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 KCNQ2 3785 broad.mit.edu 37 20 62078155 62078158 + Frame_Shift_Del DEL ACAG ACAG - TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr20:62078155_62078158delACAG ENST00000359125.2 - 2 503_506 c.329_332delCTGT c.(328-333)tctgtgfs p.SV110fs KCNQ2_ENST00000370224.1_Frame_Shift_Del_p.SV110fs|RP11-358D14.2_ENST00000436263.1_RNA|KCNQ2_ENST00000357249.2_Frame_Shift_Del_p.SV110fs|KCNQ2_ENST00000360480.3_Frame_Shift_Del_p.SV110fs|KCNQ2_ENST00000344425.5_Frame_Shift_Del_p.SV110fs|KCNQ2_ENST00000354587.3_Frame_Shift_Del_p.SV110fs|KCNQ2_ENST00000344462.4_Frame_Shift_Del_p.SV110fs|KCNQ2_ENST00000359689.1_Frame_Shift_Del_p.SV110fs NM_172107.2 NP_742105.1 O43526 KCNQ2_HUMAN potassium voltage-gated channel, KQT-like subfamily, member 2 65 all_cancers(38;1.24e-11) BRCA - Breast invasive adenocarcinoma(10;1.04e-05) Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939) GGTGGAAAACACAGACAGCACGAG 0.632000 0 SO:0001589 frameshift_variant ENST00000359125.2 1 0 hg19 CCDS13520.1 TCGA-US-A77E-01A-11D-A32N-08 KCNQ2-003 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000080353.1 1 0 0 76 793 0 194 0 1.063594e-12 0 1 0 194 2 0 0 0 0 0 0 1 0.272572 124 817 16 205 91 0 0 0 0 0 0 -18.895520 1 0 0 0 1 1 2 3 2.336157 1 0.390000 2.070000 0.487868 0.530000 4.200000e-01 0.680000 0.540000 0.543852 0.530000 0 0.470000 0.600000 BRAF 673 broad.mit.edu 37 7 140477831 140477845 + In_Frame_Del DEL GAGGTGTAGGTGCTG GAGGTGTAGGTGCTG - TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr7:140477831_140477845delGAGGTGTAGGTGCTG ENST00000288602.6 - 12 1523_1537 c.1463_1477delCAGCACCTACACCTC c.(1462-1479)acagcacctacacctcag>aag p.488_493TAPTPQ>K NM_004333.4 NP_004324.2 P15056 BRAF_HUMAN B-Raf proto-oncogene, serine/threonine kinase p.L485_P490>Y(2)|p.N486_P490del(1) SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2) 27380 Melanoma(164;0.00956) Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881) TGTAACTGCTGAGGTGTAGGTGCTGTCACATTCAA 0.353000 61 Mis, T, O AKAP9, KIAA1549 melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma Cardio-facio-cutaneous syndrome Cardiofaciocutaneous syndrome Colon(40;35 892 2973 5743 27438) Dom yes 7 7q34 673 v-raf murine sarcoma viral oncogene homolog B1 yes E 3 Complex - deletion inframe(2)|Deletion - In frame(1) SO:0001651 inframe_deletion Familial Cancer Database CFC, CFCS ENST00000288602.6 0 1 hg19 CCDS5863.1 TCGA-US-A77E-01A-11D-A32N-08 BRAF-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000348886.1 1 0 0 26 281 0 51 0 2.167422e-01 0 10 0 51 2 0 0 0 0 0 0 1 1.000000 34 283 0 51 2 0 0 0 0 0 0 -2.841673 1 1 0 0 1 1 2 3 2.349308 1 0.390000 2.070000 0.489540 0.520000 3.500000e-01 0.720000 0.510000 0.533661 0.520000 0 0.430000 0.630000 NEBL 10529 broad.mit.edu 37 10 21074742 21074742 + Silent SNP G G A rs139156783 by1000genomes TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr10:21074742G>A ENST00000377122.4 - 28 3375 c.2979C>T c.(2977-2979)taC>taT p.Y993Y NEBL_ENST00000417816.2_Silent_p.Y249Y|NEBL_ENST00000377159.4_Silent_p.Y215Y NM_006393.2 NP_006384.1 O76041 NEBL_HUMAN nebulette 70 GCACTGTGCCGTACATCCAGC 0.468000 0 SO:0001819 synonymous_variant ENST00000377122.4 0 1 hg19 CCDS7134.1 TCGA-US-A77E-01A-11D-A32N-08 NEBL-004 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000047113.1 0 0 0 4 248 0 48 0 1.181304e-01 0 29 0 48 2 0 0 0 0 0 2 1 0.887304 4 244 0 47 2 0 0 0 0 0 0 -3.223479 1 1 121412 2 41 1 0 1 1 1.968530 0 0.390000 2.070000 0.388808 0.080000 2.000000e-02 0.190000 0.080000 0.100113 0.080000 0 0.050000 0.140000 MYO3A 53904 broad.mit.edu 37 10 26457784 26457784 + Silent SNP C C T rs35541310 byFrequency TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr10:26457784C>T ENST00000265944.5 + 28 3421 c.3255C>T c.(3253-3255)agC>agT p.S1085S MYO3A_ENST00000543632.1_Intron NM_017433.4 NP_059129.3 Q8NEV4 MYO3A_HUMAN myosin IIIA 146 GGAAAGAAAGCGCTATAATAA 0.328000 0 SO:0001819 synonymous_variant ENST00000265944.5 1 1 hg19 CCDS7148.1 TCGA-US-A77E-01A-11D-A32N-08 MYO3A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000047259.1 1 0 1 36 195 0 41 0 0 0 1 0 41 2 0 0 0 0 0 2 1 1.000000 36 192 0 41 2 0 0 0 0 0 0 -20.000000 1 1 121410 16 45 1 0 1 1 1.968530 0 0.390000 2.070000 0.388808 0.790000 5.700000e-01 1.000000 1.000000 0.803464 0.790000 0 0.680000 0.920000 APOA4 337 broad.mit.edu 37 11 116691783 116691783 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr11:116691783G>A ENST00000357780.3 - 3 1105 c.991C>T c.(991-993)Ccc>Tcc p.P331S NM_000482.3 NP_000473.2 P06727 APOA4_HUMAN apolipoprotein A-IV 20 all_hematologic(175;0.0487) Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0564)|all_neural(223;0.234) CCCGCATGGGGGCCCAGTTTC 0.592000 0 SO:0001583 missense ENST00000357780.3 1 1 hg19 CCDS31681.1 . . . . . . . . . . G 13.78 2.340577 0.41498 . . ENSG00000110244 ENST00000357780 T 0.76316 -1.01 5.39 4.46 0.54185 Apolipoprotein/apolipophorin (1); 0.377447 0.26019 N 0.026825 T 0.73016 0.3533 M 0.64676 1.99 0.29390 N 0.862669 P 0.50272 0.933 P 0.45167 0.472 T 0.69394 -0.5157 10 0.29301 T 0.29 -39.6749 7.0255 0.24938 0.142:0.0:0.7148:0.1432 . 331 P06727 APOA4_HUMAN S 331 ENSP00000350425:P331S ENSP00000350425:P331S P - 1 0 APOA4 116196993 0.241000 0.23857 0.999000 0.59377 0.626000 0.37791 1.085000 0.30840 2.522000 0.85027 0.557000 0.71058 CCC TCGA-US-A77E-01A-11D-A32N-08 APOA4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000106279.2 1 0 1 93 371 0 85 0 1 0 269 0 85 2 0 0 0 0 0 2 1 1.000000 93 369 0 85 2 0 0 0 0 0 0 -3.644587 1 1 0 0 1 1 2 3 1.982548 0 0.390000 2.070000 0.391187 0.990000 8.400000e-01 1.000000 1.000000 0.976487 0.990000 1 0.930000 1.000000 IFT46 56912 broad.mit.edu 37 11 118416522 118416522 + Missense_Mutation SNP A A G TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr11:118416522A>G ENST00000264021.3 - 10 1137 c.719T>C c.(718-720)aTt>aCt p.I240T TMEM25_ENST00000442938.2_Intron|IFT46_ENST00000530872.1_Missense_Mutation_p.I291T|IFT46_ENST00000264020.2_Missense_Mutation_p.I291T|TMEM25_ENST00000354284.4_Intron NM_001168618.1 NP_001162089.1 Q9NQC8 IFT46_HUMAN intraflagellar transport 46 9 GATCATGTCAATGTACTCTGC 0.507000 0 SO:0001583 missense ENST00000264021.3 1 1 hg19 CCDS53718.1 . . . . . . . . . . A 13.21 2.169425 0.38315 . . ENSG00000118096 ENST00000264021;ENST00000264020;ENST00000530872 T;T;T 0.48522 0.82;0.81;0.81 6.03 4.91 0.64330 . 0.364645 0.29335 N 0.012458 T 0.36936 0.0985 L 0.37561 1.115 0.41527 D 0.988432 B;B;B 0.21071 0.01;0.051;0.008 B;B;B 0.17433 0.012;0.018;0.011 T 0.16394 -1.0404 10 0.45353 T 0.12 -8.0521 9.5551 0.39334 0.8583:0.0:0.1417:0.0 . 291;240;291 E9PR06;Q9NQC8;Q9NQC8-2 .;IFT46_HUMAN;. T 240;291;291 ENSP00000264021:I240T;ENSP00000264020:I291T;ENSP00000432384:I291T ENSP00000264020:I291T I - 2 0 IFT46 117921732 0.998000 0.40836 0.992000 0.48379 0.823000 0.46562 3.755000 0.55197 1.104000 0.41587 0.533000 0.62120 ATT TCGA-US-A77E-01A-11D-A32N-08 IFT46-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000389627.1 1 0 1 68 394 0 78 1 9.984372e-01 26 32 0 78 2 0 0 0 0 0 2 1 1.000000 68 389 0 77 2 0 0 0 0 0 0 -20.000000 1 1 121412 4 37 1 1 2 3 1.982548 0 0.390000 2.070000 0.391187 0.750000 5.900000e-01 0.930000 0.750000 0.761391 0.750000 0 0.670000 0.850000 UPK2 7379 broad.mit.edu 37 11 118828843 118828843 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr11:118828843G>A ENST00000264031.2 + 5 490 c.455G>A c.(454-456)cGc>cAc p.R152H UPK2_ENST00000534788.1_3'UTR NM_006760.3 NP_006751.1 O00526 UPK2_HUMAN uroplakin 2 5 all_hematologic(175;0.0839) Medulloblastoma(222;0.0523)|all_hematologic(192;0.122)|all_neural(223;0.224) GGTATGGCCCGCACAGGGGGC 0.617000 0 SO:0001583 missense ENST00000264031.2 0 1 hg19 CCDS8404.1 . . . . . . . . . . g 17.59 3.427814 0.62733 . . ENSG00000110375 ENST00000534788;ENST00000264031 T 0.41400 1.0 5.43 4.51 0.55191 . 0.151206 0.31134 N 0.008188 T 0.61311 0.2337 M 0.65975 2.015 0.26235 N 0.978957 D 0.89917 1.0 D 0.87578 0.998 T 0.56908 -0.7901 10 0.46703 T 0.11 -3.4525 13.3218 0.60436 0.0836:0.0:0.9164:0.0 . 152 O00526 UPK2_HUMAN H 18;152 ENSP00000264031:R152H ENSP00000264031:R152H R + 2 0 UPK2 118334053 1.000000 0.71417 0.969000 0.41365 0.873000 0.50193 3.661000 0.54503 0.802000 0.34089 -0.937000 0.02696 CGC TCGA-US-A77E-01A-11D-A32N-08 UPK2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000389311.1 0 0 0 5 372 0 84 0 0 0 0 84 2 0 0 0 0 0 2 1 0.937064 5 370 0 83 2 0 0 0 0 0 0 -2.126169 0 1 0 0 1 1 2 3 1.982548 0 0.390000 2.070000 0.391187 0.070000 2.000000e-02 0.160000 0.070000 0.081011 0.070000 0 0.040000 0.110000 ADAMTS8 11095 broad.mit.edu 37 11 130284700 130284700 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr11:130284700G>A ENST00000257359.6 - 5 1998 c.1292C>T c.(1291-1293)gCg>gTg p.A431V NM_007037.4 NP_008968.4 Q9UP79 ATS8_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 8 10 all_hematologic(175;0.0429) Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837) GGGCAGGGCCGCAGCAGGGGC 0.652000 0 SO:0001583 missense ENST00000257359.6 1 1 hg19 CCDS41732.1 . . . . . . . . . . G 7.801 0.713736 0.15306 . . ENSG00000134917 ENST00000257359;ENST00000414575 T 0.03580 3.88 5.42 4.5 0.54988 . 0.751547 0.12761 N 0.441396 T 0.03564 0.0102 N 0.24115 0.695 0.09310 N 1 B 0.14805 0.011 B 0.10450 0.005 T 0.38329 -0.9666 10 0.59425 D 0.04 . 9.1476 0.36942 0.0:0.119:0.5962:0.2848 . 431 Q9UP79 ATS8_HUMAN V 431;460 ENSP00000257359:A431V ENSP00000257359:A431V A - 2 0 ADAMTS8 129789910 0.000000 0.05858 0.040000 0.18447 0.079000 0.17450 0.809000 0.27168 1.264000 0.44198 0.655000 0.94253 GCG TCGA-US-A77E-01A-11D-A32N-08 ADAMTS8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000385636.1 0 0 0 40 149 1 42 0 1.199467e-01 0 3 1 42 2 0 0 0 0 0 2 1 0.999919 40 146 1 42 15 0 0 0 0 0 0 -20.000000 1 1 120648 3 27 1 1 2 3 1.982548 0 0.390000 2.070000 0.391187 0.990000 8.000000e-01 1.000000 1.000000 0.976490 0.990000 1 0.930000 1.000000 FIBIN 387758 broad.mit.edu 37 11 27016362 27016362 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr11:27016362G>A ENST00000318627.2 + 1 735 c.289G>A c.(289-291)Gtg>Atg p.V97M NM_203371.1 NP_976249.1 Q8TAL6 FIBIN_HUMAN fin bud initiation factor homolog (zebrafish) 11 TGCTGGGCGCGTGCTGGAGGG 0.657000 0 SO:0001583 missense ENST00000318627.2 1 1 hg19 CCDS7861.1 1 4.578754578754579E-4 1 0.0020325203252032522 0 0.0 0 0.0 0 0.0 G 27.4 4.826858 0.90955 . . ENSG00000176971 ENST00000318627 . . . 5.7 5.7 0.88788 . 0.000000 0.85682 D 0.000000 T 0.68723 0.3032 L 0.32530 0.975 0.80722 D 1 D 0.89917 1.0 D 0.85130 0.997 T 0.70605 -0.4826 9 0.72032 D 0.01 -14.2051 18.3976 0.90504 0.0:0.0:1.0:0.0 . 97 Q8TAL6 FIBIN_HUMAN M 97 . ENSP00000321962:V97M V + 1 0 FIBIN 26972938 1.000000 0.71417 0.985000 0.45067 0.994000 0.84299 9.245000 0.95431 2.706000 0.92434 0.557000 0.71058 GTG TCGA-US-A77E-01A-11D-A32N-08 FIBIN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000387945.1 1 0 1 32 142 0 45 0 9.859475e-01 0 33 0 45 2 0 0 0 0 0 2 1 1.000000 32 142 0 45 2 0 0 0 0 0 0 -20.000000 1 1 121392 2 29 1 1 2 3 1.976461 0 0.390000 2.070000 0.391187 0.940000 6.700000e-01 1.000000 1.000000 0.914454 0.940000 1 0.800000 1.000000 EXT2 2132 broad.mit.edu 37 11 44129401 44129401 + Missense_Mutation SNP C C T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr11:44129401C>T ENST00000343631.3 + 2 268 c.139C>T c.(139-141)Ccc>Tcc p.P47S EXT2_ENST00000358681.4_Missense_Mutation_p.P47S|EXT2_ENST00000395673.3_Missense_Mutation_p.P80S|EXT2_ENST00000533608.1_Missense_Mutation_p.P47S Q93063 EXT2_HUMAN exostosin glycosyltransferase 2 32 TCAGTTTTGGCCCCATTCTAT 0.527000 Mis, N, F, S exostoses, osteosarcoma Hereditary Multiple Exostoses yes Rec Multiple Exostoses Type 2 11 11p12-p11 2132 multiple exostoses type 2 gene M 0 SO:0001583 missense Familial Cancer Database HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses ENST00000343631.3 0 1 hg19 CCDS7908.1 . . . . . . . . . . C 13.85 2.360982 0.41801 . . ENSG00000151348 ENST00000533608;ENST00000532479;ENST00000527014;ENST00000358681;ENST00000395673;ENST00000343631 T;T;T;T;T;T 0.47177 0.85;0.85;0.85;0.85;0.85;0.85 5.45 4.52 0.55395 . 0.050514 0.85682 D 0.000000 T 0.56863 0.2014 L 0.29908 0.895 0.80722 D 1 D;D;D;P;B 0.89917 1.0;0.984;0.979;0.956;0.296 D;P;P;P;B 0.83275 0.996;0.786;0.798;0.63;0.027 T 0.57636 -0.7777 10 0.44086 T 0.13 1.5466 15.282 0.73794 0.1413:0.8587:0.0:0.0 . 47;47;47;47;60 Q6NUL1;C9JU51;Q93063-2;Q93063;D3DR24 .;.;.;EXT2_HUMAN;. S 47;47;47;47;80;47 ENSP00000431173:P47S;ENSP00000433827:P47S;ENSP00000434716:P47S;ENSP00000351509:P47S;ENSP00000379032:P80S;ENSP00000342656:P47S ENSP00000342656:P47S P + 1 0 EXT2 44085977 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 7.380000 0.79704 1.253000 0.44018 0.650000 0.86243 CCC TCGA-US-A77E-01A-11D-A32N-08 EXT2-005 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000390074.1 0 0 0 5 420 0 84 0 1.999998e-01 0 58 0 84 2 0 0 0 0 0 2 1 0.936327 5 416 0 83 2 0 0 0 0 0 0 -2.259352 0 1 0 0 1 1 2 3 1.976461 0 0.390000 2.070000 0.391187 0.060000 1.000000e-02 0.140000 0.060000 0.071930 0.060000 0 0.030000 0.100000 CKAP5 9793 broad.mit.edu 37 11 46780946 46780946 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr11:46780946G>A ENST00000529230.1 - 34 4487 c.4441C>T c.(4441-4443)Cgc>Tgc p.R1481C SNORD67_ENST00000516618.1_RNA|CKAP5_ENST00000312055.5_Missense_Mutation_p.R1481C|CKAP5_ENST00000415402.1_Missense_Mutation_p.R1481C|SNORD67_ENST00000390833.1_RNA|CKAP5_ENST00000354558.3_Missense_Mutation_p.R1481C Q14008 CKAP5_HUMAN cytoskeleton associated protein 5 43 AATTCTCGGCGGACCATCTGG 0.483000 Ovarian(4;85 273 2202 4844 13323) 0 SO:0001583 missense ENST00000529230.1 0 1 hg19 CCDS31477.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 19.81|19.81 3.896803|3.896803 0.72639|0.72639 .|. .|. ENSG00000175216|ENSG00000175216 ENST00000527333|ENST00000529230;ENST00000415402;ENST00000312055;ENST00000354558;ENST00000526876 .|T;T;T;T .|0.48201 .|0.84;0.85;0.82;0.82 5.53|5.53 5.53|5.53 0.82687|0.82687 .|Armadillo-like helical (1);Armadillo-type fold (1); .|0.094061 .|0.85682 .|D .|0.000000 T|T 0.34745|0.34745 0.0908|0.0908 N|N 0.14661|0.14661 0.345|0.345 0.51767|0.51767 D|D 0.999933|0.999933 .|P;P;P .|0.49447 .|0.924;0.894;0.83 .|B;B;B .|0.39840 .|0.235;0.311;0.165 T|T 0.23084|0.23084 -1.0198|-1.0198 5|10 .|0.44086 .|T .|0.13 -9.5534|-9.5534 19.8389|19.8389 0.96675|0.96675 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|1481;1481;1481 .|Q14008-3;Q14008-2;Q14008 .|.;.;CKAP5_HUMAN L|C 37|1481;1481;1481;1481;212 .|ENSP00000432768:R1481C;ENSP00000395302:R1481C;ENSP00000310227:R1481C;ENSP00000346566:R1481C .|ENSP00000310227:R1481C P|R -|- 2|1 0|0 CKAP5|CKAP5 46737522|46737522 1.000000|1.000000 0.71417|0.71417 0.999000|0.999000 0.59377|0.59377 0.998000|0.998000 0.95712|0.95712 7.753000|7.753000 0.85153|0.85153 2.755000|2.755000 0.94549|0.94549 0.650000|0.650000 0.86243|0.86243 CCG|CGC TCGA-US-A77E-01A-11D-A32N-08 CKAP5-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000390679.1 0 0 0 5 354 0 71 0 3.410767e-01 0 73 0 71 2 0 0 0 0 0 2 1 0.937042 5 352 0 71 2 0 0 0 0 0 0 -2.916531 1 1 121412 1 33 1 1 2 3 1.976461 0 0.390000 2.070000 0.391187 0.070000 2.000000e-02 0.170000 0.070000 0.085034 0.070000 0 0.040000 0.120000 OR4A47 403253 broad.mit.edu 37 11 48510885 48510885 + Missense_Mutation SNP C C A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr11:48510885C>A ENST00000446524.1 + 1 617 c.541C>A c.(541-543)Ccc>Acc p.P181T NM_001005512.2 NP_001005512.2 Q6IF82 O4A47_HUMAN olfactory receptor, family 4, subfamily A, member 47 p.P181A(1) 29 TGACATGTATCCCTTATTGAA 0.443000 1 Substitution - Missense(1) SO:0001583 missense ENST00000446524.1 1 1 hg19 CCDS31490.1 . . . . . . . . . . N 7.778 0.708860 0.15239 . . ENSG00000237388 ENST00000446524 T 0.00216 8.53 4.84 1.9 0.25705 GPCR, rhodopsin-like superfamily (1); 0.117629 0.38778 N 0.001571 T 0.00666 0.0022 H 0.94658 3.565 0.09310 N 1 D 0.89917 1.0 D 0.97110 1.0 T 0.38045 -0.9679 10 0.72032 D 0.01 . 6.6304 0.22853 0.0:0.6819:0.147:0.171 . 181 Q6IF82 O4A47_HUMAN T 181 ENSP00000412752:P181T ENSP00000412752:P181T P + 1 0 OR4A47 48467461 0.000000 0.05858 0.219000 0.23793 0.012000 0.07955 0.174000 0.16743 0.105000 0.17753 -0.409000 0.06214 CCC TCGA-US-A77E-01A-11D-A32N-08 OR4A47-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000390559.1 0 0 0 25 619 0 154 0 0 0 0 154 2 0 0 0 0 0 2 1 1.000000 25 595 0 157 2 0 0 0 0 0 0 -4.050987 1 1 0 0 1 1 2 3 1.976461 0 0.390000 2.070000 0.391187 0.190000 1.200000e-01 0.290000 0.200000 0.206301 0.190000 0 0.160000 0.250000 OR4S2 219431 broad.mit.edu 37 11 55418776 55418776 + Missense_Mutation SNP A A C TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr11:55418776A>C ENST00000312422.2 + 1 397 c.397A>C c.(397-399)Atc>Ctc p.I133L NM_001004059.2 NP_001004059.2 Q8NH73 OR4S2_HUMAN olfactory receptor, family 4, subfamily S, member 2 45 all_epithelial(135;0.0748) TTATATGACCATCATGAACCG 0.428000 0 SO:0001583 missense ENST00000312422.2 1 1 hg19 CCDS31505.1 . . . . . . . . . . A 10.57 1.386439 0.25031 . . ENSG00000174982 ENST00000312422 T 0.00940 5.52 5.35 5.35 0.76521 GPCR, rhodopsin-like superfamily (1); 0.243922 0.28453 N 0.015284 T 0.01387 0.0045 L 0.45698 1.435 0.26071 N 0.981224 B 0.14438 0.01 B 0.10450 0.005 T 0.38564 -0.9655 10 0.72032 D 0.01 . 10.9264 0.47193 0.8431:0.1569:0.0:0.0 . 133 Q8NH73 OR4S2_HUMAN L 133 ENSP00000310337:I133L ENSP00000310337:I133L I + 1 0 OR4S2 55175352 0.008000 0.16893 0.997000 0.53966 0.193000 0.23685 0.647000 0.24812 2.028000 0.59812 0.443000 0.29094 ATC TCGA-US-A77E-01A-11D-A32N-08 OR4S2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391503.1 1 0 0 42 839 0 184 0 0 0 0 184 2 0 0 0 0 0 2 1 1.000000 41 828 0 181 2 0 0 0 0 0 0 -6.012469 1 1 0 0 1 1 2 3 1.976461 0 0.390000 2.070000 0.391187 0.240000 1.700000e-01 0.330000 0.240000 0.249778 0.240000 0 0.200000 0.290000 CHRM1 1128 broad.mit.edu 37 11 62677297 62677297 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr11:62677297G>A ENST00000306960.3 - 2 1817 c.1276C>T c.(1276-1278)Cgg>Tgg p.R426W AP000438.2_ENST00000543624.1_RNA NM_000738.2 NP_000729.2 P11229 ACM1_HUMAN cholinergic receptor, muscarinic 1 9 Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Benzatropine(DB00245)|Biperiden(DB00810)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbachol(DB00411)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clidinium(DB00771)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyclopentolate(DB00979)|Cycrimine(DB00942)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Doxylamine(DB00366)|Escitalopram(DB01175)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Flupentixol(DB00875)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methantheline(DB00940)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Oxyphenonium(DB00219)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pirenzepine(DB00670)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propantheline(DB00782)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Trospium(DB00209)|Ziprasidone(DB00246) AAGGTGTCCCGGAAGGCTTTG 0.632000 0 SO:0001583 missense ENST00000306960.3 0 1 hg19 CCDS8040.1 . . . . . . . . . . G 15.89 2.966720 0.53507 . . ENSG00000168539 ENST00000306960;ENST00000543973 T;T 0.58358 0.34;0.34 3.98 1.97 0.26223 . 0.792889 0.10240 N 0.698549 T 0.64972 0.2647 L 0.57536 1.79 0.39146 D 0.962134 D 0.89917 1.0 D 0.64321 0.924 T 0.62148 -0.6915 10 0.87932 D 0 -13.9234 9.6941 0.40147 0.0:0.0:0.4009:0.5991 . 426 P11229 ACM1_HUMAN W 426 ENSP00000306490:R426W;ENSP00000441188:R426W ENSP00000306490:R426W R - 1 2 CHRM1 62433873 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 5.136000 0.64783 0.263000 0.21812 0.561000 0.74099 CGG TCGA-US-A77E-01A-11D-A32N-08 CHRM1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000396178.1 0 0 0 6 820 0 183 0 0 0 0 183 2 0 0 0 0 0 2 1 0.962859 6 804 0 183 2 0 0 0 0 0 0 -1.903257 0 1 121412 1 33 1 1 2 3 1.982548 0 0.390000 2.070000 0.391187 0.030000 0 0.080000 0.040000 0.043167 0.030000 0 0.020000 0.060000 RCOR2 283248 broad.mit.edu 37 11 63680166 63680166 + Nonsense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr11:63680166G>A ENST00000301459.4 - 10 1396 c.1009C>T c.(1009-1011)Cag>Tag p.Q337* RCOR2_ENST00000473926.2_5'Flank NM_173587.3 NP_775858.2 Q8IZ40 RCOR2_HUMAN REST corepressor 2 17 GCCAAAAGCTGCTCATCTGTG 0.532000 0 SO:0001587 stop_gained ENST00000301459.4 0 1 hg19 CCDS8052.1 . . . . . . . . . . G 41 8.641449 0.98897 . . ENSG00000167771 ENST00000301459 . . . 4.45 4.45 0.53987 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.66056 D 0.02 . 16.4081 0.83697 0.0:0.0:1.0:0.0 . . . . X 337 . ENSP00000301459:Q337X Q - 1 0 RCOR2 63436742 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 9.524000 0.98036 2.479000 0.83701 0.561000 0.74099 CAG TCGA-US-A77E-01A-11D-A32N-08 RCOR2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000318233.1 1 0 1 229 656 0 173 0 6.699958e-02 0 2 0 173 2 0 0 0 0 0 2 1 1.000000 228 651 0 171 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 1.982548 0 0.390000 2.070000 0.391187 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 ESRRA 2101 broad.mit.edu 37 11 64082689 64082689 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr11:64082689G>A ENST00000405666.1 + 6 1193 c.959G>A c.(958-960)cGg>cAg p.R320Q ESRRA_ENST00000000442.6_Missense_Mutation_p.R320Q|PRDX5_ENST00000265462.4_5'Flank|PRDX5_ENST00000352435.4_5'Flank|PRDX5_ENST00000347941.4_5'Flank|ESRRA_ENST00000406310.1_Missense_Mutation_p.R319Q NM_001282450.1 NP_001269379.1 P11474 ERR1_HUMAN estrogen-related receptor alpha 14 CAGGCCCTGCGGCTGGAGCGA 0.627000 0 SO:0001583 missense ENST00000405666.1 1 1 hg19 CCDS41667.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 9.914|9.914 1.210433|1.210433 0.22289|0.22289 0.0|0.0 1.2E-4|1.2E-4 ENSG00000173153|ENSG00000173153 ENST00000545035|ENST00000406310;ENST00000000442;ENST00000405666 .|D;D;D .|0.96334 .|-3.98;-3.98;-3.98 4.14|4.14 4.14|4.14 0.48551|0.48551 .|Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2); .|0.192229 .|0.44483 .|D .|0.000441 D|D 0.89269|0.89269 0.6667|0.6667 N|N 0.16903|0.16903 0.455|0.455 0.44073|0.44073 D|D 0.996821|0.996821 .|B;P .|0.51449 .|0.033;0.945 .|B;B .|0.31547 .|0.0;0.132 D|D 0.90139|0.90139 0.4212|0.4212 5|10 .|0.39692 .|T .|0.17 .|. 14.3272|14.3272 0.66528|0.66528 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|319;320 .|P11474-2;P11474 .|.;ERR1_HUMAN S|Q 101|319;320;320 .|ENSP00000385971:R319Q;ENSP00000000442:R320Q;ENSP00000384851:R320Q .|ENSP00000000442:R320Q G|R +|+ 1|2 0|0 ESRRA|ESRRA 63839265|63839265 0.082000|0.082000 0.21442|0.21442 0.944000|0.944000 0.38274|0.38274 0.203000|0.203000 0.24098|0.24098 2.216000|2.216000 0.42871|0.42871 2.309000|2.309000 0.77851|0.77851 0.462000|0.462000 0.41574|0.41574 GGC|CGG TCGA-US-A77E-01A-11D-A32N-08 ESRRA-003 KNOWN alternative_5_UTR|NAGNAG_splice_site|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000319304.1 1 0 1 51 174 0 38 1 1 43 124 0 38 2 0 0 0 0 0 2 1 1.000000 49 170 0 38 2 0 0 0 0 0 0 -20.000000 1 1 120840 5 33 1 1 2 3 1.982548 0 0.390000 2.070000 0.391187 0.990000 8.900000e-01 1.000000 1.000000 0.992830 0.990000 1 0.990000 1.000000 FOXN4 121643 broad.mit.edu 37 12 109719343 109719343 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr12:109719343G>A ENST00000299162.5 - 9 1267 c.1163C>T c.(1162-1164)cCg>cTg p.P388L FOXN4_ENST00000355216.1_Missense_Mutation_p.P208L NM_213596.2 NP_998761.2 Q96NZ1 FOXN4_HUMAN forkhead box N4 16 GCTGAGGTCCGGCAGGGCGTG 0.657000 0 SO:0001583 missense ENST00000299162.5 1 1 hg19 CCDS9126.2 . . . . . . . . . . G 17.27 3.347910 0.61183 . . ENSG00000139445 ENST00000355216;ENST00000299162 D;D 0.95482 -3.72;-3.4 4.49 3.58 0.41010 . 0.472963 0.19054 N 0.123947 D 0.96901 0.8988 M 0.71581 2.175 0.80722 D 1 D;D 0.89917 1.0;0.981 D;P 0.69654 0.965;0.57 D 0.96418 0.9309 10 0.52906 T 0.07 -12.9682 13.1717 0.59602 0.0:0.0:0.8395:0.1605 . 388;388 A6H901;Q96NZ1 .;FOXN4_HUMAN L 208;388 ENSP00000347354:P208L;ENSP00000299162:P388L ENSP00000299162:P388L P - 2 0 FOXN4 108203726 1.000000 0.71417 0.819000 0.32651 0.417000 0.31264 4.115000 0.57865 1.212000 0.43366 0.561000 0.74099 CCG TCGA-US-A77E-01A-11D-A32N-08 FOXN4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000328306.1 1 0 1 29 105 0 27 0 0 0 0 27 2 0 0 0 0 0 2 1 1.000000 29 100 0 27 2 0 0 0 0 0 0 -20.000000 1 1 121376 1 23 1 1 2 3 1.973903 0 0.390000 2.070000 0.391187 0.990000 7.800000e-01 1.000000 1.000000 0.974490 0.990000 1 0.930000 1.000000 RPH3A 22895 broad.mit.edu 37 12 113266105 113266105 + Splice_Site SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr12:113266105G>A ENST00000389385.4 + 3 479 c.e3-1 RPH3A_ENST00000543106.2_Splice_Site|RPH3A_ENST00000551052.1_Splice_Site|RPH3A_ENST00000415485.3_Splice_Site|RPH3A_ENST00000548866.1_Splice_Site|RPH3A_ENST00000447659.2_Splice_Site|RPH3A_ENST00000420983.2_5'Flank NM_001143854.1|NM_014954.3 NP_001137326.1|NP_055769.2 Q9Y2J0 RP3A_HUMAN rabphilin 3A 47 ATGTTTTCCAGGAGCACTAGA 0.488000 0 SO:0001630 splice_region_variant ENST00000389385.4 0 1 hg19 CCDS44979.1 TCGA-US-A77E-01A-11D-A32N-08 RPH3A-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000405561.1 0 0 0 6 313 0 73 0 0 0 0 73 2 0 0 0 0 0 2 1 0.964325 6 310 0 71 2 0 0 0 0 0 0 -2.870380 1 1 0 0 1 1 2 3 1.973903 0 0.390000 2.070000 0.391187 0.100000 3.000000e-02 0.210000 0.100000 0.111507 0.100000 0 0.060000 0.150000 KRT72 140807 broad.mit.edu 37 12 52994910 52994910 + Silent SNP C C T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr12:52994910C>T ENST00000537672.2 - 1 337 c.327G>A c.(325-327)ccG>ccA p.P109P RP11-641A6.2_ENST00000551089.1_RNA|KRT72_ENST00000398066.3_5'UTR|KRT72_ENST00000354310.4_Silent_p.P109P|KRT72_ENST00000293745.2_Silent_p.P109P NM_001146225.1 NP_001139697.1 Q14CN4 K2C72_HUMAN keratin 72 p.P109P(1) 36 CCACGTTGAGCGGGGCCAGGA 0.667000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000537672.2 0 1 hg19 CCDS8833.1 . . . . . . . . . . C 13.45 2.239736 0.39598 . . ENSG00000170486 ENST00000549979 . . . 4.49 -1.94 0.07571 . . . . . T 0.39279 0.1072 . . . 0.80722 D 1 . . . . . . T 0.27123 -1.0083 4 . . . . 1.5914 0.02655 0.2117:0.371:0.1662:0.2511 . . . . H 95 . . R - 2 0 KRT72 51281177 0.000000 0.05858 0.947000 0.38551 0.805000 0.45488 -2.331000 0.01110 -0.362000 0.08113 -1.083000 0.02208 CGC TCGA-US-A77E-01A-11D-A32N-08 KRT72-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000405693.1 0 0 0 6 291 0 63 0 0 0 0 63 2 0 0 0 0 0 2 1 0.963522 6 286 0 62 2 0 0 0 0 0 0 -2.785011 1 1 121412 2 34 1 1 2 3 1.980614 0 0.390000 2.070000 0.391187 0.100000 4.000000e-02 0.220000 0.100000 0.119667 0.100000 0 0.070000 0.160000 SPRYD4 283377 broad.mit.edu 37 12 56863123 56863123 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr12:56863123G>A ENST00000338146.5 + 2 461 c.386G>A c.(385-387)cGc>cAc p.R129H MIP_ENST00000555551.1_5'Flank NM_207344.3 NP_997227 Q8WW59 SPRY4_HUMAN SPRY domain containing 4 7 TATGCCCAGCGCAAGTGGTAC 0.572000 0 SO:0001583 missense ENST00000338146.5 0 1 hg19 CCDS8920.1 . . . . . . . . . . G 35 5.514600 0.96402 . . ENSG00000176422 ENST00000338146;ENST00000543121 T 0.61158 0.13 5.46 5.46 0.80206 Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1); 0.102358 0.64402 D 0.000003 T 0.71796 0.3382 L 0.49126 1.545 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.73380 0.98;0.95 T 0.71101 -0.4690 10 0.51188 T 0.08 -18.1887 18.4593 0.90732 0.0:0.0:1.0:0.0 . 51;129 B4DUC9;Q8WW59 .;SPRY4_HUMAN H 129;51 ENSP00000338034:R129H ENSP00000338034:R129H R + 2 0 SPRYD4 55149390 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 3.921000 0.56454 2.735000 0.93741 0.561000 0.74099 CGC TCGA-US-A77E-01A-11D-A32N-08 SPRYD4-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding 0 0 0 6 626 0 134 0 8.336658e-02 0 42 0 134 2 0 0 0 0 0 2 1 0.963333 6 616 0 134 2 0 0 0 0 0 0 -2.126141 0 1 0 0 1 1 2 3 1.976042 0 0.390000 2.070000 0.391187 0.040000 1.000000e-02 0.110000 0.050000 0.056609 0.040000 0 0.020000 0.080000 LRP1 4035 broad.mit.edu 37 12 57590012 57590012 + Missense_Mutation SNP G G T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr12:57590012G>T ENST00000243077.3 + 55 9310 c.8844G>T c.(8842-8844)aaG>aaT p.K2948N MIR1228_ENST00000408438.1_RNA NM_002332.2 NP_002323.2 Q07954 LRP1_HUMAN low density lipoprotein receptor-related protein 1 184 Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031) TCAGCCGCAAGCTCAGTGGCT 0.632000 0 SO:0001583 missense ENST00000243077.3 0 1 hg19 CCDS8932.1 . . . . . . . . . . G 13.76 2.334687 0.41297 . . ENSG00000123384 ENST00000243077 D 0.89681 -2.55 5.02 2.11 0.27256 Growth factor, receptor (1);EGF-like calcium-binding (1); 0.000000 0.64402 D 0.000001 T 0.80989 0.4730 N 0.02685 -0.53 0.80722 D 1 D 0.61697 0.99 D 0.64776 0.929 T 0.74497 -0.3646 10 0.17832 T 0.49 . 6.2253 0.20703 0.2279:0.1436:0.6285:0.0 . 2948 Q07954 LRP1_HUMAN N 2948 ENSP00000243077:K2948N ENSP00000243077:K2948N K + 3 2 LRP1 55876279 0.962000 0.33011 1.000000 0.80357 0.982000 0.71751 0.431000 0.21444 0.687000 0.31509 0.655000 0.94253 AAG TCGA-US-A77E-01A-11D-A32N-08 LRP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000412772.2 0 0 0 5 149 0 31 0 8.527393e-01 0 105 0 31 2 0 0 0 0 0 2 0 0.928190 0 145 0 31 2 0 0 0 0 0 0 -7.967799 1 0 0 0 1 1 2 3 1.976042 0 0.390000 2.070000 0.391187 0.180000 6.000000e-02 0.380000 0.160000 0.195639 0.180000 0 0.110000 0.270000 C1RL 51279 broad.mit.edu 37 12 7254566 7254566 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr12:7254566G>A ENST00000266542.4 - 3 510 c.418C>T c.(418-420)Cgc>Tgc p.R140C C1RL_ENST00000545280.1_Intron|C1RL_ENST00000544702.1_Missense_Mutation_p.R140C|C1RL_ENST00000545337.1_Missense_Mutation_p.R140C NM_016546.2 NP_057630.2 Q9NZP8 C1RL_HUMAN complement component 1, r subcomponent-like 16 GGCTGTGTGCGGAAGGTCAGC 0.622000 0 SO:0001583 missense ENST00000266542.4 0 1 hg19 CCDS8573.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 5.842|5.842 0.339585|0.339585 0.11069|0.11069 .|. .|. ENSG00000139178|ENSG00000139178 ENST00000534950|ENST00000266542;ENST00000396661;ENST00000544702;ENST00000543933;ENST00000545337 .|T;T;T;T .|0.30448 .|1.53;1.53;1.53;1.53 3.76|3.76 -0.133|-0.133 0.13485|0.13485 .|CUB (5); .|1.399260 .|0.04433 .|N .|0.369511 T|T 0.35799|0.35799 0.0944|0.0944 M|M 0.88640|0.88640 2.97|2.97 0.24098|0.24098 N|N 0.995883|0.995883 .|B;B;B .|0.33919 .|0.432;0.038;0.285 .|B;B;B .|0.27887 .|0.051;0.007;0.084 T|T 0.30268|0.30268 -0.9984|-0.9984 5|10 .|0.45353 .|T .|0.12 .|. 3.3529|3.3529 0.07159|0.07159 0.2989:0.0:0.5228:0.1783|0.2989:0.0:0.5228:0.1783 .|. .|140;140;140 .|F5GWF3;F5H7C8;Q9NZP8 .|.;.;C1RL_HUMAN L|C 39|140 .|ENSP00000266542:R140C;ENSP00000441885:R140C;ENSP00000437398:R140C;ENSP00000442611:R140C .|ENSP00000266542:R140C P|R -|- 2|1 0|0 C1RL|C1RL 7145842|7145842 0.147000|0.147000 0.22687|0.22687 0.103000|0.103000 0.21229|0.21229 0.289000|0.289000 0.27227|0.27227 0.193000|0.193000 0.17116|0.17116 -0.034000|-0.034000 0.13713|0.13713 -1.529000|-1.529000 0.00923|0.00923 CCG|CGC TCGA-US-A77E-01A-11D-A32N-08 C1RL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000398367.1 0 0 0 6 618 0 157 0 2.229390e-01 0 79 0 157 2 0 0 0 0 0 2 1 0.963682 5 611 0 157 2 0 0 0 0 0 0 -2.133321 0 1 121412 1 35 1 1 2 3 1.980614 0 0.390000 2.070000 0.391187 0.050000 1.000000e-02 0.110000 0.050000 0.057333 0.050000 0 0.030000 0.080000 MMP14 4323 broad.mit.edu 37 14 23315041 23315041 + Silent SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr14:23315041G>A ENST00000311852.6 + 10 1803 c.1542G>A c.(1540-1542)ccG>ccA p.P514P MMP14_ENST00000548162.1_Intron NM_004995.2 NP_004986.1 P50281 MMP14_HUMAN matrix metallopeptidase 14 (membrane-inserted) 20 all_cancers(95;9.47e-05) Marimastat(DB00786) GAGGCCGGCCGGATGAGGGGA 0.637000 0 SO:0001819 synonymous_variant ENST00000311852.6 0 1 hg19 CCDS9577.1 TCGA-US-A77E-01A-11D-A32N-08 MMP14-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000071660.3 0 0 0 4 240 0 50 0 9.998255e-01 0 1682 0 50 2 0 0 0 0 0 2 1 0.886206 4 235 0 49 2 0 0 0 0 0 0 -2.949559 1 1 121410 2 35 1 1 2 3 1.983148 0 0.390000 2.070000 0.391187 0.090000 2.000000e-02 0.210000 0.080000 0.103761 0.090000 0 0.050000 0.150000 NKX2-8 26257 broad.mit.edu 37 14 37050517 37050517 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr14:37050517G>A ENST00000258829.5 - 2 527 c.310C>T c.(310-312)Cgg>Tgg p.R104W NM_014360.2 NP_055175.2 O15522 NKX28_HUMAN NK2 homeobox 8 1 Breast(36;0.143)|Hepatocellular(127;0.158)|Esophageal squamous(585;0.164) Lung(8;1.12e-09)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.00357)|all cancers(34;0.0113)|LUSC - Lung squamous cell carcinoma(13;0.0189) CGCTGCTGCCGGAAGCGCCGC 0.662000 0 SO:0001583 missense ENST00000258829.5 0 1 hg19 CCDS9660.1 . . . . . . . . . . G 28.3 4.911256 0.92178 . . ENSG00000136327 ENST00000258829 D 0.96459 -4.02 4.25 4.25 0.50352 Homeodomain-related (1);Homeobox (3);Homeodomain-like (1); 0.067264 0.64402 D 0.000008 D 0.97920 0.9316 M 0.80028 2.48 0.58432 D 0.999999 D 0.89917 1.0 D 0.80764 0.994 D 0.98869 1.0765 10 0.87932 D 0 . 15.8354 0.78793 0.0:0.0:1.0:0.0 . 104 O15522 NKX28_HUMAN W 104 ENSP00000258829:R104W ENSP00000258829:R104W R - 1 2 NKX2-8 36120268 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 2.079000 0.41577 2.186000 0.69663 0.549000 0.68633 CGG TCGA-US-A77E-01A-11D-A32N-08 NKX2-8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000071844.6 0 0 0 3 46 0 10 0 0 0 0 10 2 0 0 0 0 0 2 1 0.806023 3 45 0 10 2 0 0 0 0 0 0 -8.326563 1 1 0 0 1 0 1 1 1.968804 0 0.390000 2.070000 0.388808 0.350000 1.000000e-01 0.780000 0.300000 0.388295 0.350000 0 0.200000 0.560000 BTBD7 55727 broad.mit.edu 37 14 93709084 93709084 + Silent SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr14:93709084G>A ENST00000334746.5 - 11 3241 c.2934C>T c.(2932-2934)taC>taT p.Y978Y BTBD7_ENST00000554565.1_Silent_p.Y627Y|BTBD7_ENST00000393170.2_Silent_p.Y552Y NM_001002860.2 NP_001002860.2 Q9P203 BTBD7_HUMAN BTB (POZ) domain containing 7 35 all_cancers(154;0.08) TATTGTGGCTGTACAGATCGG 0.483000 0 SO:0001819 synonymous_variant ENST00000334746.5 0 1 hg19 CCDS32146.1 TCGA-US-A77E-01A-11D-A32N-08 BTBD7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000412701.1 0 0 0 5 525 0 111 0 2.143140e-02 0 19 0 111 2 0 0 0 0 0 2 1 0.936245 5 520 0 111 2 0 0 0 0 0 0 -2.465566 0 1 121412 1 28 1 0 1 1 1.968804 0 0.390000 2.070000 0.388808 0.040000 1.000000e-02 0.110000 0.050000 0.057496 0.040000 0 0.020000 0.080000 CLMN 79789 broad.mit.edu 37 14 95677190 95677190 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr14:95677190G>A ENST00000298912.4 - 7 748 c.635C>T c.(634-636)gCg>gTg p.A212V NM_024734.3 NP_079010.2 Q96JQ2 CLMN_HUMAN calmin (calponin-like, transmembrane) 44 CCAACTGCCCGCAAAGTCCTG 0.567000 0 SO:0001583 missense ENST00000298912.4 0 1 hg19 CCDS9933.1 . . . . . . . . . . G 32 5.119023 0.94385 . . ENSG00000165959 ENST00000298912 T 0.59638 0.25 5.93 5.93 0.95920 Calponin homology domain (5); 0.000000 0.39341 N 0.001394 T 0.59797 0.2220 N 0.14661 0.345 0.80722 D 1 D 0.63046 0.992 P 0.57468 0.821 T 0.65113 -0.6247 10 0.72032 D 0.01 . 20.3311 0.98718 0.0:0.0:1.0:0.0 . 212 Q96JQ2 CLMN_HUMAN V 212 ENSP00000298912:A212V ENSP00000298912:A212V A - 2 0 CLMN 94746943 1.000000 0.71417 0.260000 0.24451 0.983000 0.72400 6.642000 0.74329 2.797000 0.96272 0.655000 0.94253 GCG TCGA-US-A77E-01A-11D-A32N-08 CLMN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000414518.2 0 0 0 7 695 0 152 0 1.531691e-01 1 59 0 152 2 0 0 0 0 0 2 1 0.979113 6 681 0 151 2 0 0 0 0 0 0 -1.844680 0 1 121402 4 35 1 0 1 1 1.968804 0 0.390000 2.070000 0.388808 0.050000 1.000000e-02 0.100000 0.060000 0.058093 0.050000 0 0.030000 0.080000 TPM1 7168 broad.mit.edu 37 15 63353068 63353068 + Splice_Site SNP G G T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr15:63353068G>T ENST00000403994.3 + 5 573 c.493G>T c.(493-495)Gtg>Ttg p.V165L TPM1_ENST00000317516.7_Splice_Site_p.V129L|TPM1_ENST00000358278.3_Splice_Site_p.V165L|TPM1_ENST00000559397.1_Splice_Site_p.V165L|TPM1_ENST00000560959.1_Splice_Site_p.V129L|TPM1_ENST00000404484.4_Splice_Site_p.V129L|TPM1_ENST00000334895.5_Splice_Site_p.V129L|TPM1_ENST00000357980.4_Splice_Site_p.V207L|TPM1_ENST00000559556.1_Splice_Site_p.V165L|TPM1_ENST00000267996.7_Splice_Site_p.V165L|TPM1_ENST00000288398.6_Splice_Site_p.V165L|TPM1_ENST00000560445.1_Intron|TPM1_ENST00000559281.1_Splice_Site_p.V129L NM_001018005.1 NP_001018005.1 P09493 TPM1_HUMAN tropomyosin 1 (alpha) 4 CCTGCTGCAGGTGGCCCGTAA 0.592000 0 SO:0001630 splice_region_variant ENST00000403994.3 1 0 hg19 CCDS45273.1 . . . . . . . . . . G 24.1 4.490295 0.84962 . . ENSG00000140416 ENST00000288398;ENST00000267996;ENST00000358278;ENST00000403994;ENST00000357980;ENST00000404484;ENST00000334895;ENST00000317516 D;D;D;D;D;D 0.98150 -4.75;-4.75;-4.75;-4.75;-4.75;-4.75 5.58 5.58 0.84498 . 0.000000 0.44902 D 0.000411 D 0.99032 0.9669 M 0.92507 3.315 0.80722 D 1 P;P;D;P;B;B;P;D;D;D;D;P;P;P 0.69078 0.486;0.841;0.997;0.47;0.352;0.314;0.912;0.985;0.966;0.995;0.98;0.848;0.836;0.912 P;P;D;B;B;B;D;D;D;D;D;P;P;D 0.75020 0.622;0.846;0.985;0.337;0.261;0.366;0.919;0.957;0.961;0.965;0.979;0.817;0.87;0.919 D 0.99541 1.0963 9 . . . -30.939 18.5512 0.91065 0.0:0.0:1.0:0.0 . 129;129;165;131;129;129;165;207;165;165;165;165;165;165 B7Z722;B7Z596;P09493-6;F5H7S3;D9YZV7;Q1ZYL5;D9YZV4;Q6ZN40;D9YZV8;D9YZV5;Q9Y427;D9YZV3;D9YZV2;P09493 .;.;.;.;.;.;.;.;.;.;.;.;.;TPM1_HUMAN L 165;165;165;165;207;187;129;131 ENSP00000288398:V165L;ENSP00000267996:V165L;ENSP00000351022:V165L;ENSP00000385107:V165L;ENSP00000350667:V207L;ENSP00000334624:V129L . V + 1 0 TPM1 61140121 1.000000 0.71417 1.000000 0.80357 0.943000 0.58893 9.869000 0.99810 2.628000 0.89032 0.491000 0.48974 GTG TCGA-US-A77E-01A-11D-A32N-08 TPM1-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000417083.2 1 0 1 49 226 0 52 1 1 116 803 0 52 2 0 0 0 0 0 2 1 1.000000 49 223 0 52 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 1.986821 0 0.390000 2.070000 0.392370 0.910000 6.900000e-01 1.000000 1.000000 0.905602 0.910000 1 0.800000 1.000000 HOMER2 9455 broad.mit.edu 37 15 83561566 83561566 + Silent SNP C C T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr15:83561566C>T ENST00000304231.8 - 2 225 c.33G>A c.(31-33)gcG>gcA p.A11A HOMER2_ENST00000450735.2_Silent_p.A11A|HOMER2_ENST00000399166.2_Silent_p.A11A|HOMER2_ENST00000426485.1_Silent_p.A11A NM_199330.2 NP_955362.1 Q9NSB8 HOME2_HUMAN homer homolog 2 (Drosophila) p.A11A(1) 9 GGAAGACATGCGCTCGGGTGG 0.483000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000304231.8 0 1 hg19 CCDS45334.1 TCGA-US-A77E-01A-11D-A32N-08 HOMER2-004 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000418689.1 0 0 0 5 471 0 98 0 9.568124e-02 0 40 0 98 2 0 0 0 0 0 2 1 0.936101 5 466 0 97 2 0 0 0 0 0 0 -2.272608 0 1 120902 3 39 1 1 2 3 1.986821 0 0.390000 2.070000 0.392370 0.050000 1.000000e-02 0.130000 0.060000 0.073551 0.050000 0 0.030000 0.090000 GNPTG 84572 broad.mit.edu 37 16 1412884 1412884 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr16:1412884G>A ENST00000204679.4 + 10 843 c.800G>A c.(799-801)gGc>gAc p.G267D LA16c-316G12.2_ENST00000569831.1_RNA NM_032520.4 NP_115909.1 Q9UJJ9 GNPTG_HUMAN N-acetylglucosamine-1-phosphate transferase, gamma subunit 7 Hepatocellular(780;0.0893) ACCCAGCACGGCATCCCCTAC 0.567000 0 SO:0001583 missense ENST00000204679.4 0 1 hg19 CCDS10436.1 . . . . . . . . . . G 16.58 3.161810 0.57368 . . ENSG00000090581 ENST00000204679 D 0.88664 -2.41 5.04 4.06 0.47325 . 0.332660 0.35466 N 0.003194 D 0.87325 0.6149 M 0.71581 2.175 0.38684 D 0.952614 P 0.40578 0.722 B 0.39185 0.293 D 0.89026 0.3438 10 0.51188 T 0.08 -35.0628 12.1825 0.54220 0.0896:0.0:0.9104:0.0 . 267 Q9UJJ9 GNPTG_HUMAN D 267 ENSP00000204679:G267D ENSP00000204679:G267D G + 2 0 GNPTG 1352885 0.997000 0.39634 0.551000 0.28230 0.143000 0.21401 1.542000 0.36137 2.527000 0.85204 0.650000 0.86243 GGC TCGA-US-A77E-01A-11D-A32N-08 GNPTG-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000109058.2 0 0 0 6 467 0 110 0 9.488421e-01 1 415 0 110 2 0 0 0 0 0 2 1 0.964259 6 463 0 109 2 0 0 0 0 0 0 -2.183592 0 1 0 0 1 1 2 3 1.983116 0 0.390000 2.070000 0.391187 0.060000 2.000000e-02 0.140000 0.060000 0.075491 0.060000 0 0.040000 0.100000 XYLT1 64131 broad.mit.edu 37 16 17352929 17352929 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr16:17352929G>A ENST00000261381.6 - 3 913 c.829C>T c.(829-831)Cgc>Tgc p.R277C NM_022166.3 NP_071449.1 Q86Y38 XYLT1_HUMAN xylosyltransferase I 67 ATCTCCTGGCGGCAGTGCTTG 0.607000 0 SO:0001583 missense ENST00000261381.6 1 1 hg19 CCDS10569.1 . . . . . . . . . . G 24.2 4.508056 0.85282 . . ENSG00000103489 ENST00000261381 T 0.07444 3.19 5.43 5.43 0.79202 . 0.000000 0.85682 D 0.000000 T 0.32406 0.0828 M 0.79475 2.455 0.80722 D 1 D 0.89917 1.0 D 0.85130 0.997 T 0.03306 -1.1050 10 0.87932 D 0 -31.9029 18.2463 0.89986 0.0:0.0:1.0:0.0 . 277 Q86Y38 XYLT1_HUMAN C 277 ENSP00000261381:R277C ENSP00000261381:R277C R - 1 0 XYLT1 17260430 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 7.731000 0.84895 2.547000 0.85894 0.655000 0.94253 CGC TCGA-US-A77E-01A-11D-A32N-08 XYLT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252241.2 1 0 1 73 344 0 94 0 9.600882e-01 1 26 0 94 2 0 0 0 0 0 2 1 1.000000 73 343 0 93 2 0 0 0 0 0 0 -3.271079 1 1 121102 4 36 1 1 2 3 1.982829 0 0.390000 2.070000 0.391187 0.890000 7.100000e-01 1.000000 1.000000 0.895581 0.890000 1 0.800000 1.000000 ZNF646 9726 broad.mit.edu 37 16 31090857 31090857 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr16:31090857G>A ENST00000394979.2 + 1 3635 c.3212G>A c.(3211-3213)cGc>cAc p.R1071H ZNF646_ENST00000300850.5_Missense_Mutation_p.R1071H O15015 ZN646_HUMAN zinc finger protein 646 49 GTGAACCACCGCAAGATCCAC 0.617000 0 SO:0001583 missense ENST00000394979.2 0 1 hg19 . . . . . . . . . . G 20.5 4.004264 0.74932 0.0 1.16E-4 ENSG00000167395 ENST00000300850;ENST00000394979 T;T 0.52057 0.68;0.68 5.75 4.78 0.61160 . . . . . T 0.33147 0.0853 L 0.31065 0.9 0.33612 D 0.603727 D 0.56521 0.976 B 0.41813 0.367 T 0.51498 -0.8698 9 0.62326 D 0.03 -15.9326 5.5911 0.17301 0.1514:0.0:0.6807:0.1679 . 1071 O15015-2 . H 1071 ENSP00000300850:R1071H;ENSP00000378429:R1071H ENSP00000300850:R1071H R + 2 0 ZNF646 30998358 0.512000 0.26186 1.000000 0.80357 0.987000 0.75469 1.081000 0.30791 1.389000 0.46526 0.563000 0.77884 CGC TCGA-US-A77E-01A-11D-A32N-08 ZNF646-003 KNOWN basic protein_coding protein_coding OTTHUMT00000108510.2 0 0 0 8 1060 0 278 0 1.581895e-02 0 22 0 278 2 0 0 0 0 0 2 1 0.989029 8 1052 0 272 2 0 0 0 0 0 0 -2.188596 0 1 121412 2 38 1 1 2 3 1.982829 0 0.390000 2.070000 0.391187 0.030000 0 0.080000 0.040000 0.043305 0.030000 0 0.020000 0.060000 SLC6A2 6530 broad.mit.edu 37 16 55727937 55727937 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr16:55727937G>A ENST00000379906.2 + 6 1189 c.934G>A c.(934-936)Gca>Aca p.A312T SLC6A2_ENST00000567238.1_Missense_Mutation_p.A207T|SLC6A2_ENST00000414754.3_Missense_Mutation_p.A312T|SLC6A2_ENST00000219833.8_Missense_Mutation_p.A312T|SLC6A2_ENST00000568943.1_Missense_Mutation_p.A312T|SLC6A2_ENST00000561820.1_Missense_Mutation_p.A312T|SLC6A2_ENST00000566163.1_Missense_Mutation_p.A267T NM_001043.3 NP_001034.1 P23975 SC6A2_HUMAN solute carrier family 6 (neurotransmitter transporter), member 2 41 Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Bupropion(DB01156)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Diethylpropion(DB00937)|Dopamine(DB00988)|Doxepin(DB01142)|Droxidopa(DB06262)|Duloxetine(DB00476)|Ephedra(DB01363)|Ephedrine(DB01364)|Ergotamine(DB00696)|Escitalopram(DB01175)|Ginkgo biloba(DB01381)|Guanadrel(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Iobenguane(DB06704)|Ketamine(DB01221)|Levomilnacipran(DB08918)|Levonordefrin(DB06707)|Loxapine(DB00408)|Maprotiline(DB00934)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Orphenadrine(DB01173)|Paroxetine(DB00715)|Pethidine(DB00454)|Phendimetrazine(DB01579)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trimipramine(DB00726)|Venlafaxine(DB00285) GATTGATGCCGCAACTCAGAT 0.453000 0 SO:0001583 missense ENST00000379906.2 0 1 hg19 CCDS10754.1 . . . . . . . . . . G 14.23 2.474824 0.43942 . . ENSG00000103546 ENST00000414754;ENST00000537705;ENST00000379906;ENST00000219833 T;T;T 0.75938 -0.98;-0.98;-0.98 4.74 4.74 0.60224 . 0.000000 0.85682 D 0.000000 D 0.88418 0.6431 M 0.88031 2.925 0.58432 D 0.999998 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.87578 0.998;0.998;0.998;0.996 D 0.91031 0.4864 10 0.87932 D 0 . 17.3376 0.87286 0.0:0.0:1.0:0.0 . 312;26;207;312 Q96KH8;F5H0T4;B4DX48;P23975 .;.;.;SC6A2_HUMAN T 312;26;312;312 ENSP00000394956:A312T;ENSP00000369237:A312T;ENSP00000219833:A312T ENSP00000219833:A312T A + 1 0 SLC6A2 54285438 1.000000 0.71417 0.999000 0.59377 0.930000 0.56654 9.501000 0.97979 2.196000 0.70406 0.561000 0.74099 GCA TCGA-US-A77E-01A-11D-A32N-08 SLC6A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256922.2 0 0 0 5 541 0 94 0 0 0 0 94 2 0 0 0 0 0 2 1 0.934726 5 532 0 94 2 0 0 0 0 0 0 -2.187734 0 1 121412 1 34 1 1 2 3 1.982829 0 0.390000 2.070000 0.391187 0.040000 0 0.110000 0.050000 0.056023 0.040000 0 0.020000 0.080000 KIFC3 3801 broad.mit.edu 37 16 57803635 57803635 + Missense_Mutation SNP C C T rs146824728 byFrequency TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr16:57803635C>T ENST00000379655.4 - 9 1347 c.1090G>A c.(1090-1092)Gtc>Atc p.V364I KIFC3_ENST00000540079.2_Missense_Mutation_p.V262I|KIFC3_ENST00000543930.1_Missense_Mutation_p.V225I|KIFC3_ENST00000562903.1_Missense_Mutation_p.V225I|KIFC3_ENST00000465878.2_Missense_Mutation_p.V225I|KIFC3_ENST00000566975.1_5'Flank|KIFC3_ENST00000445690.2_Missense_Mutation_p.V364I|KIFC3_ENST00000541240.1_Missense_Mutation_p.V386I|KIFC3_ENST00000539578.1_Missense_Mutation_p.V306I|KIFC3_ENST00000421376.2_Missense_Mutation_p.V225I NM_005550.3 NP_005541.3 Q9BVG8 KIFC3_HUMAN kinesin family member C3 23 all_neural(199;0.224) TTGGTCCGGACGCCTATGGGG 0.667000 0 SO:0001583 missense ENST00000379655.4 1 1 hg19 CCDS10789.2 . . . . . . . . . . C 17.90 3.503117 0.64298 4.55E-4 0.0 ENSG00000140859 ENST00000379655;ENST00000445690;ENST00000421376;ENST00000541240;ENST00000540079;ENST00000543930;ENST00000539578 T;T;T;T;T;T;T 0.74632 -0.82;-0.8;-0.79;-0.81;-0.78;-0.86;-0.79 5.6 5.6 0.85130 . 0.000000 0.85682 D 0.000000 T 0.69504 0.3118 L 0.54323 1.7 0.58432 D 0.999999 B;P;B;B;B;B;P 0.44627 0.4;0.839;0.4;0.133;0.088;0.4;0.495 B;B;B;B;B;B;B 0.36845 0.051;0.234;0.051;0.08;0.04;0.051;0.058 T 0.71024 -0.4712 10 0.35671 T 0.21 . 18.1742 0.89756 0.0:1.0:0.0:0.0 . 386;306;225;262;69;364;225 B7Z484;F5H4I9;B7Z896;F5H3M2;B7Z3I6;Q9BVG8;A8K6S2 .;.;.;.;.;KIFC3_HUMAN;. I 364;364;225;386;262;225;306 ENSP00000368976:V364I;ENSP00000401696:V364I;ENSP00000396399:V225I;ENSP00000442008:V386I;ENSP00000438805:V262I;ENSP00000444012:V225I;ENSP00000444884:V306I ENSP00000368976:V364I V - 1 0 KIFC3 56361136 1.000000 0.71417 0.987000 0.45799 0.186000 0.23388 5.980000 0.70516 2.624000 0.88883 0.655000 0.94253 GTC TCGA-US-A77E-01A-11D-A32N-08 KIFC3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000257329.2 1 0 1 37 151 0 47 1 9.999954e-01 12 70 0 47 2 0 0 0 0 0 2 1 1.000000 37 149 0 45 2 0 0 0 0 0 0 -20.000000 1 1 121404 19 40 1 1 2 3 1.976157 0 0.390000 2.070000 0.391187 0.990000 7.400000e-01 1.000000 1.000000 0.950524 0.990000 1 0.860000 1.000000 CDH11 1009 broad.mit.edu 37 16 65032559 65032559 + Silent SNP C C T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr16:65032559C>T ENST00000268603.4 - 4 1044 c.429G>A c.(427-429)tcG>tcA p.S143S CDH11_ENST00000394156.3_Silent_p.S143S|CDH11_ENST00000566827.1_Silent_p.S17S NM_001797.2 NP_001788.2 P55287 CAD11_HUMAN cadherin 11, type 2, OB-cadherin (osteoblast) 88 Ovarian(137;0.0973) CAATGAATTCCGACGGTGGCT 0.557000 T USP6 aneurysmal bone cysts TSP Lung(24;0.17) Dom yes 16 16q22.1 1009 cadherin 11, type 2, OB-cadherin (osteoblast) M 0 SO:0001819 synonymous_variant ENST00000268603.4 1 1 hg19 CCDS10803.1 . . . . . . . . . . C 7.100 0.573882 0.13623 . . ENSG00000140937 ENST00000536902 . . . 5.77 -11.5 0.00074 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 4.1085 0.10049 0.127:0.3975:0.2727:0.2028 . . . . . -1 . . . - . . CDH11 63590060 0.000000 0.05858 0.005000 0.12908 0.809000 0.45718 -2.084000 0.01363 -3.488000 0.00154 -1.021000 0.02439 . TCGA-US-A77E-01A-11D-A32N-08 CDH11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268755.1 1 0 1 56 243 0 68 0 9.999999e-01 0 108 0 68 2 0 0 0 0 0 2 1 1.000000 56 242 1 68 15 0 0 0 0 0 0 -3.179270 1 1 121412 2 35 1 1 2 3 1.976157 0 0.390000 2.070000 0.391187 0.950000 7.400000e-01 1.000000 1.000000 0.935818 0.950000 1 0.840000 1.000000 FHOD1 29109 broad.mit.edu 37 16 67273270 67273270 + Missense_Mutation SNP C C T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr16:67273270C>T ENST00000258201.4 - 2 536 c.289G>A c.(289-291)Ggc>Agc p.G97S NM_013241.2 NP_037373.2 Q9Y613 FHOD1_HUMAN formin homology 2 domain containing 1 34 Ovarian(137;0.0563) TCATAGAAGCCCTCCAGCATC 0.582000 0 SO:0001583 missense ENST00000258201.4 1 1 hg19 CCDS10834.1 . . . . . . . . . . C 14.69 2.610778 0.46527 . . ENSG00000135723 ENST00000258201 T 0.20200 2.09 4.85 2.67 0.31697 GTPase-binding/formin homology 3 (1); 0.390655 0.28834 N 0.013983 T 0.15262 0.0368 L 0.41492 1.28 0.80722 D 1 B 0.02656 0.0 B 0.01281 0.0 T 0.07927 -1.0747 10 0.24483 T 0.36 . 8.5697 0.33561 0.0:0.8069:0.0:0.1931 . 97 Q9Y613 FHOD1_HUMAN S 97 ENSP00000258201:G97S ENSP00000258201:G97S G - 1 0 FHOD1 65830771 0.100000 0.21855 1.000000 0.80357 0.997000 0.91878 0.337000 0.19841 0.516000 0.28340 0.655000 0.94253 GGC TCGA-US-A77E-01A-11D-A32N-08 FHOD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268844.2 1 0 1 42 300 0 87 1 7.246828e-01 3 17 0 87 2 0 0 0 0 0 2 1 1.000000 39 296 0 85 2 0 0 0 0 0 0 -3.318838 1 1 0 0 1 1 2 3 1.976157 0 0.390000 2.070000 0.391187 0.630000 4.600000e-01 0.830000 0.630000 0.639354 0.630000 0 0.540000 0.730000 SLC12A4 6560 broad.mit.edu 37 16 67980419 67980419 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr16:67980419G>A ENST00000316341.3 - 18 2499 c.2359C>T c.(2359-2361)Cgg>Tgg p.R787W SLC12A4_ENST00000338335.3_Intron|LCAT_ENST00000264005.5_5'Flank|SLC12A4_ENST00000541864.2_Missense_Mutation_p.R756W|SLC12A4_ENST00000572037.1_Missense_Mutation_p.R739W|SLC12A4_ENST00000537830.2_Missense_Mutation_p.R781W|SLC12A4_ENST00000576616.1_Missense_Mutation_p.R787W|CTC-479C5.17_ENST00000590594.1_lincRNA|SLC12A4_ENST00000422611.2_Missense_Mutation_p.R789W NM_001145961.1|NM_005072.4 NP_001139433.1|NP_005063.1 Q9UP95 S12A4_HUMAN solute carrier family 12 (potassium/chloride transporter), member 4 29 Ovarian(137;0.192) Bumetanide(DB00887)|Potassium Chloride(DB00761) GAGTTATGCCGCATGCCTCCC 0.652000 0 SO:0001583 missense ENST00000316341.3 0 1 hg19 CCDS10855.1 . . . . . . . . . . G 18.93 3.728223 0.69074 0.0 1.16E-4 ENSG00000124067 ENST00000422611;ENST00000541864;ENST00000537830;ENST00000316341 D;D;D;D 0.92595 -3.07;-3.07;-3.07;-3.07 4.57 2.23 0.28157 . 0.048575 0.85682 D 0.000000 D 0.94837 0.8332 M 0.80982 2.52 0.80722 D 1 D;D;D;D;D;D 0.63046 0.989;0.986;0.992;0.992;0.992;0.986 P;P;D;P;P;P 0.63381 0.877;0.582;0.914;0.761;0.828;0.582 D 0.93878 0.7168 10 0.87932 D 0 . 11.329 0.49465 0.0:0.0:0.3051:0.6949 . 789;787;756;781;787;787 F5H3C0;B4DF30;F5H066;F5H0S9;Q9UP95-2;Q9UP95 .;.;.;.;.;S12A4_HUMAN W 789;756;781;787 ENSP00000395983:R789W;ENSP00000438334:R756W;ENSP00000445962:R781W;ENSP00000318557:R787W ENSP00000318557:R787W R - 1 2 SLC12A4 66537920 1.000000 0.71417 1.000000 0.80357 0.983000 0.72400 3.502000 0.53332 0.220000 0.20860 -0.262000 0.10625 CGG TCGA-US-A77E-01A-11D-A32N-08 SLC12A4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268864.4 0 0 0 6 341 1 86 0 3.981331e-02 0 82 1 86 5 0 0 0 0 0 2 0 0.036408 6 341 1 86 15 0 0 0 0 0 0 -2.414368 0 1 121396 1 32 1 1 2 3 1.976157 0 0.390000 2.070000 0.391187 0.090000 3.000000e-02 0.190000 0.090000 0.102604 0.090000 0 0.050000 0.140000 WWP2 11060 broad.mit.edu 37 16 69832593 69832593 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr16:69832593G>A ENST00000359154.2 + 3 180 c.79G>A c.(79-81)Gca>Aca p.A27T WWP2_ENST00000356003.2_Missense_Mutation_p.A27T|WWP2_ENST00000448661.1_Missense_Mutation_p.A27T|WWP2_ENST00000569174.1_Missense_Mutation_p.A27T NM_001270454.1|NM_007014.4 NP_001257383.1|NP_008945.2 O00308 WWP2_HUMAN WW domain containing E3 ubiquitin protein ligase 2 42 AGTGGTGTCCGCAAAGCCCAA 0.527000 OREG0023909 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000359154.2 0 1 hg19 CCDS10885.1 . . . . . . . . . . G 24.6 4.551721 0.86127 . . ENSG00000198373 ENST00000359154;ENST00000448661;ENST00000356003 T;T;T 0.80738 -1.41;-1.41;-1.41 5.76 5.76 0.90799 C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1); 0.198406 0.45606 D 0.000349 T 0.76054 0.3934 M 0.67397 2.05 0.80722 D 1 P 0.46020 0.871 B 0.32583 0.148 T 0.78339 -0.2242 9 . . . . 16.6952 0.85333 0.0:0.0:1.0:0.0 . 27 O00308 WWP2_HUMAN T 27 ENSP00000352069:A27T;ENSP00000396871:A27T;ENSP00000348283:A27T . A + 1 0 WWP2 68390094 1.000000 0.71417 1.000000 0.80357 0.965000 0.64279 4.778000 0.62368 2.713000 0.92767 0.655000 0.94253 GCA TCGA-US-A77E-01A-11D-A32N-08 WWP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268954.1 0 0 0 6 490 1 113 0 2.503172e-02 0 41 1 113 3 0 3.173886e-01 1 693 2 360 12 0 0.024402 7 488 1 112 16 0 0 0 0 0 0 -1.705587 0 1 0 0 1 1 2 3 1.976157 0 0.390000 2.070000 0.391187 0.060000 2.000000e-02 0.140000 0.060000 0.072019 0.060000 0 0.030000 0.100000 PLCG2 5336 broad.mit.edu 37 16 81942078 81942078 + Nonsense_Mutation SNP A A T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr16:81942078A>T ENST00000359376.3 + 17 1829 c.1615A>T c.(1615-1617)Aag>Tag p.K539* NM_002661.3 NP_002652.2 P16885 PLCG2_HUMAN phospholipase C, gamma 2 (phosphatidylinositol-specific) 58 GAAGGTGGAGAAGAGGACGAG 0.547000 0 SO:0001587 stop_gained ENST00000359376.3 0 1 hg19 CCDS42204.1 . . . . . . . . . . A 40 8.275878 0.98737 . . ENSG00000197943 ENST00000359376 . . . 4.72 4.72 0.59763 . 0.385009 0.29884 N 0.010957 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.27082 T 0.32 . 7.2706 0.26254 0.8622:0.0:0.1378:0.0 . . . . X 539 . ENSP00000352336:K539X K + 1 0 PLCG2 80499579 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 5.998000 0.70653 1.770000 0.52166 0.460000 0.39030 AAG TCGA-US-A77E-01A-11D-A32N-08 PLCG2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000432429.1 1 0 1 45 191 0 44 0 3.243658e-01 0 6 0 44 2 0 0 0 0 0 2 1 1.000000 43 190 0 44 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 1.976157 0 0.390000 2.070000 0.391187 0.970000 7.300000e-01 1.000000 1.000000 0.940789 0.970000 1 0.850000 1.000000 KRT36 8689 broad.mit.edu 37 17 39643660 39643660 + Silent SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr17:39643660G>A ENST00000328119.6 - 5 929 c.930C>T c.(928-930)atC>atT p.I310I KRT36_ENST00000393986.2_Silent_p.I260I NM_003771.4 NP_003762.1 O76013 KRT36_HUMAN keratin 36 17 Breast(137;0.000286) GTCTCAGCTCGATGATCTCCG 0.627000 0 SO:0001819 synonymous_variant ENST00000328119.6 1 1 hg19 CCDS11395.1 TCGA-US-A77E-01A-11D-A32N-08 KRT36-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000259508.1 1 0 1 20 115 0 32 0 0 0 1 0 32 2 0 0 0 0 0 2 1 0.999997 20 113 0 31 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 1.988334 0 0.390000 2.070000 0.392370 0.760000 4.900000e-01 1.000000 1.000000 0.775080 0.760000 0 0.620000 0.940000 ARMC7 79637 broad.mit.edu 37 17 73124988 73124988 + Missense_Mutation SNP C C T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr17:73124988C>T ENST00000245543.1 + 3 754 c.452C>T c.(451-453)tCg>tTg p.S151L NT5C_ENST00000579082.1_5'Flank|ARMC7_ENST00000581078.1_3'UTR|ARMC7_ENST00000579096.1_3'UTR NM_024585.2 NP_078861.1 Q9H6L4 ARMC7_HUMAN armadillo repeat containing 7 9 all_lung(278;0.14)|Lung NSC(278;0.168) LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235) TTCTCCCTCTCGGCCAGCGCC 0.701000 0 SO:0001583 missense ENST00000245543.1 1 1 hg19 CCDS11714.1 . . . . . . . . . . C 26.0 4.697716 0.88830 . . ENSG00000125449 ENST00000245543 T 0.56444 0.46 5.18 5.18 0.71444 Armadillo-like helical (1);Armadillo-type fold (1); 0.071680 0.64402 D 0.000016 T 0.70228 0.3200 M 0.67397 2.05 0.80722 D 1 D 0.89917 1.0 D 0.63033 0.91 T 0.73219 -0.4052 10 0.72032 D 0.01 . 19.0722 0.93143 0.0:1.0:0.0:0.0 . 151 Q9H6L4 ARMC7_HUMAN L 151 ENSP00000245543:S151L ENSP00000245543:S151L S + 2 0 ARMC7 70636583 1.000000 0.71417 0.977000 0.42913 0.480000 0.33159 7.771000 0.85420 2.595000 0.87683 0.655000 0.94253 TCG TCGA-US-A77E-01A-11D-A32N-08 ARMC7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000445846.1 1 0 1 28 98 0 26 1 8.160037e-01 4 9 0 26 2 0 0 0 0 0 2 1 1.000000 28 98 0 26 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 1.988334 0 0.390000 2.070000 0.392370 0.990000 8.000000e-01 1.000000 1.000000 0.979937 0.990000 1 0.960000 1.000000 ZBTB4 57659 broad.mit.edu 37 17 7369754 7369754 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr17:7369754G>A ENST00000311403.4 - 3 706 c.367C>T c.(367-369)Ccc>Tcc p.P123S ZBTB4_ENST00000380599.4_Missense_Mutation_p.P123S NM_020899.3 NP_065950.2 Q9P1Z0 ZBTB4_HUMAN zinc finger and BTB domain containing 4 36 Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255) AGGACCCGGGGTGGGGAAGAA 0.592000 0 SO:0001583 missense ENST00000311403.4 0 1 hg19 CCDS11107.1 . . . . . . . . . . G 12.76 2.034919 0.35893 . . ENSG00000174282 ENST00000311403;ENST00000380599 T;T 0.46451 0.87;0.87 4.5 4.5 0.54988 BTB/POZ-like (2);BTB/POZ fold (2); 0.081322 0.48286 N 0.000193 T 0.14485 0.0350 N 0.01464 -0.85 0.34368 D 0.691707 B 0.33413 0.411 B 0.23018 0.043 T 0.16719 -1.0393 10 0.59425 D 0.04 -17.1852 8.349 0.32290 0.1059:0.0:0.8941:0.0 . 123 Q9P1Z0 ZBTB4_HUMAN S 123 ENSP00000307858:P123S;ENSP00000369973:P123S ENSP00000307858:P123S P - 1 0 ZBTB4 7310478 1.000000 0.71417 0.996000 0.52242 0.860000 0.49131 1.958000 0.40402 2.332000 0.79248 0.462000 0.41574 CCC TCGA-US-A77E-01A-11D-A32N-08 ZBTB4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000226940.2 1 0 0 7 83 0 13 1 8.041582e-01 2 36 0 13 2 0 0 0 0 0 2 1 0.981287 7 82 0 13 2 0 0 0 0 0 0 -12.065770 1 1 0 0 1 0 1 1 1.705046 1 0.390000 2.070000 0.283869 0.350000 1.500000e-01 0.620000 0.330000 0.369311 0.350000 0 0.240000 0.490000 ENGASE 64772 broad.mit.edu 37 17 77081767 77081767 + Missense_Mutation SNP C C T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr17:77081767C>T ENST00000579016.1 + 13 1766 c.1766C>T c.(1765-1767)cCg>cTg p.P589L NM_001042573.2 NP_001036038.1 Q8NFI3 ENASE_HUMAN endo-beta-N-acetylglucosaminidase 25 TCACGGCCGCCGGGTAGTCGG 0.647000 0 SO:0001583 missense ENST00000579016.1 1 1 hg19 CCDS42394.1 . . . . . . . . . . C 4.447 0.082790 0.08533 . . ENSG00000167280 ENST00000545583 . . . 5.12 -2.66 0.06077 . 0.740232 0.11997 N 0.509178 T 0.22820 0.0551 L 0.36672 1.1 0.09310 N 1 B 0.12630 0.006 B 0.06405 0.002 T 0.17992 -1.0351 9 0.28530 T 0.3 -14.6675 0.6221 0.00780 0.2261:0.2603:0.1292:0.3843 . 589 Q8NFI3 ENASE_HUMAN L 589 . ENSP00000438577:P589L P + 2 0 ENGASE 74593362 0.000000 0.05858 0.000000 0.03702 0.008000 0.06430 -0.211000 0.09332 -0.062000 0.13088 0.462000 0.41574 CCG TCGA-US-A77E-01A-11D-A32N-08 ENGASE-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000395807.1 1 0 1 56 228 0 54 1 9.999064e-01 18 41 0 54 2 0 0 0 0 0 2 1 1.000000 55 224 0 52 2 0 0 0 0 0 0 -3.423686 1 1 120930 2 30 1 1 2 3 1.988334 0 0.390000 2.070000 0.392370 0.990000 7.800000e-01 1.000000 1.000000 0.961933 0.990000 1 0.890000 1.000000 GAA 2548 broad.mit.edu 37 17 78085870 78085870 + Silent SNP C C T rs112517802 TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr17:78085870C>T ENST00000302262.3 + 12 1944 c.1725C>T c.(1723-1725)taC>taT p.Y575Y GAA_ENST00000390015.3_Silent_p.Y575Y NM_000152.3 NP_000143.2 P10253 LYAG_HUMAN glucosidase, alpha; acid 21 all_neural(118;0.117) OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139) Acarbose(DB00284)|Miglitol(DB00491) ACAACCTCTACGGCCTGACCG 0.657000 0 SO:0001819 synonymous_variant ENST00000302262.3 1 1 hg19 CCDS32760.1 TCGA-US-A77E-01A-11D-A32N-08 GAA-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000437441.1 1 0 0 86 345 0 95 1 1 9 126 0 95 2 0 0 0 0 0 2 1 1.000000 85 338 0 94 2 0 0 0 0 0 0 -20.000000 1 1 121412 2 37 1 1 2 3 1.988334 0 0.390000 2.070000 0.392370 0.990000 8.300000e-01 1.000000 1.000000 0.974530 0.990000 1 0.920000 1.000000 CELF4 56853 broad.mit.edu 37 18 34854360 34854360 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr18:34854360G>A ENST00000591282.1 - 6 714 c.715C>T c.(715-717)Cgg>Tgg p.R239W CELF4_ENST00000601019.1_Missense_Mutation_p.R238W|CELF4_ENST00000420428.2_Missense_Mutation_p.R239W|CELF4_ENST00000334919.5_Missense_Mutation_p.R229W|CELF4_ENST00000603232.1_Missense_Mutation_p.R239W|CELF4_ENST00000588597.1_Missense_Mutation_p.R228W|CELF4_ENST00000361795.5_Missense_Mutation_p.R238W|RP11-797E24.3_ENST00000588766.1_RNA|CELF4_ENST00000591287.1_Missense_Mutation_p.R238W|RP11-797E24.3_ENST00000586610.1_RNA|CELF4_ENST00000412753.1_Missense_Mutation_p.R239W Q9BZC1 CELF4_HUMAN CUGBP, Elav-like family member 4 p.R239W(1) 44 TGCATTCGCCGCATCGTGCGC 0.667000 1 Substitution - Missense(1) SO:0001583 missense ENST00000591282.1 0 1 hg19 CCDS32818.1 . . . . . . . . . . G 21.5 4.159388 0.78226 . . ENSG00000101489 ENST00000361795;ENST00000412753;ENST00000420428;ENST00000334919;ENST00000361683 T;T;T 0.06449 3.3;3.31;3.31 4.55 3.59 0.41128 . 0.000000 0.85682 D 0.000000 T 0.29882 0.0747 M 0.91510 3.215 0.80722 D 1 D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0 D;D;D;D;D 0.97110 0.999;0.993;1.0;0.999;0.996 T 0.19614 -1.0300 10 0.87932 D 0 -12.5849 12.0837 0.53686 0.0:0.0:0.7247:0.2753 . 238;228;229;238;239 Q9BZC1-3;B4DHA8;Q9BZC1-5;Q9BZC1-2;Q9BZC1 .;.;.;.;CELF4_HUMAN W 239;239;238;229;122 ENSP00000355089:R239W;ENSP00000406823:R239W;ENSP00000335631:R229W ENSP00000335631:R229W R - 1 2 CELF4 33108358 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 2.280000 0.43443 2.373000 0.80994 0.561000 0.74099 CGG TCGA-US-A77E-01A-11D-A32N-08 CELF4-004 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000440892.1 0 0 0 5 632 1 164 0 0 0 1 164 2 0 0 0 0 0 2 0 0.028245 5 622 1 162 14 0 0 0 0 0 0 -1.778118 0 1 0 0 1 1 2 3 1.976333 0 0.390000 2.070000 0.391187 0.040000 0 0.100000 0.040000 0.047934 0.040000 0 0.020000 0.070000 PGLYRP2 114770 broad.mit.edu 37 19 15586705 15586705 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr19:15586705G>A ENST00000340880.4 - 2 1256 c.776C>T c.(775-777)aCg>aTg p.T259M PGLYRP2_ENST00000292609.4_Missense_Mutation_p.T259M NM_052890.3 NP_443122.3 Q96PD5 PGRP2_HUMAN peptidoglycan recognition protein 2 28 GTCCAAAAGCGTAAAGGTCCG 0.612000 0 SO:0001583 missense ENST00000340880.4 0 1 hg19 CCDS12330.2 . . . . . . . . . . g 3.963 -0.009976 0.07727 . . ENSG00000161031 ENST00000340880;ENST00000292609 T;T 0.05025 3.53;3.51 5.31 3.19 0.36642 . 0.237201 0.32901 N 0.005502 T 0.07728 0.0194 M 0.76002 2.32 0.22819 N 0.998691 P;P 0.43431 0.807;0.576 B;B 0.37267 0.245;0.048 T 0.31943 -0.9925 10 0.66056 D 0.02 -22.5225 4.5625 0.12166 0.0828:0.1521:0.6077:0.1574 . 259;259 Q96PD5-2;Q96PD5 .;PGRP2_HUMAN M 259 ENSP00000345968:T259M;ENSP00000292609:T259M ENSP00000292609:T259M T - 2 0 PGLYRP2 15447705 0.978000 0.34361 0.446000 0.26920 0.000000 0.00434 2.391000 0.44424 0.647000 0.30713 -1.032000 0.02404 ACG TCGA-US-A77E-01A-11D-A32N-08 PGLYRP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000319626.1 0 0 0 4 223 0 43 0 0 0 0 43 2 0 0 0 0 0 2 1 0.891148 4 223 0 43 2 0 0 0 0 0 0 -5.363324 1 1 121412 18 42 1 1 2 3 1.994306 0 0.390000 2.070000 0.394721 0.100000 2.000000e-02 1.000000 0.090000 0.137632 0.100000 0 0.050000 0.170000 SHKBP1 92799 broad.mit.edu 37 19 41096643 41096643 + Silent SNP C C T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr19:41096643C>T ENST00000291842.5 + 17 1825 c.1776C>T c.(1774-1776)ggC>ggT p.G592G SHKBP1_ENST00000600733.1_Silent_p.G567G|LTBP4_ENST00000545697.1_5'Flank|LTBP4_ENST00000204005.9_5'Flank NM_138392.3 NP_612401.2 Q8TBC3 SHKB1_HUMAN SH3KBP1 binding protein 1 29 Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384) CAGCAGGTGGCCTGACGGAGC 0.662000 0 SO:0001819 synonymous_variant ENST00000291842.5 1 1 hg19 CCDS12560.1 TCGA-US-A77E-01A-11D-A32N-08 SHKBP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000462613.2 1 0 1 79 448 0 114 1 1 71 133 0 114 2 0 0 0 0 0 2 1 1.000000 77 443 0 112 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 2.001483 0 0.390000 2.070000 0.395890 0.770000 6.200000e-01 1.000000 0.780000 0.789007 0.770000 0 0.690000 0.870000 PSG6 5675 broad.mit.edu 37 19 43411874 43411874 + Missense_Mutation SNP G G A rs142652144 byFrequency TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr19:43411874G>A ENST00000292125.2 - 4 883 c.839C>T c.(838-840)cCg>cTg p.P280L PSG6_ENST00000187910.2_Missense_Mutation_p.P280L|PSG6_ENST00000402603.4_Intron NM_002782.4 NP_002773.1 Q00889 PSG6_HUMAN pregnancy specific beta-1-glycoprotein 6 44 Prostate(69;0.00899) CGGACTGACCGGGAGGCTCTG 0.478000 0 SO:0001583 missense ENST00000292125.2 1 1 hg19 CCDS12613.1 1 4.578754578754579E-4 0 0.0 1 0.0027624309392265192 0 0.0 0 0.0 N 0.009 -1.803836 0.00611 0.002499 0.0 ENSG00000170848 ENST00000187910;ENST00000292125 T;T 0.13307 2.6;2.6 1.42 -1.33 0.09172 Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); . . . . T 0.21962 0.0529 L 0.52266 1.64 0.09310 N 1 D;B 0.89917 1.0;0.015 D;B 0.97110 1.0;0.038 T 0.16453 -1.0402 9 0.39692 T 0.17 . 1.6928 0.02856 0.2473:0.0:0.4168:0.3359 . 280;280 Q00889;Q00889-2 PSG6_HUMAN;. L 280 ENSP00000187910:P280L;ENSP00000292125:P280L ENSP00000187910:P280L P - 2 0 PSG6 48103714 0.000000 0.05858 0.005000 0.12908 0.184000 0.23303 0.090000 0.15025 -0.070000 0.12908 0.134000 0.15878 CCG TCGA-US-A77E-01A-11D-A32N-08 PSG6-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000321436.1 1 0 1 256 1086 0 274 0 0 0 0 274 2 0 0 0 0 0 2 1 1.000000 253 1042 0 268 2 0 0 0 0 0 0 -2.719552 1 1 121356 23 50 1 1 2 3 2.001483 0 0.390000 2.070000 0.395890 0.980000 8.700000e-01 1.000000 1.000000 0.972773 0.980000 1 0.920000 1.000000 C5AR1 728 broad.mit.edu 37 19 47823129 47823129 + Missense_Mutation SNP C C T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr19:47823129C>T ENST00000355085.3 + 2 117 c.95C>T c.(94-96)aCg>aTg p.T32M NM_001736.3 NP_001727.1 P21730 C5AR1_HUMAN complement component 5a receptor 1 p.T32M(1) 20 all_cancers(25;2e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503) ACTTCTAACACGCTGCGTGTT 0.532000 1 Substitution - Missense(1) SO:0001583 missense ENST00000355085.3 1 1 hg19 CCDS33063.1 . . . . . . . . . . C 9.210 1.030611 0.19512 . . ENSG00000197405 ENST00000355085 T 0.37411 1.2 3.85 -7.7 0.01259 . 0.484862 0.17251 U 0.181174 T 0.10423 0.0255 N 0.08118 0 0.09310 N 1 P 0.51653 0.947 B 0.38296 0.27 T 0.32771 -0.9894 10 0.48119 T 0.1 . 2.3954 0.04388 0.2001:0.3146:0.3273:0.158 . 32 P21730 C5AR_HUMAN M 32 ENSP00000347197:T32M ENSP00000347197:T32M T + 2 0 C5AR1 52514969 0.000000 0.05858 0.000000 0.03702 0.010000 0.07245 -3.504000 0.00449 -2.504000 0.00508 -0.792000 0.03331 ACG TCGA-US-A77E-01A-11D-A32N-08 C5AR1-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000466925.1 0 0 1 69 286 0 77 0 9.188805e-01 0 20 0 77 2 0 0 0 0 0 2 1 1.000000 69 284 0 76 2 0 0 0 0 0 0 -20.000000 1 1 121412 4 38 1 1 2 3 2.001483 0 0.390000 2.070000 0.395890 0.990000 8.000000e-01 1.000000 1.000000 0.963577 0.990000 1 0.900000 1.000000 NLRP4 147945 broad.mit.edu 37 19 56369561 56369561 + Missense_Mutation SNP A A G TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr19:56369561A>G ENST00000301295.6 + 3 1224 c.802A>G c.(802-804)Aag>Gag p.K268E NLRP4_ENST00000346986.5_Missense_Mutation_p.K268E|NLRP4_ENST00000587891.1_Missense_Mutation_p.K193E NM_134444.4 NP_604393.2 Q96MN2 NALP4_HUMAN NLR family, pyrin domain containing 4 42 Colorectal(82;0.0002)|Ovarian(87;0.221) GCTGAGGAAGAAGATGCTCCC 0.592000 0 SO:0001583 missense ENST00000301295.6 1 1 hg19 CCDS12936.1 . . . . . . . . . . A 15.58 2.876238 0.51801 . . ENSG00000160505 ENST00000301295;ENST00000346986 T;T 0.79653 -1.29;-1.29 4.1 3.05 0.35203 NACHT nucleoside triphosphatase (1); . . . . T 0.81640 0.4865 L 0.41079 1.255 0.09310 N 1 D;D;D 0.89917 0.999;1.0;1.0 D;D;D 0.78314 0.947;0.984;0.991 T 0.67692 -0.5605 9 0.18276 T 0.48 . 6.9127 0.24344 0.629:0.0:0.0:0.371 . 268;193;268 Q96MN2-2;Q96MN2-3;Q96MN2 .;.;NALP4_HUMAN E 268 ENSP00000301295:K268E;ENSP00000344787:K268E ENSP00000301295:K268E K + 1 0 NLRP4 61061373 0.000000 0.05858 0.008000 0.14137 0.087000 0.18053 1.126000 0.31344 0.689000 0.31550 0.533000 0.62120 AAG TCGA-US-A77E-01A-11D-A32N-08 NLRP4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000457367.2 1 0 1 77 346 0 96 0 0 0 0 96 2 0 0 0 0 0 2 1 1.000000 76 343 0 96 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 2.011441 0 0.390000 2.070000 0.397054 0.940000 7.600000e-01 1.000000 1.000000 0.933178 0.940000 1 0.840000 1.000000 NLRP8 126205 broad.mit.edu 37 19 56467178 56467178 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr19:56467178G>A ENST00000291971.3 + 3 1825 c.1754G>A c.(1753-1755)aGg>aAg p.R585K NLRP8_ENST00000590542.1_Missense_Mutation_p.R585K NM_176811.2 NP_789781.2 Q86W28 NALP8_HUMAN NLR family, pyrin domain containing 8 35 Colorectal(82;0.000147)|Ovarian(87;0.17) GGTAATAAGAGGAAACTGCTG 0.498000 0 SO:0001583 missense ENST00000291971.3 1 1 hg19 CCDS12937.1 . . . . . . . . . . G 0.011 -1.716604 0.00706 . . ENSG00000179709 ENST00000291971 D 0.88431 -2.38 2.03 -3.26 0.05064 . . . . . T 0.70649 0.3248 N 0.08118 0 0.09310 N 1 B;B 0.20780 0.036;0.048 B;B 0.13407 0.007;0.009 T 0.56703 -0.7935 9 0.18710 T 0.47 . 4.4176 0.11465 0.2921:0.221:0.4869:0.0 . 585;585 Q86W28-2;Q86W28 .;NALP8_HUMAN K 585 ENSP00000291971:R585K ENSP00000291971:R585K R + 2 0 NLRP8 61158990 0.000000 0.05858 0.000000 0.03702 0.017000 0.09413 -0.103000 0.10940 -1.059000 0.03193 -0.507000 0.04495 AGG TCGA-US-A77E-01A-11D-A32N-08 NLRP8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000457462.1 1 0 1 31 168 0 45 0 0 0 0 45 2 0 0 0 0 0 2 1 1.000000 31 167 0 45 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 2.011441 0 0.390000 2.070000 0.397054 0.810000 5.700000e-01 1.000000 1.000000 0.821973 0.810000 0 0.680000 0.980000 MED16 10025 broad.mit.edu 37 19 868430 868430 + Nonsense_Mutation SNP C C T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr19:868430C>T ENST00000589119.1 - 14 2468 c.2469G>A c.(2467-2469)tgG>tgA p.W823* MED16_ENST00000395808.3_Nonsense_Mutation_p.W823*|MED16_ENST00000269814.4_3'UTR|MED16_ENST00000312090.6_Nonsense_Mutation_p.W842*|MED16_ENST00000325464.1_Nonsense_Mutation_p.W823* Q9Y2X0 MED16_HUMAN mediator complex subunit 16 21 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137) AGTTCTTGATCCAGCGCTGCT 0.667000 0 SO:0001587 stop_gained ENST00000589119.1 0 1 hg19 CCDS12047.1 . . . . . . . . . . C 40 8.283552 0.98742 . . ENSG00000175221 ENST00000325464;ENST00000312090;ENST00000395808 . . . 4.27 4.27 0.50696 . 0.000000 0.64402 D 0.000006 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 -18.7101 15.6761 0.77326 0.0:1.0:0.0:0.0 . . . . X 823;842;823 . ENSP00000308528:W842X W - 3 0 MED16 819430 1.000000 0.71417 1.000000 0.80357 0.961000 0.63080 7.266000 0.78452 1.941000 0.56285 0.511000 0.50034 TGG TCGA-US-A77E-01A-11D-A32N-08 MED16-006 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000457902.3 1 0 0 13 147 0 37 1 9.999975e-01 99 204 0 37 2 0 0 0 0 0 2 1 0.999589 13 146 0 37 2 0 0 0 0 0 0 -18.449790 1 1 0 0 1 1 2 3 2.013232 0 0.390000 2.070000 0.397054 0.430000 2.400000e-01 1.000000 0.410000 0.470238 0.430000 0 0.330000 0.580000 NES 10763 broad.mit.edu 37 1 156639754 156639754 + Missense_Mutation SNP G G T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr1:156639754G>T ENST00000368223.3 - 4 4358 c.4226C>A c.(4225-4227)tCc>tAc p.S1409Y NM_006617.1 NP_006608.1 P48681 NEST_HUMAN nestin 64 all_hematologic(923;0.088)|Hepatocellular(266;0.158) AAACCCATCGGACTCCCCATC 0.647000 0 SO:0001583 missense ENST00000368223.3 1 1 hg19 CCDS1151.1 . . . . . . . . . . G 16.79 3.219120 0.58560 . . ENSG00000132688 ENST00000368223 D 0.93811 -3.29 4.46 4.46 0.54185 . 0.000000 0.32640 N 0.005837 D 0.94215 0.8143 M 0.66939 2.045 0.26797 N 0.969277 D 0.76494 0.999 D 0.71184 0.972 D 0.89006 0.3425 10 0.87932 D 0 . 11.8552 0.52433 0.0:0.0:0.8245:0.1755 . 1409 P48681 NEST_HUMAN Y 1409 ENSP00000357206:S1409Y ENSP00000357206:S1409Y S - 2 0 NES 154906378 0.996000 0.38824 1.000000 0.80357 0.933000 0.57130 3.567000 0.53813 2.316000 0.78162 0.557000 0.71058 TCC TCGA-US-A77E-01A-11D-A32N-08 NES-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000082844.2 1 0 0 11 176 0 54 0 7.919837e-01 0 49 0 54 2 0 0 0 0 0 2 1 0.998442 11 175 0 53 2 0 0 0 0 0 0 -14.998890 1 1 0 0 1 1 2 3 2.005218 0 0.390000 2.070000 0.395890 0.310000 1.600000e-01 1.000000 0.300000 0.351699 0.310000 0 0.230000 0.430000 GABRD 2563 broad.mit.edu 37 1 1961076 1961076 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr1:1961076G>A ENST00000378585.4 + 8 1017 c.934G>A c.(934-936)Gtc>Atc p.V312I NM_000815.4 NP_000806.2 O14764 GBRD_HUMAN gamma-aminobutyric acid (GABA) A receptor, delta 20 all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634) all_epithelial(116;2.7e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128) Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897) GGCACTGGACGTCTACTTCTG 0.592000 0 SO:0001583 missense ENST00000378585.4 1 1 hg19 CCDS36.1 . . . . . . . . . . G 8.302 0.820039 0.16678 . . ENSG00000187730 ENST00000378585 D 0.85773 -2.03 4.0 4.0 0.46444 Neurotransmitter-gated ion-channel transmembrane domain (2); 0.145269 0.46145 D 0.000310 D 0.85969 0.5821 L 0.36672 1.1 0.58432 D 0.999996 D 0.76494 0.999 D 0.79784 0.993 T 0.80984 -0.1138 10 0.02654 T 1 -16.1297 15.6431 0.77025 0.0:0.0:1.0:0.0 . 312 O14764 GBRD_HUMAN I 312 ENSP00000367848:V312I ENSP00000367848:V312I V + 1 0 GABRD 1950936 1.000000 0.71417 0.994000 0.49952 0.343000 0.28985 9.302000 0.96175 2.239000 0.73571 0.561000 0.74099 GTC TCGA-US-A77E-01A-11D-A32N-08 GABRD-001 KNOWN mRNA_start_NF|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000098493.1 1 0 1 36 189 0 40 0 3.828524e-01 0 8 0 40 2 0 0 0 0 0 2 1 1.000000 36 189 0 40 2 0 0 0 0 0 0 -20.000000 1 1 121328 17 42 1 1 2 3 2.026464 0 0.390000 2.070000 0.399370 0.840000 6.000000e-01 1.000000 1.000000 0.846143 0.840000 0 0.710000 1.000000 CELA3A 10136 broad.mit.edu 37 1 22329556 22329556 + Missense_Mutation SNP C C T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr1:22329556C>T ENST00000290122.3 + 2 123 c.104C>T c.(103-105)gCg>gTg p.A35V RN7SL768P_ENST00000584415.1_RNA|CELA3A_ENST00000374663.1_Missense_Mutation_p.A35V NM_005747.4 NP_005738.4 P09093 CEL3A_HUMAN chymotrypsin-like elastase family, member 3A p.A35V(1) 18 GGTGAGGATGCGGTCCCCTAC 0.612000 1 Substitution - Missense(1) SO:0001583 missense ENST00000290122.3 0 1 hg19 CCDS220.1 . . . . . . . . . . C 18.75 3.689677 0.68271 . . ENSG00000142789 ENST00000290122;ENST00000374663;ENST00000374661 T;D 0.94417 2.07;-3.42 3.47 2.54 0.30619 Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3); . . . . D 0.92639 0.7661 L 0.48260 1.515 0.43756 D 0.996263 D 0.71674 0.998 P 0.52627 0.704 D 0.89403 0.3697 9 0.39692 T 0.17 -25.4813 6.7714 0.23596 0.0:0.8655:0.0:0.1345 . 35 P09093 CEL3A_HUMAN V 35;35;51 ENSP00000290122:A35V;ENSP00000363795:A35V ENSP00000290122:A35V A + 2 0 CELA3A 22202143 0.996000 0.38824 0.042000 0.18584 0.880000 0.50808 3.389000 0.52516 0.781000 0.33589 0.400000 0.26472 GCG TCGA-US-A77E-01A-11D-A32N-08 CELA3A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000007791.1 0 0 0 5 444 0 91 0 1.207299e-03 0 4 0 91 2 0 0 0 0 0 2 1 0.931308 5 427 0 91 2 0 0 0 0 0 0 -2.066993 0 1 119974 1 32 1 1 2 3 2.014975 0 0.390000 2.070000 0.397054 0.060000 1.000000e-02 1.000000 0.060000 0.112506 0.060000 0 0.030000 0.100000 CNIH3 149111 broad.mit.edu 37 1 224868727 224868727 + Splice_Site SNP C C T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr1:224868727C>T ENST00000272133.3 + 2 1031 c.149C>T c.(148-150)gCg>gTg p.A50V NM_152495.1 NP_689708.1 Q8TBE1 CNIH3_HUMAN cornichon family AMPA receptor auxiliary protein 3 9 Breast(184;0.218) CCTGTTCATGCGGTAAGTGGC 0.473000 0 SO:0001630 splice_region_variant ENST00000272133.3 1 0 hg19 CCDS1544.1 . . . . . . . . . . C 23.2 4.386315 0.82902 . . ENSG00000143786 ENST00000272133 . . . 5.32 5.32 0.75619 . 0.000000 0.85682 D 0.000000 T 0.67268 0.2875 L 0.29908 0.895 0.53688 D 0.999979 D 0.89917 1.0 D 0.91635 0.999 T 0.69800 -0.5047 9 0.59425 D 0.04 -0.2012 17.7753 0.88505 0.0:1.0:0.0:0.0 . 50 Q8TBE1 CNIH3_HUMAN V 50 . ENSP00000272133:A50V A + 2 0 CNIH3 222935350 1.000000 0.71417 1.000000 0.80357 0.835000 0.47333 5.322000 0.65852 2.504000 0.84457 0.551000 0.68910 GCG TCGA-US-A77E-01A-11D-A32N-08 CNIH3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000091752.2 1 0 1 53 297 1 97 0 4.662368e-01 0 10 1 97 2 0 0 0 0 0 2 1 1.000000 50 291 1 97 13 0 0 0 0 0 0 -3.022584 1 1 121412 3 37 1 1 2 3 1.991274 0 0.390000 2.070000 0.392370 0.770000 5.900000e-01 1.000000 0.780000 0.787582 0.770000 0 0.680000 0.890000 PTCH2 8643 broad.mit.edu 37 1 45294946 45294946 + Silent SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr1:45294946G>A ENST00000372192.3 - 10 1384 c.1254C>T c.(1252-1254)tgC>tgT p.C418C PTCH2_ENST00000447098.2_Silent_p.C418C NM_003738.4 NP_003729.3 Q9Y6C5 PTC2_HUMAN patched 2 50 Acute lymphoblastic leukemia(166;0.155) GGGACTGGGCGCAGTCCCACC 0.687000 Basal Cell Nevus syndrome 0 SO:0001819 synonymous_variant Familial Cancer Database Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS ENST00000372192.3 0 1 hg19 CCDS516.1 TCGA-US-A77E-01A-11D-A32N-08 PTCH2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000023428.4 0 0 0 5 237 0 54 0 4.035170e-03 0 4 0 54 2 0 0 0 0 0 2 1 0.936124 5 234 0 52 2 0 0 0 0 0 0 -6.115855 1 1 121380 1 28 1 1 2 3 2.014431 0 0.390000 2.070000 0.397054 0.110000 4.000000e-02 1.000000 0.110000 0.167791 0.110000 0 0.070000 0.190000 INSM1 3642 broad.mit.edu 37 20 20350394 20350394 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr20:20350394G>A ENST00000310227.1 + 1 1630 c.1483G>A c.(1483-1485)Gaa>Aaa p.E495K NM_002196.2 NP_002187.1 Q01101 INSM1_HUMAN insulinoma-associated 1 6 CCACCCATCCGAAAACAGACA 0.672000 0 SO:0001583 missense ENST00000310227.1 1 1 hg19 CCDS13143.1 . . . . . . . . . . G 24.4 4.524404 0.85600 . . ENSG00000173404 ENST00000310227 T 0.00856 5.61 5.41 5.41 0.78517 Zinc finger, C2H2 (1); 0.000000 0.64402 U 0.000001 T 0.01661 0.0053 M 0.61703 1.905 0.51482 D 0.999923 D 0.58620 0.983 B 0.39660 0.306 T 0.61589 -0.7032 10 0.87932 D 0 -11.8587 14.4248 0.67207 0.0729:0.0:0.9271:0.0 . 495 Q01101 INSM1_HUMAN K 495 ENSP00000312631:E495K ENSP00000312631:E495K E + 1 0 INSM1 20298394 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 7.963000 0.87922 2.522000 0.85027 0.650000 0.86243 GAA TCGA-US-A77E-01A-11D-A32N-08 INSM1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000078223.1 1 0 1 31 186 0 37 0 2.191781e-02 0 2 0 37 2 0 0 0 0 0 2 1 1.000000 31 183 0 36 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 2.336157 1 0.390000 2.070000 0.487868 0.870000 6.100000e-01 1.000000 1.000000 0.869705 0.870000 1 0.730000 1.000000 NNAT 4826 broad.mit.edu 37 20 36149750 36149750 + Missense_Mutation SNP C C G TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr20:36149750C>G ENST00000062104.2 + 1 134 c.17C>G c.(16-18)gCg>gGg p.A6G BLCAP_ENST00000397131.1_Intron|BLCAP_ENST00000397135.1_Intron|BLCAP_ENST00000373537.2_Intron|BLCAP_ENST00000414542.2_5'UTR|NNAT_ENST00000346199.2_Missense_Mutation_p.A6G|BLCAP_ENST00000397137.1_Intron|BLCAP_ENST00000397134.1_5'Flank NM_005386.2 NP_005377.1 Q16517 NNAT_HUMAN neuronatin 3 Myeloproliferative disorder(115;0.00878) GCAGTGGCGGCGGCCTCGGCT 0.627000 0 SO:0001583 missense ENST00000062104.2 1 1 hg19 CCDS13296.1 . . . . . . . . . . C 16.19 3.052781 0.55218 . . ENSG00000053438 ENST00000062104;ENST00000346199 . . . 4.59 4.59 0.56863 . 0.000000 0.48767 D 0.000176 T 0.71600 0.3359 . . . 0.33830 D 0.630072 D;D 0.61080 0.989;0.989 D;D 0.64237 0.923;0.923 T 0.80132 -0.1510 8 0.87932 D 0 -8.0572 13.2076 0.59807 0.0:1.0:0.0:0.0 . 6;6 Q16517-2;Q16517 .;NNAT_HUMAN G 6 . ENSP00000062104:A6G A + 2 0 NNAT 35583164 1.000000 0.71417 0.998000 0.56505 0.991000 0.79684 2.991000 0.49409 2.836000 0.97738 0.655000 0.94253 GCG TCGA-US-A77E-01A-11D-A32N-08 NNAT-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000079116.2 0 0 0 34 1244 0 283 0 1.065260e-02 1 5 0 283 2 0 0 0 0 0 2 1 1.000000 31 1207 0 281 2 0 0 0 0 0 0 -1.905460 0 1 0 0 1 1 2 3 2.336157 1 0.390000 2.070000 0.487868 0.160000 1.000000e-01 0.240000 0.160000 0.175047 0.160000 0 0.130000 0.200000 PREX1 57580 broad.mit.edu 37 20 47324917 47324917 + Missense_Mutation SNP C C T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr20:47324917C>T ENST00000371941.3 - 6 686 c.664G>A c.(664-666)Gcg>Acg p.A222T PREX1_ENST00000396220.1_Missense_Mutation_p.A222T NM_020820.3 NP_065871 Q8TCU6 PREX1_HUMAN phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1 110 BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198) CTCTGGACCGCGGGGTGGTCT 0.582000 0 SO:0001583 missense ENST00000371941.3 1 1 hg19 CCDS13410.1 . . . . . . . . . . C 15.89 2.965570 0.53507 . . ENSG00000124126 ENST00000371941;ENST00000396220 T;T 0.64085 -0.08;-0.08 5.64 5.64 0.86602 Dbl homology (DH) domain (5); 0.000000 0.53938 U 0.000049 T 0.65575 0.2704 L 0.40543 1.245 0.41921 D 0.990515 D 0.55800 0.973 P 0.51777 0.679 T 0.61337 -0.7083 10 0.29301 T 0.29 . 19.7013 0.96054 0.0:1.0:0.0:0.0 . 222 Q8TCU6 PREX1_HUMAN T 222 ENSP00000361009:A222T;ENSP00000379522:A222T ENSP00000361009:A222T A - 1 0 PREX1 46758324 1.000000 0.71417 0.163000 0.22734 0.196000 0.23810 4.780000 0.62382 2.657000 0.90304 0.655000 0.94253 GCG TCGA-US-A77E-01A-11D-A32N-08 PREX1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000079623.1 1 0 1 176 1040 0 233 0 3.275801e-01 0 8 0 233 2 0 0 0 0 0 2 1 1.000000 174 1017 0 227 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 2.336157 1 0.390000 2.070000 0.487868 0.880000 7.600000e-01 1.000000 0.890000 0.886949 0.880000 1 0.810000 0.950000 GNAS 2778 broad.mit.edu 37 20 57484421 57484421 + Missense_Mutation SNP G G A rs121913495 TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr20:57484421G>A ENST00000371085.3 + 8 1026 c.602G>A c.(601-603)cGt>cAt p.R201H GNAS_ENST00000313949.7_3'UTR|GNAS_ENST00000371075.3_3'UTR|GNAS_ENST00000265620.7_Missense_Mutation_p.R186H|GNAS_ENST00000371102.4_Missense_Mutation_p.R830H|GNAS_ENST00000354359.7_Missense_Mutation_p.R202H|GNAS_ENST00000371095.3_Missense_Mutation_p.R187H|GNAS_ENST00000306090.10_Missense_Mutation_p.R187H|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000371100.4_Missense_Mutation_p.R844H NM_000516.4 NP_000507.1 P63092 GNAS2_HUMAN GNAS complex locus p.R201H(81)|p.R844H(4)|p.R201L(2)|p.R844L(1) 441 all_lung(29;0.0104) BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109) CTTCGCTGCCGTGTCCTGACT 0.423000 Mis pituitary adenoma McCune-Albright syndrome; pseudohypoparathyroidism, type IA TSP Lung(22;0.16) Colon(117;935 1597 6045 8307 46442) Dom yes 20 20q13.2 2778 guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1 yes E 88 Substitution - Missense(88) SO:0001583 missense ENST00000371085.3 1 1 hg19 CCDS13472.1 . . . . . . . . . . G 35 5.430570 0.96150 . . ENSG00000087460 ENST00000371100;ENST00000371102;ENST00000371095;ENST00000371085;ENST00000354359;ENST00000265620;ENST00000306090 D;D;D;D;D;D;D 0.99458 -5.93;-5.93;-5.93;-5.93;-5.93;-2.96;-5.93 5.53 5.53 0.82687 G protein alpha subunit, helical insertion (2); 0.000000 0.85682 D 0.000000 D 0.99799 0.9914 H 0.98965 4.385 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.97110 0.997;0.994;0.983;1.0 D 0.96812 0.9597 10 0.87932 D 0 . 19.4606 0.94915 0.0:0.0:1.0:0.0 . 201;202;186;844 P63092;A6NI00;P63092-3;Q5JWF2 GNAS2_HUMAN;.;.;GNAS1_HUMAN H 844;830;187;201;202;186;187 ENSP00000360141:R844H;ENSP00000360143:R830H;ENSP00000360136:R187H;ENSP00000360126:R201H;ENSP00000346328:R202H;ENSP00000265620:R186H;ENSP00000304472:R187H ENSP00000265620:R186H R + 2 0 GNAS 56917816 1.000000 0.71417 0.963000 0.40424 0.936000 0.57629 9.291000 0.96070 2.596000 0.87737 0.563000 0.77884 CGT TCGA-US-A77E-01A-11D-A32N-08 GNAS-015 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000080431.2 1 0 1 113 255 0 51 1 1 1287 1966 0 51 2 1 1 229 556 0 408 2 1 1.000000 111 252 0 50 2 0 0 0 0 0 0 -9.037880 1 1 121412 10 32 1 1 2 3 2.336157 1 0.390000 2.070000 0.487868 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 U2AF1 7307 broad.mit.edu 37 21 44524456 44524456 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr21:44524456G>A ENST00000291552.4 - 2 193 c.101C>T c.(100-102)tCt>tTt p.S34F U2AF1_ENST00000459639.1_5'UTR|U2AF1_ENST00000398137.1_5'UTR|U2AF1_ENST00000486519.1_5'UTR|U2AF1_ENST00000380276.2_Missense_Mutation_p.S34F NM_006758.2 NP_006749.1 Q01081 U2AF1_HUMAN U2 small nuclear RNA auxiliary factor 1 p.S34F(45)|p.S34Y(12) 126 GTGCAACCGAGAGCACCTGTC 0.358000 Mis CLL, MDS Dom yes 21 21q22.3 7307 U2 small nuclear RNA auxiliary factor 1 L 57 Substitution - Missense(57) SO:0001583 missense ENST00000291552.4 1 1 hg19 CCDS13694.1 . . . . . . . . . . G 29.7 5.025187 0.93518 2.27E-4 0.0 ENSG00000160201 ENST00000380276;ENST00000291552 T;T 0.46063 0.88;0.88 5.47 5.47 0.80525 Zinc finger, CCCH-type (3); 0.000000 0.85682 D 0.000000 T 0.77239 0.4101 H 0.96430 3.82 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.97110 1.0;0.997;0.997 D 0.84864 0.0821 10 0.87932 D 0 -15.7954 19.3169 0.94218 0.0:0.0:1.0:0.0 . 34;34;34 Q69YM7;Q01081;Q701P4 .;U2AF1_HUMAN;. F 34 ENSP00000369629:S34F;ENSP00000291552:S34F ENSP00000291552:S34F S - 2 0 U2AF1 43397525 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 8.864000 0.92294 2.560000 0.86352 0.563000 0.77884 TCT TCGA-US-A77E-01A-11D-A32N-08 U2AF1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000195541.1 1 0 1 32 166 0 43 1 1 85 202 0 43 2 1 1 102 444 0 283 2 1 1.000000 31 164 0 43 2 0 0 0 0 0 0 -3.186309 1 1 121412 5 36 1 1 2 3 1.980002 0 0.390000 2.070000 0.391187 0.830000 5.900000e-01 1.000000 1.000000 0.832257 0.830000 0 0.700000 0.970000 COL6A2 1292 broad.mit.edu 37 21 47552344 47552344 + Missense_Mutation SNP G G A rs140020002 TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr21:47552344G>A ENST00000300527.4 + 28 3042 c.2938G>A c.(2938-2940)Gtg>Atg p.V980M NM_001849.3 NP_001840.3 P12110 CO6A2_HUMAN collagen, type VI, alpha 2 43 Breast(49;0.245) GGGCAGCGACGTGGACATGGA 0.662000 0 SO:0001583 missense ENST00000300527.4 1 1 hg19 CCDS13728.1 . . . . . . . . . . G 11.70 1.717812 0.30413 4.54E-4 0.0 ENSG00000142173 ENST00000300527 T 0.80393 -1.37 4.4 4.4 0.53042 von Willebrand factor, type A (3); 0.388276 0.26069 N 0.026522 D 0.86887 0.6041 M 0.68317 2.08 0.80722 D 1 D 0.89917 1.0 D 0.76575 0.988 D 0.87150 0.2208 10 0.56958 D 0.05 -16.4704 10.6536 0.45663 0.0893:0.0:0.9107:0.0 . 980 P12110 CO6A2_HUMAN M 980 ENSP00000300527:V980M ENSP00000300527:V980M V + 1 0 COL6A2 46376772 1.000000 0.71417 0.994000 0.49952 0.290000 0.27261 5.117000 0.64667 2.001000 0.58596 0.297000 0.19635 GTG TCGA-US-A77E-01A-11D-A32N-08 COL6A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000206971.1 1 0 1 37 120 0 48 0 1 1 3128 0 48 2 0 0 0 0 0 2 1 1.000000 37 118 0 47 2 0 0 0 0 0 0 -20.000000 1 1 121176 9 40 1 1 2 3 1.980002 0 0.390000 2.070000 0.391187 0.990000 8.900000e-01 1.000000 1.000000 0.992813 0.990000 1 0.990000 1.000000 MCM3AP 8888 broad.mit.edu 37 21 47664991 47664991 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr21:47664991G>A ENST00000397708.1 - 24 5022 c.4768C>T c.(4768-4770)Cat>Tat p.H1590Y MCM3AP-AS1_ENST00000444998.1_RNA|MCM3AP-AS1_ENST00000432735.1_RNA|MCM3AP-AS1_ENST00000591223.1_RNA|MCM3AP-AS1_ENST00000455567.1_RNA|MCM3AP-AS1_ENST00000421927.1_RNA|MCM3AP_ENST00000291688.1_Missense_Mutation_p.H1590Y|MCM3AP-AS1_ENST00000588753.1_RNA|AP001469.7_ENST00000444966.1_RNA|MCM3AP_ENST00000467026.1_5'UTR|MCM3AP-AS1_ENST00000414659.1_RNA|MCM3AP-AS1_ENST00000590829.1_RNA O60318 GANP_HUMAN minichromosome maintenance complex component 3 associated protein 72 Breast(49;0.112) CTTCTGTCATGGAAAAAGCGG 0.552000 0 SO:0001583 missense ENST00000397708.1 1 1 hg19 CCDS13734.1 . . . . . . . . . . G 8.432 0.848790 0.17034 . . ENSG00000160294 ENST00000397708;ENST00000291688;ENST00000539647 T;T 0.03272 3.99;3.99 5.45 4.37 0.52481 . 0.551176 0.21218 N 0.078193 T 0.04182 0.0116 L 0.31294 0.92 0.31865 N 0.620481 B;B 0.06786 0.001;0.001 B;B 0.10450 0.001;0.005 T 0.06789 -1.0807 10 0.39692 T 0.17 -10.1882 15.096 0.72235 0.0801:0.0:0.9199:0.0 . 1590;85 O60318;B3KT88 MCM3A_HUMAN;. Y 1590;1590;85 ENSP00000380820:H1590Y;ENSP00000291688:H1590Y ENSP00000291688:H1590Y H - 1 0 MCM3AP 46489419 0.996000 0.38824 0.984000 0.44739 0.846000 0.48090 2.460000 0.45031 2.545000 0.85829 0.655000 0.94253 CAT TCGA-US-A77E-01A-11D-A32N-08 MCM3AP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207254.1 1 0 1 53 262 0 52 1 9.999926e-01 28 61 0 52 2 0 0 0 0 0 2 1 1.000000 53 258 0 50 2 0 0 0 0 0 0 -3.055940 1 1 0 0 1 1 2 3 1.980002 0 0.390000 2.070000 0.391187 0.860000 6.600000e-01 1.000000 1.000000 0.864055 0.860000 1 0.750000 0.980000 ST6GAL2 84620 broad.mit.edu 37 2 107450522 107450522 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr2:107450522G>A ENST00000409382.3 - 3 1634 c.1024C>T c.(1024-1026)Cgc>Tgc p.R342C ST6GAL2_ENST00000409087.3_Missense_Mutation_p.R342C|AC016994.2_ENST00000425419.1_RNA|ST6GAL2_ENST00000361686.4_Missense_Mutation_p.R342C NM_001142351.1 NP_001135823.1 Q96JF0 SIAT2_HUMAN ST6 beta-galactosamide alpha-2,6-sialyltranferase 2 p.R342C(1) 65 TTAATGATGCGTATGGTGGTT 0.393000 1 Substitution - Missense(1) SO:0001583 missense ENST00000409382.3 1 1 hg19 CCDS2073.1 . . . . . . . . . . G 25.1 4.606524 0.87157 . . ENSG00000144057 ENST00000361686;ENST00000409382;ENST00000409087 T;T;T 0.78924 -1.22;-1.22;-1.22 6.03 6.03 0.97812 Glycoside hydrolase/deacetylase, beta/alpha-barrel (1); 0.000000 0.85682 D 0.000000 D 0.92740 0.7692 H 0.96604 3.85 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 D 0.94296 0.7533 10 0.87932 D 0 -37.1524 19.545 0.95291 0.0:0.0:1.0:0.0 . 342;342 Q96JF0-2;Q96JF0 .;SIAT2_HUMAN C 342 ENSP00000355273:R342C;ENSP00000386942:R342C;ENSP00000387332:R342C ENSP00000355273:R342C R - 1 0 ST6GAL2 106816954 1.000000 0.71417 0.990000 0.47175 0.813000 0.45954 9.869000 0.99810 2.861000 0.98227 0.655000 0.94253 CGC TCGA-US-A77E-01A-11D-A32N-08 ST6GAL2-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000330065.1 1 0 1 67 327 0 64 0 0 0 1 0 64 2 0 0 0 0 0 2 1 1.000000 66 319 0 63 2 0 0 0 0 0 0 -20.000000 1 1 121412 2 40 1 1 2 3 1.974951 0 0.390000 2.070000 0.391187 0.870000 6.900000e-01 1.000000 1.000000 0.873282 0.870000 1 0.770000 0.980000 POLR1B 84172 broad.mit.edu 37 2 113322044 113322044 + Missense_Mutation SNP C C T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr2:113322044C>T ENST00000263331.5 + 10 2294 c.1714C>T c.(1714-1716)Cca>Tca p.P572S POLR1B_ENST00000537335.1_Missense_Mutation_p.P361S|POLR1B_ENST00000541869.1_Missense_Mutation_p.P610S|POLR1B_ENST00000409894.3_Intron|POLR1B_ENST00000417433.2_Missense_Mutation_p.P516S NM_019014.4 NP_061887.2 Q9H9Y6 RPA2_HUMAN polymerase (RNA) I polypeptide B, 128kDa 42 GGATCTTGCTCCAGGCATCGC 0.498000 Ovarian(16;256 576 9537 23969 41147) 0 SO:0001583 missense ENST00000263331.5 1 1 hg19 CCDS2097.1 . . . . . . . . . . C 8.254 0.809758 0.16537 . . ENSG00000125630 ENST00000263331;ENST00000541869;ENST00000537335;ENST00000417433;ENST00000458012 T;T;T;T;T 0.75477 -0.94;-0.94;-0.94;-0.94;-0.51 5.83 3.97 0.46021 RNA polymerase I, Rpa2 specific (1); 0.150076 0.64402 D 0.000009 T 0.68274 0.2983 L 0.43152 1.355 0.58432 D 0.999992 B;B;B 0.25105 0.118;0.0;0.094 B;B;B 0.33254 0.108;0.003;0.16 T 0.59306 -0.7479 10 0.12766 T 0.61 -13.5536 15.3557 0.74425 0.0:0.7349:0.265:0.0 . 610;516;572 F5GZX4;Q9H9Y6-2;Q9H9Y6 .;.;RPA2_HUMAN S 572;610;361;516;36 ENSP00000263331:P572S;ENSP00000444136:P610S;ENSP00000437914:P361S;ENSP00000405358:P516S;ENSP00000394408:P36S ENSP00000263331:P572S P + 1 0 POLR1B 113038515 1.000000 0.71417 0.534000 0.28014 0.274000 0.26718 3.052000 0.49893 0.738000 0.32606 0.650000 0.86243 CCA TCGA-US-A77E-01A-11D-A32N-08 POLR1B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254083.1 1 0 1 92 458 0 107 1 8.025777e-01 4 13 0 107 2 0 0 0 0 0 2 1 1.000000 91 452 0 104 2 0 0 0 0 0 0 -3.087977 1 1 0 0 1 1 2 3 1.974951 0 0.390000 2.070000 0.391187 0.850000 7.000000e-01 1.000000 1.000000 0.861290 0.850000 1 0.770000 0.940000 ZEB2 9839 broad.mit.edu 37 2 145162490 145162490 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr2:145162490G>A ENST00000558170.2 - 5 1689 c.505C>T c.(505-507)Cgc>Tgc p.R169C ZEB2_ENST00000303660.4_Missense_Mutation_p.R169C|ZEB2_ENST00000409487.3_Missense_Mutation_p.R169C|ZEB2_ENST00000539609.3_Missense_Mutation_p.R145C NM_014795.3 NP_055610.1 O60315 ZEB2_HUMAN zinc finger E-box binding homeobox 2 107 GTGTCACTGCGCTGAAGGTAC 0.493000 Melanoma(33;1235 1264 5755 16332) 0 SO:0001583 missense ENST00000558170.2 1 1 hg19 CCDS2186.1 . . . . . . . . . . G 17.85 3.489988 0.64074 . . ENSG00000169554 ENST00000392860;ENST00000539609;ENST00000303660;ENST00000409487;ENST00000427902;ENST00000392861 T;T;T;T;T 0.77358 -1.09;-1.09;-1.09;-1.09;-1.09 5.62 5.62 0.85841 . 0.000000 0.85682 D 0.000000 D 0.86560 0.5962 L 0.54323 1.7 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.77004 0.989;0.948;0.948;0.948 D 0.86852 0.2024 10 0.87932 D 0 -8.3326 20.0114 0.97452 0.0:0.0:1.0:0.0 . 145;34;168;169 F5H814;Q53TD9;A0JP08;O60315 .;.;.;ZEB2_HUMAN C 164;145;169;169;169;169 ENSP00000443792:R145C;ENSP00000302501:R169C;ENSP00000386854:R169C;ENSP00000395496:R169C;ENSP00000376601:R169C ENSP00000302501:R169C R - 1 0 ZEB2 144878960 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.820000 0.86633 2.795000 0.96236 0.655000 0.94253 CGC TCGA-US-A77E-01A-11D-A32N-08 ZEB2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254778.5 1 0 1 31 154 0 44 0 6.696461e-01 0 13 0 44 2 0 0 0 0 0 2 1 1.000000 31 152 0 44 2 0 0 0 0 0 0 -20.000000 1 1 121412 1 26 1 1 2 3 1.974951 0 0.390000 2.070000 0.391187 0.860000 6.000000e-01 1.000000 1.000000 0.856880 0.860000 1 0.720000 1.000000 TTN 7273 broad.mit.edu 37 2 179466769 179466769 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr2:179466769G>A ENST00000591111.1 - 234 50530 c.50306C>T c.(50305-50307)tCa>tTa p.S16769L TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.S15842L|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.S9345L|TTN_ENST00000589042.1_Missense_Mutation_p.S18410L|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.S9537L|TTN_ENST00000359218.5_Missense_Mutation_p.S9470L|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA Q8WZ42 TITIN_HUMAN titin 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) TTCCCAAGATGATTTTGGTGT 0.403000 0 SO:0001583 missense ENST00000591111.1 1 1 hg19 . . . . . . . . . . G 14.36 2.512432 0.44660 . . ENSG00000155657 ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127 T;T;T;T 0.64618 -0.11;-0.11;-0.11;-0.11 6.07 6.07 0.98685 Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1); . . . . T 0.50803 0.1637 N 0.11789 0.175 0.34748 D 0.731475 B;B;B;B 0.28128 0.101;0.101;0.201;0.101 B;B;B;B 0.28385 0.089;0.089;0.089;0.089 T 0.59778 -0.7390 9 0.87932 D 0 . 20.6593 0.99626 0.0:0.0:1.0:0.0 . 9345;9470;9537;16769 D3DPF9;E7EQE6;E7ET18;Q8WZ42 .;.;.;TITIN_HUMAN L 15842;9345;9537;9470;9345 ENSP00000343764:S15842L;ENSP00000434586:S9345L;ENSP00000340554:S9537L;ENSP00000352154:S9470L ENSP00000340554:S9537L S - 2 0 TTN 179175014 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 7.331000 0.79192 2.885000 0.99019 0.655000 0.94253 TCA TCGA-US-A77E-01A-11D-A32N-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 1 0 1 85 363 0 84 0 0 0 0 84 2 0 0 0 0 0 2 1 1.000000 82 361 0 84 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 1.974951 0 0.390000 2.070000 0.391187 0.970000 7.900000e-01 1.000000 1.000000 0.950199 0.970000 1 0.870000 1.000000 COL5A2 1290 broad.mit.edu 37 2 189929337 189929337 + Silent SNP T T C TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 T C T T Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr2:189929337T>C ENST00000374866.3 - 25 1936 c.1662A>G c.(1660-1662)aaA>aaG p.K554K NM_000393.3 NP_000384.2 P05997 CO5A2_HUMAN collagen, type V, alpha 2 95 OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127) CCTGGCTTCCTTTGGGTCCTG 0.507000 0 SO:0001819 synonymous_variant ENST00000374866.3 1 1 hg19 CCDS33350.1 TCGA-US-A77E-01A-11D-A32N-08 COL5A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000313523.1 1 0 0 46 300 0 63 0 1 0 283 0 63 2 0 0 0 0 0 2 1 1.000000 46 295 0 63 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 1.974951 0 0.390000 2.070000 0.391187 0.680000 5.100000e-01 0.880000 0.680000 0.690797 0.680000 0 0.590000 0.780000 DOCK10 55619 broad.mit.edu 37 2 225651759 225651759 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr2:225651759G>A ENST00000258390.7 - 50 5702 c.5635C>T c.(5635-5637)Cgt>Tgt p.R1879C DOCK10_ENST00000409592.3_Missense_Mutation_p.R1873C NM_014689.2 NP_055504.2 Q96BY6 DOC10_HUMAN dedicator of cytokinesis 10 87 Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14) AATGCCACACGATAGTAGCGA 0.433000 0 SO:0001583 missense ENST00000258390.7 1 1 hg19 CCDS46528.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 22.1|22.1 4.238466|4.238466 0.79800|0.79800 .|. .|. ENSG00000135905|ENSG00000135905 ENST00000409592;ENST00000258390;ENST00000373702|ENST00000535663 T;T|. 0.32988|. 1.43;1.43|. 5.99|5.99 5.09|5.09 0.68999|0.68999 .|. 0.000000|. 0.85682|. D|. 0.000000|. D|D 0.85483|0.85483 0.5707|0.5707 M|M 0.93507|0.93507 3.425|3.425 0.58432|0.58432 D|D 0.999999|0.999999 D;D;D;D|. 0.89917|. 1.0;1.0;1.0;1.0|. D;D;D;D|. 0.97110|. 0.994;1.0;0.991;0.997|. D|D 0.89507|0.89507 0.3768|0.3768 10|5 0.87932|. D|. 0|. .|. 15.2244|15.2244 0.73339|0.73339 0.0:0.0:0.7376:0.2624|0.0:0.0:0.7376:0.2624 .|. 1879;700;1873;541|. Q96BY6;B4DF07;B3FL70;B4DEY4|. DOC10_HUMAN;.;.;.|. C|L 1873;1879;384|26 ENSP00000386694:R1873C;ENSP00000258390:R1879C|. ENSP00000258390:R1879C|. R|S -|- 1|2 0|0 DOCK10|DOCK10 225360003|225360003 1.000000|1.000000 0.71417|0.71417 0.999000|0.999000 0.59377|0.59377 0.996000|0.996000 0.88848|0.88848 4.329000|4.329000 0.59260|0.59260 1.477000|1.477000 0.48234|0.48234 0.655000|0.655000 0.94253|0.94253 CGT|TCG TCGA-US-A77E-01A-11D-A32N-08 DOCK10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000331246.1 1 0 1 69 359 0 83 0 3.826724e-01 0 8 0 83 2 0 0 0 0 0 2 1 1.000000 69 353 0 83 2 0 0 0 0 0 0 -3.328643 1 1 0 0 1 1 2 3 1.974951 0 0.390000 2.070000 0.391187 0.820000 6.500000e-01 1.000000 0.830000 0.831826 0.820000 0 0.730000 0.920000 C2orf54 79919 broad.mit.edu 37 2 241827790 241827790 + Silent SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr2:241827790G>A ENST00000388934.4 - 4 1328 c.1170C>T c.(1168-1170)tcC>tcT p.S390S C2orf54_ENST00000402775.2_Silent_p.S222S|C2orf54_ENST00000307486.8_Silent_p.S241S NM_001085437.1 NP_001078906 Q08AI8 CB054_HUMAN chromosome 2 open reading frame 54 6 all_epithelial(40;3.99e-16)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244) CCTTGAGCCCGGAGCCGATGC 0.721000 0 SO:0001819 synonymous_variant ENST00000388934.4 1 1 hg19 CCDS42839.1 TCGA-US-A77E-01A-11D-A32N-08 C2orf54-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000324353.1 1 0 0 10 44 0 16 0 0 1 0 0 16 2 0 0 0 0 0 2 1 0.997028 10 41 0 15 2 0 0 0 0 0 0 -19.487670 1 1 115602 22 36 1 0 1 1 1.972134 0 0.390000 2.070000 0.388808 0.950000 5.100000e-01 1.000000 1.000000 0.883321 0.950000 1 0.710000 1.000000 ITSN2 50618 broad.mit.edu 37 2 24531532 24531532 + Silent SNP C C T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr2:24531532C>T ENST00000355123.4 - 8 1190 c.747G>A c.(745-747)cgG>cgA p.R249R ITSN2_ENST00000406921.3_Silent_p.R249R|ITSN2_ENST00000361999.3_Silent_p.R249R|ITSN2_ENST00000407704.1_5'Flank NM_006277.2 NP_006268.2 Q9NZM3 ITSN2_HUMAN intersectin 2 61 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) TAAATTTTTGCCGATATTTTA 0.428000 0 SO:0001819 synonymous_variant ENST00000355123.4 0 1 hg19 CCDS1710.2 TCGA-US-A77E-01A-11D-A32N-08 ITSN2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000207620.2 0 0 0 5 422 0 88 0 9.243794e-03 0 10 0 88 2 0 0 0 0 0 2 1 0.937885 5 422 0 87 2 0 0 0 0 0 0 -2.321241 0 1 0 0 1 1 2 3 1.974951 0 0.390000 2.070000 0.391187 0.060000 1.000000e-02 0.140000 0.060000 0.071595 0.060000 0 0.030000 0.100000 POMC 5443 broad.mit.edu 37 2 25384178 25384178 + Silent SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr2:25384178G>A ENST00000405623.1 - 3 1031 c.576C>T c.(574-576)gaC>gaT p.D192D POMC_ENST00000264708.3_Silent_p.D192D|RP11-509E16.1_ENST00000567599.1_lincRNA|POMC_ENST00000395826.2_Silent_p.D192D|POMC_ENST00000380794.1_Silent_p.D192D P01189 COLI_HUMAN proopiomelanocortin 12 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) Loperamide(DB00836) CGGCAGGGCCGTCGGGGCCAT 0.697000 Colon(110;1515 1566 8452 10082 43216) 0 SO:0001819 synonymous_variant ENST00000405623.1 1 1 hg19 CCDS1717.1 TCGA-US-A77E-01A-11D-A32N-08 POMC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000211573.3 1 0 0 19 73 0 22 0 4.542598e-01 0 7 0 22 2 0 0 0 0 0 2 1 0.999993 17 70 0 21 2 0 0 0 0 0 0 -20.000000 1 1 121012 1 26 1 1 2 3 1.974951 0 0.390000 2.070000 0.391187 0.990000 6.800000e-01 1.000000 1.000000 0.949142 0.990000 1 0.850000 1.000000 NRXN1 9378 broad.mit.edu 37 2 50765563 50765563 + Silent SNP C C T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr2:50765563C>T ENST00000406316.2 - 10 3447 c.1971G>A c.(1969-1971)cgG>cgA p.R657R NRXN1_ENST00000406859.3_Silent_p.R657R|NRXN1_ENST00000404971.1_Silent_p.R697R|NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000401669.2_Silent_p.R657R|NRXN1_ENST00000402717.3_Silent_p.R649R|NRXN1_ENST00000405472.3_Silent_p.R649R NM_004801.4 NP_004792.1 Q9ULB1 NRX1A_HUMAN neurexin 1 58 all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192) Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116) CAGCCATTTGCCGGATATCTT 0.502000 0 SO:0001819 synonymous_variant ENST00000406316.2 0 1 hg19 CCDS54360.1 TCGA-US-A77E-01A-11D-A32N-08 NRXN1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000325291.2 0 0 0 7 1303 1 303 0 0 0 1 303 2 0 0 0 0 0 2 0 0.043074 7 1288 1 299 16 0 0 0 0 0 0 -2.349706 0 1 0 0 1 1 2 3 1.974951 0 0.390000 2.070000 0.391187 0.020000 0 0.060000 0.020000 0.030122 0.020000 0 0.010000 0.050000 PVRL3 25945 broad.mit.edu 37 3 110852707 110852707 + Missense_Mutation SNP G G A rs15611 by1000genomes TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr3:110852707G>A ENST00000485303.1 + 6 1570 c.1295G>A c.(1294-1296)cGg>cAg p.R432Q PVRL3_ENST00000493615.1_Intron|PVRL3_ENST00000319792.3_3'UTR NM_001243286.1|NM_015480.2 NP_001230215.1|NP_056295.1 Q9NQS3 PVRL3_HUMAN poliovirus receptor-related 3 19 AGGAGAAGACGGACGTTTCGT 0.413000 0 SO:0001583 missense ENST00000485303.1 1 1 hg19 CCDS2957.1 . . . . . . . . . . G 13.25 2.181044 0.38511 . . ENSG00000177707 ENST00000485303 T 0.15834 2.39 5.87 5.87 0.94306 Cytochrome c1, transmembrane anchor, C-terminal (1); 0.064498 0.64402 D 0.000010 T 0.08714 0.0216 N 0.21097 0.63 0.80722 D 1 P 0.48503 0.911 B 0.28991 0.097 T 0.16660 -1.0395 10 0.33940 T 0.23 . 11.0918 0.48121 0.0834:0.0:0.9166:0.0 . 432 Q9NQS3 PVRL3_HUMAN Q 432 ENSP00000418070:R432Q ENSP00000418070:R432Q R + 2 0 PVRL3 112335397 1.000000 0.71417 1.000000 0.80357 0.976000 0.68499 5.640000 0.67875 2.801000 0.96364 0.454000 0.30748 CGG TCGA-US-A77E-01A-11D-A32N-08 PVRL3-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000354045.1 1 0 1 98 383 0 123 1 9.984107e-01 7 33 0 123 2 0 0 0 0 0 2 1 1.000000 97 379 0 123 2 0 0 0 0 0 0 -3.618345 1 1 121412 2 40 1 1 2 3 1.977426 0 0.390000 2.070000 0.391187 0.990000 8.600000e-01 1.000000 1.000000 0.982550 0.990000 1 0.950000 1.000000 ATP2C1 27032 broad.mit.edu 37 3 130718462 130718462 + Missense_Mutation SNP C C G TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr3:130718462C>G ENST00000510168.1 + 27 3138 c.2588C>G c.(2587-2589)cCg>cGg p.P863R ATP2C1_ENST00000504381.1_Missense_Mutation_p.P808R|ATP2C1_ENST00000428331.2_Missense_Mutation_p.P863R|ATP2C1_ENST00000328560.8_Missense_Mutation_p.P863R|ATP2C1_ENST00000359644.3_Missense_Mutation_p.P863R|ATP2C1_ENST00000507488.2_Missense_Mutation_p.P847R|ATP2C1_ENST00000504948.1_Missense_Mutation_p.P847R|ATP2C1_ENST00000513801.1_Missense_Mutation_p.P847R|ATP2C1_ENST00000505330.1_Missense_Mutation_p.P847R|ATP2C1_ENST00000508532.1_Missense_Mutation_p.P863R|ATP2C1_ENST00000393221.4_Missense_Mutation_p.P897R|ATP2C1_ENST00000422190.2_Missense_Mutation_p.P863R|ATP2C1_ENST00000533801.2_Missense_Mutation_p.P858R P98194 AT2C1_HUMAN ATPase, Ca++ transporting, type 2C, member 1 39 Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236) TACTTTCCTCCGCTTCAGAAG 0.343000 Hailey-Hailey disease Esophageal Squamous(99;456 1443 27647 34099 42636) 0 SO:0001583 missense Familial Cancer Database HHD, Familial Benign Chronic Pemphigus, Benign Familial Pemphigus ENST00000510168.1 1 1 hg19 CCDS46914.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 25.8|25.8 4.678165|4.678165 0.88542|0.88542 .|. .|. ENSG00000017260|ENSG00000017260 ENST00000505330;ENST00000504381;ENST00000507488;ENST00000393221;ENST00000533801;ENST00000510168;ENST00000508532;ENST00000504948;ENST00000513801;ENST00000328560;ENST00000428331;ENST00000359644;ENST00000422190;ENST00000347421|ENST00000504612 D;D;D;D;D;D;D;D;D;D;D;D;D|. 0.89123|. -2.47;-2.47;-2.47;-2.47;-2.47;-2.47;-2.47;-2.47;-2.47;-2.47;-2.47;-2.47;-2.47|. 5.91|5.91 5.91|5.91 0.95273|0.95273 ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type, transmembrane domain (1);|. 0.000000|. 0.85682|. D|. 0.000000|. D|D 0.87107|0.87107 0.6095|0.6095 M|M 0.92833|0.92833 3.35|3.35 0.80722|0.80722 D|D 1|1 D;D;D;D;D;D;D|. 0.89917|. 1.0;1.0;1.0;1.0;1.0;1.0;1.0|. D;D;D;D;D;D;D|. 0.91635|. 0.999;0.999;0.996;0.999;0.996;0.999;0.999|. D|D 0.89107|0.89107 0.3493|0.3493 10|5 0.41790|. T|. 0.15|. .|. 20.2985|20.2985 0.98592|0.98592 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. 897;858;897;863;897;863;863|. G3XAH8;B4DSW3;B4E2Q0;P98194-5;B7Z3X9;P98194-2;P98194|. .;.;.;.;.;.;AT2C1_HUMAN|. R|G 847;808;847;897;858;863;863;847;847;863;863;863;863;862|817 ENSP00000423774:P847R;ENSP00000425320:P808R;ENSP00000421326:P847R;ENSP00000376914:P897R;ENSP00000432956:P858R;ENSP00000427461:P863R;ENSP00000424783:P863R;ENSP00000423330:P847R;ENSP00000422872:P847R;ENSP00000329664:P863R;ENSP00000395809:P863R;ENSP00000352665:P863R;ENSP00000402677:P863R|. ENSP00000329664:P863R|. P|R +|+ 2|1 0|0 ATP2C1|ATP2C1 132201152|132201152 1.000000|1.000000 0.71417|0.71417 0.997000|0.997000 0.53966|0.53966 0.925000|0.925000 0.55904|0.55904 7.812000|7.812000 0.86109|0.86109 2.793000|2.793000 0.96121|0.96121 0.655000|0.655000 0.94253|0.94253 CCG|CGC TCGA-US-A77E-01A-11D-A32N-08 ATP2C1-008 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000356648.2 1 0 1 39 200 0 41 1 1 80 159 0 41 2 0 0 0 0 0 2 1 1.000000 37 198 0 41 2 0 0 0 0 0 0 -2.679540 1 1 0 0 1 1 2 3 1.977426 0 0.390000 2.070000 0.391187 0.830000 6.100000e-01 1.000000 1.000000 0.840070 0.830000 0 0.720000 0.970000 DNAJC13 23317 broad.mit.edu 37 3 132175223 132175223 + Silent SNP C C A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr3:132175223C>A ENST00000260818.6 + 10 1325 c.1077C>A c.(1075-1077)ctC>ctA p.L359L DNAJC13_ENST00000486798.1_3'UTR NM_015268.3 NP_056083.3 O75165 DJC13_HUMAN DnaJ (Hsp40) homolog, subfamily C, member 13 34 GCCTTCACCTCAGGTTCTTAG 0.378000 0 SO:0001819 synonymous_variant ENST00000260818.6 1 1 hg19 CCDS33857.1 TCGA-US-A77E-01A-11D-A32N-08 DNAJC13-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000356807.2 1 0 1 47 211 0 45 1 7.860263e-01 5 10 0 45 2 0 0 0 0 0 2 1 1.000000 47 207 0 45 2 0 0 0 0 0 0 -2.844505 1 1 0 0 1 1 2 3 1.977426 0 0.390000 2.070000 0.391187 0.930000 7.000000e-01 1.000000 1.000000 0.916596 0.930000 1 0.810000 1.000000 FBLN2 2199 broad.mit.edu 37 3 13672892 13672892 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr3:13672892G>A ENST00000295760.7 + 15 3077 c.3008G>A c.(3007-3009)gGg>gAg p.G1003E FBLN2_ENST00000492059.1_Missense_Mutation_p.G1050E|FBLN2_ENST00000404922.3_Missense_Mutation_p.G1050E|FBLN2_ENST00000535798.1_Missense_Mutation_p.G1029E NM_001998.2 NP_001989.2 P98095 FBLN2_HUMAN fibulin 2 24 UCEC - Uterine corpus endometrioid carcinoma (1;0.00416) AACGTGCCAGGGAGCTACCAG 0.637000 0 SO:0001583 missense ENST00000295760.7 0 1 hg19 CCDS46762.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 33|33 5.288281|5.288281 0.95517|0.95517 .|. .|. ENSG00000163520|ENSG00000163520 ENST00000535798;ENST00000404922;ENST00000295760;ENST00000492059|ENST00000295761 D;D;D;D|D 0.90504|0.99557 -2.56;-2.56;-2.68;-2.56|-6.16 5.39|5.39 5.39|5.39 0.77823|0.77823 EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);|. 0.000000|0.000000 0.85682|0.85682 D|D 0.000000|0.000000 D|D 0.99775|0.99775 0.9907|0.9907 H|H 0.95294|0.95294 3.65|3.65 0.80722|0.80722 D|D 1|1 D;D;D|. 0.89917|. 1.0;1.0;1.0|. D;D;D|. 0.97110|. 1.0;1.0;1.0|. D|D 0.97158|0.97158 0.9836|0.9836 10|8 0.87932|0.87932 D|D 0|0 .|. 19.1574|19.1574 0.93517|0.93517 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. 1003;1050;1029|. P98095;P98095-2;F5H1F3|. FBLN2_HUMAN;.;.|. E|R 1029;1050;1003;1050|22 ENSP00000445705:G1029E;ENSP00000384169:G1050E;ENSP00000295760:G1003E;ENSP00000420042:G1050E|ENSP00000295761:G22R ENSP00000295760:G1003E|ENSP00000295761:G22R G|G +|+ 2|1 0|0 FBLN2|FBLN2 13647893|13647893 1.000000|1.000000 0.71417|0.71417 0.996000|0.996000 0.52242|0.52242 0.977000|0.977000 0.68977|0.68977 9.839000|9.839000 0.99476|0.99476 2.525000|2.525000 0.85131|0.85131 0.655000|0.655000 0.94253|0.94253 GGG|GGA TCGA-US-A77E-01A-11D-A32N-08 FBLN2-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000340083.3 1 0 1 26 45 0 11 0 1 1 322 0 11 2 1 1 530 1085 0 1028 2 1 1.000000 26 45 0 10 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 2 2 1.968864 1 0.390000 2.070000 0.390000 0.990000 9.900000e-01 1.000000 1.000000 0.999968 0.990000 1 0.990000 1.000000 CPA3 1359 broad.mit.edu 37 3 148599357 148599357 + Nonsense_Mutation SNP C C T rs141357361 byFrequency TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr3:148599357C>T ENST00000296046.3 + 7 677 c.625C>T c.(625-627)Cga>Tga p.R209* RP11-680B3.2_ENST00000488190.1_RNA NM_001870.2 NP_001861.2 P15088 CBPA3_HUMAN carboxypeptidase A3 (mast cell) p.R209R(1) 35 LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115) ACTCTTGGACCGAATGAATTT 0.343000 1 Substitution - coding silent(1) SO:0001587 stop_gained ENST00000296046.3 0 1 hg19 CCDS3138.1 . . . . . . . . . . C 20.9 4.071142 0.76301 . . ENSG00000163751 ENST00000296046 . . . 5.06 3.09 0.35607 . 0.546116 0.18299 N 0.145492 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.14656 T 0.56 . 10.9886 0.47537 0.5206:0.4794:0.0:0.0 . . . . X 209 . ENSP00000296046:R209X R + 1 2 CPA3 150082047 0.162000 0.22906 0.643000 0.29450 0.200000 0.23975 1.401000 0.34589 1.325000 0.45301 -0.182000 0.12963 CGA TCGA-US-A77E-01A-11D-A32N-08 CPA3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000355974.1 1 0 1 32 222 0 67 0 2.765583e-01 0 8 0 67 2 0 0 0 0 0 2 1 1.000000 31 219 0 67 2 0 0 0 0 0 0 -3.142530 1 1 121408 60 50 1 1 2 3 1.977426 0 0.390000 2.070000 0.391187 0.640000 4.500000e-01 0.880000 0.640000 0.658225 0.640000 0 0.540000 0.760000 ALS2CL 259173 broad.mit.edu 37 3 46729748 46729748 + Missense_Mutation SNP G G A rs143519761 TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr3:46729748G>A ENST00000318962.4 - 3 225 c.142C>T c.(142-144)Cgg>Tgg p.R48W ALS2CL_ENST00000415953.1_Missense_Mutation_p.R48W NM_147129.3 NP_667340.2 Q60I27 AL2CL_HUMAN ALS2 C-terminal like 29 TGCAAGAGCCGCAGGCACTCT 0.612000 0 SO:0001583 missense ENST00000318962.4 1 1 hg19 CCDS2743.1 . . . . . . . . . . G 9.542 1.113617 0.20795 0.0 1.16E-4 ENSG00000178038 ENST00000318962;ENST00000415953 T;T 0.17691 2.26;2.26 4.15 2.19 0.27852 . 0.879668 0.09620 N 0.777724 T 0.11196 0.0273 L 0.29908 0.895 0.19300 N 0.999979 D 0.56968 0.978 B 0.36504 0.226 T 0.20338 -1.0278 10 0.72032 D 0.01 . 8.7355 0.34525 0.0:0.0:0.5869:0.4131 . 48 Q60I27 AL2CL_HUMAN W 48 ENSP00000313670:R48W;ENSP00000413223:R48W ENSP00000313670:R48W R - 1 2 ALS2CL 46704752 0.003000 0.15002 0.255000 0.24374 0.221000 0.24807 0.312000 0.19397 1.098000 0.41479 -0.196000 0.12772 CGG TCGA-US-A77E-01A-11D-A32N-08 ALS2CL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250567.3 1 0 1 32 176 0 50 1 9.912157e-01 22 22 0 50 2 0 0 0 0 0 2 1 1.000000 32 175 0 50 2 0 0 0 0 0 0 -20.000000 1 1 121358 9 38 1 1 2 3 1.977426 0 0.390000 2.070000 0.391187 0.790000 5.600000e-01 1.000000 1.000000 0.797108 0.790000 0 0.660000 0.930000 DNAH1 25981 broad.mit.edu 37 3 52392752 52392752 + Splice_Site SNP C C T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr3:52392752C>T ENST00000420323.2 + 25 4526 c.4265C>T c.(4264-4266)aCg>aTg p.T1422M NM_015512.4 NP_056327 Q9P2D7 DYH1_HUMAN dynein, axonemal, heavy chain 1 62 GCCTACCCCACGGTGAGCCGC 0.672000 0 SO:0001630 splice_region_variant ENST00000420323.2 1 0 hg19 CCDS46842.1 . . . . . . . . . . c 14.44 2.535864 0.45176 . . ENSG00000114841 ENST00000420323 T 0.57752 0.38 5.4 -1.98 0.07480 . 1.606480 0.03543 N 0.224331 T 0.55353 0.1915 M 0.85197 2.74 0.09310 N 1 P 0.38767 0.646 B 0.36989 0.238 T 0.52223 -0.8604 10 0.52906 T 0.07 . 6.2438 0.20805 0.4428:0.3398:0.0:0.2173 . 1422 C9JXH6 . M 1422 ENSP00000401514:T1422M ENSP00000401514:T1422M T + 2 0 DNAH1 52367792 0.000000 0.05858 0.032000 0.17829 0.425000 0.31504 0.412000 0.21131 -0.236000 0.09753 -0.119000 0.15052 ACG TCGA-US-A77E-01A-11D-A32N-08 DNAH1-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000350816.1 1 0 1 21 171 0 55 1 1.040082e-01 3 2 0 55 2 0 0 0 0 0 2 1 0.999998 21 170 0 55 2 0 0 0 0 0 0 -20.000000 1 1 121158 5 34 1 1 2 3 1.977426 0 0.390000 2.070000 0.391187 0.560000 3.600000e-01 0.820000 0.560000 0.577949 0.560000 0 0.450000 0.690000 OR5H1 26341 broad.mit.edu 37 3 97852400 97852400 + Missense_Mutation SNP C C T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr3:97852400C>T ENST00000354565.2 + 1 859 c.859C>T c.(859-861)Cct>Tct p.P287S RP11-343D2.11_ENST00000508964.1_RNA NM_001005338.1 NP_001005338.1 A6NKK0 OR5H1_HUMAN olfactory receptor, family 5, subfamily H, member 1 34 TTTGTTAAATCCTATCATCTA 0.363000 0 SO:0001583 missense ENST00000354565.2 1 1 hg19 CCDS33797.1 . . . . . . . . . . C 9.923 1.212625 0.22289 . . ENSG00000231192 ENST00000354565 T 0.63417 -0.04 3.38 3.38 0.38709 GPCR, rhodopsin-like superfamily (1); 0.000000 0.46758 D 0.000271 T 0.68833 0.3044 M 0.88842 2.985 0.35061 D 0.761587 B 0.33238 0.403 B 0.37239 0.244 T 0.81182 -0.1049 10 0.87932 D 0 . 12.2602 0.54647 0.0:1.0:0.0:0.0 . 287 A6NKK0 OR5H1_HUMAN S 287 ENSP00000346575:P287S ENSP00000346575:P287S P + 1 0 OR5H1 99335090 1.000000 0.71417 0.685000 0.30070 0.005000 0.04900 6.901000 0.75693 1.712000 0.51347 0.195000 0.17529 CCT TCGA-US-A77E-01A-11D-A32N-08 OR5H1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000359100.2 1 0 1 66 302 0 67 0 0 0 0 67 2 0 0 0 0 0 2 1 1.000000 65 301 0 66 2 0 0 0 0 0 0 -3.224316 1 1 0 0 1 1 2 3 1.977426 0 0.390000 2.070000 0.391187 0.910000 7.200000e-01 1.000000 1.000000 0.911651 0.910000 1 0.810000 1.000000 TBC1D9 23158 broad.mit.edu 37 4 141622724 141622724 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr4:141622724G>A ENST00000442267.2 - 2 249 c.175C>T c.(175-177)Cgg>Tgg p.R59W Y_RNA_ENST00000384426.1_RNA NM_015130.2 NP_055945.2 Q6ZT07 TBCD9_HUMAN TBC1 domain family, member 9 (with GRAM domain) 31 all_hematologic(180;0.162) Medulloblastoma(177;0.00498) GGAGCGACCCGGGCGCTGGAG 0.517000 0 SO:0001583 missense ENST00000442267.2 1 1 hg19 CCDS47136.1 . . . . . . . . . . G 21.4 4.148616 0.78001 . . ENSG00000109436 ENST00000442267 T 0.23552 1.9 5.39 4.45 0.53987 . 0.000000 0.85682 D 0.000000 T 0.48822 0.1521 M 0.74258 2.255 0.80722 D 1 D 0.89917 1.0 D 0.87578 0.998 T 0.51403 -0.8710 10 0.87932 D 0 -4.7968 10.5771 0.45233 0.0:0.0:0.4702:0.5298 . 59 Q6ZT07 TBCD9_HUMAN W 59 ENSP00000411197:R59W ENSP00000411197:R59W R - 1 2 TBC1D9 141842174 1.000000 0.71417 0.998000 0.56505 0.930000 0.56654 4.245000 0.58734 1.314000 0.45095 0.655000 0.94253 CGG TCGA-US-A77E-01A-11D-A32N-08 TBC1D9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000364806.1 1 0 1 31 161 0 26 0 3.887059e-01 0 8 0 26 2 0 0 0 0 0 2 1 1.000000 31 157 0 26 2 0 0 0 0 0 0 -2.924440 1 1 120842 1 28 1 1 2 3 1.996179 0 0.390000 2.070000 0.394721 0.830000 5.900000e-01 1.000000 1.000000 0.840335 0.830000 0 0.700000 1.000000 GBA3 57733 broad.mit.edu 37 4 22749669 22749669 + RNA SNP T T G TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr4:22749669T>G ENST00000503442.1 + 0 377 GBA3_ENST00000508166.1_RNA|GBA3_ENST00000511446.2_RNA NM_001128432.2 NP_001121904.1 Q9H227 GBA3_HUMAN glucosidase, beta, acid 3 (gene/pseudogene) 33 GTGGATTGGATCTACGTGGTA 0.383000 0 ENST00000503442.1 0 1 hg19 TCGA-US-A77E-01A-11D-A32N-08 GBA3-003 KNOWN basic polymorphic_pseudogene polymorphic_pseudogene OTTHUMT00000360620.2 0 0 0 12 63 0 24 0 2.042507e-01 0 5 0 24 2 0 0 0 0 0 2 1 0.999331 12 62 0 23 2 0 0 0 0 0 0 -19.983290 1 1 0 0 1 1 2 3 1.996179 0 0.390000 2.070000 0.394721 0.840000 4.700000e-01 1.000000 1.000000 0.825446 0.840000 0 0.640000 1.000000 PCDHA5 56143 broad.mit.edu 37 5 140201497 140201497 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr5:140201497G>A ENST00000529859.1 + 1 137 c.137G>A c.(136-138)cGc>cAc p.R46H PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000378126.3_Missense_Mutation_p.R46H|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Missense_Mutation_p.R46H NM_018908.2 NP_061731.1 Q9Y5H7 PCDA5_HUMAN protocadherin alpha 5 p.R46H(2) 60 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) TTCGTTGGCCGCATCGCGCAG 0.657000 2 Substitution - Missense(2) SO:0001583 missense ENST00000529859.1 0 1 hg19 CCDS54917.1 . . . . . . . . . . G 17.07 3.294143 0.60086 . . ENSG00000204965 ENST00000529619;ENST00000529859;ENST00000378126 T;T;T 0.27256 1.68;1.68;1.68 3.87 2.98 0.34508 Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1); . . . . T 0.25827 0.0629 M 0.63428 1.95 0.25612 N 0.986495 P;P;P 0.46987 0.848;0.888;0.609 B;B;B 0.38803 0.282;0.253;0.185 T 0.11275 -1.0594 9 0.72032 D 0.01 . 10.3243 0.43783 0.1721:0.0:0.8279:0.0 . 46;46;46 Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2 PCDA5_HUMAN;.;. H 46 ENSP00000433416:R46H;ENSP00000436557:R46H;ENSP00000367366:R46H ENSP00000367366:R46H R + 2 0 PCDHA5 140181681 0.004000 0.15560 1.000000 0.80357 0.960000 0.62799 1.772000 0.38552 0.719000 0.32188 0.585000 0.79938 CGC TCGA-US-A77E-01A-11D-A32N-08 PCDHA5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000372883.2 0 0 0 7 479 0 115 0 0 0 0 115 2 0 0 0 0 0 2 1 0.980177 7 475 0 115 2 0 0 0 0 0 0 -2.229413 0 1 0 0 1 1 2 3 1.991597 0 0.390000 2.070000 0.392370 0.070000 2.000000e-02 0.160000 0.080000 0.093106 0.070000 0 0.040000 0.120000 FOXI1 2299 broad.mit.edu 37 5 169533243 169533243 + Silent SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr5:169533243G>A ENST00000306268.6 + 1 343 c.282G>A c.(280-282)ccG>ccA p.P94P FOXI1_ENST00000449804.2_Silent_p.P94P Q12951 FOXI1_HUMAN forkhead box I1 35 Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04) Medulloblastoma(196;0.0109)|all_neural(177;0.0298) Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525) TGCAGAGGCCGCTGCTGCCCA 0.697000 Pendred syndrome 0 SO:0001819 synonymous_variant Familial Cancer Database Goiter-Deafness syndrome ENST00000306268.6 1 1 hg19 CCDS4372.1 TCGA-US-A77E-01A-11D-A32N-08 FOXI1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252827.2 1 0 0 9 37 0 17 0 0 0 1 0 17 2 0 0 0 0 0 2 1 0.995341 9 36 0 17 2 0 0 0 0 0 0 -18.510660 1 1 0 0 1 1 2 3 1.991597 0 0.390000 2.070000 0.392370 0.990000 5.300000e-01 1.000000 1.000000 0.904822 0.990000 1 0.740000 1.000000 STC2 8614 broad.mit.edu 37 5 172744926 172744926 + Missense_Mutation SNP C C T rs145310530 TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr5:172744926C>T ENST00000265087.4 - 4 2142 c.833G>A c.(832-834)gGc>gAc p.G278D STC2_ENST00000520593.1_5'Flank NM_003714.2 NP_003705.1 O76061 STC2_HUMAN stanniocalcin 2 25 Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004) Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|Ovarian(839;0.223) Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183) AGCCCCAAGGCCCCCGACTCT 0.612000 0 SO:0001583 missense ENST00000265087.4 1 1 hg19 CCDS4388.1 . . . . . . . . . . C 12.57 1.978009 0.34942 . . ENSG00000113739 ENST00000265087 . . . 5.31 1.1 0.20463 . 0.502817 0.22661 N 0.057194 T 0.22205 0.0535 N 0.24115 0.695 0.09310 N 0.999996 B 0.10296 0.003 B 0.09377 0.004 T 0.10064 -1.0646 9 0.38643 T 0.18 -5.3352 2.7467 0.05268 0.2356:0.2927:0.3461:0.1256 . 278 O76061 STC2_HUMAN D 278 . ENSP00000265087:G278D G - 2 0 STC2 172677532 0.000000 0.05858 0.000000 0.03702 0.913000 0.54294 -0.238000 0.08977 0.181000 0.19994 0.650000 0.86243 GGC TCGA-US-A77E-01A-11D-A32N-08 STC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252965.1 0 0 1 125 498 0 151 0 9.946677e-01 0 33 0 151 2 0 0 0 0 0 2 1 1.000000 123 490 0 148 2 0 0 0 0 0 0 -20.000000 1 1 121412 1 33 1 1 2 3 1.991597 0 0.390000 2.070000 0.392370 0.990000 8.700000e-01 1.000000 1.000000 0.982136 0.990000 1 0.940000 1.000000 C7 730 broad.mit.edu 37 5 40981607 40981607 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr5:40981607G>A ENST00000313164.9 + 18 2823 c.2464G>A c.(2464-2466)Gct>Act p.A822T NM_000587.2 NP_000578.2 P10643 CO7_HUMAN complement component 7 Ovarian(839;0.0112) TGAGGCGGGCGCTCTGAGATG 0.567000 0 SO:0001583 missense ENST00000313164.9 1 1 hg19 CCDS47201.1 . . . . . . . . . . G 4.186 0.033170 0.08101 . . ENSG00000112936 ENST00000313164 T 0.65364 -0.15 5.83 -0.108 0.13588 Factor I / membrane attack complex (1); 1.811360 0.02513 N 0.091774 T 0.48857 0.1523 L 0.37850 1.14 0.09310 N 1 B 0.06786 0.001 B 0.06405 0.002 T 0.10200 -1.0640 10 0.27082 T 0.32 0.8429 2.9604 0.05890 0.462:0.1118:0.3117:0.1144 . 822 P10643 CO7_HUMAN T 822 ENSP00000322061:A822T ENSP00000322061:A822T A + 1 0 C7 41017364 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 -0.255000 0.08769 -0.082000 0.12640 -0.992000 0.02543 GCT TCGA-US-A77E-01A-11D-A32N-08 C7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000317680.1 1 0 1 24 101 0 17 0 1 1 171 0 17 2 0 0 0 0 0 2 1 1.000000 24 99 0 16 2 0 0 0 0 0 0 -20.000000 1 1 121058 5 34 1 1 2 3 1.991597 0 0.390000 2.070000 0.392370 0.990000 6.700000e-01 1.000000 1.000000 0.929971 0.990000 1 0.810000 1.000000 VCAN 1462 broad.mit.edu 37 5 82876174 82876174 + Missense_Mutation SNP C C T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr5:82876174C>T ENST00000265077.3 + 15 10677 c.10112C>T c.(10111-10113)tCa>tTa p.S3371L VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000342785.4_Missense_Mutation_p.S1617L|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000343200.5_Missense_Mutation_p.S2384L|VCAN_ENST00000512590.2_Missense_Mutation_p.S1569L|VCAN_ENST00000502527.2_Missense_Mutation_p.S630L NM_004385.4 NP_004376.2 P13611 CSPG2_HUMAN versican 190 Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142) Hyaluronan(DB08818) AAAAATTCCTCATCAGCAAAG 0.393000 0 SO:0001583 missense ENST00000265077.3 1 1 hg19 CCDS4060.1 . . . . . . . . . . C 15.86 2.957027 0.53293 . . ENSG00000038427 ENST00000265077;ENST00000343200;ENST00000342785;ENST00000512590;ENST00000502527 D;D;D;D;D 0.87029 -2.19;-2.2;-1.94;-1.94;-1.85 5.8 5.8 0.92144 . 0.000000 0.44483 D 0.000456 D 0.89750 0.6805 N 0.24115 0.695 0.38290 D 0.942687 D;B;P;D 0.89917 0.999;0.386;0.502;1.0 D;B;B;D 0.74023 0.964;0.23;0.403;0.982 D 0.91528 0.5240 10 0.72032 D 0.01 . 20.0706 0.97721 0.0:1.0:0.0:0.0 . 1617;630;2384;3371 P13611-3;P13611-4;P13611-2;P13611 .;.;.;CSPG2_HUMAN L 3371;2384;1617;1569;630 ENSP00000265077:S3371L;ENSP00000340062:S2384L;ENSP00000342768:S1617L;ENSP00000425959:S1569L;ENSP00000421362:S630L ENSP00000265077:S3371L S + 2 0 VCAN 82911930 1.000000 0.71417 1.000000 0.80357 0.954000 0.61252 4.512000 0.60469 2.744000 0.94065 0.655000 0.94253 TCA TCGA-US-A77E-01A-11D-A32N-08 VCAN-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000254092.3 1 0 1 59 186 0 56 0 1 0 550 0 56 2 0 0 0 0 0 2 1 1.000000 59 184 0 56 2 0 0 0 0 0 0 -4.083793 1 1 0 0 1 1 2 3 1.991597 0 0.390000 2.070000 0.392370 0.990000 9.700000e-01 1.000000 1.000000 0.998263 0.990000 1 0.990000 1.000000 SERINC1 57515 broad.mit.edu 37 6 122773086 122773086 + Missense_Mutation SNP T T C TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr6:122773086T>C ENST00000339697.4 - 6 790 c.706A>G c.(706-708)Aac>Gac p.N236D NM_020755.2 NP_065806.1 Q9NRX5 SERC1_HUMAN serine incorporator 1 13 AGGAGCATGTTGACACTGATG 0.393000 0 SO:0001583 missense ENST00000339697.4 1 1 hg19 CCDS5125.1 . . . . . . . . . . T 32 5.185893 0.94885 . . ENSG00000111897 ENST00000339697;ENST00000368454 T;T 0.20069 2.1;2.1 5.71 5.71 0.89125 . 0.000000 0.85682 D 0.000000 T 0.53899 0.1825 H 0.95917 3.74 0.80722 D 1 D 0.58268 0.982 D 0.72075 0.976 T 0.70699 -0.4800 10 0.87932 D 0 -14.7994 15.9701 0.80008 0.0:0.0:0.0:1.0 . 236 Q9NRX5 SERC1_HUMAN D 236 ENSP00000342962:N236D;ENSP00000357439:N236D ENSP00000342962:N236D N - 1 0 SERINC1 122814785 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 8.040000 0.89188 2.166000 0.68216 0.528000 0.53228 AAC TCGA-US-A77E-01A-11D-A32N-08 SERINC1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000042031.2 1 0 1 53 198 0 49 1 1 82 183 0 49 2 0 0 0 0 0 2 1 1.000000 53 194 0 49 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 1.979114 0 0.390000 2.070000 0.391187 0.990000 8.300000e-01 1.000000 1.000000 0.981579 0.990000 1 0.950000 1.000000 TRDN 10345 broad.mit.edu 37 6 123539785 123539785 + Silent SNP A A G TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr6:123539785A>G ENST00000398178.3 - 41 2172 c.2151T>C c.(2149-2151)ggT>ggC p.G717G TRDN_ENST00000334268.4_Silent_p.G709G NM_006073.3 NP_006064.2 Q13061 TRDN_HUMAN triadin 41 AATTTGCTTGACCAGAGCTCT 0.438000 0 SO:0001819 synonymous_variant ENST00000398178.3 0 1 hg19 CCDS55053.1 TCGA-US-A77E-01A-11D-A32N-08 TRDN-201 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding 1 0 1 18 97 0 15 0 0 0 0 15 2 0 0 0 0 0 2 1 0.999989 18 96 0 15 2 0 0 0 0 0 0 -11.907530 1 1 0 0 1 1 2 3 1.979114 0 0.390000 2.070000 0.391187 0.800000 5.000000e-01 1.000000 1.000000 0.807459 0.800000 0 0.640000 0.990000 PHACTR1 221692 broad.mit.edu 37 6 13206098 13206098 + Missense_Mutation SNP C C T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr6:13206098C>T ENST00000379350.1 + 7 845 c.716C>T c.(715-717)cCg>cTg p.P239L PHACTR1_ENST00000379345.2_Intron|PHACTR1_ENST00000332995.7_Missense_Mutation_p.P239L|PHACTR1_ENST00000457702.2_Missense_Mutation_p.P94L Q9C0D0 PHAR1_HUMAN phosphatase and actin regulator 1 26 Breast(50;0.0427)|Ovarian(93;0.12) all_hematologic(90;0.122)|Lung SC(78;0.195) Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239) CTGTCGCCTCCGCTACCTCCA 0.587000 0 SO:0001583 missense ENST00000379350.1 0 1 hg19 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 25.1|25.1 4.605951|4.605951 0.87157|0.87157 .|. .|. ENSG00000112137|ENSG00000112137 ENST00000379350;ENST00000332995;ENST00000432934;ENST00000457702|ENST00000415087 T;T;T|. 0.44482|. 0.92;1.13;1.25|. 5.15|5.15 5.15|5.15 0.70609|0.70609 .|. 0.000000|. 0.85682|. D|. 0.000000|. T|T 0.44871|0.44871 0.1314|0.1314 L|L 0.27053|0.27053 0.805|0.805 0.80722|0.80722 D|D 1|1 D;D;D|. 0.89917|. 1.0;1.0;1.0|. D;D;D|. 0.87578|. 0.992;0.997;0.998|. T|T 0.34502|0.34502 -0.9826|-0.9826 10|5 0.72032|. D|. 0.01|. -16.0863|-16.0863 17.7928|17.7928 0.88561|0.88561 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. 308;239;239|. E7ESR5;Q9C0D0;Q9C0D0-2|. .;PHAR1_HUMAN;.|. L|C 239;239;308;94|74 ENSP00000368655:P239L;ENSP00000329880:P239L;ENSP00000397669:P94L|. ENSP00000329880:P239L|. P|R +|+ 2|1 0|0 PHACTR1|PHACTR1 13314077|13314077 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.995000|0.995000 0.86356|0.86356 7.012000|7.012000 0.76366|0.76366 2.665000|2.665000 0.90641|0.90641 0.561000|0.561000 0.74099|0.74099 CCG|CGC TCGA-US-A77E-01A-11D-A32N-08 PHACTR1-001 KNOWN basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000039876.1 0 0 0 5 356 0 96 0 0 0 0 96 2 0 0 0 0 0 2 1 0.935646 5 351 0 95 2 0 0 0 0 0 0 -2.029818 0 1 120926 1 30 1 1 2 3 1.996224 0 0.390000 2.070000 0.394721 0.070000 2.000000e-02 1.000000 0.070000 0.111398 0.070000 0 0.040000 0.120000 NUP153 9972 broad.mit.edu 37 6 17706578 17706578 + Missense_Mutation SNP C C T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr6:17706578C>T ENST00000262077.2 - 1 40 c.41G>A c.(40-42)gGc>gAc p.G14D NUP153_ENST00000537253.1_Missense_Mutation_p.G14D|RP11-500C11.3_ENST00000606771.1_RNA NM_005124.2 NP_005115.2 P49790 NU153_HUMAN nucleoporin 153kDa 53 Breast(50;0.0259)|Ovarian(93;0.0584) all_hematologic(90;0.125) all cancers(50;0.0981)|Epithelial(50;0.112) CCGGATCTTGCCGCCACCGCC 0.726000 0 SO:0001583 missense ENST00000262077.2 0 1 hg19 CCDS4541.1 . . . . . . . . . . C 20.5 4.008788 0.75046 . . ENSG00000124789 ENST00000262077;ENST00000430136;ENST00000537253 T;T 0.35048 1.33;1.43 3.12 3.12 0.35913 . 0.000000 0.35525 N 0.003147 T 0.40015 0.1100 L 0.46157 1.445 0.42084 D 0.991265 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.91635 0.999;0.998;0.998 T 0.33548 -0.9864 10 0.87932 D 0 -8.5848 10.0092 0.41975 0.0:1.0:0.0:0.0 . 14;36;14 F6QR24;Q4LE47;P49790 .;.;NU153_HUMAN D 14;36;14 ENSP00000262077:G14D;ENSP00000444029:G14D ENSP00000262077:G14D G - 2 0 NUP153 17814557 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 3.110000 0.50352 2.085000 0.62840 0.591000 0.81541 GGC TCGA-US-A77E-01A-11D-A32N-08 NUP153-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000039953.1 0 0 0 6 258 0 52 0 4.173195e-02 0 12 0 52 2 0 0 0 0 0 2 1 0.963787 6 254 0 51 2 0 0 0 0 0 0 -3.085488 1 1 0 0 1 1 2 3 1.996224 0 0.390000 2.070000 0.394721 0.120000 4.000000e-02 1.000000 0.120000 0.160111 0.120000 0 0.080000 0.190000 TNXB 7148 broad.mit.edu 37 6 32046862 32046862 + Silent SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr6:32046862G>A ENST00000375244.3 - 11 4524 c.4323C>T c.(4321-4323)taC>taT p.Y1441Y TNXB_ENST00000375247.2_Silent_p.Y1441Y|RNA5SP206_ENST00000516703.1_RNA P22105 TENX_HUMAN tenascin XB 8 CGTGGAGGCCGTACAGGTGCA 0.697000 0 SO:0001819 synonymous_variant ENST00000375244.3 0 1 hg19 TCGA-US-A77E-01A-11D-A32N-08 TNXB-001 PUTATIVE not_organism_supported|basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000268927.2 0 0 0 5 377 0 105 0 2.725191e-03 0 5 0 105 2 0 0 0 0 0 2 1 0.936193 5 373 0 102 2 0 0 0 0 0 0 -2.602696 1 1 120864 5 39 1 1 2 3 1.996224 0 0.390000 2.070000 0.394721 0.070000 2.000000e-02 1.000000 0.070000 0.106896 0.070000 0 0.040000 0.120000 DST 667 broad.mit.edu 37 6 56492887 56492887 + Nonsense_Mutation SNP C C T rs149154059 TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr6:56492887C>T ENST00000361203.3 - 29 3922 c.3915G>A c.(3913-3915)tgG>tgA p.W1305* DST_ENST00000370788.2_Nonsense_Mutation_p.W1305*|DST_ENST00000421834.2_Nonsense_Mutation_p.W1305*|DST_ENST00000370754.5_Nonsense_Mutation_p.W1483*|DST_ENST00000446842.2_Nonsense_Mutation_p.W979*|DST_ENST00000370765.6_Nonsense_Mutation_p.W979*|DST_ENST00000312431.6_Nonsense_Mutation_p.W1305*|DST_ENST00000518935.1_Nonsense_Mutation_p.W979*|DST_ENST00000244364.6_Nonsense_Mutation_p.W979*|DST_ENST00000370769.4_Nonsense_Mutation_p.W1305* Q03001 DYST_HUMAN dystonin 105 Lung NSC(77;0.103) LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956) CCTGCTGGATCCAATCATCTA 0.403000 0 SO:0001587 stop_gained ENST00000361203.3 0 1 hg19 . . . . . . . . . . C 42 9.322677 0.99137 . . ENSG00000151914 ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203;ENST00000439203;ENST00000520645;ENST00000370765;ENST00000518935 . . . 5.45 5.45 0.79879 . 0.000000 0.49305 D 0.000156 . . . . . . 0.80722 A 1.000000 . . . . . . . . . . 0.02654 T 1 . 19.6695 0.95905 0.0:1.0:0.0:0.0 . . . . X 979;1483;1305;1305;979;1305;1305;1305;979;1345;979;979 . ENSP00000244364:W979X W - 3 0 DST 56600846 1.000000 0.71417 1.000000 0.80357 0.893000 0.52053 5.880000 0.69698 2.701000 0.92244 0.650000 0.86243 TGG TCGA-US-A77E-01A-11D-A32N-08 DST-004 NOVEL not_organism_supported|basic|appris_candidate protein_coding protein_coding OTTHUMT00000041021.3 1 0 0 15 252 0 52 0 3.123456e-01 1 18 0 52 2 0 0 0 0 0 2 1 0.999881 16 250 0 52 2 0 0 0 0 0 0 -17.959750 1 0 0 0 1 1 2 3 1.979114 0 0.390000 2.070000 0.391187 0.290000 1.700000e-01 0.460000 0.280000 0.303844 0.290000 0 0.220000 0.380000 COL12A1 1303 broad.mit.edu 37 6 75901461 75901461 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr6:75901461G>A ENST00000322507.8 - 5 659 c.350C>T c.(349-351)tCg>tTg p.S117L COL12A1_ENST00000416123.2_Missense_Mutation_p.S117L|COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000483888.2_Missense_Mutation_p.S117L NM_004370.5 NP_004361.3 Q99715 COCA1_HUMAN collagen, type XII, alpha 1 169 TGGCTTTGTCGAACTACCTGT 0.299000 0 SO:0001583 missense ENST00000322507.8 1 1 hg19 CCDS43482.1 . . . . . . . . . . G 12.54 1.967274 0.34754 . . ENSG00000111799 ENST00000322507;ENST00000432784;ENST00000416123;ENST00000483888 D;D;D 0.86769 -2.17;-2.16;-2.15 5.97 5.97 0.96955 Fibronectin, type III (1);Immunoglobulin-like fold (1); 0.488510 0.20737 N 0.086602 T 0.56232 0.1971 N 0.08118 0 0.21579 N 0.99963 B 0.02656 0.0 B 0.01281 0.0 T 0.30822 -0.9965 10 0.22706 T 0.39 . 8.1231 0.30982 0.0784:0.0:0.7627:0.1589 . 117 Q99715 COCA1_HUMAN L 117 ENSP00000325146:S117L;ENSP00000412864:S117L;ENSP00000421216:S117L ENSP00000325146:S117L S - 2 0 COL12A1 75958181 0.123000 0.22298 0.822000 0.32727 0.868000 0.49771 1.943000 0.40253 2.833000 0.97629 0.585000 0.79938 TCG TCGA-US-A77E-01A-11D-A32N-08 COL12A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041249.3 1 0 1 47 306 0 65 0 9.726732e-01 0 39 0 65 2 0 0 0 0 0 2 1 1.000000 47 303 0 64 2 0 0 0 0 0 0 -19.461560 1 1 120760 3 39 1 1 2 3 1.979114 0 0.390000 2.070000 0.391187 0.680000 5.100000e-01 0.880000 0.680000 0.691649 0.680000 0 0.590000 0.780000 KIAA1549 57670 broad.mit.edu 37 7 138566147 138566147 + Missense_Mutation SNP G G C TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr7:138566147G>C ENST00000422774.1 - 11 4264 c.4216C>G c.(4216-4218)Cgt>Ggt p.R1406G KIAA1549_ENST00000242365.4_Missense_Mutation_p.R1356G|KIAA1549_ENST00000440172.1_Missense_Mutation_p.R1406G Q9HCM3 K1549_HUMAN KIAA1549 KIAA1549/BRAF(703) 7 CCTCTGTGACGAACATTCTTG 0.502000 O BRAF pilocytic astrocytoma NSCLC(119;1534 1718 44213 46230 50068) Dom yes 7 7q34 57670 KIAA1549 O 0 SO:0001583 missense ENST00000422774.1 1 1 hg19 CCDS56513.1 . . . . . . . . . . G 21.9 4.221722 0.79464 . . ENSG00000122778 ENST00000440172;ENST00000242365;ENST00000422774 T;T;T 0.27557 1.66;1.66;1.68 5.23 5.23 0.72850 . 0.101100 0.64402 D 0.000003 T 0.55242 0.1908 M 0.65975 2.015 0.80722 D 1 D;D;D;D 0.89917 1.0;0.999;1.0;0.999 D;D;D;D 0.81914 0.995;0.965;0.991;0.965 T 0.56547 -0.7961 10 0.72032 D 0.01 . 17.5362 0.87832 0.0:0.0:1.0:0.0 . 1406;190;1406;190 Q9HCM3;Q9HCM3-4;Q9HCM3-2;Q9HCM3-3 K1549_HUMAN;.;.;. G 1406;1356;1406 ENSP00000406661:R1406G;ENSP00000242365:R1356G;ENSP00000416040:R1406G ENSP00000242365:R1356G R - 1 0 KIAA1549 138216687 1.000000 0.71417 0.942000 0.38095 0.793000 0.44817 5.140000 0.64807 2.716000 0.92895 0.655000 0.94253 CGT TCGA-US-A77E-01A-11D-A32N-08 KIAA1549-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000348092.1 1 0 1 68 385 0 79 1 5.601395e-01 5 7 0 79 2 0 0 0 0 0 2 1 1.000000 66 380 0 79 2 0 0 0 0 0 0 -2.880992 1 1 0 0 1 1 2 3 2.349308 1 0.390000 2.070000 0.489540 0.910000 7.200000e-01 1.000000 1.000000 0.911890 0.910000 1 0.810000 1.000000 ZNF212 7988 broad.mit.edu 37 7 148951330 148951330 + Missense_Mutation SNP C C T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr7:148951330C>T ENST00000335870.2 + 5 1440 c.1312C>T c.(1312-1314)Cac>Tac p.H438Y NM_012256.3 NP_036388.2 Q9UDV6 ZN212_HUMAN zinc finger protein 212 9 Melanoma(164;0.15) OV - Ovarian serous cystadenocarcinoma(82;0.00171) GAGCTTCAGTCACCCATCTGA 0.587000 0 SO:0001583 missense ENST00000335870.2 1 1 hg19 CCDS5896.1 . . . . . . . . . . C 19.24 3.789182 0.70337 . . ENSG00000170260 ENST00000335870 T 0.06528 3.29 5.1 5.1 0.69264 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.000000 0.53938 D 0.000051 T 0.10895 0.0266 N 0.19112 0.55 0.37851 D 0.92938 D 0.67145 0.996 D 0.65010 0.931 T 0.43147 -0.9409 10 0.16420 T 0.52 -15.4352 14.3872 0.66953 0.0:1.0:0.0:0.0 . 438 Q9UDV6 ZN212_HUMAN Y 438 ENSP00000338572:H438Y ENSP00000338572:H438Y H + 1 0 ZNF212 148582263 0.000000 0.05858 1.000000 0.80357 0.932000 0.56968 0.028000 0.13644 2.536000 0.85505 0.561000 0.74099 CAC TCGA-US-A77E-01A-11D-A32N-08 ZNF212-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000352710.1 1 0 1 59 287 0 61 1 9.923151e-01 14 25 0 61 2 0 0 0 0 0 2 1 1.000000 59 287 0 60 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 2.349308 1 0.390000 2.070000 0.489540 0.990000 8.100000e-01 1.000000 1.000000 0.973299 0.990000 1 0.920000 1.000000 DPP6 1804 broad.mit.edu 37 7 154667694 154667694 + Silent SNP C C T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr7:154667694C>T ENST00000377770.3 + 20 2103 c.1962C>T c.(1960-1962)ggC>ggT p.G654G DPP6_ENST00000427557.1_Silent_p.G547G|DPP6_ENST00000332007.3_Silent_p.G592G|DPP6_ENST00000404039.1_Silent_p.G590G P42658 DPP6_HUMAN dipeptidyl-peptidase 6 71 all_neural(206;0.181) all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204) OV - Ovarian serous cystadenocarcinoma(82;0.0562) GCAGCCACGGCGCGGTGGTGG 0.647000 NSCLC(125;1384 1783 2490 7422 34254) 0 SO:0001819 synonymous_variant ENST00000377770.3 1 1 hg19 TCGA-US-A77E-01A-11D-A32N-08 DPP6-003 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000322932.1 1 0 0 10 129 0 26 0 1.857956e-02 0 3 0 26 2 0 0 0 0 0 2 1 0.997221 10 129 0 26 2 0 0 0 0 0 0 -14.490230 1 1 0 0 1 1 2 3 2.349308 1 0.390000 2.070000 0.489540 0.450000 2.300000e-01 0.750000 0.450000 0.474469 0.450000 0 0.330000 0.600000 CARD11 84433 broad.mit.edu 37 7 2984085 2984085 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr7:2984085G>A ENST00000396946.4 - 5 848 c.445C>T c.(445-447)Cgc>Tgc p.R149C AC004906.3_ENST00000423194.1_RNA NM_032415.4 NP_115791.3 Q9BXL7 CAR11_HUMAN caspase recruitment domain family, member 11 150 Ovarian(82;0.0115) AGCTCGCAGCGTTGCAGGTCC 0.607000 Mis DLBCL Dom yes 7 7p22 84433 caspase recruitment domain family, member 11 L 0 SO:0001583 missense ENST00000396946.4 1 1 hg19 CCDS5336.2 . . . . . . . . . . G 16.44 3.124918 0.56613 . . ENSG00000198286 ENST00000396946 T 0.35048 1.33 4.38 4.38 0.52667 . 0.370990 0.28766 N 0.014207 T 0.44265 0.1285 L 0.43152 1.355 0.58432 D 0.999992 D 0.76494 0.999 P 0.55871 0.786 T 0.42799 -0.9430 10 0.72032 D 0.01 -31.7767 12.44 0.55619 0.0:0.0:0.8323:0.1677 . 149 Q9BXL7 CAR11_HUMAN C 149 ENSP00000380150:R149C ENSP00000380150:R149C R - 1 0 CARD11 2950611 1.000000 0.71417 1.000000 0.80357 0.937000 0.57800 4.048000 0.57390 2.153000 0.67306 0.655000 0.94253 CGC TCGA-US-A77E-01A-11D-A32N-08 CARD11-011 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000059344.4 1 0 1 87 466 0 118 1 9.456846e-01 9 19 0 118 2 0 0 0 0 0 2 1 1.000000 85 460 0 118 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 2.339105 1 0.390000 2.070000 0.480210 0.950000 7.700000e-01 1.000000 1.000000 0.939554 0.950000 1 0.850000 1.000000 TECPR1 25851 broad.mit.edu 37 7 97858456 97858456 + Missense_Mutation SNP G G T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr7:97858456G>T ENST00000447648.2 - 16 2604 c.2305C>A c.(2305-2307)Cac>Aac p.H769N TECPR1_ENST00000542604.1_Missense_Mutation_p.H699N|TECPR1_ENST00000479975.1_5'Flank|TECPR1_ENST00000379795.3_Missense_Mutation_p.H770N Q7Z6L1 TCPR1_HUMAN tectonin beta-propeller repeat containing 1 26 ATCCGCAGGTGGCCTCCCATC 0.642000 0 SO:0001583 missense ENST00000447648.2 0 1 hg19 CCDS47648.1 . . . . . . . . . . G 33 5.208596 0.95069 . . ENSG00000205356 ENST00000447648;ENST00000379795;ENST00000542604 T;T;T 0.49432 1.02;1.02;0.78 5.12 5.12 0.69794 . 0.051894 0.85682 D 0.000000 T 0.68449 0.3002 M 0.76002 2.32 0.50171 D 0.999851 D;D 0.58970 0.984;0.979 D;P 0.66084 0.941;0.761 T 0.72577 -0.4251 10 0.72032 D 0.01 -30.3075 17.6109 0.88053 0.0:0.0:1.0:0.0 . 699;769 F5GX57;Q7Z6L1 .;TCPR1_HUMAN N 769;770;699 ENSP00000404923:H769N;ENSP00000369121:H770N;ENSP00000441121:H699N ENSP00000369121:H770N H - 1 0 TECPR1 97696392 1.000000 0.71417 1.000000 0.80357 0.987000 0.75469 9.830000 0.99415 2.389000 0.81357 0.549000 0.68633 CAC TCGA-US-A77E-01A-11D-A32N-08 TECPR1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000334661.1 1 0 1 7 27 0 10 1 9.828066e-01 6 27 0 10 2 0 0 0 0 0 2 1 0.982807 7 26 0 10 2 0 0 0 0 0 0 -15.917780 1 1 0 0 1 1 2 3 2.348736 1 0.390000 2.070000 0.489540 0.990000 6.100000e-01 1.000000 1.000000 0.958050 0.990000 1 0.900000 1.000000 DGAT1 8694 broad.mit.edu 37 8 145541605 145541605 + Missense_Mutation SNP C C T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr8:145541605C>T ENST00000332324.4 - 9 1100 c.827G>A c.(826-828)cGc>cAc p.R276H GS1-393G12.12_ENST00000525023.1_RNA|DGAT1_ENST00000531896.1_Silent_p.A306A|DGAT1_ENST00000527438.1_5'Flank NM_012079.4 NP_036211.2 O75907 DGAT1_HUMAN diacylglycerol O-acyltransferase 1 9 all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;7.67e-40)|all cancers(56;7.88e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055) CAGCAGAAAGCGCTTCCGGAT 0.622000 0 SO:0001583 missense ENST00000332324.4 0 1 hg19 CCDS6420.1 . . . . . . . . . . C 21.9 4.213109 0.79352 . . ENSG00000185000 ENST00000332324 T 0.72942 -0.7 4.77 4.77 0.60923 . 0.000000 0.85682 D 0.000000 T 0.66336 0.2779 M 0.66439 2.03 0.80722 D 1 P 0.46457 0.878 B 0.36845 0.234 T 0.71457 -0.4587 10 0.42905 T 0.14 -15.1045 15.3179 0.74095 0.0:1.0:0.0:0.0 . 276 O75907 DGAT1_HUMAN H 276 ENSP00000332258:R276H ENSP00000332258:R276H R - 2 0 DGAT1 145512413 1.000000 0.71417 1.000000 0.80357 0.967000 0.64934 7.047000 0.76599 2.481000 0.83766 0.555000 0.69702 CGC TCGA-US-A77E-01A-11D-A32N-08 DGAT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000382059.3 0 0 0 8 205 0 46 1 9.948823e-01 14 235 0 46 2 0 0 0 0 0 2 1 0.989158 8 202 0 45 2 0 0 0 0 0 0 -9.903371 1 1 0 0 1 0 1 1 1.967067 0 0.390000 2.070000 0.388808 0.190000 9.000000e-02 0.350000 0.190000 0.212676 0.190000 0 0.130000 0.280000 IDO1 3620 broad.mit.edu 37 8 39775725 39775725 + Splice_Site SNP A A T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr8:39775725A>T ENST00000518237.1 + 3 941 c.302A>T c.(301-303)aAg>aTg p.K101M RP11-44K6.4_ENST00000522970.1_RNA|IDO1_ENST00000522495.1_Splice_Site_p.K101M|RP11-44K6.2_ENST00000520185.1_RNA|RP11-44K6.3_ENST00000517623.1_RNA NM_002164.5 NP_002155.1 P14902 I23O1_HUMAN indoleamine 2,3-dioxygenase 1 12 L-Tryptophan(DB00150)|Melatonin(DB01065) GATGTCCGTAAGGTTTGGAGA 0.398000 0 SO:0001630 splice_region_variant ENST00000518237.1 1 0 hg19 CCDS47847.1 . . . . . . . . . . A 16.87 3.243130 0.58995 . . ENSG00000131203 ENST00000519154;ENST00000522495;ENST00000518237 T;T;T 0.50277 0.75;0.75;0.75 5.65 5.65 0.86999 . 0.166139 0.38605 N 0.001628 T 0.67767 0.2928 M 0.83953 2.67 0.41481 D 0.98816 D 0.65815 0.995 D 0.64144 0.922 T 0.72384 -0.4310 9 . . . -19.5956 12.2669 0.54683 1.0:0.0:0.0:0.0 . 101 P14902 I23O1_HUMAN M 101 ENSP00000428716:K101M;ENSP00000430505:K101M;ENSP00000430950:K101M . K + 2 0 IDO1 39894882 0.998000 0.40836 0.974000 0.42286 0.281000 0.26958 4.977000 0.63792 2.154000 0.67381 0.477000 0.44152 AAG TCGA-US-A77E-01A-11D-A32N-08 IDO1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000376987.1 1 0 1 76 270 0 63 0 3.070964e-01 1 4 0 63 2 0 0 0 0 0 2 1 1.000000 74 267 0 60 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 1 1 1.967067 0 0.390000 2.070000 0.388808 0.990000 9.000000e-01 1.000000 1.000000 0.993234 0.990000 1 0.990000 1.000000 SOX17 64321 broad.mit.edu 37 8 55372148 55372148 + Missense_Mutation SNP G G T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr8:55372148G>T ENST00000297316.4 + 2 1042 c.838G>T c.(838-840)Ggt>Tgt p.G280C NM_022454.3 NP_071899.1 Q9H6I2 SOX17_HUMAN SRY (sex determining region Y)-box 17 18 Lung NSC(129;0.109)|all_epithelial(80;0.176)|all_lung(136;0.181) OV - Ovarian serous cystadenocarcinoma(7;1.9e-07)|Epithelial(17;1.7e-05)|all cancers(17;0.000159) AGAGCCCGCGGGTCCCTCGAT 0.761000 0 SO:0001583 missense ENST00000297316.4 0 1 hg19 CCDS6159.1 . . . . . . . . . . G 6.286 0.420879 0.11928 . . ENSG00000164736 ENST00000297316 T 0.77620 -1.11 4.44 3.49 0.39957 . 0.789630 0.11802 N 0.527999 T 0.73583 0.3605 M 0.63843 1.955 0.25014 N 0.99138 B 0.33345 0.409 B 0.34489 0.184 T 0.64394 -0.6418 10 0.37606 T 0.19 . 9.5602 0.39364 0.0:0.153:0.6895:0.1574 . 280 Q9H6I2 SOX17_HUMAN C 280 ENSP00000297316:G280C ENSP00000297316:G280C G + 1 0 SOX17 55534701 0.009000 0.17119 0.185000 0.23176 0.085000 0.17905 1.627000 0.37050 2.006000 0.58801 0.455000 0.32223 GGT TCGA-US-A77E-01A-11D-A32N-08 SOX17-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000378526.2 1 0 0 7 12 0 8 0 3.320158e-01 0 3 0 8 2 0 0 0 0 0 2 1 0.985060 7 11 0 8 2 0 0 0 0 0 0 -19.982810 1 1 0 0 1 0 1 1 1.967067 0 0.390000 2.070000 0.388808 0.990000 8.400000e-01 1.000000 1.000000 0.990877 0.990000 1 0.990000 1.000000 LAPTM4B 55353 broad.mit.edu 37 8 98817579 98817579 + Splice_Site SNP A A T rs149932386 TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr8:98817579A>T ENST00000521545.2 + 2 333 c.e2-1 LAPTM4B_ENST00000445593.2_Splice_Site Q86VI4 LAP4B_HUMAN lysosomal protein transmembrane 4 beta 10 Breast(36;1.59e-06) OV - Ovarian serous cystadenocarcinoma(57;0.149) TTCTTGTTGCAGATCATCAAT 0.388000 0 SO:0001630 splice_region_variant ENST00000521545.2 1 0 hg19 . . . . . . . . . . A 19.74 3.884628 0.72410 . . ENSG00000104341 ENST00000445593;ENST00000378722;ENST00000517924;ENST00000521545 . . . 5.07 5.07 0.68467 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 12.653 0.56772 1.0:0.0:0.0:0.0 . . . . . -1 . . . + . . LAPTM4B 98886755 1.000000 0.71417 1.000000 0.80357 0.952000 0.60782 7.723000 0.84788 2.036000 0.60181 0.533000 0.62120 . TCGA-US-A77E-01A-11D-A32N-08 LAPTM4B-002 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000380016.2 1 0 0 22 483 0 95 0 0 0 0 95 2 0 0 0 0 0 2 1 0.999998 12 461 0 93 2 0 0 0 0 0 0 -1.522542 0 1 0 0 1 0 1 1 1.967067 0 0.390000 2.070000 0.388808 0.220000 1.400000e-01 0.320000 0.220000 0.231466 0.220000 0 0.170000 0.280000 KLF4 9314 broad.mit.edu 37 9 110249341 110249341 + Missense_Mutation SNP G G T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr9:110249341G>T ENST00000374672.4 - 4 1705 c.1232C>A c.(1231-1233)tCc>tAc p.S411Y NM_004235.4 NP_004226.3 O43474 KLF4_HUMAN Kruppel-like factor 4 (gut) 16 CTTGAGATGGGAACTCTTTGT 0.592000 0 SO:0001583 missense ENST00000374672.4 1 1 hg19 CCDS6770.2 . . . . . . . . . . G 24.9 4.579183 0.86645 . . ENSG00000136826 ENST00000374672 T 0.35605 1.3 5.57 4.68 0.58851 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.347798 0.21123 N 0.079795 T 0.66208 0.2766 M 0.89601 3.045 0.80722 D 1 D;D 0.76494 0.989;0.999 P;D 0.72625 0.641;0.978 T 0.74041 -0.3792 10 0.87932 D 0 . 14.0741 0.64880 0.0732:0.0:0.9268:0.0 . 445;411 O43474;O43474-1 KLF4_HUMAN;. Y 411 ENSP00000363804:S411Y ENSP00000363804:S411Y S - 2 0 KLF4 109289162 1.000000 0.71417 1.000000 0.80357 0.974000 0.67602 9.824000 0.99380 1.358000 0.45922 -0.136000 0.14681 TCC TCGA-US-A77E-01A-11D-A32N-08 KLF4-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053556.2 1 0 1 125 651 0 191 1 1 63 70 0 191 2 0 0 0 0 0 2 1 1.000000 122 642 0 190 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 1 1 1.968358 0 0.390000 2.070000 0.388808 0.810000 6.900000e-01 0.950000 0.820000 0.827054 0.810000 0 0.750000 0.890000 ELAVL2 1993 broad.mit.edu 37 9 23692693 23692693 + Missense_Mutation SNP A A C TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr9:23692693A>C ENST00000397312.2 - 7 1216 c.942T>G c.(940-942)aaT>aaG p.N314K ELAVL2_ENST00000223951.6_Missense_Mutation_p.N301K|ELAVL2_ENST00000544538.1_Missense_Mutation_p.N314K|ELAVL2_ENST00000380117.1_Missense_Mutation_p.N314K|ELAVL2_ENST00000380110.4_Missense_Mutation_p.N344K NM_004432.3 NP_004423.2 Q12926 ELAV2_HUMAN ELAV like neuron-specific RNA binding protein 2 39 CTTTGCATTTATTGGTGTTAA 0.473000 0 SO:0001583 missense ENST00000397312.2 1 1 hg19 CCDS6515.1 . . . . . . . . . . A 12.36 1.913291 0.33815 . . ENSG00000107105 ENST00000223951;ENST00000397312;ENST00000544538;ENST00000380110;ENST00000380117;ENST00000359598 T;T;T;T 0.05996 3.36;3.36;3.36;3.36 5.94 4.81 0.61882 Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3); 0.000000 0.85682 D 0.000000 T 0.12178 0.0296 L 0.28740 0.885 0.80722 D 1 P;D 0.61080 0.776;0.989 B;D 0.66497 0.377;0.944 T 0.05435 -1.0885 10 0.51188 T 0.08 . 8.3434 0.32258 0.7382:0.0:0.2618:0.0 . 314;301 Q12926;Q12926-2 ELAV2_HUMAN;. K 301;314;314;301;314;342 ENSP00000223951:N301K;ENSP00000380479:N314K;ENSP00000440998:N314K;ENSP00000369460:N314K ENSP00000223951:N301K N - 3 2 ELAVL2 23682693 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 4.183000 0.58317 1.074000 0.40909 0.528000 0.53228 AAT TCGA-US-A77E-01A-11D-A32N-08 ELAVL2-201 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000051943.2 1 0 0 20 465 0 111 0 0 0 0 111 2 0 0 0 0 0 2 1 0.999995 20 458 0 110 2 0 0 0 0 0 0 -19.576970 1 1 0 0 1 0 2 2 1.971494 1 0.390000 2.070000 0.390000 0.210000 1.300000e-01 0.310000 0.210000 0.220407 0.210000 0 0.160000 0.270000 TRPM3 80036 broad.mit.edu 37 9 73442926 73442926 + Silent SNP C C T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr9:73442926C>T ENST00000377111.2 - 6 1053 c.810G>A c.(808-810)cgG>cgA p.R270R TRPM3_ENST00000360823.2_Silent_p.R117R|TRPM3_ENST00000396283.1_Silent_p.R117R|TRPM3_ENST00000361823.5_Silent_p.R117R|TRPM3_ENST00000396285.1_Silent_p.R117R|TRPM3_ENST00000423814.3_Silent_p.R272R|TRPM3_ENST00000396292.4_Silent_p.R117R|TRPM3_ENST00000377105.1_Silent_p.R117R|TRPM3_ENST00000358082.3_Silent_p.R117R|TRPM3_ENST00000377101.1_Silent_p.R117R|TRPM3_ENST00000377110.3_Silent_p.R270R|TRPM3_ENST00000408909.2_Silent_p.R117R|TRPM3_ENST00000396280.5_Silent_p.R117R|TRPM3_ENST00000377106.1_Silent_p.R117R|TRPM3_ENST00000357533.2_Silent_p.R272R NM_001007471.2 NP_001007472.2 Q9HCF6 TRPM3_HUMAN transient receptor potential cation channel, subfamily M, member 3 95 TCTGGTATGGCCGGACAACCT 0.458000 0 SO:0001819 synonymous_variant ENST00000377111.2 0 1 hg19 . . . . . . . . . . C 9.804 1.181369 0.21787 0.0 1.16E-4 ENSG00000083067 ENST00000396280 . . . 5.83 1.69 0.24217 . . . . . T 0.46502 0.1396 . . . 0.80722 D 1 . . . . . . T 0.27365 -1.0076 4 . . . -20.7328 4.1127 0.10067 0.2451:0.4474:0.0:0.3075 . . . . T 117 . . A - 1 0 TRPM3 72632746 0.626000 0.27120 0.998000 0.56505 0.980000 0.70556 -0.166000 0.09954 0.371000 0.24564 0.650000 0.86243 GCC TCGA-US-A77E-01A-11D-A32N-08 TRPM3-007 NOVEL basic|exp_conf protein_coding protein_coding OTTHUMT00000214157.5 0 0 0 5 523 0 128 0 0 0 0 128 2 0 0 0 0 0 2 1 0.936874 5 520 0 126 2 0 0 0 0 0 0 -2.167190 0 1 121410 2 35 1 0 1 1 1.968358 0 0.390000 2.070000 0.388808 0.040000 1.000000e-02 0.110000 0.050000 0.057714 0.040000 0 0.020000 0.080000 KIF27 55582 broad.mit.edu 37 9 86504131 86504131 + Missense_Mutation SNP A A C TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chr9:86504131A>C ENST00000297814.2 - 7 1990 c.1847T>G c.(1846-1848)aTa>aGa p.I616R KIF27_ENST00000334204.2_Missense_Mutation_p.I616R|KIF27_ENST00000413982.1_Missense_Mutation_p.I616R|KIF27_ENST00000376347.1_Missense_Mutation_p.I7R NM_017576.1 NP_060046.1 Q86VH2 KIF27_HUMAN kinesin family member 27 43 TCCAGCAAATATTCGATCCAG 0.403000 0 SO:0001583 missense ENST00000297814.2 1 1 hg19 CCDS6665.1 . . . . . . . . . . A 17.75 3.465512 0.63513 . . ENSG00000165115 ENST00000297814;ENST00000413982;ENST00000334204;ENST00000376347 T;T;T;T 0.53206 0.63;0.63;0.63;0.63 4.85 3.62 0.41486 . 0.461427 0.16718 U 0.202373 T 0.30448 0.0765 N 0.08118 0 0.38420 D 0.946164 P;P;B 0.42993 0.467;0.797;0.337 B;P;B 0.44359 0.133;0.447;0.054 T 0.11446 -1.0587 10 0.29301 T 0.29 . 10.6689 0.45747 0.8568:0.0:0.0:0.1432 . 616;616;616 Q86VH2-3;Q86VH2-2;Q86VH2 .;.;KIF27_HUMAN R 616;616;616;7 ENSP00000297814:I616R;ENSP00000401688:I616R;ENSP00000333928:I616R;ENSP00000365525:I7R ENSP00000297814:I616R I - 2 0 KIF27 85693951 1.000000 0.71417 0.999000 0.59377 0.826000 0.46750 5.222000 0.65277 1.949000 0.56562 0.455000 0.32223 ATA TCGA-US-A77E-01A-11D-A32N-08 KIF27-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052861.1 0 0 0 32 714 0 118 0 0 0 1 0 118 2 0 0 0 0 0 2 1 1.000000 31 700 0 118 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 1 1 1.968358 0 0.390000 2.070000 0.388808 0.210000 1.400000e-01 0.300000 0.220000 0.225328 0.210000 0 0.180000 0.260000 DRP2 1821 broad.mit.edu 37 X 100500426 100500426 + Missense_Mutation SNP T T A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chrX:100500426T>A ENST00000395209.3 + 11 1692 c.1165T>A c.(1165-1167)Tac>Aac p.Y389N DRP2_ENST00000541709.1_Missense_Mutation_p.Y311N|DRP2_ENST00000538510.1_Missense_Mutation_p.Y389N|DRP2_ENST00000402866.1_Missense_Mutation_p.Y389N NM_001939.2 NP_001930.2 Q13474 DRP2_HUMAN dystrophin related protein 2 31 GACAGAGTTATACCAAACCCT 0.468000 0 SO:0001583 missense ENST00000395209.3 0 1 hg19 CCDS14480.2 . . . . . . . . . . T 27.7 4.854763 0.91355 . . ENSG00000102385 ENST00000402866;ENST00000395209;ENST00000541709;ENST00000538510 T;T;T;T 0.63913 -0.07;-0.07;-0.07;-0.07 5.84 5.84 0.93424 EF-hand domain, type 1 (1); 0.059046 0.64402 D 0.000001 T 0.77485 0.4137 M 0.73962 2.25 0.80722 D 1 D 0.76494 0.999 D 0.63793 0.918 T 0.80616 -0.1303 10 0.87932 D 0 -13.6727 15.1354 0.72562 0.0:0.0:0.0:1.0 . 389 Q13474 DRP2_HUMAN N 389;389;311;389 ENSP00000385038:Y389N;ENSP00000378635:Y389N;ENSP00000444752:Y311N;ENSP00000441051:Y389N ENSP00000378635:Y389N Y + 1 0 DRP2 100387082 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 8.040000 0.89188 1.957000 0.56846 0.486000 0.48141 TAC TCGA-US-A77E-01A-11D-A32N-08 DRP2-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000057522.3 0 0 0 3 44 0 8 0 0 0 0 8 2 0 0 0 0 0 2 1 0.805743 2 44 0 8 2 0 0 0 0 0 0 -7.624812 1 0 0 0 1 0 1 1 0.390000 2.070000 0.390000 0.180000 5.000000e-02 0.400000 0.160000 0.202488 0.180000 0 0.100000 0.290000 KIF4A 24137 broad.mit.edu 37 X 69521814 69521814 + Missense_Mutation SNP G G A TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chrX:69521814G>A ENST00000374403.3 + 6 663 c.581G>A c.(580-582)gGc>gAc p.G194D KIF4A_ENST00000374388.3_Missense_Mutation_p.G194D NM_012310.4 NP_036442.3 O95239 KIF4A_HUMAN kinesin family member 4A 51 TTGGAACAGGGCAACAACTCT 0.438000 0 SO:0001583 missense ENST00000374403.3 0 1 hg19 CCDS14401.1 . . . . . . . . . . G 25.5 4.645442 0.87859 . . ENSG00000090889 ENST00000374388;ENST00000374403 D;D 0.83837 -1.77;-1.77 5.1 5.1 0.69264 Kinesin, motor domain (4); 0.000000 0.53938 D 0.000051 D 0.95214 0.8448 H 0.99357 4.53 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.85130 0.997;0.995 D 0.97585 1.0113 10 0.87932 D 0 . 16.5735 0.84631 0.0:0.0:1.0:0.0 . 194;194 O95239;O95239-2 KIF4A_HUMAN;. D 194 ENSP00000363509:G194D;ENSP00000363524:G194D ENSP00000363509:G194D G + 2 0 KIF4A 69438539 1.000000 0.71417 1.000000 0.80357 0.965000 0.64279 9.316000 0.96319 2.115000 0.64714 0.538000 0.68166 GGC TCGA-US-A77E-01A-11D-A32N-08 KIF4A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057068.1 0 0 0 4 220 0 47 0 1.718410e-03 0 3 0 47 2 0 0 0 0 0 2 1 0.886880 4 216 0 46 2 0 0 0 0 0 0 -2.733447 1 1 0 0 1 0 1 1 0.390000 2.070000 0.390000 0.040000 1.000000e-02 0.110000 0.050000 0.056321 0.040000 0 0.020000 0.080000 ATP7A 538 broad.mit.edu 37 X 77244909 77244909 + Missense_Mutation SNP A A T TCGA-US-A77E-01A-11D-A32N-08 TCGA-US-A77E-11A-11D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 41e7b7ba-2ad3-461e-b034-9012b11b0ac6 d4212d5b-eb9c-4720-a339-23763029e0e2 g.chrX:77244909A>T ENST00000341514.6 + 4 946 c.791A>T c.(790-792)gAa>gTa p.E264V ATP7A_ENST00000350425.4_Intron|ATP7A_ENST00000343533.5_Missense_Mutation_p.E264V NM_000052.5 NP_000043.4 Q04656 ATP7A_HUMAN ATPase, Cu++ transporting, alpha polypeptide 53 Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526) AAATCCTCAGAAGGGTCACAG 0.403000 0 SO:0001583 missense ENST00000341514.6 1 1 hg19 CCDS35339.1 . . . . . . . . . . A 3.798 -0.042338 0.07452 . . ENSG00000165240 ENST00000343533;ENST00000341514;ENST00000400860;ENST00000355691 D;D 0.96334 -3.98;-3.98 4.78 2.24 0.28232 . 0.471910 0.20943 N 0.082889 D 0.95519 0.8544 M 0.88450 2.955 0.80722 D 1 B;B 0.28783 0.002;0.222 B;B 0.35688 0.007;0.208 D 0.91217 0.5003 10 0.30078 T 0.28 -11.1068 4.7038 0.12839 0.5353:0.2948:0.1699:0.0 . 264;274 Q04656;Q59HD1 ATP7A_HUMAN;. V 264;264;264;274 ENSP00000343026:E264V;ENSP00000345728:E264V ENSP00000345728:E264V E + 2 0 ATP7A 77131565 0.959000 0.32827 0.899000 0.35326 0.225000 0.24961 1.880000 0.39628 0.694000 0.31654 0.422000 0.28245 GAA TCGA-US-A77E-01A-11D-A32N-08 ATP7A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057306.1 1 0 1 114 222 0 83 0 2.691430e-01 1 2 0 83 2 0 0 0 0 0 2 1 1.000000 113 222 0 82 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 1 1 0.390000 2.070000 0.390000 0.860000 7.300000e-01 0.980000 0.870000 0.864439 0.860000 1 0.790000 0.930000