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 PLSCR2 57047 broad.mit.edu 37 3 146177707 146177707 + Frame_Shift_Del DEL A A - TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr3:146177707delA ENST00000497985.1 - 4 643 c.204delT c.(202-204)cctfs p.P68fs PLSCR2_ENST00000336685.2_5'UTR NM_001199978.1 NP_001186907.1 Q9NRY7 PLS2_HUMAN phospholipid scramblase 2 15 GTACCCCTTCAGGTCTACCTG 0.507000 0 SO:0001589 frameshift_variant ENST00000497985.1 1 1 hg19 CCDS56284.1 TCGA-2L-AAQE-01A-11D-A397-08 PLSCR2-002 PUTATIVE basic|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000355264.1 1 0 0 64 321 0 63 0 7.586917e-02 0 3 0 63 2 0 0 0 0 0 0 1 1 65 318 0 62 2 0 0 0 0 0 0 -2.989177 1 1 0 0 1 1 2 3 2.162847 0 0.530000 1.810000 0.536146 0.630000 5.000000e-01 1.000000 0.630000 0.654406 0.630000 0 5.600000e-01 0.720000 EIF3A 8661 broad.mit.edu 37 10 120830492 120830492 + Missense_Mutation SNP G G A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr10:120830492G>A ENST00000369144.3 - 5 774 c.647C>T c.(646-648)aCg>aTg p.T216M EIF3A_ENST00000541549.1_Missense_Mutation_p.T182M NM_003750.2 NP_003741.1 P56537 IF6_HUMAN eukaryotic translation initiation factor 3, subunit A 56 Lung NSC(174;0.094)|all_lung(145;0.123) ATTGATTGCCGTACTTTGGTT 0.443000 0 SO:0001583 missense ENST00000369144.3 0 1 hg19 CCDS7608.1 . . . . . . . . . . G 17.57 3.422747 0.62733 . . ENSG00000107581 ENST00000369144;ENST00000541549 T;T 0.44083 0.93;0.93 5.69 5.69 0.88448 . 0.000000 0.40469 N 0.001098 T 0.63815 0.2543 M 0.61703 1.905 0.80722 D 1 D 0.89917 1.0 D 0.83275 0.996 T 0.58025 -0.7709 10 0.34782 T 0.22 -22.9502 19.813 0.96554 0.0:0.0:1.0:0.0 . 216 Q14152 EIF3A_HUMAN M 216;182 ENSP00000358140:T216M;ENSP00000438178:T182M ENSP00000358140:T216M T - 2 0 EIF3A 120820482 1.000000 0.71417 0.994000 0.49952 0.993000 0.82548 9.827000 0.99397 2.683000 0.91414 0.591000 0.81541 ACG TCGA-2L-AAQE-01A-11D-A397-08 EIF3A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050634.1 0 0 0 5 273 0 57 0 7.283483e-01 0 136 0 57 2 0 0 0 0 0 2 1 9.375043e-01 5 272 0 56 2 0 0 0 0 0 2 -2.742045 1 1 121412 1 31 1 2 2 4 2.213109 0 0.530000 1.810000 0.553656 0.070000 2.000000e-02 1.000000 0.070000 0.158934 0.070000 0 4.000000e-02 0.140000 INPP5F 22876 broad.mit.edu 37 10 121541192 121541192 + Missense_Mutation SNP G G A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr10:121541192G>A ENST00000361976.2 + 3 390 c.224G>A c.(223-225)gGc>gAc p.G75D INPP5F_ENST00000369081.1_5'UTR|INPP5F_ENST00000369083.3_Missense_Mutation_p.G75D NM_014937.3 NP_055752.1 Q01968 OCRL_HUMAN inositol polyphosphate-5-phosphatase F 42 Lung NSC(174;0.109)|all_lung(145;0.142) GCATTGGTGGGCAAACTCCCA 0.438000 0 SO:0001583 missense ENST00000361976.2 0 1 hg19 CCDS7616.1 . . . . . . . . . . G 25.6 4.655701 0.88056 . . ENSG00000198825 ENST00000361976;ENST00000369083 T;T 0.59502 0.26;0.26 5.96 5.04 0.67666 Synaptojanin, N-terminal (1); 0.000000 0.85682 D 0.000000 T 0.81009 0.4734 M 0.91768 3.24 0.80722 D 1 D;D 0.89917 1.0;0.999 D;D 0.73380 0.98;0.962 D 0.86073 0.1539 10 0.87932 D 0 -18.5695 16.4613 0.84055 0.0:0.0:0.8678:0.1322 . 75;75 Q9Y2H2;Q9Y2H2-3 SAC2_HUMAN;. D 75 ENSP00000354519:G75D;ENSP00000358079:G75D ENSP00000354519:G75D G + 2 0 INPP5F 121531182 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 9.091000 0.94151 1.474000 0.48178 0.655000 0.94253 GGC TCGA-2L-AAQE-01A-11D-A397-08 INPP5F-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050679.1 0 0 0 4 183 0 44 0 9.595635e-02 0 19 0 44 2 0 0 0 0 0 2 1 8.887247e-01 4 181 0 44 2 0 0 0 0 0 2 -2.919370 1 1 0 0 1 2 2 4 2.213109 0 0.530000 1.810000 0.553656 0.090000 2.000000e-02 1.000000 0.090000 0.177086 0.090000 0 5.000000e-02 0.170000 GPR123 84435 broad.mit.edu 37 10 134896361 134896361 + Splice_Site SNP C C T TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr10:134896361C>T ENST00000607359.1 + 7 1373 c.1373C>T c.(1372-1374)gCg>gTg p.A458V RP13-439H18.4_ENST00000444433.1_RNA Q86SQ6 GP123_HUMAN G protein-coupled receptor 123 14 all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203) AGGCCCTGTGCGGTGAGGCCT 0.662000 0 SO:0001630 splice_region_variant ENST00000607359.1 0 1 hg19 . . . . . . . . . . C 2.107 -0.404715 0.04832 3.21E-4 0.0 ENSG00000197177 ENST00000368577;ENST00000392609 . . . 1.64 -3.28 0.05033 . 11.146600 0.01144 U 0.006263 T 0.08626 0.0214 . . . 0.21020 N 0.999803 P 0.50272 0.933 B 0.22880 0.042 T 0.31392 -0.9945 7 0.87932 D 0 . 1.3877 0.02243 0.1983:0.2487:0.394:0.159 . 458 Q86SQ6-1 . V 458 . ENSP00000357566:A458V A + 2 0 GPR123 134746351 0.000000 0.05858 0.000000 0.03702 0.004000 0.04260 -1.344000 0.02639 -1.142000 0.02869 0.306000 0.20318 GCG TCGA-2L-AAQE-01A-11D-A397-08 GPR123-004 PUTATIVE basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000316904.2 0 0 0 7 33 0 8 0 0 0 0 8 2 0 0 0 0 0 2 1 9.840074e-01 7 33 0 8 2 0 0 0 0 0 2 -15.315740 1 1 117816 5 30 1 1 2 3 2.179679 0 0.530000 1.810000 0.538560 0.710000 3.300000e-01 1.000000 1.000000 0.718482 0.710000 0 4.900000e-01 1.000000 RET 5979 broad.mit.edu 37 10 43622039 43622039 + Missense_Mutation SNP C C T TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr10:43622039C>T ENST00000355710.3 + 19 3288 c.3056C>T c.(3055-3057)gCg>gTg p.A1019V RET_ENST00000340058.5_Missense_Mutation_p.A1019V NM_020975.4 NP_066124.1 P07949 RET_HUMAN ret proto-oncogene CCDC6/RET(4)|KIF5B/RET(79) 607 Ovarian(717;0.0423) Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398) TTGGACCTTGCGGCGTCCACT 0.557000 1 T, Mis, N, F H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6 medullary thyroid, papillary thyroid, pheochromocytoma, NSCLC medullary thyroid, papillary thyroid, pheochromocytoma Hirschsprung disease Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149) yes Dom yes Multiple endocrine neoplasia 2A/2B 10 10q11.2 5979 ret proto-oncogene yes E, O 0 SO:0001583 missense Familial Cancer Database MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC ENST00000355710.3 0 1 hg19 CCDS7200.1 . . . . . . . . . . C 20.6 4.010130 0.75046 . . ENSG00000165731 ENST00000355710;ENST00000340058 T;T 0.80304 -1.24;-1.36 5.09 5.09 0.68999 . 0.000000 0.85682 D 0.000000 D 0.83922 0.5359 N 0.24115 0.695 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.91635 0.997;0.998;0.999 D 0.85682 0.1301 10 0.52906 T 0.07 . 18.5126 0.90923 0.0:1.0:0.0:0.0 . 765;1019;1019 B4DGX8;P07949;P07949-2 .;RET_HUMAN;. V 1019 ENSP00000347942:A1019V;ENSP00000344798:A1019V ENSP00000344798:A1019V A + 2 0 RET 42942045 1.000000 0.71417 0.735000 0.30896 0.550000 0.35303 7.786000 0.85741 2.374000 0.81015 0.655000 0.94253 GCG TCGA-2L-AAQE-01A-11D-A397-08 RET-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000047694.2 0 0 0 8 1098 1 253 0 0 0 1 1 253 2 0 0 0 0 0 2 0 7.157282e-02 8 1090 1 253 16 0 0 0 0 0 2 -1.889802 0 1 0 0 1 1 2 3 2.165270 0 0.530000 1.810000 0.537356 0.020000 0 1.000000 0.020000 0.075259 0.020000 0 1.000000e-02 0.050000 C10orf71 118461 broad.mit.edu 37 10 50532475 50532475 + Missense_Mutation SNP G G A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr10:50532475G>A ENST00000374144.3 + 3 2173 c.1885G>A c.(1885-1887)Gga>Aga p.G629R C10orf71_ENST00000323868.4_Missense_Mutation_p.G629R Q711Q0 CJ071_HUMAN chromosome 10 open reading frame 71 p.G629*(1) 1 GGGTCCTGCCGGATCCAGCTG 0.567000 1 Substitution - Nonsense(1) SO:0001583 missense ENST00000374144.3 1 1 hg19 CCDS44387.1 . . . . . . . . . . G 0.328 -0.958059 0.02267 0.0 1.2E-4 ENSG00000177354 ENST00000323868;ENST00000374144 T;T 0.13196 2.61;3.69 5.74 -0.929 0.10444 . 1.066660 0.07463 N 0.901009 T 0.03434 0.0099 N 0.00538 -1.39 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.42865 -0.9426 10 0.23891 T 0.37 . 6.3022 0.21119 0.5432:0.0:0.34:0.1168 . 629 Q711Q0-3 . R 629 ENSP00000318713:G629R;ENSP00000363259:G629R ENSP00000318713:G629R G + 1 0 C10orf71 50202481 0.000000 0.05858 0.002000 0.10522 0.002000 0.02628 -0.233000 0.09041 -0.118000 0.11851 -1.239000 0.01543 GGA TCGA-2L-AAQE-01A-11D-A397-08 C10orf71-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000047984.2 1 0 1 20 60 0 16 0 0 0 0 16 2 0 0 0 0 0 2 1 9.999984e-01 20 60 0 16 2 0 0 0 0 0 2 -20.000000 1 1 120874 5 35 1 2 2 4 2.213109 0 0.530000 1.810000 0.553656 0.990000 6.600000e-01 1.000000 1.000000 0.934301 0.990000 1 8.200000e-01 1.000000 KIAA1377 57562 broad.mit.edu 37 11 101834466 101834466 + Silent SNP G G A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr11:101834466G>A ENST00000263468.8 + 6 2970 c.2700G>A c.(2698-2700)cgG>cgA p.R900R KIAA1377_ENST00000537689.1_Silent_p.R701R NM_020802.2 NP_065853.2 Q9P2H0 K1377_HUMAN KIAA1377 53 all_epithelial(12;0.0104) Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931) CAGTTGCCCGGCAAGATGCGA 0.413000 0 SO:0001819 synonymous_variant ENST00000263468.8 0 1 hg19 CCDS31658.1 TCGA-2L-AAQE-01A-11D-A397-08 KIAA1377-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000394140.1 0 0 0 5 504 0 144 0 1.865306e-02 0 17 0 144 2 0 0 0 0 0 2 1 9.361954e-01 5 499 0 144 2 0 0 0 0 0 2 -2.300723 0 1 0 0 1 1 2 3 2.185977 0 0.530000 1.810000 0.539757 0.030000 0 1.000000 0.040000 0.106294 0.030000 0 2.000000e-02 0.070000 ANO3 63982 broad.mit.edu 37 11 26556047 26556047 + Missense_Mutation SNP G G A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr11:26556047G>A ENST00000256737.3 + 9 1766 c.914G>A c.(913-915)cGa>cAa p.R305Q ANO3_ENST00000531568.1_Missense_Mutation_p.R159Q|ANO3_ENST00000537978.1_Missense_Mutation_p.R289Q|ANO3_ENST00000525139.1_Missense_Mutation_p.R289Q NM_031418.2 NP_113606.2 Q9BYT9 ANO3_HUMAN anoctamin 3 p.R305Q(1) 68 AATGCTACTCGAAGCAGAATA 0.348000 1 Substitution - Missense(1) SO:0001583 missense ENST00000256737.3 1 1 hg19 CCDS31447.1 . . . . . . . . . . G 32 5.138511 0.94560 . . ENSG00000134343 ENST00000537978;ENST00000525139;ENST00000256737;ENST00000538001;ENST00000531568 T;T;T;T 0.69806 -0.43;-0.43;-0.43;-0.43 5.03 5.03 0.67393 . 0.000000 0.85682 D 0.000000 D 0.87120 0.6098 H 0.94183 3.505 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.87578 0.998;0.998 D 0.90997 0.4839 10 0.87932 D 0 . 17.9596 0.89081 0.0:0.0:1.0:0.0 . 207;305 B7Z7Y6;Q9BYT9 .;ANO3_HUMAN Q 289;289;305;207;159 ENSP00000440737:R289Q;ENSP00000432576:R289Q;ENSP00000256737:R305Q;ENSP00000432394:R159Q ENSP00000256737:R305Q R + 2 0 ANO3 26512623 1.000000 0.71417 1.000000 0.80357 0.978000 0.69477 9.516000 0.98017 2.349000 0.79799 0.460000 0.39030 CGA TCGA-2L-AAQE-01A-11D-A397-08 ANO3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000387806.1 1 0 1 102 288 1 97 0 0 0 1 97 2 0 0 0 0 0 2 1 1 101 288 1 97 15 0 0 0 0 0 2 -6.159810 1 1 121406 1 36 1 1 2 3 2.185977 0 0.530000 1.810000 0.539757 0.990000 8.400000e-01 1.000000 1.000000 0.972668 0.990000 1 9.200000e-01 1.000000 ELP4 26610 broad.mit.edu 37 11 31541617 31541617 + Missense_Mutation SNP G G A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr11:31541617G>A ENST00000350638.5 + 2 273 c.238G>A c.(238-240)Gtt>Att p.V80I ELP4_ENST00000395934.2_Missense_Mutation_p.V80I|ELP4_ENST00000379163.5_Missense_Mutation_p.V80I NM_019040.3 NP_061913.3 Q96EB1 ELP4_HUMAN elongator acetyltransferase complex subunit 4 20 Lung SC(675;0.225) AGGTTTAGCCGTTGGAACAGT 0.348000 0 SO:0001583 missense ENST00000350638.5 1 1 hg19 CCDS7875.2 2 9.157509157509158E-4 0 0.0 0 0.0 0 0.0 2 0.002638522427440633 G 10.03 1.239257 0.22711 0.0 1.22E-4 ENSG00000109911 ENST00000350638;ENST00000379163;ENST00000395934 T;T;T 0.40756 1.02;1.02;1.02 5.15 4.23 0.50019 . 0.125811 0.53938 N 0.000059 T 0.52837 0.1759 L 0.41710 1.295 0.33585 D 0.600371 D;D;D 0.89917 0.994;1.0;1.0 P;D;D 0.87578 0.869;0.995;0.998 T 0.57957 -0.7721 10 0.15066 T 0.55 -12.2988 15.406 0.74877 0.0731:0.0:0.9269:0.0 . 80;80;80 B4E3W0;G5E9D4;Q96EB1 .;.;ELP4_HUMAN I 80 ENSP00000298937:V80I;ENSP00000368461:V80I;ENSP00000379267:V80I ENSP00000298937:V80I V + 1 0 ELP4 31498193 1.000000 0.71417 0.922000 0.36590 0.892000 0.51952 4.374000 0.59543 0.692000 0.31613 -1.151000 0.01829 GTT TCGA-2L-AAQE-01A-11D-A397-08 ELP4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000286640.1 1 0 1 76 221 0 70 1 9.042740e-01 5 9 0 70 2 0 0 0 0 0 2 1 1 76 220 0 70 2 0 0 0 0 0 2 -5.289739 1 1 120798 22 43 1 1 2 3 2.185977 0 0.530000 1.810000 0.539757 0.990000 8.000000e-01 1.000000 1.000000 0.958488 0.990000 1 8.900000e-01 1.000000 OR5M11 219487 broad.mit.edu 37 11 56310189 56310189 + Missense_Mutation SNP G G A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr11:56310189G>A ENST00000528616.2 - 1 568 c.545C>T c.(544-546)cCg>cTg p.P182L NM_001005245.1 NP_001005245.1 Q96RB7 OR5MB_HUMAN olfactory receptor, family 5, subfamily M, member 11 18 CTTAATGAGCGGCGGGTCAGC 0.502000 0 SO:0001583 missense ENST00000528616.2 1 1 hg19 CCDS53629.1 . . . . . . . . . . A 11.09 1.535136 0.27475 0.0 4.74E-4 ENSG00000255223 ENST00000528616 T 0.00224 8.51 4.89 1.97 0.26223 GPCR, rhodopsin-like superfamily (1); . . . . T 0.00496 0.0016 M 0.80422 2.495 0.21445 N 0.99969 D 0.89917 1.0 D 0.74348 0.983 T 0.47032 -0.9148 9 0.72032 D 0.01 . 7.6395 0.28286 0.1337:0.0:0.6314:0.2349 . 182 Q96RB7 OR5MB_HUMAN L 182 ENSP00000432417:P182L ENSP00000432417:P182L P - 2 0 OR5M11 56066765 0.003000 0.15002 0.493000 0.27502 0.234000 0.25298 1.152000 0.31663 0.040000 0.15660 -1.789000 0.00628 CCG TCGA-2L-AAQE-01A-11D-A397-08 OR5M11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391608.1 1 0 1 43 131 0 30 0 0 0 0 30 2 0 0 0 0 0 2 1 1 42 121 0 28 2 0 0 0 0 0 2 -2.895511 1 1 121030 32 48 1 1 2 3 2.185977 0 0.530000 1.810000 0.539757 0.960000 7.200000e-01 1.000000 1.000000 0.931059 0.960000 1 8.300000e-01 1.000000 GLYATL1 92292 broad.mit.edu 37 11 58723412 58723412 + Missense_Mutation SNP G G A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr11:58723412G>A ENST00000317391.4 + 8 1161 c.821G>A c.(820-822)cGc>cAc p.R274H RP11-142C4.6_ENST00000525714.1_RNA|GLYATL1_ENST00000300079.5_Missense_Mutation_p.R305H|RP11-142C4.6_ENST00000533954.1_RNA NM_001220494.1 NP_001207423.1 Q969I3 GLYL1_HUMAN glycine-N-acyltransferase-like 1 p.R305H(1) 34 Glycine(DB00145) GAAGACTCCCGCAGATTTGTG 0.448000 1 Substitution - Missense(1) SO:0001583 missense ENST00000317391.4 1 1 hg19 CCDS55768.1 0 0.0 0 0.0 0 0.0 0 0.0 0 0.0 . 0.271 -0.993172 0.02145 . . ENSG00000166840 ENST00000444580;ENST00000317391;ENST00000300079 T;T 0.18657 2.2;2.2 1.97 -2.28 0.06826 Acyl-CoA N-acyltransferase (2);Glycine N-acyltransferase, C-terminal (1); 0.732987 0.11663 N 0.541605 T 0.06280 0.0162 N 0.04508 -0.205 0.09310 N 1 B;B 0.17465 0.022;0.01 B;B 0.12156 0.004;0.007 T 0.36529 -0.9744 10 0.13853 T 0.58 . 1.8117 0.03092 0.4455:0.0:0.2831:0.2714 . 305;274 Q969I3-2;Q969I3 .;GLYL1_HUMAN H 251;274;305 ENSP00000322223:R274H;ENSP00000300079:R305H ENSP00000300079:R305H R + 2 0 GLYATL1 58479988 0.000000 0.05858 0.000000 0.03702 0.003000 0.03518 -1.478000 0.02329 -0.626000 0.05596 0.411000 0.27672 CGC TCGA-2L-AAQE-01A-11D-A397-08 GLYATL1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000393783.1 1 0 1 89 233 0 64 0 0 0 1 0 64 2 0 0 0 0 0 2 1 1 88 229 0 63 2 0 0 0 0 0 2 -6.211773 1 1 121412 4 41 1 1 2 3 2.185977 0 0.530000 1.810000 0.539757 0.990000 8.800000e-01 1.000000 1.000000 0.987679 0.990000 1 9.700000e-01 1.000000 AHNAK 79026 broad.mit.edu 37 11 62287090 62287090 + Silent SNP T T C TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr11:62287090T>C ENST00000378024.4 - 5 15073 c.14799A>G c.(14797-14799)tcA>tcG p.S4933S AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000525875.1_5'Flank|AHNAK_ENST00000257247.7_Intron NM_001620.1 NP_001611.1 Q09666 AHNK_HUMAN AHNAK nucleoprotein 268 Melanoma(852;0.155) ACTTCGGACCTGAAAATCCAA 0.458000 0 SO:0001819 synonymous_variant ENST00000378024.4 0 1 hg19 CCDS31584.1 TCGA-2L-AAQE-01A-11D-A397-08 AHNAK-005 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000395572.1 0 0 0 5 521 0 139 0 9.812960e-01 1 788 0 139 2 0 0 0 0 0 2 1 9.371875e-01 5 519 0 139 2 0 0 0 0 0 2 -2.385043 0 1 0 0 1 1 2 3 2.185977 0 0.530000 1.810000 0.539757 0.030000 0 1.000000 0.040000 0.104887 0.030000 0 1.000000e-02 0.070000 SRRM4 84530 broad.mit.edu 37 12 119568554 119568554 + Missense_Mutation SNP T T A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr12:119568554T>A ENST00000267260.4 + 8 1074 c.686T>A c.(685-687)cTc>cAc p.L229H SRRM4_ENST00000537597.1_3'UTR NM_194286.3 NP_919262.2 A7MD48 SRRM4_HUMAN serine/arginine repetitive matrix 4 24 TCCAAGACCCTCTGCAAGGAC 0.652000 0 SO:0001583 missense ENST00000267260.4 1 1 hg19 CCDS44994.1 . . . . . . . . . . T 14.62 2.590902 0.46214 . . ENSG00000139767 ENST00000267260 T 0.23552 1.9 5.07 2.5 0.30297 . 0.407083 0.22564 N 0.058424 T 0.11239 0.0274 N 0.19112 0.55 0.09310 N 1 B 0.06786 0.001 B 0.08055 0.003 T 0.21381 -1.0247 10 0.15066 T 0.55 -8.4824 1.5524 0.02578 0.1784:0.0995:0.1716:0.5504 . 229 A7MD48 SRRM4_HUMAN H 229 ENSP00000267260:L229H ENSP00000267260:L229H L + 2 0 SRRM4 118052937 0.059000 0.20769 0.996000 0.52242 0.987000 0.75469 0.734000 0.26101 0.734000 0.32515 0.368000 0.22195 CTC TCGA-2L-AAQE-01A-11D-A397-08 SRRM4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000401640.2 0 0 1 29 71 0 23 0 0 0 0 23 2 0 0 0 0 0 2 1 1 25 65 0 22 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 1.758242 1 0.530000 1.810000 0.378471 0.810000 5.800000e-01 1.000000 1.000000 0.815603 0.810000 0 6.900000e-01 0.940000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 C T C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr12:25398284C>T ENST00000256078.4 - 2 98 c.35G>A c.(34-36)gGt>gAt p.G12D KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 23.4 4.409094 0.83340 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.85919 0.5809 M 0.91818 3.245 0.80722 D 1 B;P 0.35714 0.385;0.517 B;B 0.41619 0.257;0.361 D 0.87870 0.2670 10 0.87932 D 0 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN D 12 ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D ENSP00000256078:G12D G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-2L-AAQE-01A-11D-A397-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 72 173 0 79 1 9.965879e-01 16 8 0 79 2 1 1 73 264 0 271 2 1 1 72 172 0 79 2 1 1 2983 5037 13 8012 23 -20.000000 1 1 121404 2 44 1 0 2 2 2.090760 1 0.530000 1.810000 0.530000 0.990000 9.000000e-01 1.000000 1.000000 0.993266 0.990000 1 9.900000e-01 1.000000 RND1 27289 broad.mit.edu 37 12 49254866 49254866 + Missense_Mutation SNP T T A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr12:49254866T>A ENST00000309739.5 - 4 497 c.367A>T c.(367-369)Att>Ttt p.I123F NM_014470.3 NP_055285.1 Q92730 RND1_HUMAN Rho family GTPase 1 10 TTGCAGCCAATGAGCAAAACG 0.552000 0 SO:0001583 missense ENST00000309739.5 1 1 hg19 CCDS8771.1 . . . . . . . . . . T 21.7 4.185328 0.78677 . . ENSG00000172602 ENST00000550607;ENST00000309739 T;T 0.79352 -1.26;-1.26 5.66 3.33 0.38152 Small GTP-binding protein domain (1); 0.051099 0.85682 D 0.000000 T 0.74718 0.3753 L 0.61387 1.9 0.58432 D 0.999998 P 0.47962 0.903 B 0.44108 0.441 T 0.76266 -0.3022 10 0.87932 D 0 -22.6091 9.2452 0.37520 0.0:0.1499:0.0:0.8501 . 123 Q92730 RND1_HUMAN F 17;123 ENSP00000447059:I17F;ENSP00000308461:I123F ENSP00000308461:I123F I - 1 0 RND1 47541133 0.915000 0.31059 0.998000 0.56505 0.935000 0.57460 1.352000 0.34033 1.084000 0.41184 -0.274000 0.10170 ATT TCGA-2L-AAQE-01A-11D-A397-08 RND1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000408915.1 1 0 1 118 240 0 75 1 9.685573e-01 6 8 0 75 2 0 0 0 0 0 2 1 1 118 238 0 75 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 2 2 2.094693 1 0.530000 1.810000 0.530000 0.990000 9.900000e-01 1.000000 1.000000 0.999929 0.990000 1 9.900000e-01 1.000000 ANKS1B 56899 broad.mit.edu 37 12 99898356 99898356 + Missense_Mutation SNP A A T TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr12:99898356A>T ENST00000547776.2 - 10 1335 c.1336T>A c.(1336-1338)Ttt>Att p.F446I ANKS1B_ENST00000329257.7_Missense_Mutation_p.F446I|ANKS1B_ENST00000547010.1_Missense_Mutation_p.F26I NM_152788.4 NP_690001.3 Q7Z6G8 ANS1B_HUMAN ankyrin repeat and sterile alpha motif domain containing 1B 70 all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209) TCTGAAGGAAATGTATCCAGA 0.383000 0 SO:0001583 missense ENST00000547776.2 1 1 hg19 CCDS55872.1 . . . . . . . . . . A 15.63 2.890646 0.52014 . . ENSG00000185046 ENST00000547776;ENST00000547010;ENST00000329257;ENST00000538702;ENST00000549866 T;T;T;T 0.61742 0.92;0.08;0.92;0.78 5.68 5.68 0.88126 . 0.136396 0.48767 D 0.000169 T 0.41766 0.1173 L 0.29908 0.895 0.80722 D 1 B;B;B 0.32829 0.386;0.386;0.02 B;B;B 0.27170 0.077;0.077;0.006 T 0.33828 -0.9853 9 . . . -6.2914 11.418 0.49965 0.8382:0.1618:0.0:0.0 . 412;26;446 F8VVQ4;Q7Z6G8-6;Q7Z6G8 .;.;ANS1B_HUMAN I 446;26;446;25;412 ENSP00000449629:F446I;ENSP00000448512:F26I;ENSP00000331381:F446I;ENSP00000449894:F412I . F - 1 0 ANKS1B 98422487 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 3.066000 0.50002 2.175000 0.68902 0.528000 0.53228 TTT TCGA-2L-AAQE-01A-11D-A397-08 ANKS1B-003 KNOWN basic|appris_candidate_longest|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000408421.3 1 0 1 17 48 0 31 0 0 0 0 31 2 0 0 0 0 0 2 1 9.999869e-01 17 48 0 31 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 1.758242 1 0.530000 1.810000 0.378471 0.730000 4.600000e-01 1.000000 1.000000 0.739562 0.730000 0 5.900000e-01 0.880000 LTB4R 1241 broad.mit.edu 37 14 24784967 24784967 + Missense_Mutation SNP G G C TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr14:24784967G>C ENST00000396789.4 + 2 1835 c.110G>C c.(109-111)aGc>aCc p.S37T LTB4R_ENST00000345363.3_Missense_Mutation_p.S37T|LTB4R_ENST00000396782.2_Missense_Mutation_p.S37T NM_181657.3 NP_858043.1 Q15722 LT4R1_HUMAN leukotriene B4 receptor 8 CCCGGCAACAGCTTTGTGGTG 0.577000 0 SO:0001583 missense ENST00000396789.4 1 1 hg19 CCDS9626.1 . . . . . . . . . . G 5.085 0.201347 0.09652 . . ENSG00000213903 ENST00000553481;ENST00000345363;ENST00000396789;ENST00000396782 T;T;T;T 0.37752 1.18;1.18;1.18;1.18 5.89 0.269 0.15631 GPCR, rhodopsin-like superfamily (1); 0.568969 0.17126 U 0.186005 T 0.19846 0.0477 L 0.28115 0.83 0.18873 N 0.999986 B 0.22003 0.063 B 0.18263 0.021 T 0.28933 -1.0028 10 0.10377 T 0.69 . 8.9335 0.35686 0.0:0.4012:0.3233:0.2755 . 37 Q15722 LT4R1_HUMAN T 37 ENSP00000450457:S37T;ENSP00000307445:S37T;ENSP00000380008:S37T;ENSP00000380002:S37T ENSP00000307445:S37T S + 2 0 LTB4R 23854807 0.015000 0.18098 0.089000 0.20774 0.999000 0.98932 0.329000 0.19698 0.050000 0.15949 0.655000 0.94253 AGC TCGA-2L-AAQE-01A-11D-A397-08 LTB4R-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000073198.4 1 0 1 170 467 0 131 1 9.620468e-01 5 12 0 131 2 0 0 0 0 0 2 1 1 169 463 0 129 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.130831 0 0.530000 1.810000 0.532478 0.990000 8.800000e-01 1.000000 1.000000 0.979970 0.990000 1 9.400000e-01 1.000000 SNRPN 6638 broad.mit.edu 37 15 25223413 25223413 + Silent SNP G G A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr15:25223413G>A ENST00000400100.1 + 12 1523 c.633G>A c.(631-633)acG>acA p.T211T SNRPN_ENST00000577565.1_Silent_p.T211T|SNRPN_ENST00000444203.2_Silent_p.T215T|SNRPN_ENST00000390687.4_Silent_p.T211T|SNURF_ENST00000551312.2_Intron|SNRPN_ENST00000400098.1_Silent_p.T211T|SNHG14_ENST00000551631.2_RNA|SNURF_ENST00000338094.6_3'UTR|SNRPN_ENST00000400097.1_Silent_p.T211T|SNRPN_ENST00000346403.6_Silent_p.T211T|SNRPN_ENST00000554227.2_Silent_p.T215T NM_022807.2 NP_073718.1 P63162 RSMN_HUMAN small nuclear ribonucleoprotein polypeptide N 24 all_cancers(20;9.33e-22)|Breast(32;0.000625) CTCGAGGGACGCCAATAGGCA 0.557000 Prader-Willi syndrome 0 SO:0001819 synonymous_variant Familial Cancer Database Prader-Labhart-Willi syndrome ENST00000400100.1 1 1 hg19 CCDS10017.1 TCGA-2L-AAQE-01A-11D-A397-08 SNRPN-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000413849.10 1 0 1 191 499 1 140 1 1 262 143 1 140 12 0 0 0 0 0 2 1 1 185 495 1 136 17 0 0 0 0 0 2 -20.000000 1 1 120858 9 44 1 1 2 3 2.120405 0 0.530000 1.810000 0.531242 0.990000 9.100000e-01 1.000000 1.000000 0.991671 0.990000 1 9.700000e-01 1.000000 ABCC1 4363 broad.mit.edu 37 16 16150130 16150130 + Missense_Mutation SNP C C T TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr16:16150130C>T ENST00000399410.3 + 12 1830 c.1655C>T c.(1654-1656)aCc>aTc p.T552I ABCC1_ENST00000399408.2_Missense_Mutation_p.T552I|ABCC1_ENST00000351154.5_Missense_Mutation_p.T552I|ABCC1_ENST00000349029.5_Missense_Mutation_p.T552I|ABCC1_ENST00000345148.5_Missense_Mutation_p.T552I|ABCC1_ENST00000346370.5_Missense_Mutation_p.T552I NM_004996.3 NP_004987.2 P33527 MRP1_HUMAN ATP-binding cassette, sub-family C (CFTR/MRP), member 1 56 Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399) GGCACCTTCACCTGGGTCTGC 0.517000 0 SO:0001583 missense ENST00000399410.3 1 1 hg19 CCDS42122.1 . . . . . . . . . . C 9.579 1.123011 0.20959 . . ENSG00000103222 ENST00000399410;ENST00000399408;ENST00000346370;ENST00000351154;ENST00000345148;ENST00000349029;ENST00000536381 D;D;D;D;D;D 0.90069 -2.61;-2.61;-2.61;-2.61;-2.61;-2.61 5.29 4.34 0.51931 ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1); 0.046759 0.85682 D 0.000000 D 0.88265 0.6390 N 0.21448 0.665 0.49915 D 0.99983 D;D;P;D;D;P;P 0.89917 0.998;0.996;0.821;1.0;0.999;0.806;0.923 D;P;P;D;D;P;P 0.76071 0.923;0.898;0.599;0.987;0.973;0.848;0.764 D 0.83738 0.0202 10 0.09338 T 0.73 -45.3552 13.1912 0.59711 0.0:0.9229:0.0:0.0771 . 552;552;552;552;552;552;552 P33527-6;P33527-5;P33527-4;P33527-3;P33527-2;P33527;P33527-9 .;.;.;.;.;MRP1_HUMAN;. I 552;552;552;552;552;552;226 ENSP00000382342:T552I;ENSP00000382340:T552I;ENSP00000263019:T552I;ENSP00000263017:T552I;ENSP00000263014:T552I;ENSP00000263016:T552I ENSP00000263014:T552I T + 2 0 ABCC1 16057631 1.000000 0.71417 1.000000 0.80357 0.937000 0.57800 7.450000 0.80656 1.216000 0.43427 0.462000 0.41574 ACC TCGA-2L-AAQE-01A-11D-A397-08 ABCC1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000109701.1 1 0 1 39 162 0 41 1 9.991354e-01 19 29 0 41 2 0 0 0 0 0 2 1 1 39 160 0 41 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.189608 0 0.530000 1.810000 0.539757 0.750000 5.500000e-01 1.000000 0.740000 0.771166 0.750000 0 6.400000e-01 0.890000 XYLT1 64131 broad.mit.edu 37 16 17235134 17235134 + Missense_Mutation SNP G G A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr16:17235134G>A ENST00000261381.6 - 7 1547 c.1463C>T c.(1462-1464)gCc>gTc p.A488V CTD-2576D5.4_ENST00000567344.1_RNA NM_022166.3 NP_071449.1 Q86Y38 XYLT1_HUMAN xylosyltransferase I 67 GCCATCCACGGCAATGCCCTC 0.577000 0 SO:0001583 missense ENST00000261381.6 0 1 hg19 CCDS10569.1 . . . . . . . . . . G 8.165 0.790357 0.16258 . . ENSG00000103489 ENST00000261381 T 0.11385 2.78 5.92 5.92 0.95590 . 0.342297 0.36374 N 0.002632 T 0.04770 0.0129 N 0.02142 -0.665 0.09310 N 0.999997 P 0.45044 0.849 B 0.40702 0.338 T 0.45527 -0.9255 10 0.20046 T 0.44 -20.7778 14.1696 0.65500 0.0:0.0:0.8505:0.1495 . 488 Q86Y38 XYLT1_HUMAN V 488 ENSP00000261381:A488V ENSP00000261381:A488V A - 2 0 XYLT1 17142635 0.894000 0.30519 0.015000 0.15790 0.196000 0.23810 4.775000 0.62346 2.797000 0.96272 0.555000 0.69702 GCC TCGA-2L-AAQE-01A-11D-A397-08 XYLT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252241.2 0 0 0 5 510 1 129 0 9.182503e-04 0 4 1 129 2 0 0 0 0 0 2 0 1.752358e-02 7 498 1 125 15 0 0 0 0 0 2 -2.495725 0 1 0 0 1 1 2 3 2.189608 0 0.530000 1.810000 0.539757 0.030000 0 1.000000 0.040000 0.105788 0.030000 0 1.000000e-02 0.070000 TMC7 79905 broad.mit.edu 37 16 19067891 19067891 + Silent SNP G G A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr16:19067891G>A ENST00000304381.5 + 14 2029 c.1899G>A c.(1897-1899)ccG>ccA p.P633P TMC7_ENST00000569532.1_Silent_p.P633P|TMC7_ENST00000421369.3_Silent_p.P523P NM_024847.3 NP_079123.3 Q7Z402 TMC7_HUMAN transmembrane channel-like 7 28 CCTGTGGGCCGTTCACCAACT 0.602000 0 SO:0001819 synonymous_variant ENST00000304381.5 0 1 hg19 CCDS10573.1 TCGA-2L-AAQE-01A-11D-A397-08 TMC7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254276.3 0 0 0 5 324 0 78 0 3.182076e-01 0 64 0 78 2 0 0 0 0 0 2 1 9.369998e-01 5 322 0 76 2 0 0 0 0 0 2 -2.835645 1 1 121412 9 42 1 1 2 3 2.189608 0 0.530000 1.810000 0.539757 0.060000 1.000000e-02 1.000000 0.060000 0.129508 0.060000 0 3.000000e-02 0.110000 ITGAX 3687 broad.mit.edu 37 16 31391078 31391078 + Splice_Site SNP G G T TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 G T G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr16:31391078G>T ENST00000268296.4 + 25 2990 c.2869G>T c.(2869-2871)Gtc>Ttc p.V957F ITGAX_ENST00000562522.1_Splice_Site_p.V957F NM_000887.3 NP_000878.2 P20702 ITAX_HUMAN integrin, alpha X (complement component 3 receptor 4 subunit) 77 CTCTGTGCAGGTCAATAACCT 0.627000 0 SO:0001630 splice_region_variant ENST00000268296.4 1 0 hg19 CCDS10711.1 . . . . . . . . . . G 12.97 2.096174 0.36952 . . ENSG00000140678 ENST00000268296 T 0.56776 0.44 4.58 4.58 0.56647 Integrin alpha-2 (1); . . . . T 0.58206 0.2106 L 0.33485 1.01 0.80722 D 1 D;D 0.67145 0.996;0.992 D;D 0.65573 0.936;0.918 T 0.54043 -0.8352 8 . . . . 13.0477 0.58937 0.0:0.0:1.0:0.0 . 957;142 P20702;Q8TES5 ITAX_HUMAN;. F 957 ENSP00000268296:V957F . V + 1 0 ITGAX 31298579 1.000000 0.71417 0.998000 0.56505 0.211000 0.24417 2.460000 0.45031 2.535000 0.85469 0.313000 0.20887 GTC TCGA-2L-AAQE-01A-11D-A397-08 ITGAX-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000255628.2 1 0 1 34 59 0 18 0 9.947066e-01 0 18 0 18 2 0 0 0 0 0 2 1 1 34 58 0 18 2 0 0 0 0 0 2 -20.000000 1 1 121410 3 36 1 1 2 3 2.189608 0 0.530000 1.810000 0.539757 0.990000 9.900000e-01 1.000000 1.000000 0.999363 0.990000 1 9.900000e-01 1.000000 TEX14 56155 broad.mit.edu 37 17 56659016 56659016 + Missense_Mutation SNP C C G TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr17:56659016C>G ENST00000240361.8 - 20 3350 c.3265G>C c.(3265-3267)Gaa>Caa p.E1089Q TEX14_ENST00000349033.5_Intron|TEX14_ENST00000389934.3_Missense_Mutation_p.E1083Q Q8IWB6 TEX14_HUMAN testis expressed 14 81 Medulloblastoma(34;0.127)|all_neural(34;0.237) TAAAAATATTCACCGTCTGGA 0.368000 0 SO:0001583 missense ENST00000240361.8 1 1 hg19 CCDS56042.1 . . . . . . . . . . C 13.82 2.352360 0.41700 . . ENSG00000121101 ENST00000240361;ENST00000389934 T;T 0.80214 -1.35;-1.35 5.34 4.37 0.52481 . 0.200908 0.34603 N 0.003829 T 0.73048 0.3537 L 0.27053 0.805 0.29767 N 0.835083 P;P 0.52061 0.917;0.95 B;P 0.49887 0.421;0.625 T 0.68368 -0.5427 10 0.31617 T 0.26 -4.298 8.9678 0.35887 0.0:0.9008:0.0:0.0992 . 1089;1083 Q8IWB6;Q8IWB6-2 TEX14_HUMAN;. Q 1089;1083 ENSP00000240361:E1089Q;ENSP00000374584:E1083Q ENSP00000240361:E1089Q E - 1 0 TEX14 54014015 0.751000 0.28327 0.573000 0.28510 0.696000 0.40369 2.632000 0.46511 2.504000 0.84457 0.462000 0.41574 GAA TCGA-2L-AAQE-01A-11D-A397-08 TEX14-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000445446.1 1 0 1 65 234 0 58 0 0 0 0 58 2 0 0 0 0 0 2 1 1 64 230 0 58 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.182309 0 0.530000 1.810000 0.546813 0.860000 6.700000e-01 1.000000 1.000000 0.869288 0.860000 1 7.600000e-01 1.000000 TP53 7157 broad.mit.edu 37 17 7579575 7579575 + Nonsense_Mutation SNP G G A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr17:7579575G>A ENST00000269305.4 - 4 301 c.112C>T c.(112-114)Caa>Taa p.Q38* TP53_ENST00000445888.2_Nonsense_Mutation_p.Q38*|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Nonsense_Mutation_p.Q38*|TP53_ENST00000420246.2_Nonsense_Mutation_p.Q38*|TP53_ENST00000359597.4_Nonsense_Mutation_p.Q38*|TP53_ENST00000413465.2_Nonsense_Mutation_p.Q38* 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.Q38*(8)|p.0?(8)|p.P36fs*4(3)|p.?(1)|p.S33fs*23(1)|p.P13fs*18(1)|p.S37fs*79(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) TCCATTGCTTGGGACGGCAAG 0.592000 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 23 Substitution - Nonsense(8)|Whole gene deletion(8)|Deletion - Frameshift(6)|Unknown(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 . . . . . . . . . . G 14.56 2.571091 0.45798 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000508793;ENST00000503591 . . . 3.41 -1.11 0.09840 . 3.135740 0.02989 U 0.146625 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.09338 T 0.73 0.2222 0.8266 0.01122 0.224:0.1841:0.4032:0.1887 . . . . X 38 . ENSP00000269305:Q38X Q - 1 0 TP53 7520300 0.000000 0.05858 0.000000 0.03702 0.042000 0.13812 -0.754000 0.04787 -0.145000 0.11294 0.561000 0.74099 CAA TCGA-2L-AAQE-01A-11D-A397-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 245 464 0 204 1 9.999999e-01 30 19 0 204 2 1 1 155 251 0 335 2 1 1 243 460 0 200 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 1.646491 1 0.530000 1.810000 0.369635 0.960000 8.600000e-01 1.000000 1.000000 0.959032 0.960000 1 9.100000e-01 1.000000 DAND5 199699 broad.mit.edu 37 19 13084387 13084387 + Missense_Mutation SNP G G A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr19:13084387G>A ENST00000317060.2 + 2 688 c.509G>A c.(508-510)cGt>cAt p.R170H DAND5_ENST00000585548.1_3'UTR NM_152654.2 NP_689867.1 Q8N907 DAND5_HUMAN DAN domain family member 5, BMP antagonist 6 OV - Ovarian serous cystadenocarcinoma(19;1.87e-18) TCAGCCTCCCGTCGACGGGTG 0.602000 0 SO:0001583 missense ENST00000317060.2 1 1 hg19 CCDS12291.1 . . . . . . . . . . G 11.08 1.534859 0.27475 2.27E-4 2.33E-4 ENSG00000179284 ENST00000317060 T 0.33654 1.4 5.49 -3.42 0.04825 DAN (1); 0.906086 0.09091 N 0.849807 T 0.23410 0.0566 L 0.40543 1.245 0.09310 N 1 B 0.15141 0.012 B 0.12837 0.008 T 0.29088 -1.0023 10 0.30854 T 0.27 -1.7171 5.2395 0.15464 0.3965:0.2644:0.3391:0.0 . 170 Q8N907 DAND5_HUMAN H 170 ENSP00000323155:R170H ENSP00000323155:R170H R + 2 0 DAND5 12945387 0.000000 0.05858 0.001000 0.08648 0.059000 0.15707 -0.058000 0.11750 -0.216000 0.10048 -0.136000 0.14681 CGT TCGA-2L-AAQE-01A-11D-A397-08 DAND5-001 KNOWN upstream_ATG|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000452761.1 1 0 1 91 240 0 83 0 0 1 0 0 83 2 0 0 0 0 0 2 1 1 91 238 0 81 2 0 0 0 0 0 2 -6.565702 1 1 121412 6 43 1 1 2 3 2.128114 0 0.530000 1.810000 0.532478 0.990000 8.600000e-01 1.000000 1.000000 0.981746 0.990000 1 9.400000e-01 1.000000 DMKN 93099 broad.mit.edu 37 19 36004243 36004243 + Silent SNP G G A rs113646456 TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr19:36004243G>A ENST00000339686.3 - 1 311 c.135C>T c.(133-135)gaC>gaT p.D45D DMKN_ENST00000451297.2_Silent_p.D45D|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000440396.1_Silent_p.D45D|DMKN_ENST00000419602.1_Silent_p.D45D|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000447113.2_Silent_p.D45D|DMKN_ENST00000418261.1_Silent_p.D45D|DMKN_ENST00000424570.2_Silent_p.D45D|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000429837.1_Silent_p.D45D|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000443640.1_5'Flank NM_033317.4 NP_201574 Q6E0U4 DMKN_HUMAN dermokine 27 all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0724) CGCTCAGGGCGTCTCCCAGGC 0.642000 0 SO:0001819 synonymous_variant ENST00000339686.3 1 1 hg19 CCDS12463.1 TCGA-2L-AAQE-01A-11D-A397-08 DMKN-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000109461.2 1 0 1 65 270 0 66 0 0 1 0 0 66 2 0 0 0 0 0 2 1 1 65 269 0 63 2 0 0 0 0 0 2 -20.000000 1 1 121412 27 47 1 0 0 0 2.020278 0 0.530000 1.810000 0.509190 0.690000 5.500000e-01 0.850000 0.700000 0.705670 0.690000 0 6.200000e-01 0.780000 ZNF780B 163131 broad.mit.edu 37 19 40541025 40541025 + Missense_Mutation SNP C C T TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr19:40541025C>T ENST00000434248.1 - 5 1806 c.1741G>A c.(1741-1743)Gga>Aga p.G581R ZNF780B_ENST00000221355.6_Missense_Mutation_p.G433R NM_001005851.2 NP_001005851.1 Q9Y6R6 Z780B_HUMAN zinc finger protein 780B p.G581R(1) 23 all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925) GGTTTCTTTCCGGTATGAATA 0.388000 1 Substitution - Missense(1) SO:0001583 missense ENST00000434248.1 1 1 hg19 CCDS46077.1 . . . . . . . . . . C 20.3 3.970459 0.74246 2.27E-4 0.0 ENSG00000128000 ENST00000434248;ENST00000221355 T;T 0.26223 1.75;1.75 2.56 1.45 0.22620 Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.43277 0.1240 M 0.69248 2.105 0.31143 N 0.706402 D 0.89917 1.0 D 0.97110 1.0 T 0.42582 -0.9443 9 0.56958 D 0.05 . 6.4082 0.21676 0.0:0.8247:0.0:0.1753 . 581 Q9Y6R6 Z780B_HUMAN R 581;433 ENSP00000391641:G581R;ENSP00000221355:G433R ENSP00000221355:G433R G - 1 0 ZNF780B 45232865 0.000000 0.05858 0.017000 0.16124 0.602000 0.36980 0.958000 0.29227 0.214000 0.20742 0.462000 0.41574 GGA TCGA-2L-AAQE-01A-11D-A397-08 ZNF780B-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000338466.1 1 0 1 70 473 1 113 1 2.805598e-01 3 5 1 113 2 0 0 0 0 0 2 1 1 70 471 1 113 17 0 0 0 0 0 2 -2.920857 1 1 121412 7 41 1 0 0 0 2.020278 0 0.530000 1.810000 0.509190 0.460000 3.600000e-01 0.570000 0.460000 0.469926 0.460000 0 4.100000e-01 0.520000 HIF3A 64344 broad.mit.edu 37 19 46834437 46834437 + Silent SNP C C T TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr19:46834437C>T ENST00000377670.4 + 13 1768 c.1737C>T c.(1735-1737)gaC>gaT p.D579D HIF3A_ENST00000244303.6_Silent_p.D510D|AC007193.10_ENST00000596807.1_RNA|HIF3A_ENST00000472815.1_Intron|HIF3A_ENST00000300862.3_Silent_p.D577D|HIF3A_ENST00000420102.2_Silent_p.D528D|HIF3A_ENST00000600383.1_Silent_p.D510D|HIF3A_ENST00000339613.2_Silent_p.D523D NM_152795.3 NP_690008.2 Q9Y2N7 HIF3A_HUMAN hypoxia inducible factor 3, alpha subunit p.D577D(1) 33 Ovarian(192;0.00965)|all_neural(266;0.0887) GCTCAGAGGACGAGGACGAGG 0.552000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000377670.4 1 1 hg19 CCDS12681.2 TCGA-2L-AAQE-01A-11D-A397-08 HIF3A-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000280556.3 1 0 1 37 150 0 46 0 0 0 0 46 2 0 0 0 0 0 2 1 1 37 148 0 43 2 0 0 0 0 0 2 -20.000000 1 1 121412 2 30 1 1 2 3 2.131241 0 0.530000 1.810000 0.536146 0.760000 5.500000e-01 1.000000 0.750000 0.773132 0.760000 0 6.500000e-01 0.890000 BCAT2 587 broad.mit.edu 37 19 49300574 49300574 + Missense_Mutation SNP C C T rs139881168 TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr19:49300574C>T ENST00000316273.6 - 7 724 c.712G>A c.(712-714)Gtg>Atg p.V238M BCAT2_ENST00000402551.1_Missense_Mutation_p.V198M|BCAT2_ENST00000598162.1_Missense_Mutation_p.V238M|BCAT2_ENST00000599246.1_Missense_Mutation_p.V146M|BCAT2_ENST00000597011.1_Missense_Mutation_p.V198M|BCAT2_ENST00000545387.2_Missense_Mutation_p.V146M NM_001190.3 NP_001181.2 O15382 BCAT2_HUMAN branched chain amino-acid transaminase 2, mitochondrial 12 all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261) L-Isoleucine(DB00167)|L-Leucine(DB00149) TGCACTAACACGGTGGGCCCA 0.617000 0 SO:0001583 missense ENST00000316273.6 1 1 hg19 CCDS12735.1 . . . . . . . . . . C 15.76 2.928560 0.52759 0.0 1.16E-4 ENSG00000105552 ENST00000316273;ENST00000545387;ENST00000402551 T;T;T 0.21543 2.0;2.0;2.0 5.06 5.06 0.68205 . 0.061208 0.64402 D 0.000005 T 0.31575 0.0801 L 0.35414 1.06 0.37282 D 0.907881 D;D;D;D 0.89917 0.999;1.0;0.976;1.0 D;D;P;D 0.68483 0.937;0.937;0.458;0.958 T 0.17379 -1.0371 10 0.87932 D 0 -16.3767 9.8608 0.41114 0.0:0.9059:0.0:0.094 . 198;238;146;238 B3KSI3;Q53EW7;O15382-2;O15382 .;.;.;BCAT2_HUMAN M 238;146;198 ENSP00000322991:V238M;ENSP00000440973:V146M;ENSP00000385161:V198M ENSP00000322991:V238M V - 1 0 BCAT2 53992386 0.991000 0.36638 0.476000 0.27291 0.493000 0.33554 2.602000 0.46257 2.523000 0.85059 0.491000 0.48974 GTG TCGA-2L-AAQE-01A-11D-A397-08 BCAT2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000466202.1 1 0 1 23 95 0 24 1 9.999561e-01 34 38 0 24 2 0 0 0 0 0 2 1 9.999997e-01 22 95 0 24 2 0 0 0 0 0 2 -3.604268 1 1 121412 3 34 1 1 2 3 2.131241 0 0.530000 1.810000 0.536146 0.750000 5.000000e-01 1.000000 1.000000 0.765225 0.750000 0 6.100000e-01 0.920000 FBN3 84467 broad.mit.edu 37 19 8155007 8155007 + Missense_Mutation SNP C C T rs149936210 TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr19:8155007C>T ENST00000600128.1 - 49 6574 c.6160G>A c.(6160-6162)Gaa>Aaa p.E2054K FBN3_ENST00000601739.1_Missense_Mutation_p.E2054K|FBN3_ENST00000270509.2_Missense_Mutation_p.E2054K Q75N90 FBN3_HUMAN fibrillin 3 132 GGACACAGTTCGCAGGGGTCT 0.612000 0 SO:0001583 missense ENST00000600128.1 1 1 hg19 CCDS12196.1 2 9.157509157509158E-4 0 0.0 2 0.0055248618784530384 0 0.0 0 0.0 C 21.7 4.181062 0.78677 2.27E-4 0.0 ENSG00000142449 ENST00000270509 D 0.95885 -3.84 4.13 4.13 0.48395 Matrix fibril-associated (3);TGF-beta binding (1); 0.000000 0.85682 U 0.000000 D 0.95478 0.8531 M 0.82193 2.58 0.80722 D 1 D 0.69078 0.997 P 0.52758 0.708 D 0.94770 0.7944 10 0.51188 T 0.08 . 16.3935 0.83548 0.0:1.0:0.0:0.0 . 2054 Q75N90 FBN3_HUMAN K 2054 ENSP00000270509:E2054K ENSP00000270509:E2054K E - 1 0 FBN3 8061007 1.000000 0.71417 0.942000 0.38095 0.333000 0.28666 5.572000 0.67411 1.836000 0.53414 0.462000 0.41574 GAA TCGA-2L-AAQE-01A-11D-A397-08 FBN3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000461428.2 1 0 1 51 136 0 40 0 0 0 0 40 2 0 0 0 0 0 2 1 1 50 133 0 38 2 0 0 0 0 0 2 -20.000000 1 1 121412 3 38 1 1 2 3 2.124373 0 0.530000 1.810000 0.532478 0.990000 8.000000e-01 1.000000 1.000000 0.968762 0.990000 1 9.100000e-01 1.000000 OR7D2 162998 broad.mit.edu 37 19 9296821 9296821 + Missense_Mutation SNP C C T rs150499443 TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr19:9296821C>T ENST00000344248.2 + 1 543 c.364C>T c.(364-366)Cgg>Tgg p.R122W NM_175883.2 NP_787079.1 Q96RA2 OR7D2_HUMAN olfactory receptor, family 7, subfamily D, member 2 20 GGCCTATGACCGGTTTGTGGC 0.507000 0 SO:0001583 missense ENST00000344248.2 0 1 hg19 CCDS32900.1 . . . . . . . . . . C 11.95 1.790563 0.31685 4.54E-4 0.0 ENSG00000188000 ENST00000344248 T 0.77620 -1.11 2.21 -0.197 0.13228 GPCR, rhodopsin-like superfamily (1); 0.200776 0.24490 U 0.038067 D 0.82309 0.5009 H 0.98314 4.2 0.22226 N 0.999272 P 0.35684 0.515 B 0.30572 0.117 T 0.77032 -0.2738 10 0.87932 D 0 . 8.8799 0.35367 0.5707:0.4293:0.0:0.0 . 122 Q96RA2 OR7D2_HUMAN W 122 ENSP00000345563:R122W ENSP00000345563:R122W R + 1 2 OR7D2 9157821 0.418000 0.25440 0.996000 0.52242 0.822000 0.46500 0.150000 0.16263 0.051000 0.15978 0.511000 0.50034 CGG TCGA-2L-AAQE-01A-11D-A397-08 OR7D2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000449002.1 0 0 0 9 652 0 137 0 0 0 0 137 2 0 0 0 0 0 2 1 9.938478e-01 9 642 0 136 2 0 0 0 0 0 2 -2.019665 0 1 121412 3 45 1 1 2 3 2.124373 0 0.530000 1.810000 0.532478 0.050000 1.000000e-02 0.110000 0.060000 0.066441 0.050000 0 3.000000e-02 0.080000 FLG 2312 broad.mit.edu 37 1 152286796 152286796 + Missense_Mutation SNP T T A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr1:152286796T>A ENST00000368799.1 - 3 601 c.566A>T c.(565-567)gAa>gTa p.E189V FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA NM_002016.1 NP_002007.1 P20930 FILA_HUMAN filaggrin 424 Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127) LUSC - Lung squamous cell carcinoma(543;0.206) TCTAGTATTTTCAGTCTTGTT 0.308000 Ichthyosis 0 SO:0001583 missense Familial Cancer Database X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris ENST00000368799.1 1 1 hg19 CCDS30860.1 . . . . . . . . . . T 10.59 1.391622 0.25118 . . ENSG00000143631 ENST00000368799 T 0.00801 5.68 3.68 -3.27 0.05048 . . . . . T 0.00328 0.0010 N 0.08118 0 0.09310 N 1 D 0.53885 0.963 P 0.53035 0.716 T 0.48502 -0.9030 9 0.29301 T 0.29 0.9076 4.776 0.13180 0.0:0.3342:0.3439:0.322 . 189 P20930 FILA_HUMAN V 189 ENSP00000357789:E189V ENSP00000357789:E189V E - 2 0 FLG 150553420 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -1.049000 0.03514 -0.583000 0.05921 0.378000 0.23410 GAA TCGA-2L-AAQE-01A-11D-A397-08 FLG-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000033742.1 1 0 0 10 206 0 76 0 0 0 0 76 2 0 0 0 0 0 2 1 9.970829e-01 10 206 0 76 2 0 0 0 0 0 2 -4.509725 1 1 0 0 1 0 1 1 1.973246 0 0.530000 1.810000 0.489408 0.160000 8.000000e-02 0.280000 0.160000 0.174429 0.160000 0 1.100000e-01 0.220000 TMEM63A 9725 broad.mit.edu 37 1 226037743 226037743 + Silent SNP C C T TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr1:226037743C>T ENST00000366835.3 - 21 2211 c.1941G>A c.(1939-1941)cgG>cgA p.R647R NM_014698.2 NP_055513.2 O94886 CSCL1_HUMAN transmembrane protein 63A 24 Breast(184;0.197) AGAGGTTGTGCCGGTCCACCA 0.602000 0 SO:0001819 synonymous_variant ENST00000366835.3 0 1 hg19 CCDS31042.1 TCGA-2L-AAQE-01A-11D-A397-08 TMEM63A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000091154.2 0 0 0 5 422 0 95 0 6.921161e-01 0 192 0 95 2 0 0 0 0 0 2 1 9.367252e-01 5 419 0 95 2 0 0 0 0 0 2 -1.923306 0 1 0 0 1 0 1 1 1.973246 0 0.530000 1.810000 0.489408 0.040000 0 0.090000 0.040000 0.048395 0.040000 0 2.000000e-02 0.070000 OBSCN 84033 broad.mit.edu 37 1 228451984 228451984 + Missense_Mutation SNP G G A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr1:228451984G>A ENST00000422127.1 + 16 4797 c.4753G>A c.(4753-4755)Gtg>Atg p.V1585M OBSCN_ENST00000359599.6_Missense_Mutation_p.V241M|OBSCN_ENST00000284548.11_Missense_Mutation_p.V1585M|OBSCN_ENST00000570156.2_Missense_Mutation_p.V1769M|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR NM_001098623.2 NP_001092093.2 Q5VST9 OBSCN_HUMAN obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF 223 Prostate(94;0.0405) AATGGAGGCCGTGGGCTGCAC 0.662000 0 SO:0001583 missense ENST00000422127.1 0 1 hg19 CCDS58065.1 . . . . . . . . . . . 9.689 1.151336 0.21371 . . ENSG00000154358 ENST00000284548;ENST00000422127;ENST00000359599 T;T;T 0.67523 -0.27;-0.27;-0.27 4.82 -9.64 0.00541 Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 2.685180 0.02136 N 0.056724 T 0.57519 0.2059 L 0.34521 1.04 0.09310 N 0.999999 D;D 0.59767 0.965;0.986 P;P 0.52881 0.712;0.462 T 0.65611 -0.6126 10 0.48119 T 0.1 . 3.3118 0.07020 0.2018:0.2166:0.4408:0.1408 . 1585;1585 Q5VST9;Q5VST9-3 OBSCN_HUMAN;. M 1585;1585;241 ENSP00000284548:V1585M;ENSP00000409493:V1585M;ENSP00000352613:V241M ENSP00000284548:V1585M V + 1 0 OBSCN 226518607 0.002000 0.14202 0.000000 0.03702 0.000000 0.00434 0.071000 0.14594 -2.145000 0.00801 -0.218000 0.12543 GTG TCGA-2L-AAQE-01A-11D-A397-08 OBSCN-204 KNOWN basic|CCDS protein_coding protein_coding 0 0 0 5 317 0 89 0 0 0 1 0 89 2 0 0 0 0 0 2 1 9.364698e-01 5 314 0 87 2 0 0 0 0 0 2 -2.778025 1 1 121122 5 41 1 0 1 1 1.973246 0 0.530000 1.810000 0.489408 0.050000 1.000000e-02 0.120000 0.050000 0.064111 0.050000 0 3.000000e-02 0.090000 CHD6 84181 broad.mit.edu 37 20 40052243 40052243 + Missense_Mutation SNP G G A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr20:40052243G>A ENST00000373233.3 - 30 4621 c.4444C>T c.(4444-4446)Cgc>Tgc p.R1482C NM_032221.3 NP_115597.3 Q8TD26 CHD6_HUMAN chromodomain helicase DNA binding protein 6 129 Myeloproliferative disorder(115;0.00425) GAAATGATGCGGAACTGTGTC 0.443000 0 SO:0001583 missense ENST00000373233.3 0 1 hg19 CCDS13317.1 . . . . . . . . . . G 28.5 4.928613 0.92389 . . ENSG00000124177 ENST00000373233 D 0.94793 -3.52 6.07 6.07 0.98685 SANT domain, DNA binding (1); 0.000000 0.64402 D 0.000007 D 0.97876 0.9302 M 0.89287 3.02 0.80722 D 1 D 0.89917 1.0 D 0.85130 0.997 D 0.97909 1.0307 10 0.87932 D 0 -12.954 20.6439 0.99570 0.0:0.0:1.0:0.0 . 1482 Q8TD26 CHD6_HUMAN C 1482 ENSP00000362330:R1482C ENSP00000362330:R1482C R - 1 0 CHD6 39485657 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 6.405000 0.73272 2.884000 0.98904 0.655000 0.94253 CGC TCGA-2L-AAQE-01A-11D-A397-08 CHD6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079270.1 0 0 0 5 787 0 214 0 3.446151e-03 0 11 0 214 2 0 0 0 0 0 2 1 9.372926e-01 5 785 0 212 2 0 0 0 0 0 2 -1.736653 0 1 0 0 1 1 2 3 2.177491 0 0.530000 1.810000 0.538560 0.020000 0 1.000000 0.020000 0.082419 0.020000 0 0 0.050000 PTK6 5753 broad.mit.edu 37 20 62166328 62166328 + Silent SNP C C T TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr20:62166328C>T ENST00000217185.2 - 2 342 c.315G>A c.(313-315)agG>agA p.R105R PTK6_ENST00000542869.1_Intron NM_005975.3 NP_005966.1 Q13882 PTK6_HUMAN protein tyrosine kinase 6 15 all_cancers(38;2.51e-11) Epithelial(9;1.5e-08)|all cancers(9;8.67e-08)|BRCA - Breast invasive adenocarcinoma(10;6.43e-06) Vandetanib(DB05294) TCTCGCTGACCCTGATCAGGA 0.692000 0 SO:0001819 synonymous_variant ENST00000217185.2 1 1 hg19 CCDS13524.1 TCGA-2L-AAQE-01A-11D-A397-08 PTK6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000080313.1 1 0 0 16 77 0 20 1 9.999998e-01 80 87 0 20 2 0 0 0 0 0 2 1 9.999570e-01 16 76 0 20 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.177491 0 0.530000 1.810000 0.538560 0.670000 4.100000e-01 1.000000 0.660000 0.697733 0.670000 0 5.300000e-01 0.870000 TIAM1 7074 broad.mit.edu 37 21 32502539 32502539 + Missense_Mutation SNP G G A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr21:32502539G>A ENST00000286827.3 - 26 4508 c.4037C>T c.(4036-4038)gCg>gTg p.A1346V TIAM1_ENST00000541036.1_Missense_Mutation_p.A1286V NM_003253.2 NP_003244.2 Q13009 TIAM1_HUMAN T-cell lymphoma invasion and metastasis 1 115 ACCTGCACTCGCCAAAGCTCG 0.473000 0 SO:0001583 missense ENST00000286827.3 0 1 hg19 CCDS13609.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 14.02|14.02 2.411603|2.411603 0.42817|0.42817 .|. .|. ENSG00000156299|ENSG00000156299 ENST00000286827;ENST00000541036|ENST00000423206 T;T|. 0.43294|. 0.95;0.96|. 6.03|6.03 6.03|6.03 0.97812|0.97812 Pleckstrin homology-type (1);Pleckstrin homology domain (1);|. 0.249575|. 0.39544|. N|. 0.001336|. T|. 0.69495|. 0.3117|. L|L 0.44542|0.44542 1.39|1.39 0.38497|0.38497 D|D 0.948125|0.948125 B;B;B|. 0.28971|. 0.229;0.016;0.147|. B;B;B|. 0.27170|. 0.077;0.003;0.035|. T|. 0.65055|. -0.6261|. 10|. 0.46703|. T|. 0.11|. .|. 20.5666|20.5666 0.99351|0.99351 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. 1286;1286;1346|. F5GZ53;B7ZLR6;Q13009|. .;.;TIAM1_HUMAN|. V|X 1346;1286|1 ENSP00000286827:A1346V;ENSP00000441570:A1286V|. ENSP00000286827:A1346V|. A|R -|- 2|1 0|2 TIAM1|TIAM1 31424410|31424410 1.000000|1.000000 0.71417|0.71417 0.983000|0.983000 0.44433|0.44433 0.291000|0.291000 0.27294|0.27294 7.077000|7.077000 0.76814|0.76814 2.854000|2.854000 0.98071|0.98071 0.655000|0.655000 0.94253|0.94253 GCG|CGA TCGA-2L-AAQE-01A-11D-A397-08 TIAM1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000192552.1 0 0 0 6 733 0 209 0 1.015770e-04 0 2 0 209 2 0 0 0 0 0 2 1 9.632487e-01 6 722 0 209 2 0 0 0 0 0 2 -1.857569 0 1 121412 1 35 1 0 1 1 1.897546 1 0.530000 1.810000 0.463133 0.020000 0 0.060000 0.030000 0.030917 0.020000 0 1.000000e-02 0.040000 DOPEY2 9980 broad.mit.edu 37 21 37609569 37609569 + Missense_Mutation SNP C C T TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr21:37609569C>T ENST00000399151.3 + 16 2717 c.2632C>T c.(2632-2634)Cgt>Tgt p.R878C NM_005128.2 NP_005119.2 Q9Y3R5 DOP2_HUMAN dopey family member 2 58 GAGGGTGGCTCGTGTGCTTTG 0.587000 0 SO:0001583 missense ENST00000399151.3 1 1 hg19 CCDS13643.1 . . . . . . . . . . C 14.48 2.547731 0.45383 . . ENSG00000142197 ENST00000399151 T 0.67523 -0.27 5.3 5.3 0.74995 . 0.368606 0.30076 N 0.010472 T 0.56601 0.1996 L 0.36672 1.1 0.26838 N 0.968431 B 0.18461 0.028 B 0.10450 0.005 T 0.52442 -0.8575 10 0.48119 T 0.1 -8.3965 12.7613 0.57365 0.0:0.9152:0.0:0.0848 . 878 Q9Y3R5 DOP2_HUMAN C 878 ENSP00000382104:R878C ENSP00000382104:R878C R + 1 0 DOPEY2 36531439 0.604000 0.26932 0.983000 0.44433 0.978000 0.69477 5.633000 0.67825 2.489000 0.83994 0.591000 0.81541 CGT TCGA-2L-AAQE-01A-11D-A397-08 DOPEY2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000194636.1 1 0 1 46 261 0 60 0 1.134076e-01 0 4 0 60 2 0 0 0 0 0 2 1 1 46 250 0 59 2 0 0 0 0 0 2 -2.926773 1 1 0 0 1 0 1 1 1.897546 1 0.530000 1.810000 0.463133 0.490000 3.700000e-01 0.630000 0.490000 0.500596 0.490000 0 4.200000e-01 0.570000 ZNF280A 129025 broad.mit.edu 37 22 22869193 22869193 + Silent SNP G G A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr22:22869193G>A ENST00000302097.3 - 2 1014 c.762C>T c.(760-762)gaC>gaT p.D254D snoU13_ENST00000459485.1_RNA NM_080740.3 NP_542778.1 P59817 Z280A_HUMAN zinc finger protein 280A 18 all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17) all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22) GACTTGAAATGTCTGTCATTG 0.408000 0 SO:0001819 synonymous_variant ENST00000302097.3 1 1 hg19 CCDS13800.1 TCGA-2L-AAQE-01A-11D-A397-08 ZNF280A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000075433.3 1 0 1 181 286 0 142 0 0 0 0 142 2 0 0 0 0 0 2 1 1 176 285 0 141 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 1.751573 1 0.530000 1.810000 0.365122 0.990000 9.100000e-01 1.000000 1.000000 0.984755 0.990000 1 9.500000e-01 1.000000 RGPD2 729857 broad.mit.edu 37 2 88125207 88125207 + Silent SNP C C T TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr2:88125207C>T ENST00000398146.3 - 1 264 c.42G>A c.(40-42)tcG>tcA p.S14S RGPD2_ENST00000420840.2_Intron|RGPD2_ENST00000327544.6_5'UTR P0DJD1 RGPD2_HUMAN RANBP2-like and GRIP domain containing 2 2 AGCCCTGCACCGAGGCGAGGT 0.721000 0 SO:0001819 synonymous_variant ENST00000398146.3 0 1 hg19 CCDS42710.2 TCGA-2L-AAQE-01A-11D-A397-08 RGPD2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000330534.2 0 0 0 14 40 0 11 0 0 0 0 11 2 0 0 0 0 0 2 0 0 0 0 0 2 0 0 0 0 0 2 -13.483960 1 0 0 0 1 1 2 3 2.159731 0 0.530000 1.810000 0.536146 0.990000 6.000000e-01 1.000000 1.000000 0.919173 0.990000 1 7.800000e-01 1.000000 NCBP2 22916 broad.mit.edu 37 3 196664485 196664485 + Missense_Mutation SNP G G A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr3:196664485G>A ENST00000321256.5 - 3 388 c.295C>T c.(295-297)Cgg>Tgg p.R99W NCBP2_ENST00000447325.1_Missense_Mutation_p.R29W|NCBP2_ENST00000467803.1_5'UTR|NCBP2_ENST00000452404.2_Missense_Mutation_p.R81W|NCBP2_ENST00000427641.2_Missense_Mutation_p.R46W|NCBP2-AS1_ENST00000447775.1_RNA|NCBP2_ENST00000422610.1_Missense_Mutation_p.R29W NM_007362.3 NP_031388.2 P52298 NCBP2_HUMAN nuclear cap binding protein subunit 2, 20kDa p.R99W(1) 5 all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135) Epithelial(36;3.42e-24)|all cancers(36;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(49;4.13e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06) TTTATGTACCGCATGGCGTTT 0.488000 1 Substitution - Missense(1) SO:0001583 missense ENST00000321256.5 0 1 hg19 CCDS3323.1 . . . . . . . . . . G 17.74 3.462954 0.63513 . . ENSG00000114503 ENST00000447325;ENST00000321256;ENST00000427641;ENST00000452404;ENST00000422610;ENST00000411704 T;T;T;T;T;T 0.75260 -0.92;2.27;-0.92;2.27;-0.92;-0.92 4.96 2.05 0.26809 Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3); 0.057701 0.64402 D 0.000003 D 0.85248 0.5653 M 0.82823 2.61 0.80722 D 1 P;D;P 0.89917 0.716;1.0;0.844 B;D;B 0.80764 0.138;0.994;0.217 D 0.84961 0.0877 10 0.48119 T 0.1 . 13.3628 0.60665 0.0:0.0:0.4238:0.5762 . 81;46;99 P52298-2;E9PAR5;P52298 .;.;NCBP2_HUMAN W 29;99;46;81;29;29 ENSP00000413518:R29W;ENSP00000326806:R99W;ENSP00000397619:R46W;ENSP00000412785:R81W;ENSP00000394105:R29W;ENSP00000389315:R29W ENSP00000326806:R99W R - 1 2 NCBP2 198148882 1.000000 0.71417 1.000000 0.80357 0.991000 0.79684 0.449000 0.21744 0.323000 0.23307 -0.182000 0.12963 CGG TCGA-2L-AAQE-01A-11D-A397-08 NCBP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000340470.2 0 0 0 5 494 1 93 0 5.516925e-03 0 201 1 93 9 0 0 0 0 0 2 0 4.553594e-03 5 490 1 91 18 0 0 0 0 0 2 -2.167731 0 1 0 0 1 1 2 3 2.162847 0 0.530000 1.810000 0.536146 0.030000 0 1.000000 0.040000 0.081679 0.030000 0 2.000000e-02 0.070000 FBXL5 26234 broad.mit.edu 37 4 15628553 15628553 + Missense_Mutation SNP G G T TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr4:15628553G>T ENST00000341285.3 - 8 1191 c.1067C>A c.(1066-1068)cCt>cAt p.P356H FBXL5_ENST00000412094.2_Missense_Mutation_p.P339H|FBXL5_ENST00000382358.4_Missense_Mutation_p.P230H NM_001193534.1|NM_001193535.1|NM_012161.3 NP_001180463.1|NP_001180464.1|NP_036293.1 Q9UKA1 FBXL5_HUMAN F-box and leucine-rich repeat protein 5 13 CTCCAGGTTAGGACAAAGCTC 0.328000 0 SO:0001583 missense ENST00000341285.3 0 1 hg19 CCDS3415.1 . . . . . . . . . . G 29.0 4.966766 0.92855 . . ENSG00000118564 ENST00000341285;ENST00000412094;ENST00000382358 T;T;T 0.19669 2.13;2.13;2.13 5.98 5.98 0.97165 . 0.000000 0.85682 D 0.000000 T 0.49795 0.1578 M 0.71581 2.175 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.998 T 0.43718 -0.9374 10 0.87932 D 0 -27.9909 20.0624 0.97681 0.0:0.0:1.0:0.0 . 339;356 Q9UKA1-2;Q9UKA1 .;FBXL5_HUMAN H 356;339;230 ENSP00000344866:P356H;ENSP00000408679:P339H;ENSP00000371795:P230H ENSP00000344866:P356H P - 2 0 FBXL5 15237651 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 9.230000 0.95299 2.838000 0.97847 0.591000 0.81541 CCT TCGA-2L-AAQE-01A-11D-A397-08 FBXL5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000214235.2 0 0 0 5 224 0 52 0 5.886872e-01 0 82 0 52 2 0 0 0 0 0 2 1 9.382227e-01 5 224 0 52 2 0 0 0 0 0 2 -3.095176 1 1 0 0 1 0 1 1 1.907445 0 0.530000 1.810000 0.474273 0.070000 2.000000e-02 0.160000 0.080000 0.087206 0.070000 0 4.000000e-02 0.120000 VDAC1 7416 broad.mit.edu 37 5 133316519 133316519 + Missense_Mutation SNP G G A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr5:133316519G>A ENST00000265333.3 - 6 696 c.452C>T c.(451-453)gCc>gTc p.A151V VDAC1_ENST00000395044.3_Missense_Mutation_p.A151V|VDAC1_ENST00000395047.2_Missense_Mutation_p.A151V NM_003374.2 NP_003365.1 P21796 VDAC1_HUMAN voltage-dependent anion channel 1 4 KIRC - Kidney renal clear cell carcinoma(527;0.00806)|Kidney(363;0.02) Dihydroxyaluminium(DB01375) CTGGTAGCCGGCCAGCCAGCC 0.527000 NSCLC(127;1776 1806 35523 41489 48154) 0 SO:0001583 missense ENST00000265333.3 0 1 hg19 CCDS4168.1 . . . . . . . . . . G 35 5.499741 0.96355 . . ENSG00000213585 ENST00000265333;ENST00000395044;ENST00000395047;ENST00000425992 T;T;T;T 0.39997 1.05;1.05;1.05;1.05 5.27 5.27 0.74061 . 0.000000 0.85682 D 0.000000 T 0.51770 0.1694 L 0.52573 1.65 0.80722 D 1 P 0.48089 0.905 P 0.51079 0.658 T 0.49476 -0.8936 10 0.48119 T 0.1 . 19.2582 0.93955 0.0:0.0:1.0:0.0 . 151 P21796 VDAC1_HUMAN V 151 ENSP00000265333:A151V;ENSP00000378484:A151V;ENSP00000378487:A151V;ENSP00000390129:A151V ENSP00000265333:A151V A - 2 0 VDAC1 133344418 1.000000 0.71417 0.978000 0.43139 0.973000 0.67179 7.885000 0.87282 2.622000 0.88805 0.655000 0.94253 GCC TCGA-2L-AAQE-01A-11D-A397-08 VDAC1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000259208.1 0 0 0 5 324 0 50 0 9.949625e-01 1 710 0 50 2 0 0 0 0 0 2 1 9.369998e-01 5 322 0 49 2 0 0 0 0 0 2 -3.132440 1 1 0 0 1 1 2 3 2.173791 0 0.530000 1.810000 0.537356 0.060000 1.000000e-02 1.000000 0.060000 0.113003 0.060000 0 3.000000e-02 0.100000 SPOCK1 6695 broad.mit.edu 37 5 136315143 136315143 + Missense_Mutation SNP C C T TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr5:136315143C>T ENST00000394945.1 - 10 1176 c.1007G>A c.(1006-1008)cGg>cAg p.R336Q SPOCK1_ENST00000509978.1_5'UTR|SPOCK1_ENST00000282223.7_Missense_Mutation_p.R336Q NM_004598.3 NP_004589.1 Q08629 TICN1_HUMAN sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1 18 KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233) CTCATTACACCGAGGTATGAA 0.542000 0 SO:0001583 missense ENST00000394945.1 1 1 hg19 CCDS4191.1 . . . . . . . . . . C 15.13 2.743313 0.49151 . . ENSG00000152377 ENST00000394945;ENST00000282223 T;T 0.61040 0.14;0.14 4.95 4.95 0.65309 Thyroglobulin type-1 (6); 0.000000 0.85682 D 0.000000 T 0.48642 0.1511 N 0.02334 -0.595 0.51767 D 0.999933 D 0.89917 1.0 D 0.85130 0.997 T 0.51639 -0.8680 10 0.16896 T 0.51 . 12.3181 0.54969 0.169:0.831:0.0:0.0 . 336 Q08629 TICN1_HUMAN Q 336 ENSP00000378401:R336Q;ENSP00000282223:R336Q ENSP00000282223:R336Q R - 2 0 SPOCK1 136343042 0.998000 0.40836 0.996000 0.52242 0.927000 0.56198 3.885000 0.56182 2.277000 0.76020 0.650000 0.86243 CGG TCGA-2L-AAQE-01A-11D-A397-08 SPOCK1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251222.1 1 0 1 64 194 0 51 0 5.526920e-01 0 7 0 51 2 0 0 0 0 0 2 1 1 63 191 0 50 2 0 0 0 0 0 2 -4.153474 1 1 121412 2 30 1 1 2 3 2.173791 0 0.530000 1.810000 0.537356 0.950000 7.500000e-01 1.000000 1.000000 0.935591 0.950000 1 8.500000e-01 1.000000 PCDHA7 56141 broad.mit.edu 37 5 140216036 140216036 + Missense_Mutation SNP G G A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr5:140216036G>A ENST00000525929.1 + 1 2068 c.2068G>A c.(2068-2070)Gag>Aag p.E690K PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA7_ENST00000378125.3_Missense_Mutation_p.E690K|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529619.1_Intron NM_018910.2 NP_061733.1 Q9UN72 PCDA7_HUMAN protocadherin alpha 7 63 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) TGCAGGCCCAGAGACCGAGCT 0.637000 NSCLC(160;258 2013 5070 22440 28951) 0 SO:0001583 missense ENST00000525929.1 1 1 hg19 CCDS54918.1 . . . . . . . . . . G 9.958 1.222045 0.22457 . . ENSG00000204963 ENST00000525929;ENST00000378125 T;T 0.52754 0.65;0.66 3.57 1.55 0.23275 . 3.216130 0.05786 U 0.609423 T 0.50188 0.1601 M 0.82132 2.575 0.09310 N 1 B;B 0.09022 0.002;0.001 B;B 0.15052 0.012;0.005 T 0.41822 -0.9487 10 0.33940 T 0.23 . 7.687 0.28546 0.0:0.2711:0.5139:0.215 . 690;690 Q9UN72-2;Q9UN72 .;PCDA7_HUMAN K 690 ENSP00000436426:E690K;ENSP00000367365:E690K ENSP00000367365:E690K E + 1 0 PCDHA7 140196220 0.000000 0.05858 0.002000 0.10522 0.003000 0.03518 0.072000 0.14617 0.812000 0.34326 -0.467000 0.05162 GAG TCGA-2L-AAQE-01A-11D-A397-08 PCDHA7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000372887.2 1 0 1 54 416 0 76 0 0 0 0 76 2 0 0 0 0 0 2 1 1 53 411 0 74 2 0 0 0 0 0 2 -19.689040 1 1 0 0 1 1 2 3 2.173791 0 0.530000 1.810000 0.537356 0.440000 3.300000e-01 1.000000 0.440000 0.471915 0.440000 0 3.800000e-01 0.510000 POU4F3 5459 broad.mit.edu 37 5 145719822 145719822 + Missense_Mutation SNP C C T TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr5:145719822C>T ENST00000230732.4 + 2 921 c.832C>T c.(832-834)Cgc>Tgc p.R278C CTC-359M8.1_ENST00000515598.1_RNA NM_002700.2 NP_002691.1 Q15319 PO4F3_HUMAN POU class 4 homeobox 3 17 KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) GAAGCGCAAACGCACGTCCAT 0.612000 0 SO:0001583 missense ENST00000230732.4 1 1 hg19 CCDS4281.1 . . . . . . . . . . C 20.5 4.004800 0.74932 . . ENSG00000091010 ENST00000230732 D 0.99186 -5.53 4.62 4.62 0.57501 Homeodomain-related (1);Homeobox (3);POU (1);Homeodomain-like (1); 0.000000 0.85682 D 0.000000 D 0.99638 0.9867 H 0.99130 4.44 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.97244 0.9893 10 0.87932 D 0 . 16.3979 0.83621 0.0:1.0:0.0:0.0 . 278 Q15319 PO4F3_HUMAN C 278 ENSP00000230732:R278C ENSP00000230732:R278C R + 1 0 POU4F3 145700015 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 7.629000 0.83207 2.372000 0.80975 0.462000 0.41574 CGC TCGA-2L-AAQE-01A-11D-A397-08 POU4F3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251887.2 1 0 1 56 218 1 55 0 0 0 1 55 2 0 0 0 0 0 2 1 9.999998e-01 55 218 1 55 17 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 2 3 2.173791 0 0.530000 1.810000 0.537356 0.780000 6.100000e-01 1.000000 0.780000 0.798587 0.780000 0 6.900000e-01 0.900000 UGT3A2 167127 broad.mit.edu 37 5 36049023 36049023 + Missense_Mutation SNP A A T TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr5:36049023A>T ENST00000282507.3 - 4 912 c.811T>A c.(811-813)Ttg>Atg p.L271M UGT3A2_ENST00000504954.1_Intron|UGT3A2_ENST00000513300.1_Missense_Mutation_p.L237M|UGT3A2_ENST00000545528.1_Intron NM_174914.3 NP_777574.2 Q3SY77 UD3A2_HUMAN UDP glycosyltransferase 3 family, polypeptide A2 43 all_lung(31;0.000179) Lung(74;0.111)|Epithelial(62;0.113)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202) TTTTCCATCAAGCCTCCAACA 0.453000 0 SO:0001583 missense ENST00000282507.3 1 1 hg19 CCDS3914.1 . . . . . . . . . . A 16.16 3.044979 0.55110 . . ENSG00000168671 ENST00000282507;ENST00000513300 T;T 0.63580 -0.05;-0.05 3.45 0.914 0.19360 . 0.107344 0.38492 N 0.001677 T 0.67050 0.2852 L 0.60067 1.865 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.80764 0.987;0.994 T 0.64398 -0.6417 10 0.72032 D 0.01 . 1.5646 0.02602 0.5509:0.1761:0.1021:0.171 . 237;271 E9PFK7;Q3SY77 .;UD3A2_HUMAN M 271;237 ENSP00000282507:L271M;ENSP00000427404:L237M ENSP00000282507:L271M L - 1 2 UGT3A2 36084780 0.139000 0.22563 0.911000 0.35937 0.961000 0.63080 0.431000 0.21444 0.186000 0.20125 0.533000 0.62120 TTG TCGA-2L-AAQE-01A-11D-A397-08 UGT3A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253771.2 1 0 1 40 274 0 70 0 0 0 0 70 2 0 0 0 0 0 2 1 1 40 270 0 70 2 0 0 0 0 0 2 -17.383150 1 1 0 0 1 1 2 3 2.173791 0 0.530000 1.810000 0.537356 0.490000 3.500000e-01 1.000000 0.490000 0.519704 0.490000 0 4.200000e-01 0.580000 BCLAF1 9774 broad.mit.edu 37 6 136599814 136599814 + Nonsense_Mutation SNP G G A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr6:136599814G>A ENST00000531224.1 - 4 457 c.205C>T c.(205-207)Cga>Tga p.R69* BCLAF1_ENST00000527536.1_Nonsense_Mutation_p.R69*|BCLAF1_ENST00000353331.4_Nonsense_Mutation_p.R67*|BCLAF1_ENST00000527759.1_Nonsense_Mutation_p.R67*|BCLAF1_ENST00000530767.1_Nonsense_Mutation_p.R69*|BCLAF1_ENST00000392348.2_Nonsense_Mutation_p.R67* NM_001077441.1|NM_014739.2 NP_001070909.1|NP_055554.1 Q9NYF8 BCLF1_HUMAN BCL2-associated transcription factor 1 9 Colorectal(23;0.24) CCATAAGGTCGTCTCATTCCT 0.433000 Colon(142;1534 1789 5427 7063 28491) 0 SO:0001587 stop_gained ENST00000531224.1 0 1 hg19 CCDS5177.1 . . . . . . . . . . G 21.8 4.201669 0.79015 . . ENSG00000029363 ENST00000531224;ENST00000353331;ENST00000527536;ENST00000530767;ENST00000527759;ENST00000392348;ENST00000529826 . . . 5.64 3.59 0.41128 . 0.000000 0.52532 D 0.000064 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 -4.5909 16.2474 0.82450 0.0:0.0:0.7701:0.2299 . . . . X 69;67;69;69;67;67;69 . ENSP00000229446:R67X R - 1 2 BCLAF1 136641507 1.000000 0.71417 1.000000 0.80357 0.991000 0.79684 4.151000 0.58105 1.318000 0.45170 0.557000 0.71058 CGA TCGA-2L-AAQE-01A-11D-A397-08 BCLAF1-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000042375.2 1 0 0 45 332 0 123 0 8.155079e-01 0 25 0 123 2 0 0 0 0 0 2 1 1 39 329 0 120 2 0 0 0 0 0 2 -17.769040 1 1 121406 18 38 1 0 1 1 1.603364 1 0.530000 1.810000 0.360544 0.320000 2.400000e-01 0.420000 0.330000 0.335053 0.320000 0 2.800000e-01 0.380000 ABRA 137735 broad.mit.edu 37 8 107782214 107782214 + Missense_Mutation SNP G G A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr8:107782214G>A ENST00000311955.3 - 1 259 c.205C>T c.(205-207)Cct>Tct p.P69S NM_139166.4 NP_631905.1 actin-binding Rho activating protein 27 OV - Ovarian serous cystadenocarcinoma(57;3.83e-09) TGTGAAGTAGGGGGTGTGATT 0.592000 0 SO:0001583 missense ENST00000311955.3 1 1 hg19 CCDS6305.1 . . . . . . . . . . G 3.421 -0.118071 0.06838 . . ENSG00000174429 ENST00000311955 D 0.92446 -3.04 5.07 0.834 0.18880 . 0.373311 0.30020 N 0.010608 D 0.82926 0.5143 N 0.25647 0.755 0.09310 N 1 B 0.26809 0.16 B 0.24701 0.055 T 0.66452 -0.5920 10 0.10902 T 0.67 . 10.6755 0.45783 0.0:0.3894:0.4775:0.1331 . 69 Q8N0Z2 ABRA_HUMAN S 69 ENSP00000311436:P69S ENSP00000311436:P69S P - 1 0 ABRA 107851390 0.103000 0.21917 0.000000 0.03702 0.001000 0.01503 0.268000 0.18571 0.341000 0.23771 0.655000 0.94253 CCT TCGA-2L-AAQE-01A-11D-A397-08 ABRA-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000380416.1 1 0 1 61 501 0 95 0 0 0 0 95 2 0 0 0 0 0 2 1 1 58 500 0 94 2 0 0 0 0 0 2 -2.879461 1 1 0 0 1 1 2 3 2.648027 1 0.530000 1.810000 0.626895 0.510000 3.900000e-01 0.670000 0.510000 0.526688 0.510000 0 4.500000e-01 0.590000 COL22A1 169044 broad.mit.edu 37 8 139820045 139820045 + Missense_Mutation SNP C C T TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr8:139820045C>T ENST00000303045.6 - 10 1906 c.1460G>A c.(1459-1461)gGa>gAa p.G487E COL22A1_ENST00000435777.1_Missense_Mutation_p.G487E NM_152888.1 NP_690848.1 Q8NFW1 COMA1_HUMAN collagen, type XXII, alpha 1 211 all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155) BRCA - Breast invasive adenocarcinoma(115;0.0517) GCCAGCAACTCCCATTTCACC 0.443000 HNSCC(7;0.00092) 0 SO:0001583 missense ENST00000303045.6 1 1 hg19 CCDS6376.1 . . . . . . . . . . C 14.78 2.636991 0.47049 . . ENSG00000169436 ENST00000303045;ENST00000435777 D;D 0.94184 -3.37;-3.37 4.61 4.61 0.57282 . 0.000000 0.46758 U 0.000262 D 0.96537 0.8870 H 0.96833 3.89 0.38814 D 0.955498 D 0.60160 0.987 P 0.50352 0.638 D 0.98256 1.0496 9 . . . . 13.7328 0.62799 0.0:1.0:0.0:0.0 . 487 Q8NFW1 COMA1_HUMAN E 487 ENSP00000303153:G487E;ENSP00000387655:G487E . G - 2 0 COL22A1 139889227 0.715000 0.27946 0.317000 0.25265 0.125000 0.20455 3.700000 0.54786 2.520000 0.84964 0.644000 0.83932 GGA TCGA-2L-AAQE-01A-11D-A397-08 COL22A1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000315905.2 1 0 0 50 673 0 115 0 3.890634e-01 1 18 0 115 2 0 0 0 0 0 2 1 1 50 667 0 115 2 0 0 0 0 0 2 -9.797079 1 1 0 0 1 1 3 4 2.724615 1 0.530000 1.810000 0.634582 0.350000 2.500000e-01 1.000000 0.340000 0.499856 0.350000 0 2.900000e-01 1.000000 ANK1 286 broad.mit.edu 37 8 41572577 41572577 + Silent SNP G G A TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr8:41572577G>A ENST00000347528.4 - 15 1701 c.1618C>T c.(1618-1620)Ctg>Ttg p.L540L ANK1_ENST00000396945.1_Silent_p.L540L|ANK1_ENST00000289734.7_Silent_p.L540L|ANK1_ENST00000396942.1_Silent_p.L540L|ANK1_ENST00000379758.2_Silent_p.L540L|ANK1_ENST00000352337.4_Silent_p.L540L|ANK1_ENST00000265709.8_Silent_p.L573L NM_020475.2|NM_020476.2|NM_020477.2 NP_065208.2|NP_065209.2|NP_065210.2 P16157 ANK1_HUMAN ankyrin 1, erythrocytic 122 Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211) all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188) OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264) GCCACGTGCAGAGGGGTAAAT 0.622000 0 SO:0001819 synonymous_variant ENST00000347528.4 1 1 hg19 CCDS6119.1 TCGA-2L-AAQE-01A-11D-A397-08 ANK1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000317297.1 1 0 1 191 180 0 54 0 0 0 0 54 2 0 0 0 0 0 2 1 1 189 178 0 53 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 1 4 5 3.201363 1 0.530000 1.810000 0.705560 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1.000000 ZNF189 7743 broad.mit.edu 37 9 104170526 104170526 + Missense_Mutation SNP G G A rs146668775 TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr9:104170526G>A ENST00000339664.2 + 3 605 c.476G>A c.(475-477)cGc>cAc p.R159H ZNF189_ENST00000374861.3_Missense_Mutation_p.R145H|ZNF189_ENST00000259395.4_Missense_Mutation_p.R117H NM_001278240.1 NP_001265169.1 O75820 ZN189_HUMAN zinc finger protein 189 26 Acute lymphoblastic leukemia(62;0.0559) GGTTTTGTCCGCAAGGCCCAT 0.383000 0 SO:0001583 missense ENST00000339664.2 0 1 hg19 CCDS6754.1 1 4.578754578754579E-4 0 0.0 0 0.0 1 0.0017482517482517483 0 0.0 G 3.003 -0.205670 0.06180 0.0 2.33E-4 ENSG00000136870 ENST00000374861;ENST00000339664;ENST00000259395 T;T;T 0.15718 2.4;2.4;2.4 4.66 4.66 0.58398 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.000000 0.49916 D 0.000138 T 0.10809 0.0264 L 0.28776 0.89 0.32692 N 0.513987 B;B;B 0.26902 0.033;0.163;0.163 B;B;B 0.15870 0.003;0.014;0.003 T 0.09250 -1.0683 10 0.16896 T 0.51 . 10.5539 0.45105 0.0:0.0:0.8078:0.1922 . 144;145;159 B7ZLK9;Q5T7D8;O75820 .;.;ZN189_HUMAN H 145;159;117 ENSP00000363995:R145H;ENSP00000342019:R159H;ENSP00000259395:R117H ENSP00000259395:R117H R + 2 0 ZNF189 103210347 0.000000 0.05858 1.000000 0.80357 0.998000 0.95712 0.052000 0.14163 2.873000 0.98535 0.563000 0.77884 CGC TCGA-2L-AAQE-01A-11D-A397-08 ZNF189-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053447.1 0 0 0 5 277 0 77 0 2.013852e-02 0 10 0 77 2 0 0 0 0 0 2 1 9.380859e-01 5 277 0 76 2 0 0 0 0 0 2 -2.314507 0 1 121410 6 41 1 0 1 1 1.895776 1 0.530000 1.810000 0.469556 0.060000 1.000000e-02 0.130000 0.060000 0.070354 0.060000 0 3.000000e-02 0.100000 SMC2 10592 broad.mit.edu 37 9 106864325 106864325 + Silent SNP C C T TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr9:106864325C>T ENST00000286398.7 + 8 1009 c.721C>T c.(721-723)Ctg>Ttg p.L241L SMC2_ENST00000303219.8_Silent_p.L241L|SMC2_ENST00000374793.3_Silent_p.L241L|SMC2_ENST00000374787.3_Silent_p.L241L NM_001042551.1|NM_001265602.1|NM_006444.2 NP_001036016.1|NP_001252531.1|NP_006435.2 O95347 SMC2_HUMAN structural maintenance of chromosomes 2 48 TCAGTTTTTGCTGGCTGAAGA 0.333000 0 SO:0001819 synonymous_variant ENST00000286398.7 0 1 hg19 CCDS35086.1 TCGA-2L-AAQE-01A-11D-A397-08 SMC2-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053470.1 0 0 0 6 427 1 115 0 5.789190e-03 0 7 1 115 2 0 0 0 0 0 2 0 5.381804e-02 6 425 1 115 14 0 0 0 0 0 2 -2.129470 0 1 0 0 1 0 1 1 1.895776 1 0.530000 1.810000 0.469556 0.040000 1.000000e-02 0.100000 0.050000 0.053677 0.040000 0 2.000000e-02 0.070000 GTF3C5 9328 broad.mit.edu 37 9 135917536 135917536 + Silent SNP C C T TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr9:135917536C>T ENST00000372097.5 + 2 539 c.216C>T c.(214-216)caC>caT p.H72H GTF3C5_ENST00000372108.5_Silent_p.H72H|GTF3C5_ENST00000372099.6_Silent_p.H63H|GTF3C5_ENST00000372095.5_Intron|GTF3C5_ENST00000485692.1_Intron|GTF3C5_ENST00000342018.8_Silent_p.H72H NM_012087.3 NP_036219.2 Q9Y5Q8 TF3C5_HUMAN general transcription factor IIIC, polypeptide 5, 63kDa 21 CATACTGCCACCCAGTGTGCG 0.612000 0 SO:0001819 synonymous_variant ENST00000372097.5 1 1 hg19 CCDS6958.1 TCGA-2L-AAQE-01A-11D-A397-08 GTF3C5-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054826.1 1 0 0 51 287 0 90 1 9.997530e-01 25 47 0 90 2 0 0 0 0 0 2 1 1 50 286 0 88 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 1.908518 0 0.530000 1.810000 0.472710 0.500000 3.800000e-01 0.640000 0.510000 0.512738 0.500000 0 4.400000e-01 0.580000 CDKN2A 1029 broad.mit.edu 37 9 21971111 21971111 + Missense_Mutation SNP G G A rs121913385 TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chr9:21971111G>A ENST00000304494.5 - 2 517 c.247C>T c.(247-249)Cac>Tac p.H83Y CDKN2A_ENST00000530628.2_Missense_Mutation_p.A97V|CDKN2A_ENST00000498124.1_Missense_Mutation_p.H83Y|CDKN2A_ENST00000579755.1_Missense_Mutation_p.A97V|CDKN2A_ENST00000494262.1_Missense_Mutation_p.H32Y|CDKN2A_ENST00000497750.1_Missense_Mutation_p.H32Y|CDKN2A_ENST00000578845.2_Missense_Mutation_p.H32Y|CDKN2A_ENST00000446177.1_Missense_Mutation_p.H83Y|CDKN2A_ENST00000361570.3_Missense_Mutation_p.A138V|CDKN2A_ENST00000498628.2_Missense_Mutation_p.H32Y|CDKN2A_ENST00000579122.1_Missense_Mutation_p.H83Y|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000479692.2_Missense_Mutation_p.H32Y NM_000077.4 NP_000068.1 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A p.0?(1315)|p.?(44)|p.H83Y(30)|p.A138V(2)|p.H83fs*2(2)|p.H83N(1)|p.V82fs*62(1)|p.0(1)|p.V82_G89>G(1)|p.E61_L94del(1)|p.R137fs*48(1)|p.A68fs*3(1)|p.P81_A85del(1)|p.R80fs*34(1)|p.V82_E88del(1) 4199 all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172) GCAGCGTCGTGCACGGGTCGG 0.741000 H83Y(CALU3_LUNG)|H83Y(HS944T_SKIN)|H83Y(JHH2_LIVER)|H83Y(OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|H83Y(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE) 17 HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07) 1403 Whole gene deletion(1316)|Unknown(44)|Substitution - Missense(33)|Deletion - Frameshift(6)|Deletion - In frame(3)|Complex - deletion inframe(1) GRCh37 CM053801|CM056557 CDKN2A M rs121913385 SO:0001583 missense ENST00000304494.5 1 1 hg19 CCDS6510.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 26.7|26.7 4.762523|4.762523 0.89932|0.89932 .|. .|. ENSG00000147889|ENSG00000147889 ENST00000361570;ENST00000530628|ENST00000304494;ENST00000446177 T;T|T;T 0.80393|0.71222 -1.37;-1.31|-0.55;-0.55 5.93|5.93 5.93|5.93 0.95920|0.95920 .|Ankyrin repeat-containing domain (4); 0.000000|. 0.37261|. N|. 0.002164|. T|T 0.77579|0.77579 0.4151|0.4151 L|L 0.27053|0.27053 0.805|0.805 0.46521|0.46521 D|D 0.999085|0.999085 P|D 0.47191|0.76494 0.891|0.999 B|D 0.44044|0.75484 0.439|0.986 T|T 0.79024|0.79024 -0.1972|-0.1972 10|9 0.62326|0.66056 D|D 0.03|0.02 -15.192|-15.192 19.1026|19.1026 0.93279|0.93279 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. 138|83 Q8N726|P42771 CD2A2_HUMAN|CD2A1_HUMAN V|Y 138;97|83 ENSP00000355153:A138V;ENSP00000432664:A97V|ENSP00000307101:H83Y;ENSP00000394932:H83Y ENSP00000355153:A138V|ENSP00000307101:H83Y A|H -|- 2|1 0|0 CDKN2A|CDKN2A 21961111|21961111 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.915000|0.915000 0.54546|0.54546 8.665000|8.665000 0.91144|0.91144 2.803000|2.803000 0.96430|0.96430 0.650000|0.650000 0.86243|0.86243 GCA|CAC TCGA-2L-AAQE-01A-11D-A397-08 CDKN2A-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000051915.1 1 0 0 16 51 0 23 1 1 351 2 0 23 2 1 9.999996e-01 28 76 0 111 2 1 9.998878e-01 14 43 0 18 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 0 0 1.326982 1 0.530000 1.810000 0.252782 0.490000 3.200000e-01 0.600000 0.550000 0.495243 0.490000 0 4.100000e-01 0.570000 MAGEB2 4113 broad.mit.edu 37 X 30237553 30237553 + Missense_Mutation SNP A A T TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chrX:30237553A>T ENST00000378988.4 + 2 957 c.856A>T c.(856-858)Atg>Ttg p.M286L NM_002364.4 NP_002355.2 O15479 MAGB2_HUMAN melanoma antigen family B, 2 23 AACCAGCAAGATGAAAGTCCT 0.507000 0 SO:0001583 missense ENST00000378988.4 1 1 hg19 CCDS14219.1 . . . . . . . . . . A 19.14 3.768852 0.69878 . . ENSG00000099399 ENST00000378988 T 0.05025 3.51 3.27 -0.453 0.12201 . 0.242459 0.43579 D 0.000556 T 0.11922 0.0290 M 0.80183 2.485 0.09310 N 1 P 0.35982 0.531 P 0.44422 0.449 T 0.09796 -1.0658 10 0.66056 D 0.02 . 5.7074 0.17915 0.5317:0.0:0.4683:0.0 . 286 O15479 MAGB2_HUMAN L 286 ENSP00000368273:M286L ENSP00000368273:M286L M + 1 0 MAGEB2 30147474 0.001000 0.12720 0.000000 0.03702 0.922000 0.55478 0.354000 0.20146 -0.185000 0.10550 0.356000 0.21956 ATG TCGA-2L-AAQE-01A-11D-A397-08 MAGEB2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056157.1 1 0 1 20 71 0 19 0 0 0 0 19 2 0 0 0 0 0 2 1 9.999981e-01 20 71 0 19 2 0 0 0 0 0 2 -15.736300 1 1 121402 2 31 1 0 1 1 0.530000 1.810000 0.530000 0.410000 2.600000e-01 0.580000 0.410000 0.421942 0.410000 0 3.300000e-01 0.500000 MAGEE2 139599 broad.mit.edu 37 X 75004114 75004114 + Missense_Mutation SNP T T C TCGA-2L-AAQE-01A-11D-A397-08 TCGA-2L-AAQE-11A-11D-A39A-08 Untested Somatic Phase_I WXS none Illumina GAIIx d57069ad-4f07-4f3d-93a2-16b0c4a51325 43d83c90-8211-4c2a-92c4-eee9c092680e g.chrX:75004114T>C ENST00000373359.2 - 1 965 c.773A>G c.(772-774)cAc>cGc p.H258R NM_138703.4 NP_619648.1 Q8TD90 MAGE2_HUMAN melanoma antigen family E, 2 34 GATTTCCCTGTGGGCTCTAGA 0.498000 0 SO:0001583 missense ENST00000373359.2 1 1 hg19 CCDS14431.1 . . . . . . . . . . T 8.525 0.869554 0.17322 . . ENSG00000186675 ENST00000373359 T 0.04654 3.58 3.1 0.589 0.17452 . . . . . T 0.05227 0.0139 L 0.60455 1.87 0.09310 N 1 B 0.25850 0.136 B 0.27262 0.078 T 0.41716 -0.9493 9 0.33940 T 0.23 . 2.0976 0.03672 0.2592:0.1513:0.0:0.5895 . 258 Q8TD90 MAGE2_HUMAN R 258 ENSP00000362457:H258R ENSP00000362457:H258R H - 2 0 MAGEE2 74920839 0.685000 0.27652 0.009000 0.14445 0.688000 0.40055 0.561000 0.23515 0.015000 0.14971 0.345000 0.21793 CAC TCGA-2L-AAQE-01A-11D-A397-08 MAGEE2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057288.1 1 0 1 49 173 0 53 0 0 0 0 53 2 0 0 0 0 0 2 1 1 49 172 0 53 2 0 0 0 0 0 2 -20.000000 1 1 0 0 1 0 1 1 0.530000 1.810000 0.530000 0.410000 3.100000e-01 0.520000 0.410000 0.419483 0.410000 0 3.600000e-01 0.470000