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 ABI2 10152 broad.mit.edu 37 2 204267424 204267427 + Frame_Shift_Del DEL ATGA ATGA - TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr2:204267424_204267427delATGA ENST00000422511.2 + 9 1091_1094 c.1060_1063delATGA c.(1060-1065)atgaatfs p.MN354fs ABI2_ENST00000430418.1_Frame_Shift_Del_p.MN332fs|ABI2_ENST00000295851.5_Frame_Shift_Del_p.MN387fs|RAPH1_ENST00000457812.1_Intron|ABI2_ENST00000261016.6_Frame_Shift_Del_p.MN275fs|ABI2_ENST00000261017.5_Frame_Shift_Del_p.MN320fs|ABI2_ENST00000261018.7_Frame_Shift_Del_p.MN173fs|ABI2_ENST00000430574.1_3'UTR|ABI2_ENST00000424558.1_Frame_Shift_Del_p.MN381fs Q9NYB9 ABI2_HUMAN abl-interactor 2 15 TCAGAATCAGATGAATGGAGGACC 0.407000 0 SO:0001589 frameshift_variant ENST00000422511.2 0 1 hg19 TCGA-HZ-A4BH-01A-11D-A26I-08 ABI2-007 NOVEL not_organism_supported|basic|appris_candidate|exp_conf protein_coding protein_coding OTTHUMT00000336179.2 1 0 0 65 566 0 52 1 9.111372e-01 3 35 0 52 2 0 0 0 0 0 0 1 1.000000 80 574 0 52 2 -20.000000 1 1 0 0 1 1 2 3 2.064020 0 0.310000 1.820000 0.312132 0.660000 0.520000 0.850000 0.670000 0.675619 0.660000 0 5.800000e-01 7.500000e-01 RSU1 6251 broad.mit.edu 37 10 16794556 16794556 + Missense_Mutation SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr10:16794556C>T ENST00000377921.3 - 6 881 c.580G>A c.(580-582)Gtt>Att p.V194I RSU1_ENST00000345264.5_Missense_Mutation_p.V194I|RSU1_ENST00000602389.1_Missense_Mutation_p.V141I|RSU1_ENST00000464074.2_5'UTR Q15404 RSU1_HUMAN Ras suppressor protein 1 14 GGGGGCAGAACGGTGAGGCGG 0.468000 0 SO:0001583 missense ENST00000377921.3 1 1 hg19 CCDS7112.1 . . . . . . . . . . C 21.9 4.212821 0.79352 . . ENSG00000148484 ENST00000345264;ENST00000377921;ENST00000377911 T;T 0.09255 3.0;3.0 5.26 5.26 0.73747 . 0.000000 0.85682 D 0.000000 T 0.19446 0.0467 N 0.20610 0.595 0.80722 D 1 D;D 0.76494 0.981;0.999 P;D 0.63703 0.899;0.917 T 0.04017 -1.0984 10 0.42905 T 0.14 -5.5557 18.8996 0.92437 0.0:1.0:0.0:0.0 . 194;194 B0YJ73;Q15404 .;RSU1_HUMAN I 194;194;141 ENSP00000339521:V194I;ENSP00000367154:V194I ENSP00000339521:V194I V - 1 0 RSU1 16834562 1.000000 0.71417 0.972000 0.41901 0.836000 0.47400 7.456000 0.80751 2.471000 0.83476 0.585000 0.79938 GTT TCGA-HZ-A4BH-01A-11D-A26I-08 RSU1-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047006.1 1 0 1 57 668 1 101 1 9.913823e-01 41 251 1 101 12 0 0 0 0 0 2 1 1.000000 53 649 0 97 2 -13.148030 1 1 121410 2 34 1 0 1 1 1.909855 0 0.310000 1.820000 0.250774 0.460000 0.350000 0.590000 0.460000 0.472071 0.460000 0 4.000000e-01 5.300000e-01 ANKRD30A 91074 broad.mit.edu 37 10 37506771 37506771 + Missense_Mutation SNP A A G TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr10:37506771A>G ENST00000602533.1 + 33 3163 c.3064A>G c.(3064-3066)Ata>Gta p.I1022V ANKRD30A_ENST00000374660.1_Missense_Mutation_p.I1141V|ANKRD30A_ENST00000361713.1_Missense_Mutation_p.I1022V Q9BXX3 AN30A_HUMAN ankyrin repeat domain 30A 158 AATACAAGATATAGAATTGAA 0.274000 0 SO:0001583 missense ENST00000602533.1 1 1 hg19 . . . . . . . . . . a 0.004 -2.272481 0.00257 . . ENSG00000148513 ENST00000361713;ENST00000374660 T;T 0.16457 2.34;2.34 2.78 -5.55 0.02536 . . . . . T 0.05640 0.0148 N 0.16368 0.405 0.09310 N 1 B 0.06786 0.001 B 0.01281 0.0 T 0.41215 -0.9521 9 0.02654 T 1 . 1.7614 0.02992 0.2387:0.2515:0.3726:0.1371 . 1078 Q9BXX3 AN30A_HUMAN V 1022;1141 ENSP00000354432:I1022V;ENSP00000363792:I1141V ENSP00000354432:I1022V I + 1 0 ANKRD30A 37546777 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -1.305000 0.02738 -1.298000 0.02348 -0.435000 0.05868 ATA TCGA-HZ-A4BH-01A-11D-A26I-08 ANKRD30A-001 KNOWN NMD_exception|basic|appris_principal protein_coding protein_coding OTTHUMT00000047588.2 1 0 1 29 161 0 18 0 0 0 1 0 18 2 0 0 0 0 0 2 1 1.000000 29 160 0 18 2 -20.000000 1 1 0 0 1 0 1 1 1.912229 0 0.310000 1.820000 0.272804 0.920000 0.650000 1.000000 1.000000 0.903843 0.920000 1 7.800000e-01 1 FRMPD2 143162 broad.mit.edu 37 10 49457187 49457187 + Silent SNP G G A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr10:49457187G>A ENST00000374201.3 - 3 488 c.186C>T c.(184-186)gcC>gcT p.A62A FRMPD2_ENST00000407470.4_Silent_p.A53A|FRMPD2_ENST00000305531.3_Silent_p.A60A NM_001018071.3|NM_001042512.2 NP_001018081|NP_001035977.2 Q68DX3 FRPD2_HUMAN FERM and PDZ domain containing 2 66 CAGAAAGCAGGGCTGACCAGG 0.552000 0 SO:0001819 synonymous_variant ENST00000374201.3 1 1 hg19 CCDS31195.1 TCGA-HZ-A4BH-01A-11D-A26I-08 FRMPD2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047923.3 1 0 1 39 179 0 77 0 0 0 0 77 2 0 0 0 0 0 2 1 1.000000 39 179 0 77 2 -20.000000 1 1 0 0 1 0 1 1 1.912229 0 0.310000 1.820000 0.272804 0.990000 0.800000 1.000000 1.000000 0.976317 0.990000 1 9.300000e-01 1 CHAT 1103 broad.mit.edu 37 10 50833616 50833616 + Missense_Mutation SNP G G A rs146236256 TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr10:50833616G>A ENST00000337653.2 + 6 1003 c.850G>A c.(850-852)Ggc>Agc p.G284S CHAT_ENST00000455728.2_Missense_Mutation_p.G166S|CHAT_ENST00000395559.2_Missense_Mutation_p.G166S|CHAT_ENST00000395562.2_Missense_Mutation_p.G202S|CHAT_ENST00000339797.1_Missense_Mutation_p.G166S|CHAT_ENST00000351556.3_Missense_Mutation_p.G166S 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) CCGGCTCCCCGGCCATACCCA 0.592000 0 SO:0001583 missense ENST00000337653.2 1 1 hg19 CCDS7232.1 . . . . . . . . . . G 24.0 4.486814 0.84854 0.0 1.16E-4 ENSG00000070748 ENST00000339797;ENST00000351556;ENST00000395559;ENST00000337653;ENST00000395562;ENST00000455728 D;D;D;D;D;D 0.92099 -2.97;-2.97;-2.97;-2.97;-2.97;-2.97 5.23 5.23 0.72850 . 0.000000 0.85682 D 0.000000 D 0.96589 0.8887 M 0.87758 2.905 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.73708 0.975;0.981 D 0.97201 0.9864 10 0.87932 D 0 -30.9801 18.8 0.92013 0.0:0.0:1.0:0.0 . 166;284 F8W8I2;P28329 .;CLAT_HUMAN S 166;166;166;284;202;166 ENSP00000343486:G166S;ENSP00000345878:G166S;ENSP00000378926:G166S;ENSP00000337103:G284S;ENSP00000378929:G202S;ENSP00000390521:G166S ENSP00000337103:G284S G + 1 0 CHAT 50503622 1.000000 0.71417 0.836000 0.33094 0.196000 0.23810 9.852000 0.99516 2.439000 0.82584 0.411000 0.27672 GGC TCGA-HZ-A4BH-01A-11D-A26I-08 CHAT-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000047997.1 1 0 1 15 71 0 26 0 0 0 1 0 26 2 0 0 0 0 0 2 1 0.999916 15 70 0 26 2 -10.979210 1 1 121400 10 38 1 0 1 1 1.912229 0 0.310000 1.820000 0.272804 0.990000 0.640000 1.000000 1.000000 0.939377 0.990000 1 8.300000e-01 1 GRID1 2894 broad.mit.edu 37 10 87362370 87362370 + Missense_Mutation SNP G G A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr10:87362370G>A ENST00000327946.7 - 16 2775 c.2690C>T c.(2689-2691)tCg>tTg p.S897L GRID1_ENST00000536331.1_Missense_Mutation_p.S468L|RP11-93H12.2_ENST00000443311.1_RNA|GRID1_ENST00000552278.2_5'UTR NM_017551.2 NP_060021.1 Q9ULK0 GRID1_HUMAN glutamate receptor, ionotropic, delta 1 106 GAGCTCAATCGACGCTGGGGA 0.592000 Multiple Myeloma(13;0.14) 0 SO:0001583 missense ENST00000327946.7 1 1 hg19 CCDS31236.1 . . . . . . . . . . G 18.84 3.708583 0.68615 . . ENSG00000182771 ENST00000327946;ENST00000536331 T;T 0.16457 2.59;2.34 5.74 4.84 0.62591 . 0.047518 0.85682 D 0.000000 T 0.34424 0.0897 L 0.55481 1.735 0.58432 D 0.999998 D 0.64830 0.994 D 0.64042 0.921 T 0.05971 -1.0853 10 0.62326 D 0.03 . 13.749 0.62894 0.0737:0.0:0.9263:0.0 . 897 Q9ULK0 GRID1_HUMAN L 897;468 ENSP00000330148:S897L;ENSP00000444455:S468L ENSP00000330148:S897L S - 2 0 GRID1 87352350 1.000000 0.71417 0.619000 0.29118 0.608000 0.37181 9.869000 0.99810 1.430000 0.47334 -0.218000 0.12543 TCG TCGA-HZ-A4BH-01A-11D-A26I-08 GRID1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000049148.3 1 0 1 28 120 0 26 0 7.718569e-01 0 14 0 26 2 0 0 0 0 0 2 1 1.000000 28 119 0 26 2 -20.000000 1 1 121410 1 25 1 0 1 1 1.912229 0 0.310000 1.820000 0.272804 0.990000 0.800000 1.000000 1.000000 0.980450 0.990000 1 9.600000e-01 1 OR5L1 219437 broad.mit.edu 37 11 55579400 55579400 + Missense_Mutation SNP C C T rs144467940 by1000genomes TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr11:55579400C>T ENST00000333973.2 + 1 547 c.458C>T c.(457-459)aCg>aTg p.T153M NM_001004738.1 NP_001004738.1 Q8NGL2 OR5L1_HUMAN olfactory receptor, family 5, subfamily L, member 1 78 all_epithelial(135;0.208) TTCTGTGGGACGGTGTGTTCT 0.453000 0 SO:0001583 missense ENST00000333973.2 1 1 hg19 CCDS31509.1 6 0.0027472527472527475 0 0.0 0 0.0 0 0.0 6 0.0079155672823219 c 9.351 1.065546 0.20067 . . ENSG00000186117 ENST00000333973 T 0.00091 8.74 3.98 -3.09 0.05331 GPCR, rhodopsin-like superfamily (1); 0.729368 0.12300 N 0.481164 T 0.00073 0.0002 N 0.04705 -0.18 0.09310 N 1 B 0.25105 0.118 B 0.28991 0.097 T 0.09292 -1.0681 10 0.44086 T 0.13 -0.6723 10.911 0.47108 0.0:0.2882:0.0:0.7118 . 153 Q8NGL2 OR5L1_HUMAN M 153 ENSP00000335529:T153M ENSP00000335529:T153M T + 2 0 OR5L1 55335976 0.000000 0.05858 0.000000 0.03702 0.520000 0.34377 -0.308000 0.08156 -0.861000 0.04094 -0.516000 0.04426 ACG TCGA-HZ-A4BH-01A-11D-A26I-08 OR5L1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391514.1 1 0 1 168 871 0 108 0 0 0 0 108 2 0 0 0 0 0 2 1 1.000000 168 866 0 108 2 -20.000000 1 1 121410 218 59 1 1 2 3 2.063691 0 0.310000 1.820000 0.312132 0.990000 0.900000 1.000000 1.000000 0.988936 0.990000 1 9.700000e-01 1 RARRES3 5920 broad.mit.edu 37 11 63307030 63307030 + Missense_Mutation SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr11:63307030C>T ENST00000255688.3 + 2 100 c.52C>T c.(52-54)Cgc>Tgc p.R18C RARRES3_ENST00000439013.2_Missense_Mutation_p.R18C|RARRES3_ENST00000537871.1_Intron|RARRES3_ENST00000354445.2_Missense_Mutation_p.R18C NM_004585.3 NP_004576.2 Q9UL19 HRSL4_HUMAN retinoic acid receptor responder (tazarotene induced) 3 6 TGAGATTTTCCGCCTTGGCTA 0.483000 0 SO:0001583 missense ENST00000255688.3 1 1 hg19 CCDS41662.1 . . . . . . . . . . C 15.22 2.768386 0.49680 . . ENSG00000133321 ENST00000439013;ENST00000255688;ENST00000354445 T;T;T 0.46063 0.88;0.88;0.88 4.35 2.47 0.30058 . 0.263285 0.27636 N 0.018488 T 0.65523 0.2699 M 0.90369 3.11 0.09310 N 0.999993 D 0.89917 1.0 D 0.73380 0.98 T 0.57388 -0.7820 10 0.87932 D 0 . 8.3897 0.32520 0.0:0.8054:0.0:0.1946 . 18 Q9UL19 TIG3_HUMAN C 18 ENSP00000402943:R18C;ENSP00000255688:R18C;ENSP00000346431:R18C ENSP00000255688:R18C R + 1 0 RARRES3 63063606 0.005000 0.15991 0.002000 0.10522 0.002000 0.02628 1.900000 0.39828 0.591000 0.29711 -0.251000 0.11542 CGC TCGA-HZ-A4BH-01A-11D-A26I-08 RARRES3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000396629.1 1 0 0 31 419 0 57 1 1 91 560 0 57 2 0 0 0 0 0 2 1 1.000000 31 416 0 57 2 -2.774718 1 1 121406 8 42 1 1 2 3 2.063691 0 0.310000 1.820000 0.312132 0.440000 0.310000 0.640000 0.440000 0.461257 0.440000 0 3.700000e-01 5.400000e-01 NRXN2 9379 broad.mit.edu 37 11 64434761 64434761 + Missense_Mutation SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr11:64434761C>T ENST00000377551.1 - 8 1970 c.1759G>A c.(1759-1761)Gag>Aag p.E587K NRXN2_ENST00000265459.6_Missense_Mutation_p.E587K|NRXN2_ENST00000377559.3_Missense_Mutation_p.E556K|NRXN2_ENST00000409571.1_Missense_Mutation_p.E580K Q9P2S2 NRX2A_HUMAN neurexin 2 p.E587K(1) 71 TGACACCACTCGCCATCATTG 0.592000 1 Substitution - Missense(1) SO:0001583 missense ENST00000377551.1 1 1 hg19 CCDS8077.1 . . . . . . . . . . C 31 5.087169 0.94100 . . ENSG00000110076 ENST00000377551;ENST00000377559;ENST00000265459;ENST00000345863;ENST00000409571 T;T;T;T 0.77229 -1.08;-1.08;-1.08;-1.08 4.61 4.61 0.57282 Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1); 0.000000 0.42821 U 0.000657 T 0.80491 0.4633 L 0.28115 0.83 0.58432 D 0.999999 D;D;D 0.76494 0.998;0.995;0.999 D;D;D 0.69479 0.964;0.936;0.909 T 0.83054 -0.0151 10 0.72032 D 0.01 . 14.9631 0.71171 0.0:1.0:0.0:0.0 . 556;587;333 Q9P2S2-2;Q9P2S2;E7EV67 .;NRX2A_HUMAN;. K 587;556;587;556;580 ENSP00000366774:E587K;ENSP00000366782:E556K;ENSP00000265459:E587K;ENSP00000386416:E580K ENSP00000265459:E587K E - 1 0 NRXN2 64191337 1.000000 0.71417 1.000000 0.80357 0.991000 0.79684 7.637000 0.83313 2.383000 0.81215 0.448000 0.29417 GAG TCGA-HZ-A4BH-01A-11D-A26I-08 NRXN2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000104967.3 1 0 1 81 492 0 120 0 0 0 1 0 120 2 0 0 0 0 0 2 1 1.000000 80 486 0 118 2 -3.142769 1 1 0 0 1 1 2 3 2.063691 0 0.310000 1.820000 0.312132 0.910000 0.730000 1.000000 1.000000 0.909411 0.910000 1 8.200000e-01 1 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr12:25398284C>T ENST00000256078.4 - 2 98 c.35G>A c.(34-36)gGt>gAt p.G12D KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 0 1 hg19 CCDS8703.1 . . . . . . . . . . C 23.4 4.409094 0.83340 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.85919 0.5809 M 0.91818 3.245 0.80722 D 1 B;P 0.35714 0.385;0.517 B;B 0.41619 0.257;0.361 D 0.87870 0.2670 10 0.87932 D 0 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN D 12 ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D ENSP00000256078:G12D G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-HZ-A4BH-01A-11D-A26I-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 21 90 0 10 1 8.023678e-01 11 4 0 10 2 1 1 28 131 0 389 2 1 0.999999 21 89 0 10 2 -14.884310 1 1 121404 2 44 1 0 1 1 1.717647 1 0.310000 1.820000 0.183432 0.870000 0.620000 1.000000 0.990000 0.862398 0.870000 1 7.500000e-01 9.700000e-01 AGAP2 116986 broad.mit.edu 37 12 58127884 58127884 + Missense_Mutation SNP G G A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr12:58127884G>A ENST00000547588.1 - 5 1473 c.1474C>T c.(1474-1476)Cgt>Tgt p.R492C AGAP2_ENST00000257897.3_Missense_Mutation_p.R156C NM_001122772.2 NP_001116244.1 Q99490 AGAP2_HUMAN ArfGAP with GTPase domain, ankyrin repeat and PH domain 2 p.R156S(1) 48 CCATGGAGACGGCTCACAGCC 0.592000 1 Substitution - Missense(1) SO:0001583 missense ENST00000547588.1 1 1 hg19 CCDS44932.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 16.31|16.31 3.086143|3.086143 0.55861|0.55861 .|. .|. ENSG00000135439|ENSG00000135439 ENST00000328568|ENST00000257897;ENST00000547588 .|T;T .|0.23552 .|1.9;1.9 5.43|5.43 3.6|3.6 0.41247|0.41247 .|Mitochondrial Rho-like (1); .|0.401538 .|0.26092 .|N .|0.026393 T|T 0.43986|0.43986 0.1272|0.1272 L|L 0.52905|0.52905 1.665|1.665 0.39166|0.39166 D|D 0.962491|0.962491 .|D;D;D .|0.89917 .|0.996;1.0;1.0 .|P;D;D .|0.70487 .|0.671;0.948;0.969 T|T 0.34850|0.34850 -0.9812|-0.9812 5|10 .|0.56958 .|D .|0.05 .|. 13.0081|13.0081 0.58717|0.58717 0.1502:0.0:0.8498:0.0|0.1502:0.0:0.8498:0.0 .|. .|156;492;492 .|Q99490-2;F8VVT9;Q99490 .|.;.;AGAP2_HUMAN L|C 355|156;492 .|ENSP00000257897:R156C;ENSP00000449241:R492C .|ENSP00000257897:R156C P|R -|- 2|1 0|0 AGAP2|AGAP2 56414151|56414151 0.258000|0.258000 0.24033|0.24033 1.000000|1.000000 0.80357|0.80357 0.947000|0.947000 0.59692|0.59692 0.557000|0.557000 0.23454|0.23454 0.378000|0.378000 0.24764|0.24764 -1.134000|-1.134000 0.01955|0.01955 CCG|CGT TCGA-HZ-A4BH-01A-11D-A26I-08 AGAP2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000408367.1 1 0 0 15 196 0 37 0 9.462908e-02 0 7 0 37 2 0 0 0 0 0 2 1 0.999886 15 195 0 36 2 -3.319119 1 1 0 0 1 1 2 3 2.068349 0 0.310000 1.820000 0.312132 0.460000 0.270000 0.760000 0.460000 0.486154 0.460000 0 3.600000e-01 6.000000e-01 MSRB3 253827 broad.mit.edu 37 12 65857005 65857005 + Missense_Mutation SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr12:65857005C>T ENST00000355192.3 + 6 608 c.482C>T c.(481-483)tCg>tTg p.S161L MSRB3_ENST00000308259.5_Missense_Mutation_p.S154L|MSRB3_ENST00000535664.1_Missense_Mutation_p.S154L NM_198080.3 NP_932346.1 Q8IXL7 MSRB3_HUMAN methionine sulfoxide reductase B3 p.S161L(1)|p.S154L(1) 13 LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975) TGCATAAATTCGGCTGCCTTG 0.547000 2 Substitution - Missense(2) SO:0001583 missense ENST00000355192.3 1 1 hg19 CCDS8973.1 . . . . . . . . . . C 34 5.393034 0.96009 . . ENSG00000174099 ENST00000355192;ENST00000308259;ENST00000535664;ENST00000535239 D;D;D;D 0.82893 -1.66;-1.66;-1.66;-1.66 5.76 5.76 0.90799 Mss4-like (1);Methionine sulphoxide reductase B (4); 0.000000 0.85682 D 0.000000 D 0.95310 0.8478 H 0.98629 4.285 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.91635 0.998;0.999 D 0.96448 0.9332 9 . . . -2.9871 20.3325 0.98724 0.0:1.0:0.0:0.0 . 161;154 Q8IXL7;Q8IXL7-2 MSRB3_HUMAN;. L 161;154;154;154 ENSP00000347324:S161L;ENSP00000312274:S154L;ENSP00000441650:S154L;ENSP00000445843:S154L . S + 2 0 MSRB3 64143272 1.000000 0.71417 0.196000 0.23383 0.071000 0.16799 6.792000 0.75125 2.890000 0.99128 0.655000 0.94253 TCG TCGA-HZ-A4BH-01A-11D-A26I-08 MSRB3-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000401421.1 1 0 1 82 510 0 85 0 9.920609e-01 0 48 0 85 2 0 0 0 0 0 2 1 1.000000 80 503 0 84 2 -2.966636 1 1 0 0 1 1 2 3 2.068349 0 0.310000 1.820000 0.312132 0.890000 0.720000 1.000000 1.000000 0.894774 0.890000 1 8.000000e-01 1 COL4A2 1284 broad.mit.edu 37 13 111121596 111121596 + Missense_Mutation SNP G G A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr13:111121596G>A ENST00000360467.5 + 28 2434 c.2128G>A c.(2128-2130)Gca>Aca p.A710T NM_001846.2 NP_001837.2 P08572 CO4A2_HUMAN collagen, type IV, alpha 2 80 all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922) Breast(118;0.212) BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151) CCCAGGCTTCGCAGGAGCTGA 0.572000 0 SO:0001583 missense ENST00000360467.5 1 1 hg19 CCDS41907.1 . . . . . . . . . . T 15.62 2.888790 0.52014 0.0 1.21E-4 ENSG00000134871 ENST00000360467;ENST00000257309 D 0.93604 -3.25 5.57 -5.12 0.02893 . 0.651803 0.13327 N 0.396252 D 0.85457 0.5701 L 0.42686 1.345 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.71048 -0.4705 10 0.30078 T 0.28 . 4.5599 0.12154 0.1987:0.4843:0.1005:0.2165 . 710 P08572 CO4A2_HUMAN T 710 ENSP00000353654:A710T ENSP00000257309:A710T A + 1 0 COL4A2 109919597 0.000000 0.05858 0.061000 0.19648 0.006000 0.05464 -0.603000 0.05674 -0.842000 0.04195 -1.221000 0.01599 GCA TCGA-HZ-A4BH-01A-11D-A26I-08 COL4A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045761.2 1 0 1 14 65 0 16 0 1 0 874 0 16 2 0 0 0 0 0 2 1 0.999834 13 65 0 16 2 -11.142240 1 1 120548 5 40 1 1 2 3 2.071293 0 0.310000 1.820000 0.312132 0.990000 0.680000 1.000000 1.000000 0.959614 0.990000 1 8.900000e-01 1 NBEA 26960 broad.mit.edu 37 13 35735929 35735929 + Nonsense_Mutation SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr13:35735929C>T ENST00000400445.3 + 23 4438 c.3904C>T c.(3904-3906)Cga>Tga p.R1302* NBEA_ENST00000310336.4_Nonsense_Mutation_p.R1302*|NBEA_ENST00000540320.1_Nonsense_Mutation_p.R1302*|NBEA_ENST00000379939.2_Nonsense_Mutation_p.R1302* NM_015678.4 NP_056493.3 Q8NFP9 NBEA_HUMAN neurobeachin 108 Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207) CCGAGATCTCCGAGTTGATTT 0.433000 0 SO:0001587 stop_gained ENST00000400445.3 0 1 hg19 CCDS45026.1 . . . . . . . . . . C 48 13.944603 0.99771 . . ENSG00000172915 ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336 . . . 5.04 1.83 0.25207 . 0.156994 0.42548 D 0.000689 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 . 14.3905 0.66975 0.4506:0.5494:0.0:0.0 . . . . X 1302 . ENSP00000308534:R1302X R + 1 2 NBEA 34633929 0.982000 0.34865 0.995000 0.50966 0.984000 0.73092 0.644000 0.24766 0.481000 0.27557 0.591000 0.81541 CGA TCGA-HZ-A4BH-01A-11D-A26I-08 NBEA-202 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding 1 0 0 5 121 0 23 0 0 0 1 0 23 2 0 0 0 0 0 2 1 0.937521 5 120 0 23 2 -3.099096 1 1 0 0 1 1 2 3 2.071293 0 0.310000 1.820000 0.312132 0.270000 0.100000 0.600000 0.250000 0.304966 0.270000 0 1.700000e-01 4.200000e-01 FAM179B 23116 broad.mit.edu 37 14 45431977 45431977 + Missense_Mutation SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr14:45431977C>T ENST00000361577.3 + 1 567 c.353C>T c.(352-354)gCt>gTt p.A118V KLHL28_ENST00000396128.4_5'Flank|FAM179B_ENST00000382233.2_Missense_Mutation_p.A118V|KLHL28_ENST00000355081.2_5'Flank|KLHL28_ENST00000553817.1_5'Flank|FAM179B_ENST00000361462.2_Missense_Mutation_p.A118V NM_015091.2 NP_055906.2 Q9Y4F4 F179B_HUMAN family with sequence similarity 179, member B 45 GCTTTGCAAGCTGCTTTGCCG 0.617000 0 SO:0001583 missense ENST00000361577.3 1 1 hg19 CCDS9681.1 . . . . . . . . . . C 20.7 4.038206 0.75617 . . ENSG00000198718 ENST00000429476;ENST00000361577;ENST00000361462;ENST00000382233 T;T;T 0.56611 0.45;0.45;0.45 4.88 4.88 0.63580 Armadillo-like helical (1); 0.146929 0.31554 N 0.007443 T 0.58235 0.2108 N 0.24115 0.695 0.31602 N 0.6526 D;D;D;D 0.71674 0.998;0.998;0.998;0.998 D;D;D;D 0.76071 0.987;0.987;0.987;0.987 T 0.64170 -0.6470 10 0.66056 D 0.02 -11.2912 13.4039 0.60900 0.0:1.0:0.0:0.0 . 118;118;118;118 Q9Y4F4-3;G3XAE9;Q9Y4F4;Q9Y4F4-2 .;.;F179B_HUMAN;. V 118 ENSP00000355045:A118V;ENSP00000354917:A118V;ENSP00000371668:A118V ENSP00000354917:A118V A + 2 0 FAM179B 44501727 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 3.581000 0.53914 2.526000 0.85167 0.655000 0.94253 GCT TCGA-HZ-A4BH-01A-11D-A26I-08 FAM179B-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000276791.1 1 0 0 51 856 0 139 0 1.844637e-02 0 4 0 139 2 0 0 0 0 0 2 1 1.000000 51 847 0 134 2 -7.919481 1 1 0 0 1 0 3 3 2.125584 1 0.310000 1.820000 0.334747 0.380000 0.280000 1.000000 0.380000 0.489637 0.380000 0 3.300000e-01 1 APBA2 321 broad.mit.edu 37 15 29346316 29346316 + Missense_Mutation SNP G G A rs140795962 TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr15:29346316G>A ENST00000558402.1 + 5 828 c.229G>A c.(229-231)Gtg>Atg p.V77M APBA2_ENST00000411764.1_Missense_Mutation_p.V77M|APBA2_ENST00000558259.1_Missense_Mutation_p.V77M|APBA2_ENST00000558330.1_Missense_Mutation_p.V77M|APBA2_ENST00000561069.1_Missense_Mutation_p.V77M Q99767 APBA2_HUMAN amyloid beta (A4) precursor protein-binding, family A, member 2 59 all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234) CTCTGACTACGTGAACAACAC 0.637000 0 SO:0001583 missense ENST00000558402.1 1 1 hg19 CCDS10022.1 . . . . . . . . . . G 19.85 3.904297 0.72868 0.0 1.16E-4 ENSG00000034053 ENST00000411764;ENST00000219865 T 0.52295 0.67 5.25 5.25 0.73442 . 0.145082 0.46145 D 0.000306 T 0.66356 0.2781 M 0.68952 2.095 0.48632 D 0.999683 D;D;D 0.89917 1.0;0.997;0.997 D;P;P 0.64237 0.923;0.797;0.797 T 0.70099 -0.4965 10 0.87932 D 0 . 17.832 0.88685 0.0:0.0:1.0:0.0 . 77;77;77 Q5XKC0;E9PGI4;Q99767 .;.;APBA2_HUMAN M 77 ENSP00000409312:V77M ENSP00000219865:V77M V + 1 0 APBA2 27133608 1.000000 0.71417 0.989000 0.46669 0.827000 0.46813 6.796000 0.75145 2.423000 0.82170 0.650000 0.86243 GTG TCGA-HZ-A4BH-01A-11D-A26I-08 APBA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251362.3 1 0 1 123 763 0 160 0 3.641623e-01 0 9 0 160 2 0 0 0 0 0 2 1 1.000000 122 757 1 160 19 -20.000000 1 1 121412 2 39 1 0 1 1 2.056661 0 0.310000 1.820000 0.308929 0.880000 0.740000 1.000000 1.000000 0.893932 0.880000 1 8.100000e-01 9.700000e-01 ZNF267 10308 broad.mit.edu 37 16 31926313 31926313 + Missense_Mutation SNP A A G TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr16:31926313A>G ENST00000300870.10 + 4 952 c.743A>G c.(742-744)gAa>gGa p.E248G NM_001265588.1|NM_003414.5 NP_001252517.1|NP_003405 Q14586 ZN267_HUMAN zinc finger protein 267 41 AAATGTAAAGAATTTGAGGAA 0.303000 0 SO:0001583 missense ENST00000300870.10 0 1 hg19 CCDS32440.1 . . . . . . . . . . . 11.49 1.655457 0.29425 . . ENSG00000185947 ENST00000300870;ENST00000394846 T 0.17528 2.27 0.458 0.458 0.16670 . . . . . T 0.16557 0.0398 M 0.63169 1.94 0.26123 N 0.980529 B 0.06786 0.001 B 0.01281 0.0 T 0.27571 -1.0070 9 0.87932 D 0 . 5.2013 0.15267 0.9999:0.0:1.0E-4:0.0 . 248 Q14586 ZN267_HUMAN G 248;215 ENSP00000300870:E248G ENSP00000300870:E248G E + 2 0 ZNF267 31833814 0.001000 0.12720 0.109000 0.21407 0.096000 0.18686 0.550000 0.23345 0.407000 0.25591 0.397000 0.26171 GAA TCGA-HZ-A4BH-01A-11D-A26I-08 ZNF267-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000432446.2 1 0 1 43 243 0 15 1 8.767708e-01 7 16 0 15 2 0 0 0 0 0 2 1 1.000000 43 243 0 15 2 -20.000000 1 1 0 0 1 0 0 0 2.012011 0 0.310000 1.820000 0.292453 0.940000 0.700000 1.000000 1.000000 0.919989 0.940000 1 8.100000e-01 1 AXIN1 8312 broad.mit.edu 37 16 343713 343713 + Missense_Mutation SNP G G A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr16:343713G>A ENST00000262320.3 - 8 2332 c.1961C>T c.(1960-1962)tCg>tTg p.S654L AXIN1_ENST00000354866.3_Missense_Mutation_p.S654L NM_003502.3 NP_003493.1 O15169 AXIN1_HUMAN axin 1 221 all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187) CCTCGTCCCCGAAGACCTTGG 0.637000 0 SO:0001583 missense ENST00000262320.3 1 1 hg19 CCDS10405.1 . . . . . . . . . . G 17.38 3.373947 0.61735 2.27E-4 0.0 ENSG00000103126 ENST00000262320;ENST00000354866 T;T 0.61742 0.08;0.08 4.17 4.17 0.49024 . 0.309451 0.34853 N 0.003624 T 0.65471 0.2694 M 0.63843 1.955 0.47153 D 0.99933 D;D 0.64830 0.994;0.99 P;P 0.52909 0.713;0.52 T 0.69068 -0.5243 10 0.48119 T 0.1 -21.2179 15.6374 0.76966 0.0:0.0:1.0:0.0 . 654;654 O15169-2;O15169 .;AXIN1_HUMAN L 654 ENSP00000262320:S654L;ENSP00000346935:S654L ENSP00000262320:S654L S - 2 0 AXIN1 283714 1.000000 0.71417 0.509000 0.27700 0.094000 0.18550 4.945000 0.63568 2.185000 0.69588 0.478000 0.44815 TCG TCGA-HZ-A4BH-01A-11D-A26I-08 AXIN1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000139441.3 1 0 0 43 524 0 109 1 9.940773e-01 24 72 0 109 2 0 0 0 0 0 2 1 1.000000 42 519 0 108 2 -10.798960 1 1 121370 2 32 1 0 1 1 2.055065 0 0.310000 1.820000 0.308929 0.480000 0.350000 0.630000 0.480000 0.496159 0.480000 0 4.100000e-01 5.700000e-01 HEATR3 55027 broad.mit.edu 37 16 50112735 50112735 + Missense_Mutation SNP G G A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr16:50112735G>A ENST00000299192.7 + 7 1038 c.847G>A c.(847-849)Gtt>Att p.V283I HEATR3_ENST00000285767.4_Missense_Mutation_p.V197I NM_182922.2 NP_891552.1 Q7Z4Q2 HEAT3_HUMAN HEAT repeat containing 3 28 CTTATCTGAAGTTTTGGGAAT 0.378000 0 SO:0001583 missense ENST00000299192.7 0 1 hg19 CCDS10739.1 . . . . . . . . . . G 19.93 3.918750 0.73098 . . ENSG00000155393 ENST00000285767;ENST00000299192 T;T 0.31769 1.48;1.48 5.74 4.79 0.61399 Armadillo-like helical (1);Armadillo-type fold (1); 0.492308 0.24010 N 0.042387 T 0.34919 0.0914 M 0.64997 1.995 0.25653 N 0.986075 P;P 0.50272 0.933;0.501 P;B 0.47251 0.542;0.039 T 0.20140 -1.0284 10 0.29301 T 0.29 . 9.7486 0.40462 0.0742:0.0:0.7542:0.1716 . 197;283 B7WNW7;Q7Z4Q2 .;HEAT3_HUMAN I 197;283 ENSP00000285767:V197I;ENSP00000299192:V283I ENSP00000285767:V197I V + 1 0 HEATR3 48670236 0.926000 0.31397 0.779000 0.31741 0.993000 0.82548 1.464000 0.35288 1.569000 0.49696 0.637000 0.83480 GTT TCGA-HZ-A4BH-01A-11D-A26I-08 HEATR3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256880.2 0 0 0 8 351 0 28 0 1.570797e-01 0 28 0 28 2 0 0 0 0 0 2 1 0.989073 8 348 0 28 2 -8.271699 1 1 0 0 1 0 0 0 2.012011 0 0.310000 1.820000 0.292453 0.140000 0.060000 0.260000 0.140000 0.155799 0.140000 0 9.000000e-02 2.000000e-01 RLTPR 146206 broad.mit.edu 37 16 67682804 67682804 + Silent SNP G G A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr16:67682804G>A ENST00000334583.6 + 17 1846 c.1518G>A c.(1516-1518)tcG>tcA p.S506S RLTPR_ENST00000545661.1_Silent_p.S470S NM_001013838.1 NP_001013860.1 Q6F5E8 LR16C_HUMAN RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing 18 Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192) AGCTGCGCTCGGCCGGCGCCC 0.682000 0 SO:0001819 synonymous_variant ENST00000334583.6 0 1 hg19 CCDS45513.1 TCGA-HZ-A4BH-01A-11D-A26I-08 RLTPR-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000467858.1 0 0 0 4 78 0 11 0 2.256845e-02 0 4 0 11 2 0 0 0 0 0 2 1 0.889214 4 77 0 11 2 -7.844712 1 1 0 0 1 0 0 0 2.012011 0 0.310000 1.820000 0.292453 0.330000 0.110000 0.690000 0.300000 0.363489 0.330000 0 2.000000e-01 5.100000e-01 ADAD2 161931 broad.mit.edu 37 16 84229512 84229512 + Missense_Mutation SNP G G A rs142081193 byFrequency TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr16:84229512G>A ENST00000315906.5 + 7 1196 c.1144G>A c.(1144-1146)Gtg>Atg p.V382M RP11-486L19.2_ENST00000536986.1_RNA|ADAD2_ENST00000268624.3_Missense_Mutation_p.V464M|RP11-486L19.2_ENST00000569834.1_RNA|RP11-486L19.2_ENST00000561900.1_RNA|RP11-486L19.2_ENST00000565643.1_RNA NM_001145400.1 NP_001138872.1 Q8NCV1 ADAD2_HUMAN adenosine deaminase domain containing 2 13 TGTGTGCTACGTGGCGCCCTC 0.716000 0 SO:0001583 missense ENST00000315906.5 1 1 hg19 CCDS45536.1 . . . . . . . . . . G 12.26 1.885176 0.33255 . . ENSG00000140955 ENST00000315906;ENST00000268624 D;D 0.94280 -3.39;-3.39 5.49 -2.27 0.06846 Adenosine deaminase/editase (2); 0.653207 0.14249 N 0.331597 D 0.86928 0.6051 L 0.53617 1.68 0.31539 N 0.660181 P;P 0.45396 0.857;0.856 B;B 0.33890 0.172;0.114 T 0.81936 -0.0705 10 0.33940 T 0.23 -14.3004 9.5447 0.39273 0.1738:0.6193:0.2068:0.0 . 382;464 Q8NCV1;Q8NCV1-2 ADAD2_HUMAN;. M 382;464 ENSP00000325153:V382M;ENSP00000268624:V464M ENSP00000268624:V464M V + 1 0 ADAD2 82787013 0.006000 0.16342 0.724000 0.30704 0.475000 0.33008 0.019000 0.13444 -0.237000 0.09739 0.561000 0.74099 GTG TCGA-HZ-A4BH-01A-11D-A26I-08 ADAD2-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000433385.1 1 0 0 12 161 0 35 0 0 0 0 35 2 0 0 0 0 0 2 1 0.999194 12 160 0 35 2 -16.876340 1 1 121100 22 41 1 0 0 0 2.037557 0 0.310000 1.820000 0.301337 0.450000 0.240000 0.710000 0.430000 0.466999 0.450000 0 3.300000e-01 5.800000e-01 ABHD15 116236 broad.mit.edu 37 17 27889843 27889843 + Silent SNP G G A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr17:27889843G>A ENST00000307201.4 - 2 1313 c.1143C>T c.(1141-1143)ttC>ttT p.F381F RP11-68I3.2_ENST00000581474.1_RNA NM_198147.2 NP_937790.2 Q6UXT9 ABH15_HUMAN abhydrolase domain containing 15 10 GCAGGAGGAAGAAGTAGGGGT 0.617000 0 SO:0001819 synonymous_variant ENST00000307201.4 1 1 hg19 CCDS32602.1 TCGA-HZ-A4BH-01A-11D-A26I-08 ABHD15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000447796.2 1 0 0 31 420 0 87 1 7.069741e-01 2 33 0 87 2 0 0 0 0 0 2 1 1.000000 30 416 0 87 2 -20.000000 1 1 0 0 1 1 2 3 2.234057 1 0.310000 1.820000 0.355923 0.510000 0.330000 1.000000 0.470000 0.610030 0.510000 0 4.100000e-01 1 OR1D2 4991 broad.mit.edu 37 17 2996105 2996105 + Silent SNP G G A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr17:2996105G>A ENST00000331459.1 - 1 185 c.186C>T c.(184-186)ttC>ttT p.F62F NM_002548.2 NP_002539.2 P34982 OR1D2_HUMAN olfactory receptor, family 1, subfamily D, member 2 15 GGTTGGCCAGGAAGAAGTACA 0.537000 0 SO:0001819 synonymous_variant ENST00000331459.1 1 1 hg19 CCDS11019.1 TCGA-HZ-A4BH-01A-11D-A26I-08 OR1D2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207207.1 1 0 0 81 822 0 159 0 0 0 0 159 2 0 0 0 0 0 2 1 1.000000 79 800 0 159 2 -19.886920 1 1 0 0 1 0 1 1 1.754142 1 0.310000 1.820000 0.183432 0.480000 0.380000 0.590000 0.490000 0.491526 0.480000 0 4.300000e-01 5.400000e-01 OR1A1 8383 broad.mit.edu 37 17 3119669 3119669 + Missense_Mutation SNP G G A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr17:3119669G>A ENST00000304094.1 + 1 755 c.755G>A c.(754-756)gGt>gAt p.G252D NM_014565.2 NP_055380.2 Q9P1Q5 OR1A1_HUMAN olfactory receptor, family 1, subfamily A, member 1 23 TTGTATTATGGTACAGTCATG 0.498000 0 SO:0001583 missense ENST00000304094.1 1 1 hg19 CCDS11022.1 . . . . . . . . . . G 16.40 3.111392 0.56398 . . ENSG00000172146 ENST00000304094 T 0.39229 1.09 5.05 5.05 0.67936 GPCR, rhodopsin-like superfamily (1); 0.000000 0.52532 D 0.000074 T 0.78748 0.4332 H 0.98333 4.205 0.32665 N 0.517561 D 0.89917 1.0 D 0.97110 1.0 D 0.88672 0.3196 10 0.87932 D 0 . 17.1395 0.86749 0.0:0.0:1.0:0.0 . 252 Q9P1Q5 OR1A1_HUMAN D 252 ENSP00000305207:G252D ENSP00000305207:G252D G + 2 0 OR1A1 3066419 0.925000 0.31364 1.000000 0.80357 0.607000 0.37147 1.912000 0.39946 2.632000 0.89209 0.511000 0.50034 GGT TCGA-HZ-A4BH-01A-11D-A26I-08 OR1A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207292.1 1 0 1 136 646 0 94 0 0 0 0 94 2 0 0 0 0 0 2 1 1.000000 136 641 0 93 2 -20.000000 1 1 121408 1 32 1 0 1 1 1.754142 1 0.310000 1.820000 0.183432 0.920000 0.790000 1.000000 0.940000 0.918875 0.920000 1 8.500000e-01 9.800000e-01 PRR11 55771 broad.mit.edu 37 17 57270937 57270937 + Silent SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr17:57270937C>T ENST00000262293.4 + 5 799 c.487C>T c.(487-489)Ctg>Ttg p.L163L NM_018304.3 NP_060774.2 Q96HE9 PRR11_HUMAN proline rich 11 16 Medulloblastoma(34;0.0922)|all_neural(34;0.101) TGCCTGCGTTCTGATCACCCC 0.532000 0 SO:0001819 synonymous_variant ENST00000262293.4 1 1 hg19 CCDS11614.1 TCGA-HZ-A4BH-01A-11D-A26I-08 PRR11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000445949.1 1 0 0 102 623 0 47 1 9.723178e-01 4 33 0 47 2 0 0 0 0 0 2 1 1.000000 88 619 0 47 2 -20.000000 1 0 0 0 1 1 6 7 3.668927 1 0.310000 1.820000 0.611268 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 PRR11 55771 broad.mit.edu 37 17 57270942 57270942 + Missense_Mutation SNP C C G TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr17:57270942C>G ENST00000262293.4 + 5 804 c.492C>G c.(490-492)atC>atG p.I164M NM_018304.3 NP_060774.2 Q96HE9 PRR11_HUMAN proline rich 11 16 Medulloblastoma(34;0.0922)|all_neural(34;0.101) GCGTTCTGATCACCCCTGGAG 0.537000 0 SO:0001583 missense ENST00000262293.4 1 1 hg19 CCDS11614.1 . . . . . . . . . . C 6.692 0.496371 0.12762 . . ENSG00000068489 ENST00000262293 . . . 5.25 1.87 0.25490 . 0.783614 0.11729 N 0.535099 T 0.18087 0.0434 N 0.08118 0 0.09310 N 1 B 0.32396 0.369 B 0.35073 0.195 T 0.19063 -1.0317 9 0.44086 T 0.13 -9.65 3.8305 0.08873 0.2002:0.5605:0.1516:0.0877 . 164 Q96HE9 PRR11_HUMAN M 164 . ENSP00000262293:I164M I + 3 3 PRR11 54625724 0.000000 0.05858 0.000000 0.03702 0.009000 0.06853 0.329000 0.19698 0.165000 0.19558 0.561000 0.74099 ATC TCGA-HZ-A4BH-01A-11D-A26I-08 PRR11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000445949.1 1 0 1 103 614 0 48 1 9.638231e-01 4 30 0 48 2 0 0 0 0 0 2 1 1.000000 87 612 0 48 2 -20.000000 1 0 0 0 1 1 6 7 3.668927 1 0.310000 1.820000 0.611268 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 PRR11 55771 broad.mit.edu 37 17 57271006 57271006 + Missense_Mutation SNP C C A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr17:57271006C>A ENST00000262293.4 + 5 868 c.556C>A c.(556-558)Cct>Act p.P186T NM_018304.3 NP_060774.2 Q96HE9 PRR11_HUMAN proline rich 11 16 Medulloblastoma(34;0.0922)|all_neural(34;0.101) CCATTTtcctcctcctcctcc 0.547000 0 SO:0001583 missense ENST00000262293.4 0 0 hg19 CCDS11614.1 . . . . . . . . . . C 13.23 2.174345 0.38413 . . ENSG00000068489 ENST00000262293 . . . 4.53 3.53 0.40419 . 0.428017 0.22147 N 0.063971 T 0.28863 0.0716 L 0.27053 0.805 0.09310 N 0.999999 P 0.47302 0.893 P 0.44811 0.461 T 0.08126 -1.0737 9 0.59425 D 0.04 -8.2827 10.3157 0.43736 0.0:0.903:0.0:0.097 . 186 Q96HE9 PRR11_HUMAN T 186 . ENSP00000262293:P186T P + 1 0 PRR11 54625788 0.000000 0.05858 0.009000 0.14445 0.863000 0.49368 0.108000 0.15396 1.000000 0.39049 0.561000 0.74099 CCT TCGA-HZ-A4BH-01A-11D-A26I-08 PRR11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000445949.1 1 0 1 92 491 0 51 1 9.967791e-01 5 43 0 51 2 0 0 0 0 0 2 1 1.000000 83 516 0 52 2 -20.000000 1 0 0 0 1 1 6 7 3.668927 1 0.310000 1.820000 0.611268 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 PRR11 55771 broad.mit.edu 37 17 57271015 57271015 + Missense_Mutation SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr17:57271015C>T ENST00000262293.4 + 5 877 c.565C>T c.(565-567)Cca>Tca p.P189S NM_018304.3 NP_060774.2 Q96HE9 PRR11_HUMAN proline rich 11 16 Medulloblastoma(34;0.0922)|all_neural(34;0.101) tcctcctcctccacctccacc 0.542000 0 SO:0001583 missense ENST00000262293.4 1 0 hg19 CCDS11614.1 . . . . . . . . . . C 14.49 2.549872 0.45383 . . ENSG00000068489 ENST00000262293 . . . 5.5 5.5 0.81552 . 0.098878 0.44902 N 0.000402 T 0.65450 0.2692 L 0.29908 0.895 0.50813 D 0.999894 D 0.71674 0.998 D 0.66979 0.948 T 0.67550 -0.5642 9 0.66056 D 0.02 -3.8599 16.467 0.84081 0.0:1.0:0.0:0.0 . 189 Q96HE9 PRR11_HUMAN S 189 . ENSP00000262293:P189S P + 1 0 PRR11 54625797 0.908000 0.30866 0.764000 0.31436 0.193000 0.23685 3.741000 0.55090 2.729000 0.93468 0.561000 0.74099 CCA TCGA-HZ-A4BH-01A-11D-A26I-08 PRR11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000445949.1 1 0 1 91 487 0 60 1 9.941523e-01 3 41 0 60 2 0 0 0 0 0 2 1 1.000000 82 492 0 61 2 -3.144808 1 0 0 0 1 1 6 7 3.668927 1 0.310000 1.820000 0.611268 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 PRR11 55771 broad.mit.edu 37 17 57271016 57271016 + Missense_Mutation SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr17:57271016C>T ENST00000262293.4 + 5 878 c.566C>T c.(565-567)cCa>cTa p.P189L NM_018304.3 NP_060774.2 Q96HE9 PRR11_HUMAN proline rich 11 16 Medulloblastoma(34;0.0922)|all_neural(34;0.101) cctcctcctccacctccacct 0.547000 0 SO:0001583 missense ENST00000262293.4 1 0 hg19 CCDS11614.1 . . . . . . . . . . C 12.47 1.948265 0.34377 . . ENSG00000068489 ENST00000262293 . . . 5.5 3.47 0.39725 . 0.098878 0.44902 D 0.000402 T 0.45836 0.1362 L 0.29908 0.895 0.58432 D 0.999999 B 0.32101 0.356 B 0.38562 0.276 T 0.43015 -0.9417 9 0.44086 T 0.13 -3.8599 7.6838 0.28528 0.1648:0.7514:0.0:0.0838 . 189 Q96HE9 PRR11_HUMAN L 189 . ENSP00000262293:P189L P + 2 0 PRR11 54625798 0.901000 0.30685 0.678000 0.29963 0.136000 0.21042 3.741000 0.55090 1.420000 0.47138 0.561000 0.74099 CCA TCGA-HZ-A4BH-01A-11D-A26I-08 PRR11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000445949.1 1 0 1 93 493 0 60 1 9.945401e-01 3 41 0 60 2 0 0 0 0 0 2 1 1.000000 84 490 0 61 2 -3.145223 1 0 0 0 1 1 6 7 3.668927 1 0.310000 1.820000 0.611268 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 PRR11 55771 broad.mit.edu 37 17 57271093 57271093 + Nonsense_Mutation SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr17:57271093C>T ENST00000262293.4 + 5 955 c.643C>T c.(643-645)Cag>Tag p.Q215* NM_018304.3 NP_060774.2 Q96HE9 PRR11_HUMAN proline rich 11 16 Medulloblastoma(34;0.0922)|all_neural(34;0.101) TAAAGCACTTCAGGTAGGTAA 0.473000 0 SO:0001587 stop_gained ENST00000262293.4 0 1 hg19 CCDS11614.1 . . . . . . . . . . C 13.07 2.127327 0.37533 . . ENSG00000068489 ENST00000262293 . . . 5.5 5.5 0.81552 . 0.107189 0.41938 D 0.000783 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.05721 T 0.95 -8.9529 16.467 0.84081 0.0:1.0:0.0:0.0 . . . . X 215 . ENSP00000262293:Q215X Q + 1 0 PRR11 54625875 1.000000 0.71417 1.000000 0.80357 0.297000 0.27493 3.865000 0.56033 2.729000 0.93468 0.561000 0.74099 CAG TCGA-HZ-A4BH-01A-11D-A26I-08 PRR11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000445949.1 0 0 1 156 572 0 61 1 9.985986e-01 3 35 0 61 2 0 0 0 0 0 2 1 1.000000 154 562 0 60 2 -4.015504 1 0 121412 1 28 1 1 6 7 3.668927 1 0.310000 1.820000 0.611268 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 TP53 7157 broad.mit.edu 37 17 7578526 7578526 + Missense_Mutation SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr17:7578526C>T ENST00000269305.4 - 5 593 c.404G>A c.(403-405)tGc>tAc p.C135Y TP53_ENST00000445888.2_Missense_Mutation_p.C135Y|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Missense_Mutation_p.C135Y|TP53_ENST00000420246.2_Missense_Mutation_p.C135Y|TP53_ENST00000359597.4_Missense_Mutation_p.C135Y|TP53_ENST00000413465.2_Missense_Mutation_p.C135Y 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.C135Y(60)|p.C135F(43)|p.C135S(8)|p.0?(8)|p.C42Y(4)|p.C3Y(4)|p.C135fs*9(3)|p.N131fs*27(2)|p.C3F(2)|p.C42F(2)|p.F134_T140>S(1)|p.K132_A138delKMFCQLA(1)|p.S127_Q136del10(1)|p.C135T(1)|p.V73fs*9(1)|p.C135fs*15(1)|p.C135fs*14(1)|p.Y126fs*11(1)|p.C3fs*9(1)|p.C42fs*9(1)|p.C135_A138delCQLA(1)|p.C42S(1)|p.M133fs*13(1)|p.C3S(1)|p.C135_T140delCQLAKT(1)|p.Q136fs*13(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) GGCCAGTTGGCAAAACATCTT 0.572000 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 152 Substitution - Missense(126)|Deletion - Frameshift(10)|Whole gene deletion(8)|Deletion - In frame(4)|Insertion - Frameshift(3)|Complex - deletion inframe(1) SO:0001583 missense Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 1 1 hg19 CCDS11118.1 . . . . . . . . . . C 25.4 4.639320 0.87760 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315;ENST00000508793 D;D;D;D;D;D;D;D;D 0.99800 -6.8;-6.8;-6.8;-6.8;-6.8;-6.8;-6.8;-6.8;-6.8 5.48 5.48 0.80851 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 0.99771 0.9906 M 0.85945 2.785 0.80722 D 1 D;D;D;D;D;D;D 0.89917 1.0;1.0;0.993;1.0;1.0;1.0;1.0 D;D;D;D;D;D;D 0.97110 0.999;1.0;0.929;1.0;1.0;1.0;1.0 D 0.97312 0.9938 10 0.87932 D 0 -26.815 17.2272 0.86973 0.0:1.0:0.0:0.0 . 96;135;135;42;135;135;135 B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7 .;.;.;.;P53_HUMAN;.;. Y 135;135;135;135;135;135;124;42;3;42;3;135 ENSP00000410739:C135Y;ENSP00000352610:C135Y;ENSP00000269305:C135Y;ENSP00000398846:C135Y;ENSP00000391127:C135Y;ENSP00000391478:C135Y;ENSP00000425104:C3Y;ENSP00000423862:C42Y;ENSP00000424104:C135Y ENSP00000269305:C135Y C - 2 0 TP53 7519251 1.000000 0.71417 1.000000 0.80357 0.794000 0.44872 7.772000 0.85439 2.733000 0.93635 0.655000 0.94253 TGC TCGA-HZ-A4BH-01A-11D-A26I-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 37 183 0 40 1 9.996891e-01 31 33 0 40 2 1 1 67 256 0 1809 2 1 1.000000 37 182 0 40 2 -20.000000 1 1 0 0 1 0 1 1 1.754142 1 0.310000 1.820000 0.183432 0.860000 0.640000 0.990000 0.900000 0.856401 0.860000 1 7.500000e-01 9.500000e-01 COL5A3 50509 broad.mit.edu 37 19 10097024 10097024 + Silent SNP G G A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr19:10097024G>A ENST00000264828.3 - 30 2404 c.2319C>T c.(2317-2319)ggC>ggT p.G773G NM_015719.3 NP_056534.2 P25940 CO5A3_HUMAN collagen, type V, alpha 3 116 Epithelial(33;7.11e-05) GCCCCTCCTCGCCAGCCTGCC 0.612000 0 SO:0001819 synonymous_variant ENST00000264828.3 1 1 hg19 CCDS12222.1 TCGA-HZ-A4BH-01A-11D-A26I-08 COL5A3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000315788.1 1 0 0 25 221 0 35 0 4.343563e-01 0 14 0 35 2 0 0 0 0 0 2 1 1.000000 24 210 0 34 2 -20.000000 1 1 121222 2 31 1 1 2 3 2.408486 1 0.310000 1.820000 0.402597 0.760000 0.510000 1.000000 1.000000 0.771331 0.760000 0 6.200000e-01 9.100000e-01 KCNN1 3780 broad.mit.edu 37 19 18099263 18099263 + Missense_Mutation SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr19:18099263C>T ENST00000222249.9 + 7 1418 c.1099C>T c.(1099-1101)Cgg>Tgg p.R367W NM_002248.3 NP_002239.2 Q92952 KCNN1_HUMAN potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1 8 Miconazole(DB01110)|Procaine(DB00721) TGTGGTGGCTCGGAAGCTGGA 0.637000 0 SO:0001583 missense ENST00000222249.9 1 1 hg19 . . . . . . . . . . C 19.27 3.795298 0.70452 . . ENSG00000105642 ENST00000222249;ENST00000536713 . . . 4.61 4.61 0.57282 Ion transport 2 (1);Calmodulin-binding domain (1); 0.000000 0.85682 D 0.000000 T 0.79052 0.4381 M 0.86028 2.79 0.51482 D 0.999927 D 0.89917 1.0 D 0.85130 0.997 T 0.81927 -0.0709 9 0.87932 D 0 -29.1479 10.2569 0.43403 0.1978:0.8022:0.0:0.0 . 367 Q92952 KCNN1_HUMAN W 384;367 . ENSP00000222249:R384W R + 1 2 KCNN1 17960263 0.920000 0.31207 0.996000 0.52242 0.910000 0.53928 0.876000 0.28092 2.116000 0.64780 0.561000 0.74099 CGG TCGA-HZ-A4BH-01A-11D-A26I-08 KCNN1-001 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000471896.2 1 0 1 34 107 0 22 0 0 0 0 22 2 0 0 0 0 0 2 1 1.000000 33 102 0 22 2 -20.000000 1 1 0 0 1 1 2 3 2.378492 1 0.310000 1.820000 0.402597 0.990000 0.990000 1.000000 1.000000 0.999986 0.990000 1 9.900000e-01 1 GRAMD1A 57655 broad.mit.edu 37 19 35500042 35500042 + Missense_Mutation SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr19:35500042C>T ENST00000317991.5 + 2 220 c.28C>T c.(28-30)Cgg>Tgg p.R10W GRAMD1A_ENST00000598073.1_3'UTR|GRAMD1A_ENST00000504615.2_5'UTR|GRAMD1A_ENST00000424536.2_Missense_Mutation_p.R10W|GRAMD1A_ENST00000599564.1_Missense_Mutation_p.R97W|GRAMD1A_ENST00000411896.2_Missense_Mutation_p.R10W NM_020895.3 NP_065946.2 Q96CP6 GRM1A_HUMAN GRAM domain containing 1A 19 all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0849) CCACTCTGGCCGGAGCACGCC 0.622000 0 SO:0001583 missense ENST00000317991.5 1 1 hg19 CCDS42546.1 . . . . . . . . . . c 15.81 2.944466 0.53079 . . ENSG00000089351 ENST00000453966;ENST00000317991;ENST00000411896 T;T 0.34859 1.36;1.34 4.83 3.79 0.43588 . 0.000000 0.64402 D 0.000002 T 0.43122 0.1233 N 0.19112 0.55 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.79108 0.977;0.948;0.977;0.992 T 0.45934 -0.9227 10 0.87932 D 0 . 12.3312 0.55041 0.1697:0.8302:0.0:0.0 . 10;10;10;97 Q96CP6-3;Q96CP6;Q96CP6-2;F5GZ02 .;GRM1A_HUMAN;.;. W 97;10;10 ENSP00000441032:R10W;ENSP00000439267:R10W ENSP00000441032:R10W R + 1 2 GRAMD1A 40191882 1.000000 0.71417 1.000000 0.80357 0.913000 0.54294 2.429000 0.44758 1.250000 0.43966 0.561000 0.74099 CGG TCGA-HZ-A4BH-01A-11D-A26I-08 GRAMD1A-003 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000461557.1 0 0 0 47 655 0 112 1 9.814592e-01 14 75 0 112 2 0 0 0 0 0 2 1 1.000000 46 650 0 110 2 -3.075755 1 1 120926 2 34 1 0 1 1 1.820828 1 0.310000 1.820000 0.239250 0.380000 0.280000 0.500000 0.390000 0.397169 0.380000 0 3.300000e-01 4.500000e-01 PRODH2 58510 broad.mit.edu 37 19 36302895 36302895 + Missense_Mutation SNP T T A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr19:36302895T>A ENST00000301175.3 - 5 811 c.794A>T c.(793-795)gAg>gTg p.E265V NM_021232.1 NP_067055.1 Q9UF12 PROD2_HUMAN proline dehydrogenase (oxidase) 2 21 all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0515) AGCCAGCCTCTCGGGGCTCAG 0.637000 0 SO:0001583 missense ENST00000301175.3 1 1 hg19 CCDS12478.1 . . . . . . . . . . T 15.74 2.922070 0.52653 . . ENSG00000250799 ENST00000301175 T 0.05855 3.38 4.86 3.84 0.44239 . . . . . T 0.08758 0.0217 L 0.57536 1.79 0.80722 D 1 B 0.34103 0.437 B 0.38616 0.277 T 0.16630 -1.0396 9 0.33940 T 0.23 . 7.7224 0.28740 0.3387:0.0:0.0:0.6613 . 265 Q9UF12 PROD2_HUMAN V 265 ENSP00000301175:E265V ENSP00000301175:E265V E - 2 0 PRODH2 40994735 0.997000 0.39634 0.565000 0.28409 0.819000 0.46315 4.364000 0.59479 0.977000 0.38444 0.533000 0.62120 GAG TCGA-HZ-A4BH-01A-11D-A26I-08 PRODH2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000452552.2 1 0 0 16 259 0 67 0 0 0 0 67 2 0 0 0 0 0 2 1 0.999937 16 257 0 67 2 -19.012940 1 1 0 0 1 0 1 1 1.820828 1 0.310000 1.820000 0.239250 0.340000 0.200000 0.520000 0.340000 0.354987 0.340000 0 2.600000e-01 4.300000e-01 PRODH2 58510 broad.mit.edu 37 19 36302896 36302896 + Nonsense_Mutation SNP C C A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr19:36302896C>A ENST00000301175.3 - 5 810 c.793G>T c.(793-795)Gag>Tag p.E265* NM_021232.1 NP_067055.1 Q9UF12 PROD2_HUMAN proline dehydrogenase (oxidase) 2 21 all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0515) GCCAGCCTCTCGGGGCTCAGC 0.637000 0 SO:0001587 stop_gained ENST00000301175.3 0 1 hg19 CCDS12478.1 . . . . . . . . . . C 34 5.398174 0.96030 . . ENSG00000250799 ENST00000301175 . . . 4.86 2.75 0.32379 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . 0.09843 T 0.71 . 10.2938 0.43612 0.0:0.8654:0.0:0.1346 . . . . X 265 . ENSP00000301175:E265X E - 1 0 PRODH2 40994736 0.346000 0.24844 0.463000 0.27130 0.810000 0.45777 1.290000 0.33319 0.785000 0.33685 0.655000 0.94253 GAG TCGA-HZ-A4BH-01A-11D-A26I-08 PRODH2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000452552.2 1 0 0 17 257 0 67 0 0 0 0 67 2 0 0 0 0 0 2 1 0.999968 17 255 0 67 2 -3.222690 1 1 0 0 1 0 1 1 1.820828 1 0.310000 1.820000 0.239250 0.360000 0.220000 0.550000 0.360000 0.377214 0.360000 0 2.800000e-01 4.600000e-01 PRODH2 58510 broad.mit.edu 37 19 36303115 36303115 + Missense_Mutation SNP C C A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr19:36303115C>A ENST00000301175.3 - 4 676 c.659G>T c.(658-660)gGc>gTc p.G220V NM_021232.1 NP_067055.1 Q9UF12 PROD2_HUMAN proline dehydrogenase (oxidase) 2 21 all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.0515) CTCCAGGAGGCCCCGTGACAG 0.652000 0 SO:0001583 missense ENST00000301175.3 1 1 hg19 CCDS12478.1 . . . . . . . . . . C 1.117 -0.656468 0.03480 . . ENSG00000250799 ENST00000301175 T 0.27557 1.66 4.85 -0.471 0.12119 . . . . . T 0.21962 0.0529 L 0.51422 1.61 0.20307 N 0.999911 B 0.27625 0.183 B 0.22386 0.039 T 0.25502 -1.0130 9 0.54805 T 0.06 . 2.2746 0.04099 0.1245:0.4534:0.1295:0.2926 . 220 Q9UF12 PROD2_HUMAN V 220 ENSP00000301175:G220V ENSP00000301175:G220V G - 2 0 PRODH2 40994955 0.521000 0.26258 0.004000 0.12327 0.020000 0.10135 0.698000 0.25571 -0.384000 0.07845 -0.797000 0.03246 GGC TCGA-HZ-A4BH-01A-11D-A26I-08 PRODH2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000452552.2 1 0 0 42 393 0 75 0 0 0 0 75 2 0 0 0 0 0 2 1 1.000000 42 388 0 75 2 -20.000000 1 1 0 0 1 0 1 1 1.820828 1 0.310000 1.820000 0.239250 0.560000 0.410000 0.730000 0.560000 0.571589 0.560000 0 4.800000e-01 6.500000e-01 PLD3 23646 broad.mit.edu 37 19 40882579 40882579 + Silent SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr19:40882579C>T ENST00000409587.1 + 11 1480 c.1083C>T c.(1081-1083)cgC>cgT p.R361R PLD3_ENST00000409735.4_Silent_p.R361R|PLD3_ENST00000409281.1_Silent_p.R361R|PLD3_ENST00000356508.5_Silent_p.R361R|PLD3_ENST00000409419.1_Silent_p.R361R Q8IV08 PLD3_HUMAN phospholipase D family, member 3 20 Lung(22;0.000636)|LUSC - Lung squamous cell carcinoma(20;0.00248) TCAAGGTGCGCCTGCTCATCA 0.642000 0 SO:0001819 synonymous_variant ENST00000409587.1 1 1 hg19 CCDS33027.1 TCGA-HZ-A4BH-01A-11D-A26I-08 PLD3-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000327721.1 0 0 1 79 316 0 90 1 1 94 576 0 90 2 0 0 0 0 0 2 1 1.000000 79 311 0 89 2 -20.000000 1 1 0 0 1 0 0 0 1.903023 0 0.310000 1.820000 0.252033 0.990000 0.960000 1.000000 1.000000 0.997783 0.990000 1 9.900000e-01 1 ERCC2 2068 broad.mit.edu 37 19 45860929 45860929 + Silent SNP G G A rs142702501 byFrequency TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr19:45860929G>A ENST00000391945.4 - 13 1343 c.1266C>T c.(1264-1266)gaC>gaT p.D422D ERCC2_ENST00000391944.3_Silent_p.D344D NM_000400.3 NP_000391.1 P18074 ERCC2_HUMAN excision repair cross-complementation group 2 9 Ovarian(192;0.0728)|all_neural(266;0.112) GGGTTCTGTCGTCAAAGGGCT 0.627000 Mis, N, F, S skin basal cell, skin squamous cell, melanoma Nucleotide excision repair (NER) Xeroderma Pigmentosum yes Rec Xeroderma pigmentosum (D) 19 19q13.2-q13.3 2068 excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D) E 0 SO:0001819 synonymous_variant Familial Cancer Database incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV ENST00000391945.4 1 0 hg19 CCDS33049.1 TCGA-HZ-A4BH-01A-11D-A26I-08 ERCC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000109626.2 1 0 0 49 521 0 58 1 9.989058e-01 16 93 0 58 2 0 0 0 0 0 2 1 1.000000 49 517 0 57 2 -13.704700 1 1 121412 41 49 1 1 7 8 3.787199 1 0.310000 1.820000 0.633661 0.990000 0.780000 1.000000 1.000000 0.969189 0.990000 1 9.100000e-01 1 CCDC61 729440 broad.mit.edu 37 19 46506729 46506729 + Silent SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr19:46506729C>T ENST00000595358.1 + 3 250 c.201C>T c.(199-201)ttC>ttT p.F67F CCDC61_ENST00000594087.1_Silent_p.F67F|CCDC61_ENST00000536603.1_Silent_p.F67F|CCDC61_ENST00000263284.2_Silent_p.F124F NM_001267723.1 NP_001254652.1 Q9Y6R9 CCD61_HUMAN coiled-coil domain containing 61 13 all_neural(266;0.113)|Ovarian(192;0.127) TCAACATCTTCTGTCATATGC 0.567000 0 SO:0001819 synonymous_variant ENST00000595358.1 1 1 hg19 CCDS46120.2 TCGA-HZ-A4BH-01A-11D-A26I-08 CCDC61-001 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000461689.1 1 0 1 37 156 0 24 1 9.999139e-01 3 61 0 24 2 0 0 0 0 0 2 1 1.000000 36 154 0 24 2 -20.000000 1 1 0 0 1 0.310000 1.820000 0 0 MAP2K7 5609 broad.mit.edu 37 19 7976364 7976364 + Missense_Mutation SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr19:7976364C>T ENST00000397979.3 + 9 1034 c.980C>T c.(979-981)aCg>aTg p.T327M MAP2K7_ENST00000397983.3_Missense_Mutation_p.T343M|MAP2K7_ENST00000545011.1_Missense_Mutation_p.T369M|MAP2K7_ENST00000397981.3_Missense_Mutation_p.T334M|CTD-3193O13.13_ENST00000595655.1_RNA NM_145185.2 NP_660186.1 O14733 MP2K7_HUMAN mitogen-activated protein kinase kinase 7 19 AACTGCAAGACGGACTTTGAG 0.592000 0 SO:0001583 missense ENST00000397979.3 1 1 hg19 CCDS42491.1 . . . . . . . . . . C 27.3 4.819928 0.90873 . . ENSG00000076984 ENST00000397981;ENST00000397983;ENST00000545011;ENST00000425613;ENST00000397979 T;T;T;T 0.15139 2.45;2.45;2.45;2.45 4.85 4.85 0.62838 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 0.85682 D 0.000000 T 0.32164 0.0820 L 0.53780 1.695 0.80722 D 1 D;D 0.61697 0.978;0.99 P;P 0.56751 0.507;0.805 T 0.02156 -1.1204 10 0.87932 D 0 -9.4511 15.8291 0.78739 0.0:1.0:0.0:0.0 . 334;327 O14733-4;O14733 .;MP2K7_HUMAN M 334;343;369;343;327 ENSP00000381068:T334M;ENSP00000381070:T343M;ENSP00000443946:T369M;ENSP00000381066:T327M ENSP00000381066:T327M T + 2 0 MAP2K7 7882364 0.999000 0.42202 1.000000 0.80357 0.997000 0.91878 3.697000 0.54764 2.675000 0.91044 0.655000 0.94253 ACG TCGA-HZ-A4BH-01A-11D-A26I-08 MAP2K7-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000267980.1 1 0 1 53 157 0 45 1 9.997191e-01 15 25 0 45 2 0 0 0 0 0 2 1 1.000000 53 154 0 45 2 -20.000000 1 1 0 0 1 0 1 1 1.754381 1 0.310000 1.820000 0.184927 0.970000 0.850000 1.000000 1.000000 0.966691 0.970000 1 9.200000e-01 1 NTNG1 22854 broad.mit.edu 37 1 107979392 107979392 + Missense_Mutation SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr1:107979392C>T ENST00000370068.1 + 7 2207 c.1361C>T c.(1360-1362)cCg>cTg p.P454L NTNG1_ENST00000370070.2_Intron|NTNG1_ENST00000542803.1_Missense_Mutation_p.P454L|NTNG1_ENST00000370073.2_Missense_Mutation_p.P454L|NTNG1_ENST00000370066.1_Intron|NTNG1_ENST00000370074.4_Intron|NTNG1_ENST00000370065.1_Intron|NTNG1_ENST00000370072.3_Intron|NTNG1_ENST00000370067.1_Intron|NTNG1_ENST00000370061.3_Missense_Mutation_p.P420L|NTNG1_ENST00000370071.2_Intron Q9Y2I2 NTNG1_HUMAN netrin G1 37 all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243) GAGTGTCTGCCGGGAAATTCC 0.517000 0 SO:0001583 missense ENST00000370068.1 1 1 hg19 CCDS44180.1 . . . . . . . . . . C 16.99 3.274201 0.59649 . . ENSG00000162631 ENST00000370073;ENST00000542803;ENST00000370061;ENST00000370064;ENST00000370062;ENST00000370068 T;T;T;T 0.63580 -0.05;-0.05;-0.05;-0.05 5.87 5.87 0.94306 EGF-like, laminin (3); 0.000000 0.64402 D 0.000017 T 0.64034 0.2562 M 0.84773 2.715 0.80722 D 1 D;P 0.53462 0.96;0.935 P;P 0.46940 0.532;0.449 T 0.64972 -0.6281 10 0.30078 T 0.28 . 16.7906 0.85589 0.0:0.8715:0.1285:0.0 . 420;454 B4DKF0;Q9Y2I2 .;NTNG1_HUMAN L 454;454;420;257;201;454 ENSP00000359090:P454L;ENSP00000440561:P454L;ENSP00000359078:P420L;ENSP00000359085:P454L ENSP00000359078:P420L P + 2 0 NTNG1 107780915 1.000000 0.71417 1.000000 0.80357 1.000000 0.99986 4.584000 0.60971 2.941000 0.99782 0.655000 0.94253 CCG TCGA-HZ-A4BH-01A-11D-A26I-08 NTNG1-006 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000030340.1 1 0 1 32 178 0 29 0 0 0 0 29 2 0 0 0 0 0 2 1 1.000000 31 177 0 29 2 -3.037354 1 1 0 0 1 1 2 3 2.068002 0 0.310000 1.820000 0.312132 0.980000 0.700000 1.000000 1.000000 0.935610 0.980000 1 8.300000e-01 1 WDR47 22911 broad.mit.edu 37 1 109560150 109560150 + Missense_Mutation SNP C C A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr1:109560150C>A ENST00000369962.3 - 3 454 c.232G>T c.(232-234)Gac>Tac p.D78Y WDR47_ENST00000361054.3_Intron|WDR47_ENST00000369965.4_Missense_Mutation_p.D78Y|WDR47_ENST00000357672.3_Intron|WDR47_ENST00000400794.3_Missense_Mutation_p.D78Y O94967 WDR47_HUMAN WD repeat domain 47 20 all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822) CTTTTTTTGTCAAATTTTTCC 0.289000 0 SO:0001583 missense ENST00000369962.3 0 1 hg19 CCDS44187.1 . . . . . . . . . . C 24.7 4.564866 0.86439 . . ENSG00000085433 ENST00000400794;ENST00000369962;ENST00000369965;ENST00000530772;ENST00000529074;ENST00000528747 T;T;T 0.60171 0.23;0.25;0.21 5.97 5.97 0.96955 CTLH, C-terminal LisH motif (2); 0.000000 0.85682 D 0.000000 T 0.72003 0.3407 M 0.62723 1.935 0.80722 D 1 D;D;D 0.89917 0.999;0.999;1.0 D;D;D 0.87578 0.995;0.995;0.998 T 0.72510 -0.4271 10 0.87932 D 0 -14.641 20.4239 0.99064 0.0:1.0:0.0:0.0 . 78;78;78 A8MX09;O94967;O94967-3 .;WDR47_HUMAN;. Y 78;78;78;78;5;78 ENSP00000383599:D78Y;ENSP00000358979:D78Y;ENSP00000358982:D78Y ENSP00000358979:D78Y D - 1 0 WDR47 109361673 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 7.466000 0.80914 2.828000 0.97474 0.655000 0.94253 GAC TCGA-HZ-A4BH-01A-11D-A26I-08 WDR47-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000032414.2 1 0 1 47 310 0 20 0 2.914210e-01 1 7 0 20 2 0 0 0 0 0 2 1 1.000000 47 307 0 20 2 -3.318982 1 1 0 0 1 1 2 3 2.068002 0 0.310000 1.820000 0.312132 0.850000 0.640000 1.000000 1.000000 0.854115 0.850000 1 7.400000e-01 9.800000e-01 PRAMEF4 400735 broad.mit.edu 37 1 12943068 12943068 + Missense_Mutation SNP G G A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr1:12943068G>A ENST00000235349.5 - 2 218 c.148C>T c.(148-150)Cgc>Tgc p.R50C NM_001009611.2 NP_001009611.1 O60810 PRAM4_HUMAN PRAME family member 4 p.R50C(1) 24 Ovarian(185;0.249) Lung NSC(185;3.67e-05)|all_lung(284;4.03e-05)|Renal(390;0.000147)|Breast(348;0.000278)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255) GCCTCACAGCGTCTCCTGCTG 0.607000 1 Substitution - Missense(1) SO:0001583 missense ENST00000235349.5 1 1 hg19 CCDS30592.1 . . . . . . . . . . g 5.461 0.270195 0.10349 . . ENSG00000243073 ENST00000235349 T 0.04970 3.52 1.48 1.48 0.22813 . 0.786987 0.11561 N 0.551731 T 0.05686 0.0149 L 0.38838 1.175 0.09310 N 1 B 0.10296 0.003 B 0.06405 0.002 T 0.31110 -0.9955 10 0.54805 T 0.06 . 6.4564 0.21932 0.0:0.0:1.0:0.0 . 50 O60810 PRAM4_HUMAN C 50 ENSP00000235349:R50C ENSP00000235349:R50C R - 1 0 PRAMEF4 12865655 0.000000 0.05858 0.003000 0.11579 0.008000 0.06430 0.224000 0.17738 1.137000 0.42214 0.400000 0.26472 CGC TCGA-HZ-A4BH-01A-11D-A26I-08 PRAMEF4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000005518.1 1 0 0 79 766 0 144 0 0 0 0 144 2 0 0 0 0 0 2 1 1.000000 56 560 0 147 2 -2.966611 1 1 120658 15 45 1 0 1 1 1.905258 0 0.310000 1.820000 0.250774 0.550000 0.440000 0.670000 0.550000 0.559210 0.550000 0 4.900000e-01 6.200000e-01 KDM5B 10765 broad.mit.edu 37 1 202714993 202714993 + Silent SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr1:202714993C>T ENST00000367265.3 - 16 3480 c.2316G>A c.(2314-2316)aaG>aaA p.K772K KDM5B_ENST00000367264.2_Silent_p.K808K NM_006618.3 NP_006609.3 Q9UGL1 KDM5B_HUMAN lysine (K)-specific demethylase 5B 6 TACTTTTCTTCTTGTTGATCT 0.383000 0 SO:0001819 synonymous_variant ENST00000367265.3 1 1 hg19 CCDS30974.1 TCGA-HZ-A4BH-01A-11D-A26I-08 KDM5B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000099184.2 1 0 0 73 813 0 81 1 8.689619e-01 7 35 0 81 2 0 0 0 0 0 2 1 1.000000 73 805 0 81 2 -16.528350 1 1 0 0 1 0 2 2 2.041686 1 0.310000 1.820000 0.310000 0.550000 0.420000 1.000000 0.530000 0.644935 0.550000 0 4.800000e-01 1 DISC1 27185 broad.mit.edu 37 1 231830151 231830151 + Missense_Mutation SNP C C T rs139420445 byFrequency TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr1:231830151C>T ENST00000602281.1 + 2 700 c.647C>T c.(646-648)tCg>tTg p.S216L TSNAX-DISC1_ENST00000602962.1_3'UTR|DISC1_ENST00000366637.3_5'UTR|DISC1_ENST00000366633.3_Missense_Mutation_p.S216L|DISC1_ENST00000537876.1_Missense_Mutation_p.S216L|DISC1_ENST00000317586.4_Missense_Mutation_p.S216L|DISC1_ENST00000602873.1_Intron|DISC1_ENST00000439617.2_Missense_Mutation_p.S216L|DISC1_ENST00000539444.1_Missense_Mutation_p.S216L|DISC1_ENST00000535983.1_Missense_Mutation_p.S216L|DISC1_ENST00000366636.4_Missense_Mutation_p.S216L NM_001164542.1|NM_001164544.1 NP_001158014.1|NP_001158016.1 Q9NRI5 DISC1_HUMAN disrupted in schizophrenia 1 15 all_cancers(173;0.0208)|Prostate(94;0.0975) ATTCGGCTCTCGCTTGGCTCT 0.607000 0 SO:0001583 missense ENST00000602281.1 1 1 hg19 CCDS59205.1 . . . . . . . . . . C 13.70 2.314498 0.40996 6.81E-4 0.0 ENSG00000162946 ENST00000439617;ENST00000366637;ENST00000317586;ENST00000366636;ENST00000366638;ENST00000532576;ENST00000535983;ENST00000537876;ENST00000366633;ENST00000539444;ENST00000295051;ENST00000535944;ENST00000366632 T;T;T;T;T;T;T;T;T 0.30714 1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52 4.61 3.69 0.42338 . 0.354936 0.29900 N 0.010911 T 0.49406 0.1555 L 0.59436 1.845 0.28799 N 0.898879 D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D 0.89917 0.999;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999 P;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D 0.91635 0.846;0.998;0.998;0.997;0.998;0.999;0.998;0.998;0.998;0.998;0.933;0.997;0.997;0.998;0.998;0.997;0.997;0.998;0.997;0.997;0.933 T 0.45934 -0.9227 10 0.87932 D 0 -6.3648 11.6928 0.51525 0.0:0.8064:0.1936:0.0 . 216;216;216;216;216;216;216;216;216;216;216;216;216;216;216;216;216;216;216;216;216 C4P094;C4P0A3;C4P098;C4P0A1;C4P0A4;A6NLH2;C4P0A5;C4P095;C4P0B6;C4P0C4;C4P091;C4P0D2;C4P0D3;C4P0B1;A7E2W8;Q5T409;C4P0D0;Q9NRI5-2;Q9NRI5;Q9NRI5-3;Q9NRI5-4 .;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;DISC1_HUMAN;.;. L 216;216;216;216;216;216;216;216;216;216;216;216;67 ENSP00000403888:S216L;ENSP00000320784:S216L;ENSP00000355596:S216L;ENSP00000443996:S216L;ENSP00000440909:S216L;ENSP00000355593:S216L;ENSP00000440953:S216L;ENSP00000295051:S216L;ENSP00000441193:S216L ENSP00000295051:S216L S + 2 0 DISC1 229896774 0.940000 0.31905 0.056000 0.19401 0.071000 0.16799 2.506000 0.45433 1.127000 0.42034 0.561000 0.74099 TCG TCGA-HZ-A4BH-01A-11D-A26I-08 DISC1-019 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000467451.1 1 0 0 28 368 0 75 0 2.943613e-02 0 4 0 75 2 0 0 0 0 0 2 1 1.000000 28 365 0 74 2 -3.318792 1 1 121412 7 42 1 1 2 3 2.382850 1 0.310000 1.820000 0.402597 0.520000 0.360000 0.730000 0.520000 0.540927 0.520000 0 4.300000e-01 6.300000e-01 CHML 1122 broad.mit.edu 37 1 241799053 241799053 + Missense_Mutation SNP G G A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr1:241799053G>A ENST00000366553.1 - 1 179 c.16C>T c.(16-18)Ccc>Tcc p.P6S OPN3_ENST00000331838.5_Intron|OPN3_ENST00000469376.1_Intron|OPN3_ENST00000366554.2_Intron NM_001821.3 NP_001812.2 P26374 RAE2_HUMAN choroideremia-like (Rab escort protein 2) 26 Ovarian(103;0.103)|all_lung(81;0.23) all_cancers(173;0.0231) OV - Ovarian serous cystadenocarcinoma(106;0.0125) AACTCTGTGGGAAGATTGTCC 0.433000 0 SO:0001583 missense ENST00000366553.1 1 1 hg19 CCDS31073.1 . . . . . . . . . . G 14.90 2.674542 0.47781 . . ENSG00000203668 ENST00000366553 T 0.59224 0.28 5.14 5.14 0.70334 . 0.000000 0.85682 U 0.000000 T 0.74816 0.3766 . . . 0.41587 D 0.988775 D 0.89917 1.0 D 0.97110 1.0 T 0.76405 -0.2971 9 0.59425 D 0.04 -8.0953 14.3144 0.66437 0.0:0.0:1.0:0.0 . 6 P26374 RAE2_HUMAN S 6 ENSP00000355511:P6S ENSP00000355511:P6S P - 1 0 CHML 239865676 1.000000 0.71417 0.959000 0.39883 0.543000 0.35085 4.210000 0.58500 2.840000 0.97914 0.655000 0.94253 CCC TCGA-HZ-A4BH-01A-11D-A26I-08 CHML-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000095712.1 1 0 0 35 523 0 38 0 3.223040e-01 1 17 0 38 2 0 0 0 0 0 2 1 1.000000 33 516 0 37 2 -7.981680 1 1 0 0 1 1 2 3 2.382850 1 0.310000 1.820000 0.402597 0.460000 0.330000 0.630000 0.460000 0.477760 0.460000 0 3.900000e-01 5.500000e-01 EXO1 9156 broad.mit.edu 37 1 242030320 242030320 + Silent SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr1:242030320C>T ENST00000366548.3 + 11 1823 c.1230C>T c.(1228-1230)ctC>ctT p.L410L EXO1_ENST00000518483.1_Silent_p.L410L|EXO1_ENST00000348581.5_Silent_p.L410L NM_130398.3 NP_569082.2 Q9UQ84 EXO1_HUMAN exonuclease 1 45 Ovarian(103;0.103) all_cancers(173;0.0555) OV - Ovarian serous cystadenocarcinoma(106;0.0107) GGTTAAATCTCCCAAGGAAAT 0.408000 Editing and processing nucleases 0 SO:0001819 synonymous_variant ENST00000366548.3 0 1 hg19 CCDS1620.1 TCGA-HZ-A4BH-01A-11D-A26I-08 EXO1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000096405.1 0 0 0 11 302 0 39 0 6.594001e-02 0 11 0 39 2 0 0 0 0 0 2 1 0.998292 11 298 0 39 2 -11.734300 1 1 0 0 1 1 2 3 2.382850 1 0.310000 1.820000 0.402597 0.260000 0.130000 0.440000 0.270000 0.282525 0.260000 0 1.900000e-01 3.600000e-01 GJB4 127534 broad.mit.edu 37 1 35227279 35227279 + Missense_Mutation SNP G G A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr1:35227279G>A ENST00000339480.1 + 2 794 c.424G>A c.(424-426)Gat>Aat p.D142N RP1-34M23.5_ENST00000542839.1_RNA NM_153212.2 NP_694944.1 Q9NTQ9 CXB4_HUMAN gap junction protein, beta 4, 30.3kDa 16 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234) GGCCGCCGTGGATGCTGGCTT 0.612000 0 SO:0001583 missense ENST00000339480.1 1 1 hg19 CCDS383.1 . . . . . . . . . . G 17.63 3.436444 0.62955 . . ENSG00000189433 ENST00000339480 D 0.95724 -3.79 5.73 4.82 0.62117 Gap junction protein, cysteine-rich domain (1); 0.000000 0.85682 D 0.000000 D 0.97467 0.9171 M 0.81112 2.525 0.47153 D 0.999335 D 0.76494 0.999 D 0.73708 0.981 D 0.98052 1.0388 10 0.87932 D 0 . 14.4153 0.67145 0.0715:0.0:0.9285:0.0 . 142 Q9NTQ9 CXB4_HUMAN N 142 ENSP00000345868:D142N ENSP00000345868:D142N D + 1 0 GJB4 34999866 1.000000 0.71417 0.136000 0.22124 0.034000 0.12701 7.966000 0.87956 1.440000 0.47531 0.655000 0.94253 GAT TCGA-HZ-A4BH-01A-11D-A26I-08 GJB4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000011560.1 1 0 0 47 246 0 50 1 9.999922e-01 53 42 0 50 2 0 0 0 0 0 2 1 1.000000 44 243 0 50 2 -20.000000 1 1 121412 2 29 1 0 1 1 1.899383 1 0.310000 1.820000 0.252033 0.940000 0.710000 1.000000 1.000000 0.925772 0.940000 1 8.200000e-01 1 C1orf173 0 broad.mit.edu 37 1 75036840 75036840 + Silent SNP G G A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr1:75036840G>A ENST00000326665.5 - 14 4772 c.4554C>T c.(4552-4554)agC>agT p.S1518S C1orf173_ENST00000433746.2_5'UTR NM_001002912.4 NP_001002912.4 Q5RHP9 ERIC3_HUMAN 184 CTGCAGTCTCGCTTTCTCCTT 0.493000 0 SO:0001819 synonymous_variant ENST00000326665.5 1 1 hg19 CCDS30755.1 TCGA-HZ-A4BH-01A-11D-A26I-08 C1orf173-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000026516.1 0 0 0 25 836 0 131 0 0 0 0 131 2 0 0 0 0 0 2 1 1.000000 25 832 0 131 2 -2.827852 1 1 0 0 1 0 1 1 1.935132 0 0.310000 1.820000 0.263175 0.170000 0.110000 0.250000 0.170000 0.181427 0.170000 0 1.400000e-01 2.200000e-01 BAGE2 85319 broad.mit.edu 37 21 11058247 11058247 + RNA SNP G G A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr21:11058247G>A ENST00000470054.1 - 0 400 Q86Y30 BAGE2_HUMAN B melanoma antigen family, member 2 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) TGCAGCACAAGGATAATGATA 0.433000 0 ENST00000470054.1 0 1 hg19 TCGA-HZ-A4BH-01A-11D-A26I-08 BAGE2-001 KNOWN basic processed_transcript pseudogene OTTHUMT00000157417.3 0 0 0 22 581 1 68 0 0 0 1 68 2 0 9.782009e-02 7 188 12 432 12 0 0.522537 20 567 1 87 22 -2.676343 1 1 0 0 1 0 3 3 1.976330 1 0.310000 1.820000 0.402597 0.270000 0.170000 0.400000 0.270000 0.282584 0.270000 0 2.100000e-01 3.400000e-01 CLTCL1 8218 broad.mit.edu 37 22 19184149 19184149 + Missense_Mutation SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr22:19184149C>T ENST00000263200.10 - 25 3964 c.3892G>A c.(3892-3894)Gag>Aag p.E1298K CLTCL1_ENST00000442042.2_5'UTR|CLTCL1_ENST00000353891.5_Missense_Mutation_p.E1298K|CLTCL1_ENST00000427926.1_Missense_Mutation_p.E1298K NM_007098.3 NP_009029.3 P53675 CLH2_HUMAN clathrin, heavy chain-like 1 49 Colorectal(54;0.0993) AAGATCAGCTCCTCAAAGTAG 0.612000 T ? ALCL Dom yes 22 22q11.21 8218 clathrin, heavy polypeptide-like 1 L 0 SO:0001583 missense ENST00000263200.10 0 1 hg19 CCDS46662.1 . . . . . . . . . . C 19.95 3.921732 0.73213 . . ENSG00000070371 ENST00000353891;ENST00000263200;ENST00000427926 T;T;T 0.35048 1.33;1.33;1.33 3.5 3.5 0.40072 Tetratricopeptide-like helical (1);Armadillo-type fold (1); 0.000000 0.64402 D 0.000001 T 0.67126 0.2860 M 0.93106 3.38 0.80722 D 1 P;D;P;P 0.59767 0.528;0.986;0.882;0.745 P;D;P;P 0.70016 0.628;0.967;0.852;0.677 T 0.78370 -0.2230 10 0.87932 D 0 -16.3906 15.1691 0.72854 0.0:1.0:0.0:0.0 . 1298;121;121;1298 P53675-2;B7Z1Z7;B7Z2Y4;P53675 .;.;.;CLH2_HUMAN K 1298 ENSP00000439662:E1298K;ENSP00000445677:E1298K;ENSP00000441158:E1298K ENSP00000445677:E1298K E - 1 0 CLTCL1 17564149 1.000000 0.71417 1.000000 0.80357 0.222000 0.24845 5.268000 0.65536 1.802000 0.52723 0.491000 0.48974 GAG TCGA-HZ-A4BH-01A-11D-A26I-08 CLTCL1-001 KNOWN non_canonical_genome_sequence_error|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000316397.5 1 0 0 9 112 0 12 0 5.931435e-02 0 5 0 12 2 0 0 0 0 0 2 1 0.994590 9 111 0 12 2 -13.966830 1 1 0 0 1 0 1 1 1.912810 0 0.310000 1.820000 0.253287 0.450000 0.220000 0.760000 0.430000 0.472892 0.450000 0 3.200000e-01 6.100000e-01 CCDC116 164592 broad.mit.edu 37 22 21991276 21991276 + Missense_Mutation SNP G G T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr22:21991276G>T ENST00000292779.3 + 5 1920 c.1759G>T c.(1759-1761)Gat>Tat p.D587Y NM_152612.2 NP_689825.2 Q8IYX3 CC116_HUMAN coiled-coil domain containing 116 22 Colorectal(54;0.105) TGAGGGCCGTGATAAAGCCGA 0.557000 0 SO:0001583 missense ENST00000292779.3 1 1 hg19 CCDS13791.1 . . . . . . . . . . G 10.48 1.360852 0.24598 . . ENSG00000161180 ENST00000292779 T 0.12255 2.7 3.35 2.3 0.28687 . 3.410210 0.00674 N 0.000657 T 0.25195 0.0612 . . . 0.09310 N 1 D 0.60160 0.987 P 0.52217 0.693 T 0.13602 -1.0503 9 0.62326 D 0.03 -3.8567 8.4003 0.32581 0.0:0.2736:0.7264:0.0 . 587 Q8IYX3-2 . Y 587 ENSP00000292779:D587Y ENSP00000292779:D587Y D + 1 0 CCDC116 20321276 0.019000 0.18553 0.002000 0.10522 0.004000 0.04260 1.152000 0.31663 0.706000 0.31912 0.491000 0.48974 GAT TCGA-HZ-A4BH-01A-11D-A26I-08 CCDC116-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000320199.1 1 0 0 32 413 0 74 0 0 0 0 74 2 0 0 0 0 0 2 1 1.000000 32 409 0 72 2 -8.777760 1 1 0 0 1 0 1 1 1.912810 0 0.310000 1.820000 0.253287 0.420000 0.290000 0.580000 0.420000 0.437211 0.420000 0 3.500000e-01 5.100000e-01 KCNJ4 3761 broad.mit.edu 37 22 38823340 38823340 + Silent SNP G G A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr22:38823340G>A ENST00000303592.3 - 2 1056 c.798C>T c.(796-798)gaC>gaT p.D266D RP3-434P1.6_ENST00000433230.1_RNA NM_004981.1|NM_152868.2 NP_004972.1|NP_690607.1 P48050 KCNJ4_HUMAN potassium inwardly-rectifying channel, subfamily J, member 4 23 Melanoma(58;0.0286) GGCTGTCCTCGTCGATCTCGT 0.607000 0 SO:0001819 synonymous_variant ENST00000303592.3 1 1 hg19 CCDS13971.1 TCGA-HZ-A4BH-01A-11D-A26I-08 KCNJ4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000321447.1 1 0 0 22 244 0 48 0 0 0 0 48 2 0 0 0 0 0 2 1 0.999999 22 243 0 48 2 -20.000000 1 1 121412 4 38 1 0 1 1 1.894235 1 0.310000 1.820000 0.248243 0.490000 0.310000 0.700000 0.490000 0.502433 0.490000 0 3.900000e-01 6.000000e-01 IL1RN 3557 broad.mit.edu 37 2 113885304 113885304 + Missense_Mutation SNP A A T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 A T A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr2:113885304A>T ENST00000409930.3 + 1 167 c.103A>T c.(103-105)Atg>Ttg p.M35L IL1RN_ENST00000259206.5_Missense_Mutation_p.M38L|IL1RN_ENST00000409052.1_Start_Codon_SNP_p.M1L|IL1RN_ENST00000361779.3_Start_Codon_SNP_p.M1L|IL1RN_ENST00000354115.2_Missense_Mutation_p.M17L NM_173842.2 NP_776214.1 P18510 IL1RA_HUMAN interleukin 1 receptor antagonist 10 Rilonacept(DB06372) ATCCAGCAAGATGCAAGCCTT 0.562000 Lichen Sclerosis et Atrophicus, Familial Clustering of 0 SO:0001583 missense Familial Cancer Database Lichen Sclerosis, Familial ENST00000409930.3 1 1 hg19 CCDS46396.1 . . . . . . . . . . A 15.59 2.878314 0.51801 . . ENSG00000136689 ENST00000409052;ENST00000361779;ENST00000259206;ENST00000354115;ENST00000409930 T;T;T;T;T 0.35973 1.28;1.28;3.02;3.02;3.02 5.24 5.24 0.73138 . 0.361602 0.37809 N 0.001934 T 0.34919 0.0914 M 0.63428 1.95 0.33072 D 0.535518 B;B;B 0.02656 0.0;0.0;0.0 B;B;B 0.04013 0.001;0.001;0.0 T 0.42649 -0.9439 10 0.27785 T 0.31 -24.0838 11.8146 0.52202 1.0:0.0:0.0:0.0 . 35;17;38 P18510;P18510-2;Q53SC2 IL1RA_HUMAN;.;. L 1;1;38;17;35 ENSP00000387210:M1L;ENSP00000354816:M1L;ENSP00000259206:M38L;ENSP00000329072:M17L;ENSP00000387173:M35L ENSP00000259206:M38L M + 1 0 IL1RN 113601775 1.000000 0.71417 1.000000 0.80357 0.849000 0.48306 4.129000 0.57957 2.104000 0.64026 0.533000 0.62120 ATG TCGA-HZ-A4BH-01A-11D-A26I-08 IL1RN-005 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000330802.1 1 0 1 38 303 0 55 1 9.999985e-01 61 104 0 55 2 0 0 0 0 0 2 1 1.000000 38 299 0 55 2 -20.000000 1 1 0 0 1 1 2 3 2.064020 0 0.310000 1.820000 0.312132 0.720000 0.520000 0.990000 0.710000 0.733196 0.720000 0 6.100000e-01 8.400000e-01 TPO 7173 broad.mit.edu 37 2 1520713 1520713 + Silent SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr2:1520713C>T ENST00000345913.4 + 15 2668 c.2577C>T c.(2575-2577)atC>atT p.I859I TPO_ENST00000382198.1_Silent_p.I686I|TPO_ENST00000329066.4_Silent_p.I859I|TPO_ENST00000382201.3_Silent_p.I802I|TPO_ENST00000337415.3_Silent_p.I859I|TPO_ENST00000497517.2_3'UTR|TPO_ENST00000349624.3_Silent_p.I686I|TPO_ENST00000346956.3_Silent_p.I815I NM_000547.5 NP_000538.3 P07202 PERT_HUMAN thyroid peroxidase 95 all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627) all_cancers(51;0.0338) Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550) CTCTGCTGATCGGAGGCTTCG 0.547000 0 SO:0001819 synonymous_variant ENST00000345913.4 1 1 hg19 CCDS1643.1 . . . . . . . . . . C 0.144 -1.099164 0.01843 . . ENSG00000115705 ENST00000446278 . . . 5.52 -5.29 0.02747 . . . . . T 0.26702 0.0653 . . . 0.09310 N 0.999999 . . . . . . T 0.27088 -1.0084 4 . . . -27.4266 6.7432 0.23447 0.0:0.3461:0.3029:0.3509 . . . . L 334 . . S + 2 0 TPO 1499720 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 -2.732000 0.00804 -1.770000 0.01295 -0.904000 0.02843 TCG TCGA-HZ-A4BH-01A-11D-A26I-08 TPO-202 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000206594.2 1 0 1 25 235 0 43 0 0 0 0 43 2 0 0 0 0 0 2 1 1.000000 25 235 0 43 2 -3.318795 1 1 121402 4 38 1 0 1 1 2.053131 0 0.310000 1.820000 0.308929 0.620000 0.410000 0.860000 0.620000 0.633629 0.620000 0 5.100000e-01 7.500000e-01 KCNS3 3790 broad.mit.edu 37 2 18112314 18112314 + Silent SNP C C T rs35186900 byFrequency TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr2:18112314C>T ENST00000403915.1 + 3 490 c.39C>T c.(37-39)gaC>gaT p.D13D KCNS3_ENST00000304101.4_Silent_p.D13D|KCNS3_ENST00000465292.1_Intron NM_001282428.1 NP_001269357.1 Q9BQ31 KCNS3_HUMAN potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3 32 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158) CTGGACAAGACGAGGAACTTG 0.537000 0 SO:0001819 synonymous_variant ENST00000403915.1 1 0 hg19 CCDS1692.1 TCGA-HZ-A4BH-01A-11D-A26I-08 KCNS3-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000323808.1 0 0 1 69 408 0 54 1 6.622274e-01 2 13 0 54 2 0 0 0 0 0 2 1 1.000000 68 404 0 54 2 -3.047587 1 1 121412 2842 67 1 0 1 1 2.053131 0 0.310000 1.820000 0.308929 0.920000 0.730000 1.000000 1.000000 0.919127 0.920000 1 8.200000e-01 1 NBEAL1 65065 broad.mit.edu 37 2 204009874 204009874 + Silent SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr2:204009874C>T ENST00000449802.1 + 32 5541 c.5208C>T c.(5206-5208)ctC>ctT p.L1736L NM_001114132.1 NP_001107604.1 Q6ZS30 NBEL1_HUMAN neurobeachin-like 1 37 AAAGCAAGCTCAAATTTCAGG 0.333000 0 SO:0001819 synonymous_variant ENST00000449802.1 0 1 hg19 CCDS46495.1 TCGA-HZ-A4BH-01A-11D-A26I-08 NBEAL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000333982.4 1 0 0 21 348 0 21 0 0 0 1 0 21 2 0 0 0 0 0 2 1 0.999997 21 344 0 21 2 -5.024666 1 1 0 0 1 1 2 3 2.064020 0 0.310000 1.820000 0.312132 0.370000 0.230000 0.570000 0.370000 0.387534 0.370000 0 2.900000e-01 4.600000e-01 DYSF 8291 broad.mit.edu 37 2 71741003 71741003 + Missense_Mutation SNP T T A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr2:71741003T>A ENST00000258104.3 + 6 892 c.615T>A c.(613-615)agT>agA p.S205R DYSF_ENST00000429174.2_Missense_Mutation_p.S205R|DYSF_ENST00000410020.3_Missense_Mutation_p.S237R|DYSF_ENST00000413539.2_Missense_Mutation_p.S236R|DYSF_ENST00000409762.1_Missense_Mutation_p.S236R|DYSF_ENST00000409651.1_Missense_Mutation_p.S237R|DYSF_ENST00000409744.1_Missense_Mutation_p.S206R|DYSF_ENST00000409582.3_Missense_Mutation_p.S236R|DYSF_ENST00000409366.1_Missense_Mutation_p.S206R|DYSF_ENST00000394120.2_Missense_Mutation_p.S206R|DYSF_ENST00000410041.1_Missense_Mutation_p.S237R NM_001130976.1|NM_003494.3 NP_001124448.1|NP_003485.1 O75923 DYSF_HUMAN dysferlin 111 GAAAGCGAAGTGCGCCTACAT 0.582000 0 SO:0001583 missense ENST00000258104.3 1 1 hg19 CCDS1918.1 . . . . . . . . . . T 0.964 -0.702308 0.03255 . . ENSG00000135636 ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041 D;D;D;D;D;D;D;D;D;D;D 0.83163 -1.69;-1.69;-1.69;-1.68;-1.67;-1.68;-1.67;-1.67;-1.67;-1.68;-1.68 4.79 0.606 0.17559 . 0.256158 0.39475 N 0.001360 T 0.67590 0.2909 N 0.16478 0.41 0.20307 N 0.999918 B;B;B;B;B;B;B;B;B;B;B;B;B;B 0.19445 0.036;0.036;0.036;0.02;0.0;0.0;0.0;0.0;0.036;0.0;0.02;0.02;0.036;0.012 B;B;B;B;B;B;B;B;B;B;B;B;B;B 0.31290 0.127;0.127;0.127;0.088;0.003;0.001;0.003;0.005;0.127;0.002;0.088;0.127;0.127;0.06 T 0.52756 -0.8533 10 0.17832 T 0.49 -14.3939 7.9678 0.30109 0.0:0.5926:0.0:0.4074 . 237;237;206;206;237;206;236;205;236;236;205;205;206;205 O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923 .;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN R 236;236;236;205;205;237;206;206;206;237;237 ENSP00000407046:S236R;ENSP00000387137:S236R;ENSP00000386547:S236R;ENSP00000398305:S205R;ENSP00000258104:S205R;ENSP00000386683:S237R;ENSP00000377678:S206R;ENSP00000386285:S206R;ENSP00000386512:S206R;ENSP00000386881:S237R;ENSP00000386617:S237R ENSP00000258104:S205R S + 3 2 DYSF 71594511 0.086000 0.21541 0.034000 0.17996 0.020000 0.10135 0.392000 0.20801 -0.114000 0.11936 -0.384000 0.06662 AGT TCGA-HZ-A4BH-01A-11D-A26I-08 DYSF-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000251970.3 1 0 0 17 277 0 63 0 4.870360e-02 0 6 0 63 2 0 0 0 0 0 2 1 0.999960 16 269 0 63 2 -19.652540 1 1 0 0 1 1 2 3 2.064020 0 0.310000 1.820000 0.312132 0.380000 0.220000 0.610000 0.370000 0.396573 0.380000 0 2.900000e-01 4.800000e-01 MYLK 4638 broad.mit.edu 37 3 123383037 123383037 + Silent SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr3:123383037C>T ENST00000475616.1 - 20 3899 c.3900G>A c.(3898-3900)gcG>gcA p.A1300A MYLK_ENST00000510775.1_5'Flank|MYLK_ENST00000354792.5_Silent_p.A100A|MYLK_ENST00000360772.3_Silent_p.A1300A|MYLK_ENST00000359169.1_Silent_p.A1300A|MYLK_ENST00000346322.5_Silent_p.A1231A|MYLK_ENST00000360304.3_Silent_p.A1300A Q15746 MYLK_HUMAN myosin light chain kinase 113 Lung NSC(201;0.0496) GCTCCTGGCGCGCGGCCAGGA 0.627000 0 SO:0001819 synonymous_variant ENST00000475616.1 1 1 hg19 CCDS46896.1 TCGA-HZ-A4BH-01A-11D-A26I-08 MYLK-004 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000356464.1 1 0 0 109 1320 0 225 0 9.360167e-01 0 57 0 225 2 0 0 0 0 0 2 1 1.000000 108 1305 0 218 2 -19.949160 1 1 121412 7 43 1 0 0 0 2.035354 0 0.310000 1.820000 0.301337 0.480000 0.390000 0.570000 0.480000 0.488988 0.480000 0 4.300000e-01 5.300000e-01 RYBP 23429 broad.mit.edu 37 3 72427709 72427709 + Missense_Mutation SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr3:72427709C>T ENST00000477973.2 - 4 778 c.779G>A c.(778-780)aGa>aAa p.R260K NM_012234.5 NP_036366.3 Q8N488 RYBP_HUMAN RING1 and YY1 binding protein 2 Prostate(10;0.00174)|Lung NSC(201;0.0659)|Myeloproliferative disorder(1037;0.204) TCCTTAAAGTCTGTGATAATG 0.552000 0 SO:0001583 missense ENST00000477973.2 0 1 hg19 . . . . . . . . . . C 27.5 4.834301 0.91036 . . ENSG00000163602 ENST00000477973 . . . 5.86 5.86 0.93980 . . . . . T 0.79482 0.4453 M 0.66939 2.045 . . . . . . . . . T 0.75534 -0.3284 4 . . . -15.2615 20.5632 0.99335 0.0:1.0:0.0:0.0 . . . . K 260 . . R - 2 0 RYBP 72510399 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 7.776000 0.85560 2.937000 0.99478 0.650000 0.86243 AGA TCGA-HZ-A4BH-01A-11D-A26I-08 RYBP-001 KNOWN mRNA_start_NF|cds_start_NF|basic|appris_principal protein_coding protein_coding OTTHUMT00000353762.3 1 0 1 47 238 0 51 1 9.974967e-01 8 41 0 51 2 0 0 0 0 0 2 1 1.000000 47 236 0 51 2 -20.000000 1 1 0 0 1 0 0 0 2.035354 0 0.310000 1.820000 0.301337 0.990000 0.790000 1.000000 1.000000 0.969222 0.990000 1 9.100000e-01 1 GPR15 2838 broad.mit.edu 37 3 98251438 98251438 + Missense_Mutation SNP G G C TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr3:98251438G>C ENST00000284311.3 + 1 696 c.561G>C c.(559-561)aaG>aaC p.K187N NM_005290.1 NP_005281.1 P49685 GPR15_HUMAN G protein-coupled receptor 15 p.K187N(1) 19 Lung NSC(201;7.93e-06)|all_neural(597;0.00172)|Hepatocellular(537;0.00825)|Myeloproliferative disorder(1037;0.0255) CAGAGAAAAAGGCAACTCCAA 0.473000 1 Substitution - Missense(1) SO:0001583 missense ENST00000284311.3 1 1 hg19 CCDS2931.1 . . . . . . . . . . G 0.009 -1.809317 0.00606 . . ENSG00000154165 ENST00000284311 T 0.39592 1.07 4.74 -5.96 0.02234 GPCR, rhodopsin-like superfamily (1); 1.101080 0.06952 N 0.814708 T 0.25158 0.0611 N 0.24115 0.695 0.09310 N 1 B 0.26147 0.143 B 0.24394 0.053 T 0.22765 -1.0207 10 0.27082 T 0.32 -0.0397 10.5559 0.45117 0.7354:0.1051:0.1594:0.0 . 187 P49685 GPR15_HUMAN N 187 ENSP00000284311:K187N ENSP00000284311:K187N K + 3 2 GPR15 99734128 0.000000 0.05858 0.000000 0.03702 0.004000 0.04260 -1.676000 0.01946 -1.282000 0.02396 -0.982000 0.02568 AAG TCGA-HZ-A4BH-01A-11D-A26I-08 GPR15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000358907.1 1 0 0 45 627 0 53 0 0 0 0 53 2 0 0 0 0 0 2 1 1.000000 45 622 0 52 2 -9.421888 1 1 0 0 1 0 0 0 2.035354 0 0.310000 1.820000 0.301337 0.420000 0.310000 0.550000 0.430000 0.433359 0.420000 0 3.600000e-01 4.900000e-01 PCDH18 54510 broad.mit.edu 37 4 138451227 138451227 + Silent SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr4:138451227C>T ENST00000344876.4 - 1 2402 c.2016G>A c.(2014-2016)ctG>ctA p.L672L PCDH18_ENST00000507846.1_Silent_p.L452L|PCDH18_ENST00000511115.1_Intron|PCDH18_ENST00000412923.2_Silent_p.L672L|PCDH18_ENST00000510305.1_Intron NM_019035.3 NP_061908.1 Q9HCL0 PCD18_HUMAN protocadherin 18 86 all_hematologic(180;0.24) TCATGCACTTCAGAAGGACTT 0.423000 0 SO:0001819 synonymous_variant ENST00000344876.4 1 1 hg19 CCDS34064.1 TCGA-HZ-A4BH-01A-11D-A26I-08 PCDH18-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000364614.1 1 0 0 81 881 0 139 0 2.072071e-01 0 10 0 139 2 0 0 0 0 0 2 1 1.000000 81 877 0 139 2 -18.466390 1 1 0 0 1 0 1 1 1.789989 1 0.310000 1.820000 0.184927 0.450000 0.360000 0.550000 0.460000 0.462449 0.450000 0 4.000000e-01 5.100000e-01 SEPSECS 51091 broad.mit.edu 37 4 25158572 25158572 + Silent SNP G G A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr4:25158572G>A ENST00000382103.2 - 3 366 c.294C>T c.(292-294)tcC>tcT p.S98S SEPSECS_ENST00000302922.3_Silent_p.S19S NM_016955.3 NP_058651.3 Q9HD40 SPCS_HUMAN Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase 8 Breast(46;0.173) AAATATCACCGGATCGTCCAA 0.398000 0 SO:0001819 synonymous_variant ENST00000382103.2 1 1 hg19 CCDS3432.2 TCGA-HZ-A4BH-01A-11D-A26I-08 SEPSECS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250414.2 1 0 1 77 383 0 54 0 2.688507e-01 1 5 0 54 2 0 0 0 0 0 2 1 1.000000 77 378 0 54 2 -2.825206 1 1 121412 6 40 1 1 2 3 2.082443 0 0.310000 1.820000 0.315306 0.990000 0.870000 1.000000 1.000000 0.988114 0.990000 1 9.700000e-01 1 PCDHA3 56145 broad.mit.edu 37 5 140180975 140180975 + Missense_Mutation SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr5:140180975C>T ENST00000522353.2 + 1 193 c.193C>T c.(193-195)Cgg>Tgg p.R65W PCDHA2_ENST00000520672.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000532566.2_Missense_Mutation_p.R65W|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron NM_018906.2 NP_061729.1 Q9Y5H8 PCDA3_HUMAN protocadherin alpha 3 95 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) GCGCCTGTTCCGGGTGGCGTC 0.617000 0 SO:0001583 missense ENST00000522353.2 1 1 hg19 CCDS54915.1 . . . . . . . . . . c 20.4 3.980912 0.74474 . . ENSG00000255408 ENST00000522353;ENST00000532566 T;T 0.38887 1.11;1.11 4.48 3.58 0.41010 Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1); 0.000000 0.37955 U 0.001876 T 0.78130 0.4235 H 0.99117 4.435 0.40488 D 0.980514 D;D 0.89917 1.0;1.0 D;D 0.80764 0.994;0.993 D 0.87025 0.2131 10 0.87932 D 0 . 13.635 0.62217 0.1614:0.8386:0.0:0.0 . 65;65 Q9Y5H8-2;Q9Y5H8 .;PCDA3_HUMAN W 65 ENSP00000429808:R65W;ENSP00000434086:R65W ENSP00000429808:R65W R + 1 2 PCDHA3 140161159 0.994000 0.37717 1.000000 0.80357 0.978000 0.69477 3.208000 0.51114 0.963000 0.38082 0.586000 0.80456 CGG TCGA-HZ-A4BH-01A-11D-A26I-08 PCDHA3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000372848.2 1 0 0 61 935 1 152 0 0 0 1 1 152 2 0 0 0 0 0 2 1 0.999998 56 877 1 162 20 -2.559126 1 1 0 0 1 0 0 0 1.973607 0 0.310000 1.820000 0.278695 0.370000 0.280000 0.470000 0.380000 0.382412 0.370000 0 3.200000e-01 4.300000e-01 PCDH12 51294 broad.mit.edu 37 5 141335640 141335640 + Missense_Mutation SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr5:141335640C>T ENST00000231484.3 - 1 2987 c.1777G>A c.(1777-1779)Gag>Aag p.E593K AC005740.6_ENST00000607378.1_RNA|PCDH12_ENST00000512221.1_5'Flank NM_016580.2 NP_057664.1 Q9NPG4 PCD12_HUMAN protocadherin 12 38 all_hematologic(541;0.0999) KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) TTGGGAGTCTCGATGGGCACC 0.597000 0 SO:0001583 missense ENST00000231484.3 1 1 hg19 CCDS4269.1 . . . . . . . . . . C 11.58 1.681193 0.29872 . . ENSG00000113555 ENST00000231484 T 0.53423 0.62 5.38 5.38 0.77491 . 0.194702 0.44285 D 0.000471 T 0.37019 0.0988 L 0.54323 1.7 0.43430 D 0.995596 P 0.41710 0.76 B 0.22152 0.038 T 0.39292 -0.9621 10 0.44086 T 0.13 . 14.5119 0.67794 0.0:1.0:0.0:0.0 . 593 Q9NPG4 PCD12_HUMAN K 593 ENSP00000231484:E593K ENSP00000231484:E593K E - 1 0 PCDH12 141315824 1.000000 0.71417 0.755000 0.31263 0.059000 0.15707 5.396000 0.66297 2.802000 0.96397 0.655000 0.94253 GAG TCGA-HZ-A4BH-01A-11D-A26I-08 PCDH12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251858.1 1 0 1 51 246 0 66 0 9.615120e-01 0 28 0 66 2 0 0 0 0 0 2 1 1.000000 51 242 0 66 2 -3.021709 1 1 121412 1 28 1 0 0 0 1.973607 0 0.310000 1.820000 0.278695 0.990000 0.800000 1.000000 1.000000 0.973418 0.990000 1 9.200000e-01 1 GABRG2 2566 broad.mit.edu 37 5 161576159 161576159 + Missense_Mutation SNP G G A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr5:161576159G>A ENST00000361925.4 + 8 1188 c.968G>A c.(967-969)cGg>cAg p.R323Q GABRG2_ENST00000393933.4_Missense_Mutation_p.R228Q|GABRG2_ENST00000414552.2_Missense_Mutation_p.R363Q|GABRG2_ENST00000356592.3_Missense_Mutation_p.R323Q P18507 GBRG2_HUMAN gamma-aminobutyric acid (GABA) A receptor, gamma 2 62 Renal(175;0.000319) Medulloblastoma(196;0.0208)|all_neural(177;0.0672) Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897) ACCATTGCCCGGAAATCGCTC 0.473000 0 SO:0001583 missense ENST00000361925.4 1 1 hg19 CCDS4358.1 . . . . . . . . . . G 36 5.909224 0.97093 . . ENSG00000113327 ENST00000356592;ENST00000414552;ENST00000361925;ENST00000393933 D;D;D;D 0.86432 -2.12;-2.12;-2.12;-2.12 5.88 5.88 0.94601 Neurotransmitter-gated ion-channel transmembrane domain (2); 0.000000 0.85682 D 0.000000 D 0.92789 0.7707 L 0.58925 1.835 0.80722 D 1 D;D;D 0.89917 1.0;0.998;1.0 D;D;D 0.97110 1.0;0.954;0.969 D 0.92716 0.6187 10 0.87932 D 0 . 20.2381 0.98363 0.0:0.0:1.0:0.0 . 363;323;323 F5HB82;P18507;P18507-2 .;GBRG2_HUMAN;. Q 323;363;323;228 ENSP00000349000:R323Q;ENSP00000410732:R363Q;ENSP00000354651:R323Q;ENSP00000377510:R228Q ENSP00000349000:R323Q R + 2 0 GABRG2 161508737 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 9.751000 0.98889 2.779000 0.95612 0.650000 0.86243 CGG TCGA-HZ-A4BH-01A-11D-A26I-08 GABRG2-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000252706.1 1 0 0 40 418 0 65 0 9.464194e-02 0 6 0 65 2 0 0 0 0 0 2 1 1.000000 40 416 0 65 2 -2.522913 1 1 0 0 1 0 0 0 1.973607 0 0.310000 1.820000 0.278695 0.530000 0.390000 0.700000 0.540000 0.546976 0.530000 0 4.600000e-01 6.300000e-01 SKP2 6502 broad.mit.edu 37 5 36170522 36170522 + Missense_Mutation SNP A A G TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr5:36170522A>G ENST00000274255.6 + 6 944 c.748A>G c.(748-750)Act>Gct p.T250A SKP2_ENST00000274254.5_Missense_Mutation_p.T250A|SKP2_ENST00000546211.1_Missense_Mutation_p.T36A|SKP2_ENST00000508514.1_Intron NM_005983.3 NP_005974.2 Q13309 SKP2_HUMAN S-phase kinase-associated protein 2, E3 ubiquitin protein ligase 4 all_lung(31;5.63e-05) Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202) TGCCCTGCAGACTTTGCTAAG 0.383000 0 SO:0001583 missense ENST00000274255.6 1 1 hg19 CCDS3916.1 . . . . . . . . . . A 8.341 0.828751 0.16749 . . ENSG00000145604 ENST00000274254;ENST00000274255;ENST00000308927;ENST00000513151;ENST00000546211 T;T;T;T 0.48836 0.8;0.8;0.8;0.8 5.53 3.19 0.36642 . 0.419284 0.28365 N 0.015605 T 0.31199 0.0789 L 0.37507 1.11 0.24045 N 0.996061 B;B;B 0.02656 0.0;0.0;0.0 B;B;B 0.06405 0.002;0.001;0.0 T 0.24083 -1.0170 10 0.07644 T 0.81 -7.1949 8.9256 0.35639 0.8857:0.0:0.1143:0.0 . 36;250;250 B4DJT4;Q13309-2;Q13309 .;.;SKP2_HUMAN A 250;250;216;205;36 ENSP00000274254:T250A;ENSP00000274255:T250A;ENSP00000423188:T205A;ENSP00000443492:T36A ENSP00000274254:T250A T + 1 0 SKP2 36206279 0.702000 0.27816 0.988000 0.46212 0.883000 0.51084 1.206000 0.32321 0.546000 0.28920 0.533000 0.62120 ACT TCGA-HZ-A4BH-01A-11D-A26I-08 SKP2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253769.2 1 0 0 25 418 0 48 0 1.968732e-01 1 13 0 48 2 0 0 0 0 0 2 1 1.000000 25 415 0 48 2 -20.000000 1 1 0 0 1 0 0 0 2.035507 0 0.310000 1.820000 0.301337 0.360000 0.230000 0.510000 0.360000 0.370330 0.360000 0 2.900000e-01 4.400000e-01 ADAMTS16 170690 broad.mit.edu 37 5 5239938 5239938 + Missense_Mutation SNP G G A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr5:5239938G>A ENST00000274181.7 + 16 2561 c.2423G>A c.(2422-2424)cGg>cAg p.R808Q NM_139056.2 NP_620687.2 Q8TE57 ATS16_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 16 107 TGGCCCGGCCGGTACAAATTT 0.512000 0 SO:0001583 missense ENST00000274181.7 1 1 hg19 CCDS43299.1 . . . . . . . . . . G 14.86 2.660533 0.47572 . . ENSG00000145536 ENST00000274181;ENST00000536857 T 0.50277 0.75 5.56 4.69 0.59074 ADAM-TS Spacer 1 (1); 0.275899 0.31020 N 0.008407 T 0.32041 0.0816 L 0.35542 1.07 0.09310 N 0.999998 B;B 0.26081 0.141;0.085 B;B 0.18561 0.02;0.022 T 0.14868 -1.0457 10 0.26408 T 0.33 . 7.7049 0.28644 0.246:0.0:0.754:0.0 . 808;808 Q8TE57;Q8TE57-2 ATS16_HUMAN;. Q 808 ENSP00000274181:R808Q ENSP00000274181:R808Q R + 2 0 ADAMTS16 5292938 0.005000 0.15991 0.498000 0.27564 0.973000 0.67179 1.239000 0.32719 1.355000 0.45865 0.655000 0.94253 CGG TCGA-HZ-A4BH-01A-11D-A26I-08 ADAMTS16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000365657.1 1 0 0 50 672 0 75 0 2.857254e-01 0 15 0 75 2 0 0 0 0 0 2 1 1.000000 50 662 0 73 2 -2.774725 1 1 120814 9 41 1 0 0 0 2.035507 0 0.310000 1.820000 0.301337 0.430000 0.330000 0.560000 0.440000 0.447389 0.430000 0 3.800000e-01 5.100000e-01 CKMT2 1160 broad.mit.edu 37 5 80550266 80550266 + Missense_Mutation SNP G G A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr5:80550266G>A ENST00000424301.2 + 5 641 c.403G>A c.(403-405)Gac>Aac p.D135N CKMT2-AS1_ENST00000503483.2_RNA|CKMT2-AS1_ENST00000505295.1_RNA|CKMT2-AS1_ENST00000511495.1_RNA|CKMT2_ENST00000437669.1_Missense_Mutation_p.D135N|CKMT2-AS1_ENST00000500148.2_RNA|CKMT2-AS1_ENST00000502041.2_RNA|CKMT2-AS1_ENST00000501927.2_RNA|CKMT2-AS1_ENST00000512287.1_RNA|CKMT2_ENST00000254035.4_Missense_Mutation_p.D135N NM_001825.2 NP_001816.2 P17540 KCRS_HUMAN creatine kinase, mitochondrial 2 (sarcomeric) 17 Lung NSC(167;0.00475)|all_lung(232;0.00502)|Ovarian(174;0.0336) Creatine(DB00148) CAACGGCTATGACCCCAGGGT 0.532000 0 SO:0001583 missense ENST00000424301.2 1 1 hg19 CCDS4053.1 . . . . . . . . . . G 19.09 3.760757 0.69763 . . ENSG00000131730 ENST00000254035;ENST00000511719;ENST00000437669;ENST00000424301;ENST00000505060 T;T;T;T;T 0.63913 -0.07;-0.07;-0.07;-0.07;-0.07 5.61 5.61 0.85477 ATP:guanido phosphotransferase, N-terminal (2); 0.000000 0.85682 D 0.000000 T 0.64605 0.2613 M 0.69185 2.1 0.80722 D 1 B 0.06786 0.001 B 0.06405 0.002 T 0.61267 -0.7097 10 0.54805 T 0.06 -10.8422 19.6449 0.95773 0.0:0.0:1.0:0.0 . 135 P17540 KCRS_HUMAN N 135 ENSP00000254035:D135N;ENSP00000423264:D135N;ENSP00000410289:D135N;ENSP00000404203:D135N;ENSP00000427635:D135N ENSP00000254035:D135N D + 1 0 CKMT2 80586022 1.000000 0.71417 1.000000 0.80357 0.634000 0.38068 7.641000 0.83368 2.627000 0.88993 0.563000 0.77884 GAC TCGA-HZ-A4BH-01A-11D-A26I-08 CKMT2-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000369600.1 1 0 0 25 347 0 86 0 1.039398e-01 0 8 0 86 2 0 0 0 0 0 2 1 1.000000 24 344 0 85 2 -7.418816 1 1 0 0 1 0 0 0 1.973607 0 0.310000 1.820000 0.278695 0.410000 0.270000 0.580000 0.410000 0.426065 0.410000 0 3.400000e-01 5.000000e-01 SLC16A10 117247 broad.mit.edu 37 6 111498424 111498424 + Missense_Mutation SNP G G C TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr6:111498424G>C ENST00000368851.5 + 3 673 c.498G>C c.(496-498)gaG>gaC p.E166D SLC16A10_ENST00000368850.3_5'UTR|SLC16A10_ENST00000465319.1_3'UTR NM_018593.4 NP_061063.2 Q8TF71 MOT10_HUMAN solute carrier family 16 (aromatic amino acid transporter), member 10 12 all_cancers(87;0.00172)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0313)|Colorectal(196;0.0466) Droxidopa(DB06262)|Glycine(DB00145)|L-Alanine(DB00160)|L-Arginine(DB00125)|L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)|L-Cysteine(DB00151)|L-Cystine(DB00138)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Histidine(DB00117)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Lysine(DB00123)|L-Methionine(DB00134)|L-Phenylalanine(DB00120)|L-Proline(DB00172)|L-Serine(DB00133)|L-Threonine(DB00156)|L-Tryptophan(DB00150)|L-Tyrosine(DB00135)|L-Valine(DB00161)|Liothyronine(DB00279)|Liotrix(DB01583)|Pyruvic acid(DB00119) GTTCCATCGAGCCTCTGTACC 0.398000 0 SO:0001583 missense ENST00000368851.5 1 1 hg19 CCDS5089.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 12.30|12.30 1.897900|1.897900 0.33535|0.33535 .|. .|. ENSG00000112394|ENSG00000112394 ENST00000535637;ENST00000368851;ENST00000368853|ENST00000419619;ENST00000439288 T|. 0.37058|. 1.22|. 5.22|5.22 2.37|2.37 0.29283|0.29283 Major facilitator superfamily domain, general substrate transporter (1);|. 0.144833|. 0.64402|. N|. 0.000008|. T|T 0.43500|0.43500 0.1250|0.1250 M|M 0.64404|0.64404 1.975|1.975 0.80722|0.80722 D|D 1|1 P;D|. 0.56521|. 0.786;0.976|. P;P|. 0.62298|. 0.76;0.9|. T|T 0.42447|0.42447 -0.9451|-0.9451 10|5 0.19147|. T|. 0.46|. .|. 4.3484|4.3484 0.11143|0.11143 0.2966:0.0:0.542:0.1614|0.2966:0.0:0.542:0.1614 .|. 166;166|. Q8TF71;Q05BR4|. MOT10_HUMAN;.|. D|T 166;166;57|52 ENSP00000357844:E166D|. ENSP00000357844:E166D|. E|S +|+ 3|2 2|0 SLC16A10|SLC16A10 111605117|111605117 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.986000|0.986000 0.74619|0.74619 0.672000|0.672000 0.25187|0.25187 0.653000|0.653000 0.30826|0.30826 0.563000|0.563000 0.77884|0.77884 GAG|AGC TCGA-HZ-A4BH-01A-11D-A26I-08 SLC16A10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041822.2 1 0 1 45 384 0 56 0 2.482022e-01 0 9 0 56 2 0 0 0 0 0 2 1 1.000000 45 377 0 55 2 -20.000000 1 1 0 0 1 0 1 1 1.912280 0 0.310000 1.820000 0.258264 0.620000 0.460000 0.810000 0.630000 0.636262 0.620000 0 5.400000e-01 7.200000e-01 PRL 5617 broad.mit.edu 37 6 22294688 22294688 + Missense_Mutation SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr6:22294688C>T ENST00000306482.1 - 2 672 c.154G>A c.(154-156)Gtc>Atc p.V52I RP3-404K8.2_ENST00000561912.1_RNA NM_000948.5|NM_001163558.2 NP_000939.1|NP_001157030.1 P01236 PRL_HUMAN prolactin 16 Ovarian(93;0.163) TGGGACAGGACGACGGCGCGG 0.582000 0 SO:0001583 missense ENST00000306482.1 1 1 hg19 CCDS4548.1 . . . . . . . . . . C 12.63 1.996710 0.35226 . . ENSG00000172179 ENST00000306482 D 0.88741 -2.42 5.85 0.828 0.18841 Four-helical cytokine-like, core (1);Four-helical cytokine, core (1); 0.538216 0.21188 N 0.078687 T 0.49795 0.1578 N 0.02854 -0.475 0.19945 N 0.999948 B;B 0.02656 0.0;0.0 B;B 0.04013 0.001;0.001 T 0.52495 -0.8568 10 0.28530 T 0.3 0.6696 5.8852 0.18878 0.0:0.2086:0.129:0.6624 . 52;53 P01236;Q5I0G2 PRL_HUMAN;. I 52 ENSP00000302150:V52I ENSP00000302150:V52I V - 1 0 PRL 22402667 0.999000 0.42202 0.922000 0.36590 0.815000 0.46073 0.547000 0.23299 0.122000 0.18314 -0.471000 0.05019 GTC TCGA-HZ-A4BH-01A-11D-A26I-08 PRL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000043327.1 1 0 1 44 336 0 74 0 0 0 0 74 2 0 0 0 0 0 2 1 1.000000 43 334 0 74 2 -17.293210 1 1 121412 2 32 1 1 2 3 2.059508 0 0.310000 1.820000 0.311068 0.740000 0.550000 0.980000 0.740000 0.756057 0.740000 0 6.400000e-01 8.600000e-01 EYS 346007 broad.mit.edu 37 6 66063415 66063415 + Missense_Mutation SNP G G C TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr6:66063415G>C ENST00000370621.3 - 9 1921 c.1395C>G c.(1393-1395)ttC>ttG p.F465L EYS_ENST00000370618.3_Missense_Mutation_p.F465L|EYS_ENST00000370616.2_Missense_Mutation_p.F465L|EYS_ENST00000393380.2_Missense_Mutation_p.F465L|EYS_ENST00000503581.1_Missense_Mutation_p.F465L|EYS_ENST00000342421.5_Missense_Mutation_p.F465L Q5T1H1 EYS_HUMAN eyes shut homolog (Drosophila) 69 AAATACCATGGAAGGTGACTC 0.373000 0 SO:0001583 missense ENST00000370621.3 1 1 hg19 . . . . . . . . . . g 7.119 0.577517 0.13686 . . ENSG00000188107 ENST00000503581;ENST00000370621;ENST00000370616;ENST00000393380;ENST00000342421;ENST00000370618 T;T;T;T;T;T 0.18174 2.23;2.23;2.23;2.23;2.23;2.23 4.14 0.278 0.15673 . . . . . T 0.01800 0.0057 N 0.08118 0 0.09310 N 1 B;B;B 0.09022 0.001;0.002;0.001 B;B;B 0.09377 0.004;0.003;0.003 T 0.48875 -0.8996 9 0.11794 T 0.64 . 6.6386 0.22897 0.4292:0.0:0.5708:0.0 . 465;465;465 Q5T1H1-1;Q5T1H1-2;Q5SZM4 .;.;. L 465 ENSP00000424243:F465L;ENSP00000359655:F465L;ENSP00000359650:F465L;ENSP00000377042:F465L;ENSP00000341818:F465L;ENSP00000359652:F465L ENSP00000341818:F465L F - 3 2 EYS 66120136 0.000000 0.05858 0.000000 0.03702 0.066000 0.16364 -0.195000 0.09546 -0.034000 0.13713 0.591000 0.81541 TTC TCGA-HZ-A4BH-01A-11D-A26I-08 EYS-001 KNOWN basic protein_coding protein_coding OTTHUMT00000351351.3 1 0 1 70 448 0 44 0 0 0 0 44 2 0 0 0 0 0 2 1 1.000000 70 448 0 44 2 -20.000000 1 1 0 0 1 1 2 3 2.058211 0 0.310000 1.820000 0.311068 0.870000 0.690000 1.000000 1.000000 0.872952 0.870000 1 7.700000e-01 9.700000e-01 MYO1G 64005 broad.mit.edu 37 7 45003667 45003667 + Missense_Mutation SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr7:45003667C>T ENST00000258787.7 - 20 2862 c.2726G>A c.(2725-2727)cGg>cAg p.R909Q NM_033054.2 NP_149043.2 B0I1T2 MYO1G_HUMAN myosin IG 28 GGGCACGGCCCGCATCACCCG 0.637000 0 SO:0001583 missense ENST00000258787.7 0 1 hg19 CCDS34629.1 . . . . . . . . . . C 20.3 3.962493 0.74016 2.28E-4 0.0 ENSG00000136286 ENST00000258787 T 0.39056 1.1 4.24 4.24 0.50183 Myosin tail 2 (1); 0.000000 0.33792 N 0.004548 T 0.32194 0.0821 M 0.62016 1.91 0.35794 D 0.82262 P 0.38677 0.642 B 0.26416 0.069 T 0.41875 -0.9484 10 0.15952 T 0.53 . 12.0407 0.53452 0.0:0.8248:0.1752:0.0 . 909 B0I1T2 MYO1G_HUMAN Q 909 ENSP00000258787:R909Q ENSP00000258787:R909Q R - 2 0 MYO1G 44970192 0.998000 0.40836 0.994000 0.49952 0.695000 0.40330 3.509000 0.53386 2.286000 0.76751 0.655000 0.94253 CGG TCGA-HZ-A4BH-01A-11D-A26I-08 MYO1G-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000341832.2 1 0 0 7 40 0 8 0 9.217702e-01 0 29 0 8 2 0 0 0 0 0 2 1 0.983479 7 40 0 8 2 -14.005020 1 1 120834 5 32 1 0 2 2 1.883342 1 0.310000 1.820000 0.310000 0.990000 0.470000 1.000000 1.000000 0.896844 0.990000 1 7.100000e-01 1 DEFB136 613210 broad.mit.edu 37 8 11831528 11831528 + Missense_Mutation SNP G G A TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr8:11831528G>A ENST00000382209.2 - 2 154 c.155C>T c.(154-156)gCg>gTg p.A52V NM_001033018.2 NP_001028190.2 Q30KP8 DB136_HUMAN defensin, beta 136 7 STAD - Stomach adenocarcinoma(15;0.033) GTGGCAGAACGCAATCCACCT 0.458000 0 SO:0001583 missense ENST00000382209.2 1 1 hg19 CCDS43709.1 . . . . . . . . . . G 13.05 2.122435 0.37436 . . ENSG00000205884 ENST00000382209 T 0.17691 2.26 4.06 2.2 0.27929 . 0.810105 0.10785 N 0.634395 T 0.23727 0.0574 . . . 0.09310 N 1 D 0.63046 0.992 P 0.52066 0.689 T 0.12016 -1.0564 9 0.66056 D 0.02 0.1607 5.4674 0.16650 0.1106:0.2046:0.6848:0.0 . 52 Q30KP8 DB136_HUMAN V 52 ENSP00000371644:A52V ENSP00000371644:A52V A - 2 0 DEFB136 11868937 0.000000 0.05858 0.001000 0.08648 0.002000 0.02628 0.184000 0.16939 0.628000 0.30357 0.555000 0.69702 GCG TCGA-HZ-A4BH-01A-11D-A26I-08 DEFB136-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000351889.1 1 0 0 85 1083 0 169 0 0 0 0 169 2 0 0 0 0 0 2 1 1.000000 84 1076 0 169 2 -15.381800 1 1 120920 1 37 1 0 1 1 1.961253 0 0.310000 1.820000 0.258264 0.430000 0.340000 0.530000 0.440000 0.440060 0.430000 0 3.800000e-01 4.800000e-01 NTNG2 84628 broad.mit.edu 37 9 135073821 135073821 + Missense_Mutation SNP C C T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr9:135073821C>T ENST00000393229.3 + 3 1458 c.682C>T c.(682-684)Cgc>Tgc p.R228C NTNG2_ENST00000372179.3_Missense_Mutation_p.R228C|NTNG2_ENST00000393228.4_Missense_Mutation_p.R228C|NTNG2_ENST00000360670.3_Missense_Mutation_p.R228C NM_032536.2 NP_115925.2 Q96CW9 NTNG2_HUMAN netrin G2 29 CCCCGACCTGCGCAACATGGA 0.667000 0 SO:0001583 missense ENST00000393229.3 0 1 hg19 CCDS6946.1 . . . . . . . . . . C 21.2 4.113959 0.77210 . . ENSG00000196358 ENST00000393229;ENST00000393228;ENST00000360670;ENST00000372179 T;T;T;T 0.75821 -0.97;-0.97;-0.97;-0.97 5.22 5.22 0.72569 Laminin, N-terminal (3); 0.068253 0.64402 D 0.000020 T 0.77054 0.4074 L 0.57536 1.79 0.49915 D 0.999837 D 0.71674 0.998 P 0.52309 0.695 T 0.79227 -0.1890 10 0.62326 D 0.03 . 11.6166 0.51094 0.284:0.716:0.0:0.0 . 228 Q96CW9 NTNG2_HUMAN C 228 ENSP00000376921:R228C;ENSP00000376920:R228C;ENSP00000353888:R228C;ENSP00000361252:R228C ENSP00000353888:R228C R + 1 0 NTNG2 134063642 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 3.164000 0.50770 2.417000 0.82017 0.561000 0.74099 CGC TCGA-HZ-A4BH-01A-11D-A26I-08 NTNG2-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000054779.1 0 0 0 11 413 0 116 0 2.106905e-02 0 8 0 116 2 0 0 0 0 0 2 1 0.998222 11 406 0 115 2 -3.125807 1 1 0 0 1 0 2 2 1.904342 1 0.310000 1.820000 0.310000 0.180000 0.080000 1.000000 0.160000 0.294703 0.180000 0 1.200000e-01 3.000000e-01 FAM154A 158297 broad.mit.edu 37 9 18941744 18941744 + Silent SNP C C T rs112030642 TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr9:18941744C>T ENST00000380534.4 - 3 591 c.312G>A c.(310-312)acG>acA p.T104T FAM154A_ENST00000542071.1_Intron|FAM154A_ENST00000380530.1_Intron NM_153707.2 NP_714918.2 Q8IYX7 F154A_HUMAN family with sequence similarity 154, member A 26 CTTTCTTATACGTCGTGAGCA 0.478000 0 SO:0001819 synonymous_variant ENST00000380534.4 1 1 hg19 CCDS6487.1 TCGA-HZ-A4BH-01A-11D-A26I-08 FAM154A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051811.1 1 0 1 104 412 0 76 0 0 0 0 76 2 0 0 0 0 0 2 1 1.000000 101 405 0 76 2 -20.000000 1 1 121412 1 38 1 0 1 1 1.728485 1 0.310000 1.820000 0.183432 0.960000 0.850000 1.000000 0.990000 0.956610 0.960000 1 9.100000e-01 9.900000e-01 CDKN2A 1029 broad.mit.edu 37 9 21971111 21971111 + Missense_Mutation SNP G G C rs121913385 TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr9:21971111G>C ENST00000304494.5 - 2 517 c.247C>G c.(247-249)Cac>Gac p.H83D CDKN2A_ENST00000530628.2_Missense_Mutation_p.A97G|CDKN2A_ENST00000498124.1_Missense_Mutation_p.H83D|CDKN2A_ENST00000579755.1_Missense_Mutation_p.A97G|CDKN2A_ENST00000494262.1_Missense_Mutation_p.H32D|CDKN2A_ENST00000497750.1_Missense_Mutation_p.H32D|CDKN2A_ENST00000578845.2_Missense_Mutation_p.H32D|CDKN2A_ENST00000446177.1_Missense_Mutation_p.H83D|CDKN2A_ENST00000361570.3_Missense_Mutation_p.A138G|CDKN2A_ENST00000498628.2_Missense_Mutation_p.H32D|CDKN2A_ENST00000579122.1_Missense_Mutation_p.H83D|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000479692.2_Missense_Mutation_p.H32D NM_000077.4 NP_000068.1 P42771 CD2A1_HUMAN cyclin-dependent kinase inhibitor 2A p.0?(1315)|p.?(44)|p.H83Y(30)|p.A138V(2)|p.H83fs*2(2)|p.H83N(1)|p.V82fs*62(1)|p.0(1)|p.V82_G89>G(1)|p.E61_L94del(1)|p.R137fs*48(1)|p.A68fs*3(1)|p.P81_A85del(1)|p.R80fs*34(1)|p.V82_E88del(1) 4199 all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172) GCAGCGTCGTGCACGGGTCGG 0.741000 H83Y(CALU3_LUNG)|H83Y(HS944T_SKIN)|H83Y(JHH2_LIVER)|H83Y(OPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|H83Y(SEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE) 17 HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07) 1403 Whole gene deletion(1316)|Unknown(44)|Substitution - Missense(33)|Deletion - Frameshift(6)|Deletion - In frame(3)|Complex - deletion inframe(1) GRCh37 CM053801|CM056557 CDKN2A M rs121913385 SO:0001583 missense ENST00000304494.5 1 1 hg19 CCDS6510.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 22.6|22.6 4.311283|4.311283 0.81358|0.81358 .|. .|. ENSG00000147889|ENSG00000147889 ENST00000361570;ENST00000530628|ENST00000304494;ENST00000446177 T;T|T;T 0.80393|0.71341 -1.37;-1.3|-0.56;-0.56 5.93|5.93 5.93|5.93 0.95920|0.95920 .|Ankyrin repeat-containing domain (4); 0.000000|. 0.37261|. N|. 0.002164|. T|T 0.77370|0.77370 0.4120|0.4120 L|L 0.27053|0.27053 0.805|0.805 0.45962|0.45962 D|D 0.998784|0.998784 P|D 0.36144|0.71674 0.539|0.998 B|D 0.37480|0.79784 0.251|0.993 T|T 0.77773|0.77773 -0.2462|-0.2462 10|9 0.54805|0.52906 T|T 0.06|0.07 -15.192|-15.192 19.1026|19.1026 0.93279|0.93279 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. 138|83 Q8N726|P42771 CD2A2_HUMAN|CD2A1_HUMAN G|D 138;97|83 ENSP00000355153:A138G;ENSP00000432664:A97G|ENSP00000307101:H83D;ENSP00000394932:H83D ENSP00000355153:A138G|ENSP00000307101:H83D A|H -|- 2|1 0|0 CDKN2A|CDKN2A 21961111|21961111 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.915000|0.915000 0.54546|0.54546 8.665000|8.665000 0.91144|0.91144 2.803000|2.803000 0.96430|0.96430 0.650000|0.650000 0.86243|0.86243 GCA|CAC TCGA-HZ-A4BH-01A-11D-A26I-08 CDKN2A-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000051915.1 1 0 0 17 113 0 27 1 9.999954e-01 154 1 0 27 2 1 9.875572e-01 9 42 0 139 2 1 0.999904 14 96 0 26 2 -20.000000 1 1 0 0 1 0 1 1 1.728485 1 0.310000 1.820000 0.183432 0.690000 0.430000 0.950000 0.690000 0.702028 0.690000 0 5.500000e-01 8.400000e-01 NUDT2 318 broad.mit.edu 37 9 34343390 34343390 + Missense_Mutation SNP G G T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chr9:34343390G>T ENST00000379158.2 + 5 754 c.396G>T c.(394-396)aaG>aaT p.K132N NUDT2_ENST00000346365.4_Missense_Mutation_p.K132N|NUDT2_ENST00000379155.5_Missense_Mutation_p.K132N NM_001161.4 NP_001152.1 P50583 AP4A_HUMAN nudix (nucleoside diphosphate linked moiety X)-type motif 2 3 LUSC - Lung squamous cell carcinoma(29;0.0107) AGGAGATGAAGGCAGCGCTCC 0.567000 Melanoma(95;1683 1957 4276 39813) 0 SO:0001583 missense ENST00000379158.2 1 1 hg19 CCDS6552.1 . . . . . . . . . . G 13.92 2.382081 0.42207 . . ENSG00000164978 ENST00000337747;ENST00000379154;ENST00000379155;ENST00000346365;ENST00000379158 T;T;T 0.08458 3.09;3.09;3.09 5.88 4.99 0.66335 NUDIX hydrolase domain (3);NUDIX hydrolase domain-like (1); 0.205060 0.56097 D 0.000038 T 0.11665 0.0284 L 0.55481 1.735 0.51233 D 0.999916 B 0.26483 0.15 B 0.34536 0.185 T 0.03969 -1.0988 10 0.56958 D 0.05 -18.5143 9.5184 0.39120 0.1987:0.0:0.8013:0.0 . 132 P50583 AP4A_HUMAN N 132 ENSP00000368452:K132N;ENSP00000344187:K132N;ENSP00000368455:K132N ENSP00000338397:K132N K + 3 2 NUDT2 34333390 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 4.713000 0.61895 1.509000 0.48786 0.561000 0.74099 AAG TCGA-HZ-A4BH-01A-11D-A26I-08 NUDT2-001 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052160.2 0 0 0 11 300 0 52 1 5.962846e-01 3 51 0 52 2 0 0 0 0 0 2 1 0.998323 11 297 0 52 2 -11.967900 1 1 0 0 1 0 1 1 1.728485 1 0.310000 1.820000 0.183432 0.190000 0.100000 0.320000 0.190000 0.206020 0.190000 0 1.400000e-01 2.600000e-01 FAM47A 158724 broad.mit.edu 37 X 34150323 34150323 + Silent SNP G G T TCGA-HZ-A4BH-01A-11D-A26I-08 TCGA-HZ-A4BH-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 449b0a3a-5c4c-4117-852f-5b732b395e80 f65e31fb-81af-4b3c-82cf-bd086025d453 g.chrX:34150323G>T ENST00000346193.3 - 1 124 c.73C>A c.(73-75)Cgg>Agg p.R25R NM_203408.3 NP_981953.2 Q5JRC9 FA47A_HUMAN family with sequence similarity 47, member A 97 TTGGAAGGCCGTTTGTTACAG 0.612000 0 SO:0001819 synonymous_variant ENST00000346193.3 1 1 hg19 CCDS43926.1 TCGA-HZ-A4BH-01A-11D-A26I-08 FAM47A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056205.1 1 0 0 16 247 0 36 0 0 0 0 36 2 0 0 0 0 0 2 1 0.999941 16 247 0 36 2 -5.615640 1 1 0 0 1 0 1 1 0.310000 1.820000 0.310000 0.190000 0.110000 0.300000 0.190000 0.205188 0.190000 0 1.500000e-01 2.500000e-01