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 MLXIP 22877 broad.mit.edu 37 12 122623075 122623075 + Frame_Shift_Del DEL C C - TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr12:122623075delC ENST00000319080.7 + 14 2493 c.2361delC c.(2359-2361)atcfs p.I787fs MLXIP_ENST00000538698.1_Frame_Shift_Del_p.I394fs MLX interacting protein 20 all_neural(191;0.0837)|Medulloblastoma(191;0.163) Lung NSC(355;0.0659) GGGAGGAGATCGAGGAGCTCA 0.632000 Esophageal Squamous(105;787 1493 16200 18566 52466) 0 SO:0001589 frameshift_variant ENST00000319080.7 0 1 hg19 TCGA-XD-AAUI-01A-42D-A40W-08 MLXIP-001 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000401718.2 1 0 0 14 117 0 24 0 7.643365e-01 0 25 0 24 2 0 0 0 0 0 0 1 0.999811 16 115 0 23 2 -19.970870 1 1 0 0 1 0 0 0 1.988815 0 0.210000 1.910000 0.194781 0.990000 0.580000 1.000000 1.000000 0.912718 0.990000 1 7.700000e-01 1 FRMD4A 55691 broad.mit.edu 37 10 13736001 13736001 + Silent SNP G G A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr10:13736001G>A ENST00000357447.2 - 15 1382 c.1014C>T c.(1012-1014)gcC>gcT p.A338A FRMD4A_ENST00000378503.1_Silent_p.A338A|FRMD4A_ENST00000358621.4_Silent_p.A323A|FRMD4A_ENST00000492155.1_5'UTR|FRMD4A_ENST00000342409.2_Silent_p.A354A NM_018027.3 NP_060497.3 Q9P2Q2 FRM4A_HUMAN FERM domain containing 4A 41 TCAGGTCGATGGCGATCTCAC 0.572000 0 SO:0001819 synonymous_variant ENST00000357447.2 1 1 hg19 CCDS7101.1 TCGA-XD-AAUI-01A-42D-A40W-08 FRMD4A-003 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000046889.1 1 0 1 39 220 0 55 0 6.466338e-01 0 14 0 55 2 0 0 0 0 0 2 1 1.000000 38 217 0 54 2 -20.000000 1 1 0 0 1 0 1 1 1.942227 0 0.210000 1.910000 0.157827 0.990000 0.950000 1.000000 1.000000 0.997077 0.990000 1 9.900000e-01 1 PARD3 56288 broad.mit.edu 37 10 34663857 34663857 + Missense_Mutation SNP C C T TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr10:34663857C>T ENST00000374789.3 - 11 1938 c.1613G>A c.(1612-1614)gGa>gAa p.G538E PARD3_ENST00000374773.1_Missense_Mutation_p.G538E|PARD3_ENST00000545693.1_Missense_Mutation_p.G538E|PARD3_ENST00000545260.1_Missense_Mutation_p.G494E|PARD3_ENST00000374794.3_Missense_Mutation_p.G494E|PARD3_ENST00000374788.3_Missense_Mutation_p.G538E|PARD3_ENST00000544292.1_Missense_Mutation_p.G268E|PARD3_ENST00000374768.1_5'Flank|PARD3_ENST00000374776.1_Missense_Mutation_p.G538E|PARD3_ENST00000346874.4_Missense_Mutation_p.G538E|PARD3_ENST00000374790.3_Missense_Mutation_p.G494E|PARD3_ENST00000350537.4_Missense_Mutation_p.G538E|PARD3_ENST00000340077.5_Missense_Mutation_p.G538E NM_019619.3 NP_062565.2 Q8TEW0 PARD3_HUMAN par-3 family cell polarity regulator 63 Breast(68;0.0707) GCTCACAGTTCCTTCCATCTT 0.438000 0 SO:0001583 missense ENST00000374789.3 0 1 hg19 CCDS7178.1 . . . . . . . . . . c 13.72 2.321178 0.41096 . . ENSG00000148498 ENST00000545693;ENST00000545260;ENST00000374789;ENST00000374788;ENST00000346874;ENST00000374794;ENST00000350537;ENST00000374790;ENST00000374776;ENST00000340077;ENST00000374773;ENST00000544292 T;T;T;T;T;T;T;T;T;T;T;T 0.18338 2.22;2.22;2.22;2.22;2.22;2.22;2.22;2.22;2.22;2.22;2.22;2.22 5.82 5.82 0.92795 PDZ/DHR/GLGF (4); 0.000000 0.85682 D 0.000000 T 0.28200 0.0696 L 0.31157 0.91 0.80722 D 1 D;D;D;D;D;D;D;B;B;D;D;B;B;B;B 0.89917 1.0;0.993;0.998;0.997;0.994;0.998;0.997;0.195;0.324;0.997;0.994;0.217;0.008;0.026;0.001 D;P;D;P;D;D;P;B;B;D;D;B;B;B;B 0.80764 0.994;0.709;0.969;0.903;0.934;0.923;0.903;0.096;0.119;0.942;0.963;0.082;0.024;0.018;0.001 T 0.01276 -1.1398 10 0.05351 T 0.99 . 20.088 0.97803 0.0:1.0:0.0:0.0 . 494;494;538;538;538;538;538;538;494;538;538;538;538;538;268 Q8TEW0-5;Q8TEW0-3;Q8TEW0-7;Q8TEW0-6;F5H5T0;Q8TEW0-4;Q8TEW0-2;Q8TEW0;Q5VWV2;Q6IQ47;Q5VWU8;Q8TEW0-8;Q8TEW0-9;Q8TEW0-10;F5GZI3 .;.;.;.;.;.;.;PARD3_HUMAN;.;.;.;.;.;.;. E 538;494;538;538;538;494;538;494;538;538;538;268 ENSP00000443147:G538E;ENSP00000440857:G494E;ENSP00000363921:G538E;ENSP00000363920:G538E;ENSP00000340591:G538E;ENSP00000363926:G494E;ENSP00000311986:G538E;ENSP00000363922:G494E;ENSP00000363908:G538E;ENSP00000341844:G538E;ENSP00000363905:G538E;ENSP00000444429:G268E ENSP00000341844:G538E G - 2 0 PARD3 34703863 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 7.451000 0.80668 2.739000 0.93911 0.655000 0.94253 GGA TCGA-XD-AAUI-01A-42D-A40W-08 PARD3-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000047527.1 0 0 0 7 531 0 118 0 1.083584e-01 0 37 0 118 2 0 0 0 0 0 2 1 0.979938 7 525 0 118 2 -2.718959 1 1 0 0 1 0 1 1 1.942227 0 0.210000 1.910000 0.157827 0.120000 0.050000 0.230000 0.110000 0.131042 0.120000 0 8.000000e-02 1.700000e-01 CHAT 1103 broad.mit.edu 37 10 50857681 50857681 + Splice_Site SNP C C T TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr10:50857681C>T ENST00000337653.2 + 10 1663 c.1510C>T c.(1510-1512)Cga>Tga p.R504* CHAT_ENST00000455728.2_Splice_Site_p.R386*|CHAT_ENST00000395559.2_Splice_Site_p.R386*|CHAT_ENST00000395562.2_Splice_Site_p.R422*|CHAT_ENST00000339797.1_Splice_Site_p.R386*|CHAT_ENST00000351556.3_Splice_Site_p.R386* NM_001142929.1|NM_020549.4 NP_001136401.1|NP_065574 P28329 CLAT_HUMAN choline O-acetyltransferase 56 all_neural(218;0.107) Choline(DB00122)|Nicotine(DB00184) AAAACTTCAACGGTAAGGATA 0.602000 0 SO:0001630 splice_region_variant ENST00000337653.2 0 0 hg19 CCDS7232.1 . . . . . . . . . . C 36 5.855479 0.97030 0.0 1.16E-4 ENSG00000070748 ENST00000339797;ENST00000351556;ENST00000395559;ENST00000337653;ENST00000395562;ENST00000455728 . . . 4.77 0.0456 0.14231 . 0.156020 0.56097 D 0.000032 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.13470 T 0.59 -5.4337 7.7047 0.28642 0.5652:0.3444:0.0:0.0904 . . . . X 386;386;386;504;422;386 . ENSP00000337103:R504X R + 1 2 CHAT 50527687 0.999000 0.42202 0.959000 0.39883 0.135000 0.20990 2.130000 0.42064 0.376000 0.24707 0.462000 0.41574 CGA TCGA-XD-AAUI-01A-42D-A40W-08 CHAT-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000047997.1 1 0 1 37 264 0 92 0 0 0 0 92 2 0 0 0 0 0 2 1 1.000000 37 261 0 89 2 -20.000000 1 1 121392 2 33 1 0 1 1 1.942227 0 0.210000 1.910000 0.157827 0.990000 0.780000 1.000000 1.000000 0.972845 0.990000 1 9.200000e-01 1 C2CD2L 9854 broad.mit.edu 37 11 118982297 118982297 + Missense_Mutation SNP C C A rs140133210 TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr11:118982297C>A ENST00000528586.1 + 3 291 c.221C>A c.(220-222)gCg>gAg p.A74E C2CD2L_ENST00000336702.3_Missense_Mutation_p.A326E O14523 C2C2L_HUMAN C2CD2-like 13 ACCAAGCCCGCGAGGGCTGGA 0.562000 0 SO:0001583 missense ENST00000528586.1 0 1 hg19 . . . . . . . . . . C 7.519 0.656367 0.14580 . . ENSG00000172375 ENST00000336702;ENST00000528586 T;T 0.40225 1.04;1.04 5.54 -11.1 0.00147 C2 calcium/lipid-binding domain, CaLB (1); 1.839290 0.02350 N 0.075789 T 0.24547 0.0595 N 0.14661 0.345 0.09310 N 1 B;B 0.24618 0.107;0.107 B;B 0.27715 0.082;0.082 T 0.48328 -0.9045 10 0.05525 T 0.97 -3.7304 19.4928 0.95059 0.0:0.217:0.0:0.783 . 326;326 O14523;O14523-2 C2C2L_HUMAN;. E 326;74 ENSP00000338885:A326E;ENSP00000433600:A74E ENSP00000338885:A326E A + 2 0 C2CD2L 118487507 0.000000 0.05858 0.000000 0.03702 0.030000 0.12068 -1.299000 0.02754 -2.688000 0.00405 -0.140000 0.14226 GCG TCGA-XD-AAUI-01A-42D-A40W-08 C2CD2L-003 PUTATIVE basic|exp_conf protein_coding protein_coding OTTHUMT00000388199.2 0 0 0 4 155 0 36 0 2.301066e-01 0 29 0 36 2 0 0 0 0 0 2 1 0.880480 3 149 0 35 2 -6.208200 1 0 0 0 1 0 1 1 1.839385 1 0.210000 1.910000 0.117318 0.230000 0.070000 0.480000 0.210000 0.252258 0.230000 0 1.400000e-01 3.500000e-01 NUP98 4928 broad.mit.edu 37 11 3704600 3704600 + Missense_Mutation SNP G G A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr11:3704600G>A ENST00000324932.7 - 30 5168 c.4748C>T c.(4747-4749)gCt>gTt p.A1583V NUP98_ENST00000355260.3_Missense_Mutation_p.A1509V|NUP98_ENST00000359171.4_Missense_Mutation_p.A1509V NM_016320.4|NM_139132.3 NP_057404.2|NP_624358.2 P52948 NUP98_HUMAN nucleoporin 98kDa 66 Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227) AGTCTCTTTAGCCCAAGATTC 0.512000 T HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11 AML Dom yes 11 11p15 4928 nucleoporin 98kDa L 0 SO:0001583 missense ENST00000324932.7 1 1 hg19 CCDS7746.1 . . . . . . . . . . G 20.8 4.052507 0.75960 . . ENSG00000110713 ENST00000324932;ENST00000359171;ENST00000355260 . . . 6.02 5.1 0.69264 . 0.131086 0.53938 D 0.000044 T 0.59404 0.2191 M 0.74647 2.275 0.23563 N 0.997403 D;D;P 0.53462 0.96;0.96;0.933 P;P;P 0.51615 0.675;0.6;0.461 T 0.56774 -0.7923 9 0.31617 T 0.26 -18.3788 15.8043 0.78481 0.0:0.0:0.8629:0.1371 . 1509;1583;1497 P52948-2;P52948-5;P52948-6 .;.;. V 1583;1509;1509 . ENSP00000316032:A1583V A - 2 0 NUP98 3661176 1.000000 0.71417 1.000000 0.80357 0.978000 0.69477 3.236000 0.51336 1.552000 0.49463 -0.187000 0.12897 GCT TCGA-XD-AAUI-01A-42D-A40W-08 NUP98-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000032766.3 1 0 1 22 349 0 80 1 9.610911e-01 11 76 0 80 2 0 0 0 0 0 2 1 0.999999 22 345 0 80 2 -6.003247 1 1 0 0 1 1 2 3 2.045850 0 0.210000 1.910000 0.217396 0.580000 0.370000 1.000000 0.560000 0.617040 0.580000 0 4.600000e-01 7.500000e-01 FZD10 11211 broad.mit.edu 37 12 130649223 130649223 + Missense_Mutation SNP C C A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr12:130649223C>A ENST00000229030.4 + 1 2220 c.1736C>A c.(1735-1737)aCc>aAc p.T579N FZD10_ENST00000539839.1_3'UTR|FZD10-AS1_ENST00000505807.2_RNA Q9ULW2 FZD10_HUMAN frizzled class receptor 10 35 all_neural(191;0.101)|Medulloblastoma(191;0.163) CAGTCGCCCACCTGCGTGTGA 0.527000 0 SO:0001583 missense ENST00000229030.4 0 1 hg19 CCDS9267.1 . . . . . . . . . . C 12.03 1.817078 0.32145 . . ENSG00000111432 ENST00000229030 T 0.77098 -1.07 4.69 4.69 0.59074 . 0.000000 0.64402 U 0.000001 T 0.70684 0.3252 L 0.27053 0.805 0.53005 D 0.999969 B 0.32968 0.392 B 0.35813 0.211 T 0.74578 -0.3619 10 0.87932 D 0 . 17.6375 0.88127 0.0:1.0:0.0:0.0 . 579 Q9ULW2 FZD10_HUMAN N 579 ENSP00000229030:T579N ENSP00000229030:T579N T + 2 0 FZD10 129215176 1.000000 0.71417 0.989000 0.46669 0.397000 0.30659 3.619000 0.54196 2.127000 0.65507 0.561000 0.74099 ACC TCGA-XD-AAUI-01A-42D-A40W-08 FZD10-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding 0 0 0 4 97 0 30 0 3.514690e-02 0 6 0 30 2 0 0 0 0 0 2 1 0.889477 4 96 0 30 2 -7.556106 1 1 0 0 1 0 0 0 1.988815 0 0.210000 1.910000 0.194781 0.400000 0.130000 0.830000 0.360000 0.434336 0.400000 0 2.400000e-01 6.100000e-01 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C A rs121913529 TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 C A C C Valid Somatic Phase_I WXS targeted Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr12:25398284C>A ENST00000256078.4 - 2 98 c.35G>T c.(34-36)gGt>gTt p.G12V KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 27.2 4.808637 0.90707 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78707 -1.2;-1.2;-1.2;-1.2 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.90373 0.6987 M 0.90650 3.135 0.80722 D 1 D;D 0.76494 0.997;0.999 D;D 0.72625 0.969;0.978 D 0.91773 0.5429 10 0.72032 D 0.01 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN V 12 ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V ENSP00000256078:G12V G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-XD-AAUI-01A-42D-A40W-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 22 155 0 56 0 5.055540e-01 1 5 0 56 2 1 1 41 401 0 361 2 1 0.999999 22 154 0 52 2 -11.597720 1 1 0 0 1 1 2 3 2.030377 0 0.210000 1.910000 0.217396 0.990000 0.790000 1.000000 1.000000 0.981165 0.990000 1 9.800000e-01 1 ITFG2 55846 broad.mit.edu 37 12 2929953 2929953 + Missense_Mutation SNP G G T TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr12:2929953G>T ENST00000228799.2 + 6 749 c.610G>T c.(610-612)Ggt>Tgt p.G204C ITFG2_ENST00000542548.1_Missense_Mutation_p.G92C|ITFG2_ENST00000419778.2_Missense_Mutation_p.G27C NM_018463.3 NP_060933.3 Q969R8 ITFG2_HUMAN integrin alpha FG-GAP repeat containing 2 19 OV - Ovarian serous cystadenocarcinoma(31;0.000818) GTCTCAGCCAGGTTGTGCGTA 0.562000 0 SO:0001583 missense ENST00000228799.2 1 1 hg19 CCDS8513.1 . . . . . . . . . . G 28.2 4.902630 0.92035 . . ENSG00000111203 ENST00000228799;ENST00000419778;ENST00000542548 T 0.72942 -0.7 5.08 5.08 0.68730 . 0.000000 0.85682 D 0.000000 D 0.85500 0.5711 M 0.82517 2.595 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.87516 0.2443 10 0.87932 D 0 -21.1172 17.6386 0.88129 0.0:0.0:1.0:0.0 . 204 Q969R8 ITFG2_HUMAN C 204;27;92 ENSP00000228799:G204C ENSP00000228799:G204C G + 1 0 ITFG2 2800214 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 9.350000 0.97070 2.632000 0.89209 0.655000 0.94253 GGT TCGA-XD-AAUI-01A-42D-A40W-08 ITFG2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253091.1 1 0 0 14 240 0 81 0 9.667885e-02 1 8 0 81 2 0 0 0 0 0 2 1 0.999752 14 236 0 81 2 -3.221883 1 1 0 0 1 1 2 3 2.021246 0 0.210000 1.910000 0.211656 0.530000 0.300000 0.890000 0.520000 0.555264 0.530000 0 4.100000e-01 6.900000e-01 PLXNC1 10154 broad.mit.edu 37 12 94641698 94641698 + Missense_Mutation SNP C C T TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr12:94641698C>T ENST00000258526.4 + 13 2657 c.2408C>T c.(2407-2409)gCg>gTg p.A803V NM_005761.2 NP_005752.1 O60486 PLXC1_HUMAN plexin C1 64 TATTGTGTGGCGACTTACTGC 0.428000 0 SO:0001583 missense ENST00000258526.4 1 1 hg19 CCDS9049.1 . . . . . . . . . . C 3.557 -0.090472 0.07053 . . ENSG00000136040 ENST00000258526 T 0.07114 3.22 6.16 1.83 0.25207 Cell surface receptor IPT/TIG (2); 0.869786 0.10286 N 0.692988 T 0.06096 0.0158 L 0.27053 0.805 0.09310 N 1 P 0.36944 0.574 B 0.31869 0.137 T 0.39461 -0.9613 10 0.27785 T 0.31 . 10.7249 0.46061 0.6283:0.2651:0.1066:0.0 . 803 O60486 PLXC1_HUMAN V 803 ENSP00000258526:A803V ENSP00000258526:A803V A + 2 0 PLXNC1 93165829 0.000000 0.05858 0.000000 0.03702 0.066000 0.16364 -0.066000 0.11598 0.440000 0.26502 -0.175000 0.13238 GCG TCGA-XD-AAUI-01A-42D-A40W-08 PLXNC1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000408126.2 1 0 0 26 587 0 149 0 1.123669e-02 0 4 0 149 2 0 0 0 0 0 2 1 1.000000 24 575 0 146 2 -3.903845 1 1 121412 1 31 1 0 0 0 1.988815 0 0.210000 1.910000 0.194781 0.390000 0.260000 0.560000 0.400000 0.407454 0.390000 0 3.200000e-01 4.800000e-01 GPC6 10082 broad.mit.edu 37 13 95034762 95034762 + Missense_Mutation SNP C C T TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr13:95034762C>T ENST00000377047.4 + 7 1862 c.1247C>T c.(1246-1248)aCg>aTg p.T416M NM_005708.3 NP_005699.1 Q9Y625 GPC6_HUMAN glypican 6 38 all_neural(89;0.0684)|Medulloblastoma(90;0.163) all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217) ACAGCGGGCACGTCCAACGAG 0.537000 0 SO:0001583 missense ENST00000377047.4 1 1 hg19 CCDS9469.1 . . . . . . . . . . C 15.78 2.935396 0.52866 . . ENSG00000183098 ENST00000377047 T 0.51071 0.72 5.74 5.74 0.90152 . 0.262572 0.38720 N 0.001587 T 0.36496 0.0969 L 0.34521 1.04 0.28457 N 0.916084 P 0.48350 0.909 B 0.39379 0.298 T 0.44682 -0.9312 10 0.54805 T 0.06 . 12.4114 0.55469 0.0:0.923:0.0:0.077 . 416 Q9Y625 GPC6_HUMAN M 416 ENSP00000366246:T416M ENSP00000366246:T416M T + 2 0 GPC6 93832763 0.856000 0.29760 0.999000 0.59377 0.660000 0.38997 2.153000 0.42282 2.708000 0.92522 0.650000 0.86243 ACG TCGA-XD-AAUI-01A-42D-A40W-08 GPC6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045460.4 1 0 0 34 314 0 85 0 1.510796e-01 0 7 0 85 2 0 0 0 1 0 0 2 1 1.000000 34 307 0 84 2 -12.176790 1 1 121412 42 48 1 1 2 3 2.024408 0 0.210000 1.910000 0.213304 0.930000 0.660000 1.000000 1.000000 0.910749 0.930000 1 7.900000e-01 1 PYGL 5836 broad.mit.edu 37 14 51387719 51387719 + Missense_Mutation SNP G G A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr14:51387719G>A ENST00000216392.7 - 6 1059 c.727C>T c.(727-729)Cgc>Tgc p.R243C PYGL_ENST00000532462.1_Missense_Mutation_p.R243C|PYGL_ENST00000544180.2_Missense_Mutation_p.R209C NM_002863.4 NP_002854.3 P06737 PYGL_HUMAN phosphorylase, glycogen, liver 25 all_epithelial(31;0.00825)|Breast(41;0.148) Adenosine monophosphate(DB00131) GACCAGAGGCGCATGGTGTTG 0.498000 0 SO:0001583 missense ENST00000216392.7 1 1 hg19 CCDS32080.1 . . . . . . . . . . G 24.6 4.547610 0.86022 . . ENSG00000100504 ENST00000532462;ENST00000544180;ENST00000216392 D;D;D 0.96232 -3.95;-3.95;-3.95 5.77 5.77 0.91146 . 0.000000 0.85682 D 0.000000 D 0.98704 0.9565 M 0.94101 3.495 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.97110 0.999;1.0;1.0 D 0.99267 1.0892 10 0.87932 D 0 -0.3184 19.3504 0.94381 0.0:0.0:1.0:0.0 . 209;243;243 F5H816;E9PK47;P06737 .;.;PYGL_HUMAN C 243;209;243 ENSP00000431657:R243C;ENSP00000443787:R209C;ENSP00000216392:R243C ENSP00000216392:R243C R - 1 0 PYGL 50457469 1.000000 0.71417 1.000000 0.80357 0.965000 0.64279 2.626000 0.46460 2.885000 0.99019 0.655000 0.94253 CGC TCGA-XD-AAUI-01A-42D-A40W-08 PYGL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000390654.3 1 0 0 15 237 0 60 1 7.880128e-01 4 44 0 60 2 0 0 0 0 0 2 1 0.561145 15 235 1 58 15 -2.965748 1 1 0 0 1 0 0 0 1.997598 0 0.210000 1.910000 0.199919 0.560000 0.330000 0.860000 0.550000 0.582669 0.560000 0 4.300000e-01 7.200000e-01 PLEKHG3 26030 broad.mit.edu 37 14 65210050 65210050 + Missense_Mutation SNP C C T TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr14:65210050C>T ENST00000394691.1 + 17 3436 c.3289C>T c.(3289-3291)Cgc>Tgc p.R1097C PLEKHG3_ENST00000492928.1_Intron|PLEKHG3_ENST00000484731.2_Missense_Mutation_p.R602C|PLEKHG3_ENST00000471182.2_Missense_Mutation_p.R630C|PLEKHG3_ENST00000247226.7_Missense_Mutation_p.R1041C A1L390 PKHG3_HUMAN pleckstrin homology domain containing, family G (with RhoGef domain) member 3 29 CAGGGTGGGCCGCTGCCGCAG 0.731000 0 SO:0001583 missense ENST00000394691.1 1 1 hg19 . . . . . . . . . . C 13.99 2.401959 0.42613 . . ENSG00000126822 ENST00000247226;ENST00000394691;ENST00000471182;ENST00000484731 T;T;T;T 0.62364 0.48;0.03;1.37;1.37 5.22 3.38 0.38709 . 0.348750 0.24999 N 0.033935 T 0.65821 0.2728 L 0.53249 1.67 0.19300 N 0.999974 D;D;D;D 0.76494 0.999;0.998;0.988;0.997 P;P;P;P 0.53861 0.736;0.736;0.533;0.724 T 0.59026 -0.7531 10 0.87932 D 0 . 9.9514 0.41640 0.0:0.8303:0.0:0.1697 . 630;602;1097;1041 A1L390-2;G3V311;A1L390;A1L390-3 .;.;PKHG3_HUMAN;. C 1041;1097;630;602 ENSP00000247226:R1041C;ENSP00000378183:R1097C;ENSP00000450945:R630C;ENSP00000450973:R602C ENSP00000247226:R1041C R + 1 0 PLEKHG3 64279803 0.003000 0.15002 0.987000 0.45799 0.357000 0.29423 0.011000 0.13264 0.563000 0.29222 0.563000 0.77884 CGC TCGA-XD-AAUI-01A-42D-A40W-08 PLEKHG3-010 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000412028.1 1 0 0 9 108 0 29 1 9.345033e-01 20 40 0 29 2 0 0 0 0 0 2 1 0.992214 9 98 0 27 2 -14.084520 1 1 120986 3 34 1 1 2 3 2.084678 1 0.210000 1.910000 0.250901 0.900000 0.410000 1.000000 1.000000 0.836278 0.900000 1 6.100000e-01 1 RYR3 6263 broad.mit.edu 37 15 33895400 33895400 + Missense_Mutation SNP G G A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr15:33895400G>A ENST00000389232.4 + 18 2069 c.1999G>A c.(1999-2001)Gac>Aac p.D667N RYR3_ENST00000415757.3_Missense_Mutation_p.D667N NM_001036.3 NP_001027.3 Q15413 RYR3_HUMAN ryanodine receptor 3 311 all_lung(180;7.18e-09) GCTGATTATCGACCAGGTGGA 0.567000 0 SO:0001583 missense ENST00000389232.4 1 1 hg19 CCDS45210.1 . . . . . . . . . . G 31 5.058903 0.93846 . . ENSG00000198838 ENST00000389232;ENST00000415757;ENST00000361728 T;T 0.70516 -0.49;-0.49 5.42 4.5 0.54988 Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1); 0.000000 0.85682 D 0.000000 D 0.85392 0.5686 M 0.85299 2.745 0.58432 D 0.999999 D;D 0.89917 1.0;1.0 D;D 0.91635 0.996;0.999 D 0.88122 0.2832 10 0.66056 D 0.02 . 15.8752 0.79156 0.0:0.0:0.8636:0.1364 . 667;667 Q15413-2;Q15413 .;RYR3_HUMAN N 667 ENSP00000373884:D667N;ENSP00000399610:D667N ENSP00000354735:D667N D + 1 0 RYR3 31682692 1.000000 0.71417 0.994000 0.49952 0.985000 0.73830 9.522000 0.98032 1.529000 0.49120 -0.164000 0.13417 GAC TCGA-XD-AAUI-01A-42D-A40W-08 RYR3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000417514.1 0 0 0 37 540 0 146 0 0 0 0 146 2 0 0 0 0 0 2 1 1.000000 37 530 0 142 2 -7.797808 1 1 0 0 1 0 0 0 1.872458 1 0.210000 1.910000 0.145392 0.560000 0.400000 0.740000 0.560000 0.571921 0.560000 0 4.700000e-01 6.600000e-01 RYR3 6263 broad.mit.edu 37 15 34130000 34130000 + Missense_Mutation SNP C C A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr15:34130000C>A ENST00000389232.4 + 89 11889 c.11819C>A c.(11818-11820)tCc>tAc p.S3940Y RYR3_ENST00000415757.3_Missense_Mutation_p.S3935Y NM_001036.3 NP_001027.3 Q15413 RYR3_HUMAN ryanodine receptor 3 311 all_lung(180;7.18e-09) GGAATTATCTCCAAAAAAGAA 0.398000 0 SO:0001583 missense ENST00000389232.4 1 1 hg19 CCDS45210.1 . . . . . . . . . . C 17.85 3.490354 0.64074 . . ENSG00000198838 ENST00000389232;ENST00000361728 D 0.85013 -1.93 5.4 5.4 0.78164 EF-hand-like domain (1); 0.000000 0.85682 D 0.000000 D 0.93572 0.7948 M 0.86953 2.85 0.80722 D 1 D;D 0.89917 0.999;1.0 D;D 0.91635 0.988;0.999 D 0.93668 0.6987 10 0.59425 D 0.04 . 19.373 0.94498 0.0:1.0:0.0:0.0 . 3935;3940 Q15413-2;Q15413 .;RYR3_HUMAN Y 3940;3936 ENSP00000373884:S3940Y ENSP00000354735:S3936Y S + 2 0 RYR3 31917292 1.000000 0.71417 1.000000 0.80357 0.819000 0.46315 7.554000 0.82212 2.817000 0.96982 0.551000 0.68910 TCC TCGA-XD-AAUI-01A-42D-A40W-08 RYR3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000417514.1 1 0 0 18 221 0 63 0 0 0 0 63 2 0 0 0 0 0 2 1 0.999983 18 218 0 62 2 -2.920913 1 1 0 0 1 0 0 0 1.872458 1 0.210000 1.910000 0.145392 0.660000 0.410000 0.970000 0.650000 0.675355 0.660000 0 5.200000e-01 8.200000e-01 TMC3 342125 broad.mit.edu 37 15 81650502 81650502 + Missense_Mutation SNP A A G TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr15:81650502A>G ENST00000359440.5 - 7 866 c.731T>C c.(730-732)aTt>aCt p.I244T RP11-761I4.3_ENST00000559781.1_RNA|TMC3_ENST00000558726.1_Missense_Mutation_p.I244T|RP11-761I4.3_ENST00000560851.1_RNA NM_001080532.1 NP_001074001.1 transmembrane channel-like 3 34 TTTTAAAAGAATGATGAAGCT 0.408000 0 SO:0001583 missense ENST00000359440.5 0 1 hg19 CCDS45324.1 . . . . . . . . . . A 11.85 1.763052 0.31228 . . ENSG00000188869 ENST00000359440 T 0.50001 0.76 5.59 4.46 0.54185 . 0.478461 0.21754 N 0.069626 T 0.23054 0.0557 N 0.02854 -0.475 0.28128 N 0.930305 B;B 0.14805 0.004;0.011 B;B 0.17098 0.009;0.017 T 0.12863 -1.0531 10 0.39692 T 0.17 -9.4363 8.7012 0.34327 0.8534:0.0:0.1466:0.0 . 244;244 Q7Z5M5-2;Q7Z5M5 .;TMC3_HUMAN T 244 ENSP00000352413:I244T ENSP00000352413:I244T I - 2 0 TMC3 79437557 1.000000 0.71417 0.465000 0.27155 0.944000 0.59088 5.350000 0.66016 0.971000 0.38288 0.481000 0.45027 ATT TCGA-XD-AAUI-01A-42D-A40W-08 TMC3-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000417795.3 1 0 0 5 128 0 33 0 0 0 1 0 33 2 0 0 0 0 0 2 1 0.937519 5 127 0 33 2 -8.136713 1 1 0 0 1 0 0 0 1.877483 1 0.210000 1.910000 0.147329 0.350000 0.130000 0.680000 0.320000 0.375172 0.350000 0 2.200000e-01 5.100000e-01 IFT140 9742 broad.mit.edu 37 16 1633329 1633329 + Missense_Mutation SNP G G A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr16:1633329G>A ENST00000426508.2 - 12 1781 c.1418C>T c.(1417-1419)gCg>gTg p.A473V IFT140_ENST00000439987.2_5'UTR|LA16c-395F10.2_ENST00000563162.1_RNA NM_014714.3 NP_055529.2 Q96RY7 IF140_HUMAN intraflagellar transport 140 53 Hepatocellular(780;0.219) ACTCCGTATCGCGGCTCCAGA 0.567000 0 SO:0001583 missense ENST00000426508.2 0 1 hg19 CCDS10439.1 . . . . . . . . . . G 5.952 0.359713 0.11239 . . ENSG00000187535 ENST00000397417;ENST00000426508;ENST00000439987 T 0.69685 -0.42 5.48 -2.97 0.05530 . 1.408220 0.04710 N 0.417384 T 0.46483 0.1395 N 0.16478 0.41 0.09310 N 1 B;B 0.02656 0.0;0.0 B;B 0.04013 0.0;0.001 T 0.18429 -1.0337 10 0.25106 T 0.35 . 6.8317 0.23913 0.4417:0.0:0.4466:0.1116 . 473;198 Q96RY7;B4DR58 IF140_HUMAN;. V 473 ENSP00000406012:A473V ENSP00000380562:A473V A - 2 0 IFT140 1573330 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 -0.229000 0.09098 -0.918000 0.03808 -0.797000 0.03246 GCG TCGA-XD-AAUI-01A-42D-A40W-08 IFT140-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250438.2 0 0 0 5 185 0 51 0 5.712201e-02 1 11 0 51 2 0 0 0 0 0 2 1 0.933915 5 180 0 50 2 -6.885066 1 1 121412 2 30 1 0 0 0 1.926961 0 0.210000 1.910000 0.169906 0.250000 0.090000 0.510000 0.230000 0.275999 0.250000 0 1.600000e-01 3.800000e-01 PKD1 5310 broad.mit.edu 37 16 2162878 2162878 + Silent SNP G G A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr16:2162878G>A ENST00000262304.4 - 13 3280 c.3072C>T c.(3070-3072)gtC>gtT p.V1024V RP11-304L19.4_ENST00000568795.1_RNA|PKD1_ENST00000423118.1_Silent_p.V1024V NM_001009944.2 NP_001009944 P98161 PKD1_HUMAN polycystic kidney disease 1 (autosomal dominant) 72 GCACTGTGGAGACCTGCAGAC 0.642000 0 SO:0001819 synonymous_variant ENST00000262304.4 1 1 hg19 CCDS32369.1 TCGA-XD-AAUI-01A-42D-A40W-08 PKD1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000341688.1 1 0 0 12 156 0 59 0 1.504626e-01 0 9 0 59 2 0 0 0 0 0 2 1 0.999136 12 153 0 59 2 -16.376080 1 1 120976 1 34 1 0 0 0 1.926961 0 0.210000 1.910000 0.169906 0.650000 0.360000 1.000000 1.000000 0.668789 0.650000 0 4.900000e-01 8.400000e-01 CHST5 23563 broad.mit.edu 37 16 75564081 75564081 + Silent SNP G G A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr16:75564081G>A ENST00000336257.3 - 3 1596 c.202C>T c.(202-204)Ctg>Ttg p.L68L RP11-77K12.7_ENST00000460606.1_3'UTR|CHST5_ENST00000541075.1_Silent_p.L74L NM_024533.4 NP_078809.2 Q9GZS9 CHST5_HUMAN carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5 24 CACGAGGACAGCACCAGCACG 0.662000 0 SO:0001819 synonymous_variant ENST00000336257.3 0 1 hg19 CCDS10919.1 TCGA-XD-AAUI-01A-42D-A40W-08 CHST5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000269025.2 0 0 0 5 251 0 51 0 6.337115e-02 0 17 0 51 2 0 0 0 0 0 2 1 0.937505 5 250 0 50 2 -6.337946 1 1 0 0 1 0.210000 1.910000 0 0 IL17C 27189 broad.mit.edu 37 16 88706390 88706390 + Silent SNP G G A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr16:88706390G>A ENST00000244241.4 + 3 553 c.504G>A c.(502-504)tcG>tcA p.S168S NM_013278.3 NP_037410.1 Q9P0M4 IL17C_HUMAN interleukin 17C 2 GCGACGGCTCGGGGCTCCCCA 0.716000 0 SO:0001819 synonymous_variant ENST00000244241.4 1 1 hg19 CCDS42217.1 TCGA-XD-AAUI-01A-42D-A40W-08 IL17C-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000422575.1 1 0 1 18 288 0 85 1 2.826653e-01 4 13 0 85 2 0 0 0 0 0 2 1 0.999980 18 281 0 82 2 -2.506811 1 1 120554 4 34 1 2 2 4 2.173436 1 0.210000 1.910000 0.268383 0.660000 0.380000 1.000000 0.600000 0.712927 0.660000 0 5.000000e-01 1 DNAH9 1770 broad.mit.edu 37 17 11725368 11725368 + Nonsense_Mutation SNP C C T TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr17:11725368C>T ENST00000262442.4 + 46 8907 c.8839C>T c.(8839-8841)Cga>Tga p.R2947* DNAH9_ENST00000454412.2_Nonsense_Mutation_p.R2947* NM_001372.3 NP_001363.2 Q9NYC9 DYH9_HUMAN dynein, axonemal, heavy chain 9 290 Breast(5;0.0122)|all_epithelial(5;0.131) TCGGATCCGGCGACAGCTGAA 0.463000 0 SO:0001587 stop_gained ENST00000262442.4 0 1 hg19 CCDS11160.1 . . . . . . . . . . C 48 14.878058 0.99813 . . ENSG00000007174 ENST00000262442;ENST00000454412;ENST00000413703 . . . 4.21 -1.36 0.09085 . 0.146107 0.23074 U 0.052233 . . . . . . 0.21762 N 0.999553 . . . . . . . . . . 0.02654 T 1 . 13.2049 0.59790 0.5135:0.4865:0.0:0.0 . . . . X 2947;2947;1529 . ENSP00000262442:R2947X R + 1 2 DNAH9 11666093 0.296000 0.24398 0.019000 0.16419 0.046000 0.14306 0.403000 0.20982 0.203000 0.20529 0.467000 0.42956 CGA TCGA-XD-AAUI-01A-42D-A40W-08 DNAH9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252756.2 1 0 1 17 130 0 36 0 0 0 0 36 2 0 0 0 0 0 2 1 0.999974 17 129 0 36 2 -20.000000 1 1 121412 7 36 1 0 1 1 1.862336 1 0.210000 1.910000 0.123488 0.870000 0.570000 1.000000 1.000000 0.860084 0.870000 1 7.200000e-01 1 LRRC37B 114659 broad.mit.edu 37 17 30374829 30374829 + Silent SNP A A G TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr17:30374829A>G ENST00000341671.7 + 9 2297 c.2292A>G c.(2290-2292)ttA>ttG p.L764L LRRC37B_ENST00000543378.2_Silent_p.L682L|LRRC37B_ENST00000394713.3_Silent_p.L713L|LRRC37B_ENST00000584368.1_Silent_p.L725L|LRRC37B_ENST00000327564.7_Silent_p.L791L NM_052888.2 NP_443120.2 Q96QE4 LR37B_HUMAN leucine rich repeat containing 37B 29 Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.111)|Ovarian(249;0.182)|Breast(31;0.244) TGAAGATGTTACAAGCCCGGA 0.488000 0 SO:0001819 synonymous_variant ENST00000341671.7 1 1 hg19 CCDS32609.1 TCGA-XD-AAUI-01A-42D-A40W-08 LRRC37B-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000446508.1 1 0 1 64 587 0 182 1 8.211094e-01 4 27 0 182 2 0 0 0 0 0 2 1 1.000000 64 577 0 181 2 -20.000000 1 1 0 0 1 2 2 4 2.236854 1 0.210000 1.910000 0.289121 0.990000 0.820000 1.000000 1.000000 0.978822 0.990000 1 9.400000e-01 1 CASC3 22794 broad.mit.edu 37 17 38320039 38320039 + Missense_Mutation SNP C C T TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr17:38320039C>T ENST00000264645.7 + 7 1317 c.1091C>T c.(1090-1092)cCa>cTa p.P364L NM_007359.4 NP_031385.2 O15234 CASC3_HUMAN cancer susceptibility candidate 3 16 GATCCATCTCCAGAAGCAGAT 0.587000 0 SO:0001583 missense ENST00000264645.7 1 1 hg19 CCDS11362.1 . . . . . . . . . . C 23.5 4.426140 0.83667 . . ENSG00000108349 ENST00000264645;ENST00000418132;ENST00000394114 . . . 5.61 5.61 0.85477 . 0.056403 0.64402 D 0.000001 T 0.73434 0.3586 L 0.36672 1.1 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.85130 0.997;0.997 T 0.75187 -0.3406 9 0.72032 D 0.01 -8.0315 19.2489 0.93914 0.0:1.0:0.0:0.0 . 364;364 B4DKR6;O15234 .;CASC3_HUMAN L 364 . ENSP00000264645:P364L P + 2 0 CASC3 35573565 1.000000 0.71417 1.000000 0.80357 0.932000 0.56968 5.784000 0.68990 2.648000 0.89879 0.563000 0.77884 CCA TCGA-XD-AAUI-01A-42D-A40W-08 CASC3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257127.3 1 0 0 33 736 0 172 1 7.201792e-01 4 54 0 172 2 0 0 0 0 0 2 1 1.000000 33 720 0 170 2 -3.072344 1 1 0 0 1 1 3 4 2.263984 1 0.210000 1.910000 0.315009 0.490000 0.330000 1.000000 0.470000 0.580754 0.490000 0 4.000000e-01 1 DHX58 79132 broad.mit.edu 37 17 40260081 40260081 + Missense_Mutation SNP C C A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr17:40260081C>A ENST00000251642.3 - 7 946 c.724G>T c.(724-726)Gac>Tac p.D242Y NM_024119.2 NP_077024.2 Q96C10 DHX58_HUMAN DEXH (Asp-Glu-X-His) box polypeptide 58 16 all_cancers(22;9.73e-07)|all_epithelial(22;3.58e-05)|Breast(137;0.000143) TCCAGGTGGTCATGGATTTGG 0.557000 0 SO:0001583 missense ENST00000251642.3 0 1 hg19 CCDS11416.1 . . . . . . . . . . C 13.11 2.139297 0.37728 . . ENSG00000108771 ENST00000251642;ENST00000423748;ENST00000413196 T;T 0.24350 2.0;1.86 5.08 1.82 0.25136 . 0.408706 0.26991 N 0.021480 T 0.27967 0.0689 M 0.64997 1.995 0.09310 N 0.999996 B;D 0.55385 0.245;0.971 B;P 0.47645 0.08;0.553 T 0.11348 -1.0591 10 0.45353 T 0.12 -12.1084 6.7211 0.23330 0.0:0.5553:0.2787:0.166 . 235;242 B7Z455;Q96C10 .;DHX58_HUMAN Y 242;205;242 ENSP00000251642:D242Y;ENSP00000416389:D242Y ENSP00000251642:D242Y D - 1 0 DHX58 37513607 0.000000 0.05858 0.515000 0.27774 0.061000 0.15899 0.163000 0.16520 0.117000 0.18138 0.563000 0.77884 GAC TCGA-XD-AAUI-01A-42D-A40W-08 DHX58-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257396.1 0 0 0 8 372 0 105 0 8.365598e-02 0 20 0 105 2 0 0 0 0 0 2 1 0.988345 8 362 0 104 2 -2.934218 1 1 0 0 1 1 2 3 2.082176 0 0.210000 1.910000 0.224654 0.220000 0.100000 1.000000 0.200000 0.334120 0.220000 0 1.500000e-01 4.000000e-01 BPTF 2186 broad.mit.edu 37 17 65925454 65925454 + Missense_Mutation SNP G G A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr17:65925454G>A ENST00000321892.4 + 19 6440 c.6379G>A c.(6379-6381)Gtt>Att p.V2127I BPTF_ENST00000335221.5_Missense_Mutation_p.V2127I|BPTF_ENST00000424123.3_Missense_Mutation_p.V1988I|BPTF_ENST00000306378.6_Missense_Mutation_p.V2001I Q12830 BPTF_HUMAN bromodomain PHD finger transcription factor 78 all_cancers(12;6e-11) BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24) TTTTTAAGGCGTTGTTCAAGT 0.433000 0 SO:0001583 missense ENST00000321892.4 1 1 hg19 . . . . . . . . . . G 10.43 1.348665 0.24426 . . ENSG00000171634 ENST00000306378;ENST00000335221;ENST00000321892 T;T;T 0.64803 -0.06;-0.12;-0.09 5.84 4.85 0.62838 . . . . . T 0.44808 0.1311 N 0.17082 0.46 0.33129 D 0.542898 P;P 0.47034 0.466;0.889 B;B 0.36922 0.029;0.236 T 0.56786 -0.7921 9 0.34782 T 0.22 -11.045 15.4007 0.74838 0.0676:0.0:0.9324:0.0 . 2001;2127 Q12830-2;Q12830-4 .;. I 2001;2127;2127 ENSP00000307208:V2001I;ENSP00000334351:V2127I;ENSP00000315454:V2127I ENSP00000307208:V2001I V + 1 0 BPTF 63355916 1.000000 0.71417 0.990000 0.47175 0.981000 0.71138 3.766000 0.55280 1.443000 0.47586 0.650000 0.86243 GTT TCGA-XD-AAUI-01A-42D-A40W-08 BPTF-201 KNOWN basic protein_coding protein_coding 1 0 0 12 234 0 77 1 3.570716e-01 4 20 0 77 2 0 0 0 0 0 2 1 0.999162 12 233 0 77 2 -13.869140 1 1 121412 15 44 1 0 1 1 1.853394 1 0.210000 1.910000 0.117318 0.410000 0.220000 0.660000 0.400000 0.433162 0.410000 0 3.100000e-01 5.400000e-01 ABCA9 10350 broad.mit.edu 37 17 66979885 66979885 + Silent SNP G G A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr17:66979885G>A ENST00000340001.4 - 36 4816 c.4605C>T c.(4603-4605)atC>atT p.I1535I ABCA9_ENST00000370732.2_3'UTR|ABCA9_ENST00000482072.1_5'Flank|ABCA9_ENST00000453985.2_Silent_p.I1497I NM_080283.3 NP_525022.2 Q8IUA7 ABCA9_HUMAN ATP-binding cassette, sub-family A (ABC1), member 9 91 Breast(10;1.47e-12) AAAGCCTCAGGATCTCTGCAT 0.463000 0 SO:0001819 synonymous_variant ENST00000340001.4 1 1 hg19 CCDS11681.1 TCGA-XD-AAUI-01A-42D-A40W-08 ABCA9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000277072.2 1 0 1 47 286 0 85 0 4.291758e-01 0 10 0 85 2 0 0 0 0 0 2 1 1.000000 47 284 0 85 2 -19.981730 1 0 0 0 1 0 1 1 1.853394 1 0.210000 1.910000 0.117318 0.940000 0.790000 1.000000 0.990000 0.937043 0.940000 1 8.700000e-01 9.900000e-01 TP53 7157 broad.mit.edu 37 17 7577538 7577538 + Missense_Mutation SNP C C T rs11540652 TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr17:7577538C>T ENST00000269305.4 - 7 932 c.743G>A c.(742-744)cGg>cAg p.R248Q TP53_ENST00000445888.2_Missense_Mutation_p.R248Q|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.R248Q|TP53_ENST00000420246.2_Missense_Mutation_p.R248Q|TP53_ENST00000359597.4_Missense_Mutation_p.R248Q|TP53_ENST00000413465.2_Missense_Mutation_p.R248Q 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.R248Q(580)|p.R248L(75)|p.R248P(19)|p.R155Q(18)|p.0?(8)|p.?(5)|p.R155L(3)|p.R155P(2)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*96(1)|p.R248fs*>39(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) GATGGGCCTCCGGTTCATGCC 0.572000 R248Q(BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(CI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(EM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(HCC1143_BREAST)|R248Q(HCC70_BREAST)|R248Q(HEC1A_ENDOMETRIUM)|R248Q(HS683_CENTRAL_NERVOUS_SYSTEM)|R248Q(HSC4_UPPER_AERODIGESTIVE_TRACT)|R248Q(KASUMI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(KYSE150_OESOPHAGUS)|R248Q(MOLM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NAMALWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NB4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(NCIH211_LUNG)|R248Q(NCIN87_STOMACH)|R248Q(NIHOVCAR3_OVARY)|R248Q(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(P12ICHIKAWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(PANC0203_PANCREAS)|R248Q(PC14_LUNG)|R248Q(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(RT112_URINARY_TRACT)|R248Q(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SF295_CENTRAL_NERVOUS_SYSTEM)|R248Q(SKUT1_SOFT_TISSUE)|R248Q(SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248Q(SW1463_LARGE_INTESTINE)|R248Q(WSUDLCL2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE) 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 725 Substitution - Missense(698)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(2)|Complex - compound substitution(1) GRCh37 CM920675 TP53 M rs11540652 SO:0001583 missense Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 1 1 hg19 CCDS11118.1 . . . . . . . . . . C 27.3 4.822907 0.90873 0.0 1.16E-4 ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944 D;D;D;D;D;D;D;D 0.99864 -7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28;-7.28 4.62 3.65 0.41850 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.000000 0.85682 D 0.000000 D 0.99840 0.9927 M 0.88640 2.97 0.58432 A 0.999994 D;D;D;D;D;D 0.89917 1.0;0.994;1.0;1.0;1.0;1.0 D;P;D;D;D;D 0.91635 0.996;0.882;0.999;0.995;0.996;0.995 D 0.96819 0.9602 9 0.72032 D 0.01 -9.5643 10.6687 0.45745 0.0:0.9059:0.0:0.0941 rs11540652;rs11540652 248;248;155;248;248;248 P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7 .;.;.;P53_HUMAN;.;. Q 248;248;248;248;248;248;237;155;116;155 ENSP00000410739:R248Q;ENSP00000352610:R248Q;ENSP00000269305:R248Q;ENSP00000398846:R248Q;ENSP00000391127:R248Q;ENSP00000391478:R248Q;ENSP00000425104:R116Q;ENSP00000423862:R155Q ENSP00000269305:R248Q R - 2 0 TP53 7518263 1.000000 0.71417 1.000000 0.80357 0.887000 0.51463 5.884000 0.69729 1.305000 0.44909 0.462000 0.41574 CGG TCGA-XD-AAUI-01A-42D-A40W-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 28 156 0 72 1 9.996647e-01 27 46 0 72 2 1 1 84 845 2 899 8 1 1.000000 28 150 0 72 2 -2.603265 1 1 121412 7 38 1 0 1 1 1.862336 1 0.210000 1.910000 0.123488 0.980000 0.760000 1.000000 1.000000 0.953148 0.980000 1 8.800000e-01 1 DSC1 1823 broad.mit.edu 37 18 28710559 28710559 + Missense_Mutation SNP C C G TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr18:28710559C>G ENST00000257198.5 - 16 2864 c.2603G>C c.(2602-2604)cGg>cCg p.R868P DSC1_ENST00000257197.3_3'UTR|RP11-408H20.3_ENST00000582307.1_RNA|RP11-408H20.2_ENST00000581836.1_RNA NM_024421.2 NP_077739.1 Q08554 DSC1_HUMAN desmocollin 1 53 OV - Ovarian serous cystadenocarcinoma(10;0.00778) TTCTTCCTGCCGATCGCTGCA 0.438000 0 SO:0001583 missense ENST00000257198.5 1 1 hg19 CCDS11894.1 . . . . . . . . . . C 14.19 2.460536 0.43736 . . ENSG00000134765 ENST00000257198 T 0.76839 -1.05 6.17 1.38 0.22167 Cadherin, cytoplasmic domain (1); 0.137951 0.33235 N 0.005138 T 0.67878 0.2940 M 0.63843 1.955 0.09310 N 1 B 0.15719 0.014 B 0.20955 0.032 T 0.60383 -0.7274 10 0.59425 D 0.04 . 1.3924 0.02253 0.1426:0.3912:0.1396:0.3265 . 868 Q08554 DSC1_HUMAN P 868 ENSP00000257198:R868P ENSP00000257198:R868P R - 2 0 DSC1 26964557 0.926000 0.31397 0.445000 0.26908 0.605000 0.37080 0.758000 0.26447 0.492000 0.27815 0.655000 0.94253 CGG TCGA-XD-AAUI-01A-42D-A40W-08 DSC1-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000254946.1 1 0 0 36 505 0 147 0 0 0 0 147 2 0 0 0 0 0 2 1 1.000000 36 496 0 144 2 -2.879449 1 1 0 0 1 0 0 0 1.913322 0 0.210000 1.910000 0.164375 0.590000 0.420000 0.790000 0.590000 0.607759 0.590000 0 5.000000e-01 7.000000e-01 C19orf57 79173 broad.mit.edu 37 19 14006193 14006193 + Silent SNP G G A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr19:14006193G>A ENST00000586783.1 - 2 197 c.198C>T c.(196-198)gcC>gcT p.A66A C19orf57_ENST00000346736.2_Silent_p.A66A|C19orf57_ENST00000454313.1_Silent_p.A66A|C19orf57_ENST00000591586.1_Silent_p.A66A Q0VDD7 CS057_HUMAN chromosome 19 open reading frame 57 14 OV - Ovarian serous cystadenocarcinoma(19;2e-21) ACCTGGAGACGGCCTTTCCTG 0.562000 0 SO:0001819 synonymous_variant ENST00000586783.1 0 1 hg19 TCGA-XD-AAUI-01A-42D-A40W-08 C19orf57-003 NOVEL basic protein_coding protein_coding OTTHUMT00000457947.1 0 0 0 7 377 1 86 0 4.795013e-04 0 2 1 86 2 0 0 0 0 0 2 0 0.041244 7 374 1 86 16 -2.718714 1 1 121412 1 34 1 1 2 3 2.028289 0 0.210000 1.910000 0.214126 0.180000 0.070000 1.000000 0.170000 0.227040 0.180000 0 1.200000e-01 2.800000e-01 LSR 51599 broad.mit.edu 37 19 35753531 35753531 + Silent SNP G G A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr19:35753531G>A ENST00000361790.3 + 5 1017 c.858G>A c.(856-858)ccG>ccA p.P286P AD000684.2_ENST00000602262.1_RNA|LSR_ENST00000347609.4_Silent_p.P249P|LSR_ENST00000602122.1_Silent_p.P267P|LSR_ENST00000597933.1_3'UTR|LSR_ENST00000427250.1_Intron|LSR_ENST00000354900.3_Silent_p.P267P|LSR_ENST00000360798.3_Intron NM_205834.3 NP_991403.1 Q86X29 LSR_HUMAN lipolysis stimulated lipoprotein receptor 13 all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162) Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417) AGTGCTGCCCGCACACTTGCT 0.622000 0 SO:0001819 synonymous_variant ENST00000361790.3 0 1 hg19 CCDS12450.1 TCGA-XD-AAUI-01A-42D-A40W-08 LSR-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000465513.2 0 0 0 6 429 0 87 1 9.853121e-01 2 560 0 87 2 0 0 0 0 0 2 1 0.963160 6 421 0 87 2 -2.513202 1 1 121412 4 37 1 1 3 4 2.395528 1 0.210000 1.910000 0.329656 0.170000 0.060000 1.000000 0.150000 0.276476 0.170000 0 1.100000e-01 3.100000e-01 USP29 57663 broad.mit.edu 37 19 57641566 57641566 + Missense_Mutation SNP T T A rs145552693 TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr19:57641566T>A ENST00000254181.4 + 4 1977 c.1523T>A c.(1522-1524)aTc>aAc p.I508N USP29_ENST00000598197.1_Missense_Mutation_p.I508N NM_020903.2 NP_065954.1 Q9HBJ7 UBP29_HUMAN ubiquitin specific peptidase 29 85 Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157) AGGGTCCTTATCATTCATCTG 0.368000 0 SO:0001583 missense ENST00000254181.4 0 1 hg19 CCDS33124.1 . . . . . . . . . . T 11.77 1.737455 0.30774 . . ENSG00000131864 ENST00000254181 T 0.77229 -1.08 2.69 1.66 0.24008 Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2); 0.000000 0.32819 U 0.005605 D 0.84483 0.5482 M 0.78916 2.43 0.31512 N 0.663476 D 0.89917 1.0 D 0.97110 1.0 T 0.81992 -0.0678 10 0.87932 D 0 -10.247 5.9622 0.19305 0.0:0.138:0.0:0.8619 . 508 Q9HBJ7 UBP29_HUMAN N 508 ENSP00000254181:I508N ENSP00000254181:I508N I + 2 0 USP29 62333378 1.000000 0.71417 0.168000 0.22838 0.221000 0.24807 3.064000 0.49986 0.430000 0.26230 0.482000 0.46254 ATC TCGA-XD-AAUI-01A-42D-A40W-08 USP29-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000465075.1 0 0 0 5 435 0 103 0 0 0 0 103 2 0 0 0 0 0 2 1 0.936748 5 432 0 103 2 -5.220647 1 1 0 0 1 0 2 2 1.961025 1 0.210000 1.910000 0.210000 0.120000 0.040000 1.000000 0.110000 0.205652 0.120000 0 7.000000e-02 2.100000e-01 LRRC8E 80131 broad.mit.edu 37 19 7965572 7965572 + Missense_Mutation SNP G G A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr19:7965572G>A ENST00000306708.6 + 3 2266 c.2165G>A c.(2164-2166)cGc>cAc p.R722H RN7SL115P_ENST00000392196.5_RNA|AC010336.1_ENST00000539278.1_5'UTR NM_001268284.1|NM_001268285.1|NM_025061.4 NP_001255213.1|NP_001255214.1|NP_079337.2 Q6NSJ5 LRC8E_HUMAN leucine rich repeat containing 8 family, member E 35 TTCTTCTGCCGCAAGCTGCGG 0.657000 0 SO:0001583 missense ENST00000306708.6 0 1 hg19 CCDS12189.1 2 9.157509157509158E-4 0 0.0 1 0.0027624309392265192 0 0.0 1 0.0013192612137203166 G 7.848 0.723462 0.15439 . . ENSG00000171017 ENST00000306708 T 0.10382 2.88 4.35 2.07 0.26955 . 0.307696 0.29444 N 0.012138 T 0.06826 0.0174 L 0.31578 0.945 0.24912 N 0.992033 B 0.13594 0.008 B 0.10450 0.005 T 0.24693 -1.0153 10 0.40728 T 0.16 . 4.6497 0.12589 0.3968:0.0:0.6032:0.0 . 722 Q6NSJ5 LRC8E_HUMAN H 722 ENSP00000306524:R722H ENSP00000306524:R722H R + 2 0 LRRC8E 7871572 0.992000 0.36948 0.479000 0.27329 0.045000 0.14185 2.928000 0.48908 1.028000 0.39785 0.585000 0.79938 CGC TCGA-XD-AAUI-01A-42D-A40W-08 LRRC8E-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000461354.1 0 0 0 5 250 0 79 0 2.900688e-02 0 11 0 79 2 0 0 0 0 0 2 1 0.934172 5 244 0 78 2 -2.308896 0 1 121410 11 41 1 0 1 1 1.923094 0 0.210000 1.910000 0.153087 0.180000 0.060000 0.370000 0.170000 0.202923 0.180000 0 1.100000e-01 2.800000e-01 MTOR 2475 broad.mit.edu 37 1 11193143 11193143 + Missense_Mutation SNP C C G TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr1:11193143C>G ENST00000361445.4 - 38 5434 c.5358G>C c.(5356-5358)tgG>tgC p.W1786C MTOR_ENST00000495435.1_5'UTR|MTOR_ENST00000376838.1_5'Flank NM_004958.3 NP_004949.1 P42345 MTOR_HUMAN mechanistic target of rapamycin (serine/threonine kinase) 149 Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287) TCACCTTGTACCAGCTGCGGT 0.577000 0 SO:0001583 missense ENST00000361445.4 1 1 hg19 CCDS127.1 . . . . . . . . . . C 15.58 2.875568 0.51695 . . ENSG00000198793 ENST00000361445 T 0.72835 -0.69 5.65 4.74 0.60224 PIK-related kinase (1);PIK-related kinase, FAT (1);Armadillo-like helical (1); 0.059201 0.64402 N 0.000001 T 0.73393 0.3581 M 0.80616 2.505 0.80722 D 1 B 0.02656 0.0 B 0.01281 0.0 T 0.71741 -0.4501 10 0.51188 T 0.08 -12.1729 16.7143 0.85394 0.0:0.8706:0.1294:0.0 . 1786 P42345 MTOR_HUMAN C 1786 ENSP00000354558:W1786C ENSP00000354558:W1786C W - 3 0 MTOR 11115730 1.000000 0.71417 1.000000 0.80357 0.987000 0.75469 7.456000 0.80751 1.367000 0.46095 0.655000 0.94253 TGG TCGA-XD-AAUI-01A-42D-A40W-08 MTOR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000005558.1 1 0 0 33 392 0 106 1 3.951495e-01 8 9 0 106 2 0 0 0 0 0 2 1 1.000000 33 387 0 104 2 -9.515631 1 1 0 0 1 1 2 3 2.034459 0 0.210000 1.910000 0.214946 0.750000 0.520000 1.000000 1.000000 0.766159 0.750000 0 6.300000e-01 9.100000e-01 KRTAP24-1 643803 broad.mit.edu 37 21 31654596 31654596 + Nonsense_Mutation SNP G G A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr21:31654596G>A ENST00000340345.4 - 1 680 c.655C>T c.(655-657)Cga>Tga p.R219* NM_001085455.1 NP_001078924.1 Q3LI83 KR241_HUMAN keratin associated protein 24-1 14 CTCAGTGGTCGGCAGCTCGTA 0.443000 0 SO:0001587 stop_gained ENST00000340345.4 0 1 hg19 CCDS42915.1 . . . . . . . . . . G 15.89 2.967829 0.53507 . . ENSG00000188694 ENST00000340345 . . . 4.04 3.15 0.36227 . 1.427210 0.04871 N 0.445896 . . . . . . 0.47214 D 0.999352 . . . . . . . . . . 0.02654 T 1 2.7357 8.2674 0.31821 0.1164:0.0:0.8836:0.0 . . . . X 219 . ENSP00000339238:R219X R - 1 2 KRTAP24-1 30576467 0.010000 0.17322 0.013000 0.15412 0.022000 0.10575 1.624000 0.37018 0.998000 0.38996 -0.251000 0.11542 CGA TCGA-XD-AAUI-01A-42D-A40W-08 KRTAP24-1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000246806.2 0 0 0 14 407 0 112 0 0 0 0 112 2 0 0 0 0 0 2 1 0.999738 13 402 0 112 2 -2.621413 1 1 120808 2 34 1 0 0 0 1.978313 0 0.210000 1.910000 0.191319 0.310000 0.170000 0.490000 0.310000 0.326617 0.310000 0 2.300000e-01 4.100000e-01 LRP1B 53353 broad.mit.edu 37 2 141533746 141533746 + Silent SNP G G A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr2:141533746G>A ENST00000389484.3 - 33 6392 c.5421C>T c.(5419-5421)gaC>gaT p.D1807D NM_018557.2 NP_061027.2 Q9NZR2 LRP1B_HUMAN low density lipoprotein receptor-related protein 1B 606 all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101) GGTTTCTTCCGTCTCTTTTGC 0.383000 TSP Lung(27;0.18) Colon(99;50 2074 2507 20106) 0 SO:0001819 synonymous_variant ENST00000389484.3 1 1 hg19 CCDS2182.1 TCGA-XD-AAUI-01A-42D-A40W-08 LRP1B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254736.2 1 0 1 30 203 0 50 0 0 0 0 50 2 0 0 0 0 0 2 1 1.000000 30 201 0 49 2 -14.093960 1 1 121412 6 38 1 1 2 3 2.075048 0 0.210000 1.910000 0.223053 0.990000 0.880000 1.000000 1.000000 0.992440 0.990000 1 9.900000e-01 1 MYCN 4613 broad.mit.edu 37 2 16086019 16086019 + Missense_Mutation SNP T T A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr2:16086019T>A ENST00000281043.3 + 3 1492 c.1195T>A c.(1195-1197)Tcc>Acc p.S399T NM_005378.4 NP_005369.2 P04198 MYCN_HUMAN v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog 31 all_cancers(1;1.35e-08)|all_neural(1;2.92e-24)|Lung SC(1;3.26e-07)|Medulloblastoma(1;6.9e-06)|all_lung(1;1.26e-05)|Glioma(3;0.135)|Acute lymphoblastic leukemia(172;0.155)|all_epithelial(1;0.169)|all_hematologic(175;0.197) GBM - Glioblastoma multiforme(3;0.000332) CGACCTTCGGTCCAGCTTTCT 0.562000 A neuroblastoma Dom yes 2 2p24.1 4613 v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian) O 0 SO:0001583 missense ENST00000281043.3 1 1 hg19 CCDS1687.1 . . . . . . . . . . T 15.43 2.831915 0.50845 . . ENSG00000134323 ENST00000281043;ENST00000426211 D 0.98120 -4.73 5.14 3.98 0.46160 Helix-loop-helix DNA-binding (5); 0.000000 0.85682 D 0.000000 D 0.95335 0.8486 N 0.05078 -0.115 0.53688 D 0.999976 D 0.64830 0.994 D 0.64506 0.926 D 0.92718 0.6189 10 0.22109 T 0.4 -18.6908 10.7944 0.46451 0.0:0.0748:0.0:0.9252 . 399 P04198 MYCN_HUMAN T 399;317 ENSP00000281043:S399T ENSP00000281043:S399T S + 1 0 MYCN 16003470 1.000000 0.71417 0.850000 0.33497 0.991000 0.79684 5.091000 0.64505 0.931000 0.37242 0.496000 0.49642 TCC TCGA-XD-AAUI-01A-42D-A40W-08 MYCN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000095469.2 0 0 1 51 449 1 145 0 3.028889e-02 0 3 1 145 2 0 0 0 0 0 2 1 1.000000 50 442 1 145 13 -20.000000 1 1 0 0 1 1 2 3 2.075048 0 0.210000 1.910000 0.223053 0.990000 0.750000 1.000000 1.000000 0.952667 0.990000 1 8.700000e-01 1 SCN9A 6335 broad.mit.edu 37 2 167056341 167056341 + Missense_Mutation SNP A A G TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr2:167056341A>G ENST00000409435.1 - 26 4807 c.4808T>C c.(4807-4809)tTt>tCt p.F1603S AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000409672.1_Missense_Mutation_p.F1592S|SCN9A_ENST00000303354.6_Missense_Mutation_p.F1604S|SCN9A_ENST00000375387.4_Missense_Mutation_p.F1604S Q15858 SCN9A_HUMAN sodium channel, voltage-gated, type IX, alpha subunit 108 Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909) AGGGGACACAAAATACGTTTC 0.423000 0 SO:0001583 missense ENST00000409435.1 1 1 hg19 CCDS46441.1 . . . . . . . . . . A 19.39 3.817625 0.70912 . . ENSG00000169432 ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435 D;D;D;D 0.98296 -4.85;-4.85;-4.85;-4.85 5.74 5.74 0.90152 . 0.000000 0.64402 D 0.000009 D 0.98425 0.9476 M 0.65498 2.005 0.80722 D 1 D 0.55172 0.97 P 0.58820 0.846 D 0.99548 1.0965 10 0.87932 D 0 . 16.0249 0.80536 1.0:0.0:0.0:0.0 . 1592 E7EUN6 . S 1592;1604;1604;1603 ENSP00000386306:F1592S;ENSP00000364536:F1604S;ENSP00000304748:F1604S;ENSP00000386330:F1603S ENSP00000304748:F1604S F - 2 0 SCN9A 166764587 1.000000 0.71417 0.998000 0.56505 0.855000 0.48748 9.157000 0.94714 2.181000 0.69327 0.528000 0.53228 TTT TCGA-XD-AAUI-01A-42D-A40W-08 SCN9A-004 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000333639.1 1 0 0 43 373 0 89 0 0 0 0 89 2 0 0 0 0 0 2 1 1.000000 43 364 0 88 2 -20.000000 1 1 0 0 1 1 2 3 2.075048 0 0.210000 1.910000 0.223053 0.990000 0.740000 1.000000 1.000000 0.954575 0.990000 1 8.700000e-01 1 XIRP2 129446 broad.mit.edu 37 2 168103840 168103840 + Missense_Mutation SNP A A C TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr2:168103840A>C ENST00000409195.1 + 9 6027 c.5938A>C c.(5938-5940)Aag>Cag p.K1980Q XIRP2_ENST00000295237.9_Missense_Mutation_p.K1980Q|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.K1758Q|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409756.2_Intron NM_152381.5 NP_689594.4 A4UGR9 XIRP2_HUMAN xin actin-binding repeat containing 2 315 TCTTCAGCCAAAGCCAGGTCC 0.468000 0 SO:0001583 missense ENST00000409195.1 1 1 hg19 CCDS42769.1 . . . . . . . . . . A 0.052 -1.247707 0.01469 . . ENSG00000163092 ENST00000409195;ENST00000295237;ENST00000409273 T;T;T 0.02552 4.25;4.25;4.25 5.73 2.16 0.27623 . 0.674670 0.15536 N 0.257239 T 0.01558 0.0050 N 0.14661 0.345 0.09310 N 1 B;B;B 0.26258 0.09;0.145;0.091 B;B;B 0.24541 0.024;0.054;0.034 T 0.48399 -0.9039 10 0.12766 T 0.61 -1.5086 3.3189 0.07043 0.5633:0.0:0.2707:0.1659 . 1805;1805;1758 A4UGR9;A4UGR9-3;A4UGR9-2 XIRP2_HUMAN;.;. Q 1980;1980;1758 ENSP00000386840:K1980Q;ENSP00000295237:K1980Q;ENSP00000387255:K1758Q ENSP00000295237:K1980Q K + 1 0 XIRP2 167812086 0.000000 0.05858 0.947000 0.38551 0.012000 0.07955 -0.097000 0.11042 0.465000 0.27167 -0.263000 0.10527 AAG TCGA-XD-AAUI-01A-42D-A40W-08 XIRP2-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000333547.1 1 0 0 16 220 0 61 0 0 0 0 61 2 0 0 0 0 0 2 1 0.999938 14 220 0 61 2 -19.894760 1 1 0 0 1 1 2 3 2.075048 0 0.210000 1.910000 0.223053 0.690000 0.400000 1.000000 1.000000 0.719264 0.690000 0 5.300000e-01 9.800000e-01 ALS2CR12 130540 broad.mit.edu 37 2 202172323 202172323 + Silent SNP G G A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr2:202172323G>A ENST00000286190.5 - 10 844 c.798C>T c.(796-798)ttC>ttT p.F266F ALS2CR12_ENST00000392257.3_Silent_p.F266F|ALS2CR12_ENST00000448967.1_5'Flank|ALS2CR12_ENST00000405148.2_Silent_p.F266F|ALS2CR12_ENST00000439709.1_Silent_p.F266F Q96Q35 AL2SB_HUMAN amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 12 p.F266F(1) 21 ACTCCATTTCGAATTTTTTGG 0.383000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000286190.5 1 1 hg19 CCDS2346.1 . . . . . . . . . . G 0.508 -0.867740 0.02590 . . ENSG00000155749 ENST00000415745 . . . 5.53 -0.054 0.13816 . . . . . T 0.50888 0.1642 . . . 0.80722 D 1 . . . . . . T 0.35919 -0.9769 4 . . . -8.4115 5.6157 0.17430 0.6368:0.1427:0.2205:0.0 . . . . L 41 . . S - 2 0 ALS2CR12 201880568 0.992000 0.36948 0.993000 0.49108 0.026000 0.11368 0.295000 0.19065 -0.114000 0.11936 -0.300000 0.09419 TCG TCGA-XD-AAUI-01A-42D-A40W-08 ALS2CR12-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000256286.1 1 0 0 26 462 0 137 0 0 0 0 137 2 0 0 0 0 0 2 1 1.000000 26 458 0 137 2 -5.217164 1 1 121404 6 41 1 1 2 3 2.067490 0 0.210000 1.910000 0.221445 0.530000 0.350000 1.000000 0.510000 0.581268 0.530000 0 4.300000e-01 7.000000e-01 SIX2 10736 broad.mit.edu 37 2 45233480 45233480 + Silent SNP C C T rs146943650 byFrequency TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr2:45233480C>T ENST00000303077.6 - 2 1024 c.705G>A c.(703-705)ccG>ccA p.P235P NM_016932.4 NP_058628.3 Q9NPC8 SIX2_HUMAN SIX homeobox 2 p.P235P(1) 22 all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17) CAGGGGGCGGCGGGCTGAGGA 0.706000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000303077.6 1 1 hg19 CCDS1822.1 TCGA-XD-AAUI-01A-42D-A40W-08 SIX2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000326188.2 0 0 0 16 296 0 106 0 3.947501e-02 1 5 0 106 2 0 0 0 0 0 2 1 0.999921 16 286 0 105 2 -3.317208 1 1 121410 48 49 1 1 2 3 2.075048 0 0.210000 1.910000 0.223053 0.520000 0.300000 1.000000 0.500000 0.578975 0.520000 0 4.000000e-01 7.500000e-01 FBXO11 80204 broad.mit.edu 37 2 48066031 48066031 + Missense_Mutation SNP C C T TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr2:48066031C>T ENST00000403359.3 - 4 626 c.554G>A c.(553-555)cGc>cAc p.R185H FBXO11_ENST00000480038.1_5'UTR|FBXO11_ENST00000402508.1_Missense_Mutation_p.R101H|FBXO11_ENST00000378314.3_Missense_Mutation_p.R67H|FBXO11_ENST00000316377.4_Missense_Mutation_p.R101H NM_001190274.1 NP_001177203.1 Q86XK2 FBX11_HUMAN F-box protein 11 p.0?(2) 26 Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358) Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151) TTCACTGAAGCGTTTACATAC 0.363000 Mis, F, D DLBCL Rec yes 2 2p16.3 80204 F-box protein 11 L 2 Whole gene deletion(2) SO:0001583 missense ENST00000403359.3 0 1 hg19 CCDS54357.1 . . . . . . . . . . C 34 5.310469 0.95629 . . ENSG00000138081 ENST00000402508;ENST00000403359;ENST00000316377;ENST00000424163;ENST00000378314 T;T;T;T;T 0.51325 0.71;0.71;0.71;0.71;0.71 5.5 5.5 0.81552 F-box domain, cyclin-like (2);F-box domain, Skp2-like (1); 0.000000 0.85682 D 0.000000 T 0.69070 0.3070 M 0.72118 2.19 0.80722 D 1 D 0.76494 0.999 D 0.68621 0.959 T 0.71906 -0.4451 10 0.87932 D 0 -4.1684 19.3886 0.94570 0.0:1.0:0.0:0.0 . 185 Q86XK2 FBX11_HUMAN H 101;185;101;101;67 ENSP00000385398:R101H;ENSP00000384823:R185H;ENSP00000323822:R101H;ENSP00000392272:R101H;ENSP00000367565:R67H ENSP00000323822:R101H R - 2 0 FBXO11 47919535 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.818000 0.86416 2.573000 0.86826 0.563000 0.77884 CGC TCGA-XD-AAUI-01A-42D-A40W-08 FBXO11-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000251181.3 0 0 1 33 227 1 65 1 3.817560e-01 6 11 1 65 3 0 0 0 0 0 2 1 0.998886 32 226 1 65 14 -14.982660 1 1 0 0 1 1 2 3 2.075048 0 0.210000 1.910000 0.223053 0.990000 0.880000 1.000000 1.000000 0.992454 0.990000 1 9.900000e-01 1 BOC 91653 broad.mit.edu 37 3 112998688 112998688 + Nonsense_Mutation SNP C C T TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr3:112998688C>T ENST00000495514.1 + 13 2742 c.2038C>T c.(2038-2040)Cga>Tga p.R680* BOC_ENST00000273395.4_Nonsense_Mutation_p.R681*|BOC_ENST00000355385.3_Nonsense_Mutation_p.R680* Q9BWV1 BOC_HUMAN BOC cell adhesion associated, oncogene regulated 68 Epithelial(53;0.227) CTACAAGTTTCGAGTCCGGGC 0.622000 0 SO:0001587 stop_gained ENST00000495514.1 0 1 hg19 CCDS2971.1 . . . . . . . . . . C 43 10.022862 0.99319 . . ENSG00000144857 ENST00000495514;ENST00000273395;ENST00000355385 . . . 5.53 5.53 0.82687 . 0.065151 0.64402 D 0.000007 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 . 19.4493 0.94860 0.0:1.0:0.0:0.0 . . . . X 680;681;680 . ENSP00000273395:R681X R + 1 2 BOC 114481378 1.000000 0.71417 1.000000 0.80357 0.725000 0.41563 5.444000 0.66587 2.593000 0.87608 0.563000 0.77884 CGA TCGA-XD-AAUI-01A-42D-A40W-08 BOC-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000354485.3 1 0 0 27 433 0 95 0 2.757958e-01 0 17 0 95 2 0 0 0 0 0 2 1 1.000000 24 425 0 91 2 -6.147839 1 1 0 0 1 1 2 3 2.064228 0 0.210000 1.910000 0.220638 0.580000 0.380000 1.000000 0.560000 0.624300 0.580000 0 4.700000e-01 7.500000e-01 DHX36 170506 broad.mit.edu 37 3 154018839 154018839 + Missense_Mutation SNP T T A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr3:154018839T>A ENST00000496811.1 - 10 1375 c.1295A>T c.(1294-1296)aAa>aTa p.K432I DHX36_ENST00000308361.6_Missense_Mutation_p.K432I|DHX36_ENST00000329463.5_Missense_Mutation_p.K432I|DHX36_ENST00000544526.1_Missense_Mutation_p.K432I NM_020865.2 NP_065916.2 Q9H2U1 DHX36_HUMAN DEAH (Asp-Glu-Ala-His) box polypeptide 36 35 LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173) TTTTTCTTCTTTTTCTTGTCT 0.353000 0 SO:0001583 missense ENST00000496811.1 1 1 hg19 CCDS3171.1 . . . . . . . . . . T 19.36 3.813041 0.70912 . . ENSG00000174953 ENST00000496811;ENST00000308361;ENST00000544526;ENST00000329463;ENST00000481941 T;T;T;T;T 0.03801 3.98;3.9;3.81;3.8;3.99 5.73 5.73 0.89815 . 0.000000 0.85682 D 0.000000 T 0.12475 0.0303 L 0.60845 1.875 0.54753 D 0.999989 P;P;B 0.42456 0.78;0.78;0.27 P;P;B 0.48400 0.576;0.576;0.092 T 0.00240 -1.1887 10 0.72032 D 0.01 . 16.0307 0.80574 0.0:0.0:0.0:1.0 . 432;432;432 Q9H2U1-2;Q9H2U1-3;Q9H2U1 .;.;DHX36_HUMAN I 432;432;432;432;346 ENSP00000417078:K432I;ENSP00000309296:K432I;ENSP00000444247:K432I;ENSP00000330113:K432I;ENSP00000419862:K346I ENSP00000309296:K432I K - 2 0 DHX36 155501533 1.000000 0.71417 1.000000 0.80357 0.966000 0.64601 6.502000 0.73695 2.190000 0.69967 0.455000 0.32223 AAA TCGA-XD-AAUI-01A-42D-A40W-08 DHX36-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000353349.1 1 0 1 61 402 0 97 1 9.072670e-01 3 26 0 97 2 0 0 0 0 0 2 1 1.000000 60 400 0 97 2 -20.000000 1 0 0 0 1 1 2 3 2.064228 0 0.210000 1.910000 0.220638 0.990000 0.990000 1.000000 1.000000 0.998838 0.990000 1 9.900000e-01 1 DHX36 170506 broad.mit.edu 37 3 154018849 154018849 + Missense_Mutation SNP T T C TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr3:154018849T>C ENST00000496811.1 - 10 1365 c.1285A>G c.(1285-1287)Aga>Gga p.R429G DHX36_ENST00000308361.6_Missense_Mutation_p.R429G|DHX36_ENST00000329463.5_Missense_Mutation_p.R429G|DHX36_ENST00000544526.1_Missense_Mutation_p.R429G NM_020865.2 NP_065916.2 Q9H2U1 DHX36_HUMAN DEAH (Asp-Glu-Ala-His) box polypeptide 36 35 LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173) TTTTCTTGTCTATTTACATGC 0.343000 0 SO:0001583 missense ENST00000496811.1 1 1 hg19 CCDS3171.1 . . . . . . . . . . T 11.26 1.587020 0.28268 0.0 1.16E-4 ENSG00000174953 ENST00000496811;ENST00000308361;ENST00000544526;ENST00000329463;ENST00000481941 T;T;T;T;T 0.03635 4.04;3.97;3.86;3.86;4.05 5.73 3.31 0.37934 . 0.050847 0.85682 D 0.000000 T 0.05502 0.0145 L 0.60455 1.87 0.42665 D 0.993495 B;P;B 0.47106 0.002;0.89;0.001 B;B;B 0.44224 0.011;0.444;0.004 T 0.48937 -0.8990 10 0.28530 T 0.3 . 8.1451 0.31106 0.1262:0.0:0.2626:0.6112 . 429;429;429 Q9H2U1-2;Q9H2U1-3;Q9H2U1 .;.;DHX36_HUMAN G 429;429;429;429;343 ENSP00000417078:R429G;ENSP00000309296:R429G;ENSP00000444247:R429G;ENSP00000330113:R429G;ENSP00000419862:R343G ENSP00000309296:R429G R - 1 2 DHX36 155501543 1.000000 0.71417 0.935000 0.37517 0.661000 0.39034 2.751000 0.47508 0.425000 0.26087 -1.580000 0.00857 AGA TCGA-XD-AAUI-01A-42D-A40W-08 DHX36-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000353349.1 1 0 1 60 386 0 90 1 9.446982e-01 6 27 0 90 2 0 0 0 0 0 2 1 1.000000 60 384 0 90 2 -6.888420 1 0 121408 18 47 1 1 2 3 2.064228 0 0.210000 1.910000 0.220638 0.990000 0.990000 1.000000 1.000000 0.999196 0.990000 1 9.900000e-01 1 ANKRD28 23243 broad.mit.edu 37 3 15720986 15720986 + Missense_Mutation SNP G G A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr3:15720986G>A ENST00000399451.2 - 22 2751 c.2384C>T c.(2383-2385)gCc>gTc p.A795V ANKRD28_ENST00000497037.1_5'UTR|ANKRD28_ENST00000383777.1_Missense_Mutation_p.A828V NM_001195098.1|NM_001195099.1|NM_015199.3 NP_001182027.1|NP_001182028.1|NP_056014.2 O15084 ANR28_HUMAN ankyrin repeat domain 28 6 TACTTACACGGCACAATGCAA 0.378000 0 SO:0001583 missense ENST00000399451.2 0 1 hg19 CCDS46769.1 . . . . . . . . . . G 36 5.755213 0.96898 . . ENSG00000206560 ENST00000399451;ENST00000383777;ENST00000412318 T;T;T 0.79653 -1.29;-1.29;-1.29 6.06 6.06 0.98353 Ankyrin repeat-containing domain (4); 0.000000 0.85682 D 0.000000 D 0.91751 0.7391 M 0.87547 2.89 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 D 0.91917 0.5544 10 0.87932 D 0 . 20.6208 0.99490 0.0:0.0:1.0:0.0 . 795 O15084 ANR28_HUMAN V 795;828;795 ENSP00000382379:A795V;ENSP00000373287:A828V;ENSP00000397341:A795V ENSP00000373287:A828V A - 2 0 ANKRD28 15695990 1.000000 0.71417 0.997000 0.53966 0.919000 0.55068 9.869000 0.99810 2.882000 0.98803 0.655000 0.94253 GCC TCGA-XD-AAUI-01A-42D-A40W-08 ANKRD28-003 PUTATIVE basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000339758.1 0 0 0 5 182 0 47 0 1.484274e-01 0 21 0 47 2 0 0 0 0 0 2 1 0.935712 5 179 0 47 2 -3.019073 1 1 0 0 1 1 2 3 2.064228 0 0.210000 1.910000 0.220638 0.290000 0.100000 1.000000 0.250000 0.373596 0.290000 0 1.800000e-01 5.000000e-01 TLR9 54106 broad.mit.edu 37 3 52257685 52257685 + Missense_Mutation SNP C C T TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr3:52257685C>T ENST00000360658.2 - 2 1280 c.647G>A c.(646-648)cGc>cAc p.R216H TLR9_ENST00000494383.1_Silent_p.P369P|TLR9_ENST00000597542.1_Missense_Mutation_p.R240H NM_017442.3 NP_059138.1 Q9NR96 TLR9_HUMAN toll-like receptor 9 p.R216H(1) 30 Chloroquine(DB00608)|Hydroxychloroquine(DB01611) AGGCAGGTTGCGGGGCACCAC 0.632000 1 Substitution - Missense(1) SO:0001583 missense ENST00000360658.2 0 1 hg19 CCDS2848.1 . . . . . . . . . . C 15.78 2.934649 0.52866 . . ENSG00000239732 ENST00000360658 T 0.57273 0.41 5.57 1.0 0.19881 . 0.000000 0.37012 N 0.002294 T 0.45955 0.1368 N 0.11870 0.19 0.09310 N 1 P;D 0.89917 0.476;1.0 B;D 0.76575 0.057;0.988 T 0.23655 -1.0182 10 0.52906 T 0.07 . 3.8792 0.09071 0.3023:0.4532:0.0:0.2445 . 313;216 B4E0A1;Q9NR96 .;TLR9_HUMAN H 216 ENSP00000353874:R216H ENSP00000353874:R216H R - 2 0 TLR9 52232725 0.000000 0.05858 0.326000 0.25389 0.560000 0.35617 -0.644000 0.05415 0.263000 0.21812 0.655000 0.94253 CGC TCGA-XD-AAUI-01A-42D-A40W-08 TLR9-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000350203.1 1 0 0 6 123 0 32 0 0 0 1 0 32 2 0 0 0 0 0 2 1 0.962635 5 120 0 32 2 -3.149805 1 1 121364 1 23 1 1 2 3 2.064228 0 0.210000 1.910000 0.220638 0.500000 0.200000 1.000000 0.440000 0.552728 0.500000 0 3.200000e-01 8.100000e-01 ITIH3 3699 broad.mit.edu 37 3 52829637 52829637 + Missense_Mutation SNP G G A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr3:52829637G>A ENST00000449956.2 + 2 118 c.112G>A c.(112-114)Ggg>Agg p.G38R ITIH3_ENST00000416872.2_Missense_Mutation_p.G38R NM_002217.3 NP_002208.3 Q06033 ITIH3_HUMAN inter-alpha-trypsin inhibitor heavy chain 3 25 CCTCCCGGAAGGGGTAAGAAC 0.567000 0 SO:0001583 missense ENST00000449956.2 1 1 hg19 CCDS46845.1 . . . . . . . . . . G 9.970 1.225261 0.22457 . . ENSG00000162267 ENST00000398670;ENST00000536431;ENST00000273291;ENST00000416872;ENST00000449956 T;T 0.02631 4.22;4.88 4.17 2.37 0.29283 Vault protein inter-alpha-trypsin (1);Vault protein inter-alpha-trypsin, metazoa (1); 0.950075 0.08821 N 0.888844 T 0.01489 0.0048 N 0.03608 -0.345 0.34715 D 0.728176 B;B 0.09022 0.002;0.0 B;B 0.06405 0.002;0.001 T 0.40327 -0.9569 10 0.16420 T 0.52 -9.1591 6.4221 0.21750 0.2186:0.0:0.7814:0.0 . 38;38 E7ET33;Q06033 .;ITIH3_HUMAN R 38;38;33;38;38 ENSP00000413922:G38R;ENSP00000415769:G38R ENSP00000273291:G33R G + 1 0 ITIH3 52804677 0.984000 0.35163 0.991000 0.47740 0.958000 0.62258 0.768000 0.26590 0.716000 0.32124 0.591000 0.81541 GGG TCGA-XD-AAUI-01A-42D-A40W-08 ITIH3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000352668.2 1 0 1 12 56 0 16 0 7.369483e-01 0 14 0 16 2 0 0 0 0 0 2 1 0.999354 12 55 0 15 2 -19.991840 1 1 0 0 1 1 2 3 2.064228 0 0.210000 1.910000 0.220638 0.990000 0.950000 1.000000 1.000000 0.996052 0.990000 1 9.900000e-01 1 CDH18 1016 broad.mit.edu 37 5 19838947 19838947 + Missense_Mutation SNP C C T TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr5:19838947C>T ENST00000507958.1 - 5 1139 c.149G>A c.(148-150)cGt>cAt p.R50H CDH18_ENST00000506372.1_Missense_Mutation_p.R50H|CDH18_ENST00000274170.4_Missense_Mutation_p.R50H|CDH18_ENST00000382275.1_Missense_Mutation_p.R50H|CDH18_ENST00000511273.1_Missense_Mutation_p.R50H|CDH18_ENST00000502796.1_Missense_Mutation_p.R50H Q13634 CAD18_HUMAN cadherin 18, type 2 138 Lung NSC(1;0.00734)|all_lung(1;0.0197) CCTTTTGGGACGATGATGGAC 0.418000 0 SO:0001583 missense ENST00000507958.1 1 1 hg19 CCDS3889.1 . . . . . . . . . . C 33 5.262701 0.95399 . . ENSG00000145526 ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170;ENST00000506372;ENST00000502796;ENST00000511273 T;T;T;T;T;T 0.00585 6.39;6.39;6.39;6.39;6.39;6.39 5.93 5.93 0.95920 . 0.000000 0.85682 D 0.000000 T 0.04003 0.0112 M 0.87900 2.915 0.49582 D 0.999802 D;D 0.89917 1.0;1.0 D;D 0.91635 0.987;0.999 T 0.23013 -1.0200 9 . . . . 18.9006 0.92440 0.0:1.0:0.0:0.0 . 50;50 B4DHG6;Q13634 .;CAD18_HUMAN H 50 ENSP00000371710:R50H;ENSP00000425093:R50H;ENSP00000274170:R50H;ENSP00000424931:R50H;ENSP00000422138:R50H;ENSP00000425854:R50H . R - 2 0 CDH18 19874704 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 7.452000 0.80683 2.805000 0.96524 0.655000 0.94253 CGT TCGA-XD-AAUI-01A-42D-A40W-08 CDH18-005 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000366747.1 1 0 0 24 285 0 99 0 0 0 0 99 2 0 0 0 0 0 2 1 1.000000 24 282 0 99 2 -8.080602 1 1 0 0 1 0 0 0 1.939433 0 0.210000 1.910000 0.175365 0.700000 0.460000 0.990000 1.000000 0.720265 0.700000 0 5.700000e-01 8.500000e-01 DDX43 55510 broad.mit.edu 37 6 74104815 74104815 + Missense_Mutation SNP G G A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr6:74104815G>A ENST00000370336.4 + 1 345 c.187G>A c.(187-189)Gct>Act p.A63T OOEP_ENST00000370363.1_5'UTR|snoU13_ENST00000459178.1_RNA|DDX43_ENST00000539829.1_Missense_Mutation_p.A63T NM_018665.2 NP_061135.2 Q9NXZ2 DDX43_HUMAN DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 24 GGCCGTGGCCGCTGGTCACGA 0.617000 OREG0003900 type=REGULATORY REGION|Gene=BC024931|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay 0 SO:0001583 missense ENST00000370336.4 0 1 hg19 CCDS4977.1 . . . . . . . . . . G 10.38 1.335280 0.24253 . . ENSG00000080007 ENST00000370336;ENST00000539829 T;T 0.47528 2.45;0.84 3.78 -0.215 0.13157 . 1.510900 0.04111 N 0.314678 T 0.14013 0.0339 L 0.50333 1.59 0.09310 N 1 P 0.41420 0.749 B 0.28385 0.089 T 0.15150 -1.0447 10 0.48119 T 0.1 . 1.0278 0.01531 0.2122:0.1786:0.4258:0.1834 . 63 Q9NXZ2 DDX43_HUMAN T 63 ENSP00000359361:A63T;ENSP00000441636:A63T ENSP00000359361:A63T A + 1 0 DDX43 74161536 0.000000 0.05858 0.000000 0.03702 0.070000 0.16714 0.092000 0.15066 -0.064000 0.13043 -0.391000 0.06502 GCT TCGA-XD-AAUI-01A-42D-A40W-08 DDX43-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041219.3 0 0 0 11 185 1 40 0 0 0 1 40 2 0 0 0 0 0 2 1 0.997904 10 174 0 40 2 -13.957130 1 1 0 0 1 0 0 0 1.974494 0 0.210000 1.910000 0.189577 0.530000 0.280000 0.860000 0.520000 0.549996 0.530000 0 3.900000e-01 7.000000e-01 TRRAP 8295 broad.mit.edu 37 7 98533290 98533290 + Missense_Mutation SNP C C T TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr7:98533290C>T ENST00000359863.4 + 28 4312 c.4103C>T c.(4102-4104)gCg>gTg p.A1368V TRRAP_ENST00000446306.3_Missense_Mutation_p.A1367V|TRRAP_ENST00000355540.3_Missense_Mutation_p.A1368V NM_001244580.1 NP_001231509.1 Q9Y4A5 TRRAP_HUMAN transformation/transcription domain-associated protein 176 all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274) STAD - Stomach adenocarcinoma(171;0.215) TTACGAATTGCGGCATTAAGT 0.393000 0 SO:0001583 missense ENST00000359863.4 0 1 hg19 CCDS59066.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 24.2|24.2 4.501952|4.501952 0.85176|0.85176 .|. .|. ENSG00000196367|ENSG00000196367 ENST00000359863;ENST00000355540;ENST00000446306|ENST00000456197 T;T|. 0.66280|. -0.2;-0.2|. 6.17|6.17 6.17|6.17 0.99709|0.99709 Armadillo-type fold (1);|. 0.051888|. 0.85682|. D|. 0.000000|. T|T 0.43166|0.43166 0.1235|0.1235 N|N 0.02751|0.02751 -0.505|-0.505 0.80722|0.80722 D|D 1|1 D;D;D|. 0.62365|. 0.991;0.975;0.987|. P;B;P|. 0.48654|. 0.585;0.335;0.461|. T|T 0.40831|0.40831 -0.9542|-0.9542 10|5 0.32370|. T|. 0.25|. .|. 20.8794|20.8794 0.99867|0.99867 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. 1368;1082;1368|. Q9Y4A5-2;Q59FH1;Q9Y4A5|. .;.;TRRAP_HUMAN|. V|W 1368;1368;1366|1083 ENSP00000352925:A1368V;ENSP00000347733:A1368V|. ENSP00000347733:A1368V|. A|R +|+ 2|1 0|2 TRRAP|TRRAP 98371226|98371226 1.000000|1.000000 0.71417|0.71417 0.997000|0.997000 0.53966|0.53966 0.393000|0.393000 0.30537|0.30537 7.622000|7.622000 0.83099|0.83099 2.941000|2.941000 0.99782|0.99782 0.655000|0.655000 0.94253|0.94253 GCG|CGG TCGA-XD-AAUI-01A-42D-A40W-08 TRRAP-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000317978.1 0 0 0 5 229 0 70 0 4.306397e-03 0 4 0 70 2 0 0 0 0 0 2 1 0.935348 5 225 0 70 2 -2.972344 1 1 121410 3 25 1 1 2 3 2.061193 0 0.210000 1.910000 0.220638 0.230000 0.080000 1.000000 0.210000 0.320778 0.230000 0 1.400000e-01 4.100000e-01 COL14A1 7373 broad.mit.edu 37 8 121243763 121243763 + Missense_Mutation SNP G G A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr8:121243763G>A ENST00000297848.3 + 19 2525 c.2255G>A c.(2254-2256)cGg>cAg p.R752Q COL14A1_ENST00000537875.1_3'UTR|COL14A1_ENST00000247781.3_Missense_Mutation_p.R657Q|COL14A1_ENST00000309791.4_Missense_Mutation_p.R752Q|COL14A1_ENST00000432943.2_3'UTR NM_021110.1 NP_066933.1 collagen, type XIV, alpha 1 119 Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161) OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503) TCTAGCCTGCGGGTAAAATGG 0.438000 0 SO:0001583 missense ENST00000297848.3 1 1 hg19 CCDS34938.1 . . . . . . . . . . G 11.43 1.636123 0.29068 . . ENSG00000187955 ENST00000309791;ENST00000297848;ENST00000247781;ENST00000434620 T;T;T;T 0.56444 0.46;0.46;0.46;0.46 5.55 4.68 0.58851 Fibronectin, type III (4);Immunoglobulin-like fold (1); 0.400288 0.24985 N 0.034030 T 0.43322 0.1242 L 0.33093 0.98 0.80722 D 1 B;P 0.40794 0.189;0.729 B;B 0.42798 0.03;0.398 T 0.25467 -1.0131 10 0.31617 T 0.26 . 9.6977 0.40167 0.1605:0.0:0.8395:0.0 . 752;752 Q05707-2;Q05707 .;COEA1_HUMAN Q 752;752;657;565 ENSP00000311809:R752Q;ENSP00000297848:R752Q;ENSP00000247781:R657Q;ENSP00000409461:R565Q ENSP00000247781:R657Q R + 2 0 COL14A1 121312944 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 2.599000 0.46231 1.365000 0.46057 0.561000 0.74099 CGG TCGA-XD-AAUI-01A-42D-A40W-08 COL14A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000313657.2 1 0 0 11 241 0 54 0 8.081325e-01 0 69 0 54 2 0 0 0 0 0 2 1 0.998330 11 238 0 54 2 -2.558700 1 1 121410 3 32 1 0 0 0 1.976688 0 0.210000 1.910000 0.191319 0.410000 0.220000 0.680000 0.400000 0.432199 0.410000 0 3.000000e-01 5.500000e-01 KIAA1045 23349 broad.mit.edu 37 9 34971545 34971545 + Missense_Mutation SNP G G A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chr9:34971545G>A ENST00000242315.3 + 2 332 c.250G>A c.(250-252)Gat>Aat p.D84N KIAA1045_ENST00000544237.1_Missense_Mutation_p.D84N|KIAA1045_ENST00000476115.2_Intron NM_015297.1 NP_056112.1 Q9UPV7 K1045_HUMAN KIAA1045 19 LUSC - Lung squamous cell carcinoma(32;0.00575) GCGGCTCCGAGATGGGCGCGG 0.632000 0 SO:0001583 missense ENST00000242315.3 1 1 hg19 CCDS43796.1 . . . . . . . . . . g 36 5.915546 0.97099 . . ENSG00000122733 ENST00000544237;ENST00000242315 . . . 6.03 6.03 0.97812 . 0.000000 0.85682 D 0.000000 T 0.78240 0.4252 M 0.64997 1.995 0.80722 D 1 D 0.89917 1.0 D 0.87578 0.998 T 0.75127 -0.3427 8 . . . -3.6405 19.545 0.95291 0.0:0.0:1.0:0.0 . 84 Q9UPV7 K1045_HUMAN N 84 . . D + 1 0 KIAA1045 34961545 1.000000 0.71417 1.000000 0.80357 0.949000 0.60115 9.258000 0.95555 2.861000 0.98227 0.655000 0.94253 GAT TCGA-XD-AAUI-01A-42D-A40W-08 KIAA1045-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052256.2 1 0 0 27 452 0 137 0 0 0 0 137 2 0 0 0 0 0 2 1 1.000000 25 436 0 136 2 -20.000000 1 1 0 0 1 0 1 1 1.878350 1 0.210000 1.910000 0.117318 0.470000 0.320000 0.660000 0.470000 0.488410 0.470000 0 3.900000e-01 5.700000e-01 NRK 203447 broad.mit.edu 37 X 105150491 105150491 + Missense_Mutation SNP C C G TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chrX:105150491C>G ENST00000243300.9 + 11 1233 c.930C>G c.(928-930)caC>caG p.H310Q NRK_ENST00000428173.2_Missense_Mutation_p.H310Q NM_198465.2 NP_940867.2 Q7Z2Y5 NRK_HUMAN Nik related kinase 76 TGCTTCAACACCCATTTGTTC 0.343000 HNSCC(51;0.14) 0 SO:0001583 missense ENST00000243300.9 0 1 hg19 . . . . . . . . . . C 12.96 2.093751 0.36952 . . ENSG00000123572 ENST00000243300;ENST00000428173 T;T 0.34275 1.37;1.37 5.27 -2.09 0.07232 Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); 0.000000 0.45126 D 0.000386 T 0.57961 0.2089 M 0.86268 2.805 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 T 0.61734 -0.7002 10 0.87932 D 0 . 11.5948 0.50966 0.0:0.2133:0.0:0.7867 . 310 Q7Z2Y5 NRK_HUMAN Q 310 ENSP00000434830:H310Q;ENSP00000438378:H310Q ENSP00000434830:H310Q H + 3 2 NRK 105037147 0.998000 0.40836 0.981000 0.43875 0.125000 0.20455 0.774000 0.26675 -0.459000 0.07013 -0.192000 0.12808 CAC TCGA-XD-AAUI-01A-42D-A40W-08 NRK-001 KNOWN non_canonical_conserved|basic|appris_candidate protein_coding protein_coding OTTHUMT00000106480.6 0 0 0 6 83 0 19 0 0 0 0 19 2 0 0 0 0 0 2 1 0.966713 6 83 0 19 2 -10.721740 1 1 0 0 1 0 1 1 0.210000 1.910000 0.210000 0.660000 0.280000 1.000000 1.000000 0.681621 0.660000 0 4.400000e-01 9.400000e-01 MORC4 79710 broad.mit.edu 37 X 106229348 106229348 + Missense_Mutation SNP G G A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chrX:106229348G>A ENST00000355610.4 - 4 665 c.391C>T c.(391-393)Cgg>Tgg p.R131W MORC4_ENST00000535534.1_Intron|MORC4_ENST00000255495.7_Missense_Mutation_p.R131W NM_001085354.2|NM_024657.4 NP_001078823.1|NP_078933.3 Q8TE76 MORC4_HUMAN MORC family CW-type zinc finger 4 28 TTTCCTAGCCGCATGGAGCCT 0.473000 0 SO:0001583 missense ENST00000355610.4 0 1 hg19 CCDS14525.2 . . . . . . . . . . G 27.5 4.835024 0.91117 . . ENSG00000133131 ENST00000355610;ENST00000255495 T;T 0.74315 -0.83;-0.83 5.35 5.35 0.76521 ATPase-like, ATP-binding domain (3); 0.000000 0.85682 D 0.000000 D 0.87834 0.6277 M 0.87381 2.88 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;0.999 D 0.89717 0.3916 10 0.87932 D 0 -9.9831 15.875 0.79154 0.0:0.0:1.0:0.0 . 131;131 A1YR23;Q8TE76 .;MORC4_HUMAN W 131 ENSP00000347821:R131W;ENSP00000255495:R131W ENSP00000255495:R131W R - 1 2 MORC4 106116004 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 7.562000 0.82300 2.565000 0.86533 0.600000 0.82982 CGG TCGA-XD-AAUI-01A-42D-A40W-08 MORC4-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000057816.3 0 0 0 11 673 0 163 0 6.494867e-03 0 7 0 163 2 0 0 0 0 0 2 1 0.998175 11 661 0 159 2 -2.046025 0 1 0 0 1 0 1 1 0.210000 1.910000 0.210000 0.150000 0.070000 0.260000 0.160000 0.165666 0.150000 0 1.100000e-01 2.100000e-01 FRMPD4 9758 broad.mit.edu 37 X 12704277 12704277 + Missense_Mutation SNP A A G TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chrX:12704277A>G ENST00000380682.1 + 7 1141 c.635A>G c.(634-636)aAt>aGt p.N212S NM_014728.3 NP_055543.2 Q14CM0 FRPD4_HUMAN FERM and PDZ domain containing 4 22 TATCTGGAAAATGGGCAGACC 0.398000 0 SO:0001583 missense ENST00000380682.1 0 1 hg19 CCDS35201.1 . . . . . . . . . . A 22.8 4.335472 0.81801 . . ENSG00000169933 ENST00000380682;ENST00000429478;ENST00000304087 T 0.76060 -0.99 5.33 5.33 0.75918 Band 4.1 domain (1);FERM domain (1); 0.000000 0.85682 D 0.000000 D 0.85106 0.5621 M 0.78456 2.415 0.47905 D 0.999546 P;P 0.51537 0.946;0.869 D;P 0.64506 0.926;0.805 D 0.86474 0.1787 10 0.56958 D 0.05 . 14.4062 0.67083 1.0:0.0:0.0:0.0 . 204;212 B7ZLE1;Q14CM0 .;FRPD4_HUMAN S 212;203;201 ENSP00000370057:N212S ENSP00000304583:N201S N + 2 0 FRMPD4 12614198 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 8.850000 0.92190 1.781000 0.52344 0.486000 0.48141 AAT TCGA-XD-AAUI-01A-42D-A40W-08 FRMPD4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055771.1 0 0 0 10 367 0 72 0 0 0 0 72 2 0 0 0 0 0 2 1 0.996672 10 361 0 72 2 -3.456681 1 1 0 0 1 0 1 1 0.210000 1.910000 0.210000 0.250000 0.130000 0.440000 0.250000 0.273651 0.250000 0 1.800000e-01 3.500000e-01 F8 2157 broad.mit.edu 37 X 154134766 154134766 + Missense_Mutation SNP G G A TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chrX:154134766G>A ENST00000360256.4 - 15 5502 c.5302C>T c.(5302-5304)Cgt>Tgt p.R1768C NM_000132.3 NP_000123.1 P00451 FA8_HUMAN coagulation factor VIII, procoagulant component 120 all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055) AGTTCTCCACGGTATAAGGGC 0.423000 0 GRCh37 CM055192 F8 M SO:0001583 missense ENST00000360256.4 1 1 hg19 CCDS35457.1 . . . . . . . . . . G 19.82 3.899120 0.72754 . . ENSG00000185010 ENST00000360256 D 0.99287 -5.69 5.6 5.6 0.85130 Cupredoxin (2); 0.161419 0.53938 D 0.000042 D 0.99471 0.9812 M 0.87971 2.92 0.58432 D 0.999999 D 0.89917 1.0 D 0.83275 0.996 D 0.98619 1.0666 10 0.87932 D 0 -8.5673 17.091 0.86622 0.0:0.0:1.0:0.0 . 1768 P00451 FA8_HUMAN C 1768 ENSP00000353393:R1768C ENSP00000353393:R1768C R - 1 0 F8 153787960 0.963000 0.33076 1.000000 0.80357 0.988000 0.76386 3.384000 0.52478 2.350000 0.79820 0.600000 0.82982 CGT TCGA-XD-AAUI-01A-42D-A40W-08 F8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000058869.4 1 0 0 33 567 0 138 0 0 0 0 138 2 0 0 0 0 0 2 1 1.000000 33 558 0 136 2 -2.239660 0 1 0 0 1 0 1 1 0.210000 1.910000 0.210000 0.520000 0.360000 0.710000 0.520000 0.534513 0.520000 0 4.400000e-01 6.200000e-01 TMLHE 55217 broad.mit.edu 37 X 154741370 154741370 + Missense_Mutation SNP C C T TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chrX:154741370C>T ENST00000334398.3 - 5 867 c.722G>A c.(721-723)cGg>cAg p.R241Q TMLHE-AS1_ENST00000452506.1_RNA|TMLHE_ENST00000369439.4_Missense_Mutation_p.R241Q NM_018196.3 NP_060666.1 Q9NVH6 TMLH_HUMAN trimethyllysine hydroxylase, epsilon 20 all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214) Succinic acid(DB00139)|Vitamin C(DB00126) GTCAGTGTGCCGATCCAGAGC 0.413000 0 SO:0001583 missense ENST00000334398.3 0 1 hg19 CCDS14768.1 0 0.0 0 0.0 0 0.0 0 0.0 0 0.0 C 17.79 3.476247 0.63737 0.0 4.46E-4 ENSG00000185973 ENST00000334398;ENST00000369439 D;D 0.82081 -1.57;-1.57 3.64 2.77 0.32553 . 0.125013 0.53938 N 0.000049 D 0.82318 0.5011 L 0.44542 1.39 0.47949 D 0.999558 D;D;D 0.71674 0.997;0.998;0.998 P;P;P 0.57960 0.756;0.83;0.778 T 0.77275 -0.2648 10 0.29301 T 0.29 -7.3997 8.53 0.33329 0.0:0.8754:0.0:0.1246 . 241;241;241 Q9NVH6-2;A8K6M9;Q9NVH6 .;.;TMLH_HUMAN Q 241 ENSP00000335261:R241Q;ENSP00000358447:R241Q ENSP00000335261:R241Q R - 2 0 TMLHE 154394564 0.999000 0.42202 0.989000 0.46669 0.855000 0.48748 4.043000 0.57354 0.507000 0.28148 -0.322000 0.08575 CGG TCGA-XD-AAUI-01A-42D-A40W-08 TMLHE-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000058817.1 0 0 0 7 527 0 94 0 1.542070e-01 0 46 0 94 2 0 0 0 0 0 2 1 0.979521 7 518 0 93 2 -2.391118 0 1 121384 25 48 1 0 1 1 0.210000 1.910000 0.210000 0.130000 0.050000 0.240000 0.120000 0.141130 0.130000 0 8.000000e-02 1.900000e-01 USP9X 8239 broad.mit.edu 37 X 41029282 41029282 + Nonsense_Mutation SNP C C T TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chrX:41029282C>T ENST00000324545.8 + 19 3304 c.2671C>T c.(2671-2673)Cga>Tga p.R891* USP9X_ENST00000378308.2_Nonsense_Mutation_p.R891* NM_001039590.2|NM_001039591.2 NP_001034679.2|NP_001034680.2 Q93008 USP9X_HUMAN ubiquitin specific peptidase 9, X-linked 87 TTTTGTAGTTCGATTTCCAAA 0.408000 Ovarian(172;1807 2695 35459 49286) 0 SO:0001587 stop_gained ENST00000324545.8 0 1 hg19 CCDS43930.1 . . . . . . . . . . c 41 8.770551 0.98948 . . ENSG00000124486 ENST00000378308;ENST00000324545 . . . 5.85 4.05 0.47172 . 0.104565 0.64402 D 0.000005 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 . 8.21 0.31478 0.2778:0.6494:0.0:0.0728 . . . . X 891 . ENSP00000316357:R891X R + 1 2 USP9X 40914226 1.000000 0.71417 1.000000 0.80357 0.976000 0.68499 3.205000 0.51090 0.575000 0.29434 -0.178000 0.13098 CGA TCGA-XD-AAUI-01A-42D-A40W-08 USP9X-003 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000056250.4 1 0 0 39 550 0 127 0 1.690497e-01 0 11 0 127 2 0 0 0 0 0 2 1 1.000000 39 537 0 126 2 -3.142698 1 1 0 0 1 0 1 1 0.210000 1.910000 0.210000 0.620000 0.450000 0.830000 0.620000 0.640451 0.620000 0 5.300000e-01 7.300000e-01 CYSLTR1 10800 broad.mit.edu 37 X 77528527 77528527 + Silent SNP G G T TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chrX:77528527G>T ENST00000373304.3 - 3 1009 c.717C>A c.(715-717)acC>acA p.T239T NM_001282187.1|NM_001282188.1|NM_006639.3 NP_001269116.1|NP_001269117.1|NP_006630.1 Q9Y271 CLTR1_HUMAN cysteinyl leukotriene receptor 1 14 Cinalukast(DB00587)|Montelukast(DB00471)|Nedocromil(DB00716)|Pranlukast(DB01411)|Zafirlukast(DB00549) AAAAGGCAGCGGTCACGACCA 0.338000 0 SO:0001819 synonymous_variant ENST00000373304.3 1 1 hg19 CCDS14439.1 TCGA-XD-AAUI-01A-42D-A40W-08 CYSLTR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057315.1 0 0 0 12 321 0 63 0 9.083371e-03 0 4 0 63 2 0 0 0 0 0 2 1 0.999042 12 314 0 62 2 -2.695737 1 1 0 0 1 0 1 1 0.210000 1.910000 0.210000 0.350000 0.190000 0.560000 0.340000 0.365405 0.350000 0 2.600000e-01 4.600000e-01 PCDH19 57526 broad.mit.edu 37 X 99551638 99551638 + Missense_Mutation SNP C C G TCGA-XD-AAUI-01A-42D-A40W-08 TCGA-XD-AAUI-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx d8c4cafb-cf40-4343-9fab-78b2e1914ad1 768e3081-1fbc-418f-9000-9721e854cc35 g.chrX:99551638C>G ENST00000373034.4 - 6 4759 c.3084G>C c.(3082-3084)gaG>gaC p.E1028D PCDH19_ENST00000255531.7_Missense_Mutation_p.E981D|PCDH19_ENST00000420881.2_Missense_Mutation_p.E980D|PCDH19_ENST00000464981.1_5'Flank NM_001184880.1 NP_001171809.1 Q8TAB3 PCD19_HUMAN protocadherin 19 68 TAGGCCTCTCCTCAGCCGGGT 0.577000 0 SO:0001583 missense ENST00000373034.4 1 1 hg19 CCDS55462.1 . . . . . . . . . . C 4.652 0.121262 0.08881 . . ENSG00000165194 ENST00000420881;ENST00000373034;ENST00000255531 T;T;T 0.54071 0.59;0.64;0.6 5.73 3.95 0.45737 . 0.115763 0.56097 D 0.000025 T 0.34279 0.0892 L 0.34521 1.04 0.47862 D 0.999531 B;B;B 0.09022 0.002;0.002;0.001 B;B;B 0.09377 0.003;0.004;0.002 T 0.10382 -1.0632 10 0.14656 T 0.56 . 5.4949 0.16797 0.14:0.6354:0.0:0.2245 . 1028;981;980 Q8TAB3;Q8TAB3-2;E9PAM6 PCD19_HUMAN;.;. D 980;1028;981 ENSP00000400327:E980D;ENSP00000362125:E1028D;ENSP00000255531:E981D ENSP00000255531:E981D E - 3 2 PCDH19 99438294 0.998000 0.40836 1.000000 0.80357 0.996000 0.88848 0.647000 0.24812 1.181000 0.42912 0.600000 0.82982 GAG TCGA-XD-AAUI-01A-42D-A40W-08 PCDH19-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000057479.2 1 0 0 10 234 0 45 0 0 0 0 45 2 0 0 0 0 0 2 1 0.996862 9 232 0 44 2 -3.199164 1 1 0 0 1 0 1 1 0.210000 1.910000 0.210000 0.400000 0.200000 0.670000 0.380000 0.419303 0.400000 0 2.900000e-01 5.400000e-01