_variant ENST00000376234.3 1 1 hg19 CCDS41904.1 TCGA-IB-7890-01A-12D-2201-08 TMTC4-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045649.2 1 0 1 167 371 0 137 1 9.584764e-01 2 12 0 137 2 0 0 0 0 0 2 1 1.000000 164 364 0 135 2 0 0 0 0 137 2 -12.041230 1 1 121410 5 39 1 1 2 3 2.045309 1 0.360000 2.800000 0.457627 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 LCP1 3936 broad.mit.edu 37 13 46701838 46701838 + Missense_Mutation SNP C C T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr13:46701838C>T ENST00000398576.2 - 19 2160 c.1772G>A c.(1771-1773)cGa>cAa p.R591Q LCP1_ENST00000435666.2_Missense_Mutation_p.R160Q|LCP1_ENST00000323076.2_Missense_Mutation_p.R591Q P13796 PLSL_HUMAN lymphocyte cytosolic protein 1 (L-plastin) 34 Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262) KIRC - Kidney renal clear cell carcinoma(16;0.234) TCCAATTTTTCGGGCCATAGA 0.488000 T BCL6 NHL Dom yes 13 13q14.1-q14.3 3936 lymphocyte cytosolic protein 1 (L-plastin) L 0 SO:0001583 missense ENST00000398576.2 1 1 hg19 CCDS9403.1 . . . . . . . . . . C 36 5.769574 0.96914 . . ENSG00000136167 ENST00000323076;ENST00000398576;ENST00000435666 D;D;D 0.94650 -3.48;-3.48;-3.48 5.54 5.54 0.83059 Calponin homology domain (5); 0.000000 0.85682 D 0.000000 D 0.97823 0.9285 M 0.90369 3.11 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.83275 0.986;0.996 D 0.98204 1.0469 10 0.66056 D 0.02 -8.2981 18.8301 0.92135 0.0:1.0:0.0:0.0 . 160;591 B4DUA0;P13796 .;PLSL_HUMAN Q 591;591;160 ENSP00000315757:R591Q;ENSP00000381581:R591Q;ENSP00000405134:R160Q ENSP00000315757:R591Q R - 2 0 LCP1 45599839 1.000000 0.71417 0.998000 0.56505 0.999000 0.98932 7.776000 0.85560 2.764000 0.94973 0.655000 0.94253 CGA TCGA-IB-7890-01A-12D-2201-08 LCP1-006 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044800.3 1 0 1 93 610 0 147 0 9.999994e-01 0 132 0 147 2 0 0 0 0 0 2 1 1.000000 93 588 0 147 2 0 0 0 0 147 2 -3.142703 1 1 0 0 1 1 2 3 2.045309 1 0.360000 2.800000 0.457627 0.860000 0.700000 1.000000 1.000000 0.869744 0.860000 1 0.780000 0.950000 SLC8A3 6547 broad.mit.edu 37 14 70634760 70634760 + Missense_Mutation SNP C C T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr14:70634760C>T ENST00000381269.2 - 2 1133 c.380G>A c.(379-381)cGg>cAg p.R127Q SLC8A3_ENST00000356921.2_Missense_Mutation_p.R127Q|SLC8A3_ENST00000528359.1_Missense_Mutation_p.R127Q|SLC8A3_ENST00000357887.3_Missense_Mutation_p.R127Q|SLC8A3_ENST00000534137.1_Missense_Mutation_p.R127Q NM_058240.2|NM_183002.1 NP_489479.1|NP_892114.1 P57103 NAC3_HUMAN solute carrier family 8 (sodium/calcium exchanger), member 3 54 ATTCCAGACCCGAATAGTGGT 0.483000 0 SO:0001583 missense ENST00000381269.2 1 1 hg19 CCDS35498.1 1 4.578754578754579E-4 0 0.0 0 0.0 1 0.0017482517482517483 0 0.0 C 20.9 4.070178 0.76301 . . ENSG00000100678 ENST00000356921;ENST00000381269;ENST00000357887;ENST00000534137;ENST00000528359 T;T;T;T;T 0.63580 -0.05;-0.05;-0.05;-0.05;-0.05 5.48 5.48 0.80851 Sodium/calcium exchanger membrane region (1); 0.000000 0.85682 D 0.000000 D 0.84243 0.5429 M 0.91663 3.23 0.80722 D 1 D;D;D;D 0.76494 0.999;0.999;0.999;0.999 D;D;D;D 0.87578 0.997;0.998;0.993;0.993 D 0.87094 0.2174 10 0.62326 D 0.03 . 19.3613 0.94440 0.0:1.0:0.0:0.0 . 127;127;127;127 P57103-2;P57103;Q96QG2;Q96QG1 .;NAC3_HUMAN;.;. Q 127 ENSP00000349392:R127Q;ENSP00000370669:R127Q;ENSP00000350560:R127Q;ENSP00000436688:R127Q;ENSP00000433531:R127Q ENSP00000349392:R127Q R - 2 0 SLC8A3 69704513 1.000000 0.71417 0.997000 0.53966 0.971000 0.66376 7.811000 0.86092 2.573000 0.86826 0.650000 0.86243 CGG TCGA-IB-7890-01A-12D-2201-08 SLC8A3-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000390736.1 1 0 1 48 297 0 85 0 9.933579e-02 0 4 0 85 2 0 0 0 0 0 2 1 1.000000 46 292 0 85 2 0 0 0 0 85 2 -2.599474 1 1 121412 1 38 1 1 2 3 2.059402 1 0.360000 2.800000 0.457627 0.910000 0.690000 1.000000 1.000000 0.902066 0.910000 1 0.790000 1.000000 SERPINA3 12 broad.mit.edu 37 14 95080911 95080911 + Missense_Mutation SNP G G A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr14:95080911G>A ENST00000467132.1 + 2 1281 c.133G>A c.(133-135)Gtg>Atg p.V45M RP11-986E7.7_ENST00000553947.1_3'UTR|SERPINA3_ENST00000393078.3_Missense_Mutation_p.V45M|SERPINA3_ENST00000393080.4_Missense_Mutation_p.V45M P01011 AACT_HUMAN serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3 p.V45M(1) 40 all_cancers(154;0.0525)|all_epithelial(191;0.179) AGGGACACACGTGGACCTCGG 0.572000 1 Substitution - Missense(1) SO:0001583 missense ENST00000467132.1 1 1 hg19 CCDS32150.1 . . . . . . . . . . G 14.00 2.404725 0.42613 . . ENSG00000196136 ENST00000553947;ENST00000393078;ENST00000393080;ENST00000555820;ENST00000467132;ENST00000380354 D;D;D;D 0.88046 -2.33;-2.33;-2.33;-2.33 4.68 -0.036 0.13890 Serpin domain (1); 1.940150 0.03623 U 0.236685 T 0.81418 0.4818 N 0.19112 0.55 0.09310 N 1 D;P 0.53885 0.963;0.661 B;B 0.43809 0.432;0.154 T 0.72527 -0.4266 10 0.72032 D 0.01 . 10.9606 0.47383 0.0825:0.5309:0.3866:0.0 . 45;70 P01011;G3V5I3 AACT_HUMAN;. M 70;45;45;45;45;45 ENSP00000452367:V70M;ENSP00000376793:V45M;ENSP00000376795:V45M;ENSP00000450540:V45M ENSP00000369712:V45M V + 1 0 SERPINA3 94150664 0.000000 0.05858 0.000000 0.03702 0.002000 0.02628 -0.456000 0.06754 0.073000 0.16731 0.561000 0.74099 GTG TCGA-IB-7890-01A-12D-2201-08 SERPINA3-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268080.3 1 0 1 118 632 0 193 1 9.998222e-01 19 49 0 193 2 0 0 0 0 0 2 1 1.000000 115 617 0 192 2 0 0 0 0 193 2 -20.000000 1 1 121412 5 39 1 1 2 3 2.059402 1 0.360000 2.800000 0.457627 0.990000 0.860000 1.000000 1.000000 0.980263 0.990000 1 0.940000 1.000000 EPB42 2038 broad.mit.edu 37 15 43499591 43499591 + Missense_Mutation SNP G G A rs115972761 by1000genomes TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr15:43499591G>A ENST00000441366.2 - 9 1349 c.1124C>T c.(1123-1125)aCg>aTg p.T375M EPB42_ENST00000540029.1_Missense_Mutation_p.T297M|EPB42_ENST00000563128.1_5'Flank|EPB42_ENST00000300215.3_Missense_Mutation_p.T405M NM_000119.2|NM_001114134.1 NP_000110.2|NP_001107606.1 P16452 EPB42_HUMAN erythrocyte membrane protein band 4.2 20 all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215) CAGCCCCAGCGTCCCCTCCTT 0.582000 0 SO:0001583 missense ENST00000441366.2 1 1 hg19 CCDS45249.1 2 9.157509157509158E-4 2 0.0040650406504065045 0 0.0 0 0.0 0 0.0 G 7.005 0.555666 0.13436 . . ENSG00000166947 ENST00000300215;ENST00000540029;ENST00000441366 T;T;T 0.51071 0.72;0.72;0.72 6.02 -12.0 0.00017 . 1.311570 0.04307 N 0.348294 T 0.28333 0.0700 L 0.51422 1.61 0.09310 N 1 B;B;B;B 0.27823 0.029;0.068;0.19;0.068 B;B;B;B 0.16289 0.005;0.006;0.015;0.006 T 0.08330 -1.0727 10 0.38643 T 0.18 4.7421 1.2729 0.02025 0.4301:0.1641:0.1298:0.276 . 297;375;405;375 F5H563;B7Z4C3;P16452-2;P16452 .;.;.;EPB42_HUMAN M 405;297;375 ENSP00000300215:T405M;ENSP00000444699:T297M;ENSP00000396616:T375M ENSP00000300215:T405M T - 2 0 EPB42 41286883 0.000000 0.05858 0.000000 0.03702 0.024000 0.10985 -1.186000 0.03070 -2.622000 0.00439 -0.769000 0.03391 ACG TCGA-IB-7890-01A-12D-2201-08 EPB42-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000432219.1 1 0 1 47 165 0 63 0 0 0 0 63 2 0 0 0 0 0 2 1 1.000000 46 159 0 62 2 0 0 0 0 63 2 -20.000000 1 1 121412 18 43 1 0 2 2 1.793594 1 0.360000 2.800000 0.360000 0.990000 0.930000 1.000000 1.000000 0.996392 0.990000 1 0.990000 1.000000 CORO2B 10391 broad.mit.edu 37 15 68937512 68937512 + Missense_Mutation SNP C C T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr15:68937512C>T ENST00000566799.1 + 2 58 c.29C>T c.(28-30)cCg>cTg p.P10L CORO2B_ENST00000543950.1_Missense_Mutation_p.P5L|CORO2B_ENST00000261861.5_Missense_Mutation_p.P5L|CORO2B_ENST00000540068.1_Missense_Mutation_p.P5L Q9UQ03 COR2B_HUMAN coronin, actin binding protein, 2B 36 TCCTGGCGTCCGCAATACCGT 0.622000 0 SO:0001583 missense ENST00000566799.1 1 1 hg19 CCDS10229.2 . . . . . . . . . . C 24.3 4.518852 0.85495 0.0 1.16E-4 ENSG00000103647 ENST00000261861;ENST00000540068;ENST00000543950 T;T 0.56941 0.43;0.43 4.38 4.38 0.52667 . 0.053861 0.85682 D 0.000000 T 0.66147 0.2760 M 0.66939 2.045 0.80722 D 1 P 0.52170 0.951 P 0.57371 0.819 T 0.69394 -0.5157 10 0.51188 T 0.08 -21.1529 15.8812 0.79207 0.0:1.0:0.0:0.0 . 10 Q9UQ03 COR2B_HUMAN L 10;5;5 ENSP00000446250:P5L;ENSP00000443819:P5L ENSP00000261861:P10L P + 2 0 CORO2B 66724566 1.000000 0.71417 1.000000 0.80357 0.762000 0.43233 7.565000 0.82337 2.142000 0.66516 0.563000 0.77884 CCG TCGA-IB-7890-01A-12D-2201-08 CORO2B-203 KNOWN basic|CCDS protein_coding protein_coding 1 0 1 19 103 0 60 0 0 0 1 0 60 2 0 0 0 0 0 2 1 0.999992 19 98 0 59 2 0 0 0 0 60 2 -20.000000 1 1 121412 5 36 1 0 2 2 1.793594 1 0.360000 2.800000 0.360000 0.860000 0.550000 1.000000 1.000000 0.853216 0.860000 1 0.690000 1.000000 CELF6 60677 broad.mit.edu 37 15 72579635 72579635 + Missense_Mutation SNP G G A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr15:72579635G>A ENST00000569547.1 - 12 1488 c.1417C>T c.(1417-1419)Cgg>Tgg p.R473W CELF6_ENST00000569311.1_5'Flank|RP11-106M3.2_ENST00000379915.4_RNA|RP11-106M3.3_ENST00000570175.1_RNA|CELF6_ENST00000395258.2_Missense_Mutation_p.R360W|CELF6_ENST00000567083.1_Missense_Mutation_p.R446W|CELF6_ENST00000539635.1_Missense_Mutation_p.R334W|CELF6_ENST00000287202.5_Missense_Mutation_p.R473W|CELF6_ENST00000543764.2_Missense_Mutation_p.R336W Q96J87 CELF6_HUMAN CUGBP, Elav-like family member 6 13 TCCTTGGGCCGCTTTAGCTGG 0.517000 0 SO:0001583 missense ENST00000569547.1 1 1 hg19 CCDS10242.1 . . . . . . . . . . G 16.84 3.234720 0.58886 . . ENSG00000140488 ENST00000287202;ENST00000437872;ENST00000543764;ENST00000379915;ENST00000395258;ENST00000539635 T;T;T;T 0.06449 3.3;3.3;3.3;3.3 5.79 -1.42 0.08913 Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1); 0.000000 0.64402 U 0.000006 T 0.23492 0.0568 M 0.77103 2.36 0.53005 D 0.999967 D;D;D;D;D 0.89917 1.0;1.0;1.0;0.998;1.0 D;D;D;D;D 0.91635 0.998;0.993;0.985;0.967;0.999 T 0.27226 -1.0080 10 0.87932 D 0 -14.4833 16.9829 0.86333 0.0:0.0:0.6119:0.3881 . 446;336;360;334;473 B4DJB6;B4DG28;Q96J87-2;B3KWE6;Q96J87 .;.;.;.;CELF6_HUMAN W 473;446;336;297;360;334 ENSP00000287202:R473W;ENSP00000439956:R336W;ENSP00000378677:R360W;ENSP00000443162:R334W ENSP00000287202:R473W R - 1 2 CELF6 70366689 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 1.311000 0.33562 0.107000 0.17824 0.561000 0.74099 CGG TCGA-IB-7890-01A-12D-2201-08 CELF6-001 KNOWN basic|appris_principal|readthrough_transcript|CCDS nonsense_mediated_decay protein_coding OTTHUMT00000420180.1 1 0 1 75 303 0 112 0 1.816005e-01 0 4 0 112 2 0 0 0 0 0 2 1 1.000000 75 295 0 110 2 0 0 0 0 112 2 -3.611022 1 1 0 0 1 0 2 2 1.793594 1 0.360000 2.800000 0.360000 0.990000 0.880000 1.000000 1.000000 0.989997 0.990000 1 0.980000 1.000000 TMC3 342125 broad.mit.edu 37 15 81654605 81654605 + Missense_Mutation SNP A A G TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr15:81654605A>G ENST00000359440.5 - 4 485 c.350T>C c.(349-351)gTg>gCg p.V117A RP11-761I4.3_ENST00000559781.1_RNA|TMC3_ENST00000558726.1_Missense_Mutation_p.V117A|RP11-761I4.3_ENST00000560851.1_RNA NM_001080532.1 NP_001074001.1 transmembrane channel-like 3 34 GAAGATGACCACAAAGTTACA 0.478000 0 SO:0001583 missense ENST00000359440.5 0 1 hg19 CCDS45324.1 . . . . . . . . . . A 10.65 1.409904 0.25465 . . ENSG00000188869 ENST00000359440 T 0.63580 -0.05 5.26 4.15 0.48705 . 0.183784 0.34268 N 0.004111 T 0.40448 0.1117 N 0.16743 0.435 0.30774 N 0.742708 B;B 0.14012 0.0;0.009 B;B 0.12156 0.002;0.007 T 0.33445 -0.9868 10 0.15066 T 0.55 -11.5679 7.9842 0.30202 0.8433:0.0:0.1567:0.0 . 117;117 Q7Z5M5-2;Q7Z5M5 .;TMC3_HUMAN A 117 ENSP00000352413:V117A ENSP00000352413:V117A V - 2 0 TMC3 79441660 0.967000 0.33354 0.990000 0.47175 0.990000 0.78478 3.776000 0.55356 0.856000 0.35383 0.455000 0.32223 GTG TCGA-IB-7890-01A-12D-2201-08 TMC3-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000417795.3 1 0 0 6 118 0 22 0 0 0 0 22 2 0 0 0 0 0 2 1 0.960559 6 112 0 22 2 0 0 0 0 22 2 -9.698396 1 1 0 0 1 0 2 2 1.793594 1 0.360000 2.800000 0.360000 0.280000 0.110000 0.530000 0.260000 0.304238 0.280000 0 0.180000 0.410000 FURIN 5045 broad.mit.edu 37 15 91419516 91419516 + Missense_Mutation SNP G G A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr15:91419516G>A ENST00000268171.3 + 3 488 c.209G>A c.(208-210)cGa>cAa p.R70Q NM_002569.2 NP_002560.1 P09958 FURIN_HUMAN furin (paired basic amino acid cleaving enzyme) 36 Lung NSC(78;0.0771)|all_lung(78;0.137) Lung(145;0.189) TTCTGGCATCGAGGAGTGACG 0.657000 0 SO:0001583 missense ENST00000268171.3 1 1 hg19 CCDS10364.1 . . . . . . . . . . G 17.65 3.441351 0.63067 . . ENSG00000140564 ENST00000268171 T 0.31510 1.49 4.58 4.58 0.56647 Proteinase inhibitor, propeptide (1); 0.000000 0.85682 D 0.000000 T 0.41719 0.1171 M 0.69248 2.105 0.58432 D 0.999998 D 0.59767 0.986 P 0.48738 0.588 T 0.45629 -0.9248 10 0.59425 D 0.04 -2.4622 15.8038 0.78477 0.0:0.0:1.0:0.0 . 70 P09958 FURIN_HUMAN Q 70 ENSP00000268171:R70Q ENSP00000268171:R70Q R + 2 0 FURIN 89220520 0.978000 0.34361 0.999000 0.59377 0.083000 0.17756 2.778000 0.47726 2.396000 0.81511 0.555000 0.69702 CGA TCGA-IB-7890-01A-12D-2201-08 FURIN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000313492.1 1 0 1 102 545 0 235 1 1 43 159 0 235 2 0 0 0 0 0 2 1 1.000000 100 532 0 234 2 0 0 0 0 235 2 -3.144086 1 1 0 0 1 0 2 2 1.793594 1 0.360000 2.800000 0.360000 0.870000 0.720000 1.000000 1.000000 0.876650 0.870000 1 0.790000 0.960000 RGMA 56963 broad.mit.edu 37 15 93588562 93588562 + Missense_Mutation SNP C C T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr15:93588562C>T ENST00000329082.7 - 4 1290 c.1019G>A c.(1018-1020)cGc>cAc p.R340H RGMA_ENST00000425933.2_Missense_Mutation_p.R324H|RGMA_ENST00000542321.2_Missense_Mutation_p.R324H|RGMA_ENST00000557301.1_Missense_Mutation_p.R348H|RGMA_ENST00000556658.1_Missense_Mutation_p.R231H|RGMA_ENST00000538818.1_Missense_Mutation_p.R231H|RGMA_ENST00000543599.1_Missense_Mutation_p.R324H|RGMA_ENST00000557420.1_3'UTR NM_020211.2 NP_064596 Q96B86 RGMA_HUMAN repulsive guidance molecule family member a 9 Lung NSC(78;0.0542)|all_lung(78;0.0786) BRCA - Breast invasive adenocarcinoma(143;0.0312)|OV - Ovarian serous cystadenocarcinoma(32;0.108) TGCCAGCCTGCGGGCACCGGT 0.672000 0 SO:0001583 missense ENST00000329082.7 1 1 hg19 CCDS45357.1 . . . . . . . . . . C 10.84 1.464028 0.26335 0.0 6.01E-4 ENSG00000182175 ENST00000543599;ENST00000425933;ENST00000329082;ENST00000542321;ENST00000538818;ENST00000557301 D;D;D;D;D;D 0.91351 -2.83;-2.83;-2.82;-2.83;-2.44;-2.83 4.4 -0.978 0.10279 Repulsive guidance molecule, C-terminal (1); 0.646923 0.14204 N 0.334497 T 0.81138 0.4760 N 0.14661 0.345 0.09310 N 1 D;P 0.53151 0.958;0.952 P;P 0.49597 0.616;0.564 T 0.74038 -0.3793 10 0.11794 T 0.64 -24.0079 5.3558 0.16059 0.0:0.4763:0.1344:0.3894 . 348;340 G3V518;Q96B86 .;RGMA_HUMAN H 324;324;340;324;231;348 ENSP00000442498:R324H;ENSP00000404442:R324H;ENSP00000330005:R340H;ENSP00000440025:R324H;ENSP00000442546:R231H;ENSP00000452126:R348H ENSP00000330005:R340H R - 2 0 RGMA 91389566 0.004000 0.15560 0.003000 0.11579 0.011000 0.07611 0.075000 0.14686 -0.582000 0.05929 -0.658000 0.03865 CGC TCGA-IB-7890-01A-12D-2201-08 RGMA-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000415091.1 1 0 1 36 44 0 39 0 9.286910e-01 0 8 0 39 2 0 0 0 0 0 2 1 1.000000 33 44 0 38 2 0 0 0 0 39 2 -3.221883 1 1 120770 43 45 1 0 2 2 1.793594 1 0.360000 2.800000 0.360000 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 BFAR 51283 broad.mit.edu 37 16 14749057 14749057 + Missense_Mutation SNP G G C TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr16:14749057G>C ENST00000261658.2 + 5 1050 c.773G>C c.(772-774)tGg>tCg p.W258S BFAR_ENST00000563971.1_Missense_Mutation_p.W133S|BFAR_ENST00000426842.2_Missense_Mutation_p.W130S NM_016561.2 NP_057645.1 Q9NZS9 BFAR_HUMAN bifunctional apoptosis regulator 11 CAGAATCTCTGGGAATATAAG 0.333000 0 SO:0001583 missense ENST00000261658.2 1 1 hg19 CCDS10554.1 . . . . . . . . . . G 17.53 3.412066 0.62511 . . ENSG00000103429 ENST00000261658;ENST00000426842 T;T 0.56776 2.77;0.44 4.86 4.86 0.63082 . 0.000000 0.85682 D 0.000000 T 0.61937 0.2387 L 0.27053 0.805 0.80722 D 1 D;D;D 0.89917 0.998;1.0;1.0 D;D;D 0.85130 0.99;0.997;0.997 T 0.67409 -0.5678 10 0.87932 D 0 . 16.9649 0.86283 0.0:0.0:1.0:0.0 . 130;258;258 B4DUT0;B2R9R6;Q9NZS9 .;.;BFAR_HUMAN S 258;130 ENSP00000261658:W258S;ENSP00000400634:W130S ENSP00000261658:W258S W + 2 0 BFAR 14656558 1.000000 0.71417 1.000000 0.80357 0.561000 0.35649 9.561000 0.98142 2.239000 0.73571 0.313000 0.20887 TGG TCGA-IB-7890-01A-12D-2201-08 BFAR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252088.1 1 0 0 127 337 0 111 1 1 131 99 0 111 2 0 0 0 0 0 2 1 1.000000 124 326 0 108 2 0 0 0 0 111 2 -7.039860 1 1 0 0 1 2 2 4 2.345296 1 0.360000 2.800000 0.523100 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 AXIN1 8312 broad.mit.edu 37 16 347159 347159 + Missense_Mutation SNP C C T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr16:347159C>T ENST00000262320.3 - 7 2223 c.1852G>A c.(1852-1854)Gag>Aag p.E618K AXIN1_ENST00000354866.3_Missense_Mutation_p.E618K|AXIN1_ENST00000481769.1_5'Flank NM_003502.3 NP_003493.1 O15169 AXIN1_HUMAN axin 1 221 all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187) CCTGGCACCTCGGTGCTGGCG 0.612000 0 SO:0001583 missense ENST00000262320.3 1 1 hg19 CCDS10405.1 . . . . . . . . . . C 14.91 2.676683 0.47886 . . ENSG00000103126 ENST00000262320;ENST00000354866 T;T 0.60672 0.17;0.18 4.98 4.02 0.46733 . 0.156231 0.56097 D 0.000026 T 0.45935 0.1367 M 0.61703 1.905 0.41038 D 0.985201 P;P 0.45715 0.865;0.494 B;B 0.28305 0.088;0.029 T 0.47873 -0.9083 10 0.25106 T 0.35 -1.1885 13.1589 0.59533 0.0:0.9217:0.0:0.0782 . 618;618 O15169-2;O15169 .;AXIN1_HUMAN K 618 ENSP00000262320:E618K;ENSP00000346935:E618K ENSP00000262320:E618K E - 1 0 AXIN1 287160 0.510000 0.26171 0.287000 0.24848 0.008000 0.06430 1.583000 0.36579 1.088000 0.41272 0.478000 0.44815 GAG TCGA-IB-7890-01A-12D-2201-08 AXIN1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000139441.3 1 0 1 350 1167 0 400 1 1 31 72 0 400 2 0 0 0 0 0 2 1 1.000000 337 1147 0 398 2 0 0 0 0 400 2 -20.000000 1 1 121412 1 36 1 2 2 4 2.345296 1 0.360000 2.800000 0.523100 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 ZFHX3 463 broad.mit.edu 37 16 72830417 72830417 + Missense_Mutation SNP G G A rs144401383 TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr16:72830417G>A ENST00000268489.5 - 9 6836 c.6164C>T c.(6163-6165)cCg>cTg p.P2055L ZFHX3_ENST00000397992.5_Missense_Mutation_p.P1141L NM_006885.3 NP_008816.3 Q15911 ZFHX3_HUMAN zinc finger homeobox 3 153 Ovarian(137;0.13) CGGCTGAGGCGGCGCTGCCGG 0.662000 0 SO:0001583 missense ENST00000268489.5 1 1 hg19 CCDS10908.1 . . . . . . . . . . G 5.395 0.258120 0.10239 2.28E-4 0.0 ENSG00000140836 ENST00000268489;ENST00000397992 T;T 0.74947 -0.89;-0.89 5.4 5.4 0.78164 . 0.000000 0.46442 D 0.000284 T 0.73830 0.3637 L 0.46157 1.445 0.80722 D 1 D 0.57899 0.981 P 0.46685 0.524 T 0.73626 -0.3923 10 0.36615 T 0.2 . 18.7943 0.91988 0.0:0.0:1.0:0.0 . 2055 Q15911 ZFHX3_HUMAN L 2055;1141 ENSP00000268489:P2055L;ENSP00000438926:P1141L ENSP00000268489:P2055L P - 2 0 ZFHX3 71387918 1.000000 0.71417 0.099000 0.21106 0.103000 0.19146 7.142000 0.77339 2.523000 0.85059 0.655000 0.94253 CCG TCGA-IB-7890-01A-12D-2201-08 ZFHX3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000269008.1 1 0 0 54 380 0 86 0 1.616526e-02 1 1 0 86 2 0 0 0 0 0 2 1 1.000000 48 343 0 84 2 0 0 0 0 86 2 -3.221892 1 1 120878 1 24 1 2 2 4 2.360506 1 0.360000 2.800000 0.528163 0.930000 0.710000 1.000000 1.000000 0.921320 0.930000 1 0.820000 1.000000 SLC6A4 6532 broad.mit.edu 37 17 28537580 28537580 + Missense_Mutation SNP C C A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr17:28537580C>A ENST00000401766.2 - 10 1914 c.1402G>T c.(1402-1404)Gcc>Tcc p.A468S SLC6A4_ENST00000261707.3_Missense_Mutation_p.A468S P31645 SC6A4_HUMAN solute carrier family 6 (neurotransmitter transporter), member 4 25 Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexfenfluramine(DB01191)|Dexmethylphenidate(DB06701)|Dextromethorphan(DB00514)|Dopamine(DB00988)|Doxepin(DB01142)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fluoxetine(DB00472)|Fluvoxamine(DB00176)|Imipramine(DB00458)|Levomilnacipran(DB08918)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Pethidine(DB00454)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684) ATGACCACGGCGAGCACGAAC 0.597000 0 SO:0001583 missense ENST00000401766.2 1 1 hg19 CCDS11256.1 . . . . . . . . . . C 10.07 1.248984 0.22880 . . ENSG00000108576 ENST00000394821;ENST00000401766;ENST00000261707 T;T 0.74632 -0.86;-0.86 6.04 -0.373 0.12516 . 0.664706 0.17075 N 0.188038 T 0.50786 0.1636 N 0.21324 0.655 0.09310 N 1 B 0.06786 0.001 B 0.14023 0.01 T 0.22521 -1.0214 10 0.17369 T 0.5 . 3.284 0.06925 0.1179:0.3322:0.3805:0.1694 . 468 P31645 SC6A4_HUMAN S 510;468;468 ENSP00000385822:A468S;ENSP00000261707:A468S ENSP00000261707:A468S A - 1 0 SLC6A4 25561706 0.000000 0.05858 0.000000 0.03702 0.274000 0.26718 0.560000 0.23500 -0.236000 0.09753 0.561000 0.74099 GCC TCGA-IB-7890-01A-12D-2201-08 SLC6A4-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256115.3 1 0 1 166 332 0 114 0 0 0 1 0 114 2 0 0 0 0 0 2 1 1.000000 165 327 0 112 2 0 0 0 0 114 2 -15.033990 1 1 0 0 1 1 2 3 2.115199 1 0.360000 2.800000 0.457627 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 ATAD5 79915 broad.mit.edu 37 17 29167753 29167753 + Missense_Mutation SNP C C G TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr17:29167753C>G ENST00000321990.4 + 4 2573 c.2195C>G c.(2194-2196)tCt>tGt p.S732C CTD-2349P21.11_ENST00000580873.1_RNA NM_024857.3 NP_079133.3 Q96QE3 ATAD5_HUMAN ATPase family, AAA domain containing 5 51 all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393) AGGCGCTCCTCTAGACATCAG 0.348000 0 SO:0001583 missense ENST00000321990.4 1 1 hg19 CCDS11260.1 . . . . . . . . . . C 14.03 2.413979 0.42817 . . ENSG00000176208 ENST00000321990 T 0.13089 2.62 6.05 6.05 0.98169 . 0.809409 0.11693 N 0.538668 T 0.41373 0.1156 M 0.63843 1.955 0.40418 D 0.979817 D;D 0.89917 1.0;1.0 D;D 0.85130 0.997;0.991 T 0.06006 -1.0851 10 0.72032 D 0.01 . 20.6013 0.99457 0.0:1.0:0.0:0.0 . 732;732 Q96QE3-2;Q96QE3 .;ATAD5_HUMAN C 732 ENSP00000313171:S732C ENSP00000313171:S732C S + 2 0 ATAD5 26191879 0.984000 0.35163 1.000000 0.80357 0.882000 0.50991 3.568000 0.53820 2.878000 0.98634 0.650000 0.86243 TCT TCGA-IB-7890-01A-12D-2201-08 ATAD5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256206.2 1 0 1 74 428 0 78 0 0 0 1 0 78 2 0 0 0 0 0 2 1 1.000000 74 424 0 78 2 0 0 0 0 78 2 -2.967187 1 1 121410 1 40 1 1 2 3 2.115199 1 0.360000 2.800000 0.457627 0.960000 0.770000 1.000000 1.000000 0.943385 0.960000 1 0.860000 1.000000 NMT1 4836 broad.mit.edu 37 17 43174523 43174523 + Silent SNP C C A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr17:43174523C>A ENST00000592782.1 + 7 755 c.624C>A c.(622-624)ccC>ccA p.P208P NMT1_ENST00000258960.2_Silent_p.P208P|NMT1_ENST00000590114.1_Intron P30419 NMT1_HUMAN N-myristoyltransferase 1 8 Prostate(33;0.155) GCTGGCTCCCCCAGTGGCACT 0.597000 OREG0024469 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001819 synonymous_variant ENST00000592782.1 1 1 hg19 CCDS11494.1 TCGA-IB-7890-01A-12D-2201-08 NMT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000449239.1 1 0 1 95 591 0 233 1 9.999984e-01 22 95 0 233 2 0 0 0 0 0 2 1 1.000000 90 565 0 228 2 0 0 0 0 233 2 -2.841679 1 1 0 0 1 1 2 3 2.115199 1 0.360000 2.800000 0.457627 0.900000 0.740000 1.000000 1.000000 0.905311 0.900000 1 0.820000 1.000000 HEXIM1 10614 broad.mit.edu 37 17 43226570 43226570 + Missense_Mutation SNP T T C TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr17:43226570T>C ENST00000332499.2 + 1 1887 c.13T>C c.(13-15)Ttc>Ctc p.F5L AC002117.1_ENST00000452741.1_RNA|AC002117.1_ENST00000589950.1_RNA NM_006460.2 NP_006451.1 O94992 HEXI1_HUMAN hexamethylene bis-acetamide inducible 1 11 GGCCGAGCCATTCTTGTCAGA 0.458000 OREG0024474 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000332499.2 1 1 hg19 CCDS11495.1 . . . . . . . . . . T 0.625 -0.819580 0.02776 . . ENSG00000186834 ENST00000332499 . . . 3.94 1.93 0.25924 . . . . . T 0.08758 0.0217 N 0.02011 -0.69 0.19575 N 0.999967 B 0.02656 0.0 B 0.01281 0.0 T 0.37596 -0.9699 8 0.02654 T 1 -0.0421 5.2187 0.15356 0.0:0.727:0.0:0.273 . 5 O94992 HEXI1_HUMAN L 5 . ENSP00000328773:F5L F + 1 0 HEXIM1 40582353 0.400000 0.25295 0.983000 0.44433 0.946000 0.59487 0.061000 0.14366 0.997000 0.38969 -0.242000 0.12053 TTC TCGA-IB-7890-01A-12D-2201-08 HEXIM1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000449821.2 1 0 1 243 480 0 221 1 1 32 49 0 221 2 0 0 0 0 0 2 1 1.000000 219 460 0 217 2 0 0 0 0 221 2 -20.000000 1 1 121404 1 35 1 1 2 3 2.115199 1 0.360000 2.800000 0.457627 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 XYLT2 64132 broad.mit.edu 37 17 48435627 48435627 + Silent SNP G G A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr17:48435627G>A ENST00000017003.2 + 10 2050 c.2001G>A c.(1999-2001)ggG>ggA p.G667G XYLT2_ENST00000507602.1_Intron NM_022167.2 NP_071450.2 Q9H1B5 XYLT2_HUMAN xylosyltransferase II 12 Breast(11;7.18e-19) GGTTACTGGGGCCGCTGGACG 0.627000 0 SO:0001819 synonymous_variant ENST00000017003.2 1 1 hg19 CCDS11563.1 TCGA-IB-7890-01A-12D-2201-08 XYLT2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367046.1 1 0 1 33 137 0 62 1 9.560030e-01 9 15 0 62 2 0 0 0 0 0 2 1 1.000000 32 130 0 61 2 0 0 0 0 62 2 -20.000000 1 1 0 0 1 1 2 3 2.104474 1 0.360000 2.800000 0.457627 0.990000 0.910000 1.000000 1.000000 0.995151 0.990000 1 0.990000 1.000000 DLG4 1742 broad.mit.edu 37 17 7106623 7106623 + Silent SNP G G A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr17:7106623G>A ENST00000399506.2 - 7 722 c.531C>T c.(529-531)ggC>ggT p.G177G DLG4_ENST00000485100.1_Silent_p.G174G|DLG4_ENST00000399510.2_Silent_p.G220G|DLG4_ENST00000302955.6_Silent_p.G174G P78352 DLG4_HUMAN discs, large homolog 4 (Drosophila) 18 Guanidine(DB00536) GGTTCCCTACGCCCCCTGCGA 0.587000 0 SO:0001819 synonymous_variant ENST00000399506.2 1 1 hg19 TCGA-IB-7890-01A-12D-2201-08 DLG4-002 KNOWN non_canonical_TEC|not_organism_supported|basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000259419.2 1 0 1 26 92 0 46 0 9.783003e-01 1 24 0 46 2 0 0 0 0 0 2 1 1.000000 25 86 0 46 2 0 0 0 0 46 2 -3.150560 1 1 120950 56 46 1 0 2 2 1.785620 1 0.360000 2.800000 0.360000 0.990000 0.840000 1.000000 1.000000 0.988287 0.990000 1 0.990000 1.000000 TP53 7157 broad.mit.edu 37 17 7578254 7578254 + Nonsense_Mutation SNP C C A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 C A C C Valid Somatic Phase_I WXS targeted Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr17:7578254C>A ENST00000269305.4 - 6 784 c.595G>T c.(595-597)Gga>Tga p.G199* TP53_ENST00000445888.2_Nonsense_Mutation_p.G199*|TP53_ENST00000574684.1_Intron|TP53_ENST00000455263.2_Nonsense_Mutation_p.G199*|TP53_ENST00000420246.2_Nonsense_Mutation_p.G199*|TP53_ENST00000359597.4_Nonsense_Mutation_p.G199*|TP53_ENST00000413465.2_Nonsense_Mutation_p.G199* 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.G199R(9)|p.0?(8)|p.?(5)|p.G199*(3)|p.E198_L201>V(1)|p.N200fs*4(1)|p.E198_G199ins21(1)|p.E198fs*7(1)|p.P191fs*6(1)|p.I195_G199delIRVEG(1)|p.G199fs*48(1)|p.G199fs*42(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) CGCAAATTTCCTTCCACTCGG 0.547000 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 33 Substitution - Missense(9)|Whole gene deletion(8)|Unknown(6)|Deletion - Frameshift(4)|Substitution - Nonsense(3)|Deletion - In frame(1)|Complex - frameshift(1)|Insertion - In frame(1) SO:0001587 stop_gained 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 0 1 hg19 CCDS11118.1 . . . . . . . . . . C 14.72 2.620630 0.46736 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315 . . . 5.28 4.32 0.51571 . 0.052866 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.87932 D 0 -10.2871 12.0218 0.53348 0.0:0.9154:0.0:0.0846 . . . . X 199;199;199;199;199;199;188;106;67;106;67 . ENSP00000269305:G199X G - 1 0 TP53 7518979 1.000000 0.71417 0.996000 0.52242 0.023000 0.10783 7.775000 0.85489 1.374000 0.46228 -0.253000 0.11424 GGA TCGA-IB-7890-01A-12D-2201-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 100 180 0 72 0 9.999867e-01 1 33 0 72 2 1 1 367 671 0 1634 2 1 1.000000 99 178 0 72 2 0 0 0 0 72 2 -20.000000 1 1 0 0 1 0 2 2 1.785620 1 0.360000 2.800000 0.360000 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 EPB41L3 23136 broad.mit.edu 37 18 5415859 5415859 + Silent SNP G G A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr18:5415859G>A ENST00000341928.2 - 13 2365 c.2025C>T c.(2023-2025)agC>agT p.S675S EPB41L3_ENST00000540638.2_Intron|EPB41L3_ENST00000427684.2_Intron|EPB41L3_ENST00000542146.1_Intron|EPB41L3_ENST00000542652.2_Intron|EPB41L3_ENST00000544123.1_Intron|EPB41L3_ENST00000342933.3_Silent_p.S675S|EPB41L3_ENST00000400111.3_Intron NM_012307.2 NP_036439.2 Q9Y2J2 E41L3_HUMAN erythrocyte membrane protein band 4.1-like 3 105 CTAGGGAGGCGCTCAAGGAGG 0.577000 0 SO:0001819 synonymous_variant ENST00000341928.2 1 1 hg19 CCDS11838.1 TCGA-IB-7890-01A-12D-2201-08 EPB41L3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000254424.1 1 0 0 72 241 0 81 0 0 0 0 81 2 0 0 0 0 0 2 1 1.000000 72 234 0 77 2 0 0 0 0 81 2 -4.280753 1 1 0 0 1 2 2 4 1.887211 1 0.360000 2.800000 0.408940 0.990000 0.990000 1.000000 1.000000 0.999949 0.990000 1 0.990000 1.000000 ATP4A 495 broad.mit.edu 37 19 36053403 36053403 + Silent SNP G G A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr19:36053403G>A ENST00000262623.3 - 4 382 c.354C>T c.(352-354)gcC>gcT p.A118A NM_000704.2 NP_000695.2 P20648 ATP4A_HUMAN ATPase, H+/K+ exchanging, alpha polypeptide 53 all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0724) Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129) AGATGGCGGCGGCAACCCACA 0.657000 0 SO:0001819 synonymous_variant ENST00000262623.3 1 1 hg19 CCDS12467.1 TCGA-IB-7890-01A-12D-2201-08 ATP4A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000109470.2 0 0 0 11 194 0 58 0 0 0 0 58 2 0 0 0 0 0 2 1 0.997864 11 182 0 57 2 0 0 0 0 58 2 -4.788962 1 1 121404 2 37 1 1 2 3 2.000861 1 0.360000 2.800000 0.444058 0.370000 0.190000 1.000000 0.340000 0.447910 0.370000 0 0.260000 0.570000 STAP2 55620 broad.mit.edu 37 19 4328730 4328730 + Missense_Mutation SNP G G A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr19:4328730G>A ENST00000594605.1 - 6 655 c.532C>T c.(532-534)Cgg>Tgg p.R178W STAP2_ENST00000600324.1_Missense_Mutation_p.R178W|STAP2_ENST00000597593.1_5'Flank NM_001013841.1 NP_001013863.1 Q9UGK3 STAP2_HUMAN signal transducing adaptor family member 2 23 Hepatocellular(1079;0.137) CCGCTGGGCCGCAGCAGCAGG 0.711000 0 SO:0001583 missense ENST00000594605.1 0 1 hg19 CCDS45926.1 . . . . . . . . . . G 25.5 4.644273 0.87859 . . ENSG00000178078 ENST00000314714;ENST00000424810 . . . 4.47 2.02 0.26589 SH2 motif (3); 0.082621 0.50627 U 0.000106 T 0.76608 0.4011 M 0.82716 2.605 0.43857 D 0.996459 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 T 0.78964 -0.1996 9 0.87932 D 0 -13.5939 9.2504 0.37551 0.0:0.0:0.6804:0.3196 . 178;178 Q9UGK3-2;Q9UGK3 .;STAP2_HUMAN W 178 . ENSP00000317912:R178W R - 1 2 STAP2 4279730 0.986000 0.35501 1.000000 0.80357 0.894000 0.52154 0.524000 0.22940 2.035000 0.60131 0.479000 0.44913 CGG TCGA-IB-7890-01A-12D-2201-08 STAP2-003 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000458114.2 0 0 0 3 74 0 30 0 2.690479e-01 0 20 0 30 2 0 0 0 0 0 2 1 0.804153 2 73 0 30 2 0 0 0 0 30 2 -6.450746 1 0 0 0 1 1 2 3 2.059460 1 0.360000 2.800000 0.455967 0.290000 0.080000 0.750000 0.250000 0.332354 0.290000 0 0.160000 0.490000 PTPRS 5802 broad.mit.edu 37 19 5210704 5210704 + Silent SNP G G T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr19:5210704G>T ENST00000587303.1 - 33 5446 c.5347C>A c.(5347-5349)Cgg>Agg p.R1783R PTPRS_ENST00000348075.2_Silent_p.R1745R|PTPRS_ENST00000372412.4_Silent_p.R1784R|PTPRS_ENST00000592099.1_Silent_p.R1336R|PTPRS_ENST00000357368.4_Silent_p.R1783R|PTPRS_ENST00000353284.2_Silent_p.R1336R|PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000588012.1_Silent_p.R1745R|PTPRS_ENST00000262963.6_Silent_p.R1763R Q13332 PTPRS_HUMAN protein tyrosine phosphatase, receptor type, S 61 Alendronate(DB00630)|Etidronic acid(DB01077) CCCATCTCCCGCAGCTTGGTC 0.647000 0 SO:0001819 synonymous_variant ENST00000587303.1 1 1 hg19 CCDS45930.1 TCGA-IB-7890-01A-12D-2201-08 PTPRS-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000450762.2 1 0 1 68 217 0 85 1 1 4 105 0 85 2 0 0 0 0 0 2 1 1.000000 67 210 0 84 2 0 0 0 0 85 2 -4.621529 1 1 0 0 1 1 2 3 2.059460 1 0.360000 2.800000 0.455967 0.990000 0.990000 1.000000 1.000000 0.999998 0.990000 1 0.990000 1.000000 GZMM 3004 broad.mit.edu 37 19 547332 547332 + Silent SNP G G A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr19:547332G>A ENST00000264553.3 + 2 146 c.108G>A c.(106-108)tcG>tcA p.S36S NM_001258351.1|NM_005317.3 NP_001245280.1|NP_005308 P51124 GRAM_HUMAN granzyme M (lymphocyte met-ase 1) 3 all_cancers(10;1.94e-35)|all_epithelial(18;5.94e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228) TCCCCCACTCGCGCCCGTACA 0.667000 0 SO:0001819 synonymous_variant ENST00000264553.3 1 1 hg19 CCDS12031.1 TCGA-IB-7890-01A-12D-2201-08 GZMM-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000451895.2 0 0 0 27 558 0 205 0 1.317565e-02 0 4 0 205 2 0 0 0 0 0 2 1 1.000000 26 547 0 204 2 0 0 0 0 205 2 -4.888592 1 1 121388 1 36 1 1 2 3 1.998603 1 0.360000 2.800000 0.445791 0.300000 0.190000 1.000000 0.290000 0.382899 0.300000 0 0.240000 0.400000 PEG3 5178 broad.mit.edu 37 19 57328017 57328017 + Missense_Mutation SNP C C T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr19:57328017C>T ENST00000326441.9 - 10 2156 c.1793G>A c.(1792-1794)cGt>cAt p.R598H PEG3_ENST00000598410.1_Missense_Mutation_p.R474H|PEG3_ENST00000423103.2_Missense_Mutation_p.R598H|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000593695.1_Missense_Mutation_p.R472H|ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000221722.5_Intron NM_006210.2 NP_006201.1 Q9GZU2 PEG3_HUMAN paternally expressed 3 p.R598H(2) 170 Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243) ttcacgttcacgttcatgttc 0.458000 2 Substitution - Missense(2) SO:0001583 missense ENST00000326441.9 1 1 hg19 CCDS12948.1 . . . . . . . . . . C 0.743 -0.775804 0.02951 . . ENSG00000198300 ENST00000326441;ENST00000423103 T;T 0.02863 4.13;4.13 1.08 -0.0769 0.13721 . . . . . T 0.02193 0.0068 L 0.50333 1.59 . . . B;B;P 0.40107 0.055;0.291;0.703 B;B;B 0.23150 0.001;0.013;0.044 T 0.41251 -0.9519 8 0.56958 D 0.05 . 3.4582 0.07523 0.0:0.7126:0.0:0.2874 . 474;598;533 A7E2B8;Q9GZU2;Q96Q96 .;PEG3_HUMAN;. H 598 ENSP00000326581:R598H;ENSP00000403051:R598H ENSP00000326581:R598H R - 2 0 ZIM2 62019829 0.000000 0.05858 0.010000 0.14722 0.165000 0.22458 -0.044000 0.12023 0.063000 0.16370 0.525000 0.51046 CGT TCGA-IB-7890-01A-12D-2201-08 PEG3-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000416099.2 1 0 1 54 246 0 60 0 8.835486e-02 0 3 0 60 2 0 0 0 0 0 2 1 1.000000 54 244 0 59 2 0 0 0 0 60 2 -20.000000 1 1 0 0 1 1 2 3 2.074068 1 0.360000 2.800000 0.457627 0.990000 0.910000 1.000000 1.000000 0.994469 0.990000 1 0.990000 1.000000 MUC16 94025 broad.mit.edu 37 19 9070332 9070332 + Missense_Mutation SNP G G A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr19:9070332G>A ENST00000397910.4 - 3 17317 c.17114C>T c.(17113-17115)gCg>gTg p.A5705V NM_024690.2 NP_078966.2 Q8WXI7 MUC16_HUMAN mucin 16, cell surface associated 590 TTCTGTGTGCGCAGTGTCTTT 0.502000 0 SO:0001583 missense ENST00000397910.4 1 1 hg19 CCDS54212.1 . . . . . . . . . . g 5.554 0.287072 0.10513 7.16E-4 0.0 ENSG00000181143 ENST00000397910 T 0.17854 2.25 1.54 -1.16 0.09678 . . . . . T 0.04952 0.0133 N 0.08118 0 . . . P 0.44578 0.838 B 0.24155 0.051 T 0.31806 -0.9930 8 0.87932 D 0 . 3.5904 0.07986 0.0:0.2807:0.4342:0.285 . 5705 B5ME49 . V 5705 ENSP00000381008:A5705V ENSP00000381008:A5705V A - 2 0 MUC16 8931332 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -0.207000 0.09384 -0.197000 0.10350 0.456000 0.33151 GCG TCGA-IB-7890-01A-12D-2201-08 MUC16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000402806.1 1 0 1 57 338 0 74 0 0 0 0 74 2 0 0 0 0 0 2 1 1.000000 58 336 0 73 2 0 0 0 0 74 2 -3.222927 1 1 121054 11 44 1 1 2 3 2.059460 1 0.360000 2.800000 0.455967 0.940000 0.730000 1.000000 1.000000 0.925974 0.940000 1 0.830000 1.000000 MUC16 94025 broad.mit.edu 37 19 9090831 9090831 + Silent SNP A A G TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr19:9090831A>G ENST00000397910.4 - 1 1187 c.984T>C c.(982-984)ccT>ccC p.P328P NM_024690.2 NP_078966.2 Q8WXI7 MUC16_HUMAN mucin 16, cell surface associated 590 TCATGGAAAAAGGGATAGCTG 0.522000 0 SO:0001819 synonymous_variant ENST00000397910.4 0 1 hg19 CCDS54212.1 TCGA-IB-7890-01A-12D-2201-08 MUC16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000402806.1 0 0 0 7 429 0 122 0 0 0 0 122 2 0 0 0 0 0 2 1 0.979809 6 424 0 120 2 0 0 0 0 122 2 -2.339787 0 1 0 0 1 1 2 3 2.059460 1 0.360000 2.800000 0.455967 0.110000 0.040000 0.230000 0.110000 0.127691 0.110000 0 0.070000 0.160000 HSD3B1 3283 broad.mit.edu 37 1 120056677 120056677 + Silent SNP C C T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr1:120056677C>T ENST00000369413.3 + 4 676 c.531C>T c.(529-531)ggC>ggT p.G177G HSD3B1_ENST00000235547.6_Silent_p.G179G|HSD3B1_ENST00000528909.1_Silent_p.G177G P14060 3BHS1_HUMAN hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1 32 all_neural(166;0.219) all_lung(203;3.16e-06)|Lung NSC(69;2.19e-05)|all_epithelial(167;0.000624) Trilostane(DB01108) TGAAAAACGGCGGCACCCTGT 0.512000 0 SO:0001819 synonymous_variant ENST00000369413.3 1 1 hg19 CCDS903.1 TCGA-IB-7890-01A-12D-2201-08 HSD3B1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000034993.3 1 0 1 89 358 0 152 0 0 0 0 152 2 0 0 0 0 0 2 1 1.000000 87 350 0 147 2 0 0 0 0 152 2 -3.107943 1 1 121412 22 47 1 1 2 3 1.807388 0 0.360000 2.800000 0.372426 0.990000 0.920000 1.000000 1.000000 0.995412 0.990000 1 0.990000 1.000000 CDC42 998 broad.mit.edu 37 1 22405018 22405018 + Missense_Mutation SNP A A G TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr1:22405018A>G ENST00000344548.3 + 3 298 c.47A>G c.(46-48)aAa>aGa p.K16R CDC42_ENST00000498236.1_3'UTR|CDC42_ENST00000400259.1_Missense_Mutation_p.K16R|CDC42_ENST00000315554.8_Missense_Mutation_p.K16R|CDC42_ENST00000421089.2_5'UTR NM_001039802.1 NP_001034891.1 P60953 CDC42_HUMAN cell division cycle 42 12 Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;6.55e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)|Prostate(1639;0.0792) GCTGTTGGTAAAACATGTCTC 0.358000 0 SO:0001583 missense ENST00000344548.3 1 1 hg19 CCDS221.1 . . . . . . . . . . a 26.3 4.721851 0.89298 . . ENSG00000070831 ENST00000400259;ENST00000344548;ENST00000315554;ENST00000411827 D;D;D;D 0.90324 -2.65;-2.65;-2.65;-2.65 4.91 4.91 0.64330 Small GTP-binding protein domain (1); 0.048902 0.85682 D 0.000000 D 0.98118 0.9379 H 0.99997 5.475 0.80722 D 1 D;D;D 0.71674 0.985;0.998;0.987 D;D;P 0.73380 0.928;0.98;0.88 D 0.98100 1.0414 10 0.87932 D 0 . 13.365 0.60678 1.0:0.0:0.0:0.0 . 16;16;16 B4E1U9;P60953;P60953-1 .;CDC42_HUMAN;. R 16 ENSP00000383118:K16R;ENSP00000341072:K16R;ENSP00000314458:K16R;ENSP00000398327:K16R ENSP00000314458:K16R K + 2 0 CDC42 22277605 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 8.630000 0.90987 1.854000 0.53819 0.528000 0.53228 AAA TCGA-IB-7890-01A-12D-2201-08 CDC42-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000007787.1 1 0 1 75 349 0 89 1 1 103 469 0 89 2 0 0 0 0 0 2 1 1.000000 69 340 0 88 2 0 0 0 0 89 2 -20.000000 1 1 0 0 1 1 2 3 1.828731 0 0.360000 2.800000 0.375732 0.990000 0.810000 1.000000 1.000000 0.967916 0.990000 1 0.910000 1.000000 FMN2 56776 broad.mit.edu 37 1 240370125 240370125 + Silent SNP A A G TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr1:240370125A>G ENST00000319653.9 + 5 2243 c.2013A>G c.(2011-2013)ggA>ggG p.G671G NM_020066.4 NP_064450.3 Q9NZ56 FMN2_HUMAN formin 2 178 Ovarian(103;0.127) all_cancers(173;0.013) OV - Ovarian serous cystadenocarcinoma(106;0.0106) AGTCTGAGGGACAGGCCACTG 0.433000 0 SO:0001819 synonymous_variant ENST00000319653.9 1 1 hg19 CCDS31069.2 TCGA-IB-7890-01A-12D-2201-08 FMN2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000096217.2 1 0 1 37 202 0 71 0 2.426887e-01 0 6 0 71 2 0 0 0 0 0 2 1 1.000000 37 200 0 71 2 0 0 0 0 71 2 -19.001430 1 1 0 0 1 1 3 4 2.138298 1 0.360000 2.800000 0.470549 0.990000 0.770000 1.000000 1.000000 0.970587 0.990000 1 0.910000 1.000000 AJAP1 55966 broad.mit.edu 37 1 4772349 4772349 + Missense_Mutation SNP C C T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr1:4772349C>T ENST00000378191.4 + 2 800 c.419C>T c.(418-420)gCg>gTg p.A140V AJAP1_ENST00000378190.3_Missense_Mutation_p.A140V NM_018836.3 NP_061324.1 Q9UKB5 AJAP1_HUMAN adherens junctions associated protein 1 24 all_cancers(77;0.071)|Ovarian(185;0.0721) all_cancers(23;1.77e-36)|all_epithelial(116;1.26e-21)|all_lung(118;3.51e-08)|Lung NSC(185;3.47e-06)|all_neural(13;8.84e-06)|all_hematologic(16;7.61e-05)|Breast(487;0.000507)|Renal(390;0.0007)|Colorectal(325;0.00117)|Hepatocellular(190;0.0071)|Glioma(11;0.0155)|Myeloproliferative disorder(586;0.0258)|Ovarian(437;0.0409)|Lung SC(97;0.133)|Medulloblastoma(700;0.215) TCGTCCTCCGCGGTGGCCGGT 0.716000 0 SO:0001583 missense ENST00000378191.4 1 1 hg19 CCDS54.1 . . . . . . . . . . C 1.639 -0.516965 0.04171 . . ENSG00000196581 ENST00000378190;ENST00000378191 T;T 0.44482 0.92;0.92 4.55 -0.916 0.10489 . 2.012640 0.02618 N 0.102845 T 0.26484 0.0647 N 0.14661 0.345 0.09310 N 1 B 0.06786 0.001 B 0.04013 0.001 T 0.15954 -1.0419 10 0.30078 T 0.28 1.4174 7.1766 0.25749 0.0:0.4287:0.0:0.5713 . 140 Q9UKB5 AJAP1_HUMAN V 140 ENSP00000367432:A140V;ENSP00000367433:A140V ENSP00000367432:A140V A + 2 0 AJAP1 4672209 0.000000 0.05858 0.000000 0.03702 0.177000 0.22998 -1.001000 0.03690 -0.051000 0.13334 -0.362000 0.07510 GCG TCGA-IB-7890-01A-12D-2201-08 AJAP1-001 KNOWN NMD_exception|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000001542.3 1 0 0 10 35 0 17 0 0 0 0 17 2 0 0 0 0 0 2 1 0.996697 10 31 0 17 2 0 0 0 0 17 2 -19.928010 1 1 118208 7 29 1 1 2 3 1.787418 0 0.360000 2.800000 0.367964 0.990000 0.680000 1.000000 1.000000 0.967865 0.990000 1 0.940000 1.000000 GLMN 11146 broad.mit.edu 37 1 92737124 92737124 + Missense_Mutation SNP A A G TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr1:92737124A>G ENST00000370360.3 - 8 902 c.821T>C c.(820-822)tTt>tCt p.F274S GLMN_ENST00000534881.1_Missense_Mutation_p.F274S NM_053274.2 NP_444504.1 Q92990 GLMN_HUMAN glomulin, FKBP associated protein 17 all_lung(203;0.00827)|Lung NSC(277;0.0295) TTCTTCTTCAAATTCAAGGTA 0.353000 Multiple Glomus Tumors (of the Skin), Familial 0 SO:0001583 missense Familial Cancer Database Multiple Familial Glomangiomas, Hereditary Multiple Glomus Tumors, Familial Multiple Glomangiomatosis, Inherited Cutaneous Venous Anomalies, incl. Familial Multiple Glomangiomyoma ENST00000370360.3 1 1 hg19 CCDS738.1 . . . . . . . . . . A 16.61 3.171313 0.57584 . . ENSG00000174842 ENST00000370360;ENST00000534881 T;T 0.47528 0.84;0.84 5.08 5.08 0.68730 . 0.151067 0.64402 D 0.000010 T 0.38081 0.1027 L 0.56769 1.78 0.40471 D 0.980344 P;P 0.43633 0.813;0.492 P;B 0.44647 0.456;0.193 T 0.35076 -0.9803 10 0.45353 T 0.12 -13.5471 14.0348 0.64638 1.0:0.0:0.0:0.0 . 274;274 B4DJ85;Q92990 .;GLMN_HUMAN S 274 ENSP00000359385:F274S;ENSP00000440156:F274S ENSP00000359385:F274S F - 2 0 GLMN 92509712 1.000000 0.71417 1.000000 0.80357 0.978000 0.69477 5.565000 0.67365 1.902000 0.55061 0.482000 0.46254 TTT TCGA-IB-7890-01A-12D-2201-08 GLMN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000028358.1 1 0 1 82 357 0 91 0 3.890263e-01 0 7 0 91 2 0 0 0 0 0 2 1 1.000000 82 351 0 91 2 0 0 0 0 91 2 -20.000000 1 1 0 0 1 1 2 3 1.807388 0 0.360000 2.800000 0.372426 0.990000 0.860000 1.000000 1.000000 0.984102 0.990000 1 0.950000 1.000000 MC3R 4159 broad.mit.edu 37 20 54824818 54824818 + Missense_Mutation SNP C C T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr20:54824818C>T ENST00000243911.2 + 1 1031 c.919C>T c.(919-921)Cgc>Tgc p.R307C NM_019888.3 NP_063941.3 P41968 MC3R_HUMAN melanocortin 3 receptor p.R344C(1) 26 Colorectal(105;0.202) CCTGGAATTGCGCAACACCTT 0.517000 1 Substitution - Missense(1) SO:0001583 missense ENST00000243911.2 1 1 hg19 CCDS13449.2 . . . . . . . . . . C 12.54 1.967174 0.34754 . . ENSG00000124089 ENST00000243911 T 0.58358 0.34 5.09 3.06 0.35304 . 0.000000 0.64402 D 0.000014 T 0.80989 0.4730 H 0.97440 4.005 0.54753 D 0.999986 D 0.89917 1.0 D 0.83275 0.996 D 0.85842 0.1398 10 0.87932 D 0 . 13.1951 0.59734 0.4134:0.5866:0.0:0.0 . 344 P41968 MC3R_HUMAN C 307 ENSP00000243911:R307C ENSP00000243911:R307C R + 1 0 MC3R 54258225 1.000000 0.71417 0.993000 0.49108 0.191000 0.23601 2.103000 0.41806 0.477000 0.27464 0.555000 0.69702 CGC TCGA-IB-7890-01A-12D-2201-08 MC3R-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079786.2 1 0 0 47 1071 0 167 0 0 0 0 167 2 0 0 0 0 0 2 1 1.000000 47 1052 0 164 2 0 0 0 0 167 2 -4.402638 1 1 0 0 1 2 2 4 2.306405 1 0.360000 2.800000 0.515298 0.310000 0.220000 1.000000 0.300000 0.375074 0.310000 0 0.260000 0.380000 ZNF831 128611 broad.mit.edu 37 20 57769548 57769548 + Silent SNP G G A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr20:57769548G>A ENST00000371030.2 + 1 3474 c.3474G>A c.(3472-3474)acG>acA p.T1158T NM_178457.1 NP_848552.1 Q5JPB2 ZN831_HUMAN zinc finger protein 831 p.T1158T(1) 125 all_lung(29;0.0085) ACTCAGGGACGTCCCGGAGCC 0.672000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000371030.2 1 1 hg19 CCDS42894.1 TCGA-IB-7890-01A-12D-2201-08 ZNF831-001 NOVEL basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000079916.2 1 0 1 84 480 0 161 0 0 0 0 161 2 0 0 0 0 0 2 1 1.000000 82 468 0 158 2 0 0 0 0 161 2 -20.000000 1 1 120958 1 31 1 2 2 4 2.306405 1 0.360000 2.800000 0.515298 0.990000 0.880000 1.000000 1.000000 0.990513 0.990000 1 0.990000 1.000000 TCN2 6948 broad.mit.edu 37 22 31011344 31011344 + Missense_Mutation SNP C C T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr22:31011344C>T ENST00000215838.3 + 5 1131 c.637C>T c.(637-639)Cct>Tct p.P213S TCN2_ENST00000405742.3_Missense_Mutation_p.P209S|TCN2_ENST00000407817.3_Missense_Mutation_p.P186S P20062 TCO2_HUMAN transcobalamin II 22 Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200) AAACTTCAACCCTGGTCGGAG 0.557000 0 SO:0001583 missense ENST00000215838.3 1 1 hg19 CCDS13881.1 . . . . . . . . . . C 10.23 1.293005 0.23564 . . ENSG00000185339 ENST00000215838;ENST00000405742;ENST00000407817 T;T;T 0.33865 1.39;1.39;1.39 5.82 2.59 0.31030 . 0.407958 0.29684 N 0.011470 T 0.20129 0.0484 N 0.22421 0.69 0.80722 D 1 B;B;B 0.27166 0.17;0.113;0.113 B;B;B 0.30029 0.11;0.031;0.031 T 0.05386 -1.0888 10 0.14252 T 0.57 -3.8544 5.8302 0.18577 0.1552:0.6812:0.0:0.1636 . 186;209;213 Q96FD4;B5MBX2;P20062 .;.;TCO2_HUMAN S 213;209;186 ENSP00000215838:P213S;ENSP00000385914:P209S;ENSP00000384914:P186S ENSP00000215838:P213S P + 1 0 TCN2 29341344 0.001000 0.12720 0.636000 0.29352 0.333000 0.28666 0.476000 0.22180 0.357000 0.24183 0.561000 0.74099 CCT TCGA-IB-7890-01A-12D-2201-08 TCN2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000321282.2 1 0 1 63 383 0 123 1 9.997559e-01 6 70 0 123 2 0 0 0 0 0 2 1 1.000000 63 379 0 121 2 0 0 0 0 123 2 -3.222205 1 1 0 0 1 1 2 3 2.080136 1 0.360000 2.800000 0.457627 0.920000 0.720000 1.000000 1.000000 0.915268 0.920000 1 0.820000 1.000000 BUB1 699 broad.mit.edu 37 2 111399371 111399371 + Missense_Mutation SNP G G T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr2:111399371G>T ENST00000302759.6 - 21 2591 c.2473C>A c.(2473-2475)Cct>Act p.P825T BUB1_ENST00000478175.1_5'UTR|BUB1_ENST00000409311.1_Missense_Mutation_p.P825T|BUB1_ENST00000535254.1_Missense_Mutation_p.P805T NM_004336.3 NP_004327.1 O43683 BUB1_HUMAN BUB1 mitotic checkpoint serine/threonine kinase 45 Ovarian(717;0.0822) GGGTTGGCAGGCTTTTGGACC 0.398000 0 SO:0001583 missense ENST00000302759.6 1 1 hg19 CCDS33273.1 . . . . . . . . . . G 22.7 4.326955 0.81690 . . ENSG00000169679 ENST00000535254;ENST00000409311;ENST00000302759 T;T;T 0.64085 -0.08;2.08;-0.08 6.16 5.29 0.74685 Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); 0.049093 0.85682 D 0.000000 T 0.80380 0.4612 M 0.83312 2.635 0.80722 D 1 D;D;D 0.89917 0.999;1.0;1.0 D;D;D 0.97110 0.998;1.0;0.999 D 0.83628 0.0143 10 0.87932 D 0 -15.6873 14.2663 0.66121 0.0712:0.0:0.9288:0.0 . 805;825;825 F5GXI5;E9PC26;O43683 .;.;BUB1_HUMAN T 805;825;825 ENSP00000441013:P805T;ENSP00000386701:P825T;ENSP00000302530:P825T ENSP00000302530:P825T P - 1 0 BUB1 111115843 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 6.376000 0.73141 1.631000 0.50456 0.650000 0.86243 CCT TCGA-IB-7890-01A-12D-2201-08 BUB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000331925.1 1 0 1 128 738 0 180 1 8.169202e-01 9 11 0 180 2 0 0 0 0 0 2 1 1.000000 127 730 0 179 2 0 0 0 0 180 2 -20.000000 1 1 0 0 1 1 2 3 2.079998 1 0.360000 2.800000 0.457627 0.960000 0.810000 1.000000 1.000000 0.952582 0.960000 1 0.880000 1.000000 GAD1 2571 broad.mit.edu 37 2 171687567 171687567 + Missense_Mutation SNP G G T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr2:171687567G>T ENST00000358196.3 + 5 962 c.412G>T c.(412-414)Gtg>Ttg p.V138L GAD1_ENST00000429023.1_3'UTR|GAD1_ENST00000375272.1_Missense_Mutation_p.V138L|GAD1_ENST00000344257.5_Missense_Mutation_p.V138L NM_000817.2 NP_000808.2 Q99259 DCE1_HUMAN glutamate decarboxylase 1 (brain, 67kDa) 35 CTCCACCAAGGTGCTGGACTT 0.547000 0 SO:0001583 missense ENST00000358196.3 1 1 hg19 CCDS2239.1 . . . . . . . . . . G 32 5.180048 0.94846 . . ENSG00000128683 ENST00000358196;ENST00000375272;ENST00000344257 T;T;T 0.44083 0.93;0.93;0.93 5.9 5.9 0.94986 Pyridoxal phosphate-dependent transferase, major domain (1); 0.167622 0.51477 D 0.000087 T 0.53818 0.1820 M 0.75615 2.305 0.80722 D 1 B;P 0.35348 0.023;0.496 B;B 0.40228 0.088;0.323 T 0.56854 -0.7910 10 0.87932 D 0 -18.4861 20.2673 0.98463 0.0:0.0:1.0:0.0 . 138;138 Q99259;Q99259-3 DCE1_HUMAN;. L 138 ENSP00000350928:V138L;ENSP00000364421:V138L;ENSP00000341167:V138L ENSP00000341167:V138L V + 1 0 GAD1 171395813 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 7.638000 0.83328 2.786000 0.95864 0.643000 0.83706 GTG TCGA-IB-7890-01A-12D-2201-08 GAD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000102664.2 1 0 1 61 377 0 96 0 2.012987e-02 1 1 0 96 2 0 0 0 0 0 2 1 1.000000 57 369 0 92 2 0 0 0 0 96 2 -20.000000 1 1 0 0 1 1 2 3 2.079998 1 0.360000 2.800000 0.457627 0.910000 0.710000 1.000000 1.000000 0.905526 0.910000 1 0.800000 1.000000 DCAF17 80067 broad.mit.edu 37 2 172330428 172330428 + Missense_Mutation SNP T T A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr2:172330428T>A ENST00000375255.3 + 10 1361 c.1034T>A c.(1033-1035)aTc>aAc p.I345N DCAF17_ENST00000539783.1_Intron|DCAF17_ENST00000468592.1_3'UTR NM_025000.3 NP_079276.2 Q5H9S7 DCA17_HUMAN DDB1 and CUL4 associated factor 17 17 TCTGACTGGATCTATTTCCAT 0.348000 0 SO:0001583 missense ENST00000375255.3 1 1 hg19 CCDS2243.2 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. T|T 24.5|24.5 4.534753|4.534753 0.85812|0.85812 .|. .|. ENSG00000115827|ENSG00000115827 ENST00000375255;ENST00000429466|ENST00000339506;ENST00000431110 T|. 0.53423|. 0.62|. 5.53|5.53 5.53|5.53 0.82687|0.82687 .|. 0.048318|. 0.85682|. D|. 0.000000|. T|T 0.70579|0.70579 0.3240|0.3240 L|L 0.60455|0.60455 1.87|1.87 0.80722|0.80722 D|D 1|1 D|. 0.76494|. 0.999|. D|. 0.79108|. 0.992|. T|T 0.69383|0.69383 -0.5160|-0.5160 10|5 0.66056|. D|. 0.02|. -10.6448|-10.6448 15.6457|15.6457 0.77049|0.77049 0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0 .|. 345|. Q5H9S7|. DCA17_HUMAN|. N|T 345;95|96;47 ENSP00000364404:I345N|. ENSP00000364404:I345N|. I|S +|+ 2|1 0|0 DCAF17|DCAF17 172038674|172038674 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.999000|0.999000 0.98932|0.98932 7.618000|7.618000 0.83043|0.83043 2.075000|2.075000 0.62263|0.62263 0.533000|0.533000 0.62120|0.62120 ATC|TCT TCGA-IB-7890-01A-12D-2201-08 DCAF17-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000255342.2 1 0 1 32 242 0 44 1 2.013880e-01 2 5 0 44 2 0 0 0 0 0 2 1 1.000000 32 238 0 44 2 0 0 0 0 44 2 -20.000000 1 1 0 0 1 1 2 3 2.079998 1 0.360000 2.800000 0.457627 0.760000 0.540000 1.000000 1.000000 0.777277 0.760000 0 0.640000 0.900000 TTN 7273 broad.mit.edu 37 2 179638314 179638314 + Missense_Mutation SNP C C T rs148920986 by1000genomes TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr2:179638314C>T ENST00000591111.1 - 32 7693 c.7469G>A c.(7468-7470)cGt>cAt p.R2490H TTN_ENST00000360870.5_Missense_Mutation_p.R2490H|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R2490H|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R2444H|TTN_ENST00000589042.1_Missense_Mutation_p.R2490H|TTN_ENST00000342175.6_Missense_Mutation_p.R2444H|TTN_ENST00000359218.5_Missense_Mutation_p.R2444H|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) GGCCTGTACACGGTCATCAGG 0.438000 0 SO:0001583 missense ENST00000591111.1 0 1 hg19 . . . . . . . . . . C 12.75 2.031724 0.35797 . . ENSG00000155657 ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870 T;T;T;T;T 0.52057 0.68;0.68;0.68;0.68;0.68 5.82 5.82 0.92795 Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1); . . . . T 0.70334 0.3212 M 0.70903 2.155 0.31701 N 0.640681 D;D;D;D;D 0.89917 0.999;0.999;0.999;1.0;1.0 D;D;D;D;D 0.74348 0.947;0.947;0.947;0.971;0.983 T 0.72988 -0.4124 9 0.87932 D 0 . 20.1143 0.97922 0.0:1.0:0.0:0.0 . 2444;2444;2444;2490;2490 D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6 .;.;.;TITIN_HUMAN;. H 2490;2444;2444;2444;2444;2490 ENSP00000343764:R2490H;ENSP00000434586:R2444H;ENSP00000340554:R2444H;ENSP00000352154:R2444H;ENSP00000354117:R2490H ENSP00000340554:R2444H R - 2 0 TTN 179346559 1.000000 0.71417 0.966000 0.40874 0.554000 0.35429 7.818000 0.86416 2.765000 0.95021 0.650000 0.86243 CGT TCGA-IB-7890-01A-12D-2201-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 0 0 0 13 529 0 73 0 0 0 0 73 2 0 0 0 0 0 2 1 0.999506 13 523 0 73 2 0 0 0 0 73 2 -2.613097 1 1 121406 1 39 1 1 2 3 2.027219 1 0.360000 2.800000 0.450077 0.160000 0.080000 1.000000 0.150000 0.226666 0.160000 0 0.110000 0.230000 ZNF804A 91752 broad.mit.edu 37 2 185801329 185801329 + Silent SNP A A G TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr2:185801329A>G ENST00000302277.6 + 4 1800 c.1206A>G c.(1204-1206)tcA>tcG p.S402S NM_194250.1 NP_919226.1 Q7Z570 Z804A_HUMAN zinc finger protein 804A 146 TGGCCCCTTCAAATACTGAAG 0.388000 0 SO:0001819 synonymous_variant ENST00000302277.6 1 1 hg19 CCDS2291.1 TCGA-IB-7890-01A-12D-2201-08 ZNF804A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255871.1 1 0 1 57 379 0 73 0 0 0 0 73 2 0 0 0 0 0 2 1 1.000000 56 377 0 71 2 0 0 0 0 73 2 -20.000000 1 1 0 0 1 1 2 3 2.027219 1 0.360000 2.800000 0.450077 0.850000 0.650000 1.000000 1.000000 0.860113 0.850000 1 0.740000 0.990000 PKDCC 91461 broad.mit.edu 37 2 42281326 42281326 + Missense_Mutation SNP C C T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr2:42281326C>T ENST00000294964.5 + 3 1093 c.913C>T c.(913-915)Ccg>Tcg p.P305S NM_138370.2 NP_612379.2 protein kinase domain containing, cytoplasmic 8 GGAGGAGACGCCGTGTGCAGG 0.637000 0 SO:0001583 missense ENST00000294964.5 1 1 hg19 CCDS33186.2 . . . . . . . . . . C 8.736 0.917815 0.17982 . . ENSG00000162878 ENST00000294964 . . . 5.08 5.08 0.68730 Protein kinase, catalytic domain (1); 0.270435 0.42548 D 0.000699 T 0.33352 0.0860 N 0.21194 0.64 0.45015 D 0.998034 B 0.30326 0.276 B 0.29267 0.1 T 0.13764 -1.0497 9 0.07482 T 0.82 -25.5501 10.9735 0.47452 0.0:0.9047:0.0:0.0953 . 305 Q504Y2 PKDCC_HUMAN S 305 . ENSP00000294964:P305S P + 1 0 PKDCC 42134830 0.232000 0.23762 0.252000 0.24328 0.754000 0.42855 1.211000 0.32382 2.367000 0.80283 0.561000 0.74099 CCG TCGA-IB-7890-01A-12D-2201-08 PKDCC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000325745.3 1 0 1 11 54 0 27 0 9.999338e-01 0 101 0 27 2 0 0 0 0 0 2 1 0.998717 11 53 0 27 2 0 0 0 0 27 2 -19.869220 1 1 0 0 1 0 2 2 1.840964 1 0.360000 2.800000 0.360000 0.940000 0.520000 1.000000 1.000000 0.882651 0.940000 1 0.710000 1.000000 ALMS1 7840 broad.mit.edu 37 2 73675916 73675916 + Silent SNP T T C TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr2:73675916T>C ENST00000264448.6 + 8 2370 c.2259T>C c.(2257-2259)acT>acC p.T753T ALMS1_ENST00000377715.1_Silent_p.T753T|ALMS1_ENST00000409009.1_Silent_p.T711T NM_015120.4 NP_055935 Q8TCU4 ALMS1_HUMAN Alstrom syndrome 1 147 ACCAGAAGACTGAGATACCAG 0.443000 0 SO:0001819 synonymous_variant ENST00000264448.6 1 1 hg19 CCDS42697.1 TCGA-IB-7890-01A-12D-2201-08 ALMS1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000327776.1 1 0 1 149 1010 0 207 0 1.281800e-01 1 4 0 207 2 0 0 0 0 0 2 1 1.000000 144 997 0 205 2 0 0 0 0 207 2 -20.000000 1 1 0 0 1 1 2 3 2.079998 1 0.360000 2.800000 0.457627 0.830000 0.710000 0.970000 0.840000 0.845819 0.830000 0 0.770000 0.910000 TMCC1 23023 broad.mit.edu 37 3 129370592 129370592 + Missense_Mutation SNP T T A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr3:129370592T>A ENST00000393238.3 - 6 2034 c.1694A>T c.(1693-1695)cAg>cTg p.Q565L TMCC1_ENST00000329333.5_Missense_Mutation_p.Q386L|TMCC1_ENST00000426664.2_Missense_Mutation_p.Q451L|TMCC1_ENST00000432054.2_Missense_Mutation_p.Q241L NM_001017395.3 NP_001017395.2 O94876 TMCC1_HUMAN transmembrane and coiled-coil domain family 1 PLXND1/TMCC1(4) 25 CTGCTGCTGCTGCAGCTCCAT 0.572000 0 SO:0001583 missense ENST00000393238.3 0 1 hg19 CCDS33855.1 . . . . . . . . . . T 20.6 4.009576 0.75046 . . ENSG00000172765 ENST00000432054;ENST00000393238;ENST00000426664;ENST00000329333 T;T;T;T 0.50001 0.76;0.76;0.76;0.76 5.16 5.16 0.70880 . 0.000000 0.85682 D 0.000000 T 0.61261 0.2333 L 0.46614 1.455 0.80722 D 1 D;D 0.67145 0.996;0.985 D;D 0.85130 0.997;0.973 T 0.58278 -0.7664 10 0.33940 T 0.23 -18.4911 15.1509 0.72696 0.0:0.0:0.0:1.0 . 386;565 B4DE04;O94876 .;TMCC1_HUMAN L 241;565;451;386 ENSP00000404711:Q241L;ENSP00000376930:Q565L;ENSP00000389892:Q451L;ENSP00000327349:Q386L ENSP00000327349:Q386L Q - 2 0 TMCC1 130853282 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 7.735000 0.84939 2.172000 0.68678 0.533000 0.62120 CAG TCGA-IB-7890-01A-12D-2201-08 TMCC1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000356418.2 0 0 0 7 454 0 102 0 3.361927e-01 0 70 0 102 2 0 0 0 0 0 2 1 0.982627 6 468 0 103 2 0 0 0 0 102 2 -2.087369 0 1 0 0 1 1 3 4 2.397542 1 0.360000 2.800000 0.529412 0.120000 0.040000 0.230000 0.120000 0.130371 0.120000 0 0.070000 0.180000 IGSF10 285313 broad.mit.edu 37 3 151155880 151155880 + Missense_Mutation SNP C C A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr3:151155880C>A ENST00000282466.3 - 6 6468 c.6469G>T c.(6469-6471)Gac>Tac p.D2157Y 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) ACAGCTGTGTCTCCAGCTTTG 0.443000 0 SO:0001583 missense ENST00000282466.3 1 1 hg19 CCDS3160.1 . . . . . . . . . . C 16.61 3.170322 0.57584 . . ENSG00000152580 ENST00000282466 T 0.30714 1.52 5.86 5.86 0.93980 Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.270973 0.25968 N 0.027154 T 0.51669 0.1688 L 0.47016 1.485 0.58432 D 0.999999 D;D 0.63880 0.993;0.984 D;P 0.68192 0.956;0.847 T 0.47787 -0.9090 10 0.87932 D 0 . 20.1865 0.98220 0.0:1.0:0.0:0.0 . 2157;184 Q6WRI0;Q6WRI0-2 IGS10_HUMAN;. Y 2157 ENSP00000282466:D2157Y ENSP00000282466:D2157Y D - 1 0 IGSF10 152638570 1.000000 0.71417 0.734000 0.30879 0.291000 0.27294 5.741000 0.68638 2.775000 0.95449 0.655000 0.94253 GAC TCGA-IB-7890-01A-12D-2201-08 IGSF10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000357782.1 1 0 1 69 433 0 73 0 0 0 0 73 2 0 0 0 0 0 2 1 1.000000 67 428 0 71 2 0 0 0 0 73 2 -20.000000 1 1 0 0 1 1 3 4 2.397542 1 0.360000 2.800000 0.529412 0.990000 0.820000 1.000000 1.000000 0.973781 0.990000 1 0.920000 1.000000 CCDC39 339829 broad.mit.edu 37 3 180334120 180334120 + Missense_Mutation SNP T T G TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr3:180334120T>G ENST00000442201.2 - 19 2737 c.2618A>C c.(2617-2619)aAa>aCa p.K873T TTC14_ENST00000382584.4_Intron|CCDC39_ENST00000273654.4_3'UTR NM_181426.1 NP_852091.1 Q9UFE4 CCD39_HUMAN coiled-coil domain containing 39 45 all_cancers(143;9.31e-15)|Ovarian(172;0.0212) OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558) ACGACTGCCTTTTGTGCTAGC 0.373000 0 SO:0001583 missense ENST00000442201.2 1 1 hg19 CCDS46964.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. T|T 13.12|13.12 2.143344|2.143344 0.37825|0.37825 .|. .|. ENSG00000145075|ENSG00000145075 ENST00000473854|ENST00000489868;ENST00000442201 .|. .|. .|. 5.23|5.23 0.0174|0.0174 0.14112|0.14112 .|. .|. .|. .|. .|. T|T 0.16854|0.16854 0.0405|0.0405 N|N 0.20685|0.20685 0.6|0.6 0.09310|0.09310 N|N 1|1 .|B .|0.13145 .|0.007 .|B .|0.15484 .|0.013 T|T 0.24297|0.24297 -1.0164|-1.0164 6|8 0.41790|0.21014 T|T 0.15|0.42 .|. 0.3031|0.3031 0.00276|0.00276 0.2106:0.1895:0.2605:0.3393|0.2106:0.1895:0.2605:0.3393 .|. .|873 .|Q9UFE4 .|CCD39_HUMAN Q|T 57|45;873 .|. ENSP00000418482:K57Q|ENSP00000405708:K873T K|K -|- 1|2 0|0 CCDC39|CCDC39 181816814|181816814 0.000000|0.000000 0.05858|0.05858 0.005000|0.005000 0.12908|0.12908 0.089000|0.089000 0.18198|0.18198 -0.057000|-0.057000 0.11768|0.11768 0.399000|0.399000 0.25367|0.25367 0.374000|0.374000 0.22700|0.22700 AAG|AAA TCGA-IB-7890-01A-12D-2201-08 CCDC39-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000349783.3 1 0 1 113 182 0 26 0 4.962553e-01 0 4 0 26 2 0 0 0 0 0 2 1 1.000000 113 176 0 26 2 0 0 0 0 26 2 -20.000000 1 1 0 0 1 1 3 4 2.397542 1 0.360000 2.800000 0.529412 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 ZNF385D 79750 broad.mit.edu 37 3 21462858 21462858 + Missense_Mutation SNP C C T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr3:21462858C>T ENST00000281523.2 - 8 1554 c.1036G>A c.(1036-1038)Gca>Aca p.A346T NM_024697.2 NP_078973.1 Q9H6B1 Z385D_HUMAN zinc finger protein 385D 46 actgctgctgcggctgctgca 0.517000 0 SO:0001583 missense ENST00000281523.2 1 1 hg19 CCDS2636.1 . . . . . . . . . . C 8.978 0.974663 0.18736 . . ENSG00000151789 ENST00000281523 T 0.33865 1.39 6.08 6.08 0.98989 . 0.053442 0.85682 D 0.000000 T 0.31009 0.0783 L 0.34521 1.04 0.48452 D 0.999653 B 0.25390 0.125 B 0.13407 0.009 T 0.05582 -1.0876 10 0.19590 T 0.45 -47.3476 20.6593 0.99626 0.0:1.0:0.0:0.0 . 346 Q9H6B1 Z385D_HUMAN T 346 ENSP00000281523:A346T ENSP00000281523:A346T A - 1 0 ZNF385D 21437862 0.998000 0.40836 0.210000 0.23637 0.083000 0.17756 3.858000 0.55979 2.887000 0.99086 0.650000 0.86243 GCA TCGA-IB-7890-01A-12D-2201-08 ZNF385D-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252884.1 1 0 1 20 88 0 32 0 0 0 0 32 2 0 0 0 0 0 2 1 0.999994 18 81 0 32 2 0 0 0 0 32 2 -20.000000 1 1 121336 6 35 1 1 2 3 1.763537 0 0.360000 2.800000 0.364575 0.990000 0.670000 1.000000 1.000000 0.943939 0.990000 1 0.840000 1.000000 GLB1 2720 broad.mit.edu 37 3 33038656 33038656 + Missense_Mutation SNP C C T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr3:33038656C>T ENST00000399402.3 - 16 1956 c.1825G>A c.(1825-1827)Gtg>Atg p.V609M GLB1_ENST00000445488.2_Missense_Mutation_p.V687M|GLB1_ENST00000307363.5_Missense_Mutation_p.V639M|GLB1_ENST00000307377.8_Missense_Mutation_p.V508M NM_001079811.1 NP_001073279 P16278 BGAL_HUMAN galactosidase, beta 1 21 Melanoma(143;0.104) GGCCTGTCCACGAACGTCACA 0.527000 0 SO:0001583 missense ENST00000399402.3 1 1 hg19 CCDS43062.1 . . . . . . . . . . C 13.45 2.241095 0.39598 . . ENSG00000170266 ENST00000399402;ENST00000307363;ENST00000445488;ENST00000307377 D;D;D;D 0.95853 -3.83;-3.83;-3.83;-3.83 5.44 4.54 0.55810 Galactose-binding domain-like (1); 0.238643 0.42964 D 0.000639 D 0.94971 0.8373 M 0.67700 2.07 0.37730 D 0.925223 D;D;D;D 0.64830 0.987;0.994;0.987;0.987 P;P;P;P 0.46299 0.46;0.511;0.46;0.46 D 0.95168 0.8287 10 0.48119 T 0.1 -10.5338 15.5983 0.76606 0.0:0.8614:0.1386:0.0 . 639;508;639;687 Q53G40;E7EQ29;P16278;B7Z6Q5 .;.;BGAL_HUMAN;. M 609;639;687;508 ENSP00000382333:V609M;ENSP00000306920:V639M;ENSP00000393377:V687M;ENSP00000305920:V508M ENSP00000306920:V639M V - 1 0 GLB1 33013660 0.991000 0.36638 0.794000 0.32065 0.166000 0.22503 2.596000 0.46205 1.253000 0.44018 0.555000 0.69702 GTG TCGA-IB-7890-01A-12D-2201-08 GLB1-002 NOVEL basic|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000341570.2 0 0 1 74 390 0 136 1 1 23 119 0 136 2 0 0 0 0 0 2 1 1.000000 73 380 0 133 2 0 0 0 0 136 2 -20.000000 1 1 0 0 1 1 2 3 1.763537 0 0.360000 2.800000 0.364575 0.890000 0.710000 1.000000 1.000000 0.892979 0.890000 1 0.790000 1.000000 COL25A1 84570 broad.mit.edu 37 4 109784536 109784536 + Missense_Mutation SNP C C T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr4:109784536C>T ENST00000399132.1 - 21 1621 c.1091G>A c.(1090-1092)cGg>cAg p.R364Q COL25A1_ENST00000399126.1_Missense_Mutation_p.R364Q|COL25A1_ENST00000399127.1_Missense_Mutation_p.R360Q NM_198721.2 NP_942014.1 collagen, type XXV, alpha 1 49 Hepatocellular(203;0.217) TGCTTCCCCCCGTTCACCCTG 0.502000 0 SO:0001583 missense ENST00000399132.1 1 1 hg19 CCDS43258.1 . . . . . . . . . . C 17.78 3.472391 0.63737 0.0 1.22E-4 ENSG00000188517 ENST00000399132;ENST00000333642;ENST00000401873;ENST00000399127;ENST00000399126;ENST00000443653 D;T;D 0.93547 -3.24;2.3;-3.24 5.52 4.69 0.59074 . 0.121454 0.50627 D 0.000106 D 0.94019 0.8084 L 0.33293 1 0.42993 D 0.994495 D;D 0.76494 0.999;0.998 D;D 0.79108 0.975;0.992 D 0.93272 0.6652 9 . . . -7.1172 14.6461 0.68762 0.0:0.9299:0.0:0.0701 . 364;364 Q9BXS0-2;Q9BXS0 .;COPA1_HUMAN Q 364;366;345;360;364;294 ENSP00000382083:R364Q;ENSP00000382078:R360Q;ENSP00000382077:R364Q . R - 2 0 COL25A1 110003985 0.997000 0.39634 0.997000 0.53966 0.955000 0.61496 2.451000 0.44952 1.332000 0.45431 -0.128000 0.14901 CGG TCGA-IB-7890-01A-12D-2201-08 COL25A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000315938.2 1 0 1 60 178 0 29 0 0 0 0 29 2 0 0 0 0 0 2 1 1.000000 57 175 0 29 2 0 0 0 0 29 2 -4.293586 1 1 120798 13 40 1 1 2 3 2.062099 1 0.360000 2.800000 0.457627 0.990000 0.990000 1.000000 1.000000 0.999999 0.990000 1 0.990000 1.000000 AGPAT9 84803 broad.mit.edu 37 4 84508424 84508424 + Missense_Mutation SNP A A T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr4:84508424A>T ENST00000395226.2 + 5 714 c.496A>T c.(496-498)Att>Ttt p.I166F AGPAT9_ENST00000264409.4_Missense_Mutation_p.I166F NM_001256421.1 NP_001243350.1 Q53EU6 GPAT3_HUMAN 1-acylglycerol-3-phosphate O-acyltransferase 9 13 Hepatocellular(203;0.114) CTTGGCTTTCATTGGGATCAG 0.398000 0 SO:0001583 missense ENST00000395226.2 1 1 hg19 CCDS3606.1 . . . . . . . . . . A 15.12 2.739003 0.49045 . . ENSG00000138678 ENST00000395226;ENST00000264409 T;T 0.49432 0.78;0.78 5.55 -1.01 0.10169 . 0.147943 0.64402 N 0.000012 T 0.30572 0.0769 L 0.46670 1.46 0.80722 D 1 B 0.06786 0.001 B 0.04013 0.001 T 0.04693 -1.0933 10 0.21540 T 0.41 -12.882 4.0871 0.09951 0.6087:0.1039:0.0645:0.223 . 166 Q53EU6 GPAT3_HUMAN F 166 ENSP00000378651:I166F;ENSP00000264409:I166F ENSP00000264409:I166F I + 1 0 AGPAT9 84727448 1.000000 0.71417 0.998000 0.56505 0.995000 0.86356 5.057000 0.64294 0.038000 0.15604 0.528000 0.53228 ATT TCGA-IB-7890-01A-12D-2201-08 AGPAT9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252821.3 1 0 1 182 501 0 126 1 4.032278e-01 3 2 0 126 2 0 0 0 0 0 2 1 1.000000 182 489 0 125 2 0 0 0 0 126 2 -20.000000 1 1 0 0 1 1 2 3 2.062099 1 0.360000 2.800000 0.457627 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 PCDHGA6 56109 broad.mit.edu 37 5 140755877 140755877 + Missense_Mutation SNP G G A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr5:140755877G>A ENST00000517434.1 + 1 2227 c.2227G>A c.(2227-2229)Gtg>Atg p.V743M PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron NM_018919.2|NM_032086.1 NP_061742.1|NP_114475.1 Q9Y5G7 PCDG6_HUMAN protocadherin gamma subfamily A, 6 p.V743M(1) 2 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) CTTTGTGGGCGTGGAAGGGGT 0.612000 1 Substitution - Missense(1) SO:0001583 missense ENST00000517434.1 1 1 hg19 CCDS54926.1 . . . . . . . . . . . 7.493 0.651010 0.14516 . . ENSG00000253731 ENST00000517434 T 0.50548 0.74 5.15 -0.377 0.12501 . 0.398307 0.14856 N 0.294369 T 0.45115 0.1326 M 0.81497 2.545 0.20638 N 0.99987 B;B 0.30482 0.095;0.281 B;B 0.24394 0.053;0.043 T 0.40997 -0.9533 10 0.51188 T 0.08 . 9.8004 0.40761 0.4966:0.0:0.5034:0.0 . 743;743 Q9Y5G7-2;Q9Y5G7 .;PCDG6_HUMAN M 743 ENSP00000429601:V743M ENSP00000429601:V743M V + 1 0 PCDHGA6 140736061 0.000000 0.05858 0.756000 0.31282 0.025000 0.11179 -0.171000 0.09883 0.011000 0.14865 -0.812000 0.03155 GTG TCGA-IB-7890-01A-12D-2201-08 PCDHGA6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000374743.1 1 0 1 58 360 0 146 0 9.824316e-02 0 4 0 146 2 0 0 0 0 0 2 1 1.000000 56 348 0 140 2 0 0 0 0 146 2 -19.999990 1 1 0 0 1 1 2 3 2.041096 1 0.360000 2.800000 0.452617 0.900000 0.700000 1.000000 1.000000 0.901044 0.900000 1 0.790000 1.000000 GPR151 134391 broad.mit.edu 37 5 145895652 145895652 + Missense_Mutation SNP A A C TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr5:145895652A>C ENST00000311104.2 - 1 101 c.25T>G c.(25-27)Tct>Gct p.S9A NM_194251.2 NP_919227.2 Q8TDV0 GP151_HUMAN G protein-coupled receptor 151 14 KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) CTGGAGTTAGAGTCTGCAAAG 0.498000 Pancreas(78;420 1386 18535 37114 49710) 0 SO:0001583 missense ENST00000311104.2 1 1 hg19 CCDS34266.1 . . . . . . . . . . A 2.160 -0.392320 0.04932 . . ENSG00000173250 ENST00000311104 T 0.37915 1.17 5.9 3.48 0.39840 . 0.650871 0.16005 N 0.234105 T 0.25082 0.0609 L 0.54323 1.7 0.21967 N 0.999449 B 0.06786 0.001 B 0.06405 0.002 T 0.36529 -0.9744 10 0.07482 T 0.82 . 2.9555 0.05875 0.6321:0.1483:0.0774:0.1422 . 9 Q8TDV0 GP151_HUMAN A 9 ENSP00000308733:S9A ENSP00000308733:S9A S - 1 0 GPR151 145875845 0.992000 0.36948 0.959000 0.39883 0.576000 0.36127 1.388000 0.34442 0.465000 0.27167 -0.353000 0.07706 TCT TCGA-IB-7890-01A-12D-2201-08 GPR151-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000373457.1 1 0 1 96 604 0 165 0 0 0 0 165 2 0 0 0 0 0 2 1 1.000000 95 599 0 164 2 0 0 0 0 165 2 -20.000000 1 1 0 0 1 1 2 3 2.041096 1 0.360000 2.800000 0.452617 0.890000 0.730000 1.000000 1.000000 0.896039 0.890000 1 0.800000 1.000000 GPR98 84059 broad.mit.edu 37 5 89977223 89977223 + Silent SNP T T C TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr5:89977223T>C ENST00000405460.2 + 27 5712 c.5616T>C c.(5614-5616)ttT>ttC p.F1872F NM_032119.3 NP_115495.3 Q8WXG9 GPR98_HUMAN G protein-coupled receptor 98 269 all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192) AGTCACTCTTTGTCAGTGGAA 0.423000 0 SO:0001819 synonymous_variant ENST00000405460.2 1 1 hg19 CCDS47246.1 TCGA-IB-7890-01A-12D-2201-08 GPR98-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000369993.2 1 0 1 28 132 0 22 0 0 0 0 22 2 0 0 0 0 0 2 1 1.000000 28 128 0 22 2 0 0 0 0 22 2 -17.103450 1 1 0 0 1 0 2 2 1.734642 1 0.360000 2.800000 0.360000 0.970000 0.670000 1.000000 1.000000 0.925406 0.970000 1 0.810000 1.000000 GCM2 9247 broad.mit.edu 37 6 10882008 10882008 + Nonsense_Mutation SNP G G A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr6:10882008G>A ENST00000379491.4 - 1 166 c.19C>T c.(19-21)Cag>Tag p.Q7* RP11-637O19.2_ENST00000436249.3_RNA|SYCP2L_ENST00000543878.1_Intron|RP11-637O19.3_ENST00000480294.1_Intron NM_004752.3 NP_004743.1 O75603 GCM2_HUMAN glial cells missing homolog 2 (Drosophila) 30 Breast(50;0.0838)|Ovarian(93;0.107) all_hematologic(90;0.135) ACCGCTTCCTGCACCGCGGCC 0.602000 0 SO:0001587 stop_gained ENST00000379491.4 0 1 hg19 CCDS4517.1 . . . . . . . . . . G 34 5.409039 0.96072 . . ENSG00000124827 ENST00000379491 . . . 5.23 3.37 0.38596 . 0.740013 0.12306 N 0.480643 . . . . . . 0.22552 N 0.998994 . . . . . . . . . . 0.20046 T 0.44 0.1498 8.3322 0.32193 0.0:0.401:0.476:0.123 . . . . X 7 . ENSP00000368805:Q7X Q - 1 0 GCM2 10989994 0.000000 0.05858 0.008000 0.14137 0.053000 0.15095 0.153000 0.16323 1.155000 0.42497 0.561000 0.74099 CAG TCGA-IB-7890-01A-12D-2201-08 GCM2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000039844.1 1 0 0 35 170 0 63 0 0 0 1 0 63 2 0 0 0 0 0 2 1 1.000000 34 167 0 62 2 0 0 0 0 63 2 -20.000000 1 1 0 0 1 1 2 3 1.757599 0 0.360000 2.800000 0.362296 0.950000 0.680000 1.000000 1.000000 0.920909 0.950000 1 0.810000 1.000000 NRSN1 140767 broad.mit.edu 37 6 24146060 24146060 + Silent SNP C C T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr6:24146060C>T ENST00000378491.4 + 4 775 c.474C>T c.(472-474)atC>atT p.I158I NM_080723.4 NP_542454.3 neurensin 1 p.I158I(1) 22 AAGAACGAATCGCAGACATCA 0.498000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000378491.4 1 1 hg19 CCDS4549.1 TCGA-IB-7890-01A-12D-2201-08 NRSN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000043866.1 1 0 1 47 245 0 88 0 0 0 0 88 2 0 0 0 0 0 2 1 1.000000 47 243 0 88 2 0 0 0 0 88 2 -3.097887 1 1 121412 3 32 1 1 2 3 1.757599 0 0.360000 2.800000 0.362296 0.890000 0.670000 1.000000 1.000000 0.890551 0.890000 1 0.780000 1.000000 SRPK1 6732 broad.mit.edu 37 6 35810348 35810348 + Missense_Mutation SNP C C T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr6:35810348C>T ENST00000373825.2 - 14 1939 c.1654G>A c.(1654-1656)Gaa>Aaa p.E552K SRPK1_ENST00000373822.1_Missense_Mutation_p.E444K|SRPK1_ENST00000423325.2_Missense_Mutation_p.E536K SRSF protein kinase 1 p.E551Q(1) 21 GAATGAGGTTCAAACAAATAG 0.418000 NSCLC(31;67 978 16289 24856 26454) 1 Substitution - Missense(1) SO:0001583 missense ENST00000373825.2 1 1 hg19 CCDS47415.1 . . . . . . . . . . C 35 5.529797 0.96446 . . ENSG00000096063 ENST00000373825;ENST00000361690;ENST00000423325;ENST00000373822 T;T;T;T 0.64803 -0.12;-0.12;-0.12;-0.12 5.18 5.18 0.71444 Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); . . . . T 0.58764 0.2145 N 0.11154 0.105 0.80722 D 1 D;D 0.89917 1.0;0.996 D;D 0.85130 0.997;0.991 T 0.70425 -0.4875 9 0.87932 D 0 -17.1778 19.0463 0.93020 0.0:1.0:0.0:0.0 . 536;552 B4DS61;Q96SB4 .;SRPK1_HUMAN K 552;568;536;444 ENSP00000362931:E552K;ENSP00000354674:E568K;ENSP00000391069:E536K;ENSP00000362928:E444K ENSP00000354674:E568K E - 1 0 SRPK1 35918326 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 7.442000 0.80503 2.572000 0.86782 0.491000 0.48974 GAA TCGA-IB-7890-01A-12D-2201-08 SRPK1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040319.3 1 0 1 28 130 0 32 1 9.990422e-01 21 33 0 32 2 0 0 0 0 0 2 1 1.000000 27 125 0 31 2 0 0 0 0 32 2 -20.000000 1 1 0 0 1 1 2 3 1.779925 0 0.360000 2.800000 0.366838 0.990000 0.690000 1.000000 1.000000 0.939225 0.990000 1 0.830000 1.000000 TRRAP 8295 broad.mit.edu 37 7 98609827 98609827 + Missense_Mutation SNP T T A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr7:98609827T>A ENST00000359863.4 + 72 11638 c.11429T>A c.(11428-11430)cTg>cAg p.L3810Q AC004893.11_ENST00000360902.1_RNA|TRRAP_ENST00000446306.3_Missense_Mutation_p.L3799Q|TRRAP_ENST00000355540.3_Missense_Mutation_p.L3781Q NM_001244580.1 NP_001231509.1 Q9Y4A5 TRRAP_HUMAN transformation/transcription domain-associated protein 176 all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274) STAD - Stomach adenocarcinoma(171;0.215) CTGGTGTCCCTGGTTCAGAAA 0.597000 0 SO:0001583 missense ENST00000359863.4 1 1 hg19 CCDS59066.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. T|T 14.30|14.30 2.495074|2.495074 0.44352|0.44352 .|. .|. ENSG00000196367|ENSG00000196367 ENST00000359863;ENST00000355540;ENST00000446306|ENST00000456197 D;D|. 0.84298|. -1.83;-1.83|. 5.44|5.44 4.27|4.27 0.50696|0.50696 Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (2);|. 0.000000|. 0.64402|. D|. 0.000002|. T|T 0.62024|0.62024 0.2394|0.2394 L|L 0.54323|0.54323 1.7|1.7 0.80722|0.80722 D|D 1|1 D;P;D|. 0.60160|. 0.987;0.956;0.978|. P;P;P|. 0.62089|. 0.898;0.601;0.737|. T|T 0.58323|0.58323 -0.7656|-0.7656 10|5 0.18710|. T|. 0.47|. .|. 12.5371|12.5371 0.56147|0.56147 0.0:0.0:0.1395:0.8605|0.0:0.0:0.1395:0.8605 .|. 3781;3538;3810|. Q9Y4A5-2;Q59FH1;Q9Y4A5|. .;.;TRRAP_HUMAN|. Q|R 3810;3781;3798|3539 ENSP00000352925:L3810Q;ENSP00000347733:L3781Q|. ENSP00000347733:L3781Q|. L|W +|+ 2|1 0|0 TRRAP|TRRAP 98447763|98447763 1.000000|1.000000 0.71417|0.71417 0.167000|0.167000 0.22817|0.22817 0.021000|0.021000 0.10359|0.10359 7.690000|7.690000 0.84178|0.84178 0.881000|0.881000 0.35993|0.35993 -0.313000|-0.313000 0.08912|0.08912 CTG|TGG TCGA-IB-7890-01A-12D-2201-08 TRRAP-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000317978.1 1 0 0 8 185 0 59 1 5.700693e-01 3 40 0 59 2 0 0 0 0 0 2 1 0.988668 8 180 0 57 2 0 0 0 0 59 2 -10.748270 1 1 0 0 1 1 2 3 2.079462 1 0.360000 2.800000 0.457627 0.280000 0.130000 0.500000 0.270000 0.300712 0.280000 0 0.190000 0.390000 FAM83H 286077 broad.mit.edu 37 8 144808660 144808660 + Nonsense_Mutation SNP G G A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr8:144808660G>A ENST00000388913.3 - 5 3096 c.2971C>T c.(2971-2973)Cag>Tag p.Q991* NM_198488.3 NP_940890 Q6ZRV2 FA83H_HUMAN family with sequence similarity 83, member H 21 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;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146) CCGTTCTCCTGCGGCACTGGG 0.692000 0 SO:0001587 stop_gained ENST00000388913.3 0 1 hg19 CCDS6410.2 . . . . . . . . . . g 25.1 4.597837 0.87055 . . ENSG00000180921 ENST00000388913 . . . 5.01 5.01 0.66863 . 2.505490 0.02148 N 0.057769 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 . 11.2957 0.49277 0.0:0.0:0.7074:0.2926 . . . . X 991 . ENSP00000373565:Q991X Q - 1 0 FAM83H 144880648 0.998000 0.40836 0.913000 0.36048 0.106000 0.19336 2.042000 0.41222 2.334000 0.79466 0.550000 0.68814 CAG TCGA-IB-7890-01A-12D-2201-08 FAM83H-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257632.2 1 0 0 29 103 0 35 1 9.691176e-01 7 16 0 35 2 0 0 0 0 0 2 1 1.000000 29 101 0 35 2 0 0 0 0 35 2 -20.000000 1 1 0 0 1 2 3 5 2.664308 1 0.360000 2.800000 0.582953 0.990000 0.990000 1.000000 1.000000 0.999981 0.990000 1 0.990000 1.000000 EPPK1 83481 broad.mit.edu 37 8 144945204 144945204 + Missense_Mutation SNP C C T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr8:144945204C>T ENST00000525985.1 - 2 2289 c.2218G>A c.(2218-2220)Gtg>Atg p.V740M P58107 EPIPL_HUMAN epiplakin 1 71 all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105) GCCACGTCCACGGGCACGCGG 0.657000 0 SO:0001583 missense ENST00000525985.1 1 1 hg19 . . . . . . . . . . C 20.9 4.058913 0.76074 . . ENSG00000227184 ENST00000525985 T 0.77877 -1.13 5.06 5.06 0.68205 . . . . . D 0.89298 0.6675 M 0.87971 2.92 0.32551 N 0.532326 D 0.89917 1.0 D 0.75484 0.986 D 0.91472 0.5197 9 0.59425 D 0.04 . 15.9742 0.80049 0.0:1.0:0.0:0.0 . 740 E9PPU0 . M 740 ENSP00000436337:V740M ENSP00000436337:V740M V - 1 0 EPPK1 145017192 0.723000 0.28027 1.000000 0.80357 0.892000 0.51952 1.471000 0.35365 2.643000 0.89663 0.655000 0.94253 GTG TCGA-IB-7890-01A-12D-2201-08 EPPK1-001 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000382675.1 0 0 0 76 619 0 168 0 9.761841e-02 1 4 0 168 2 0 0 0 0 0 2 1 1.000000 71 574 0 174 2 0 0 0 0 168 2 -19.999990 1 1 120830 2 37 1 3 3 6 2.621629 1 0.360000 2.800000 0.574468 0.940000 0.730000 1.000000 1.000000 0.927141 0.940000 1 0.830000 1.000000 GPR124 25960 broad.mit.edu 37 8 37692836 37692836 + Missense_Mutation SNP G G A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr8:37692836G>A ENST00000412232.2 + 12 1766 c.1753G>A c.(1753-1755)Gag>Aag p.E585K GPR124_ENST00000315215.7_Intron NM_032777.9 NP_116166.9 Q96PE1 GP124_HUMAN G protein-coupled receptor 124 37 BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10) ACCTGAGCCCGAGCCCCCAGC 0.687000 0 SO:0001583 missense ENST00000412232.2 1 1 hg19 CCDS6097.2 . . . . . . . . . . G 24.0 4.481400 0.84747 . . ENSG00000020181 ENST00000416514;ENST00000412232 T 0.57907 0.37 5.34 5.34 0.76211 . 0.000000 0.64402 D 0.000001 T 0.55545 0.1927 N 0.22421 0.69 0.58432 D 0.999996 D 0.76494 0.999 P 0.57679 0.825 T 0.53920 -0.8370 10 0.34782 T 0.22 -25.1986 18.6353 0.91376 0.0:0.0:1.0:0.0 . 585 Q96PE1 GP124_HUMAN K 578;585 ENSP00000406367:E585K ENSP00000406367:E585K E + 1 0 GPR124 37811994 1.000000 0.71417 0.565000 0.28409 0.052000 0.14988 7.123000 0.77176 2.507000 0.84556 0.655000 0.94253 GAG TCGA-IB-7890-01A-12D-2201-08 GPR124-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000343331.2 1 0 1 17 101 0 61 0 9.999996e-01 0 176 0 61 2 0 0 0 0 0 2 1 0.999974 16 100 0 61 2 0 0 0 0 61 2 -20.000000 1 1 121396 2 33 1 0 2 2 1.817945 1 0.360000 2.800000 0.360000 0.800000 0.490000 1.000000 1.000000 0.804000 0.800000 0 0.630000 0.990000 PRKDC 5591 broad.mit.edu 37 8 48790345 48790345 + Missense_Mutation SNP C C T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr8:48790345C>T ENST00000314191.2 - 41 5356 c.5300G>A c.(5299-5301)cGg>cAg p.R1767Q PRKDC_ENST00000338368.3_Missense_Mutation_p.R1767Q|PRKDC_ENST00000523565.1_5'UTR NM_006904.6 NP_008835.5 P78527 PRKDC_HUMAN protein kinase, DNA-activated, catalytic polypeptide 147 all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391) Caffeine(DB00201) CTGCTGTTCCCGACAAAGAAC 0.383000 Non-homologous end-joining Esophageal Squamous(79;1091 1253 12329 31680 40677) 0 SO:0001583 missense ENST00000314191.2 1 1 hg19 . . . . . . . . . . C 31 5.098326 0.94197 . . ENSG00000253729 ENST00000314191;ENST00000338368 T;T 0.63580 -0.05;-0.05 5.65 5.65 0.86999 Armadillo-like helical (1);Armadillo-type fold (1); 0.000000 0.85682 D 0.000000 T 0.81569 0.4850 M 0.80847 2.515 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.83275 0.994;0.996 T 0.83324 -0.0016 10 0.87932 D 0 . 19.7092 0.96085 0.0:1.0:0.0:0.0 . 1767;1768 E7EUY0;P78527 .;PRKDC_HUMAN Q 1767 ENSP00000313420:R1767Q;ENSP00000345182:R1767Q ENSP00000313420:R1767Q R - 2 0 PRKDC 48952898 1.000000 0.71417 0.996000 0.52242 0.677000 0.39632 5.203000 0.65174 2.664000 0.90586 0.585000 0.79938 CGG TCGA-IB-7890-01A-12D-2201-08 PRKDC-201 KNOWN basic|appris_principal protein_coding protein_coding 0 0 0 48 796 0 102 1 9.371534e-01 5 73 0 102 2 0 0 0 0 0 2 1 1.000000 47 787 0 102 2 0 0 0 0 102 2 -2.135519 0 1 0 0 1 2 3 5 2.664308 1 0.360000 2.800000 0.582953 0.480000 0.350000 0.640000 0.500000 0.493380 0.480000 0 0.410000 0.560000 PXDNL 137902 broad.mit.edu 37 8 52321614 52321614 + Missense_Mutation SNP G G A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr8:52321614G>A ENST00000356297.4 - 17 2670 c.2570C>T c.(2569-2571)gCg>gTg p.A857V PXDNL_ENST00000543296.1_Missense_Mutation_p.A857V NM_144651.4 NP_653252 A1KZ92 PXDNL_HUMAN peroxidasin homolog (Drosophila)-like 48 all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015) CATGCAGGGCGCGTGGGTGCC 0.682000 0 SO:0001583 missense ENST00000356297.4 1 1 hg19 CCDS47855.1 . . . . . . . . . . G 7.521 0.656623 0.14580 . . ENSG00000147485 ENST00000356297;ENST00000543296 T;T 0.68479 -0.33;-0.33 3.49 0.493 0.16878 . 0.753446 0.11213 N 0.587551 T 0.38746 0.1052 N 0.11756 0.17 0.09310 N 1 P 0.37398 0.593 B 0.29862 0.108 T 0.15009 -1.0452 10 0.30854 T 0.27 . 4.9674 0.14098 0.2166:0.1744:0.609:0.0 . 857 A1KZ92 PXDNL_HUMAN V 857 ENSP00000348645:A857V;ENSP00000444865:A857V ENSP00000348645:A857V A - 2 0 PXDNL 52484167 0.814000 0.29104 0.000000 0.03702 0.000000 0.00434 3.338000 0.52128 -0.162000 0.10964 -1.087000 0.02190 GCG TCGA-IB-7890-01A-12D-2201-08 PXDNL-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000377905.1 1 0 0 66 125 0 33 0 0 0 0 33 2 0 0 0 0 0 2 1 1.000000 66 121 0 31 2 0 0 0 0 33 2 -20.000000 1 1 0 0 1 2 3 5 2.664308 1 0.360000 2.800000 0.582953 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 COL27A1 85301 broad.mit.edu 37 9 117062960 117062960 + Missense_Mutation SNP G G A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr9:117062960G>A ENST00000356083.3 + 51 5085 c.4694G>A c.(4693-4695)gGc>gAc p.G1565D NM_032888.2 NP_116277.2 Q8IZC6 CORA1_HUMAN collagen, type XXVII, alpha 1 80 GGGCCACCTGGCTTGATGGTG 0.612000 0 SO:0001583 missense ENST00000356083.3 1 1 hg19 CCDS6802.1 . . . . . . . . . . G 18.64 3.667078 0.67814 . . ENSG00000196739 ENST00000356083;ENST00000357257 D 0.99353 -5.77 5.4 5.4 0.78164 . . . . . D 0.99694 0.9884 H 0.98646 4.29 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.97360 0.9969 9 0.87932 D 0 . 17.0516 0.86520 0.0:0.0:1.0:0.0 . 1565 Q8IZC6 CORA1_HUMAN D 1565 ENSP00000348385:G1565D ENSP00000348385:G1565D G + 2 0 COL27A1 116102781 1.000000 0.71417 0.998000 0.56505 0.120000 0.20174 8.906000 0.92626 2.711000 0.92665 0.655000 0.94253 GGC TCGA-IB-7890-01A-12D-2201-08 COL27A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053763.1 1 0 1 30 155 0 54 1 8.340496e-01 2 17 0 54 2 0 0 0 0 0 2 1 1.000000 29 152 0 54 2 0 0 0 0 54 2 -20.000000 1 1 0 0 1 1 2 3 2.067747 1 0.360000 2.800000 0.457627 0.990000 0.750000 1.000000 1.000000 0.963554 0.990000 1 0.890000 1.000000 FBXW5 54461 broad.mit.edu 37 9 139838442 139838442 + Missense_Mutation SNP C C G TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr9:139838442C>G ENST00000325285.3 - 2 173 c.94G>C c.(94-96)Gtg>Ctg p.V32L FBXW5_ENST00000483559.1_5'UTR|C8G_ENST00000224181.3_5'Flank NM_018998.3 NP_061871.1 Q969U6 FBXW5_HUMAN F-box and WD repeat domain containing 5 12 all_cancers(76;0.11) Myeloproliferative disorder(178;0.0511) STAD - Stomach adenocarcinoma(284;0.19) TGGCGGCACACCAGCCCGGCG 0.701000 0 SO:0001583 missense ENST00000325285.3 1 1 hg19 CCDS7014.1 . . . . . . . . . . c 15.55 2.867242 0.51588 . . ENSG00000159069 ENST00000325285;ENST00000428398;ENST00000443788 T;T;T 0.54479 0.57;0.57;0.57 4.02 3.12 0.35913 F-box domain, cyclin-like (2);F-box domain, Skp2-like (1); 0.216848 0.40064 N 0.001182 T 0.60573 0.2279 M 0.91249 3.19 0.26388 N 0.976624 B 0.27286 0.174 B 0.33846 0.171 T 0.57476 -0.7805 10 0.41790 T 0.15 -9.6575 8.9065 0.35526 0.0:0.8956:0.0:0.1044 . 32 Q969U6 FBXW5_HUMAN L 32 ENSP00000313034:V32L;ENSP00000404829:V32L;ENSP00000394011:V32L ENSP00000313034:V32L V - 1 0 FBXW5 138958263 1.000000 0.71417 0.993000 0.49108 0.588000 0.36517 3.941000 0.56607 0.902000 0.36520 0.479000 0.44913 GTG TCGA-IB-7890-01A-12D-2201-08 FBXW5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055227.1 1 0 0 7 27 0 21 1 9.254406e-01 7 14 0 21 2 0 0 0 0 0 2 1 0.982807 6 27 0 20 2 0 0 0 0 21 2 -16.160310 1 1 0 0 1 1 2 3 2.047008 1 0.360000 2.800000 0.457627 0.990000 0.650000 1.000000 1.000000 0.968432 0.990000 1 0.960000 1.000000 C9orf89 84270 broad.mit.edu 37 9 95875280 95875280 + Missense_Mutation SNP A A G TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chr9:95875280A>G ENST00000375464.2 + 6 571 c.443A>G c.(442-444)aAg>aGg p.K148R C9orf89_ENST00000488630.1_3'UTR NM_032310.3 NP_115686.3 Q96LW7 BINCA_HUMAN chromosome 9 open reading frame 89 7 CTAGACCCCAAGGGCCTGCCA 0.602000 0 SO:0001583 missense ENST00000375464.2 0 1 hg19 CCDS6702.2 . . . . . . . . . . A 7.776 0.708538 0.15239 . . ENSG00000165233 ENST00000375464 . . . 4.22 0.545 0.17190 . 40.080900 0.00166 N 0.000000 T 0.27594 0.0678 . . . 0.24896 N 0.992137 B 0.14805 0.011 B 0.14578 0.011 T 0.11616 -1.0580 8 0.30854 T 0.27 . 3.211 0.06682 0.519:0.0:0.3042:0.1768 . 148 Q96LW7-2 . R 148 . ENSP00000364613:K148R K + 2 0 C9orf89 94915101 0.999000 0.42202 0.998000 0.56505 0.256000 0.26092 1.016000 0.29976 0.247000 0.21414 -0.411000 0.06167 AAG TCGA-IB-7890-01A-12D-2201-08 C9orf89-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053128.1 0 0 0 3 93 0 32 0 9.460907e-01 0 178 0 32 2 0 0 0 0 0 2 1 0.787846 2 87 0 32 2 0 0 0 0 32 2 -6.482320 1 0 121150 4 33 1 1 2 3 2.067131 1 0.360000 2.800000 0.455967 0.240000 0.060000 0.610000 0.210000 0.270673 0.240000 0 0.130000 0.390000 GUCY2F 2986 broad.mit.edu 37 X 108636151 108636151 + Missense_Mutation SNP G G A TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chrX:108636151G>A ENST00000218006.2 - 13 2849 c.2558C>T c.(2557-2559)aCg>aTg p.T853M NM_001522.2 NP_001513.2 P51841 GUC2F_HUMAN guanylate cyclase 2F, retinal 67 AAGCTTTTCCGTTTTCTGTTT 0.383000 0 SO:0001583 missense ENST00000218006.2 1 1 hg19 CCDS14545.1 . . . . . . . . . . G 18.01 3.527147 0.64860 . . ENSG00000101890 ENST00000218006 D 0.90385 -2.66 4.25 3.36 0.38483 Haem NO binding associated (1);Adenylyl cyclase class-3/4/guanylyl cyclase (1); 0.108904 0.64402 D 0.000008 D 0.94473 0.8221 M 0.87097 2.86 0.58432 D 0.999998 D 0.65815 0.995 P 0.61874 0.895 D 0.94367 0.7592 10 0.87932 D 0 . 10.33 0.43816 0.0:0.0:0.8025:0.1975 . 853 P51841 GUC2F_HUMAN M 853 ENSP00000218006:T853M ENSP00000218006:T853M T - 2 0 GUCY2F 108522807 1.000000 0.71417 0.962000 0.40283 0.997000 0.91878 5.507000 0.66999 1.079000 0.41038 0.513000 0.50165 ACG TCGA-IB-7890-01A-12D-2201-08 GUCY2F-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057884.1 1 0 1 108 236 0 92 0 0 0 0 92 2 0 0 0 0 0 2 1 1.000000 103 233 1 90 14 0 0 0 0 92 2 -20.000000 1 1 121408 7 43 1 0 1 1 0.360000 2.800000 0.360000 0.860000 0.730000 0.980000 0.870000 0.865296 0.860000 1 0.790000 0.930000 AMOT 154796 broad.mit.edu 37 X 112058796 112058796 + Silent SNP C C T TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chrX:112058796C>T ENST00000524145.1 - 3 1256 c.1182G>A c.(1180-1182)caG>caA p.Q394Q AMOT_ENST00000304758.1_5'UTR|AMOT_ENST00000371962.1_Silent_p.Q162Q|AMOT_ENST00000371959.3_Silent_p.Q394Q|AMOT_ENST00000371958.1_Silent_p.Q162Q Q4VCS5 AMOT_HUMAN angiomotin p.Q394Q(1) 43 gctgctgctgctgttgttggt 0.582000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000524145.1 0 1 hg19 CCDS48154.1 TCGA-IB-7890-01A-12D-2201-08 AMOT-005 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000378570.1 0 0 0 3 93 0 33 0 1.168132e-01 0 14 0 33 2 0 0 0 0 1 2 1 0.809253 3 92 0 33 2 0 0 0 0 33 2 -2.477502 0 1 0 0 1 0 1 1 0.360000 2.800000 0.360000 0.090000 0.020000 0.230000 0.090000 0.111291 0.090000 0 0.050000 0.160000 MAGEA3 4102 broad.mit.edu 37 X 151935450 151935450 + Missense_Mutation SNP C C G rs34645170 TCGA-IB-7890-01A-12D-2201-08 TCGA-IB-7890-10A-01D-2201-08 Untested Somatic Phase_I WXS none Illumina GAIIx adbc96e9-990e-4cc9-98c9-14fffe83ed87 e2f62463-40b9-41ef-9ffb-ad2fe036c920 g.chrX:151935450C>G ENST00000393902.3 - 3 1284 c.717G>C c.(715-717)ttG>ttC p.L239F MAGEA3_ENST00000370278.3_Missense_Mutation_p.L239F P43357 MAGA3_HUMAN melanoma antigen family A, 3 15 Acute lymphoblastic leukemia(192;6.56e-05) TGGGATCCCCCAAGATACTGT 0.537000 0 SO:0001583 missense ENST00000393902.3 0 1 hg19 CCDS14715.1 15 0.009041591320072333 0 0.0 1 0.0027624309392265192 1 0.0017482517482517483 13 0.017150395778364115 c 0.243 -1.012051 0.02095 2.61E-4 1.49E-4 ENSG00000221867 ENST00000370278;ENST00000393902 T;T 0.04970 3.52;3.52 1.42 -2.84 0.05751 . 0.537671 0.21492 N 0.073674 T 0.00468 0.0015 N 0.00176 -1.92 0.80722 P 0.0 B 0.02656 0.0 B 0.01281 0.0 T 0.39781 -0.9597 9 0.09843 T 0.71 . 2.2524 0.04047 0.4558:0.312:0.2323:0.0 rs34645170 239 P43357 MAGA3_HUMAN F 239 ENSP00000359301:L239F;ENSP00000377480:L239F ENSP00000359301:L239F L - 3 2 MAGEA3 151686106 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -1.375000 0.02563 -0.539000 0.06273 -1.891000 0.00535 TTG TCGA-IB-7890-01A-12D-2201-08 MAGEA3-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000058744.1 0 0 1 163 334 0 161 0 0 0 0 161 2 0 0 0 0 0 2 1 1.000000 138 332 0 160 2 0 0 0 0 161 2 -3.318794 1 1 121202 21 45 1 0 1 1 0.360000 2.800000 0.360000 0.890000 0.790000 0.990000 0.910000 0.902064 0.890000 1 0.840000 0.960000