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 MYH7B 57644 broad.mit.edu 37 20 33586211 33586212 + Frame_Shift_Del DEL AC AC - TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr20:33586211_33586212delAC ENST00000262873.7 + 31 4079_4080 c.3987_3988delAC c.(3985-3990)ctacagfs p.Q1330fs NM_020884.3 NP_065935.2 A7E2Y1 MYH7B_HUMAN myosin, heavy chain 7B, cardiac muscle, beta 54 BRCA - Breast invasive adenocarcinoma(18;0.00691) GTGGGCGACTACAGACGGAAAG 0.649000 0 SO:0001589 frameshift_variant ENST00000262873.7 1 1 hg19 CCDS42869.1 TCGA-3A-A9J0-01A-11D-A40W-08 MYH7B-001 NOVEL basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000078833.2 1 0 0 66 458 0 97 0 1.255107e-01 0 5 0 97 2 0 0 0 0 0 0 1 0.999997 71 454 2 93 26 -20.000000 1 1 0 0 1 1 3 4 2.263571 1 0.470000 3.280000 0.639456 0.780000 6.100000e-01 0.970000 0.800000 0.795274 0.780000 0 SLC12A5 57468 broad.mit.edu 37 20 44685140 44685142 + In_Frame_Del DEL AGA AGA - TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr20:44685140_44685142delAGA ENST00000454036.2 + 23 3165_3167 c.3116_3118delAGA c.(3115-3120)gagaag>gag p.K1040del SLC12A5_ENST00000243964.3_In_Frame_Del_p.K1017del NM_001134771.1 NP_001128243.1 Q9H2X9 S12A5_HUMAN solute carrier family 12 (potassium/chloride transporter), member 5 80 Myeloproliferative disorder(115;0.0122) Bumetanide(DB00887)|Potassium Chloride(DB00761) TCGGTGGCAGAGAAGAATAAGGG 0.635000 0 SO:0001651 inframe_deletion ENST00000454036.2 0 1 hg19 CCDS46610.1 TCGA-3A-A9J0-01A-11D-A40W-08 SLC12A5-003 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000471538.1 1 0 0 18 249 0 49 0 0 0 49 0 0 0 0 0 0 1 0.241023 25 251 2 50 24 -19.995170 1 0 0 0 1 1 3 4 2.263571 1 0.470000 3.280000 0.639456 0.420000 2.600000e-01 0.630000 0.430000 0.440905 0.420000 0 ANKRD50 57182 broad.mit.edu 37 4 125599951 125599952 + Frame_Shift_Ins INS - - A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr4:125599951_125599952insA ENST00000504087.1 - 3 1658_1659 c.621_622insT c.(619-624)tctaccfs p.T208fs ANKRD50_ENST00000515641.1_Frame_Shift_Ins_p.T29fs NM_020337.2 NP_065070.1 Q9ULJ7 ANR50_HUMAN ankyrin repeat domain 50 55 GATAAGCTGGTAGACGTTTGTT 0.475000 0 SO:0001589 frameshift_variant ENST00000504087.1 0 1 hg19 CCDS34060.1 TCGA-3A-A9J0-01A-11D-A40W-08 ANKRD50-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000364775.1 1 0 0 219 735 0 130 0 0 0 130 0 0 0 0 0 0 1 1.000000 220 731 0 127 2 -20.000000 1 1 0 0 1 1 2 3 1.838072 1 0.470000 3.280000 0.566728 0.990000 9.900000e-01 1.000000 1.000000 0.999958 0.990000 1 CPXM2 119587 broad.mit.edu 37 10 125557591 125557591 + Missense_Mutation SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr10:125557591C>T ENST00000241305.3 - 6 944 c.790G>A c.(790-792)Gtc>Atc p.V264I CPXM2_ENST00000368854.3_5'UTR NM_198148.2 NP_937791.2 Q8N436 CPXM2_HUMAN carboxypeptidase X (M14 family), member 2 47 all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233) ACCATGGGGACGGGTAGCTCA 0.483000 0 SO:0001583 missense ENST00000241305.3 1 1 hg19 CCDS7637.1 . . . . . . . . . . C 6.854 0.526842 0.13066 . . ENSG00000121898 ENST00000241305;ENST00000540123;ENST00000418782 D 0.98164 -4.76 4.46 4.46 0.54185 Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1); 0.450854 0.23631 N 0.046134 D 0.95850 0.8649 L 0.45051 1.395 0.25694 N 0.985655 P 0.41420 0.749 B 0.36534 0.227 D 0.90460 0.4445 10 0.23891 T 0.37 -14.947 17.3109 0.87210 0.0:1.0:0.0:0.0 . 264 Q8N436 CPXM2_HUMAN I 264;97;264 ENSP00000241305:V264I ENSP00000241305:V264I V - 1 0 CPXM2 125547581 0.000000 0.05858 0.972000 0.41901 0.126000 0.20510 0.687000 0.25407 2.292000 0.77174 0.557000 0.71058 GTC TCGA-3A-A9J0-01A-11D-A40W-08 CPXM2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050853.1 1 0 0 19 240 0 46 0 4.267932e-01 0 19 0 46 2 0 0 0 0 0 2 1 0.999990 19 235 0 43 2 -6.781784 1 1 121412 20 43 1 0 3 3 1.934708 1 0.470000 3.280000 0.570850 0.380000 2.400000e-01 0.570000 0.390000 0.401540 0.380000 0 ARHGAP21 57584 broad.mit.edu 37 10 24959236 24959236 + Missense_Mutation SNP T T G TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr10:24959236T>G ENST00000396432.2 - 3 640 c.154A>C c.(154-156)Acg>Ccg p.T52P NM_020824.3 NP_065875.3 Q5T5U3 RHG21_HUMAN Rho GTPase activating protein 21 78 CTTTTCAACGTAACTGTTTTG 0.343000 0 SO:0001583 missense ENST00000396432.2 1 1 hg19 CCDS7144.2 . . . . . . . . . . T 10.53 1.375711 0.24857 . . ENSG00000107863 ENST00000396432;ENST00000447364;ENST00000376410;ENST00000446003;ENST00000416305 T;T;T;T 0.19250 2.16;2.16;2.16;2.16 5.19 -0.861 0.10676 PDZ/DHR/GLGF (2); 0.700803 0.15367 N 0.266050 T 0.19046 0.0457 M 0.63843 1.955 0.09310 N 1 B;B;B 0.15719 0.014;0.011;0.002 B;B;B 0.28638 0.077;0.092;0.039 T 0.29792 -1.0000 10 0.52906 T 0.07 . 3.228 0.06739 0.1417:0.131:0.5257:0.2015 . 52;51;51 F8W9U9;Q5T5U2;Q5T5U3 .;.;RHG21_HUMAN P 52;51;52;52;41 ENSP00000379709:T52P;ENSP00000365592:T52P;ENSP00000405018:T52P;ENSP00000400566:T41P ENSP00000365592:T52P T - 1 0 ARHGAP21 24999242 0.001000 0.12720 0.006000 0.13384 0.925000 0.55904 0.156000 0.16382 -0.015000 0.14150 -0.321000 0.08615 ACG TCGA-3A-A9J0-01A-11D-A40W-08 ARHGAP21-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047229.4 0 0 0 21 323 1 78 1 1.212428e-01 3 16 1 78 3 0 0 0 0 0 2 1 0.873978 20 319 1 78 15 -6.276031 1 1 0 0 1 0 3 3 1.931745 1 0.470000 3.280000 0.570850 0.320000 2.000000e-01 0.470000 0.330000 0.333422 0.320000 0 IL2RA 3559 broad.mit.edu 37 10 6063598 6063598 + Silent SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr10:6063598G>A ENST00000379959.3 - 4 599 c.426C>T c.(424-426)ttC>ttT p.F142F IL2RA_ENST00000379954.1_Intron|IL2RA_ENST00000256876.6_Silent_p.F142F NM_000417.2 NP_000408.1 P01589 IL2RA_HUMAN interleukin 2 receptor, alpha p.F142F(2) 17 Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004) GCCCCACCACGAAATGATAAA 0.512000 2 Substitution - coding silent(2) SO:0001819 synonymous_variant ENST00000379959.3 1 1 hg19 CCDS7076.1 TCGA-3A-A9J0-01A-11D-A40W-08 IL2RA-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000046627.1 1 0 1 85 303 0 76 0 3.054982e-01 0 5 0 76 2 0 0 0 0 0 2 1 1.000000 84 294 0 74 2 -20.000000 1 1 121412 1 33 1 0 3 3 1.931745 1 0.470000 3.280000 0.570850 0.990000 9.400000e-01 1.000000 1.000000 0.996612 0.990000 1 MCAM 4162 broad.mit.edu 37 11 119182565 119182565 + Missense_Mutation SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr11:119182565C>T ENST00000264036.4 - 10 1252 c.1238G>A c.(1237-1239)aGc>aAc p.S413N MCAM_ENST00000392814.1_Missense_Mutation_p.S362N NM_006500.2 NP_006491.2 P43121 MUC18_HUMAN melanoma cell adhesion molecule 22 Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112) GCCGGGTATGCTGGGCACAGA 0.617000 0 SO:0001583 missense ENST00000264036.4 0 1 hg19 CCDS31690.1 . . . . . . . . . . C 14.87 2.664926 0.47572 . . ENSG00000076706 ENST00000264036;ENST00000392814 T;T 0.15256 2.44;2.44 4.86 1.75 0.24633 Immunoglobulin subtype 2 (1);Immunoglobulin-like (1); . . . . T 0.20577 0.0495 M 0.80183 2.485 0.22354 N 0.999179 B 0.20671 0.047 B 0.20577 0.03 T 0.17684 -1.0361 9 0.38643 T 0.18 -5.4 6.2247 0.20701 0.0:0.5299:0.3693:0.1008 . 413 P43121 MUC18_HUMAN N 413;362 ENSP00000264036:S413N;ENSP00000376561:S362N ENSP00000264036:S413N S - 2 0 MCAM 118687775 0.002000 0.14202 0.803000 0.32268 0.710000 0.40934 -0.056000 0.11787 1.216000 0.43427 0.561000 0.74099 AGC TCGA-3A-A9J0-01A-11D-A40W-08 MCAM-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000388332.2 0 0 0 5 401 0 113 0 3.755845e-01 0 91 0 113 2 0 0 0 0 0 2 1 0.935436 5 395 0 110 2 -2.580035 1 1 0 0 1 1 2 3 1.848552 1 0.470000 3.280000 0.564216 0.070000 1.000000e-02 1.000000 0.060000 0.135251 0.070000 0 PKNOX2 63876 broad.mit.edu 37 11 125281736 125281736 + Missense_Mutation SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr11:125281736G>A ENST00000298282.9 + 10 1182 c.911G>A c.(910-912)cGt>cAt p.R304H PKNOX2_ENST00000542175.1_Missense_Mutation_p.R240H|PKNOX2_ENST00000530517.1_3'UTR NM_022062.2 NP_071345.2 Q96KN3 PKNX2_HUMAN PBX/knotted 1 homeobox 2 29 Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116) AATATAATGCGTTCTTGGCTC 0.517000 0 SO:0001583 missense ENST00000298282.9 1 1 hg19 CCDS41730.1 . . . . . . . . . . G 32 5.173199 0.94807 . . ENSG00000165495 ENST00000530517;ENST00000531116;ENST00000298282;ENST00000542175;ENST00000535518 D;D;D;D 0.84298 -1.83;-1.83;-1.83;-1.83 5.45 5.45 0.79879 Homeodomain-related (1);Homeobox (2);Homeodomain-like (1); 0.000000 0.85682 D 0.000000 D 0.91095 0.7197 L 0.55990 1.75 0.80722 D 1 D;D;D 0.89917 1.0;0.999;0.999 D;D;D 0.91635 0.999;0.987;0.98 D 0.91504 0.5221 10 0.87932 D 0 -4.6596 19.2404 0.93879 0.0:0.0:1.0:0.0 . 240;275;304 F5GZ15;B7Z3G7;Q96KN3 .;.;PKNX2_HUMAN H 275;275;304;240;292 ENSP00000434732:R275H;ENSP00000433971:R275H;ENSP00000298282:R304H;ENSP00000441470:R240H ENSP00000298282:R304H R + 2 0 PKNOX2 124786946 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 9.048000 0.93830 2.714000 0.92807 0.561000 0.74099 CGT TCGA-3A-A9J0-01A-11D-A40W-08 PKNOX2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000386866.3 1 0 1 87 382 0 129 0 3.522977e-02 0 2 0 129 2 0 0 0 0 0 2 1 1.000000 87 376 0 127 2 -20.000000 1 1 121012 1 33 1 1 2 3 1.859412 1 0.470000 3.280000 0.570032 0.970000 7.900000e-01 1.000000 1.000000 0.950271 0.970000 1 APLP2 334 broad.mit.edu 37 11 129993656 129993656 + Missense_Mutation SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr11:129993656G>A ENST00000263574.5 + 7 1144 c.1072G>A c.(1072-1074)Gct>Act p.A358T APLP2_ENST00000528499.1_Intron|APLP2_ENST00000543137.1_Missense_Mutation_p.A265T|APLP2_ENST00000345598.5_Intron|APLP2_ENST00000338167.5_Missense_Mutation_p.A358T|APLP2_ENST00000539648.1_Intron|APLP2_ENST00000278756.7_Missense_Mutation_p.A368T NM_001642.2 NP_001633.1 Q06481 APLP2_HUMAN amyloid beta (A4) precursor-like protein 2 31 all_hematologic(175;0.0429) Breast(109;0.00586)|Lung NSC(97;0.00785)|all_lung(97;0.0154)|Medulloblastoma(222;0.0523)|all_neural(223;0.186) TTATTGTATGGCTGTGTGTAA 0.562000 0 SO:0001583 missense ENST00000263574.5 1 1 hg19 CCDS8486.1 . . . . . . . . . . G 34 5.360245 0.95877 . . ENSG00000084234 ENST00000263574;ENST00000338167;ENST00000278756;ENST00000543137 T;T;T;T 0.58060 0.36;0.36;0.36;0.36 5.61 5.61 0.85477 Proteinase inhibitor I2, Kunitz metazoa (6); 0.050804 0.85682 D 0.000000 T 0.66470 0.2792 L 0.42686 1.345 0.80722 D 1 P;D 0.89917 0.91;1.0 P;D 0.87578 0.508;0.998 T 0.61569 -0.7036 10 0.33141 T 0.24 -17.6546 18.621 0.91321 0.0:0.0:1.0:0.0 . 358;358 Q06481;Q06481-3 APLP2_HUMAN;. T 358;358;368;265 ENSP00000263574:A358T;ENSP00000345444:A358T;ENSP00000278756:A368T;ENSP00000444122:A265T ENSP00000263574:A358T A + 1 0 APLP2 129498866 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 7.630000 0.83225 2.631000 0.89168 0.650000 0.86243 GCT TCGA-3A-A9J0-01A-11D-A40W-08 APLP2-005 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000386109.1 1 0 1 89 380 0 143 1 1 19 119 0 143 2 0 0 0 0 0 2 1 1.000000 87 374 0 139 2 -20.000000 1 1 0 0 1 1 2 3 1.859412 1 0.470000 3.280000 0.570032 0.990000 8.100000e-01 1.000000 1.000000 0.962247 0.990000 1 FAR1 84188 broad.mit.edu 37 11 13749183 13749183 + Missense_Mutation SNP G G T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr11:13749183G>T ENST00000354817.3 + 11 1482 c.1338G>T c.(1336-1338)ttG>ttT p.L446F FAR1_ENST00000532502.1_Missense_Mutation_p.L70F NM_032228.5 NP_115604.1 Q8WVX9 FACR1_HUMAN fatty acyl CoA reductase 1 13 AGTACGTATTGAATGAAGAAA 0.373000 0 SO:0001583 missense ENST00000354817.3 1 1 hg19 CCDS7813.1 . . . . . . . . . . G 15.93 2.979207 0.53827 . . ENSG00000197601 ENST00000354817;ENST00000532502 T 0.28454 1.61 5.59 5.59 0.84812 . 0.000000 0.85682 D 0.000000 T 0.50309 0.1608 L 0.55834 1.745 0.51482 D 0.999929 D 0.89917 1.0 D 0.83275 0.996 T 0.23797 -1.0178 10 0.30078 T 0.28 -8.0128 16.1581 0.81680 0.0:0.1335:0.8665:0.0 . 446 Q8WVX9 FACR1_HUMAN F 446;70 ENSP00000346874:L446F ENSP00000346874:L446F L + 3 2 FAR1 13705759 1.000000 0.71417 1.000000 0.80357 0.976000 0.68499 1.970000 0.40520 2.783000 0.95769 0.655000 0.94253 TTG TCGA-3A-A9J0-01A-11D-A40W-08 FAR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000385990.2 1 0 1 57 287 0 50 1 9.660403e-01 9 21 0 50 2 0 0 0 0 0 2 1 1.000000 57 286 0 49 2 -3.247996 1 1 0 0 1 1 2 3 1.851246 1 0.470000 3.280000 0.565894 0.860000 6.700000e-01 1.000000 1.000000 0.869408 0.860000 1 UVRAG 7405 broad.mit.edu 37 11 75851957 75851957 + Missense_Mutation SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr11:75851957G>A ENST00000356136.3 + 15 1841 c.1600G>A c.(1600-1602)Gtc>Atc p.V534I UVRAG_ENST00000531818.1_Missense_Mutation_p.V162I|UVRAG_ENST00000533454.1_Missense_Mutation_p.V162I|UVRAG_ENST00000532130.1_Missense_Mutation_p.V162I|UVRAG_ENST00000539288.1_Missense_Mutation_p.V162I|UVRAG_ENST00000528420.1_Missense_Mutation_p.V433I|UVRAG_ENST00000538870.1_Missense_Mutation_p.V90I NM_003369.3 NP_003360.2 Q9P2Y5 UVRAG_HUMAN UV radiation resistance associated 32 TGTGACCACCGTCCCCTCCAT 0.493000 0 SO:0001583 missense ENST00000356136.3 1 1 hg19 CCDS8241.1 . . . . . . . . . . G 0.634 -0.816014 0.02776 . . ENSG00000198382 ENST00000356136;ENST00000528420;ENST00000533454;ENST00000531818;ENST00000532130;ENST00000539288;ENST00000538870 T 0.44881 0.91 5.3 -10.6 0.00265 . 1.580430 0.03003 N 0.148498 T 0.18299 0.0439 N 0.03608 -0.345 0.09310 N 1 B;B 0.06786 0.001;0.0 B;B 0.01281 0.0;0.0 T 0.22382 -1.0218 10 0.12766 T 0.61 1.0426 15.3224 0.74132 0.2482:0.0:0.6594:0.0925 . 90;534 B7Z6A0;Q9P2Y5 .;UVRAG_HUMAN I 534;433;162;162;162;162;90 ENSP00000348455:V534I ENSP00000348455:V534I V + 1 0 UVRAG 75529605 0.000000 0.05858 0.000000 0.03702 0.016000 0.09150 -0.434000 0.06939 -2.212000 0.00736 -0.768000 0.03414 GTC TCGA-3A-A9J0-01A-11D-A40W-08 UVRAG-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000383430.1 1 0 1 55 227 0 64 1 9.968574e-01 6 33 0 64 2 0 0 0 0 0 2 1 1.000000 56 222 0 63 2 -3.270213 1 1 0 0 1 1 2 3 1.848552 1 0.470000 3.280000 0.564216 0.990000 7.800000e-01 1.000000 1.000000 0.962392 0.990000 1 ULK1 8408 broad.mit.edu 37 12 132396530 132396530 + Missense_Mutation SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr12:132396530C>T ENST00000321867.4 + 13 1343 c.992C>T c.(991-993)cCg>cTg p.P331L NM_003565.2 NP_003556 O75385 ULK1_HUMAN unc-51 like autophagy activating kinase 1 29 all_neural(191;0.0982)|Medulloblastoma(191;0.163) CTGGCCTCCCCGGCTGACACC 0.632000 0 SO:0001583 missense ENST00000321867.4 1 1 hg19 CCDS9274.1 . . . . . . . . . . C 15.93 2.977274 0.53720 . . ENSG00000177169 ENST00000321867 T 0.72394 -0.65 4.87 4.87 0.63330 Protein kinase-like domain (1); 0.141351 0.47852 D 0.000218 D 0.82513 0.5053 M 0.78049 2.395 0.80722 D 1 D 0.76494 0.999 P 0.59546 0.859 D 0.85704 0.1315 10 0.87932 D 0 -38.8868 17.5963 0.88013 0.0:1.0:0.0:0.0 . 331 O75385 ULK1_HUMAN L 331 ENSP00000324560:P331L ENSP00000324560:P331L P + 2 0 ULK1 130962483 1.000000 0.71417 0.303000 0.25071 0.032000 0.12392 4.382000 0.59594 2.245000 0.73994 0.561000 0.74099 CCG TCGA-3A-A9J0-01A-11D-A40W-08 ULK1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000397769.3 1 0 0 92 67 0 43 1 1 15 15 0 43 2 0 0 0 0 0 2 1 1.000000 89 65 0 41 2 -20.000000 1 1 121154 1 35 1 0 3 3 1.895325 1 0.470000 3.280000 0.558241 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 EP400 57634 broad.mit.edu 37 12 132445272 132445272 + Silent SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr12:132445272G>A ENST00000333577.4 + 2 217 c.108G>A c.(106-108)ccG>ccA p.P36P EP400_ENST00000330386.6_Silent_p.P36P|EP400_ENST00000389562.2_Silent_p.P36P|EP400_ENST00000389561.2_Silent_p.P36P|EP400_ENST00000332482.4_Silent_p.P36P Q96L91 EP400_HUMAN E1A binding protein p400 161 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_epithelial(31;0.198) ACCCACCCCCGTCCCCCGCAG 0.667000 0 SO:0001819 synonymous_variant ENST00000333577.4 1 0 hg19 TCGA-3A-A9J0-01A-11D-A40W-08 EP400-203 KNOWN basic|appris_candidate_longest protein_coding protein_coding 1 0 0 21 35 0 24 0 1.382514e-01 1 1 0 24 2 0 0 0 0 0 2 1 0.999999 20 32 0 18 2 -1.203433 0 1 119986 14 35 1 0 3 3 1.895325 1 0.470000 3.280000 0.558241 0.990000 9.900000e-01 1.000000 1.000000 0.999952 0.990000 1 ZNF605 100289635 broad.mit.edu 37 12 133502024 133502024 + Missense_Mutation SNP C C G TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr12:133502024C>G ENST00000360187.4 - 5 2209 c.1861G>C c.(1861-1863)Gag>Cag p.E621Q ZNF605_ENST00000331711.7_5'Flank|ZNF605_ENST00000392321.3_Missense_Mutation_p.E652Q NM_183238.3 NP_899061.1 Q86T29 ZN605_HUMAN zinc finger protein 605 28 all_neural(191;0.0982)|Medulloblastoma(191;0.163) all_cancers(7;0.00227)|all_epithelial(31;0.142) GTCCCACACTCATTGCATCCA 0.383000 0 SO:0001583 missense ENST00000360187.4 1 1 hg19 CCDS31938.1 . . . . . . . . . . C 15.44 2.835555 0.50951 . . ENSG00000196458 ENST00000360187;ENST00000392321 T;T 0.52057 0.68;0.68 3.72 1.76 0.24704 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.35451 0.0932 L 0.32530 0.975 0.21984 N 0.999438 B;B 0.16166 0.003;0.016 B;B 0.12156 0.006;0.007 T 0.20571 -1.0271 9 0.22706 T 0.39 . 12.2303 0.54484 0.0:0.656:0.344:0.0 . 652;621 B3KVG4;Q86T29 .;ZN605_HUMAN Q 621;652 ENSP00000353314:E621Q;ENSP00000376135:E652Q ENSP00000353314:E621Q E - 1 0 ZNF605 132012097 0.000000 0.05858 0.005000 0.12908 0.937000 0.57800 0.278000 0.18753 0.325000 0.23359 0.462000 0.41574 GAG TCGA-3A-A9J0-01A-11D-A40W-08 ZNF605-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000397135.2 1 0 1 129 196 0 104 0 1.587790e-01 0 2 0 104 2 0 0 0 0 0 2 1 1.000000 129 192 0 103 2 -20.000000 1 1 0 0 1 0 3 3 1.895325 1 0.470000 3.280000 0.558241 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 FGD4 121512 broad.mit.edu 37 12 32754273 32754273 + Missense_Mutation SNP A A G TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr12:32754273A>G ENST00000427716.2 + 6 1176 c.752A>G c.(751-753)aAt>aGt p.N251S FGD4_ENST00000531134.1_Missense_Mutation_p.N336S|FGD4_ENST00000534526.2_Missense_Mutation_p.N388S|FGD4_ENST00000381025.3_Missense_Mutation_p.N3S|FGD4_ENST00000266482.3_Missense_Mutation_p.N3S|FGD4_ENST00000546442.1_Missense_Mutation_p.N158S|FGD4_ENST00000525053.1_Missense_Mutation_p.N363S NM_139241.2 NP_640334.2 Q96M96 FGD4_HUMAN FYVE, RhoGEF and PH domain containing 4 27 Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204) GAGATGGTGAATAAAATCTTT 0.348000 0 SO:0001583 missense ENST00000427716.2 1 1 hg19 CCDS8727.1 . . . . . . . . . . A 11.96 1.794476 0.31777 . . ENSG00000139132 ENST00000534526;ENST00000531134;ENST00000427716;ENST00000266482;ENST00000546442;ENST00000525053;ENST00000381025 T;T;T;T;T;T;T 0.62941 -0.01;-0.01;-0.01;-0.01;-0.01;-0.01;-0.01 4.86 4.86 0.63082 Dbl homology (DH) domain (5); 0.000000 0.53938 D 0.000056 T 0.64800 0.2631 L 0.31578 0.945 0.42950 D 0.99437 B;B;D;B 0.58970 0.236;0.071;0.984;0.288 B;B;P;B 0.57846 0.18;0.18;0.828;0.095 T 0.67534 -0.5646 10 0.49607 T 0.09 -25.0515 14.6203 0.68579 1.0:0.0:0.0:0.0 . 363;336;251;3 E9PJX4;B7Z493;Q96M96;G3XA97 .;.;FGD4_HUMAN;. S 388;336;251;3;158;363;3 ENSP00000449273:N388S;ENSP00000431323:N336S;ENSP00000394487:N251S;ENSP00000266482:N3S;ENSP00000446695:N158S;ENSP00000433666:N363S;ENSP00000370413:N3S ENSP00000266482:N3S N + 2 0 FGD4 32645540 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 5.697000 0.68295 2.037000 0.60232 0.459000 0.35465 AAT TCGA-3A-A9J0-01A-11D-A40W-08 FGD4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268017.1 1 0 1 42 156 0 66 0 0 0 1 0 66 2 0 0 0 0 0 2 1 1.000000 42 155 0 65 2 -20.000000 1 1 0 0 1 0 3 3 1.895325 1 0.470000 3.280000 0.558241 0.990000 8.100000e-01 1.000000 1.000000 0.980028 0.990000 1 ZIC2 7546 broad.mit.edu 37 13 100637726 100637726 + Silent SNP G G T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr13:100637726G>T ENST00000376335.3 + 3 1682 c.1389G>T c.(1387-1389)gcG>gcT p.A463A ZIC2_ENST00000477213.1_3'UTR NM_007129.3 NP_009060.2 O95409 ZIC2_HUMAN Zic family member 2 13 all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184) cggcggcggcggctgcggcgg 0.816000 Pancreas(97;119 1522 31925 44771 48764) 0 SO:0001819 synonymous_variant ENST00000376335.3 0 1 hg19 CCDS9495.1 TCGA-3A-A9J0-01A-11D-A40W-08 ZIC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045618.2 0 0 0 3 25 0 9 0 0 0 0 9 2 0 0 0 0 0 2 0 0.882106 0 36 0 9 2 -4.074491 1 0 0 0 1 2 3 5 2.631542 1 0.470000 3.280000 0.689150 0.880000 2.700000e-01 1.000000 1.000000 0.799445 0.880000 1 RNF17 56163 broad.mit.edu 37 13 25444786 25444786 + Silent SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr13:25444786C>T ENST00000255324.5 + 32 4408 c.4356C>T c.(4354-4356)agC>agT p.S1452S RNF17_ENST00000339524.3_Silent_p.S462S|RNF17_ENST00000381921.1_Silent_p.S1410S NM_001184993.1|NM_031277.2 NP_001171922.1|NP_112567.2 Q9BXT8 RNF17_HUMAN ring finger protein 17 36 Lung SC(185;0.0225)|Breast(139;0.077) GTGGAGTCAGCGGGGAATCAG 0.438000 0 SO:0001819 synonymous_variant ENST00000255324.5 1 1 hg19 CCDS9308.2 TCGA-3A-A9J0-01A-11D-A40W-08 RNF17-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044217.1 0 0 1 148 357 1 87 0 0 0 1 87 2 0 0 0 0 0 2 1 1.000000 145 351 1 83 20 -9.594065 1 1 121412 2 36 1 3 3 6 2.641929 1 0.470000 3.280000 0.692540 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 KL 9365 broad.mit.edu 37 13 33635841 33635841 + Silent SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr13:33635841C>T ENST00000380099.3 + 4 2633 c.2625C>T c.(2623-2625)atC>atT p.I875I KL_ENST00000487852.1_3'UTR NM_004795.3 NP_004786.2 Q9UEF7 KLOT_HUMAN klotho 41 all_epithelial(80;0.133) Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262) CCAATGGAATCGATGACGGGC 0.517000 0 SO:0001819 synonymous_variant ENST00000380099.3 1 1 hg19 CCDS9347.1 TCGA-3A-A9J0-01A-11D-A40W-08 KL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045987.1 1 0 1 207 348 0 115 0 0 0 1 0 115 2 0 0 0 0 0 2 1 1.000000 205 344 0 109 2 -19.999950 1 1 121412 1 31 1 2 3 5 2.606114 1 0.470000 3.280000 0.689150 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 CPB2 1361 broad.mit.edu 37 13 46638808 46638808 + Silent SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr13:46638808C>T ENST00000181383.4 - 8 787 c.771G>A c.(769-771)agG>agA p.R257R CPB2_ENST00000439329.3_Silent_p.R220R|CPB2-AS1_ENST00000606243.1_RNA|CPB2-AS1_ENST00000606991.1_RNA|CPB2-AS1_ENST00000415033.2_RNA|CPB2-AS1_ENST00000606351.1_RNA NM_001872.3 NP_001863.3 Q96IY4 CBPB2_HUMAN carboxypeptidase B2 (plasma) 21 Lung NSC(96;4.21e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|all_neural(104;0.235) KIRC - Kidney renal clear cell carcinoma(16;0.234) AAGCAAAGTTCCTATTCAGGT 0.413000 0 SO:0001819 synonymous_variant ENST00000181383.4 0 1 hg19 CCDS9401.1 TCGA-3A-A9J0-01A-11D-A40W-08 CPB2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044803.2 0 0 0 5 381 1 73 0 0 0 1 73 2 0 0 0 0 0 2 0 0.004268 5 376 1 73 18 -4.637711 1 1 0 0 1 2 3 5 2.631542 1 0.470000 3.280000 0.689150 0.100000 1.000000e-02 0.210000 0.100000 0.111343 0.100000 0 PCDH8 5100 broad.mit.edu 37 13 53420319 53420319 + Silent SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr13:53420319G>A ENST00000377942.3 - 1 2456 c.2253C>T c.(2251-2253)atC>atT p.I751I PCDH8_ENST00000338862.4_Silent_p.I751I NM_002590.3 NP_002581.2 O95206 PCDH8_HUMAN protocadherin 8 36 Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173) CGATGATGACGATCAGCGGCG 0.701000 GBM(36;25 841 9273 49207) 0 SO:0001819 synonymous_variant ENST00000377942.3 1 1 hg19 CCDS9438.1 TCGA-3A-A9J0-01A-11D-A40W-08 PCDH8-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000045108.2 1 0 0 31 244 0 74 0 0 0 0 74 2 0 0 0 0 0 2 1 1.000000 29 242 0 72 2 -20.000000 1 1 0 0 1 2 3 5 2.631542 1 0.470000 3.280000 0.689150 0.820000 5.700000e-01 1.000000 1.000000 0.826789 0.820000 0 SLAIN1 122060 broad.mit.edu 37 13 78293775 78293775 + Silent SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr13:78293775G>A ENST00000466548.1 + 3 695 c.669G>A c.(667-669)gcG>gcA p.A223A SLAIN1_ENST00000418532.1_Silent_p.A4A|SLAIN1_ENST00000267219.8_Silent_p.A4A|SLAIN1_ENST00000488699.1_Silent_p.A81A NM_001242868.1 NP_001229797.1 Q8ND83 SLAI1_HUMAN SLAIN motif family, member 1 14 Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037) TGGAAGCAGCGAGACGTTCCC 0.468000 0 SO:0001819 synonymous_variant ENST00000466548.1 1 1 hg19 TCGA-3A-A9J0-01A-11D-A40W-08 SLAIN1-009 KNOWN not_organism_supported|basic protein_coding protein_coding OTTHUMT00000355018.1 1 0 1 110 811 0 116 1 3.415559e-01 4 6 0 116 2 0 0 0 0 0 2 1 1.000000 105 799 0 111 2 -3.017764 1 1 121408 2 30 1 2 3 5 2.631542 1 0.470000 3.280000 0.689150 0.860000 7.100000e-01 1.000000 1.000000 0.869848 0.860000 1 FERMT2 10979 broad.mit.edu 37 14 53386031 53386031 + Silent SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr14:53386031C>T ENST00000395631.2 - 3 417 c.201G>A c.(199-201)aaG>aaA p.K67K FERMT2_ENST00000553373.1_Silent_p.K67K|FERMT2_ENST00000343279.4_Silent_p.K67K|FERMT2_ENST00000399304.3_Silent_p.K67K|FERMT2_ENST00000341590.3_Silent_p.K67K Q96AC1 FERM2_HUMAN fermitin family member 2 ERO1L/FERMT2(2) 20 Breast(41;0.0342) AAGTTCTCTTCTTTTCCCACC 0.393000 0 SO:0001819 synonymous_variant ENST00000395631.2 1 1 hg19 CCDS9713.1 TCGA-3A-A9J0-01A-11D-A40W-08 FERMT2-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000276907.2 1 0 1 109 723 0 127 0 9.252279e-01 0 31 0 127 2 0 0 0 0 0 2 1 1.000000 105 719 0 125 2 -20.000000 1 1 0 0 1 2 3 5 2.541460 1 0.470000 3.280000 0.677134 0.920000 7.500000e-01 1.000000 1.000000 0.918918 0.920000 1 WDR89 112840 broad.mit.edu 37 14 64066609 64066609 + Missense_Mutation SNP A A T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr14:64066609A>T ENST00000394942.2 - 2 140 c.52T>A c.(52-54)Tta>Ata p.L18I CTD-2302E22.2_ENST00000553983.1_lincRNA|WDR89_ENST00000267522.3_Missense_Mutation_p.L18I NM_001008726.2|NM_001258272.1|NM_080666.3 NP_001008726.1|NP_001245201.1|NP_542397.1 Q96FK6 WDR89_HUMAN WD repeat domain 89 14 TTGGTTCCTAAGGAACATTTA 0.368000 0 SO:0001583 missense ENST00000394942.2 1 1 hg19 CCDS9759.1 . . . . . . . . . . A 3.553 -0.091356 0.07053 . . ENSG00000140006 ENST00000394942;ENST00000267522;ENST00000554717 T;T;T 0.67171 -0.25;-0.25;0.96 5.93 3.42 0.39159 . 0.938409 0.09031 N 0.858708 T 0.47040 0.1424 N 0.14661 0.345 0.09310 N 0.999998 B 0.15473 0.013 B 0.09377 0.004 T 0.29579 -1.0007 10 0.20046 T 0.44 . 8.1435 0.31097 0.6475:0.2533:0.0:0.0992 . 18 Q96FK6 WDR89_HUMAN I 18 ENSP00000378399:L18I;ENSP00000267522:L18I;ENSP00000451702:L18I ENSP00000267522:L18I L - 1 2 WDR89 63136362 0.692000 0.27719 0.971000 0.41717 0.360000 0.29518 0.704000 0.25661 1.055000 0.40461 0.533000 0.62120 TTA TCGA-3A-A9J0-01A-11D-A40W-08 WDR89-003 KNOWN alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000411879.2 1 0 1 135 385 0 93 1 8.572710e-01 3 9 0 93 2 0 0 0 0 0 2 1 1.000000 131 381 0 89 2 -20.000000 1 1 0 0 1 2 3 5 2.541460 1 0.470000 3.280000 0.677134 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 RYR3 6263 broad.mit.edu 37 15 34130031 34130031 + Silent SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr15:34130031G>A ENST00000389232.4 + 89 11920 c.11850G>A c.(11848-11850)ggG>ggA p.G3950G RYR3_ENST00000415757.3_Silent_p.G3945G NM_001036.3 NP_001027.3 Q15413 RYR3_HUMAN ryanodine receptor 3 p.G3949G(1) 311 all_lung(180;7.18e-09) CCATGGAAGGGCAAAAACAGT 0.408000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000389232.4 0 1 hg19 CCDS45210.1 TCGA-3A-A9J0-01A-11D-A40W-08 RYR3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000417514.1 0 0 0 5 427 0 61 0 0 0 0 61 2 0 0 0 0 0 2 1 0.934374 5 418 0 60 2 -2.537812 1 1 0 0 1 0 4 4 2.083936 1 0.470000 3.280000 0.621293 0.070000 1.000000e-02 1.000000 0.070000 0.190765 0.070000 0 MYO5C 55930 broad.mit.edu 37 15 52534277 52534277 + Nonsense_Mutation SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr15:52534277G>A ENST00000261839.7 - 20 2685 c.2524C>T c.(2524-2526)Cga>Tga p.R842* MYO5C_ENST00000443683.2_Intron NM_018728.3 NP_061198.2 Q9NQX4 MYO5C_HUMAN myosin VC 66 AGGAATCCTCGGCTGTAGGCC 0.542000 0 SO:0001587 stop_gained ENST00000261839.7 0 1 hg19 CCDS42036.1 . . . . . . . . . . G 39 7.406745 0.98265 . . ENSG00000128833 ENST00000261839 . . . 5.09 3.11 0.35812 . 0.068470 0.56097 D 0.000024 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 . 13.3048 0.60347 0.0:0.0:0.5797:0.4203 . . . . X 842 . ENSP00000261839:R842X R - 1 2 MYO5C 50321569 0.973000 0.33851 0.975000 0.42487 0.225000 0.24961 1.711000 0.37930 0.653000 0.30826 0.650000 0.86243 CGA TCGA-3A-A9J0-01A-11D-A40W-08 MYO5C-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000419562.1 1 0 1 341 1028 0 232 1 9.999711e-01 4 43 0 232 2 0 0 0 0 0 2 1 1.000000 337 1016 0 231 2 -8.225900 1 1 0 0 1 2 4 6 2.826299 1 0.470000 3.280000 0.711423 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 UNC13C 440279 broad.mit.edu 37 15 54825264 54825264 + Splice_Site SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr15:54825264C>T ENST00000260323.11 + 25 5696 c.5696C>T c.(5695-5697)aCa>aTa p.T1899I UNC13C_ENST00000537900.1_Splice_Site_p.T1897I|UNC13C_ENST00000545554.1_Splice_Site_p.T1899I NM_001080534.1 NP_001074003.1 Q8NB66 UN13C_HUMAN unc-13 homolog C (C. elegans) 121 TTGGACAAAACGTAAGTTTTT 0.338000 0 SO:0001630 splice_region_variant ENST00000260323.11 0 1 hg19 CCDS45264.1 . . . . . . . . . . C 12.80 2.047374 0.36085 0.0 1.23E-4 ENSG00000137766 ENST00000260323;ENST00000545554;ENST00000537900 T;T;T 0.15256 2.44;2.44;2.44 5.83 4.91 0.64330 Mammalian uncoordinated homology 13, domain 2 (1);Mammalian uncoordinated homology 13, subgroup, domain 2 (1); 0.104815 0.64402 D 0.000004 T 0.14570 0.0352 L 0.29908 0.895 0.40999 D 0.98491 B 0.16603 0.018 B 0.16722 0.016 T 0.03863 -1.0997 10 0.39692 T 0.17 . 14.2915 0.66281 0.0:0.9288:0.0:0.0712 . 1899 Q8NB66 UN13C_HUMAN I 1899;1899;1897 ENSP00000260323:T1899I;ENSP00000438156:T1899I;ENSP00000442569:T1897I ENSP00000260323:T1899I T + 2 0 UNC13C 52612556 1.000000 0.71417 1.000000 0.80357 0.919000 0.55068 1.303000 0.33470 1.472000 0.48140 0.655000 0.94253 ACA TCGA-3A-A9J0-01A-11D-A40W-08 UNC13C-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000419028.3 0 0 0 5 59 0 10 0 0 0 0 10 2 0 0 0 0 0 2 1 0.937584 5 58 0 10 2 -10.057750 1 1 120228 1 21 1 2 4 6 2.826299 1 0.470000 3.280000 0.711423 0.700000 2.600000e-01 1.000000 1.000000 0.707984 0.700000 0 CIB2 10518 broad.mit.edu 37 15 78401612 78401612 + Missense_Mutation SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr15:78401612C>T ENST00000258930.3 - 4 639 c.311G>A c.(310-312)cGa>cAa p.R104Q CIB2_ENST00000560618.1_Missense_Mutation_p.R61Q|CIB2_ENST00000539011.1_Missense_Mutation_p.R61Q|CIB2_ENST00000557846.1_Missense_Mutation_p.R55Q NM_006383.2 NP_006374.1 O75838 CIB2_HUMAN calcium and integrin binding family member 2 p.R104Q(1) 11 CTTGAGCTCTCGGGGAGCCGA 0.552000 1 Substitution - Missense(1) SO:0001583 missense ENST00000258930.3 0 1 hg19 CCDS10296.1 . . . . . . . . . . C 32 5.114424 0.94339 0.0 3.49E-4 ENSG00000136425 ENST00000258930;ENST00000539011 T;T 0.67171 -0.25;2.96 4.46 4.46 0.54185 EF-hand-like domain (1); 0.000000 0.85682 D 0.000000 T 0.77363 0.4119 L 0.58669 1.825 0.80722 D 1 D;D 0.76494 0.999;0.997 D;D 0.64506 0.926;0.925 T 0.78607 -0.2138 10 0.48119 T 0.1 -16.4882 16.4633 0.84071 0.0:1.0:0.0:0.0 . 104;104 B4DDF0;O75838 .;CIB2_HUMAN Q 104;61 ENSP00000258930:R104Q;ENSP00000442459:R61Q ENSP00000258930:R104Q R - 2 0 CIB2 76188667 1.000000 0.71417 0.981000 0.43875 0.958000 0.62258 7.617000 0.83032 2.199000 0.70637 0.591000 0.81541 CGA TCGA-3A-A9J0-01A-11D-A40W-08 CIB2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000289798.1 0 0 0 5 372 0 53 0 5.945755e-02 0 24 0 53 2 0 0 0 0 0 2 1 0.933436 5 362 0 52 2 -4.339525 1 1 0 0 1 2 3 5 2.668272 1 0.470000 3.280000 0.689150 0.100000 2.000000e-02 0.220000 0.100000 0.114076 0.100000 0 RGMA 56963 broad.mit.edu 37 15 93588701 93588701 + Missense_Mutation SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr15:93588701C>T ENST00000329082.7 - 4 1151 c.880G>A c.(880-882)Gtc>Atc p.V294I RGMA_ENST00000425933.2_Missense_Mutation_p.V278I|RGMA_ENST00000542321.2_Missense_Mutation_p.V278I|RGMA_ENST00000557301.1_Missense_Mutation_p.V302I|RGMA_ENST00000556658.1_Missense_Mutation_p.V185I|RGMA_ENST00000538818.1_Missense_Mutation_p.V185I|RGMA_ENST00000543599.1_Missense_Mutation_p.V278I|RGMA_ENST00000557420.1_3'UTR NM_020211.2 NP_064596 Q96B86 RGMA_HUMAN repulsive guidance molecule family member a 9 Lung NSC(78;0.0542)|all_lung(78;0.0786) BRCA - Breast invasive adenocarcinoma(143;0.0312)|OV - Ovarian serous cystadenocarcinoma(32;0.108) GGCATGCGGACGGCAAAGGTC 0.622000 0 SO:0001583 missense ENST00000329082.7 0 1 hg19 CCDS45357.1 1 4.578754578754579E-4 0 0.0 1 0.0027624309392265192 0 0.0 0 0.0 C 5.222 0.226549 0.09916 . . ENSG00000182175 ENST00000543599;ENST00000425933;ENST00000329082;ENST00000542321;ENST00000538818;ENST00000557301 D;D;D;D;D;D 0.84298 -1.83;-1.83;-1.83;-1.83;-1.83;-1.83 4.76 3.81 0.43845 Repulsive guidance molecule, C-terminal (1); 0.058854 0.64402 N 0.000002 T 0.71417 0.3337 N 0.25825 0.765 0.80722 D 1 B;B 0.18741 0.024;0.03 B;B 0.15052 0.012;0.012 T 0.61491 -0.7052 10 0.02654 T 1 -9.2223 10.6561 0.45675 0.0:0.8974:0.0:0.1026 . 302;294 G3V518;Q96B86 .;RGMA_HUMAN I 278;278;294;278;185;302 ENSP00000442498:V278I;ENSP00000404442:V278I;ENSP00000330005:V294I;ENSP00000440025:V278I;ENSP00000442546:V185I;ENSP00000452126:V302I ENSP00000330005:V294I V - 1 0 RGMA 91389705 0.999000 0.42202 0.400000 0.26346 0.678000 0.39670 4.046000 0.57376 0.880000 0.35969 0.491000 0.48974 GTC TCGA-3A-A9J0-01A-11D-A40W-08 RGMA-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000415091.1 1 0 1 18 135 0 26 0 4.379888e-01 0 12 0 26 2 0 0 0 0 0 2 1 0.999981 17 129 0 26 2 -20.000000 1 1 121100 13 39 1 2 3 5 2.668272 1 0.470000 3.280000 0.689150 0.860000 5.400000e-01 1.000000 1.000000 0.852002 0.860000 1 CACNA1H 8912 broad.mit.edu 37 16 1246017 1246017 + Missense_Mutation SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr16:1246017G>A ENST00000348261.5 + 5 885 c.637G>A c.(637-639)Gtg>Atg p.V213M CACNA1H_ENST00000565831.1_Missense_Mutation_p.V213M|CACNA1H_ENST00000358590.4_Missense_Mutation_p.V213M NM_021098.2 NP_066921.2 O95180 CAC1H_HUMAN calcium channel, voltage-dependent, T type, alpha 1H subunit 34 Hepatocellular(780;0.00369) Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909) CATCAACCGCGTGCCTAGTAA 0.652000 0 SO:0001583 missense ENST00000348261.5 1 1 hg19 CCDS45375.1 . . . . . . . . . . G 17.67 3.447525 0.63178 . . ENSG00000196557 ENST00000348261;ENST00000358590 D;D 0.98649 -5.05;-5.05 4.23 4.23 0.50019 Ion transport (1); 0.149470 0.44688 N 0.000436 D 0.99080 0.9684 M 0.83774 2.66 0.40988 D 0.984831 D;D 0.89917 1.0;1.0 D;D 0.91635 0.992;0.999 D 0.99875 1.1103 10 0.87932 D 0 . 15.9489 0.79817 0.0:0.0:1.0:0.0 . 213;213 O95180-2;O95180 .;CAC1H_HUMAN M 213 ENSP00000334198:V213M;ENSP00000351401:V213M ENSP00000334198:V213M V + 1 0 CACNA1H 1186018 1.000000 0.71417 0.923000 0.36655 0.020000 0.10135 9.594000 0.98254 2.061000 0.61500 0.478000 0.44815 GTG TCGA-3A-A9J0-01A-11D-A40W-08 CACNA1H-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000421601.1 1 0 1 46 258 0 69 0 1.726037e-01 0 5 0 69 2 0 0 0 0 0 2 1 1.000000 45 253 0 67 2 -20.000000 1 1 120908 2 30 1 2 2 4 2.300494 1 0.470000 3.280000 0.639456 0.940000 7.100000e-01 1.000000 1.000000 0.924757 0.940000 1 USP31 57478 broad.mit.edu 37 16 23119457 23119457 + Silent SNP A A G TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr16:23119457A>G ENST00000219689.7 - 2 680 c.681T>C c.(679-681)caT>caC p.H227H NM_020718.3 NP_065769.3 Q86UV5 UBP48_HUMAN ubiquitin specific peptidase 31 57 CCTGGGCATCATGTTGGGAAT 0.478000 0 SO:0001819 synonymous_variant ENST00000219689.7 1 1 hg19 CCDS10607.1 TCGA-3A-A9J0-01A-11D-A40W-08 USP31-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000211607.1 1 0 1 67 294 0 50 1 2.376766e-01 2 3 0 50 2 0 0 0 0 0 2 1 1.000000 66 286 0 48 2 -20.000000 1 1 0 0 1 2 2 4 2.241091 1 0.470000 3.280000 0.638299 0.990000 9.200000e-01 1.000000 1.000000 0.994906 0.990000 1 ZKSCAN2 342357 broad.mit.edu 37 16 25251421 25251421 + Missense_Mutation SNP A A C TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr16:25251421A>C ENST00000328086.7 - 7 3423 c.2620T>G c.(2620-2622)Ttc>Gtc p.F874V CTD-2547G23.2_ENST00000569456.1_RNA NM_001012981.4 NP_001012999.3 Q63HK3 ZKSC2_HUMAN zinc finger with KRAB and SCAN domains 2 36 TGGGCGCTGAAATGAGAACTG 0.458000 0 SO:0001583 missense ENST00000328086.7 1 1 hg19 CCDS32410.1 . . . . . . . . . . A 16.10 3.026466 0.54683 . . ENSG00000155592 ENST00000328086 T 0.18338 2.22 5.53 5.53 0.82687 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.173579 0.41823 D 0.000812 T 0.19886 0.0478 L 0.31120 0.905 0.36356 D 0.860369 P;D 0.53619 0.951;0.961 P;P 0.53224 0.696;0.721 T 0.10451 -1.0629 10 0.66056 D 0.02 -9.4959 8.0971 0.30835 0.913:0.0:0.087:0.0 . 670;874 B4DYF0;Q63HK3 .;ZKSC2_HUMAN V 874 ENSP00000331626:F874V ENSP00000331626:F874V F - 1 0 ZKSCAN2 25158922 0.820000 0.29190 0.998000 0.56505 0.489000 0.33432 1.465000 0.35299 2.315000 0.78130 0.533000 0.62120 TTC TCGA-3A-A9J0-01A-11D-A40W-08 ZKSCAN2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000435739.1 1 0 1 71 431 0 91 0 5.591180e-02 1 2 0 91 2 0 0 0 0 0 2 1 1.000000 68 423 0 91 2 -20.000000 1 1 0 0 1 2 2 4 2.241091 1 0.470000 3.280000 0.638299 0.880000 7.000000e-01 1.000000 1.000000 0.882631 0.880000 1 ATXN2L 11273 broad.mit.edu 37 16 28841228 28841228 + Missense_Mutation SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr16:28841228C>T ENST00000336783.4 + 8 1050 c.883C>T c.(883-885)Cgt>Tgt p.R295C ATXN2L_ENST00000325215.6_Missense_Mutation_p.R295C|ATXN2L_ENST00000395547.2_Missense_Mutation_p.R295C|ATXN2L_ENST00000382686.4_Missense_Mutation_p.R295C|RP11-24N18.1_ENST00000563565.1_RNA|ATXN2L_ENST00000564304.1_Missense_Mutation_p.R295C|ATXN2L_ENST00000570200.1_Missense_Mutation_p.R295C|ATXN2L_ENST00000340394.8_Missense_Mutation_p.R295C NM_007245.3 NP_009176.2 Q8WWM7 ATX2L_HUMAN ataxin 2-like 36 GCGAGAGCTGCGTGCGGCCCA 0.577000 0 SO:0001583 missense ENST00000336783.4 1 1 hg19 CCDS10641.1 . . . . . . . . . . . 28.0 4.882278 0.91740 . . ENSG00000168488 ENST00000340394;ENST00000395547;ENST00000336783;ENST00000359153;ENST00000382686;ENST00000325215 T;T;T;T;T 0.51817 0.7;0.7;0.69;0.7;0.7 5.85 5.85 0.93711 LsmAD domain (1); 0.000000 0.64402 D 0.000001 T 0.67711 0.2922 M 0.72118 2.19 0.80722 D 1 D;D;D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0 D;D;D;D;D;D;D;D 0.87578 0.997;0.998;0.998;0.998;0.997;0.997;0.998;0.997 T 0.69672 -0.5082 10 0.87932 D 0 -9.2431 14.4368 0.67287 0.148:0.8519:0.0:0.0 . 295;295;295;295;295;295;295;295 Q8WWM7-6;Q8WWM7-5;Q63ZY4;Q8WWM7;Q8WWM7-2;Q8WWM7-4;A8K1R6;Q8WWM7-3 .;.;.;ATX2L_HUMAN;.;.;.;. C 295 ENSP00000341459:R295C;ENSP00000378917:R295C;ENSP00000338718:R295C;ENSP00000372133:R295C;ENSP00000315650:R295C ENSP00000315650:R295C R + 1 0 ATXN2L 28748729 0.953000 0.32496 1.000000 0.80357 0.950000 0.60333 2.191000 0.42640 2.779000 0.95612 0.491000 0.48974 CGT TCGA-3A-A9J0-01A-11D-A40W-08 ATXN2L-003 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000214139.1 1 0 1 51 221 0 66 1 9.999999e-01 22 87 0 66 2 0 0 0 0 0 2 1 1.000000 51 219 0 62 2 -20.000000 1 1 0 0 1 2 2 4 2.241091 1 0.470000 3.280000 0.638299 0.990000 8.900000e-01 1.000000 1.000000 0.993174 0.990000 1 KIF22 3835 broad.mit.edu 37 16 29814108 29814108 + Missense_Mutation SNP C C A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr16:29814108C>A ENST00000160827.4 + 9 1339 c.1299C>A c.(1297-1299)agC>agA p.S433R KIF22_ENST00000400751.5_Missense_Mutation_p.S365R|KIF22_ENST00000569382.2_Missense_Mutation_p.S365R|KIF22_ENST00000561482.1_Missense_Mutation_p.S365R|KIF22_ENST00000400750.2_5'UTR NM_001256269.1|NM_007317.2 NP_001243198.1|NP_015556.1 Q14807 KIF22_HUMAN kinesin family member 22 14 AGAAGCTAAGCAGCATGGACC 0.617000 0 SO:0001583 missense ENST00000160827.4 0 1 hg19 CCDS10653.1 . . . . . . . . . . C 14.81 2.646600 0.47258 . . ENSG00000079616 ENST00000160827;ENST00000400751 T;T 0.74002 -0.72;-0.8 5.67 -4.09 0.03951 . . . . . T 0.50034 0.1592 N 0.14661 0.345 0.25229 N 0.989848 P;P 0.40731 0.483;0.728 B;B 0.37601 0.084;0.254 T 0.46020 -0.9221 9 0.23891 T 0.37 . 8.278 0.31883 0.0:0.5586:0.2028:0.2385 . 365;433 B7Z265;Q14807 .;KIF22_HUMAN R 433;365 ENSP00000160827:S433R;ENSP00000383562:S365R ENSP00000160827:S433R S + 3 2 KIF22 29721609 0.167000 0.22975 0.935000 0.37517 0.919000 0.55068 -0.212000 0.09319 -0.299000 0.08909 -0.156000 0.13503 AGC TCGA-3A-A9J0-01A-11D-A40W-08 KIF22-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000215012.2 0 0 0 5 399 0 99 0 4.681834e-01 0 112 0 99 2 0 0 0 0 0 2 1 0.934150 5 390 0 98 2 -2.924628 1 1 0 0 1 2 2 4 2.241091 1 0.470000 3.280000 0.638299 0.080000 1.000000e-02 0.180000 0.080000 0.091559 0.080000 0 SEPT1 1731 broad.mit.edu 37 16 30393182 30393182 + Silent SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr16:30393182G>A ENST00000571393.1 - 5 390 c.204C>T c.(202-204)gcC>gcT p.A68A SEPT1_ENST00000570039.1_5'Flank|SEPT1_ENST00000605106.1_Silent_p.A73A|SEPT1_ENST00000321367.3_Silent_p.A115A Q8WYJ6 SEPT1_HUMAN septin 1 24 Colorectal(24;0.193) GGCGCTCAATGGCCAGGGTCT 0.562000 0 SO:0001819 synonymous_variant ENST00000571393.1 1 1 hg19 TCGA-3A-A9J0-01A-11D-A40W-08 SEPT1-201 KNOWN basic protein_coding protein_coding 0 0 0 28 839 1 164 0 3.501273e-02 0 9 1 164 2 0 0 0 0 0 2 1 1.000000 28 813 0 157 2 -2.900864 1 1 0 0 1 2 2 4 2.241091 1 0.470000 3.280000 0.638299 0.200000 1.200000e-01 0.290000 0.200000 0.207946 0.200000 0 ABCC12 94160 broad.mit.edu 37 16 48174686 48174686 + Missense_Mutation SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr16:48174686G>A ENST00000311303.3 - 4 914 c.569C>T c.(568-570)aCg>aTg p.T190M ABCC12_ENST00000448542.1_Missense_Mutation_p.T190M|ABCC12_ENST00000416054.1_Missense_Mutation_p.T190M NM_033226.2 NP_150229.2 Q96J65 MRP9_HUMAN ATP-binding cassette, sub-family C (CFTR/MRP), member 12 90 all_cancers(37;0.0474)|all_lung(18;0.047) CCGGATGGCCGTGCGGTAGTT 0.532000 0 SO:0001583 missense ENST00000311303.3 0 1 hg19 CCDS10730.1 . . . . . . . . . . G 14.79 2.641298 0.47153 . . ENSG00000140798 ENST00000311303;ENST00000448542;ENST00000449939;ENST00000416054 D;D;D 0.90197 -2.63;-2.63;-2.63 6.07 4.13 0.48395 ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1); 0.000000 0.85682 D 0.000000 D 0.94896 0.8350 M 0.84219 2.685 0.58432 D 0.999996 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;0.998 D 0.94242 0.7486 10 0.51188 T 0.08 . 12.0291 0.53388 0.1413:0.0:0.8587:0.0 . 190;190 Q96J65-2;Q96J65 .;MRP9_HUMAN M 190 ENSP00000311030:T190M;ENSP00000401855:T190M;ENSP00000413046:T190M ENSP00000311030:T190M T - 2 0 ABCC12 46732187 1.000000 0.71417 0.755000 0.31263 0.011000 0.07611 5.520000 0.67080 0.900000 0.36469 0.655000 0.94253 ACG TCGA-3A-A9J0-01A-11D-A40W-08 ABCC12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256837.1 0 0 0 6 674 0 110 0 0 0 0 110 2 0 0 0 0 0 2 1 0.964110 6 668 0 110 2 -2.512945 1 1 121412 7 43 1 2 2 4 2.241091 1 0.470000 3.280000 0.638299 0.050000 0 0.130000 0.040000 0.062019 0.050000 0 SLC12A3 6559 broad.mit.edu 37 16 56904081 56904081 + Silent SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr16:56904081C>T ENST00000563236.1 + 5 700 c.675C>T c.(673-675)ttC>ttT p.F225F SLC12A3_ENST00000262502.5_Silent_p.F224F|SLC12A3_ENST00000438926.2_Silent_p.F225F|SLC12A3_ENST00000566786.1_Silent_p.F224F P55017 S12A3_HUMAN solute carrier family 12 (sodium/chloride transporter), member 3 50 Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325) TTTTCGCTTTCGCCAATGCCG 0.647000 0 SO:0001819 synonymous_variant ENST00000563236.1 1 1 hg19 CCDS58464.1 TCGA-3A-A9J0-01A-11D-A40W-08 SLC12A3-005 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000432337.1 1 0 1 58 299 0 77 0 0 0 0 77 2 0 0 0 0 0 2 1 1.000000 57 297 0 75 2 -3.336150 1 1 121412 8 41 1 2 2 4 2.220512 1 0.470000 3.280000 0.633598 0.990000 7.800000e-01 1.000000 1.000000 0.958304 0.990000 1 WDR90 197335 broad.mit.edu 37 16 708985 708985 + Silent SNP C C G TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr16:708985C>G ENST00000293879.4 + 24 2985 c.2985C>G c.(2983-2985)ctC>ctG p.L995L WDR90_ENST00000549091.1_Silent_p.L995L|LA16c-349E10.1_ENST00000573609.1_RNA Q96KV7 WDR90_HUMAN WD repeat domain 90 37 Hepatocellular(780;0.0218) CCGTCTTCCTCTGGGATGTCC 0.642000 0 SO:0001819 synonymous_variant ENST00000293879.4 1 1 hg19 CCDS42092.1 TCGA-3A-A9J0-01A-11D-A40W-08 WDR90-002 NOVEL basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000404335.1 1 0 0 20 423 0 91 1 4.594150e-01 3 30 0 91 2 0 0 0 0 0 2 1 0.999995 20 415 0 88 2 -4.855244 1 1 121024 3 38 1 2 2 4 2.300494 1 0.470000 3.280000 0.639456 0.280000 1.700000e-01 0.420000 0.280000 0.294826 0.280000 0 DHX38 9785 broad.mit.edu 37 16 72132878 72132878 + Nonsense_Mutation SNP A A T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 A T A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr16:72132878A>T ENST00000268482.3 + 6 1326 c.817A>T c.(817-819)Aaa>Taa p.K273* DHX38_ENST00000536867.1_Intron NM_014003.3 NP_054722.2 Q92620 PRP16_HUMAN DEAH (Asp-Glu-Ala-His) box polypeptide 38 48 Ovarian(137;0.125) TCCCTCCTACAAATATAACGA 0.592000 Melanoma(97;711 1442 7855 13832 28836) 0 SO:0001587 stop_gained ENST00000268482.3 0 1 hg19 CCDS10907.1 . . . . . . . . . . A 41 8.828726 0.98970 . . ENSG00000140829 ENST00000268482 . . . 4.87 4.87 0.63330 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 . 14.7562 0.69567 1.0:0.0:0.0:0.0 . . . . X 273 . ENSP00000268482:K273X K + 1 0 DHX38 70690379 1.000000 0.71417 1.000000 0.80357 0.741000 0.42261 8.784000 0.91818 1.958000 0.56883 0.460000 0.39030 AAA TCGA-3A-A9J0-01A-11D-A40W-08 DHX38-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000269004.3 1 0 1 55 105 0 31 1 9.999941e-01 6 34 0 31 2 0 0 0 0 0 2 1 1.000000 55 102 0 29 2 -20.000000 1 1 0 0 1 2 2 4 2.220512 1 0.470000 3.280000 0.633598 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 SPATA2L 124044 broad.mit.edu 37 16 89764252 89764252 + Silent SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr16:89764252C>T ENST00000289805.5 - 3 833 c.765G>A c.(763-765)gcG>gcA p.A255A SPATA2L_ENST00000335360.7_Intron NM_152339.3 NP_689552.2 Q8IUW3 SPA2L_HUMAN spermatogenesis associated 2-like 6 Lung NSC(15;0.00043)|all_lung(18;0.000665)|all_hematologic(23;0.0355) AGGCCAGCTCCGCCGGGGGCG 0.701000 0 SO:0001819 synonymous_variant ENST00000289805.5 1 1 hg19 CCDS10985.1 TCGA-3A-A9J0-01A-11D-A40W-08 SPATA2L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000269923.1 1 0 1 24 38 0 15 1 9.941312e-01 4 13 0 15 2 0 0 0 0 0 2 1 1.000000 16 34 0 13 2 -20.000000 1 1 121026 3 32 1 2 2 4 2.258548 1 0.470000 3.280000 0.639456 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 SCARF1 8578 broad.mit.edu 37 17 1538332 1538332 + Missense_Mutation SNP C C T rs147642060 byFrequency TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr17:1538332C>T ENST00000263071.4 - 11 2262 c.2213G>A c.(2212-2214)cGg>cAg p.R738Q SCARF1_ENST00000348987.3_Missense_Mutation_p.R652Q|SCARF1_ENST00000571272.1_3'UTR NM_003693.2|NM_145350.1 NP_003684.2|NP_663325.1 Q14162 SREC_HUMAN scavenger receptor class F, member 1 20 GCCCTTTTTCCGATTCAGGGC 0.632000 0 SO:0001583 missense ENST00000263071.4 1 1 hg19 CCDS11007.1 1 4.578754578754579E-4 1 0.0020325203252032522 0 0.0 0 0.0 0 0.0 c 10.85 1.466182 0.26335 0.00227 1.16E-4 ENSG00000074660 ENST00000263071;ENST00000348987 T;T 0.22539 1.95;2.62 4.89 2.46 0.29980 . 0.197318 0.25025 N 0.033728 T 0.17916 0.0430 M 0.63428 1.95 0.22918 N 0.998569 B;B 0.32781 0.384;0.145 B;B 0.26693 0.072;0.024 T 0.14227 -1.0480 10 0.26408 T 0.33 -6.2381 8.5352 0.33360 0.0:0.8531:0.0:0.1469 . 652;738 Q14162-2;Q14162 .;SREC_HUMAN Q 738;652 ENSP00000263071:R738Q;ENSP00000323964:R652Q ENSP00000263071:R738Q R - 2 0 SCARF1 1485082 0.995000 0.38212 0.865000 0.33974 0.372000 0.29890 0.814000 0.27239 0.257000 0.21650 0.550000 0.68814 CGG TCGA-3A-A9J0-01A-11D-A40W-08 SCARF1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000207081.4 1 0 1 18 86 0 51 1 9.437098e-01 2 24 0 51 2 0 0 0 0 0 2 1 0.999989 16 87 0 48 2 -3.634488 1 1 121406 30 44 1 0 2 2 1.636792 1 0.470000 3.280000 0.470000 0.730000 4.600000e-01 1.000000 1.000000 0.749210 0.730000 0 ERBB2 2064 broad.mit.edu 37 17 37863277 37863277 + Silent SNP T T A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 T A T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr17:37863277T>A ENST00000269571.5 + 2 267 c.108T>A c.(106-108)ccT>ccA p.P36P ERBB2_ENST00000541774.1_Silent_p.P21P|ERBB2_ENST00000584450.1_Silent_p.P36P|ERBB2_ENST00000540042.1_Silent_p.P6P|ERBB2_ENST00000445658.2_Intron|ERBB2_ENST00000578199.1_Silent_p.P6P|ERBB2_ENST00000584601.1_Silent_p.P6P|ERBB2_ENST00000406381.2_Silent_p.P6P|ERBB2_ENST00000540147.1_Silent_p.P6P P04626 ERBB2_HUMAN v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 247 all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052) Ovarian(249;0.0547)|Colorectal(1115;0.234) UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171) ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072) TGCGGCTCCCTGCCAGTCCCG 0.642000 1 A, Mis, O breast, ovarian, other tumour types, NSCLC, gastric TCGA GBM(5;<1E-08) Dom yes 17 17q21.1 2064 v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian) E 0 SO:0001819 synonymous_variant ENST00000269571.5 0 1 hg19 CCDS32642.1 TCGA-3A-A9J0-01A-11D-A40W-08 ERBB2-008 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000445621.2 0 0 0 51 4703 0 55 1 1 16 2906 0 55 2 0 0 0 0 0 2 1 1.000000 52 4489 0 50 2 -16.205390 1 1 0 0 1 1 15 16 38.437938 1 0.470000 3.280000 0.876457 0.150000 3.000000e-02 0.280000 0.160000 0.160263 0.150000 0 TTYH2 94015 broad.mit.edu 37 17 72227040 72227040 + Missense_Mutation SNP G G A rs150215307 byFrequency TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr17:72227040G>A ENST00000269346.4 + 3 390 c.316G>A c.(316-318)Gtt>Att p.V106I TTYH2_ENST00000529107.1_Missense_Mutation_p.V85I NM_032646.5 NP_116035.5 Q9BSA4 TTYH2_HUMAN tweety family member 2 36 TGCGGTGGGCGTTGGTTTCTA 0.483000 0 SO:0001583 missense ENST00000269346.4 1 0 hg19 CCDS32717.1 6 0.0027472527472527475 6 0.012195121951219513 0 0.0 0 0.0 0 0.0 g 8.083 0.772809 0.16051 0.013164 2.33E-4 ENSG00000141540 ENST00000269346;ENST00000529107 T;T 0.12984 2.63;2.63 5.35 3.38 0.38709 . 0.185685 0.46758 N 0.000263 T 0.06234 0.0161 L 0.41961 1.31 0.80722 D 1 B;B 0.33857 0.429;0.092 B;B 0.28305 0.088;0.037 T 0.24870 -1.0148 10 0.13470 T 0.59 -8.4172 7.2697 0.26250 0.3324:0.0:0.6676:0.0 . 85;106 B4DKD1;Q9BSA4 .;TTYH2_HUMAN I 106;85 ENSP00000269346:V106I;ENSP00000433089:V85I ENSP00000269346:V106I V + 1 0 TTYH2 69738635 0.567000 0.26626 0.943000 0.38184 0.688000 0.40055 1.396000 0.34531 0.658000 0.30925 -0.119000 0.15052 GTT TCGA-3A-A9J0-01A-11D-A40W-08 TTYH2-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000387459.1 0 0 1 49 302 0 66 0 3.163420e-01 0 8 0 66 2 0 0 0 0 0 2 1 1.000000 48 299 0 66 2 -3.218233 1 1 121412 205 55 1 1 3 4 2.244625 1 0.470000 3.280000 0.634785 0.860000 6.500000e-01 1.000000 1.000000 0.868288 0.860000 1 TP53 7157 broad.mit.edu 37 17 7578370 7578370 + Splice_Site SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr17:7578370C>T ENST00000269305.4 - 5 749 c.e5+1 TP53_ENST00000445888.2_Splice_Site|TP53_ENST00000574684.1_Splice_Site|TP53_ENST00000455263.2_Splice_Site|TP53_ENST00000420246.2_Splice_Site|TP53_ENST00000359597.4_Splice_Site|TP53_ENST00000413465.2_Splice_Site 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.?(54)|p.0?(8)|p.G187fs*16(2)|p.D186_P191delDGLAPP(1)|p.L188fs*19(1)|p.G187_L188delGL(1)|p.G187fs*22(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) CAGCTGCTCACCATCGCTATC 0.632000 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 68 Unknown(54)|Whole gene deletion(8)|Deletion - Frameshift(3)|Deletion - In frame(2)|Insertion - Frameshift(1) SO:0001630 splice_region_variant 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 11.89 1.774230 0.31411 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315 . . . 4.7 3.7 0.42460 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 13.0738 0.59075 0.0:0.8363:0.1637:0.0 . . . . . -1 . . . - . . TP53 7519095 1.000000 0.71417 0.967000 0.41034 0.201000 0.24016 3.085000 0.50151 1.248000 0.43934 0.655000 0.94253 . TCGA-3A-A9J0-01A-11D-A40W-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 1 74 96 0 60 0 0 0 0 60 2 1 1 400 408 0 681 2 1 1.000000 74 94 0 58 2 -20.000000 1 1 0 0 1 0 2 2 1.636792 1 0.470000 3.280000 0.470000 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 LIPG 9388 broad.mit.edu 37 18 47110141 47110141 + Missense_Mutation SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr18:47110141G>A ENST00000261292.4 + 8 1651 c.1373G>A c.(1372-1374)cGg>cAg p.R458Q LIPG_ENST00000427224.2_Missense_Mutation_p.R384Q NM_006033.2 NP_006024.1 Q9Y5X9 LIPE_HUMAN lipase, endothelial 18 GAAACCCAGCGGAAGTAAGTG 0.562000 Pancreas(126;280 1778 12814 26243 34948) 0 SO:0001583 missense ENST00000261292.4 0 1 hg19 CCDS11938.1 . . . . . . . . . . G 13.21 2.168290 0.38315 . . ENSG00000101670 ENST00000261292;ENST00000427224 T;T 0.64438 -0.1;-0.1 5.6 -1.19 0.09585 Lipoxygenase, LH2 (3);Lipase/lipooxygenase, PLAT/LH2 (1); 0.314978 0.38381 N 0.001720 T 0.21509 0.0518 N 0.00885 -1.115 0.80722 D 1 B;B 0.20550 0.001;0.046 B;B 0.12837 0.001;0.008 T 0.11131 -1.0600 10 0.09084 T 0.74 -10.3611 7.2214 0.25990 0.6792:0.0:0.1813:0.1396 . 384;458 B4DTR8;Q9Y5X9 .;LIPE_HUMAN Q 458;384 ENSP00000261292:R458Q;ENSP00000387978:R384Q ENSP00000261292:R458Q R + 2 0 LIPG 45364139 0.664000 0.27457 0.301000 0.25044 0.917000 0.54804 0.558000 0.23469 -0.126000 0.11682 0.561000 0.74099 CGG TCGA-3A-A9J0-01A-11D-A40W-08 LIPG-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000447546.1 0 0 0 3 43 0 16 0 3.757470e-01 0 16 0 16 2 0 0 0 0 0 2 1 0.798256 3 41 0 16 2 -7.404661 1 1 121394 3 27 1 0 1 1 1.264376 1 0.470000 3.280000 0.321774 0.240000 7.000000e-02 0.530000 0.210000 0.264678 0.240000 0 TCF4 6925 broad.mit.edu 37 18 52899837 52899837 + Missense_Mutation SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr18:52899837C>T ENST00000356073.4 - 17 2163 c.1552G>A c.(1552-1554)Gag>Aag p.E518K TCF4_ENST00000398339.1_Missense_Mutation_p.E620K|TCF4_ENST00000564999.1_Missense_Mutation_p.E518K|TCF4_ENST00000564403.2_Missense_Mutation_p.E524K|TCF4_ENST00000567880.1_Missense_Mutation_p.E458K|TCF4_ENST00000568740.1_Missense_Mutation_p.E493K|TCF4_ENST00000561831.3_Missense_Mutation_p.E358K|TCF4_ENST00000566286.1_Missense_Mutation_p.E515K|TCF4_ENST00000561992.1_Missense_Mutation_p.E388K|TCF4_ENST00000537578.1_Missense_Mutation_p.E494K|TCF4_ENST00000570287.2_Missense_Mutation_p.E358K|TCF4_ENST00000565018.2_Missense_Mutation_p.E518K|TCF4_ENST00000540999.1_Missense_Mutation_p.E494K|TCF4_ENST00000570177.2_Missense_Mutation_p.E388K|TCF4_ENST00000457482.3_Missense_Mutation_p.E358K|TCF4_ENST00000543082.1_Missense_Mutation_p.E476K|TCF4_ENST00000537856.3_Missense_Mutation_p.E388K|TCF4_ENST00000568673.1_Missense_Mutation_p.E494K|TCF4_ENST00000544241.2_Missense_Mutation_p.E447K|TCF4_ENST00000564228.1_Missense_Mutation_p.E447K|TCF4_ENST00000566279.1_Missense_Mutation_p.E458K|TCF4_ENST00000354452.3_Missense_Mutation_p.E518K NM_003199.2 NP_003190.1 P15884 ITF2_HUMAN transcription factor 4 41 TCATCACCCTCGTCATCGGAT 0.468000 0 SO:0001583 missense ENST00000356073.4 1 1 hg19 CCDS11960.1 . . . . . . . . . . C 15.14 2.745039 0.49151 . . ENSG00000196628 ENST00000354452;ENST00000457482;ENST00000356073;ENST00000543082;ENST00000540999;ENST00000537578;ENST00000544241;ENST00000537856;ENST00000398339 T;T;T;T;T;T;T;T;T 0.18810 2.51;2.22;2.47;2.46;2.48;2.51;2.48;2.19;2.49 5.35 5.35 0.76521 . 0.000000 0.85682 D 0.000000 T 0.35856 0.0946 L 0.49640 1.575 0.80722 D 1 B;B;B;P;D;B;B;D;B 0.65815 0.038;0.172;0.065;0.919;0.992;0.038;0.038;0.995;0.371 B;B;B;B;P;B;B;D;B 0.68192 0.007;0.017;0.025;0.394;0.905;0.007;0.007;0.956;0.095 T 0.06826 -1.0805 10 0.02654 T 1 -15.4116 17.8399 0.88712 0.0:1.0:0.0:0.0 . 494;518;358;620;518;476;447;358;515 B7Z5M6;G0LNT9;G0LNV1;E9PH57;P15884;B3KUC0;B3KT62;G0LNU9;G0LNU5 .;.;.;.;ITF2_HUMAN;.;.;.;. K 518;358;518;476;494;494;447;388;620 ENSP00000346440:E518K;ENSP00000409447:E358K;ENSP00000348374:E518K;ENSP00000439656:E476K;ENSP00000445202:E494K;ENSP00000440731:E494K;ENSP00000441562:E447K;ENSP00000439827:E388K;ENSP00000381382:E620K ENSP00000346440:E518K E - 1 0 TCF4 51050835 0.998000 0.40836 0.998000 0.56505 0.952000 0.60782 3.845000 0.55880 2.510000 0.84645 0.467000 0.42956 GAG TCGA-3A-A9J0-01A-11D-A40W-08 TCF4-002 KNOWN upstream_uORF|basic|CCDS protein_coding protein_coding OTTHUMT00000256014.1 1 0 1 49 125 0 64 0 9.968765e-01 1 25 0 64 2 0 0 0 0 0 2 1 1.000000 49 125 0 62 2 -5.456219 1 1 0 0 1 0 1 1 1.249961 1 0.470000 3.280000 0.325828 0.910000 7.100000e-01 1.000000 1.000000 0.909871 0.910000 1 KIAA1468 57614 broad.mit.edu 37 18 59912054 59912054 + Missense_Mutation SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr18:59912054G>A ENST00000398130.2 + 11 1910 c.1678G>A c.(1678-1680)Gat>Aat p.D560N RP11-173A16.2_ENST00000588561.1_RNA|KIAA1468_ENST00000256858.6_Missense_Mutation_p.D560N NM_020854.3 NP_065905.2 Q9P260 K1468_HUMAN KIAA1468 47 Colorectal(73;0.186) TAAAGAGCGAGATCAGCTTCT 0.378000 0 SO:0001583 missense ENST00000398130.2 1 1 hg19 CCDS11979.2 . . . . . . . . . . G 34 5.334181 0.95758 . . ENSG00000134444 ENST00000398130;ENST00000256858 T;T 0.39787 1.06;1.06 5.61 5.61 0.85477 Armadillo-like helical (1);Armadillo-type fold (1); 0.000000 0.85682 D 0.000000 T 0.63236 0.2494 L 0.60845 1.875 0.80722 D 1 D;D;D 0.89917 0.994;0.98;1.0 P;P;D 0.83275 0.895;0.753;0.996 T 0.57969 -0.7719 9 . . . -19.5571 20.0051 0.97433 0.0:0.0:1.0:0.0 . 560;560;204 Q9P260-2;Q9P260;B2RD46 .;K1468_HUMAN;. N 560 ENSP00000381198:D560N;ENSP00000256858:D560N . D + 1 0 KIAA1468 58063034 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 9.715000 0.98748 2.799000 0.96334 0.650000 0.86243 GAT TCGA-3A-A9J0-01A-11D-A40W-08 KIAA1468-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256187.1 1 0 1 60 118 0 28 1 9.709536e-01 9 5 0 28 2 0 0 0 0 0 2 1 1.000000 58 116 0 27 2 -20.000000 1 1 0 0 1 0 1 1 1.255422 1 0.470000 3.280000 0.307190 0.940000 8.100000e-01 1.000000 0.990000 0.941718 0.940000 1 PHLPP1 23239 broad.mit.edu 37 18 60563163 60563163 + Missense_Mutation SNP T T G TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr18:60563163T>G ENST00000262719.5 + 6 2597 c.2363T>G c.(2362-2364)cTt>cGt p.L788R PHLPP1_ENST00000400316.4_Missense_Mutation_p.L276R O60346 PHLP1_HUMAN PH domain and leucine rich repeat protein phosphatase 1 17 GTGGATAAACTTTGTATGTCT 0.383000 0 SO:0001583 missense ENST00000262719.5 1 1 hg19 CCDS45881.2 . . . . . . . . . . T 26.1 4.709037 0.89018 . . ENSG00000081913 ENST00000400316;ENST00000262719 T;T 0.59638 0.25;0.25 5.07 5.07 0.68467 . . . . . T 0.81250 0.4783 M 0.92317 3.295 0.80722 D 1 D 0.76494 0.999 D 0.91635 0.999 D 0.86211 0.1625 9 0.87932 D 0 -10.6448 15.016 0.71584 0.0:0.0:0.0:1.0 . 788 O60346 PHLP1_HUMAN R 276;788 ENSP00000383170:L276R;ENSP00000262719:L788R ENSP00000262719:L788R L + 2 0 PHLPP1 58714143 1.000000 0.71417 0.999000 0.59377 0.998000 0.95712 7.489000 0.81451 2.146000 0.66826 0.533000 0.62120 CTT TCGA-3A-A9J0-01A-11D-A40W-08 PHLPP1-001 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000319249.2 1 0 1 45 109 0 49 1 6.544192e-01 4 3 0 49 2 0 0 0 0 0 2 1 1.000000 45 108 0 49 2 -20.000000 1 1 0 0 1 0 1 1 1.255422 1 0.470000 3.280000 0.307190 0.890000 7.000000e-01 1.000000 0.940000 0.886424 0.890000 1 ZNF181 339318 broad.mit.edu 37 19 35232318 35232318 + Silent SNP T T G rs2607243 TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr19:35232318T>G ENST00000492450.1 + 4 1121 c.1032T>G c.(1030-1032)acT>acG p.T344T ZNF181_ENST00000392232.3_Silent_p.T388T|ZNF181_ENST00000459757.2_Silent_p.T343T Q2M3W8 ZN181_HUMAN zinc finger protein 181 22 all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162) LUSC - Lung squamous cell carcinoma(66;0.138) GAATTCATACTCAAGAAAAAC 0.388000 0 SO:0001819 synonymous_variant ENST00000492450.1 0 1 hg19 CCDS32990.2 TCGA-3A-A9J0-01A-11D-A40W-08 ZNF181-002 KNOWN NAGNAG_splice_site|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000349005.3 0 0 0 6 307 0 46 0 1.074758e-02 0 7 0 46 2 0 0 0 0 0 2 1 0.965022 6 306 0 46 2 -2.537562 1 1 0 0 1 0 3 3 1.942808 1 0.470000 3.280000 0.570850 0.100000 3.000000e-02 0.210000 0.100000 0.116518 0.100000 0 KLK15 55554 broad.mit.edu 37 19 51330356 51330356 + Missense_Mutation SNP G G A rs61751959 TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr19:51330356G>A ENST00000598239.1 - 3 289 c.259C>T c.(259-261)Cgg>Tgg p.R87W KLK15_ENST00000596931.1_Missense_Mutation_p.R86W|KLK15_ENST00000416184.1_Missense_Mutation_p.R87W|KLK15_ENST00000326856.4_Missense_Mutation_p.R86W|KLK15_ENST00000301421.2_Missense_Mutation_p.R87W NM_017509.2 NP_059979.2 Q9H2R5 KLK15_HUMAN kallikrein-related peptidase 15 24 all_neural(266;0.057) GACGTGGTCCGTAGTTGCTCT 0.652000 Pancreas(140;10 2513 7143 9246) 0 SO:0001583 missense ENST00000598239.1 1 1 hg19 CCDS12805.1 . . . . . . . . . . g 18.66 3.671049 0.67814 4.54E-4 6.98E-4 ENSG00000174562 ENST00000326856;ENST00000416184;ENST00000301421;ENST00000544946 D;D 0.93712 -3.27;-3.27 4.51 -0.491 0.12045 Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3); 0.354502 0.20216 N 0.096801 D 0.96519 0.8864 M 0.90814 3.15 0.09310 N 0.999999 D;D;D;D 0.89917 1.0;0.999;1.0;1.0 P;D;D;D 0.70016 0.892;0.93;0.94;0.967 D 0.92113 0.5697 10 0.87932 D 0 . 13.1286 0.59369 0.0:0.0:0.296:0.704 rs61751959 87;86;87;87 Q6UBM2;Q6ISI0;Q9H2R5-4;Q9H2R5 .;.;.;KLK15_HUMAN W 87 ENSP00000415136:R87W;ENSP00000301421:R87W ENSP00000301421:R87W R - 1 2 KLK15 56022168 0.000000 0.05858 0.000000 0.03702 0.329000 0.28539 0.668000 0.25127 -0.033000 0.13736 -0.268000 0.10319 CGG TCGA-3A-A9J0-01A-11D-A40W-08 KLK15-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000465160.1 1 0 1 79 375 0 155 0 0 0 0 155 2 0 0 0 0 0 2 1 1.000000 79 369 0 151 2 -3.901235 1 1 121346 122 54 1 0 4 4 2.013086 1 0.470000 3.280000 0.609490 0.990000 8.100000e-01 1.000000 1.000000 0.970630 0.990000 1 LILRA1 11024 broad.mit.edu 37 19 55106342 55106342 + Missense_Mutation SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr19:55106342C>T ENST00000251372.3 + 4 465 c.283C>T c.(283-285)Cgg>Tgg p.R95W LILRA1_ENST00000453777.1_Missense_Mutation_p.R95W|LILRB1_ENST00000418536.2_Intron|LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA1_ENST00000473156.1_3'UTR NM_006863.2 NP_006854.1 O75019 LIRA1_HUMAN leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1 47 ACACACAGGGCGGTATCGCTG 0.572000 0 SO:0001583 missense ENST00000251372.3 1 1 hg19 CCDS12901.1 . . . . . . . . . . C 8.318 0.823541 0.16678 0.0 1.16E-4 ENSG00000104974 ENST00000251372;ENST00000453777 T;T 0.13778 2.56;2.56 1.58 -1.3 0.09259 Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 1.639860 0.04121 N 0.316290 T 0.19604 0.0471 M 0.86740 2.835 0.09310 N 1 B;P 0.38440 0.097;0.631 B;B 0.32805 0.03;0.153 T 0.37842 -0.9688 10 0.72032 D 0.01 . 5.5529 0.17101 0.6042:0.3958:0.0:0.0 . 95;95 O75019-2;O75019 .;LIRA1_HUMAN W 95 ENSP00000251372:R95W;ENSP00000413715:R95W ENSP00000251372:R95W R + 1 2 LILRA1 59798154 0.000000 0.05858 0.001000 0.08648 0.007000 0.05969 -0.728000 0.04925 -0.245000 0.09625 0.194000 0.17425 CGG TCGA-3A-A9J0-01A-11D-A40W-08 LILRA1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000140807.2 1 0 0 88 314 0 105 0 0 0 1 0 105 2 0 0 0 0 0 2 1 1.000000 87 307 0 104 2 -20.000000 1 1 121412 14 45 1 0 4 4 2.048062 1 0.470000 3.280000 0.613505 0.990000 9.900000e-01 1.000000 1.000000 0.999800 0.990000 1 NLRP7 199713 broad.mit.edu 37 19 55450945 55450945 + Silent SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr19:55450945C>T ENST00000590030.1 - 3 1282 c.1242G>A c.(1240-1242)acG>acA p.T414T NLRP7_ENST00000446217.1_Silent_p.T442T|NLRP7_ENST00000588756.1_Silent_p.T414T|NLRP7_ENST00000592784.1_Silent_p.T414T|NLRP7_ENST00000340844.2_Silent_p.T414T|NLRP7_ENST00000328092.5_Silent_p.T414T|NLRP7_ENST00000448121.2_Silent_p.T414T Q8WX94 NALP7_HUMAN NLR family, pyrin domain containing 7 73 GGAGGCTCAGCGTCCGCAGCG 0.711000 0 SO:0001819 synonymous_variant ENST00000590030.1 1 1 hg19 CCDS33109.1 TCGA-3A-A9J0-01A-11D-A40W-08 NLRP7-003 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000451396.1 1 0 0 39 77 0 38 0 0 0 0 38 2 0 0 0 0 0 2 1 1.000000 36 67 0 52 2 -20.000000 1 1 119984 7 34 1 0 4 4 2.046693 1 0.470000 3.280000 0.612176 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 SYT5 6861 broad.mit.edu 37 19 55690401 55690401 + Silent SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr19:55690401C>T ENST00000354308.3 - 2 378 c.9G>A c.(7-9)ccG>ccA p.P3P SYT5_ENST00000537500.1_Silent_p.P3P|CTD-2587H24.5_ENST00000591665.1_RNA|SYT5_ENST00000590851.1_Missense_Mutation_p.R58Q NM_003180.2 NP_003171.2 O00445 SYT5_HUMAN synaptotagmin V 18 BRCA - Breast invasive adenocarcinoma(297;0.209) TTGGGGGCTCCGGGAACATGG 0.677000 0 SO:0001819 synonymous_variant ENST00000354308.3 0 1 hg19 CCDS12919.1 . . . . . . . . . . C 8.945 0.966705 0.18659 . . ENSG00000129990 ENST00000543844 . . . 3.54 1.3 0.21679 . . . . . T 0.23649 0.0572 . . . 0.80722 D 1 B 0.34372 0.451 B 0.18871 0.023 T 0.05178 -1.0901 7 0.27785 T 0.31 . 3.9386 0.09316 0.2358:0.6379:0.0:0.1263 . 58 B7Z300 . Q 58 . ENSP00000441336:R58Q R - 2 0 SYT5 60382213 0.974000 0.33945 1.000000 0.80357 0.304000 0.27724 -0.295000 0.08298 0.450000 0.26774 0.558000 0.71614 CGG TCGA-3A-A9J0-01A-11D-A40W-08 SYT5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000452501.1 0 0 0 5 51 0 12 0 0 0 0 12 2 0 0 0 0 0 2 1 0.934520 5 49 0 11 2 -3.233199 1 1 0 0 1 0 4 4 2.046693 1 0.470000 3.280000 0.612176 0.620000 2.300000e-01 1.000000 1.000000 0.654928 0.620000 0 FBN3 84467 broad.mit.edu 37 19 8180474 8180474 + Missense_Mutation SNP C C T rs146523311 TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr19:8180474C>T ENST00000600128.1 - 30 4177 c.3763G>A c.(3763-3765)Gag>Aag p.E1255K FBN3_ENST00000601739.1_Missense_Mutation_p.E1255K|FBN3_ENST00000270509.2_Missense_Mutation_p.E1255K Q75N90 FBN3_HUMAN fibrillin 3 132 TTCGTGTTCTCGCAGTCCCCA 0.607000 0 SO:0001583 missense ENST00000600128.1 1 1 hg19 CCDS12196.1 . . . . . . . . . . C 10.26 1.300009 0.23650 2.27E-4 0.0 ENSG00000142449 ENST00000270509 D 0.87334 -2.24 3.94 1.81 0.25067 EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1); 0.056825 0.64402 U 0.000002 T 0.76807 0.4039 L 0.37750 1.13 0.53688 D 0.999971 P 0.35050 0.482 B 0.29440 0.102 T 0.68131 -0.5490 10 0.28530 T 0.3 . 9.5212 0.39135 0.0:0.8225:0.0:0.1775 . 1255 Q75N90 FBN3_HUMAN K 1255 ENSP00000270509:E1255K ENSP00000270509:E1255K E - 1 0 FBN3 8086474 0.991000 0.36638 0.727000 0.30756 0.091000 0.18340 2.896000 0.48656 0.349000 0.23975 -0.254000 0.11334 GAG TCGA-3A-A9J0-01A-11D-A40W-08 FBN3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000461428.2 1 0 1 32 110 0 45 0 0 0 0 45 2 0 0 0 0 0 2 1 1.000000 32 107 0 44 2 -3.705161 1 1 121412 48 45 1 0 3 3 1.668820 1 0.470000 3.280000 0.545786 0.990000 8.200000e-01 1.000000 1.000000 0.983334 0.990000 1 OR7G1 125962 broad.mit.edu 37 19 9225729 9225729 + Silent SNP C C T rs138779373 byFrequency TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr19:9225729C>T ENST00000541538.1 - 1 710 c.711G>A c.(709-711)gcG>gcA p.A237A OR7G1_ENST00000293614.1_Silent_p.A237A NM_001005192.2 NP_001005192.2 Q8NGA0 OR7G1_HUMAN olfactory receptor, family 7, subfamily G, member 1 20 AGGTGGAAAACGCTTTATACT 0.418000 0 SO:0001819 synonymous_variant ENST00000541538.1 1 1 hg19 CCDS32898.2 TCGA-3A-A9J0-01A-11D-A40W-08 OR7G1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000397912.1 1 0 1 60 176 0 60 0 0 0 0 60 2 0 0 0 0 0 2 1 1.000000 59 174 0 58 2 -20.000000 1 1 121412 24 46 1 0 3 3 1.668820 1 0.470000 3.280000 0.545786 0.990000 9.900000e-01 1.000000 1.000000 0.999135 0.990000 1 ZNF562 54811 broad.mit.edu 37 19 9764114 9764114 + Missense_Mutation SNP G G T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr19:9764114G>T ENST00000448622.1 - 6 954 c.792C>A c.(790-792)aaC>aaA p.N264K ZNF562_ENST00000453792.2_Missense_Mutation_p.N195K|ZNF562_ENST00000537617.1_Missense_Mutation_p.N148K|ZNF562_ENST00000590155.1_Missense_Mutation_p.N263K|ZNF562_ENST00000453372.2_Missense_Mutation_p.N264K|ZNF562_ENST00000293648.4_Missense_Mutation_p.N192K|ZNF562_ENST00000541032.1_Missense_Mutation_p.N227K NM_001130031.1|NM_001130032.1 NP_001123503.1|NP_001123504.1 Q6V9R5 ZN562_HUMAN zinc finger protein 562 17 ATTTCCCACAGTTCTTAGTCT 0.378000 0 SO:0001583 missense ENST00000448622.1 0 1 hg19 CCDS45956.1 . . . . . . . . . . G 0.658 -0.806919 0.02819 . . ENSG00000171466 ENST00000453372;ENST00000448622;ENST00000293648;ENST00000541032;ENST00000453792;ENST00000537617 T;T;T;T;T;T 0.06768 3.28;3.28;3.35;3.26;3.36;3.38 1.67 -3.33 0.04958 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.02571 0.0078 N 0.02412 -0.56 0.09310 N 1 B;B;B;B;B 0.02656 0.0;0.0;0.0;0.0;0.0 B;B;B;B;B 0.04013 0.001;0.0;0.0;0.0;0.0 T 0.39643 -0.9604 9 0.54805 T 0.06 . 1.739 0.02948 0.1587:0.1235:0.163:0.5548 . 148;263;227;264;192 F5H1B4;B4DMG0;B4DZP9;Q6V9R5;Q6V9R5-2 .;.;.;ZN562_HUMAN;. K 264;264;192;227;195;148 ENSP00000410734:N264K;ENSP00000411784:N264K;ENSP00000293648:N192K;ENSP00000442614:N227K;ENSP00000440451:N195K;ENSP00000445816:N148K ENSP00000293648:N192K N - 3 2 ZNF562 9625114 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -6.367000 0.00069 -1.457000 0.01919 -3.756000 0.00021 AAC TCGA-3A-A9J0-01A-11D-A40W-08 ZNF562-201 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000450239.1 1 0 0 20 326 0 82 0 4.780103e-02 0 6 0 82 2 0 0 0 0 0 2 1 0.999995 20 323 0 80 2 -5.810944 1 0 121410 9 41 1 0 3 3 1.668820 1 0.470000 3.280000 0.545786 0.310000 1.800000e-01 1.000000 0.280000 0.437706 0.310000 0 PLOD1 5351 broad.mit.edu 37 1 12030859 12030859 + Missense_Mutation SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr1:12030859G>A ENST00000196061.4 + 17 1915 c.1888G>A c.(1888-1890)Ggc>Agc p.G630S PLOD1_ENST00000376369.3_Missense_Mutation_p.G677S NM_000302.3 NP_000293.2 Q02809 PLOD1_HUMAN procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1 29 Ovarian(185;0.249) Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255) Succinic acid(DB00139)|Vitamin C(DB00126) GCTCTACCCCGGCTACTACAC 0.607000 0 SO:0001583 missense ENST00000196061.4 0 1 hg19 CCDS142.1 . . . . . . . . . . G 27.8 4.864455 0.91511 . . ENSG00000083444 ENST00000414311;ENST00000376369;ENST00000196061 T;T 0.65916 -0.18;-0.17 5.94 5.94 0.96194 Prolyl 4-hydroxylase, alpha subunit (1); 0.000000 0.85682 D 0.000000 T 0.70325 0.3211 M 0.89715 3.055 0.80722 D 1 B;B 0.31435 0.323;0.323 B;B 0.23275 0.03;0.045 T 0.73864 -0.3848 10 0.87932 D 0 . 19.3514 0.94389 0.0:0.0:1.0:0.0 . 677;630 B4DR87;Q02809 .;PLOD1_HUMAN S 294;677;630 ENSP00000365548:G677S;ENSP00000196061:G630S ENSP00000196061:G630S G + 1 0 PLOD1 11953446 1.000000 0.71417 0.986000 0.45419 0.995000 0.86356 9.869000 0.99810 2.826000 0.97356 0.561000 0.74099 GGC TCGA-3A-A9J0-01A-11D-A40W-08 PLOD1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000006865.1 0 0 0 4 159 0 35 0 9.881234e-01 0 369 0 35 2 0 0 0 0 0 2 1 0.886949 4 156 0 35 2 -6.080160 1 1 121386 3 33 1 1 3 4 2.035345 1 0.470000 3.280000 0.598363 0.180000 5.000000e-02 1.000000 0.140000 0.343673 0.180000 0 HNRNPCL1 343069 broad.mit.edu 37 1 12908073 12908073 + Missense_Mutation SNP T T C TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr1:12908073T>C ENST00000317869.6 - 2 295 c.70A>G c.(70-72)Aac>Gac p.N24D NM_001013631.1|NM_001136561.2|NM_001146181.1 NP_001013653.1|NP_001130033.2|NP_001139653.1 O60812 HNRC1_HUMAN heterogeneous nuclear ribonucleoprotein C-like 1 29 ACAAGAGTGTTGAGATTCCCA 0.453000 0 SO:0001583 missense ENST00000317869.6 1 1 hg19 CCDS30591.1 . . . . . . . . . . T 18.56 3.650509 0.67472 . . ENSG00000179172 ENST00000317869 T 0.40225 1.04 1.09 -0.423 0.12325 Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3); 0.179946 0.45361 U 0.000369 T 0.24005 0.0581 N 0.17474 0.49 0.42596 D 0.993268 B 0.31931 0.347 B 0.37989 0.262 T 0.03068 -1.1076 10 0.39692 T 0.17 . 4.9313 0.13919 0.0:0.0:0.3116:0.6884 . 24 O60812 HNRCL_HUMAN D 24 ENSP00000365370:N24D ENSP00000365370:N24D N - 1 0 HNRNPCL1 12830660 1.000000 0.71417 0.489000 0.27452 0.699000 0.40488 5.399000 0.66314 -0.107000 0.12088 0.341000 0.21757 AAC TCGA-3A-A9J0-01A-11D-A40W-08 HNRNPCL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000005462.1 0 0 0 59 942 0 202 0 0 0 0 202 2 0 0 0 0 0 2 1 1.000000 59 930 0 199 2 -9.527195 1 1 0 0 1 1 3 4 2.035345 1 0.470000 3.280000 0.598363 0.340000 2.500000e-01 1.000000 0.330000 0.475043 0.340000 0 S100A3 6274 broad.mit.edu 37 1 153520200 153520200 + Missense_Mutation SNP C C A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr1:153520200C>A ENST00000368713.3 - 3 460 c.264G>T c.(262-264)gaG>gaT p.E88D S100A3_ENST00000368712.1_Missense_Mutation_p.E88D|S100A4_ENST00000481009.1_5'Flank|S100A4_ENST00000368715.1_5'Flank|S100A4_ENST00000368714.1_Intron|S100A4_ENST00000368716.4_5'Flank|S100A4_ENST00000354332.4_5'Flank NM_002960.1 NP_002951.1 P33764 S10A3_HUMAN S100 calcium binding protein A3 3 all_lung(78;5.98e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199) LUSC - Lung squamous cell carcinoma(543;0.171) CCTTGAAGTACTCGTGGCAGT 0.597000 0 SO:0001583 missense ENST00000368713.3 1 1 hg19 CCDS1043.1 . . . . . . . . . . C 10.91 1.485114 0.26598 . . ENSG00000188015 ENST00000368713;ENST00000368712 T;T 0.15139 2.45;2.45 5.02 -0.489 0.12052 EF-hand-like domain (1); 0.179337 0.47093 N 0.000253 T 0.03220 0.0094 L 0.41632 1.29 0.37075 D 0.898697 B 0.06786 0.001 B 0.06405 0.002 T 0.38779 -0.9645 10 0.08837 T 0.75 . 6.8995 0.24275 0.0:0.4367:0.3951:0.1682 . 88 P33764 S10A3_HUMAN D 88 ENSP00000357702:E88D;ENSP00000357701:E88D ENSP00000357701:E88D E - 3 2 S100A3 151786824 0.992000 0.36948 0.997000 0.53966 0.958000 0.62258 0.042000 0.13949 -0.037000 0.13646 0.655000 0.94253 GAG TCGA-3A-A9J0-01A-11D-A40W-08 S100A3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000037726.1 1 0 0 79 446 0 108 0 2.886893e-01 0 7 0 108 2 0 0 0 0 0 2 1 1.000000 79 440 0 102 2 -20.000000 1 1 0 0 1 3 3 6 2.322612 1 0.470000 3.280000 0.648448 0.990000 7.800000e-01 1.000000 1.000000 0.957669 0.990000 1 UBQLN4 56893 broad.mit.edu 37 1 156012004 156012004 + Silent SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr1:156012004G>A ENST00000368309.3 - 8 1382 c.1290C>T c.(1288-1290)ttC>ttT p.F430F NM_020131.3 NP_064516.2 Q9NRR5 UBQL4_HUMAN ubiquilin 4 16 Hepatocellular(266;0.133)|all_neural(408;0.195) GGTTCCCCGCGAAGAGCGGCA 0.617000 0 SO:0001819 synonymous_variant ENST00000368309.3 1 1 hg19 CCDS1127.1 TCGA-3A-A9J0-01A-11D-A40W-08 UBQLN4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000046193.1 1 0 1 46 320 0 66 1 9.993203e-01 15 63 0 66 2 0 0 0 0 0 2 1 0.996464 44 317 2 65 25 -20.000000 1 1 121410 5 39 1 3 3 6 2.322612 1 0.470000 3.280000 0.648448 0.850000 6.100000e-01 1.000000 1.000000 0.859474 0.850000 1 NUF2 83540 broad.mit.edu 37 1 163317716 163317716 + Missense_Mutation SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr1:163317716G>A ENST00000271452.3 + 12 1391 c.1112G>A c.(1111-1113)cGc>cAc p.R371H NUF2_ENST00000524800.1_Missense_Mutation_p.R324H|NUF2_ENST00000367900.3_Missense_Mutation_p.R371H NM_145697.2 NP_663735.2 Q9BZD4 NUF2_HUMAN NUF2, NDC80 kinetochore complex component p.R371H(1) 35 all_hematologic(923;0.101) CAATACAAACGCACAGTAATT 0.318000 1 Substitution - Missense(1) SO:0001583 missense ENST00000271452.3 1 1 hg19 CCDS1245.1 . . . . . . . . . . G 12.94 2.089136 0.36855 . . ENSG00000143228 ENST00000524800;ENST00000367900;ENST00000271452 T;T;T 0.34859 1.45;1.34;1.34 6.03 4.13 0.48395 . 0.220012 0.49916 D 0.000130 T 0.07863 0.0197 N 0.16478 0.41 0.28144 N 0.929683 P;P 0.39352 0.669;0.669 B;B 0.27076 0.076;0.046 T 0.11372 -1.0590 9 0.44086 T 0.13 -6.6183 9.1986 0.37244 0.2248:0.0:0.7752:0.0 . 324;371 E9PQC4;Q9BZD4 .;NUF2_HUMAN H 324;371;371 ENSP00000436888:R324H;ENSP00000356875:R371H;ENSP00000271452:R371H ENSP00000271452:R371H R + 2 0 NUF2 161584340 0.995000 0.38212 0.857000 0.33713 0.990000 0.78478 1.124000 0.31320 1.521000 0.48983 0.655000 0.94253 CGC TCGA-3A-A9J0-01A-11D-A40W-08 NUF2-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000082812.1 1 0 1 31 183 0 48 1 8.766069e-01 3 21 0 48 2 0 0 0 0 0 2 1 1.000000 31 181 0 47 2 -16.227440 1 1 121412 2 31 1 3 3 6 2.322612 1 0.470000 3.280000 0.648448 0.990000 6.700000e-01 1.000000 1.000000 0.930027 0.990000 1 HMCN1 83872 broad.mit.edu 37 1 186030997 186030997 + Missense_Mutation SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr1:186030997C>T ENST00000271588.4 + 47 7556 c.7327C>T c.(7327-7329)Cgg>Tgg p.R2443W HMCN1_ENST00000367492.2_Missense_Mutation_p.R2443W NM_031935.2 NP_114141.2 Q96RW7 HMCN1_HUMAN hemicentin 1 308 CAGGATGCTACGGCTGATGCA 0.398000 0 SO:0001583 missense ENST00000271588.4 1 1 hg19 CCDS30956.1 . . . . . . . . . . C 22.3 4.274075 0.80580 0.0 1.16E-4 ENSG00000143341 ENST00000271588;ENST00000367492 T;T 0.36520 1.25;1.25 5.39 4.42 0.53409 Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.000000 0.85682 D 0.000000 T 0.56529 0.1991 M 0.68317 2.08 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 T 0.53906 -0.8372 10 0.37606 T 0.19 . 14.5328 0.67939 0.1471:0.8529:0.0:0.0 . 2443 Q96RW7 HMCN1_HUMAN W 2443 ENSP00000271588:R2443W;ENSP00000356462:R2443W ENSP00000271588:R2443W R + 1 2 HMCN1 184297620 1.000000 0.71417 0.330000 0.25442 0.846000 0.48090 4.567000 0.60850 2.528000 0.85240 0.591000 0.81541 CGG TCGA-3A-A9J0-01A-11D-A40W-08 HMCN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000131848.1 1 0 1 48 212 0 13 0 0 0 1 0 13 2 0 0 0 0 0 2 1 1.000000 48 210 0 12 2 -3.289656 1 1 121402 7 40 1 3 3 6 2.360015 1 0.470000 3.280000 0.654903 0.990000 9.300000e-01 1.000000 1.000000 0.996367 0.990000 1 ASPM 259266 broad.mit.edu 37 1 197072286 197072286 + Missense_Mutation SNP C C T rs149033840 TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr1:197072286C>T ENST00000367409.4 - 18 6351 c.6095G>A c.(6094-6096)cGt>cAt p.R2032H ASPM_ENST00000294732.7_Intron|ASPM_ENST00000367408.1_Intron NM_018136.4 NP_060606.3 Q8IZT6 ASPM_HUMAN asp (abnormal spindle) homolog, microcephaly associated (Drosophila) 165 TTTCATACCACGATAAGCTGA 0.333000 0 SO:0001583 missense ENST00000367409.4 1 1 hg19 CCDS1389.1 . . . . . . . . . . c 29.9 5.043488 0.93685 0.0 1.16E-4 ENSG00000066279 ENST00000367409 T 0.77098 -1.07 5.57 5.57 0.84162 . 0.000000 0.64402 D 0.000004 D 0.93012 0.7776 H 0.98048 4.135 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.95297 0.8400 10 0.87932 D 0 . 18.5928 0.91220 0.0:1.0:0.0:0.0 . 2032 Q8IZT6 ASPM_HUMAN H 2032 ENSP00000356379:R2032H ENSP00000356379:R2032H R - 2 0 ASPM 195338909 1.000000 0.71417 0.711000 0.30485 0.987000 0.75469 4.754000 0.62191 2.635000 0.89317 0.632000 0.83419 CGT TCGA-3A-A9J0-01A-11D-A40W-08 ASPM-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000088256.1 1 0 1 84 334 0 64 1 1.851841e-01 3 1 0 64 2 0 0 0 0 0 2 1 1.000000 84 332 0 64 2 -20.000000 1 1 121386 1 31 1 0 2 2 1.605430 1 0.470000 3.280000 0.470000 0.850000 6.900000e-01 1.000000 1.000000 0.857003 0.850000 1 DISP1 84976 broad.mit.edu 37 1 223175862 223175862 + Missense_Mutation SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr1:223175862G>A ENST00000284476.6 + 8 1287 c.1123G>A c.(1123-1125)Gtt>Att p.V375I NM_032890.3 NP_116279.2 Q96F81 DISP1_HUMAN dispatched homolog 1 (Drosophila) 69 TGAGCGAGACGTTTCTCATAC 0.527000 OREG0014268|OREG0026708 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000284476.6 1 1 hg19 CCDS1536.1 . . . . . . . . . . G 11.74 1.730061 0.30684 . . ENSG00000154309 ENST00000284476 D 0.86164 -2.08 5.25 4.33 0.51752 . 0.114979 0.64402 D 0.000013 D 0.82765 0.5108 L 0.43598 1.365 0.58432 D 0.999992 P 0.43314 0.803 B 0.39935 0.314 T 0.81145 -0.1066 10 0.27785 T 0.31 -17.2678 16.1121 0.81271 0.0:0.1337:0.8663:0.0 . 375 Q96F81 DISP1_HUMAN I 375 ENSP00000284476:V375I ENSP00000284476:V375I V + 1 0 DISP1 221242485 1.000000 0.71417 0.522000 0.27862 0.672000 0.39443 5.135000 0.64777 1.433000 0.47394 0.655000 0.94253 GTT TCGA-3A-A9J0-01A-11D-A40W-08 DISP1-001 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000092512.1 1 0 1 116 240 0 44 1 7.909829e-01 3 5 0 44 2 0 0 0 0 0 2 1 1.000000 113 237 0 44 2 -20.000000 1 1 121412 1 31 1 3 3 6 2.332360 1 0.470000 3.280000 0.650626 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 CDC42BPA 8476 broad.mit.edu 37 1 227223274 227223274 + Silent SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr1:227223274G>A ENST00000366769.3 - 24 4420 c.3129C>T c.(3127-3129)aaC>aaT p.N1043N CDC42BPA_ENST00000366764.2_Silent_p.N1015N|CDC42BPA_ENST00000366767.3_Silent_p.N962N|CDC42BPA_ENST00000366766.2_Silent_p.N1078N|CDC42BPA_ENST00000334218.5_Silent_p.N1043N|CDC42BPA_ENST00000366765.3_Silent_p.N1056N|CDC42BPA_ENST00000535525.1_Silent_p.N1023N NM_003607.3 NP_003598.2 CDC42 binding protein kinase alpha (DMPK-like) 77 all_cancers(173;0.156)|Prostate(94;0.0792) TTGGAGCTTTGTTTACACAAG 0.373000 0 SO:0001819 synonymous_variant ENST00000366769.3 1 1 hg19 CCDS1558.1 . . . . . . . . . . G 9.760 1.169942 0.21621 . . ENSG00000143776 ENST00000448940;ENST00000442054;ENST00000441725 . . . 5.8 5.8 0.92144 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 20.051 0.97627 0.0:0.0:1.0:0.0 . . . . X 246;372;268 . . Q - 1 0 CDC42BPA 225289897 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 2.833000 0.48159 2.740000 0.93945 0.650000 0.86243 CAA TCGA-3A-A9J0-01A-11D-A40W-08 CDC42BPA-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000091696.1 1 0 0 69 355 0 87 0 9.367419e-01 0 26 0 87 2 0 0 0 0 0 2 1 1.000000 70 350 0 86 2 -20.000000 1 1 0 0 1 3 3 6 2.332360 1 0.470000 3.280000 0.650626 0.990000 8.400000e-01 1.000000 1.000000 0.983121 0.990000 1 WNT3A 89780 broad.mit.edu 37 1 228246856 228246856 + Missense_Mutation SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr1:228246856G>A ENST00000284523.1 + 4 827 c.749G>A c.(748-750)cGc>cAc p.R250H WNT3A_ENST00000366753.2_Missense_Mutation_p.R250H NM_033131.3 NP_149122.1 P56704 WNT3A_HUMAN wingless-type MMTV integration site family, member 3A 12 Prostate(94;0.0405) CGGGAGTCCCGCGGCTGGGTG 0.657000 0 SO:0001583 missense ENST00000284523.1 1 1 hg19 CCDS1564.1 . . . . . . . . . . G 34 5.345122 0.95807 . . ENSG00000154342 ENST00000284523;ENST00000366753 T;T 0.76448 -1.02;-1.02 4.68 4.68 0.58851 . 0.000000 0.85682 D 0.000000 D 0.85283 0.5661 L 0.51914 1.62 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.79784 0.987;0.993 D 0.86836 0.2014 10 0.66056 D 0.02 . 17.9461 0.89039 0.0:0.0:1.0:0.0 . 250;250 P56704;Q3SY79 WNT3A_HUMAN;. H 250 ENSP00000284523:R250H;ENSP00000355715:R250H ENSP00000284523:R250H R + 2 0 WNT3A 226313479 1.000000 0.71417 0.999000 0.59377 0.972000 0.66771 9.733000 0.98818 2.300000 0.77407 0.491000 0.48974 CGC TCGA-3A-A9J0-01A-11D-A40W-08 WNT3A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000091648.1 1 0 1 39 217 0 58 0 0 0 0 58 2 0 0 0 0 0 2 1 1.000000 38 211 0 58 2 -20.000000 1 1 0 0 1 3 3 6 2.332360 1 0.470000 3.280000 0.650626 0.990000 7.300000e-01 1.000000 1.000000 0.955290 0.990000 1 OR2M4 26245 broad.mit.edu 37 1 248402386 248402386 + Missense_Mutation SNP G G T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr1:248402386G>T ENST00000306687.1 + 1 156 c.156G>T c.(154-156)gaG>gaT p.E52D NM_017504.1 NP_059974.1 Q96R27 OR2M4_HUMAN olfactory receptor, family 2, subfamily M, member 4 50 all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136) OV - Ovarian serous cystadenocarcinoma(106;0.0245) TCTACATAGAGAAACAGCTCC 0.478000 0 SO:0001583 missense ENST00000306687.1 1 1 hg19 CCDS31108.1 . . . . . . . . . . g 0.001 -3.029643 0.00041 . . ENSG00000171180 ENST00000306687 T 0.02140 4.43 3.08 1.13 0.20643 GPCR, rhodopsin-like superfamily (1); 0.344625 0.20655 N 0.088135 T 0.00468 0.0015 N 0.00140 -2.01 0.09310 N 1 B 0.02656 0.0 B 0.01281 0.0 T 0.46735 -0.9170 10 0.02654 T 1 . 2.8665 0.05603 0.1816:0.523:0.1817:0.1137 . 52 Q96R27 OR2M4_HUMAN D 52 ENSP00000306688:E52D ENSP00000306688:E52D E + 3 2 OR2M4 246469009 0.000000 0.05858 0.096000 0.21009 0.114000 0.19823 -2.414000 0.01037 0.614000 0.30107 -0.268000 0.10319 GAG TCGA-3A-A9J0-01A-11D-A40W-08 OR2M4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000097352.1 1 0 1 98 646 0 89 0 0 0 0 89 2 0 0 0 0 0 2 1 1.000000 98 633 0 85 2 -3.221884 1 1 0 0 1 3 3 6 2.332360 1 0.470000 3.280000 0.650626 0.880000 7.000000e-01 1.000000 0.840000 0.889382 0.880000 1 CSMD2 114784 broad.mit.edu 37 1 34092119 34092119 + Missense_Mutation SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr1:34092119C>T ENST00000373380.1 - 12 2102 c.1882G>A c.(1882-1884)Gca>Aca p.A628T CSMD2_ENST00000373377.1_5'UTR|CSMD2_ENST00000373388.2_5'UTR|CSMD2_ENST00000373381.4_Missense_Mutation_p.A1755T Q7Z408 CSMD2_HUMAN CUB and Sushi multiple domains 2 246 Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249) CTGGCTGGTGCGAGGCCTTTG 0.542000 0 SO:0001583 missense ENST00000373380.1 1 1 hg19 . . . . . . . . . . c 9.717 1.158608 0.21454 . . ENSG00000121904 ENST00000373381;ENST00000373380 T;T 0.59083 0.29;0.29 5.87 0.757 0.18427 CUB (5); 0.497844 0.22002 N 0.065989 T 0.26340 0.0643 N 0.03903 -0.33 0.20403 N 0.999907 B;B;B 0.15473 0.002;0.013;0.002 B;B;B 0.15870 0.002;0.008;0.014 T 0.13737 -1.0498 10 0.22706 T 0.39 . 5.2569 0.15552 0.3639:0.4384:0.0:0.1976 . 628;1715;1755 Q7Z408-2;Q7Z408;E7EUA6 .;CSMD2_HUMAN;. T 1755;628 ENSP00000362479:A1755T;ENSP00000362478:A628T ENSP00000241312:A1715T A - 1 0 CSMD2 33864706 0.019000 0.18553 0.012000 0.15200 0.327000 0.28475 0.209000 0.17435 0.103000 0.17682 -0.713000 0.03633 GCA TCGA-3A-A9J0-01A-11D-A40W-08 CSMD2-002 KNOWN basic protein_coding protein_coding OTTHUMT00000030635.4 1 0 1 10 51 0 19 0 0 0 1 0 19 2 0 0 0 0 0 2 1 0.997694 10 51 0 18 2 -18.535100 1 1 121402 6 32 1 1 3 4 1.984023 1 0.470000 3.280000 0.583530 0.990000 5.000000e-01 1.000000 1.000000 0.893702 0.990000 1 HIVEP3 59269 broad.mit.edu 37 1 41976495 41976495 + Missense_Mutation SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr1:41976495C>T ENST00000372583.1 - 9 7733 c.6848G>A c.(6847-6849)gGa>gAa p.G2283E HIVEP3_ENST00000372584.1_Missense_Mutation_p.G2282E|HIVEP3_ENST00000429157.2_Missense_Mutation_p.G2282E|HIVEP3_ENST00000247584.5_Missense_Mutation_p.G2283E|HIVEP3_ENST00000460604.1_5'UTR NM_024503.4 NP_078779.2 Q5T1R4 ZEP3_HUMAN human immunodeficiency virus type I enhancer binding protein 3 85 Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0367) GCCCGGGCCTCCGCCGGTCCT 0.682000 0 SO:0001583 missense ENST00000372583.1 1 1 hg19 CCDS463.1 . . . . . . . . . . C 1.034 -0.680791 0.03353 . . ENSG00000127124 ENST00000372584;ENST00000372583;ENST00000247584;ENST00000429157 T;T;T;T 0.04917 3.54;3.53;3.53;3.54 5.27 3.27 0.37495 . 0.615288 0.14475 N 0.317317 T 0.02688 0.0081 N 0.08118 0 0.09310 N 1 B;B 0.02656 0.0;0.0 B;B 0.04013 0.001;0.001 T 0.46679 -0.9174 10 0.09843 T 0.71 -1.0496 4.9301 0.13912 0.0:0.6819:0.0:0.3181 . 2282;2283 Q5T1R4-2;Q5T1R4 .;ZEP3_HUMAN E 2282;2283;2283;2282 ENSP00000361665:G2282E;ENSP00000361664:G2283E;ENSP00000247584:G2283E;ENSP00000410828:G2282E ENSP00000247584:G2283E G - 2 0 HIVEP3 41749082 0.008000 0.16893 0.462000 0.27118 0.101000 0.19017 0.771000 0.26633 1.462000 0.47948 0.561000 0.74099 GGA TCGA-3A-A9J0-01A-11D-A40W-08 HIVEP3-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000016978.1 1 0 0 22 88 0 28 1 5.068464e-01 2 6 0 28 2 0 0 0 0 0 2 1 0.999999 20 88 0 27 2 -20.000000 1 1 0 0 1 1 3 4 1.984023 1 0.470000 3.280000 0.583530 0.990000 7.400000e-01 1.000000 1.000000 0.970960 0.990000 1 SSX2IP 117178 broad.mit.edu 37 1 85124124 85124124 + Missense_Mutation SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr1:85124124C>T ENST00000342203.3 - 9 1218 c.955G>A c.(955-957)Ggg>Agg p.G319R SSX2IP_ENST00000603677.1_Intron|SSX2IP_ENST00000437941.2_Missense_Mutation_p.G292R|SSX2IP_ENST00000605755.1_Missense_Mutation_p.G292R|SSX2IP_ENST00000370612.4_Missense_Mutation_p.G319R NM_001166293.1|NM_001166294.1|NM_014021.3 NP_001159765.1|NP_001159766.1|NP_054740.3 Q9Y2D8 ADIP_HUMAN synovial sarcoma, X breakpoint 2 interacting protein 19 CTTAGTTCCCCGGCATCTTCT 0.438000 0 SO:0001583 missense ENST00000342203.3 1 1 hg19 CCDS699.1 . . . . . . . . . . C 22.7 4.325317 0.81580 . . ENSG00000117155 ENST00000342203;ENST00000437941;ENST00000544699;ENST00000370612 T;T 0.49720 0.77;0.77 5.76 4.77 0.60923 . 0.455024 0.25037 N 0.033632 T 0.45796 0.1360 L 0.47716 1.5 0.35549 D 0.803693 D;D;D 0.63046 0.99;0.992;0.985 P;P;P 0.53760 0.615;0.734;0.648 T 0.42766 -0.9432 10 0.46703 T 0.11 . 17.5251 0.87798 0.1322:0.8678:0.0:0.0 . 315;319;292 F5H549;Q9Y2D8;B4DFE3 .;ADIP_HUMAN;. R 319;292;315;319 ENSP00000340279:G319R;ENSP00000412781:G292R ENSP00000340279:G319R G - 1 0 SSX2IP 84896712 0.967000 0.33354 0.993000 0.49108 0.938000 0.57974 4.489000 0.60309 2.732000 0.93576 0.655000 0.94253 GGG TCGA-3A-A9J0-01A-11D-A40W-08 SSX2IP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000027469.1 1 0 0 13 168 0 25 1 6.577031e-01 2 28 0 25 2 0 0 0 0 0 2 1 0.999494 13 162 0 25 2 -2.841579 1 1 0 0 1 1 3 4 1.986928 1 0.470000 3.280000 0.585062 0.440000 2.300000e-01 1.000000 0.380000 0.551462 0.440000 0 PPP1R16B 26051 broad.mit.edu 37 20 37536753 37536753 + Missense_Mutation SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr20:37536753C>T ENST00000299824.1 + 10 1300 c.1111C>T c.(1111-1113)Cgg>Tgg p.R371W PPP1R16B_ENST00000373331.2_Missense_Mutation_p.R329W NM_015568.2 NP_056383.1 Q96T49 PP16B_HUMAN protein phosphatase 1, regulatory subunit 16B 49 Myeloproliferative disorder(115;0.00878) CCTGTGGCAGCGGAGTGCAGC 0.602000 0 SO:0001583 missense ENST00000299824.1 1 1 hg19 CCDS13309.1 . . . . . . . . . . C 19.37 3.814832 0.70912 . . ENSG00000101445 ENST00000299824;ENST00000373331 T;T 0.71103 -0.41;-0.54 5.26 3.2 0.36748 . 0.204892 0.41938 D 0.000796 T 0.66317 0.2777 L 0.36672 1.1 0.27630 N 0.948065 D;D 0.71674 0.998;0.995 P;P 0.51657 0.613;0.676 T 0.61247 -0.7101 10 0.72032 D 0.01 . 8.6451 0.34000 0.3461:0.5789:0.0:0.075 . 329;371 E9PFS8;Q96T49 .;PP16B_HUMAN W 371;329 ENSP00000299824:R371W;ENSP00000362428:R329W ENSP00000299824:R371W R + 1 2 PPP1R16B 36970167 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 0.866000 0.27954 1.476000 0.48215 0.644000 0.83932 CGG TCGA-3A-A9J0-01A-11D-A40W-08 PPP1R16B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079220.2 1 0 1 39 231 1 37 0 2.208576e-02 0 2 1 37 2 0 0 0 0 0 2 1 1.000000 39 224 0 35 2 -2.846317 1 1 0 0 1 1 3 4 2.263571 1 0.470000 3.280000 0.639456 0.900000 6.600000e-01 1.000000 1.000000 0.894557 0.900000 1 ARFGEF2 10564 broad.mit.edu 37 20 47569336 47569336 + Missense_Mutation SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr20:47569336G>A ENST00000371917.4 + 5 518 c.518G>A c.(517-519)aGc>aAc p.S173N NM_006420.2 NP_006411.2 Q9Y6D5 BIG2_HUMAN ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) 63 BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198) TATTTGGCCAGCAAAAATCTC 0.443000 Esophageal Squamous(176;1738 1974 26285 33069 35354) 0 SO:0001583 missense ENST00000371917.4 0 1 hg19 CCDS13411.1 . . . . . . . . . . G 35 5.522113 0.96416 . . ENSG00000124198 ENST00000538445;ENST00000371917 T 0.33654 1.4 6.06 6.06 0.98353 Armadillo-type fold (1); 0.079509 0.85682 D 0.000000 T 0.74366 0.3707 H 0.96208 3.785 0.80722 D 1 D 0.76494 0.999 D 0.72982 0.979 T 0.81656 -0.0834 10 0.87932 D 0 . 20.6208 0.99490 0.0:0.0:1.0:0.0 . 173 Q9Y6D5 BIG2_HUMAN N 173 ENSP00000360985:S173N ENSP00000360985:S173N S + 2 0 ARFGEF2 47002743 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 9.857000 0.99534 2.882000 0.98803 0.655000 0.94253 AGC TCGA-3A-A9J0-01A-11D-A40W-08 ARFGEF2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079627.1 0 0 0 5 557 0 98 0 4.442817e-03 0 9 0 98 2 0 0 0 0 0 2 0 0.002837 5 553 1 96 19 -2.617075 1 1 0 0 1 1 3 4 2.263571 1 0.470000 3.280000 0.639456 0.050000 0 0.130000 0.050000 0.064971 0.050000 0 DSCAM 1826 broad.mit.edu 37 21 41710288 41710288 + Missense_Mutation SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr21:41710288C>T ENST00000400454.1 - 8 2000 c.1523G>A c.(1522-1524)cGa>cAa p.R508Q NM_001271534.1|NM_001389.3 NP_001258463.1|NP_001380.2 O60469 DSCAM_HUMAN Down syndrome cell adhesion molecule 142 all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103) TTTCATTGGTCGAATGCTTGC 0.403000 Melanoma(134;970 1778 1785 21664 32388) 0 SO:0001583 missense ENST00000400454.1 1 1 hg19 CCDS42929.1 . . . . . . . . . . C 33 5.256495 0.95336 . . ENSG00000171587 ENST00000400454;ENST00000404019 T;T 0.64260 -0.09;-0.09 5.77 5.77 0.91146 Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.000000 0.64402 D 0.000001 T 0.75042 0.3796 L 0.50847 1.595 0.53688 D 0.999972 D 0.76494 0.999 D 0.68192 0.956 T 0.70963 -0.4729 10 0.35671 T 0.21 . 19.9857 0.97347 0.0:1.0:0.0:0.0 . 508 O60469 DSCAM_HUMAN Q 508;260 ENSP00000383303:R508Q;ENSP00000385342:R260Q ENSP00000383303:R508Q R - 2 0 DSCAM 40632158 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.656000 0.83736 2.724000 0.93272 0.655000 0.94253 CGA TCGA-3A-A9J0-01A-11D-A40W-08 DSCAM-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000195029.1 1 0 1 57 89 0 60 0 0 0 0 60 2 0 0 0 0 0 2 1 1.000000 54 88 0 59 2 -20.000000 1 1 120828 1 35 1 0 2 2 1.590636 1 0.470000 3.280000 0.470000 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 COL6A2 1292 broad.mit.edu 37 21 47545822 47545822 + Missense_Mutation SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr21:47545822C>T ENST00000300527.4 + 26 2197 c.2093C>T c.(2092-2094)gCg>gTg p.A698V COL6A2_ENST00000357838.4_Missense_Mutation_p.A698V|COL6A2_ENST00000397763.1_Missense_Mutation_p.A698V|COL6A2_ENST00000310645.5_Missense_Mutation_p.A698V|COL6A2_ENST00000409416.1_Missense_Mutation_p.A698V NM_001849.3 NP_001840.3 P12110 CO6A2_HUMAN collagen, type VI, alpha 2 43 Breast(49;0.245) GAGTGGATTGCGGGCGGCACC 0.602000 0 SO:0001583 missense ENST00000300527.4 1 1 hg19 CCDS13728.1 . . . . . . . . . . C 18.15 3.559002 0.65538 . . ENSG00000142173 ENST00000300527;ENST00000357838;ENST00000310645;ENST00000409416;ENST00000397763 T;T;T;T;T 0.78481 -1.18;-1.18;-1.18;-1.18;-1.18 4.21 4.21 0.49690 von Willebrand factor, type A (3); 0.000000 0.85682 D 0.000000 D 0.87120 0.6098 M 0.72118 2.19 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.87578 0.998;0.998;0.998 D 0.89107 0.3493 10 0.72032 D 0.01 -18.7532 16.5536 0.84479 0.0:1.0:0.0:0.0 . 698;698;698 P12110;P12110-2;P12110-3 CO6A2_HUMAN;.;. V 698 ENSP00000300527:A698V;ENSP00000350497:A698V;ENSP00000312529:A698V;ENSP00000387115:A698V;ENSP00000380870:A698V ENSP00000300527:A698V A + 2 0 COL6A2 46370250 1.000000 0.71417 0.030000 0.17652 0.733000 0.41908 7.562000 0.82300 1.889000 0.54706 0.491000 0.48974 GCG TCGA-3A-A9J0-01A-11D-A40W-08 COL6A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000206971.1 1 0 1 37 108 0 49 1 1 2 2304 0 49 2 0 0 0 0 0 2 1 1.000000 37 105 0 46 2 -20.000000 1 1 0 0 1 0 2 2 1.590636 1 0.470000 3.280000 0.470000 0.990000 8.000000e-01 1.000000 1.000000 0.975379 0.990000 1 PPM1F 9647 broad.mit.edu 37 22 22277807 22277807 + Silent SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr22:22277807G>A ENST00000263212.5 - 8 1128 c.1023C>T c.(1021-1023)gcC>gcT p.A341A PPM1F_ENST00000407142.1_Silent_p.A173A|PPM1F_ENST00000538191.1_Silent_p.A237A NM_014634.3 NP_055449.1 P49593 PPM1F_HUMAN protein phosphatase, Mg2+/Mn2+ dependent, 1F 12 Colorectal(54;0.105) AAGCTGCATCGGCCTCCCCAG 0.632000 0 SO:0001819 synonymous_variant ENST00000263212.5 1 1 hg19 CCDS13796.1 TCGA-3A-A9J0-01A-11D-A40W-08 PPM1F-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000320267.2 1 0 1 46 151 0 52 0 7.650780e-01 1 10 0 52 2 0 0 0 0 0 2 1 1.000000 46 148 0 50 2 -4.271238 1 1 121408 1 28 1 0 3 3 1.990590 1 0.470000 3.280000 0.570850 0.990000 9.300000e-01 1.000000 1.000000 0.996304 0.990000 1 TBC1D10A 83874 broad.mit.edu 37 22 30722767 30722767 + Missense_Mutation SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr22:30722767G>A ENST00000215790.7 - 1 268 c.104C>T c.(103-105)aCc>aTc p.T35I TBC1D10A_ENST00000490449.1_5'UTR|TBC1D10A_ENST00000403477.3_Missense_Mutation_p.T35I NM_031937.2 NP_114143.1 Q9BXI6 TB10A_HUMAN TBC1 domain family, member 10A 23 GAGTTCGTCGGTGGTTGCGGC 0.711000 0 SO:0001583 missense ENST00000215790.7 1 1 hg19 CCDS13874.1 . . . . . . . . . . G 14.44 2.535300 0.45176 . . ENSG00000099992 ENST00000215790;ENST00000403477 T;T 0.18174 2.23;3.53 4.13 3.1 0.35709 . 0.783594 0.11519 N 0.555865 T 0.09730 0.0239 N 0.14661 0.345 0.80722 D 1 B;B;B 0.02656 0.0;0.0;0.0 B;B;B 0.04013 0.001;0.001;0.001 T 0.12682 -1.0538 10 0.38643 T 0.18 . 6.2359 0.20762 0.1066:0.1878:0.7056:0.0 . 35;35;35 Q20WK7;B3KXT8;Q9BXI6 .;.;TB10A_HUMAN I 35 ENSP00000215790:T35I;ENSP00000384996:T35I ENSP00000215790:T35I T - 2 0 TBC1D10A 29052767 0.815000 0.29118 0.337000 0.25536 0.754000 0.42855 1.587000 0.36622 0.843000 0.35070 0.430000 0.28490 ACC TCGA-3A-A9J0-01A-11D-A40W-08 TBC1D10A-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000320550.1 1 0 0 44 258 0 61 1 9.968197e-01 8 46 0 61 2 0 0 0 0 0 2 1 1.000000 42 245 0 58 2 -20.000000 1 1 0 0 1 0 6 6 2.712028 1 0.470000 3.280000 0.703844 0.990000 8.300000e-01 1.000000 1.000000 0.984948 0.990000 1 GCC2 9648 broad.mit.edu 37 2 109092224 109092224 + Missense_Mutation SNP A A G TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr2:109092224A>G ENST00000309863.6 + 9 3692 c.2978A>G c.(2977-2979)gAa>gGa p.E993G NM_181453.3 NP_852118 Q8IWJ2 GCC2_HUMAN GRIP and coiled-coil domain containing 2 54 ACTGTGAAGGAAGAACTTGAA 0.313000 0 SO:0001583 missense ENST00000309863.6 1 1 hg19 CCDS33268.1 . . . . . . . . . . A 18.16 3.561512 0.65538 . . ENSG00000135968 ENST00000309863 T 0.37752 1.18 5.69 4.47 0.54385 . 0.060927 0.64402 D 0.000005 T 0.36193 0.0958 M 0.65975 2.015 0.43719 D 0.996197 D 0.53619 0.961 P 0.44597 0.454 T 0.14643 -1.0465 10 0.35671 T 0.21 . 8.0869 0.30777 0.7272:0.1393:0.0:0.1335 . 993 Q8IWJ2 GCC2_HUMAN G 993 ENSP00000307939:E993G ENSP00000307939:E993G E + 2 0 GCC2 108458656 1.000000 0.71417 1.000000 0.80357 0.552000 0.35366 4.657000 0.61490 2.296000 0.77279 0.533000 0.62120 GAA TCGA-3A-A9J0-01A-11D-A40W-08 GCC2-014 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000358516.3 1 0 1 107 286 0 73 1 9.985026e-01 9 20 0 73 2 0 0 0 0 0 2 1 1.000000 105 282 0 71 2 -20.000000 1 1 0 0 1 2 2 4 2.183810 1 0.470000 3.280000 0.627547 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 CKAP2L 150468 broad.mit.edu 37 2 113514074 113514074 + Missense_Mutation SNP A A G TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr2:113514074A>G ENST00000302450.6 - 4 952 c.874T>C c.(874-876)Tca>Cca p.S292P CKAP2L_ENST00000541405.1_Missense_Mutation_p.S127P|CKAP2L_ENST00000481732.1_5'Flank NM_152515.3 NP_689728.3 Q8IYA6 CKP2L_HUMAN cytoskeleton associated protein 2-like 28 GGTTTCTTTGATGACTGAACT 0.403000 0 SO:0001583 missense ENST00000302450.6 1 1 hg19 CCDS2100.1 . . . . . . . . . . A 5.274 0.235997 0.10023 . . ENSG00000169607 ENST00000541405;ENST00000302450 T;T 0.18657 2.2;2.87 4.69 -2.55 0.06288 . 0.644272 0.13672 N 0.370817 T 0.10723 0.0262 L 0.33485 1.01 0.09310 N 1 B 0.14012 0.009 B 0.16722 0.016 T 0.27123 -1.0083 10 0.33141 T 0.24 -0.2642 0.2847 0.00249 0.3956:0.1484:0.1686:0.2874 . 292 Q8IYA6 CKP2L_HUMAN P 127;292 ENSP00000438763:S127P;ENSP00000305204:S292P ENSP00000305204:S292P S - 1 0 CKAP2L 113230545 0.527000 0.26306 0.001000 0.08648 0.091000 0.18340 0.044000 0.13992 -0.386000 0.07821 0.477000 0.44152 TCA TCGA-3A-A9J0-01A-11D-A40W-08 CKAP2L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254082.2 0 0 1 154 374 0 113 1 7.263466e-01 4 4 0 113 2 0 0 0 0 0 2 1 1.000000 153 371 0 110 2 -20.000000 1 1 0 0 1 2 2 4 2.183810 1 0.470000 3.280000 0.627547 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 GPR39 2863 broad.mit.edu 37 2 133402714 133402714 + Missense_Mutation SNP C C G TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr2:133402714C>G ENST00000329321.3 + 2 1366 c.897C>G c.(895-897)aaC>aaG p.N299K GPR39_ENST00000470071.1_3'UTR|LYPD1_ENST00000397463.2_3'UTR NM_001508.2 NP_001499.1 O43194 GPR39_HUMAN G protein-coupled receptor 39 22 GGATGCCCAACCAGATTCGGA 0.547000 0 SO:0001583 missense ENST00000329321.3 1 1 hg19 CCDS2170.1 . . . . . . . . . . C 15.31 2.795528 0.50208 . . ENSG00000183840 ENST00000329321 T 0.71817 -0.6 5.3 3.48 0.39840 GPCR, rhodopsin-like superfamily (1); 0.108898 0.64402 D 0.000010 T 0.78104 0.4231 L 0.57536 1.79 0.80722 D 1 D 0.63046 0.992 D 0.66847 0.947 T 0.77531 -0.2553 10 0.62326 D 0.03 . 9.5552 0.39334 0.0:0.7715:0.0:0.2285 . 299 O43194 GPR39_HUMAN K 299 ENSP00000327417:N299K ENSP00000327417:N299K N + 3 2 GPR39 133119184 0.998000 0.40836 1.000000 0.80357 0.995000 0.86356 0.664000 0.25068 0.799000 0.34018 0.650000 0.86243 AAC TCGA-3A-A9J0-01A-11D-A40W-08 GPR39-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254582.1 1 0 1 81 251 0 87 1 9.999954e-01 27 32 0 87 2 0 0 0 0 0 2 1 1.000000 80 250 0 87 2 -20.000000 1 1 0 0 1 2 2 4 2.183810 1 0.470000 3.280000 0.627547 0.990000 9.900000e-01 1.000000 1.000000 0.999997 0.990000 1 ABCB6 10058 broad.mit.edu 37 2 220080843 220080843 + Missense_Mutation SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr2:220080843G>A ENST00000265316.3 - 5 1346 c.1030C>T c.(1030-1032)Cgg>Tgg p.R344W ABCB6_ENST00000439002.2_Missense_Mutation_p.R298W NM_005689.2 NP_005680.1 Q9NP58 ABCB6_HUMAN ATP-binding cassette, sub-family B (MDR/TAP), member 6 (Langereis blood group) 34 Renal(207;0.0474) AGCTCCACCCGCCGAGACGTG 0.687000 0 SO:0001583 missense ENST00000265316.3 0 1 hg19 CCDS2436.1 . . . . . . . . . . G 13.59 2.282959 0.40394 . . ENSG00000115657 ENST00000265316;ENST00000439002 D;D 0.94376 -2.67;-3.41 5.07 2.06 0.26882 ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1); 0.770646 0.12487 N 0.464574 D 0.94686 0.8286 M 0.71206 2.165 0.18873 N 0.999982 D;D 0.56746 0.975;0.977 P;P 0.55303 0.663;0.773 D 0.87676 0.2544 10 0.72032 D 0.01 -1.3565 12.0339 0.53415 0.0:0.4794:0.3877:0.1328 . 298;344 Q9NP58-4;Q9NP58 .;ABCB6_HUMAN W 344;298 ENSP00000265316:R344W;ENSP00000394333:R298W ENSP00000265316:R344W R - 1 2 ABCB6 219789087 0.000000 0.05858 0.000000 0.03702 0.031000 0.12232 1.031000 0.30165 0.306000 0.22856 0.650000 0.86243 CGG TCGA-3A-A9J0-01A-11D-A40W-08 ABCB6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256820.2 1 0 0 12 63 0 10 1 9.742557e-01 6 30 0 10 2 0 0 0 0 0 2 1 0.997207 11 47 0 9 2 -19.980230 1 1 0 0 1 2 2 4 2.143198 1 0.470000 3.280000 0.620017 0.990000 5.600000e-01 1.000000 1.000000 0.910020 0.990000 1 COL4A4 1286 broad.mit.edu 37 2 227920747 227920747 + Missense_Mutation SNP C C T rs150979437 by1000genomes TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr2:227920747C>T ENST00000396625.3 - 30 2837 c.2630G>A c.(2629-2631)cGg>cAg p.R877Q COL4A4_ENST00000329662.7_Missense_Mutation_p.R877Q NM_000092.4 NP_000083.3 P53420 CO4A4_HUMAN collagen, type IV, alpha 4 98 Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242) TGCCCCAGGCCGTCCTGGGAG 0.627000 0 SO:0001583 missense ENST00000396625.3 1 0 hg19 CCDS42828.1 224 0.10256410256410256 71 0.1443089430894309 23 0.06353591160220995 44 0.07692307692307693 86 0.11345646437994723 C 3.151 -0.174203 0.06421 0.001093 0.003314 ENSG00000081052 ENST00000396625;ENST00000329662 D;D 0.93307 -3.2;-3.2 5.63 -1.9 0.07665 . . . . . T 0.02533 0.0077 N 0.16743 0.435 0.09310 N 1 B 0.13145 0.007 B 0.09377 0.004 T 0.40701 -0.9549 9 0.13470 T 0.59 . 2.2257 0.03983 0.2432:0.4338:0.1032:0.2199 . 877 P53420 CO4A4_HUMAN Q 877 ENSP00000379866:R877Q;ENSP00000328553:R877Q ENSP00000328553:R877Q R - 2 0 COL4A4 227628991 0.000000 0.05858 0.000000 0.03702 0.007000 0.05969 0.006000 0.13152 -0.756000 0.04703 -0.271000 0.10264 CGG TCGA-3A-A9J0-01A-11D-A40W-08 COL4A4-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000313770.1 0 0 1 29 186 0 37 1 1.453389e-01 3 2 0 37 2 0 0 0 0 0 2 1 1.000000 29 183 0 35 2 -2.989699 1 1 120794 502 58 1 2 2 4 2.143198 1 0.470000 3.280000 0.620017 0.830000 5.600000e-01 1.000000 1.000000 0.834406 0.830000 0 LRRFIP1 9208 broad.mit.edu 37 2 238671269 238671269 + Missense_Mutation SNP A A G TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr2:238671269A>G ENST00000392000.4 + 11 1030 c.913A>G c.(913-915)Aaa>Gaa p.K305E LRRFIP1_ENST00000244815.5_Missense_Mutation_p.K281E|LRRFIP1_ENST00000289175.6_Missense_Mutation_p.K249E|LRRFIP1_ENST00000308482.9_Intron NM_001137552.1 NP_001131024.1 Q32MZ4 LRRF1_HUMAN leucine rich repeat (in FLII) interacting protein 1 29 Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182) AGTGGAGGTGAAAAATGAAAT 0.433000 0 SO:0001583 missense ENST00000392000.4 0 1 hg19 CCDS46552.1 . . . . . . . . . . A 18.59 3.655875 0.67586 . . ENSG00000124831 ENST00000289175;ENST00000244815;ENST00000392000 T;T;T 0.47528 0.84;0.84;0.84 5.69 0.0731 0.14389 . 0.837827 0.10426 N 0.676077 T 0.37785 0.1016 L 0.51422 1.61 0.21445 N 0.999689 B;B;B 0.27882 0.192;0.046;0.1 B;B;B 0.25759 0.063;0.046;0.027 T 0.29640 -1.0005 10 0.45353 T 0.12 -15.096 6.5329 0.22336 0.6466:0.1247:0.2287:0.0 . 249;305;281 Q32MZ4-3;Q32MZ4;Q32MZ4-2 .;LRRF1_HUMAN;. E 249;281;305 ENSP00000289175:K249E;ENSP00000244815:K281E;ENSP00000375857:K305E ENSP00000244815:K281E K + 1 0 LRRFIP1 238336008 0.972000 0.33761 0.276000 0.24689 0.948000 0.59901 0.407000 0.21049 0.095000 0.17434 0.528000 0.53228 AAA TCGA-3A-A9J0-01A-11D-A40W-08 LRRFIP1-003 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000317198.1 0 0 0 4 215 0 37 0 8.366742e-01 0 179 0 37 2 0 0 0 0 0 2 1 0.883376 4 208 0 37 2 -3.118740 1 1 121412 1 27 1 2 2 4 2.137730 1 0.470000 3.280000 0.620017 0.130000 3.000000e-02 1.000000 0.110000 0.242719 0.130000 0 KIF1A 547 broad.mit.edu 37 2 241697827 241697827 + Silent SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr2:241697827G>A ENST00000320389.7 - 25 2663 c.2505C>T c.(2503-2505)acC>acT p.T835T KIF1A_ENST00000498729.2_Silent_p.T844T NM_004321.6 NP_004312.2 Q12756 KIF1A_HUMAN kinesin family member 1A p.T835T(1) 66 all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244) GGTCTCCGCCGGTCACCACGT 0.637000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000320389.7 1 1 hg19 CCDS46561.1 TCGA-3A-A9J0-01A-11D-A40W-08 KIF1A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000324536.3 1 0 1 12 95 0 29 0 0 0 0 29 2 0 0 0 0 0 2 1 0.999005 12 89 0 28 2 -18.801000 1 1 121188 4 35 1 2 2 4 2.137730 1 0.470000 3.280000 0.620017 0.710000 3.800000e-01 1.000000 1.000000 0.735511 0.710000 0 PASK 23178 broad.mit.edu 37 2 242065640 242065640 + Missense_Mutation SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr2:242065640C>T ENST00000405260.1 - 10 3388 c.2690G>A c.(2689-2691)aGc>aAc p.S897N PASK_ENST00000403638.3_Missense_Mutation_p.S897N|PASK_ENST00000544142.1_Missense_Mutation_p.S711N|PASK_ENST00000539818.1_Missense_Mutation_p.S681N|PASK_ENST00000358649.4_Missense_Mutation_p.S897N|PASK_ENST00000234040.4_Missense_Mutation_p.S897N NM_001252120.1 NP_001239049.1 Q96RG2 PASK_HUMAN PAS domain containing serine/threonine kinase 53 all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244) ATGGTAGCAGCTCCCGGAGTA 0.647000 0 SO:0001583 missense ENST00000405260.1 1 1 hg19 CCDS2545.1 . . . . . . . . . . C 8.379 0.837154 0.16891 . . ENSG00000115687 ENST00000234040;ENST00000544142;ENST00000405260;ENST00000358649;ENST00000539818;ENST00000403638 T;T;T;T;T;T 0.69175 -0.38;-0.38;-0.38;-0.34;-0.37;0.58 4.94 3.07 0.35406 . 0.267711 0.32357 N 0.006217 T 0.68943 0.3056 L 0.53249 1.67 0.26862 N 0.967935 B;B;B;D;B 0.65815 0.245;0.36;0.2;0.995;0.245 B;B;B;P;B 0.61477 0.052;0.112;0.069;0.889;0.052 T 0.57602 -0.7783 10 0.28530 T 0.3 . 5.2403 0.15467 0.0:0.644:0.1701:0.1859 . 862;711;897;897;897 B7Z7R6;F5GYW7;Q96RG2-2;G5E9F1;Q96RG2 .;.;.;.;PASK_HUMAN N 897;711;897;897;681;897 ENSP00000234040:S897N;ENSP00000441374:S711N;ENSP00000384016:S897N;ENSP00000351475:S897N;ENSP00000443083:S681N;ENSP00000384438:S897N ENSP00000234040:S897N S - 2 0 PASK 241714313 0.998000 0.40836 0.992000 0.48379 0.111000 0.19643 0.836000 0.27545 1.084000 0.41184 0.561000 0.74099 AGC TCGA-3A-A9J0-01A-11D-A40W-08 PASK-003 KNOWN alternative_5_UTR|basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000323753.1 1 0 1 55 129 0 39 1 8.428958e-01 3 7 0 39 2 0 0 0 0 0 2 1 1.000000 54 123 0 37 2 -20.000000 1 1 0 0 1 2 2 4 2.137730 1 0.470000 3.280000 0.620017 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 MYH15 22989 broad.mit.edu 37 3 108172884 108172884 + Nonsense_Mutation SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr3:108172884G>A ENST00000273353.3 - 22 2484 c.2428C>T c.(2428-2430)Cga>Tga p.R810* MYH15_ENST00000495753.2_5'Flank NM_014981.1 NP_055796.1 Q9Y2K3 MYH15_HUMAN myosin, heavy chain 15 105 AATTTGATTCGCATCAGTTTG 0.448000 0 SO:0001587 stop_gained ENST00000273353.3 0 1 hg19 CCDS43127.1 . . . . . . . . . . G 38 6.993775 0.97987 2.61E-4 1.21E-4 ENSG00000144821 ENST00000273353 . . . 5.51 -4.68 0.03309 . . . . . . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 . 5.4871 0.16755 0.2937:0.0:0.3652:0.3411 . . . . X 810 . ENSP00000273353:R810X R - 1 2 MYH15 109655574 0.146000 0.22672 0.000000 0.03702 0.931000 0.56810 -0.349000 0.07731 -0.540000 0.06265 -0.897000 0.02905 CGA TCGA-3A-A9J0-01A-11D-A40W-08 MYH15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000353935.1 1 0 1 34 225 0 46 0 0 0 0 46 2 0 0 0 0 0 2 1 1.000000 33 225 0 45 2 -15.432470 1 1 120838 3 34 1 2 2 4 2.249909 1 0.470000 3.280000 0.638299 0.820000 5.800000e-01 1.000000 1.000000 0.826477 0.820000 0 TBCCD1 55171 broad.mit.edu 37 3 186276243 186276243 + Missense_Mutation SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr3:186276243G>A ENST00000424280.1 - 3 934 c.455C>T c.(454-456)tCt>tTt p.S152F TBCCD1_ENST00000446782.1_Missense_Mutation_p.S56F|TBCCD1_ENST00000338733.5_Missense_Mutation_p.S152F NM_001134415.1 NP_001127887.1 Q9NVR7 TBCC1_HUMAN TBCC domain containing 1 17 all_cancers(143;3.75e-12)|Ovarian(172;0.0339) OV - Ovarian serous cystadenocarcinoma(80;4.3e-21) CAGGTCAGGAGACTGAGATTT 0.403000 0 SO:0001583 missense ENST00000424280.1 1 1 hg19 CCDS3276.1 . . . . . . . . . . G 20.1 3.933597 0.73442 . . ENSG00000113838 ENST00000424280;ENST00000338733;ENST00000446782;ENST00000413695;ENST00000430560 T;T;T;T;T 0.73789 -0.78;-0.78;-0.78;-0.78;0.7 5.24 5.24 0.73138 . 0.207799 0.43747 D 0.000530 T 0.77579 0.4151 M 0.61703 1.905 0.43930 D 0.996586 P;P 0.50819 0.939;0.807 P;B 0.53490 0.727;0.401 T 0.75482 -0.3302 10 0.33940 T 0.23 -19.0802 10.1928 0.43037 0.0911:0.0:0.9089:0.0 . 56;152 G5E9J4;Q9NVR7 .;TBCC1_HUMAN F 152;152;56;152;136 ENSP00000411253:S152F;ENSP00000341652:S152F;ENSP00000397091:S56F;ENSP00000391109:S152F;ENSP00000407506:S136F ENSP00000341652:S152F S - 2 0 TBCCD1 187758937 1.000000 0.71417 1.000000 0.80357 0.969000 0.65631 7.081000 0.76844 2.607000 0.88179 0.655000 0.94253 TCT TCGA-3A-A9J0-01A-11D-A40W-08 TBCCD1-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000344774.1 1 0 1 197 479 0 113 1 9.683370e-01 8 8 0 113 2 0 0 0 0 0 2 1 1.000000 195 469 0 108 2 -20.000000 1 1 0 0 1 2 2 4 2.249909 1 0.470000 3.280000 0.638299 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 RFC4 5984 broad.mit.edu 37 3 186518951 186518951 + Silent SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr3:186518951C>T ENST00000392481.2 - 3 446 c.165G>A c.(163-165)caG>caA p.Q55Q RFC4_ENST00000296273.2_Silent_p.Q55Q|RFC4_ENST00000433496.1_Silent_p.Q55Q NM_181573.2 NP_853551.1 P35249 RFC4_HUMAN replication factor C (activator 1) 4, 37kDa 26 all_cancers(143;2.92e-12)|Ovarian(172;0.0339) OV - Ovarian serous cystadenocarcinoma(80;7.41e-21) CCACTTCTTCCTGGAAAGCAA 0.383000 0 SO:0001819 synonymous_variant ENST00000392481.2 1 1 hg19 CCDS3283.1 TCGA-3A-A9J0-01A-11D-A40W-08 RFC4-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000344471.1 1 0 1 95 475 0 106 1 9.998127e-01 12 52 0 106 2 0 0 0 0 0 2 1 1.000000 94 470 0 103 2 -2.851936 1 1 0 0 1 2 2 4 2.249909 1 0.470000 3.280000 0.638299 0.990000 8.500000e-01 1.000000 1.000000 0.979696 0.990000 1 STAC 6769 broad.mit.edu 37 3 36547239 36547239 + Splice_Site SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr3:36547239G>A ENST00000273183.3 + 8 1133 c.833G>A c.(832-834)gGa>gAa p.G278E STAC_ENST00000457375.2_Splice_Site_p.G217E|STAC_ENST00000476388.1_3'UTR NM_003149.1 NP_003140.1 Q99469 STAC_HUMAN SH3 and cysteine rich domain 32 ctctttcAGGGATCTCTTTCC 0.338000 0 SO:0001630 splice_region_variant ENST00000273183.3 1 0 hg19 CCDS2662.1 . . . . . . . . . . G 8.374 0.835918 0.16820 . . ENSG00000144681 ENST00000273183;ENST00000457375;ENST00000544687;ENST00000434649 T;T;T 0.75367 -0.93;1.09;1.57 5.21 -0.896 0.10557 Src homology-3 domain (1); 0.496999 0.22073 N 0.065008 T 0.48572 0.1507 N 0.24115 0.695 0.39959 D 0.974646 B;B 0.06786 0.0;0.001 B;B 0.06405 0.002;0.001 T 0.44081 -0.9351 10 0.02654 T 1 . 6.0123 0.19582 0.3402:0.1237:0.5361:0.0 . 217;278 E9PEA7;Q99469 .;STAC_HUMAN E 278;217;210;206 ENSP00000273183:G278E;ENSP00000393713:G217E;ENSP00000398403:G206E ENSP00000273183:G278E G + 2 0 STAC 36522243 0.996000 0.38824 0.975000 0.42487 0.667000 0.39255 0.231000 0.17872 -0.428000 0.07339 -0.145000 0.13849 GGA TCGA-3A-A9J0-01A-11D-A40W-08 STAC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253338.2 1 0 1 47 104 0 23 1 6.009984e-01 3 3 0 23 2 0 0 0 0 0 2 1 1.000000 47 100 0 22 2 -20.000000 1 1 0 0 1 2 2 4 2.249909 1 0.470000 3.280000 0.638299 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 DCLK3 85443 broad.mit.edu 37 3 36779648 36779648 + Missense_Mutation SNP T T C TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr3:36779648T>C ENST00000416516.2 - 2 993 c.503A>G c.(502-504)aAg>aGg p.K168R NM_033403.1 NP_208382.1 Q9C098 DCLK3_HUMAN doublecortin-like kinase 3 48 CATTGGGCCCTTCCCCATATC 0.567000 0 SO:0001583 missense ENST00000416516.2 1 1 hg19 CCDS43064.1 . . . . . . . . . . T 5.009 0.187282 0.09547 . . ENSG00000163673 ENST00000416516 T 0.67171 -0.25 4.7 -2.05 0.07321 . 0.350599 0.17768 N 0.162674 T 0.34832 0.0911 N 0.08118 0 0.09310 N 1 B 0.06786 0.001 B 0.08055 0.003 T 0.23797 -1.0178 10 0.10377 T 0.69 . 6.1062 0.20075 0.2212:0.4608:0.0:0.318 . 168 Q9C098 DCLK3_HUMAN R 168 ENSP00000394484:K168R ENSP00000394484:K168R K - 2 0 DCLK3 36754652 0.000000 0.05858 0.001000 0.08648 0.834000 0.47266 -0.855000 0.04295 -0.571000 0.06014 0.533000 0.62120 AAG TCGA-3A-A9J0-01A-11D-A40W-08 DCLK3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000341727.1 1 0 1 173 362 0 94 0 0 0 0 94 2 0 0 0 0 0 2 1 1.000000 168 358 0 88 2 -20.000000 1 1 0 0 1 2 2 4 2.249909 1 0.470000 3.280000 0.638299 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 CTNNB1 1499 broad.mit.edu 37 3 41266136 41266136 + Missense_Mutation SNP T T C rs121913407 TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr3:41266136T>C ENST00000349496.5 + 3 413 c.133T>C c.(133-135)Tct>Cct p.S45P CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45P|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38P|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45P NM_001904.3 NP_001895.1 P35222 CTNB1_HUMAN catenin (cadherin-associated protein), beta 1, 88kDa p.S45P(168)|p.A5_A80del(53)|p.S45del(50)|p.S45A(11)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.S45T(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1) CTNNB1/PLAG1(60) 3893 CACAGCTCCTTCTCTGAGTGG 0.502000 15 H, Mis, T PLAG1 colorectal, cvarian, hepatoblastoma, others, pleomorphic salivary adenoma Pilomatrixoma, Familial Clustering of Colon(6;3 56 14213 18255) Dom yes 3 3p22-p21.3 1499 catenin (cadherin-associated protein), beta 1 E, M, O 355 Substitution - Missense(181)|Deletion - In frame(149)|Complex - deletion inframe(18)|Unknown(7) SO:0001583 missense Familial Cancer Database Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe ENST00000349496.5 1 1 hg19 CCDS2694.1 . . . . . . . . . . T 23.6 4.440246 0.83993 . . ENSG00000168036 ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708 T;T;T;T;T;T;T;T;T 0.52295 0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67 5.91 5.91 0.95273 . 0.000000 0.85682 D 0.000000 T 0.65903 0.2736 M 0.65677 2.01 0.80722 D 1 D 0.60575 0.988 P 0.62649 0.905 T 0.69083 -0.5239 10 0.87932 D 0 -13.6823 16.3453 0.83126 0.0:0.0:0.0:1.0 . 45 P35222 CTNB1_HUMAN P 38;45;45;45;45;38;45;45;45 ENSP00000400508:S38P;ENSP00000385604:S45P;ENSP00000412219:S45P;ENSP00000379486:S45P;ENSP00000344456:S45P;ENSP00000411226:S38P;ENSP00000379488:S45P;ENSP00000409302:S45P;ENSP00000401599:S45P ENSP00000344456:S45P S + 1 0 CTNNB1 41241140 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 8.040000 0.89188 2.261000 0.74972 0.533000 0.62120 TCT TCGA-3A-A9J0-01A-11D-A40W-08 CTNNB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254182.2 1 0 1 82 174 0 35 1 1 201 318 0 35 2 0 0 0 0 0 2 1 1.000000 81 173 0 35 2 -20.000000 1 1 0 0 1 2 2 4 2.249909 1 0.470000 3.280000 0.638299 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 ALS2CL 259173 broad.mit.edu 37 3 46728567 46728567 + Missense_Mutation SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr3:46728567C>T ENST00000318962.4 - 5 523 c.440G>A c.(439-441)gGc>gAc p.G147D ALS2CL_ENST00000415953.1_Missense_Mutation_p.G147D NM_147129.3 NP_667340.2 Q60I27 AL2CL_HUMAN ALS2 C-terminal like 29 CAGCGATGCGCCCACCGAGCC 0.677000 0 SO:0001583 missense ENST00000318962.4 1 1 hg19 CCDS2743.1 . . . . . . . . . . C 9.379 1.072447 0.20147 . . ENSG00000178038 ENST00000318962;ENST00000415953 T;T 0.17528 2.27;2.27 4.18 2.22 0.28083 Dbl homology (DH) domain (1); 0.498524 0.18254 N 0.146852 T 0.10208 0.0250 L 0.29908 0.895 0.09310 N 1 B 0.15141 0.012 B 0.13407 0.009 T 0.18871 -1.0323 10 0.35671 T 0.21 . 3.9061 0.09183 0.0:0.5781:0.2013:0.2207 . 147 Q60I27 AL2CL_HUMAN D 147 ENSP00000313670:G147D;ENSP00000413223:G147D ENSP00000313670:G147D G - 2 0 ALS2CL 46703571 0.005000 0.15991 0.015000 0.15790 0.001000 0.01503 0.589000 0.23939 1.103000 0.41568 0.591000 0.81541 GGC TCGA-3A-A9J0-01A-11D-A40W-08 ALS2CL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250567.3 1 0 1 14 40 0 14 1 9.998274e-01 18 33 0 14 2 0 0 0 0 0 2 1 0.999850 14 38 0 14 2 -20.000000 1 1 0 0 1 2 2 4 2.249909 1 0.470000 3.280000 0.638299 0.990000 9.900000e-01 1.000000 1.000000 0.997352 0.990000 1 ITPR1 3708 broad.mit.edu 37 3 4718357 4718357 + Missense_Mutation SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr3:4718357C>T ENST00000443694.2 + 21 2794 c.2794C>T c.(2794-2796)Cgg>Tgg p.R932W ITPR1_ENST00000354582.6_Missense_Mutation_p.R947W|ITPR1_ENST00000357086.4_Missense_Mutation_p.R938W|ITPR1_ENST00000423119.2_Missense_Mutation_p.R938W|ITPR1_ENST00000456211.2_Missense_Mutation_p.R923W|ITPR1_ENST00000302640.8_Missense_Mutation_p.R932W|ITPR1_ENST00000544951.1_Intron Q14643 ITPR1_HUMAN inositol 1,4,5-trisphosphate receptor, type 1 106 Caffeine(DB00201) GGTGGTGCTCCGGGGAGGAGG 0.562000 0 SO:0001583 missense ENST00000443694.2 1 1 hg19 CCDS54551.1 . . . . . . . . . . C 17.48 3.400893 0.62177 . . ENSG00000150995 ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694 D;D;D;D;D;D 0.91351 -2.83;-2.83;-2.83;-2.83;-2.83;-2.83 4.1 3.14 0.36123 . 0.000000 0.85682 D 0.000000 D 0.91723 0.7383 L 0.47716 1.5 0.80722 D 1 D;D;D 0.76494 0.998;0.997;0.999 P;P;D 0.63283 0.821;0.895;0.913 D 0.91805 0.5455 10 0.72032 D 0.01 . 11.6166 0.51094 0.252:0.748:0.0:0.0 . 932;947;938 E7EPX7;Q14643;G5E9P1 .;ITPR1_HUMAN;. W 947;932;947;938;938;923;932 ENSP00000306253:R932W;ENSP00000346595:R947W;ENSP00000405934:R938W;ENSP00000349597:R938W;ENSP00000397885:R923W;ENSP00000401671:R932W ENSP00000306253:R932W R + 1 2 ITPR1 4693357 1.000000 0.71417 1.000000 0.80357 0.977000 0.68977 2.115000 0.41921 2.280000 0.76307 0.313000 0.20887 CGG TCGA-3A-A9J0-01A-11D-A40W-08 ITPR1-004 KNOWN non_canonical_conserved|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000337982.3 1 0 1 35 105 0 26 0 0 0 1 0 26 2 0 0 0 0 0 2 1 1.000000 34 104 0 24 2 -3.960281 1 1 121000 1 27 1 2 2 4 2.249909 1 0.470000 3.280000 0.638299 0.990000 9.900000e-01 1.000000 1.000000 0.999850 0.990000 1 DCLK2 166614 broad.mit.edu 37 4 151160950 151160950 + Silent SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr4:151160950G>A ENST00000296550.7 + 11 2377 c.1623G>A c.(1621-1623)gcG>gcA p.A541A DCLK2_ENST00000506325.1_Silent_p.A540A|DCLK2_ENST00000302176.8_Silent_p.A558A NM_001040260.3 NP_001035350.2 Q8N568 DCLK2_HUMAN doublecortin-like kinase 2 26 all_hematologic(180;0.151) TTGGGCTTGCGACTGTGGTAG 0.458000 GBM(195;186 2215 13375 16801 37459) 0 SO:0001819 synonymous_variant ENST00000296550.7 1 1 hg19 CCDS34076.1 TCGA-3A-A9J0-01A-11D-A40W-08 DCLK2-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000364952.1 1 0 0 27 422 0 95 0 4.997810e-02 0 6 0 95 2 0 0 0 0 0 2 1 1.000000 27 419 0 91 2 -6.418375 1 1 121412 11 42 1 1 2 3 1.838072 1 0.470000 3.280000 0.566728 0.310000 2.100000e-01 1.000000 0.320000 0.348333 0.310000 0 HSD17B13 345275 broad.mit.edu 37 4 88243945 88243945 + Missense_Mutation SNP A A G TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr4:88243945A>G ENST00000328546.4 - 1 113 c.49T>C c.(49-51)Tcc>Ccc p.S17P RP11-529H2.2_ENST00000508163.1_RNA|HSD17B13_ENST00000302219.6_Missense_Mutation_p.S17P NM_178135.3 NP_835236.2 Q7Z5P4 DHB13_HUMAN hydroxysteroid (17-beta) dehydrogenase 13 8 Acute lymphoblastic leukemia(40;0.244)|all_hematologic(202;0.248) TCCAAGTAGGAGTAGATGATG 0.468000 0 SO:0001583 missense ENST00000328546.4 1 1 hg19 CCDS3618.1 . . . . . . . . . . A 14.50 2.553115 0.45487 . . ENSG00000170509 ENST00000302219;ENST00000328546 D;D 0.90133 -2.62;-1.97 4.81 3.6 0.41247 . 0.194975 0.35436 N 0.003214 D 0.92473 0.7610 M 0.79258 2.445 0.33675 D 0.611372 P;P 0.48503 0.911;0.856 P;P 0.53102 0.718;0.526 D 0.93413 0.6770 10 0.37606 T 0.19 . 11.291 0.49250 0.8469:0.1531:0.0:0.0 . 17;17 Q7Z5P4-2;Q7Z5P4 .;DHB13_HUMAN P 17 ENSP00000305438:S17P;ENSP00000333300:S17P ENSP00000305438:S17P S - 1 0 HSD17B13 88462969 1.000000 0.71417 1.000000 0.80357 0.971000 0.66376 3.554000 0.53720 0.824000 0.34613 0.477000 0.44152 TCC TCGA-3A-A9J0-01A-11D-A40W-08 HSD17B13-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253052.1 1 0 1 42 179 0 44 0 0 0 0 44 2 0 0 0 0 0 2 1 1.000000 40 177 0 42 2 -20.000000 1 1 0 0 1 1 2 3 1.838065 1 0.470000 3.280000 0.566728 0.990000 7.400000e-01 1.000000 1.000000 0.947465 0.990000 1 ADAMTS19 171019 broad.mit.edu 37 5 128863477 128863477 + Nonsense_Mutation SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr5:128863477C>T ENST00000274487.4 + 5 1250 c.1105C>T c.(1105-1107)Cag>Tag p.Q369* CTC-575N7.1_ENST00000503616.1_RNA NM_133638.3 NP_598377.3 Q8TE59 ATS19_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 19 91 all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) TCTGAGTGTGCAGGTCAATCT 0.299000 0 SO:0001587 stop_gained ENST00000274487.4 0 1 hg19 CCDS4146.1 . . . . . . . . . . C 35 5.444548 0.96187 . . ENSG00000145808 ENST00000274487 . . . 4.41 4.41 0.53225 . 0.085473 0.47455 D 0.000231 . . . . . . 0.80722 A 1 . . . . . . . . . . . . . . 18.326 0.90254 0.0:1.0:0.0:0.0 . . . . X 369 . . Q + 1 0 ADAMTS19 128891376 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 2.856000 0.48341 2.737000 0.93849 0.563000 0.77884 CAG TCGA-3A-A9J0-01A-11D-A40W-08 ADAMTS19-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250979.2 1 0 1 276 220 0 63 0 0 0 0 63 2 0 0 0 0 0 2 1 1.000000 273 219 0 60 2 -20.000000 1 1 0 0 1 0 3 3 1.941373 1 0.470000 3.280000 0.570850 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 PCDHB7 56129 broad.mit.edu 37 5 140552501 140552501 + Missense_Mutation SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr5:140552501G>A ENST00000231137.3 + 1 259 c.85G>A c.(85-87)Gaa>Aaa p.E29K NM_018940.2 NP_061763.1 Q9Y5E2 PCDB7_HUMAN protocadherin beta 7 119 KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339) GGCTGGCGCCGAACCGCTTCG 0.517000 0 SO:0001583 missense ENST00000231137.3 1 1 hg19 CCDS4249.1 . . . . . . . . . . G 12.37 1.918636 0.33908 . . ENSG00000113212 ENST00000231137 T 0.48836 0.8 4.78 4.78 0.61160 . . . . . T 0.57533 0.2060 M 0.88377 2.95 0.22017 N 0.999413 B 0.25312 0.123 B 0.21708 0.036 T 0.54029 -0.8354 9 0.40728 T 0.16 . 16.7421 0.85462 0.0:0.0:1.0:0.0 . 29 Q9Y5E2 PCDB7_HUMAN K 29 ENSP00000231137:E29K ENSP00000231137:E29K E + 1 0 PCDHB7 140532685 0.877000 0.30153 0.510000 0.27712 0.294000 0.27393 5.150000 0.64869 2.353000 0.79882 0.650000 0.86243 GAA TCGA-3A-A9J0-01A-11D-A40W-08 PCDHB7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251803.2 1 0 1 82 334 0 113 0 4.897161e-01 0 8 0 113 2 0 0 0 0 0 2 1 1.000000 80 326 0 112 2 -20.000000 1 1 121412 1 31 1 0 3 3 1.941373 1 0.470000 3.280000 0.570850 0.990000 8.400000e-01 1.000000 1.000000 0.976823 0.990000 1 MAP1B 4131 broad.mit.edu 37 5 71494871 71494871 + Missense_Mutation SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr5:71494871C>T ENST00000296755.7 + 5 5987 c.5689C>T c.(5689-5691)Cgg>Tgg p.R1897W NM_005909.3 NP_005900.2 P46821 MAP1B_HUMAN microtubule-associated protein 1B 104 Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198) GAAGACCACCCGGACCTCAGA 0.453000 Melanoma(17;367 822 11631 31730 47712) 0 SO:0001583 missense ENST00000296755.7 1 1 hg19 CCDS4012.1 . . . . . . . . . . C 3.470 -0.108223 0.06924 . . ENSG00000131711 ENST00000296755 T 0.03524 3.9 5.52 3.67 0.42095 . 0.220565 0.30658 N 0.009152 T 0.05044 0.0135 N 0.08118 0 0.09310 N 1 D;D 0.65815 0.995;0.995 P;P 0.56823 0.807;0.714 T 0.31696 -0.9934 10 0.87932 D 0 -2.6404 11.924 0.52808 0.4852:0.5148:0.0:0.0 . 1771;1897 A2BDK6;P46821 .;MAP1B_HUMAN W 1897 ENSP00000296755:R1897W ENSP00000296755:R1897W R + 1 2 MAP1B 71530627 0.001000 0.12720 0.011000 0.14972 0.113000 0.19764 0.695000 0.25527 0.645000 0.30675 0.551000 0.68910 CGG TCGA-3A-A9J0-01A-11D-A40W-08 MAP1B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000218561.6 1 0 1 180 120 0 60 0 8.185223e-01 0 4 0 60 2 0 0 0 0 0 2 1 1.000000 181 119 0 59 2 -20.000000 1 1 121412 3 36 1 0 3 3 1.932771 1 0.470000 3.280000 0.570850 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 MAP1B 4131 broad.mit.edu 37 5 71495084 71495084 + Missense_Mutation SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr5:71495084G>A ENST00000296755.7 + 5 6200 c.5902G>A c.(5902-5904)Gaa>Aaa p.E1968K NM_005909.3 NP_005900.2 P46821 MAP1B_HUMAN microtubule-associated protein 1B 104 Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198) CAGCCCCCCCGAAGTGAGTGG 0.478000 Melanoma(17;367 822 11631 31730 47712) 0 SO:0001583 missense ENST00000296755.7 1 1 hg19 CCDS4012.1 . . . . . . . . . . G 12.11 1.840480 0.32513 . . ENSG00000131711 ENST00000296755 T 0.03524 3.9 5.11 5.11 0.69529 . 0.436414 0.21672 N 0.070842 T 0.04679 0.0127 N 0.08118 0 0.36942 D 0.892433 D;P 0.58268 0.982;0.512 P;B 0.50825 0.651;0.14 T 0.57791 -0.7750 10 0.49607 T 0.09 -6.4359 16.7322 0.85438 0.0:0.0:1.0:0.0 . 1842;1968 A2BDK6;P46821 .;MAP1B_HUMAN K 1968 ENSP00000296755:E1968K ENSP00000296755:E1968K E + 1 0 MAP1B 71530840 0.787000 0.28750 0.992000 0.48379 0.246000 0.25737 4.449000 0.60034 2.381000 0.81170 0.551000 0.68910 GAA TCGA-3A-A9J0-01A-11D-A40W-08 MAP1B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000218561.6 1 0 1 81 372 0 69 0 4.364138e-01 0 8 0 69 2 0 0 0 0 0 2 1 1.000000 81 364 0 65 2 -20.000000 1 1 0 0 1 0 3 3 1.932771 1 0.470000 3.280000 0.570850 0.930000 7.600000e-01 1.000000 1.000000 0.928299 0.930000 1 LAMA4 3910 broad.mit.edu 37 6 112496518 112496518 + Missense_Mutation SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr6:112496518C>T ENST00000230538.7 - 11 1751 c.1354G>A c.(1354-1356)Gaa>Aaa p.E452K LAMA4_ENST00000522006.1_Missense_Mutation_p.E445K|LAMA4_ENST00000424408.2_Missense_Mutation_p.E445K|LAMA4_ENST00000389463.4_Missense_Mutation_p.E445K NM_001105206.2 NP_001098676.2 Q16363 LAMA4_HUMAN laminin, alpha 4 100 all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209) CACCTACGTTCGTAAGCCTCA 0.483000 0 SO:0001583 missense ENST00000230538.7 1 1 hg19 CCDS43491.1 . . . . . . . . . . C 14.97 2.694350 0.48202 . . ENSG00000112769 ENST00000230538;ENST00000522006;ENST00000389463;ENST00000424408 T;T;T;T 0.09163 3.01;3.01;3.01;3.01 5.91 5.91 0.95273 Laminin I (1); 0.213635 0.48767 D 0.000165 T 0.12433 0.0302 L 0.47716 1.5 0.80722 D 1 D;D 0.67145 0.996;0.995 P;P 0.58391 0.838;0.749 T 0.10683 -1.0619 10 0.11182 T 0.66 . 18.0694 0.89400 0.0:1.0:0.0:0.0 . 452;445 Q16363;Q16363-2 LAMA4_HUMAN;. K 452;445;445;445 ENSP00000230538:E452K;ENSP00000429488:E445K;ENSP00000374114:E445K;ENSP00000416470:E445K ENSP00000230538:E452K E - 1 0 LAMA4 112603211 0.981000 0.34729 0.343000 0.25615 0.031000 0.12232 2.957000 0.49137 2.813000 0.96785 0.655000 0.94253 GAA TCGA-3A-A9J0-01A-11D-A40W-08 LAMA4-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000041876.2 1 0 1 163 233 0 86 0 1 0 41 0 86 2 0 0 0 0 0 2 1 1.000000 158 230 0 84 2 -19.999980 1 1 0 0 1 1 2 3 1.945845 1 0.470000 3.280000 0.570850 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 IFNGR1 3459 broad.mit.edu 37 6 137524778 137524778 + Missense_Mutation SNP C C A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr6:137524778C>A ENST00000367739.4 - 5 712 c.591G>T c.(589-591)gaG>gaT p.E197D IFNGR1_ENST00000367735.2_3'UTR|IFNGR1_ENST00000478333.1_5'Flank|IFNGR1_ENST00000543628.1_Missense_Mutation_p.E169D NM_000416.2 NP_000407.1 P15260 INGR1_HUMAN interferon gamma receptor 1 18 Colorectal(23;0.24) Interferon gamma-1b(DB00033) GGCACTGAATCTCGTCACAAT 0.378000 0 SO:0001583 missense ENST00000367739.4 1 1 hg19 CCDS5185.1 . . . . . . . . . . C 12.20 1.866633 0.32977 . . ENSG00000027697 ENST00000367739;ENST00000418947;ENST00000543628;ENST00000458076 T;T;T 0.45276 0.9;0.9;0.9 5.34 -3.11 0.05299 Interferon gamma receptor, poxvirus/mammal (1);Fibronectin, type III (1);Immunoglobulin-like fold (1); 0.212273 0.23342 N 0.049224 T 0.13628 0.0330 M 0.71581 2.175 0.09310 N 1 B;B 0.09022 0.001;0.002 B;B 0.14578 0.007;0.011 T 0.18713 -1.0328 10 0.30078 T 0.28 -11.59 2.1319 0.03752 0.1234:0.2775:0.3634:0.2358 . 169;197 F5H5M7;P15260 .;INGR1_HUMAN D 197;197;169;163 ENSP00000356713:E197D;ENSP00000443282:E169D;ENSP00000389249:E163D ENSP00000356713:E197D E - 3 2 IFNGR1 137566471 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -1.316000 0.02710 -0.289000 0.09038 -0.305000 0.09177 GAG TCGA-3A-A9J0-01A-11D-A40W-08 IFNGR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042401.1 1 0 1 86 172 0 64 1 1 119 132 0 64 2 0 0 0 0 0 2 1 1.000000 86 171 0 62 2 -20.000000 1 1 0 0 1 1 2 3 1.945845 1 0.470000 3.280000 0.570850 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 LPA 4018 broad.mit.edu 37 6 161006101 161006101 + Silent SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr6:161006101C>T ENST00000316300.5 - 26 4310 c.4266G>A c.(4264-4266)agG>agA p.R1422R LPA_ENST00000447678.1_Silent_p.R1422R P08519 APOA_HUMAN lipoprotein, Lp(a) p.R1422S(1) 107 Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965) Aminocaproic Acid(DB00513) ATAATGGGATCCTCCGATGCC 0.443000 1 Substitution - Missense(1) SO:0001819 synonymous_variant ENST00000316300.5 1 1 hg19 CCDS43523.1 TCGA-3A-A9J0-01A-11D-A40W-08 LPA-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042957.1 1 0 1 288 550 0 105 0 0 0 0 105 2 0 0 0 0 0 2 1 1.000000 285 545 1 103 25 -20.000000 1 1 0 0 1 1 2 3 1.945845 1 0.470000 3.280000 0.570850 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 MUC21 394263 broad.mit.edu 37 6 30955236 30955236 + Silent SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr6:30955236C>T ENST00000376296.3 + 2 1525 c.1284C>T c.(1282-1284)acC>acT p.T428T MUC21_ENST00000486149.2_5'UTR NM_001010909.2 NP_001010909.2 Q5SSG8 MUC21_HUMAN mucin 21, cell surface associated 42 CCAGCACAACCTCCAGTGGGG 0.597000 0 SO:0001819 synonymous_variant ENST00000376296.3 1 0 hg19 CCDS34388.1 TCGA-3A-A9J0-01A-11D-A40W-08 MUC21-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000128579.3 1 0 1 91 550 0 128 0 0 0 0 128 2 0 0 0 0 0 2 1 1.000000 86 530 0 125 2 -20.000000 1 1 0 0 1 1 2 3 1.954404 1 0.470000 3.280000 0.570850 0.740000 6.000000e-01 0.890000 0.750000 0.751034 0.740000 0 TNXB 7148 broad.mit.edu 37 6 32063700 32063700 + Missense_Mutation SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr6:32063700C>T ENST00000479795.1 - 3 2070 c.1930G>A c.(1930-1932)Ggc>Agc p.G644S TNXB_ENST00000375247.2_Missense_Mutation_p.G644S|TNXB_ENST00000375244.3_Missense_Mutation_p.G644S P22105 TENX_HUMAN tenascin XB 8 CAGGTAGGGCCGGTGTAGCCT 0.687000 0 SO:0001583 missense ENST00000479795.1 1 1 hg19 . . . . . . . . . . C 14.90 2.673033 0.47781 . . ENSG00000168477 ENST00000375244;ENST00000375247;ENST00000479795 T;T;D 0.85013 1.81;1.81;-1.93 4.25 4.25 0.50352 . 0.000000 0.43416 D 0.000580 D 0.92773 0.7702 M 0.91561 3.22 0.40214 D 0.977668 D 0.89917 1.0 D 0.97110 1.0 D 0.93982 0.7259 10 0.59425 D 0.04 . 15.6045 0.76652 0.0:1.0:0.0:0.0 . 644 P22105-3 . S 644 ENSP00000364393:G644S;ENSP00000364396:G644S;ENSP00000418248:G644S ENSP00000364393:G644S G - 1 0 TNXB 32171678 . . 0.189000 0.23252 0.058000 0.15608 . . 2.198000 0.70561 0.563000 0.77884 GGC TCGA-3A-A9J0-01A-11D-A40W-08 TNXB-007 PUTATIVE basic|exp_conf protein_coding protein_coding OTTHUMT00000357059.1 1 0 1 24 82 0 32 0 5.521577e-02 0 2 0 32 2 0 0 0 0 0 2 1 1.000000 21 79 0 32 2 -20.000000 1 1 120958 2 38 1 1 2 3 1.954404 1 0.470000 3.280000 0.570850 0.990000 8.100000e-01 1.000000 1.000000 0.984096 0.990000 1 PRSS35 167681 broad.mit.edu 37 6 84233890 84233890 + Missense_Mutation SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr6:84233890G>A ENST00000369700.3 + 2 907 c.730G>A c.(730-732)Gaa>Aaa p.E244K PRSS35_ENST00000536636.1_Missense_Mutation_p.E244K NM_153362.2 NP_699193.2 Q8N3Z0 PRS35_HUMAN protease, serine, 35 32 all_cancers(76;0.000113)|Acute lymphoblastic leukemia(125;1.09e-08)|all_hematologic(105;3.12e-05)|all_epithelial(107;0.0575) GAGGATTGCCGAAGGGAGGCC 0.567000 0 SO:0001583 missense ENST00000369700.3 1 1 hg19 CCDS4999.1 . . . . . . . . . . G 10.19 1.281627 0.23392 . . ENSG00000146250 ENST00000536636;ENST00000369700 T;T 0.43294 0.95;0.95 5.65 4.76 0.60689 Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1); 0.988869 0.08242 N 0.975900 T 0.09512 0.0234 N 0.04508 -0.205 0.28907 N 0.892957 B 0.28801 0.223 B 0.16722 0.016 T 0.22312 -1.0220 10 0.17832 T 0.49 -10.6501 16.2336 0.82360 0.0:0.1375:0.8625:0.0 . 244 Q8N3Z0 PRS35_HUMAN K 244 ENSP00000440870:E244K;ENSP00000358714:E244K ENSP00000358714:E244K E + 1 0 PRSS35 84290609 0.017000 0.18338 0.008000 0.14137 0.110000 0.19582 1.679000 0.37597 1.349000 0.45751 0.462000 0.41574 GAA TCGA-3A-A9J0-01A-11D-A40W-08 PRSS35-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041352.1 1 0 1 35 152 0 33 0 0 0 1 0 33 2 0 0 0 0 0 2 1 1.000000 35 146 0 33 2 -3.267408 1 1 121412 2 32 1 1 2 3 1.945845 1 0.470000 3.280000 0.570850 0.980000 7.100000e-01 1.000000 1.000000 0.938784 0.980000 1 EPHA7 2045 broad.mit.edu 37 6 93956606 93956606 + Missense_Mutation SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr6:93956606C>T ENST00000369303.4 - 15 2814 c.2630G>A c.(2629-2631)cGt>cAt p.R877H NM_004440.3 NP_004431.1 Q15375 EPHA7_HUMAN EPH receptor A7 p.R877L(1) 112 all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142) CCTTTCAGCACGCTCCTTTTG 0.423000 1 Substitution - Missense(1) SO:0001583 missense ENST00000369303.4 1 1 hg19 CCDS5031.1 . . . . . . . . . . C 35 5.526893 0.96431 . . ENSG00000135333 ENST00000369303 T 0.62364 0.03 5.74 5.74 0.90152 Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1); 0.000000 0.85682 D 0.000000 T 0.63177 0.2489 N 0.20445 0.575 0.80722 D 1 D;D;D 0.89917 0.999;1.0;1.0 D;D;D 0.70716 0.97;0.942;0.966 T 0.69213 -0.5204 10 0.87932 D 0 . 19.9265 0.97104 0.0:1.0:0.0:0.0 . 873;872;877 Q15375-4;Q15375-2;Q15375 .;.;EPHA7_HUMAN H 877 ENSP00000358309:R877H ENSP00000358309:R877H R - 2 0 EPHA7 94013327 1.000000 0.71417 0.870000 0.34147 0.995000 0.86356 7.726000 0.84824 2.723000 0.93209 0.591000 0.81541 CGT TCGA-3A-A9J0-01A-11D-A40W-08 EPHA7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041545.1 1 0 1 115 241 0 64 0 0 0 0 64 2 0 0 0 0 0 2 1 1.000000 116 238 0 63 2 -20.000000 1 1 121412 4 38 1 1 2 3 1.945845 1 0.470000 3.280000 0.570850 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 OR2A14 135941 broad.mit.edu 37 7 143826573 143826573 + Missense_Mutation SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr7:143826573C>T ENST00000408899.2 + 1 423 c.368C>T c.(367-369)gCg>gTg p.A123V NM_001001659.1 NP_001001659.1 Q96R47 O2A14_HUMAN olfactory receptor, family 2, subfamily A, member 14 22 Melanoma(164;0.0783) GATCGCTATGCGGACATCTGC 0.493000 0 SO:0001583 missense ENST00000408899.2 0 1 hg19 CCDS43672.1 . . . . . . . . . . C 0.009 -1.806132 0.00606 . . ENSG00000221938 ENST00000408899 T 0.00402 7.56 4.18 3.02 0.34903 GPCR, rhodopsin-like superfamily (1); 0.677608 0.11236 N 0.585087 T 0.00073 0.0002 N 0.00121 -2.07 0.22684 N 0.998858 B 0.02656 0.0 B 0.01281 0.0 T 0.23261 -1.0193 10 0.02654 T 1 -8.6728 8.1672 0.31233 0.0:0.099:0.0:0.901 . 123 Q96R47 O2A14_HUMAN V 123 ENSP00000386137:A123V ENSP00000386137:A123V A + 2 0 OR2A14 143457506 0.128000 0.22383 0.910000 0.35882 0.018000 0.09664 2.090000 0.41682 0.732000 0.32470 -0.415000 0.06103 GCG TCGA-3A-A9J0-01A-11D-A40W-08 OR2A14-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000349980.1 0 0 0 7 729 0 135 0 0 0 0 135 2 0 0 0 0 0 2 1 0.979983 8 721 0 135 2 -1.816548 0 1 121204 4 35 1 2 2 4 2.315457 1 0.470000 3.280000 0.639456 0.060000 0 0.120000 0.080000 0.066212 0.060000 0 NUB1 51667 broad.mit.edu 37 7 151072988 151072988 + Missense_Mutation SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr7:151072988G>A ENST00000355851.4 + 13 1527 c.1450G>A c.(1450-1452)Gac>Aac p.D484N NUB1_ENST00000568733.1_Missense_Mutation_p.D508N|NUB1_ENST00000413040.2_Missense_Mutation_p.D494N|NUB1_ENST00000566856.1_Missense_Mutation_p.D470N|WDR86_ENST00000463000.1_5'Flank NM_001243351.1 NP_001230280.1 Q9Y5A7 NUB1_HUMAN negative regulator of ubiquitin-like proteins 1 11 OV - Ovarian serous cystadenocarcinoma(82;0.00569) TCCTGAAACCGACAACCGTCA 0.493000 0 SO:0001583 missense ENST00000355851.4 0 1 hg19 . . . . . . . . . . G 0.012 -1.671641 0.00758 . . ENSG00000013374 ENST00000413040;ENST00000355851 T 0.42513 0.97 5.29 1.42 0.22433 UBA-like (1); 0.997169 0.08136 N 0.992432 T 0.13329 0.0323 N 0.02011 -0.69 0.09310 N 1 B;B 0.02656 0.0;0.0 B;B 0.01281 0.0;0.0 T 0.30475 -0.9977 10 0.02654 T 1 -13.5194 3.5859 0.07970 0.6533:0.1362:0.0787:0.1318 . 484;470 Q9Y5A7;Q9Y5A7-2 NUB1_HUMAN;. N 470;484 ENSP00000348110:D484N ENSP00000348110:D484N D + 1 0 NUB1 150703921 0.001000 0.12720 0.000000 0.03702 0.077000 0.17291 1.025000 0.30090 0.109000 0.17891 -1.421000 0.01109 GAC TCGA-3A-A9J0-01A-11D-A40W-08 NUB1-201 KNOWN basic|appris_principal protein_coding protein_coding 0 0 0 6 756 0 148 0 2.272615e-01 0 98 0 148 2 0 0 0 0 0 2 1 0.962387 6 739 0 142 2 -2.138169 0 1 120878 1 36 1 2 2 4 2.315457 1 0.470000 3.280000 0.639456 0.040000 0 0.110000 0.040000 0.054933 0.040000 0 LMBR1 64327 broad.mit.edu 37 7 156520649 156520649 + Missense_Mutation SNP T T C TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr7:156520649T>C ENST00000353442.5 - 12 1204 c.968A>G c.(967-969)gAa>gGa p.E323G LMBR1_ENST00000354505.4_Missense_Mutation_p.E364G|LMBR1_ENST00000359422.4_Missense_Mutation_p.E171G|LMBR1_ENST00000540390.1_Missense_Mutation_p.E302G NM_022458.3 NP_071903.2 Q8WVP7 LMBR1_HUMAN limb development membrane protein 1 18 Ovarian(565;0.218) all_hematologic(28;0.0592) OV - Ovarian serous cystadenocarcinoma(82;0.00231) CATTGCTGTTTCATCAACCAA 0.363000 0 SO:0001583 missense ENST00000353442.5 0 1 hg19 CCDS5945.1 . . . . . . . . . . T 19.26 3.793587 0.70452 . . ENSG00000105983 ENST00000353442;ENST00000359422;ENST00000415428;ENST00000354505;ENST00000540390 T;T;T;T;T 0.32023 1.47;1.47;1.47;1.47;1.47 4.66 4.66 0.58398 LMBR1-like membrane protein (1); 0.000000 0.85682 D 0.000000 T 0.40423 0.1116 L 0.31752 0.955 0.80722 D 1 D;B;D 0.89917 0.999;0.084;1.0 D;B;D 0.83275 0.995;0.042;0.996 T 0.11275 -1.0594 10 0.18276 T 0.48 -11.8648 13.7733 0.63038 0.0:0.0:0.0:1.0 . 302;364;323 B7Z633;Q8WVP7-3;Q8WVP7 .;.;LMBR1_HUMAN G 323;171;362;364;302 ENSP00000326604:E323G;ENSP00000352392:E171G;ENSP00000408256:E362G;ENSP00000346500:E364G;ENSP00000445509:E302G ENSP00000326604:E323G E - 2 0 LMBR1 156213410 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 7.084000 0.76866 1.750000 0.51863 0.383000 0.25322 GAA TCGA-3A-A9J0-01A-11D-A40W-08 LMBR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347939.3 0 0 0 7 294 0 57 0 4.811309e-02 0 13 0 57 2 0 0 0 0 0 2 1 0.980472 7 292 0 56 2 -3.482006 1 1 0 0 1 2 2 4 2.315457 1 0.470000 3.280000 0.639456 0.150000 5.000000e-02 0.290000 0.160000 0.164866 0.150000 0 GLI3 2737 broad.mit.edu 37 7 42018305 42018305 + Missense_Mutation SNP C C T rs148502119 TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr7:42018305C>T ENST00000395925.3 - 11 1624 c.1540G>A c.(1540-1542)Gtg>Atg p.V514M GLI3_ENST00000479210.1_5'UTR NM_000168.5 NP_000159.3 P10071 GLI3_HUMAN GLI family zinc finger 3 112 CACCTGCACACGAACTCCTTC 0.443000 Pallister-Hall syndrome;Greig Cephalopolysyndactyly 0 SO:0001583 missense Familial Cancer Database ; ENST00000395925.3 1 1 hg19 CCDS5465.1 . . . . . . . . . . C 32 5.177605 0.94846 4.54E-4 0.0 ENSG00000106571 ENST00000395925 D 0.93811 -3.29 5.84 5.84 0.93424 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.000000 0.85682 D 0.000000 D 0.97564 0.9202 M 0.92604 3.325 0.80722 D 1 D 0.89917 1.0 D 0.66979 0.948 D 0.97919 1.0313 10 0.87932 D 0 . 20.1381 0.98040 0.0:1.0:0.0:0.0 . 514 P10071 GLI3_HUMAN M 514 ENSP00000379258:V514M ENSP00000379258:V514M V - 1 0 GLI3 41984830 1.000000 0.71417 0.989000 0.46669 0.984000 0.73092 7.770000 0.85390 2.763000 0.94921 0.650000 0.86243 GTG TCGA-3A-A9J0-01A-11D-A40W-08 GLI3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250806.3 1 0 1 125 279 0 106 0 0 0 1 0 106 2 0 0 0 0 0 2 1 1.000000 124 276 0 104 2 -20.000000 1 1 121412 2 33 1 2 2 4 2.285665 1 0.470000 3.280000 0.639456 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 ADCY1 107 broad.mit.edu 37 7 45699701 45699701 + Silent SNP G G A rs149589767 TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr7:45699701G>A ENST00000297323.7 + 7 1390 c.1368G>A c.(1366-1368)ccG>ccA p.P456P ADCY1_ENST00000432715.1_Silent_p.P231P NM_021116.2 NP_066939.1 Q08828 ADCY1_HUMAN adenylate cyclase 1 (brain) 71 Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171) AGGTAGAACCGGGTTACGGAC 0.507000 0 SO:0001819 synonymous_variant ENST00000297323.7 1 1 hg19 CCDS34631.1 TCGA-3A-A9J0-01A-11D-A40W-08 ADCY1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000340055.2 0 0 1 138 286 1 124 0 0 0 1 124 2 0 0 0 0 0 2 1 1.000000 137 281 1 121 13 -11.776190 1 1 121412 2 37 1 2 2 4 2.285665 1 0.470000 3.280000 0.639456 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 WBSCR17 64409 broad.mit.edu 37 7 71142270 71142270 + Silent SNP G G A rs145007893 TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr7:71142270G>A ENST00000333538.5 + 9 2113 c.1479G>A c.(1477-1479)ccG>ccA p.P493P WBSCR17_ENST00000498380.2_3'UTR NM_022479.1 NP_071924.1 Q6IS24 GLTL3_HUMAN Williams-Beuren syndrome chromosome region 17 100 all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125) TATTGTATCCGTGCCATGGCT 0.537000 0 SO:0001819 synonymous_variant ENST00000333538.5 0 1 hg19 CCDS5540.1 TCGA-3A-A9J0-01A-11D-A40W-08 WBSCR17-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252006.1 0 0 0 23 952 0 139 0 3.635603e-03 0 4 0 139 2 0 0 0 0 0 2 1 0.999999 23 941 0 136 2 -2.623359 1 1 121412 3 44 1 2 2 4 2.285665 1 0.470000 3.280000 0.639456 0.140000 8.000000e-02 0.220000 0.160000 0.153534 0.140000 0 LZTS1 11178 broad.mit.edu 37 8 20107374 20107374 + Silent SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr8:20107374G>A ENST00000381569.1 - 4 2007 c.1650C>T c.(1648-1650)taC>taT p.Y550Y LZTS1_ENST00000265801.6_Silent_p.Y550Y|LZTS1_ENST00000522290.1_Silent_p.Y491Y Q9Y250 LZTS1_HUMAN leucine zipper, putative tumor suppressor 1 29 ACATGGCCACGTAGCTCTGCT 0.627000 0 SO:0001819 synonymous_variant ENST00000381569.1 1 1 hg19 CCDS6015.1 TCGA-3A-A9J0-01A-11D-A40W-08 LZTS1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000214122.1 1 0 0 102 343 0 161 0 5.790849e-01 0 8 0 161 2 1 7.545493e-01 7 4 0 4 2 1 1.000000 100 340 0 155 2 -20.000000 1 1 121410 2 35 1 1 2 3 1.601012 0 0.470000 3.280000 0.482169 0.990000 8.300000e-01 1.000000 1.000000 0.968710 0.990000 1 TEK 7010 broad.mit.edu 37 9 27158047 27158047 + Nonsense_Mutation SNP G G T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr9:27158047G>T ENST00000380036.4 + 2 713 c.271G>T c.(271-273)Gaa>Taa p.E91* TEK_ENST00000406359.4_Nonsense_Mutation_p.E91*|TEK_ENST00000519097.1_Intron NM_000459.3 NP_000450 Q02763 TIE2_HUMAN TEK tyrosine kinase, endothelial 15 all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255) Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294) TTGGAAGAGAGAAAAGGCTAG 0.448000 0 SO:0001587 stop_gained ENST00000380036.4 0 1 hg19 CCDS6519.1 . . . . . . . . . . G 38 7.144543 0.98092 . . ENSG00000120156 ENST00000380036;ENST00000346448;ENST00000406359 . . . 5.92 5.92 0.95590 . 0.000000 0.52532 D 0.000066 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.52906 T 0.07 . 20.3206 0.98668 0.0:0.0:1.0:0.0 . . . . X 91 . ENSP00000343716:E91X E + 1 0 TEK 27148047 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 6.664000 0.74437 2.809000 0.96659 0.655000 0.94253 GAA TCGA-3A-A9J0-01A-11D-A40W-08 TEK-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051965.3 1 0 1 62 189 0 47 0 6.274315e-02 0 2 0 47 2 0 0 0 0 0 2 1 1.000000 59 186 0 45 2 -20.000000 1 1 0 0 1 0 2 2 1.594592 1 0.470000 3.280000 0.470000 0.990000 8.300000e-01 1.000000 1.000000 0.976859 0.990000 1 TRPM6 140803 broad.mit.edu 37 9 77376995 77376995 + Missense_Mutation SNP C C T TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr9:77376995C>T ENST00000360774.1 - 26 4829 c.4592G>A c.(4591-4593)cGc>cAc p.R1531H TRPM6_ENST00000451710.3_Missense_Mutation_p.R1531H|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000376864.4_Missense_Mutation_p.R1531H|TRPM6_ENST00000361255.3_Missense_Mutation_p.R1526H|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000449912.2_Missense_Mutation_p.R1526H NM_017662.4 NP_060132.3 Q9BX84 TRPM6_HUMAN transient receptor potential cation channel, subfamily M, member 6 126 CCTGTATCTGCGGAGAGGATT 0.418000 0 SO:0001583 missense ENST00000360774.1 1 1 hg19 CCDS6647.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 1.535|1.535 -0.543353|-0.543353 0.04053|0.04053 .|. .|. ENSG00000119121|ENSG00000119121 ENST00000448641|ENST00000360774;ENST00000451710;ENST00000449912;ENST00000361255;ENST00000376864;ENST00000312449 .|T;T;T;T;T .|0.54279 .|0.68;0.68;0.68;0.68;0.58 5.33|5.33 -5.55|-5.55 0.02536|0.02536 .|. .|1.118960 .|0.06509 .|N .|0.737619 .|T .|0.28599 .|0.0708 N|N 0.05383|0.05383 -0.06|-0.06 0.09310|0.09310 N|N 1|1 .|B;B;B .|0.10296 .|0.002;0.003;0.003 .|B;B;B .|0.06405 .|0.001;0.002;0.002 .|T .|0.27226 .|-1.0080 .|10 .|0.54805 .|T .|0.06 .|. 7.9227|7.9227 0.29857|0.29857 0.1046:0.3691:0.0:0.5263|0.1046:0.3691:0.0:0.5263 .|. .|1531;1526;1526 .|Q9BX84;Q9BX84-3;Q9BX84-2 .|TRPM6_HUMAN;.;. .|H -1|1531;1531;1526;1526;1531;1104 .|ENSP00000354006:R1531H;ENSP00000407341:R1531H;ENSP00000396672:R1526H;ENSP00000354962:R1526H;ENSP00000366060:R1531H .|ENSP00000309693:R1104H .|R -|- .|2 .|0 TRPM6|TRPM6 76566815|76566815 0.085000|0.085000 0.21516|0.21516 0.000000|0.000000 0.03702|0.03702 0.005000|0.005000 0.04900|0.04900 -0.050000|-0.050000 0.11904|0.11904 -1.668000|-1.668000 0.01471|0.01471 -0.290000|-0.290000 0.09829|0.09829 .|CGC TCGA-3A-A9J0-01A-11D-A40W-08 TRPM6-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000052693.1 1 0 1 56 212 0 57 0 0 0 0 57 2 0 0 0 0 0 2 1 1.000000 55 212 0 56 2 -3.695870 1 1 121412 5 39 1 0 2 2 1.594592 1 0.470000 3.280000 0.470000 0.880000 6.900000e-01 1.000000 1.000000 0.885130 0.880000 1 C9orf89 84270 broad.mit.edu 37 9 95869990 95869990 + Silent SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chr9:95869990G>A ENST00000375464.2 + 2 170 c.42G>A c.(40-42)acG>acA p.T14T NM_032310.3 NP_115686.3 Q96LW7 BINCA_HUMAN chromosome 9 open reading frame 89 7 TGCAGGACACGCCTTTCCTGA 0.562000 0 SO:0001819 synonymous_variant ENST00000375464.2 1 1 hg19 CCDS6702.2 TCGA-3A-A9J0-01A-11D-A40W-08 C9orf89-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053128.1 1 0 1 50 67 0 30 1 1 44 37 0 30 2 0 0 0 0 0 2 1 1.000000 49 65 0 30 2 -20.000000 1 1 121412 5 37 1 0 2 2 1.567572 1 0.470000 3.280000 0.470000 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 TMEM47 83604 broad.mit.edu 37 X 34657384 34657384 + Missense_Mutation SNP G G A TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chrX:34657384G>A ENST00000275954.3 - 2 605 c.347C>T c.(346-348)gCg>gTg p.A116V NM_031442.3 NP_113630.1 Q9BQJ4 TMM47_HUMAN transmembrane protein 47 9 AAGCATGACCGCAACAGGTCT 0.443000 0 SO:0001583 missense ENST00000275954.3 0 1 hg19 CCDS14235.1 . . . . . . . . . . G 25.4 4.638349 0.87760 . . ENSG00000147027 ENST00000275954 T 0.69926 -0.44 5.56 5.56 0.83823 . 0.000000 0.85682 D 0.000000 T 0.81049 0.4742 M 0.65975 2.015 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 T 0.82625 -0.0365 10 0.66056 D 0.02 -7.661 17.3961 0.87445 0.0:0.0:1.0:0.0 . 116 Q9BQJ4 TMM47_HUMAN V 116 ENSP00000275954:A116V ENSP00000275954:A116V A - 2 0 TMEM47 34567305 1.000000 0.71417 0.997000 0.53966 0.862000 0.49288 9.476000 0.97823 2.321000 0.78463 0.538000 0.68166 GCG TCGA-3A-A9J0-01A-11D-A40W-08 TMEM47-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056209.1 0 0 0 3 27 0 8 0 5.883815e-01 0 17 0 8 2 0 0 0 0 0 2 1 0.801814 2 27 0 8 2 -4.892002 1 0 120388 5 33 1 0 1 1 0.470000 3.280000 0.470000 0.230000 6.000000e-02 0.500000 0.210000 0.256276 0.230000 0 PCDH11Y 83259 broad.mit.edu 37 Y 4968431 4968431 + Missense_Mutation SNP G G C TCGA-3A-A9J0-01A-11D-A40W-08 TCGA-3A-A9J0-10A-01D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 9a6c492b-d3dc-4d8e-bb91-fef812140b6e 36b866cd-0189-43dc-8ebb-5839e55f48e1 g.chrY:4968431G>C ENST00000333703.4 + 5 3292 c.2779G>C c.(2779-2781)Gac>Cac p.D927H PCDH11Y_ENST00000215473.6_Missense_Mutation_p.D938H|PCDH11Y_ENST00000362095.5_Missense_Mutation_p.D938H NM_001278619.1|NM_032971.2 NP_001265548.1|NP_116753.1 Q9BZA8 PC11Y_HUMAN protocadherin 11 Y-linked 27 AGTCACACTAGACCTTCCTAT 0.428000 0 SO:0001583 missense ENST00000333703.4 0 1 hg19 CCDS14776.1 TCGA-3A-A9J0-01A-11D-A40W-08 PCDH11Y-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000084979.2 1 0 0 71 86 0 45 0 0 0 0 45 2 0 0 0 0 0 2 1 1.000000 47 61 0 55 2 -20.000000 1 1 0 0 1 0.470000 3.280000