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 TP53 7157 broad.mit.edu 37 17 7574003 7574003 + Frame_Shift_Del DEL G G - TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 G - G G Valid Somatic Phase_I WXS targeted Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr17:7574003delG ENST00000269305.4 - 10 1213 c.1024delC c.(1024-1026)cgafs p.R342fs TP53_ENST00000445888.2_Frame_Shift_Del_p.R342fs|TP53_ENST00000455263.2_3'UTR|TP53_ENST00000420246.2_3'UTR|TP53_ENST00000359597.4_Intron|TP53_ENST00000413465.2_Intron NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1 NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1 P04637 P53_HUMAN tumor protein p53 p.R342*(70)|p.0?(8)|p.R342fs*3(8)|p.?(1)|p.R342_N345delRELN(1)|p.I332fs*5(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) TTCAGCTCTCGGAACATCTCG 0.557000 111 Mis, N, F breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types Other conserved DNA damage response genes Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019) Pancreas(47;798 1329 9957 10801) yes Rec yes Li-Fraumeni syndrome 17 17p13 7157 tumor protein p53 L, E, M, O 89 Substitution - Nonsense(70)|Whole gene deletion(8)|Deletion - Frameshift(7)|Insertion - Frameshift(2)|Deletion - In frame(1)|Unknown(1) GRCh37 CM004908 TP53 M SO:0001589 frameshift_variant Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 1 1 hg19 CCDS11118.1 TCGA-HV-A5A6-01A-11D-A26I-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 0 50 111 0 33 1 9.967110e-01 5 18 0 33 2 1 1 264 699 0 1151 2 1 0.999968 54 111 2 32 22 0 0 0 0 0 0 -5.939592 1 1 0 0 1 0 1 1 1.490383 1 0.640000 1.940000 0.473068 0.650000 0.510000 0.810000 0.660000 0.663410 0.650000 0 0.580000 0.740000 WDR11 55717 broad.mit.edu 37 10 122626196 122626196 + Silent SNP A A T TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr10:122626196A>T ENST00000263461.6 + 8 1356 c.1110A>T c.(1108-1110)gcA>gcT p.A370A NM_018117.11 NP_060587.8 Q8WWQ0 PHIP_HUMAN WD repeat domain 11 38 ATGAGAATGCAGCCGCCCTCG 0.473000 0 SO:0001819 synonymous_variant ENST00000263461.6 1 1 hg19 CCDS7619.1 TCGA-HV-A5A6-01A-11D-A26I-08 WDR11-001 KNOWN non_canonical_U12|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050707.2 1 0 1 168 306 0 69 1 8.827383e-01 2 7 0 69 2 0 0 0 0 0 2 1 1.000000 166 305 0 69 2 0 0 0 0 69 2 -20.000000 1 1 0 0 1 0 1 1 1.818128 1 0.640000 1.940000 0.584104 0.950000 0.830000 1.000000 1.000000 0.950199 0.950000 1 0.890000 1.000000 USP28 57646 broad.mit.edu 37 11 113675589 113675589 + Splice_Site SNP C C T TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr11:113675589C>T ENST00000003302.4 - 20 2648 c.e20+1 USP28_ENST00000260188.5_Splice_Site|USP28_ENST00000545540.1_Splice_Site|USP28_ENST00000544967.1_Splice_Site NM_020886.2 NP_065937.1 Q96RU2 UBP28_HUMAN ubiquitin specific peptidase 28 59 all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425) TCTCTTCTCACCTTTCATCAT 0.428000 Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765) 0 SO:0001630 splice_region_variant ENST00000003302.4 1 1 hg19 CCDS31680.1 . . . . . . . . . . C 25.9 4.688412 0.88639 . . ENSG00000048028 ENST00000003302;ENST00000260188;ENST00000544967;ENST00000545540 . . . 5.95 5.95 0.96441 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 20.3748 0.98911 0.0:1.0:0.0:0.0 . . . . . -1 . . . - . . USP28 113180799 1.000000 0.71417 1.000000 0.80357 0.962000 0.63368 7.461000 0.80834 2.817000 0.96982 0.563000 0.77884 . TCGA-HV-A5A6-01A-11D-A26I-08 USP28-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000398789.1 1 0 1 97 269 0 25 0 0 1 0 0 25 2 0 0 0 0 0 2 1 1.000000 96 268 0 25 2 0 0 0 0 25 2 -6.010339 1 1 0 0 1 0 0 0 2.040351 0 0.640000 1.940000 0.640000 0.820000 0.680000 0.970000 0.820000 0.830610 0.820000 0 0.750000 0.900000 PTPN5 84867 broad.mit.edu 37 11 18763931 18763931 + Silent SNP G G A TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr11:18763931G>A ENST00000358540.2 - 7 1033 c.603C>T c.(601-603)atC>atT p.I201I PTPN5_ENST00000396170.1_Silent_p.I169I|PTPN5_ENST00000396167.2_Silent_p.I169I|PTPN5_ENST00000477854.1_Silent_p.I5I|PTPN5_ENST00000396171.4_Silent_p.I201I|PTPN5_ENST00000396168.1_Silent_p.I177I|PTPN5_ENST00000496201.2_5'UTR|RP11-1081L13.4_ENST00000527285.1_RNA NM_006906.1 NP_008837.1 P54829 PTN5_HUMAN protein tyrosine phosphatase, non-receptor type 5 (striatum-enriched) 27 AGTCATCCTCGATCTTCTCCT 0.617000 0 SO:0001819 synonymous_variant ENST00000358540.2 1 1 hg19 CCDS7845.1 TCGA-HV-A5A6-01A-11D-A26I-08 PTPN5-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000259196.2 1 0 1 52 263 0 48 0 0 0 1 0 48 2 0 0 0 0 0 2 1 1.000000 52 258 0 48 2 0 0 0 0 48 2 -20.000000 1 1 121412 23 43 1 1 2 3 2.108160 0 0.640000 1.940000 0.646782 0.520000 0.400000 1.000000 0.530000 0.553587 0.520000 0 0.460000 0.610000 AHNAK 79026 broad.mit.edu 37 11 62299013 62299013 + Missense_Mutation SNP T T G TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr11:62299013T>G ENST00000378024.4 - 5 3150 c.2876A>C c.(2875-2877)aAa>aCa p.K959T AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron NM_001620.1 NP_001611.1 Q09666 AHNK_HUMAN AHNAK nucleoprotein 268 Melanoma(852;0.155) TCCCTTTACTTTAGGACCTTT 0.483000 0 SO:0001583 missense ENST00000378024.4 1 1 hg19 CCDS31584.1 . . . . . . . . . . t 9.875 1.200010 0.22121 . . ENSG00000124942 ENST00000378024 T 0.01665 4.7 4.8 3.66 0.41972 . 0.240370 0.41823 D 0.000807 T 0.09069 0.0224 H 0.95402 3.665 0.26966 N 0.965691 P 0.50528 0.936 P 0.51415 0.669 T 0.16247 -1.0409 10 0.30078 T 0.28 -2.0869 10.1142 0.42581 0.0:0.0808:0.0:0.9192 . 959 Q09666 AHNK_HUMAN T 959 ENSP00000367263:K959T ENSP00000367263:K959T K - 2 0 AHNAK 62055589 0.273000 0.24181 0.993000 0.49108 0.053000 0.15095 1.372000 0.34261 0.683000 0.31428 0.374000 0.22700 AAA TCGA-HV-A5A6-01A-11D-A26I-08 AHNAK-005 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000395572.1 0 0 0 26 1018 0 130 0 6.529177e-03 0 5 0 130 2 0 0 0 0 0 2 1 1.000000 26 1008 0 130 2 0 0 0 0 130 2 -18.755220 1 1 0 0 1 1 2 3 2.048049 0 0.640000 1.940000 0.641148 0.070000 0.040000 0.120000 0.080000 0.080867 0.070000 0 0.050000 0.100000 SF1 7536 broad.mit.edu 37 11 64533556 64533556 + Missense_Mutation SNP C C T TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr11:64533556C>T ENST00000377390.3 - 13 1991 c.1654G>A c.(1654-1656)Gca>Aca p.A552T SF1_ENST00000227503.9_Intron|SF1_ENST00000334944.5_Missense_Mutation_p.A552T|SF1_ENST00000377387.1_Intron|SF1_ENST00000433274.2_Missense_Mutation_p.A526T|SF1_ENST00000489544.1_5'Flank|SF1_ENST00000422298.2_Intron|SF1_ENST00000377394.3_Intron NM_004630.3 NP_004621.2 Q15637 SF01_HUMAN splicing factor 1 31 GGAGAAGCTGCGGCAGCCGCC 0.682000 0 SO:0001583 missense ENST00000377390.3 1 1 hg19 CCDS31599.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 11.87|11.87 1.767095|1.767095 0.31320|0.31320 .|. .|. ENSG00000168066|ENSG00000168066 ENST00000377390;ENST00000334944;ENST00000433274|ENST00000486867 T;T;T|T 0.48836|0.54675 0.8;0.92;0.81|0.56 5.3|5.3 5.3|5.3 0.74995|0.74995 .|. .|. .|. .|. .|. T|T 0.47637|0.47637 0.1456|0.1456 N|N 0.12182|0.12182 0.205|0.205 0.80722|0.80722 D|D 1|1 B;B|. 0.31611|. 0.223;0.331|. B;B|. 0.25614|. 0.028;0.062|. T|T 0.56092|0.56092 -0.8036|-0.8036 9|7 0.87932|0.87932 D|D 0|0 .|. 16.4457|16.4457 0.83928|0.83928 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. 552;552|. Q15637;Q15637-2|. SF01_HUMAN;.|. T|H 552;552;526|271 ENSP00000366607:A552T;ENSP00000334414:A552T;ENSP00000396793:A526T|ENSP00000419062:R271H ENSP00000334414:A552T|ENSP00000419062:R271H A|R -|- 1|2 0|0 SF1|SF1 64290132|64290132 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.996000|0.996000 0.88848|0.88848 4.087000|4.087000 0.57671|0.57671 2.488000|2.488000 0.83962|0.83962 0.561000|0.561000 0.74099|0.74099 GCA|CGC TCGA-HV-A5A6-01A-11D-A26I-08 SF1-005 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000143242.1 1 0 0 76 165 0 65 1 9.999976e-01 16 30 0 65 2 0 0 0 0 0 2 1 1.000000 76 163 0 64 2 0 0 0 0 65 2 -8.089916 1 1 120562 1 31 1 0 0 0 2.040351 0 0.640000 1.940000 0.640000 0.980000 0.800000 1.000000 1.000000 0.956381 0.980000 1 0.880000 1.000000 ATG2A 23130 broad.mit.edu 37 11 64678283 64678283 + Missense_Mutation SNP G G A TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr11:64678283G>A ENST00000377264.3 - 11 1722 c.1610C>T c.(1609-1611)aCg>aTg p.T537M ATG2A_ENST00000421419.2_Missense_Mutation_p.T537M NM_015104.2 NP_055919.2 Q2TAZ0 ATG2A_HUMAN autophagy related 2A 55 CCTCACCTCCGTGTACTCAGG 0.677000 0 SO:0001583 missense ENST00000377264.3 0 1 hg19 CCDS31602.1 . . . . . . . . . . G 17.99 3.522125 0.64747 2.27E-4 0.0 ENSG00000110046 ENST00000421419;ENST00000377264 T;T 0.08984 3.03;3.03 5.11 5.11 0.69529 . 0.190202 0.41097 D 0.000944 T 0.09774 0.0240 L 0.50333 1.59 0.34319 D 0.68634 P 0.48350 0.909 B 0.38327 0.271 T 0.14643 -1.0465 10 0.66056 D 0.02 . 14.4207 0.67180 0.0:0.0:1.0:0.0 . 537 Q2TAZ0 ATG2A_HUMAN M 537 ENSP00000410522:T537M;ENSP00000366475:T537M ENSP00000366475:T537M T - 2 0 ATG2A 64434859 0.993000 0.37304 0.964000 0.40570 0.697000 0.40408 2.162000 0.42367 2.550000 0.86006 0.462000 0.41574 ACG TCGA-HV-A5A6-01A-11D-A26I-08 ATG2A-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000143224.1 0 0 0 4 72 0 12 0 1.174952e-01 0 9 0 12 2 0 0 0 0 0 2 1 0.889105 4 71 0 11 2 0 0 0 0 12 2 -7.958007 1 1 0 0 1 0 0 0 2.040351 0 0.640000 1.940000 0.640000 0.180000 0.060000 0.380000 0.160000 0.198841 0.180000 0 0.100000 0.280000 ADRBK1 156 broad.mit.edu 37 11 67048254 67048254 + Splice_Site SNP C C T TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr11:67048254C>T ENST00000308595.5 + 7 845 c.555C>T c.(553-555)caC>caT p.H185H ADRBK1_ENST00000526285.1_Splice_Site_p.H185H NM_001619.3 NP_001610.2 P25098 ARBK1_HUMAN adrenergic, beta, receptor kinase 1 22 BRCA - Breast invasive adenocarcinoma(15;2.26e-06) Adenosine triphosphate(DB00171) TCAACATCCACGTGAGTGGGC 0.597000 0 SO:0001630 splice_region_variant ENST00000308595.5 1 0 hg19 CCDS8156.1 TCGA-HV-A5A6-01A-11D-A26I-08 ADRBK1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000393153.1 1 0 1 316 707 0 234 1 1 38 79 0 234 2 0 0 0 0 0 2 1 1.000000 315 699 0 233 2 0 0 0 0 234 2 -20.000000 1 1 121412 2 41 1 0 0 0 2.040351 0 0.640000 1.940000 0.640000 0.950000 0.870000 1.000000 1.000000 0.959803 0.950000 1 0.910000 1.000000 IFT81 28981 broad.mit.edu 37 12 110655943 110655943 + Missense_Mutation SNP G G A rs150790899 by1000genomes TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr12:110655943G>A ENST00000242591.5 + 19 2449 c.1943G>A c.(1942-1944)tGt>tAt p.C648Y IFT81_ENST00000552912.1_Missense_Mutation_p.C648Y NM_014055.3 NP_054774.2 Q8WYA0 IFT81_HUMAN intraflagellar transport 81 10 TTAATGGAATGTAAGAAACAG 0.388000 0 SO:0001583 missense ENST00000242591.5 1 1 hg19 CCDS41831.1 1 4.578754578754579E-4 0 0.0 0 0.0 1 0.0017482517482517483 0 0.0 . 19.76 3.888341 0.72524 . . ENSG00000122970 ENST00000552912;ENST00000242591;ENST00000550748 . . . 5.22 4.33 0.51752 . 0.000000 0.85682 D 0.000000 T 0.78039 0.4221 M 0.78916 2.43 0.80722 D 1 D 0.71674 0.998 D 0.70487 0.969 T 0.80821 -0.1211 9 0.59425 D 0.04 -8.5873 14.297 0.66321 0.0724:0.0:0.9276:0.0 . 648 Q8WYA0 IFT81_HUMAN Y 648;648;79 . ENSP00000242591:C648Y C + 2 0 IFT81 109140326 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 9.301000 0.96167 1.338000 0.45544 0.579000 0.79373 TGT TCGA-HV-A5A6-01A-11D-A26I-08 IFT81-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000403529.1 0 0 1 157 401 1 65 1 9.858339e-01 6 25 1 65 4 0 0 0 0 0 2 1 1.000000 154 399 1 64 26 0 0 0 1 65 2 -20.000000 1 1 120846 1 32 1 0 0 0 2.008545 0 0.640000 1.940000 0.635332 0.860000 0.750000 0.980000 0.870000 0.869178 0.860000 1 0.800000 0.930000 PIWIL1 9271 broad.mit.edu 37 12 130827607 130827607 + Missense_Mutation SNP C C T rs144603967 by1000genomes TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr12:130827607C>T ENST00000245255.3 + 3 423 c.151C>T c.(151-153)Cgg>Tgg p.R51W NM_001190971.1|NM_004764.4 NP_001177900.1|NP_004755.2 Q96J94 PIWL1_HUMAN piwi-like RNA-mediated gene silencing 1 57 all_neural(191;0.101)|Medulloblastoma(191;0.163) TGGCCGTGGACGGCAGAGAGG 0.443000 0 SO:0001583 missense ENST00000245255.3 1 1 hg19 CCDS9268.1 2 9.157509157509158E-4 0 0.0 0 0.0 2 0.0034965034965034965 0 0.0 C 16.69 3.194066 0.58017 . . ENSG00000125207 ENST00000245255;ENST00000546060;ENST00000539400;ENST00000539995;ENST00000535956;ENST00000542723 T;T;T;T;T;T 0.09911 2.93;2.93;2.93;2.93;2.93;2.93 5.13 5.13 0.70059 . 0.197782 0.43579 D 0.000552 T 0.36110 0.0955 M 0.77820 2.39 0.58432 D 0.999999 D;D 0.89917 1.0;1.0 D;D 0.83275 0.996;0.994 T 0.12426 -1.0548 10 0.72032 D 0.01 -12.2295 17.5036 0.87738 0.0:1.0:0.0:0.0 . 51;51 Q96J94;Q96J94-2 PIWL1_HUMAN;. W 51 ENSP00000245255:R51W;ENSP00000442086:R51W;ENSP00000440677:R51W;ENSP00000439096:R51W;ENSP00000444353:R51W;ENSP00000438582:R51W ENSP00000245255:R51W R + 1 2 PIWIL1 129393560 1.000000 0.71417 0.836000 0.33094 0.417000 0.31264 3.696000 0.54757 2.544000 0.85801 0.467000 0.42956 CGG TCGA-HV-A5A6-01A-11D-A26I-08 PIWIL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000399510.1 1 0 1 64 131 0 19 0 0 0 0 19 2 0 0 0 0 0 2 1 1.000000 63 129 0 19 2 0 0 0 0 19 2 -8.296194 1 1 121412 7 38 1 0 0 0 2.008545 0 0.640000 1.940000 0.635332 0.990000 0.810000 1.000000 1.000000 0.965990 0.990000 1 0.900000 1.000000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr12:25398284C>T ENST00000256078.4 - 2 98 c.35G>A c.(34-36)gGt>gAt p.G12D KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 23.4 4.409094 0.83340 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.85919 0.5809 M 0.91818 3.245 0.80722 D 1 B;P 0.35714 0.385;0.517 B;B 0.41619 0.257;0.361 D 0.87870 0.2670 10 0.87932 D 0 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN D 12 ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D ENSP00000256078:G12D G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-HV-A5A6-01A-11D-A26I-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 33 57 0 12 1 9.926599e-01 10 7 0 12 2 1 1 140 334 0 453 2 1 1.000000 32 57 0 12 2 1 1 2831 5201 0 12 2 -20.000000 1 1 121404 2 44 1 0 0 0 2.008545 0 0.640000 1.940000 0.635332 0.990000 0.830000 1.000000 1.000000 0.984274 0.990000 1 0.970000 1.000000 VWF 7450 broad.mit.edu 37 12 6080794 6080794 + Missense_Mutation SNP G G A TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr12:6080794G>A ENST00000261405.5 - 44 7773 c.7519C>T c.(7519-7521)Cgg>Tgg p.R2507W NM_000552.3 NP_000543 P04275 VWF_HUMAN von Willebrand factor 129 Antihemophilic Factor(DB00025) GAGTCCCCCCGCGGTGAGCCA 0.612000 0 SO:0001583 missense ENST00000261405.5 1 1 hg19 CCDS8539.1 . . . . . . . . . . G 15.90 2.968317 0.53614 . . ENSG00000110799 ENST00000261405 T 0.37752 1.18 4.79 1.9 0.25705 . 0.194975 0.25261 N 0.031943 T 0.30947 0.0781 M 0.64404 1.975 0.47994 D 0.999565 B 0.19073 0.033 B 0.12156 0.007 T 0.10965 -1.0607 10 0.62326 D 0.03 . 5.2466 0.15500 0.1761:0.0:0.6614:0.1625 . 2507 P04275 VWF_HUMAN W 2507 ENSP00000261405:R2507W ENSP00000261405:R2507W R - 1 2 VWF 5951055 0.487000 0.25988 0.082000 0.20525 0.026000 0.11368 0.507000 0.22675 0.204000 0.20548 0.561000 0.74099 CGG TCGA-HV-A5A6-01A-11D-A26I-08 VWF-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000399020.1 1 0 1 164 299 0 87 0 1 0 130 0 87 2 0 0 0 0 0 2 1 1.000000 161 290 0 87 2 0 0 0 0 87 2 -17.624700 1 1 121412 31 47 1 1 2 3 2.049774 0 0.640000 1.940000 0.641148 0.990000 0.970000 1.000000 1.000000 0.998464 0.990000 1 0.990000 1.000000 AHNAK2 113146 broad.mit.edu 37 14 105420573 105420573 + Silent SNP G G A TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr14:105420573G>A ENST00000333244.5 - 7 1334 c.1215C>T c.(1213-1215)tgC>tgT p.C405C AHNAK2_ENST00000557457.1_5'Flank NM_138420.2 NP_612429.2 Q8IVF2 AHNK2_HUMAN AHNAK nucleoprotein 2 33 all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183) all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116) GGGTTCCCTCGCAAAGTCTAG 0.622000 0 SO:0001819 synonymous_variant ENST00000333244.5 1 1 hg19 CCDS45177.1 TCGA-HV-A5A6-01A-11D-A26I-08 AHNAK2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000410300.1 1 0 1 52 275 0 76 0 0 0 1 0 76 2 0 0 0 0 0 2 1 1.000000 52 270 0 76 2 0 0 0 0 76 2 -3.142702 1 1 121028 21 46 1 0 1 1 1.747417 1 0.640000 1.940000 0.569790 0.410000 0.310000 0.520000 0.420000 0.420292 0.410000 0 0.360000 0.470000 EXOC5 10640 broad.mit.edu 37 14 57698417 57698417 + Missense_Mutation SNP T T A TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr14:57698417T>A ENST00000413566.2 - 11 1314 c.955A>T c.(955-957)Agc>Tgc p.S319C EXOC5_ENST00000340918.7_Missense_Mutation_p.S254C NM_006544.3 NP_006535.1 O00471 EXOC5_HUMAN exocyst complex component 5 22 ATCAGCTTGCTGGAAAGATTG 0.303000 0 SO:0001583 missense ENST00000413566.2 1 1 hg19 CCDS45111.1 . . . . . . . . . . T 21.7 4.195041 0.78902 . . ENSG00000070367 ENST00000413566;ENST00000340918 T;T 0.47177 0.85;0.85 5.62 5.62 0.85841 . 0.079098 0.85682 D 0.000000 T 0.49983 0.1589 L 0.34521 1.04 0.54753 D 0.999987 P;P 0.51791 0.948;0.927 P;P 0.51582 0.545;0.674 T 0.52434 -0.8576 10 0.62326 D 0.03 -7.6021 16.1251 0.81386 0.0:0.0:0.0:1.0 . 254;319 F8W9B8;O00471 .;EXOC5_HUMAN C 319;254 ENSP00000389934:S319C;ENSP00000342100:S254C ENSP00000342100:S254C S - 1 0 EXOC5 56768170 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 5.411000 0.66386 2.267000 0.75376 0.477000 0.44152 AGC TCGA-HV-A5A6-01A-11D-A26I-08 EXOC5-001 KNOWN upstream_uORF|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000412905.1 1 0 1 73 140 0 31 1 9.494723e-01 3 9 0 31 2 0 0 0 0 0 2 1 1.000000 72 140 0 31 2 0 0 0 0 31 2 -20.000000 1 1 0 0 1 0 1 1 1.795831 1 0.640000 1.940000 0.581006 0.910000 0.740000 1.000000 1.000000 0.912202 0.910000 1 0.820000 1.000000 PGPEP1L 145814 broad.mit.edu 37 15 99512680 99512680 + Silent SNP G G A TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr15:99512680G>A ENST00000378919.6 - 4 550 c.345C>T c.(343-345)gaC>gaT p.D115D PGPEP1L_ENST00000535714.1_Silent_p.D61D|RP11-654A16.3_ENST00000559468.1_RNA NM_001102612.2 NP_001096082.2 A6NFU8 PGPIL_HUMAN pyroglutamyl-peptidase I-like 14 AAAAGATCACGTCGACACCCT 0.632000 0 SO:0001819 synonymous_variant ENST00000378919.6 1 1 hg19 CCDS53977.1 TCGA-HV-A5A6-01A-11D-A26I-08 PGPEP1L-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000415703.1 1 0 1 82 447 0 146 0 0 0 0 146 2 0 0 0 0 0 2 1 1.000000 82 442 0 146 2 0 0 0 0 146 2 -20.000000 1 1 0 0 1 0 1 1 1.798880 1 0.640000 1.940000 0.579439 0.410000 0.330000 0.500000 0.410000 0.417553 0.410000 0 0.360000 0.460000 MEFV 4210 broad.mit.edu 37 16 3293394 3293394 + Missense_Mutation SNP T T C TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr16:3293394T>C ENST00000219596.1 - 10 2132 c.2093A>G c.(2092-2094)gAg>gGg p.E698G MEFV_ENST00000339854.4_Missense_Mutation_p.E518G|MEFV_ENST00000541159.1_3'UTR|MEFV_ENST00000536379.1_Missense_Mutation_p.E487G NM_000243.2 NP_000234.1 O15553 MEFV_HUMAN Mediterranean fever 50 CGCCTGGTACTCATTTTCCTT 0.532000 0 SO:0001583 missense ENST00000219596.1 1 1 hg19 CCDS10498.1 . . . . . . . . . . T 13.37 2.217269 0.39201 . . ENSG00000103313 ENST00000219596;ENST00000339854;ENST00000536379 T;T;T 0.61040 0.14;0.14;0.14 5.32 4.23 0.50019 Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1); 0.135230 0.33691 N 0.004653 T 0.62332 0.2419 L 0.35542 1.07 0.09310 N 0.999998 D 0.89917 1.0 D 0.79108 0.992 T 0.52616 -0.8552 10 0.41790 T 0.15 -17.3674 9.3257 0.37990 0.0:0.0855:0.0:0.9145 . 698 O15553 MEFV_HUMAN G 698;518;487 ENSP00000219596:E698G;ENSP00000339639:E518G;ENSP00000445079:E487G ENSP00000219596:E698G E - 2 0 MEFV 3233395 0.118000 0.22208 0.061000 0.19648 0.659000 0.38960 2.161000 0.42358 0.979000 0.38497 0.528000 0.53228 GAG TCGA-HV-A5A6-01A-11D-A26I-08 MEFV-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251464.1 1 0 1 198 428 0 86 0 0 0 0 86 2 0 0 0 0 0 2 1 1.000000 195 423 0 86 2 0 0 0 0 86 2 -20.000000 1 1 0 0 1 1 2 3 2.081051 0 0.640000 1.940000 0.644550 0.990000 0.880000 1.000000 1.000000 0.978051 0.990000 1 0.930000 1.000000 SLC6A2 6530 broad.mit.edu 37 16 55733527 55733527 + Missense_Mutation SNP G G T TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr16:55733527G>T ENST00000379906.2 + 11 1806 c.1551G>T c.(1549-1551)tgG>tgT p.W517C SLC6A2_ENST00000567238.1_Missense_Mutation_p.W412C|SLC6A2_ENST00000414754.3_Missense_Mutation_p.W517C|SLC6A2_ENST00000219833.8_Missense_Mutation_p.W517C|SLC6A2_ENST00000568943.1_Missense_Mutation_p.W517C|SLC6A2_ENST00000561820.1_Missense_Mutation_p.W517C|SLC6A2_ENST00000566163.1_Missense_Mutation_p.W472C 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) GTCTATACTGGAGACTGTGCT 0.592000 0 SO:0001583 missense ENST00000379906.2 1 1 hg19 CCDS10754.1 . . . . . . . . . . G 23.4 4.415365 0.83449 . . ENSG00000103546 ENST00000414754;ENST00000537705;ENST00000379906;ENST00000219833 T;T;T 0.79033 -1.23;-1.23;-1.23 5.55 5.55 0.83447 . 0.000000 0.85682 D 0.000000 D 0.92227 0.7535 H 0.96142 3.775 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.91635 0.999;0.997;0.998;0.998 D 0.94353 0.7581 10 0.87932 D 0 . 18.2862 0.90114 0.0:0.0:1.0:0.0 . 517;231;412;517 Q96KH8;F5H0T4;B4DX48;P23975 .;.;.;SC6A2_HUMAN C 517;231;517;517 ENSP00000394956:W517C;ENSP00000369237:W517C;ENSP00000219833:W517C ENSP00000219833:W517C W + 3 0 SLC6A2 54291028 1.000000 0.71417 1.000000 0.80357 0.982000 0.71751 9.315000 0.96313 2.596000 0.87737 0.650000 0.86243 TGG TCGA-HV-A5A6-01A-11D-A26I-08 SLC6A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256922.2 1 0 1 39 201 0 43 0 0 0 0 43 2 0 0 0 0 0 2 1 1.000000 36 200 0 43 2 0 0 0 0 43 2 -20.000000 1 1 0 0 1 1 2 3 2.092122 0 0.640000 1.940000 0.644550 0.510000 0.370000 1.000000 0.510000 0.535703 0.510000 0 0.440000 0.610000 IL34 146433 broad.mit.edu 37 16 70688501 70688501 + Missense_Mutation SNP C C T TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr16:70688501C>T ENST00000288098.2 + 2 472 c.89C>T c.(88-90)aCg>aTg p.T30M IL34_ENST00000569641.1_Intron|IL34_ENST00000429149.2_Missense_Mutation_p.T30M|IL34_ENST00000566361.1_Missense_Mutation_p.T5M NM_001172772.1 NP_001166243.1 Q6ZMJ4 IL34_HUMAN interleukin 34 17 TGGCCCTTGACGCAGAATGAG 0.572000 OREG0023916 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000288098.2 1 1 hg19 CCDS10895.1 . . . . . . . . . . C 11.00 1.509704 0.27036 . . ENSG00000157368 ENST00000429149;ENST00000288098 T;T 0.49432 0.78;0.78 4.32 3.32 0.38043 . 0.568429 0.15866 N 0.240758 T 0.61515 0.2353 M 0.70595 2.14 0.09310 N 1 D;D 0.89917 1.0;1.0 P;P 0.60886 0.88;0.88 T 0.51434 -0.8706 10 0.66056 D 0.02 -11.2702 10.7643 0.46283 0.1886:0.8114:0.0:0.0 . 30;30 Q6ZMJ4-2;Q6ZMJ4 .;IL34_HUMAN M 30 ENSP00000397863:T30M;ENSP00000288098:T30M ENSP00000288098:T30M T + 2 0 IL34 69246002 0.002000 0.14202 0.051000 0.19133 0.015000 0.08874 1.190000 0.32126 2.258000 0.74832 0.456000 0.33151 ACG TCGA-HV-A5A6-01A-11D-A26I-08 IL34-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268971.3 1 0 1 44 385 0 94 0 4.345854e-01 0 14 0 94 2 0 0 0 0 0 2 1 1.000000 45 382 0 93 2 0 0 0 0 94 2 -15.244260 1 1 121410 1 35 1 1 2 3 2.120359 0 0.640000 1.940000 0.647887 0.320000 0.240000 1.000000 0.330000 0.370339 0.320000 0 0.280000 0.390000 ZNF821 55565 broad.mit.edu 37 16 71913839 71913839 + Missense_Mutation SNP C C T TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr16:71913839C>T ENST00000565601.1 - 2 418 c.11G>A c.(10-12)cGg>cAg p.R4Q ZNF821_ENST00000446827.2_Missense_Mutation_p.R4Q|ZNF821_ENST00000564134.1_Missense_Mutation_p.R4Q|ZNF821_ENST00000425432.1_Missense_Mutation_p.R4Q|ZNF821_ENST00000313565.6_Missense_Mutation_p.R4Q|RP11-498D10.3_ENST00000561979.1_RNA|ZNF821_ENST00000564943.1_5'UTR|ATXN1L_ENST00000569119.1_Intron NM_001201553.1 NP_001188482.1 O75541 ZN821_HUMAN zinc finger protein 821 p.R4L(1) 13 TGTCTGTTTCCGACGGGACAT 0.438000 1 Substitution - Missense(1) SO:0001583 missense ENST00000565601.1 1 1 hg19 CCDS56006.1 . . . . . . . . . . C 19.96 3.924263 0.73213 . . ENSG00000102984 ENST00000425432;ENST00000313565;ENST00000446827 T;T;T 0.01505 6.15;4.82;4.82 5.75 5.75 0.90469 . 0.197314 0.41605 D 0.000844 T 0.04861 0.0131 N 0.19112 0.55 0.52501 D 0.999955 D;D 0.64830 0.994;0.99 P;D 0.66847 0.885;0.947 T 0.57963 -0.7720 10 0.51188 T 0.08 -12.0468 16.6641 0.85248 0.0:1.0:0.0:0.0 . 4;4 B4DKK4;O75541-2 .;. Q 4 ENSP00000398089:R4Q;ENSP00000313822:R4Q;ENSP00000405908:R4Q ENSP00000313822:R4Q R - 2 0 ZNF821 70471340 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 3.962000 0.56766 2.696000 0.92011 0.655000 0.94253 CGG TCGA-HV-A5A6-01A-11D-A26I-08 ZNF821-006 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000434180.1 1 0 1 204 1157 0 165 0 4.008999e-01 0 9 0 165 2 0 0 0 0 0 2 1 1.000000 203 1152 0 164 2 0 0 0 0 165 2 -20.000000 1 1 0 0 1 1 2 3 2.120359 0 0.640000 1.940000 0.647887 0.470000 0.410000 1.000000 0.480000 0.509320 0.470000 0 0.440000 0.520000 HP 3240 broad.mit.edu 37 16 72094379 72094379 + Missense_Mutation SNP G G A TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr16:72094379G>A ENST00000355906.5 + 7 869 c.811G>A c.(811-813)Gat>Aat p.D271N HPR_ENST00000540303.2_5'Flank|HP_ENST00000357763.4_Missense_Mutation_p.D307N|HP_ENST00000562526.1_Intron|HP_ENST00000565574.1_Missense_Mutation_p.D212N|HP_ENST00000570083.1_Missense_Mutation_p.D212N|HPR_ENST00000561690.1_5'Flank|HPR_ENST00000356967.5_Intron|HP_ENST00000398131.2_Missense_Mutation_p.D212N NM_005143.3 NP_005134.1 P00738 HPT_HUMAN haptoglobin 7 Renal(780;9.67e-05)|Ovarian(137;0.00327)|Hepatocellular(780;0.114) ACCTTCAAAGGATTATGCAGA 0.458000 0 SO:0001583 missense ENST00000355906.5 0 1 hg19 CCDS45524.1 0 0.0 0 0.0 0 0.0 0 0.0 0 0.0 g 12.22 1.872195 0.33069 . . ENSG00000257017 ENST00000355906;ENST00000398131;ENST00000405951;ENST00000357763 D;D 0.88741 -2.42;-2.42 5.12 3.18 0.36537 Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3); 0.058620 0.64402 N 0.000005 D 0.82577 0.5067 L 0.33245 0.995 0.80722 D 1 B;B;B;B 0.26120 0.006;0.142;0.035;0.013 B;B;B;B 0.28784 0.02;0.094;0.053;0.065 T 0.77765 -0.2465 10 0.49607 T 0.09 . 10.5318 0.44981 0.1575:0.0:0.8425:0.0 . 93;146;212;271 Q6PEJ8;Q6NSB4;Q0VAC5;P00738 .;.;.;HPT_HUMAN N 271;212;146;247 ENSP00000348170:D271N;ENSP00000381199:D212N ENSP00000348170:D271N D + 1 0 HP 70651880 1.000000 0.71417 0.313000 0.25210 0.827000 0.46813 3.043000 0.49823 0.768000 0.33290 -0.124000 0.14976 GAT TCGA-HV-A5A6-01A-11D-A26I-08 HP-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000421680.1 0 0 0 24 282 1 50 0 2.547856e-01 0 12 1 50 2 0 0 0 0 0 2 1 0.772769 24 280 1 48 20 0 0 0 1 50 2 -2.920855 1 1 120896 10 39 1 1 2 3 2.120359 0 0.640000 1.940000 0.647887 0.250000 0.160000 1.000000 0.250000 0.300196 0.250000 0 0.200000 0.320000 EMR3 84658 broad.mit.edu 37 19 14749135 14749135 + Silent SNP G G A TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr19:14749135G>A ENST00000253673.5 - 11 1366 c.1266C>T c.(1264-1266)atC>atT p.I422I EMR3_ENST00000344373.4_Silent_p.I370I|EMR3_ENST00000443157.2_Silent_p.I296I|EMR3_ENST00000599900.1_Silent_p.I207I NM_032571.3 NP_115960.2 Q9BY15 EMR3_HUMAN egf-like module containing, mucin-like, hormone receptor-like 3 50 AAGCACCGGCGATGATGGAGC 0.582000 0 SO:0001819 synonymous_variant ENST00000253673.5 1 1 hg19 CCDS12315.1 TCGA-HV-A5A6-01A-11D-A26I-08 EMR3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000466488.1 0 0 1 29 165 0 34 0 2.408578e-02 0 2 0 34 2 0 0 0 0 0 2 1 1.000000 29 165 0 34 2 0 0 0 0 34 2 -20.000000 1 1 121412 1 27 1 0 1 1 1.787483 1 0.640000 1.940000 0.579439 0.390000 0.270000 0.540000 0.400000 0.407915 0.390000 0 0.330000 0.470000 RYR1 6261 broad.mit.edu 37 19 38939147 38939147 + Missense_Mutation SNP C C T TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr19:38939147C>T ENST00000359596.3 + 10 953 c.953C>T c.(952-954)tCc>tTc p.S318F RYR1_ENST00000360985.3_Missense_Mutation_p.S318F|RYR1_ENST00000355481.4_Missense_Mutation_p.S318F P21817 RYR1_HUMAN ryanodine receptor 1 (skeletal) 285 all_cancers(60;7.91e-06) Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272) Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786) TTCCGCATCTCCAAGGTCAGT 0.642000 0 SO:0001583 missense ENST00000359596.3 0 1 hg19 CCDS33011.1 . . . . . . . . . . C 16.29 3.080776 0.55753 . . ENSG00000196218 ENST00000359596;ENST00000355481;ENST00000360985 D;D;D 0.85955 -2.05;-2.05;-2.05 4.51 4.51 0.55191 MIR motif (2);MIR (2); 0.090463 0.46145 U 0.000315 D 0.92315 0.7562 M 0.79926 2.475 0.43863 D 0.996461 D;D 0.89917 1.0;1.0 D;D 0.97110 0.998;1.0 D 0.93476 0.6823 10 0.87932 D 0 . 16.1498 0.81605 0.0:1.0:0.0:0.0 . 318;318 P21817-2;P21817 .;RYR1_HUMAN F 318 ENSP00000352608:S318F;ENSP00000347667:S318F;ENSP00000354254:S318F ENSP00000347667:S318F S + 2 0 RYR1 43630987 1.000000 0.71417 1.000000 0.80357 0.986000 0.74619 7.239000 0.78182 2.348000 0.79779 0.491000 0.48974 TCC TCGA-HV-A5A6-01A-11D-A26I-08 RYR1-010 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000462137.1 0 0 0 13 715 0 105 0 0 0 0 105 2 0 0 0 0 0 2 1 0.999512 13 710 0 104 2 0 0 0 0 105 2 -2.849770 1 1 0 0 1 1 2 3 2.282149 1 0.640000 1.940000 0.682652 0.070000 0.020000 1.000000 0.070000 0.287849 0.070000 0 0.040000 1.000000 SYT3 84258 broad.mit.edu 37 19 51133050 51133050 + Missense_Mutation SNP A A T TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr19:51133050A>T ENST00000338916.4 - 3 1686 c.1053T>A c.(1051-1053)ttT>ttA p.F351L SYT3_ENST00000593901.1_Missense_Mutation_p.F351L|SYT3_ENST00000600079.1_Missense_Mutation_p.F351L|SYT3_ENST00000544769.1_Missense_Mutation_p.F351L NM_032298.2 NP_115674.1 Q9BQG1 SYT3_HUMAN synaptotagmin III 35 all_neural(266;0.131) CCTTGGTCTGAAACTTTTTCT 0.632000 0 SO:0001583 missense ENST00000338916.4 1 1 hg19 CCDS12798.1 . . . . . . . . . . A 10.87 1.471928 0.26423 . . ENSG00000213023 ENST00000338916;ENST00000544769 T;T 0.68624 -0.34;-0.34 4.67 -4.51 0.03483 C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1); 0.083116 0.47455 U 0.000232 T 0.44307 0.1287 N 0.12961 0.28 0.50039 D 0.999842 B 0.25955 0.138 B 0.18561 0.022 T 0.03157 -1.1066 10 0.29301 T 0.29 . 17.5164 0.87775 0.183:0.0:0.817:0.0 . 351 Q9BQG1 SYT3_HUMAN L 351 ENSP00000340914:F351L;ENSP00000438883:F351L ENSP00000340914:F351L F - 3 2 SYT3 55824862 0.967000 0.33354 0.971000 0.41717 0.461000 0.32589 0.042000 0.13949 -0.918000 0.03808 -0.250000 0.11733 TTT TCGA-HV-A5A6-01A-11D-A26I-08 SYT3-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000464910.1 1 0 0 156 217 0 54 0 1.749958e-01 0 2 0 54 2 0 0 0 0 0 2 1 1.000000 154 215 0 54 2 0 0 0 0 54 2 -20.000000 1 1 0 0 1 1 2 3 2.478776 1 0.640000 1.940000 0.696356 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 ZNF784 147808 broad.mit.edu 37 19 56135868 56135868 + Silent SNP G G A TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr19:56135868G>A ENST00000325351.4 - 1 99 c.60C>T c.(58-60)tcC>tcT p.S20S ZNF784_ENST00000591479.1_Silent_p.S20S NM_203374.1 NP_976308.1 Q8NCA9 ZN784_HUMAN zinc finger protein 784 1 BRCA - Breast invasive adenocarcinoma(297;0.18) GTGGCTCCTGGGATCGCGACT 0.716000 0 SO:0001819 synonymous_variant ENST00000325351.4 1 1 hg19 CCDS12930.1 TCGA-HV-A5A6-01A-11D-A26I-08 ZNF784-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000453355.2 1 0 0 9 48 0 15 0 2.661550e-01 1 5 0 15 2 0 0 0 0 0 2 1 0.994662 8 47 0 15 2 0 0 0 0 15 2 -17.312020 1 1 0 0 1 1 2 3 2.493615 1 0.640000 1.940000 0.699599 0.680000 0.320000 1.000000 1.000000 0.712254 0.680000 0 0.470000 1.000000 MYO1F 4542 broad.mit.edu 37 19 8609328 8609328 + Silent SNP G G A TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr19:8609328G>A ENST00000338257.8 - 14 1644 c.1377C>T c.(1375-1377)agC>agT p.S459S AC092316.2_ENST00000581156.1_RNA NM_012335.3 NP_036467.2 O00160 MYO1F_HUMAN myosin IF 42 CGTCCAAGACGCTCATGATGC 0.667000 0 SO:0001819 synonymous_variant ENST00000338257.8 1 1 hg19 CCDS42494.1 TCGA-HV-A5A6-01A-11D-A26I-08 MYO1F-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000342716.2 1 0 0 24 112 0 24 0 5.574143e-01 0 10 0 24 2 0 0 0 0 0 2 1 1.000000 24 110 0 24 2 0 0 0 0 24 2 -20.000000 1 1 0 0 1 0 1 1 1.787483 1 0.640000 1.940000 0.579439 0.470000 0.310000 0.650000 0.470000 0.482034 0.470000 0 0.380000 0.570000 CEPT1 10390 broad.mit.edu 37 1 111702113 111702113 + Nonsense_Mutation SNP G G T TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr1:111702113G>T ENST00000545121.1 + 3 659 c.451G>T c.(451-453)Gaa>Taa p.E151* CEPT1_ENST00000357172.4_Nonsense_Mutation_p.E151* NM_001007794.1 NP_001007795.1 Q9Y6K0 CEPT1_HUMAN choline/ethanolamine phosphotransferase 1 8 all_cancers(81;2.27e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359) Choline(DB00122) TCCTCTGGGAGAACTTTTTGA 0.378000 0 SO:0001587 stop_gained ENST00000545121.1 0 1 hg19 CCDS830.1 . . . . . . . . . . G 37 6.135643 0.97315 . . ENSG00000134255 ENST00000545121;ENST00000357172 . . . 5.48 5.48 0.80851 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.87932 D 0 -41.1206 16.8534 0.86000 0.0:0.0:1.0:0.0 . . . . X 151 . ENSP00000349696:E151X E + 1 0 CEPT1 111503636 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 9.476000 0.97823 2.568000 0.86640 0.655000 0.94253 GAA TCGA-HV-A5A6-01A-11D-A26I-08 CEPT1-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000034462.2 1 0 1 148 372 0 27 1 9.842258e-01 2 17 0 27 2 0 0 0 0 0 2 1 1.000000 148 370 0 27 2 0 0 0 0 27 2 -20.000000 1 1 0 0 1 1 2 3 2.140631 0 0.640000 1.940000 0.648986 0.910000 0.780000 1.000000 1.000000 0.916826 0.910000 1 0.840000 1.000000 CAPZA1 829 broad.mit.edu 37 1 113162484 113162484 + Missense_Mutation SNP T T A TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 T A T T Valid Somatic Phase_I WXS RNA Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr1:113162484T>A ENST00000263168.3 + 1 690 c.18T>A c.(16-18)gaT>gaA p.D6E ST7L_ENST00000358039.4_5'Flank|ST7L_ENST00000360743.4_5'Flank|ST7L_ENST00000369666.1_5'Flank|ST7L_ENST00000369669.1_5'Flank|CAPZA1_ENST00000476936.1_3'UTR|ST7L_ENST00000538187.1_5'Flank|ST7L_ENST00000343210.7_5'Flank|ST7L_ENST00000369668.2_5'Flank|ST7L_ENST00000544629.1_5'Flank|ST7L_ENST00000463235.1_Intron|ST7L_ENST00000543570.1_5'Flank|ST7L_ENST00000490067.1_5'Flank NM_006135.2 NP_006126.1 P52907 CAZA1_HUMAN capping protein (actin filament) muscle Z-line, alpha 1 9 Lung SC(450;0.246) all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05) ACTTCGATGATCGTGTGTCGG 0.672000 0 SO:0001583 missense ENST00000263168.3 0 1 hg19 CCDS30805.1 . . . . . . . . . . T 11.82 1.753284 0.31046 . . ENSG00000116489 ENST00000263168 . . . 6.17 6.17 0.99709 . 0.161441 0.53938 D 0.000048 T 0.19565 0.0470 N 0.02765 -0.5 0.80722 D 1 P 0.37176 0.586 P 0.47744 0.556 T 0.31779 -0.9931 9 0.02654 T 1 -1.0931 14.3455 0.66658 0.0:0.0:0.0:1.0 . 6 P52907 CAZA1_HUMAN E 6 . ENSP00000263168:D6E D + 3 2 CAPZA1 112964007 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 1.547000 0.36190 2.371000 0.80710 0.533000 0.62120 GAT TCGA-HV-A5A6-01A-11D-A26I-08 CAPZA1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000032567.2 1 0 1 13 88 0 16 1 9.983661e-01 24 55 0 16 2 0 0 0 0 0 2 1 0.999655 13 88 0 16 2 0 0 0 0 16 2 -19.981850 1 1 0 0 1 1 2 3 2.140631 0 0.640000 1.940000 0.648986 0.430000 0.240000 1.000000 0.410000 0.469779 0.430000 0 0.320000 0.570000 CAPZA1 829 broad.mit.edu 37 1 113162485 113162485 + Missense_Mutation SNP C C T TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr1:113162485C>T ENST00000263168.3 + 1 691 c.19C>T c.(19-21)Cgt>Tgt p.R7C ST7L_ENST00000358039.4_5'Flank|ST7L_ENST00000360743.4_5'Flank|ST7L_ENST00000369666.1_5'Flank|ST7L_ENST00000369669.1_5'Flank|CAPZA1_ENST00000476936.1_3'UTR|ST7L_ENST00000538187.1_5'Flank|ST7L_ENST00000343210.7_5'Flank|ST7L_ENST00000369668.2_5'Flank|ST7L_ENST00000544629.1_5'Flank|ST7L_ENST00000463235.1_Intron|ST7L_ENST00000543570.1_5'Flank|ST7L_ENST00000490067.1_5'Flank NM_006135.2 NP_006126.1 P52907 CAZA1_HUMAN capping protein (actin filament) muscle Z-line, alpha 1 9 Lung SC(450;0.246) all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05) CTTCGATGATCGTGTGTCGGA 0.667000 0 SO:0001583 missense ENST00000263168.3 0 1 hg19 CCDS30805.1 . . . . . . . . . . C 22.6 4.310470 0.81358 . . ENSG00000116489 ENST00000263168 . . . 6.17 6.17 0.99709 . 0.195980 0.45361 D 0.000364 T 0.56171 0.1967 N 0.19112 0.55 0.80722 D 1 D 0.76494 0.999 D 0.67900 0.954 T 0.59968 -0.7354 9 0.56958 D 0.05 -3.1307 17.7962 0.88572 0.0:1.0:0.0:0.0 . 7 P52907 CAZA1_HUMAN C 7 . ENSP00000263168:R7C R + 1 0 CAPZA1 112964008 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 4.595000 0.61048 2.941000 0.99782 0.655000 0.94253 CGT TCGA-HV-A5A6-01A-11D-A26I-08 CAPZA1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000032567.2 1 0 1 13 87 0 16 1 9.985749e-01 24 56 0 16 2 0 0 0 0 0 2 1 0.999657 13 87 0 16 2 0 0 0 0 16 2 -19.972810 1 1 0 0 1 1 2 3 2.140631 0 0.640000 1.940000 0.648986 0.430000 0.240000 1.000000 0.410000 0.473732 0.430000 0 0.320000 0.580000 TUFT1 7286 broad.mit.edu 37 1 151552137 151552137 + Missense_Mutation SNP A A G TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr1:151552137A>G ENST00000368849.3 + 11 999 c.937A>G c.(937-939)Aaa>Gaa p.K313E TUFT1_ENST00000353024.3_Missense_Mutation_p.K254E|TUFT1_ENST00000368848.2_Missense_Mutation_p.K288E|TUFT1_ENST00000538902.1_Missense_Mutation_p.K332E|TUFT1_ENST00000392712.3_Missense_Mutation_p.K258E NM_020127.2 NP_064512.1 Q9NNX1 TUFT1_HUMAN tuftelin 1 13 Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185) LUSC - Lung squamous cell carcinoma(543;0.181) CCAGAATTCAAAAGCTGTGAT 0.547000 0 SO:0001583 missense ENST00000368849.3 1 1 hg19 CCDS1000.1 . . . . . . . . . . A 24.6 4.553081 0.86127 . . ENSG00000143367 ENST00000368849;ENST00000392712;ENST00000353024;ENST00000368848;ENST00000538902 T;T;T;T;T 0.69806 -0.43;-0.43;-0.43;-0.43;-0.43 6.02 6.02 0.97574 . 0.050570 0.85682 D 0.000000 T 0.74921 0.3780 M 0.71581 2.175 0.35617 D 0.809083 D;D;D 0.89917 0.999;1.0;0.997 D;D;D 0.91635 0.997;0.999;0.984 T 0.76710 -0.2859 10 0.37606 T 0.19 -22.6669 14.4941 0.67674 1.0:0.0:0.0:0.0 . 332;288;313 F5H607;Q9NNX1-2;Q9NNX1 .;.;TUFT1_HUMAN E 313;258;254;288;332 ENSP00000357842:K313E;ENSP00000376476:K258E;ENSP00000343781:K254E;ENSP00000357841:K288E;ENSP00000437997:K332E ENSP00000343781:K254E K + 1 0 TUFT1 149818761 1.000000 0.71417 1.000000 0.80357 0.981000 0.71138 6.020000 0.70826 2.304000 0.77564 0.528000 0.53228 AAA TCGA-HV-A5A6-01A-11D-A26I-08 TUFT1-006 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000035022.1 1 0 1 19 98 0 21 1 9.705357e-01 9 24 0 21 2 0 0 0 0 0 2 1 0.999994 19 97 0 21 2 0 0 0 0 21 2 -20.000000 1 1 0 0 1 1 2 3 2.093433 0 0.640000 1.940000 0.644550 0.520000 0.330000 1.000000 0.510000 0.542988 0.520000 0 0.410000 0.650000 SPEN 23013 broad.mit.edu 37 1 16262018 16262018 + Nonsense_Mutation SNP C C T TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr1:16262018C>T ENST00000375759.3 + 11 9487 c.9283C>T c.(9283-9285)Cag>Tag p.Q3095* NM_015001.2 NP_055816.2 Q96T58 MINT_HUMAN spen family transcriptional repressor 149 Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255) CCACCTCTCCCAGGGCGAGGT 0.617000 0 SO:0001587 stop_gained ENST00000375759.3 0 1 hg19 CCDS164.1 . . . . . . . . . . C 50 17.181384 0.99881 . . ENSG00000065526 ENST00000375759 . . . 5.34 5.34 0.76211 . . . . . . . . . . . 0.80722 A 1 . . . . . . . . . . 0.17832 T 0.49 -12.7426 19.0275 0.92939 0.0:1.0:0.0:0.0 . . . . X 3095 . ENSP00000364912:Q3095X Q + 1 0 SPEN 16134605 0.998000 0.40836 0.977000 0.42913 0.846000 0.48090 3.935000 0.56560 2.494000 0.84150 0.491000 0.48974 CAG TCGA-HV-A5A6-01A-11D-A26I-08 SPEN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000025993.1 1 0 1 36 237 0 43 1 9.056351e-01 3 26 0 43 2 0 0 0 0 0 2 1 1.000000 36 236 0 43 2 0 0 0 0 43 2 -3.319644 1 1 0 0 1 1 2 3 2.135344 0 0.640000 1.940000 0.648986 0.420000 0.300000 1.000000 0.420000 0.467017 0.420000 0 0.360000 0.520000 NFASC 23114 broad.mit.edu 37 1 204957892 204957892 + Missense_Mutation SNP G G A TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr1:204957892G>A ENST00000401399.1 + 22 2924 c.2725G>A c.(2725-2727)Ggg>Agg p.G909R NFASC_ENST00000338586.6_Missense_Mutation_p.G1016R|NFASC_ENST00000338515.6_Missense_Mutation_p.G1016R|NFASC_ENST00000513543.1_Missense_Mutation_p.G1012R|NFASC_ENST00000367172.4_Missense_Mutation_p.G1016R|NFASC_ENST00000367170.4_Missense_Mutation_p.G1016R|NFASC_ENST00000495396.1_3'UTR|NFASC_ENST00000367171.4_Missense_Mutation_p.G1001R|NFASC_ENST00000404076.1_Missense_Mutation_p.G995R|NFASC_ENST00000367169.4_Missense_Mutation_p.G909R|NFASC_ENST00000360049.4_Missense_Mutation_p.G1012R|NFASC_ENST00000404907.1_Missense_Mutation_p.G1012R|NFASC_ENST00000539706.1_Missense_Mutation_p.G1012R|NFASC_ENST00000339876.6_Missense_Mutation_p.G909R O94856 NFASC_HUMAN neurofascin 81 all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19) KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158) GGTGGGCTCTGGGGAAGCCGT 0.592000 0 SO:0001583 missense ENST00000401399.1 0 1 hg19 CCDS53460.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 36|36 5.612808|5.612808 0.96637|0.96637 .|. .|. ENSG00000163531|ENSG00000163531 ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000404076;ENST00000401399;ENST00000404907;ENST00000513543;ENST00000430393|ENST00000413225 T;T;T;T;D;T;T;T;D;T;D;T;T;T|. 0.91996|. -0.05;-0.05;-0.05;-0.05;-2.95;-0.05;-0.05;-0.05;-2.95;-0.05;-2.95;-0.05;-0.05;-0.05|. 5.57|5.57 5.57|5.57 0.84162|0.84162 Fibronectin, type III (4);Immunoglobulin-like fold (1);|. 0.000000|. 0.49916|. D|. 0.000140|. D|. 0.86732|. 0.6003|. M|M 0.92970|0.92970 3.365|3.365 0.38365|0.38365 D|D 0.944703|0.944703 D;D;D;D;D;D;D;D;D|. 0.89917|. 1.0;1.0;0.997;1.0;1.0;1.0;1.0;1.0;1.0|. D;D;D;D;D;D;D;D;D|. 0.97110|. 1.0;0.999;0.995;1.0;0.998;1.0;1.0;0.999;0.999|. D|. 0.90619|. 0.4558|. 10|. 0.87932|. D|. 0|. .|. 19.1402|19.1402 0.93444|0.93444 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. 1016;1027;1012;1016;1016;909;1001;909;1012|. O94856;O94856-11;O94856-8;O94856-7;F8W8X7;O94856-4;F8W791;O94856-9;O94856-3|. NFASC_HUMAN;.;.;.;.;.;.;.;.|. R|X 1016;1001;1016;1016;909;1016;1027;1012;1012;909;995;909;1012;1012;1003|34 ENSP00000356140:G1016R;ENSP00000356139:G1001R;ENSP00000356138:G1016R;ENSP00000342128:G1016R;ENSP00000344786:G909R;ENSP00000343509:G1016R;ENSP00000438614:G1012R;ENSP00000353154:G1012R;ENSP00000356137:G909R;ENSP00000385676:G995R;ENSP00000385637:G909R;ENSP00000384061:G1012R;ENSP00000425908:G1012R;ENSP00000415031:G1003R|. ENSP00000295776:G1027R|. G|W +|+ 1|2 0|0 NFASC|NFASC 203224515|203224515 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.993000|0.993000 0.82548|0.82548 9.413000|9.413000 0.97351|0.97351 2.600000|2.600000 0.87896|0.87896 0.655000|0.655000 0.94253|0.94253 GGG|TGG TCGA-HV-A5A6-01A-11D-A26I-08 NFASC-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000131237.1 0 0 0 9 451 0 77 0 0 0 0 77 2 0 0 0 0 0 2 1 0.994200 9 449 0 77 2 0 0 0 0 77 2 -2.892106 1 1 0 0 1 1 2 3 2.093433 0 0.640000 1.940000 0.644550 0.060000 0.020000 1.000000 0.060000 0.095237 0.060000 0 0.040000 0.090000 KCNH1 3756 broad.mit.edu 37 1 210856924 210856924 + Missense_Mutation SNP C C T TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr1:210856924C>T ENST00000271751.4 - 11 2696 c.2669G>A c.(2668-2670)cGc>cAc p.R890H KCNH1_ENST00000367007.4_Missense_Mutation_p.R863H O95259 KCNH1_HUMAN potassium voltage-gated channel, subfamily H (eag-related), member 1 68 GTTGTCCAGGCGCAAGTCGCT 0.592000 0 SO:0001583 missense ENST00000271751.4 1 1 hg19 CCDS1496.1 . . . . . . . . . . C 19.67 3.870929 0.72065 . . ENSG00000143473 ENST00000271751;ENST00000367007 D;D 0.99537 -6.03;-6.11 4.93 4.93 0.64822 . 0.000000 0.85682 D 0.000000 D 0.99444 0.9803 L 0.58101 1.795 0.80722 D 1 D;D 0.89917 0.998;1.0 P;D 0.71184 0.858;0.972 D 0.98847 1.0757 10 0.56958 D 0.05 . 18.1618 0.89710 0.0:1.0:0.0:0.0 . 863;890 Q14CL3;O95259 .;KCNH1_HUMAN H 890;863 ENSP00000271751:R890H;ENSP00000355974:R863H ENSP00000271751:R890H R - 2 0 KCNH1 208923547 1.000000 0.71417 0.907000 0.35723 0.337000 0.28794 7.538000 0.82048 2.290000 0.77057 0.561000 0.74099 CGC TCGA-HV-A5A6-01A-11D-A26I-08 KCNH1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000088332.1 1 0 0 11 267 0 41 0 0 0 0 41 2 0 0 0 0 0 2 1 0.998326 11 264 0 41 2 0 0 0 0 41 2 -4.084644 1 1 0 0 1 1 2 3 2.093433 0 0.640000 1.940000 0.644550 0.120000 0.060000 1.000000 0.120000 0.160264 0.120000 0 0.090000 0.180000 LUZP1 7798 broad.mit.edu 37 1 23420022 23420022 + Missense_Mutation SNP C C G TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr1:23420022C>G ENST00000302291.4 - 4 1534 c.733G>C c.(733-735)Ggc>Cgc p.G245R LUZP1_ENST00000314174.5_Missense_Mutation_p.G245R|LUZP1_ENST00000418342.1_Missense_Mutation_p.G245R|LUZP1_ENST00000374623.3_Missense_Mutation_p.G245R Q86V48 LUZP1_HUMAN leucine zipper protein 1 31 Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Ovarian(437;0.00373)|Breast(348;0.00815)|Myeloproliferative disorder(586;0.0255) GAAGAGATGCCATCCTCAATC 0.393000 0 SO:0001583 missense ENST00000302291.4 1 1 hg19 CCDS30628.1 . . . . . . . . . . C 17.06 3.291930 0.59976 . . ENSG00000169641 ENST00000418342;ENST00000374623;ENST00000302291;ENST00000314174;ENST00000471849 T;T;T;T;T 0.43294 2.75;2.75;2.75;2.53;0.95 6.17 6.17 0.99709 . 0.000000 0.49305 D 0.000143 T 0.55289 0.1911 L 0.46157 1.445 0.40391 D 0.979547 D;D 0.71674 0.998;0.998 D;D 0.69142 0.962;0.962 T 0.50947 -0.8767 10 0.41790 T 0.15 . 13.0796 0.59107 0.0:0.9277:0.0:0.0723 . 245;245 Q86V48-2;Q86V48 .;LUZP1_HUMAN R 245 ENSP00000393460:G245R;ENSP00000363752:G245R;ENSP00000303758:G245R;ENSP00000313705:G245R;ENSP00000428061:G245R ENSP00000303758:G245R G - 1 0 LUZP1 23292609 1.000000 0.71417 0.666000 0.29783 0.800000 0.45204 5.782000 0.68973 2.941000 0.99782 0.655000 0.94253 GGC TCGA-HV-A5A6-01A-11D-A26I-08 LUZP1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000008900.3 1 0 1 120 282 0 28 1 8.466670e-01 3 7 0 28 2 0 0 0 0 0 2 1 1.000000 119 281 0 27 2 0 0 0 0 28 2 -20.000000 1 1 0 0 1 1 2 3 2.140631 0 0.640000 1.940000 0.648986 0.950000 0.810000 1.000000 1.000000 0.948852 0.950000 1 0.880000 1.000000 LPPR4 0 broad.mit.edu 37 1 99762345 99762345 + Missense_Mutation SNP G G C TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr1:99762345G>C ENST00000370185.3 + 3 957 c.460G>C c.(460-462)Ggg>Cgg p.G154R LPPR4_ENST00000370184.1_5'Flank|LPPR4_ENST00000457765.1_Missense_Mutation_p.G154R NM_014839.4 NP_055654.2 Q7Z2D5 LPPR4_HUMAN 72 all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202) AAGAAGAAATGGGGTCGGACT 0.463000 0 SO:0001583 missense ENST00000370185.3 1 1 hg19 CCDS757.1 . . . . . . . . . . G 13.58 2.279059 0.40294 . . ENSG00000117600 ENST00000370185;ENST00000457765;ENST00000263178 T;T 0.14640 2.49;2.49 5.58 5.58 0.84498 . 0.000000 0.85682 D 0.000000 T 0.18002 0.0432 L 0.38175 1.15 0.80722 D 1 D;B 0.69078 0.997;0.004 D;B 0.67103 0.949;0.006 T 0.03025 -1.1081 10 0.21540 T 0.41 -25.1467 19.5717 0.95423 0.0:0.0:1.0:0.0 . 154;154 E7EPS1;Q7Z2D5 .;LPPR4_HUMAN R 154 ENSP00000359204:G154R;ENSP00000394913:G154R ENSP00000263178:G154R G + 1 0 RP4-788L13.1 99534933 1.000000 0.71417 0.996000 0.52242 0.738000 0.42128 6.651000 0.74372 2.644000 0.89710 0.655000 0.94253 GGG TCGA-HV-A5A6-01A-11D-A26I-08 LPPR4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000029670.2 1 0 0 173 355 0 55 0 0 0 0 55 2 0 0 0 0 0 2 1 1.000000 171 349 0 55 2 0 0 0 0 55 2 -14.707600 1 1 0 0 1 1 2 3 2.140631 0 0.640000 1.940000 0.648986 0.990000 0.920000 1.000000 1.000000 0.992461 0.990000 1 0.980000 1.000000 PCSK2 5126 broad.mit.edu 37 20 17417442 17417442 + Missense_Mutation SNP G G A rs144151196 TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr20:17417442G>A ENST00000262545.2 + 8 1114 c.799G>A c.(799-801)Gcc>Acc p.A267T PCSK2_ENST00000377899.1_Missense_Mutation_p.A248T|PCSK2_ENST00000536609.1_Missense_Mutation_p.A232T NM_002594.3 NP_002585.2 P16519 NEC2_HUMAN proprotein convertase subtilisin/kexin type 2 53 """Insulin(DB00071)|Insulin Regular(DB00030)" CATCTACAGCGCCAGCTGGGG 0.617000 0 SO:0001583 missense ENST00000262545.2 1 1 hg19 CCDS13125.1 . . . . . . . . . . G 35 5.555701 0.96514 0.0 1.16E-4 ENSG00000125851 ENST00000377899;ENST00000262545;ENST00000536609 D;D;D 0.87729 -2.29;-2.29;-2.29 5.38 5.38 0.77491 Peptidase S8/S53, subtilisin/kexin/sedolisin (3); 0.000000 0.85682 D 0.000000 D 0.94918 0.8357 M 0.91459 3.21 0.80722 D 1 D;D 0.89917 1.0;0.999 D;D 0.76071 0.987;0.955 D 0.95800 0.8832 10 0.87932 D 0 -30.2528 17.6879 0.88261 0.0:0.0:1.0:0.0 . 232;267 B4DFQ3;P16519 .;NEC2_HUMAN T 248;267;232 ENSP00000367131:A248T;ENSP00000262545:A267T;ENSP00000437458:A232T ENSP00000262545:A267T A + 1 0 PCSK2 17365442 1.000000 0.71417 0.994000 0.49952 0.989000 0.77384 9.413000 0.97351 2.519000 0.84933 0.655000 0.94253 GCC TCGA-HV-A5A6-01A-11D-A26I-08 PCSK2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000078120.2 1 0 1 76 202 0 38 0 0 0 0 38 2 0 0 0 0 0 2 1 1.000000 76 199 0 38 2 0 0 0 0 38 2 -6.173506 1 1 121410 2 33 1 1 2 3 2.092438 0 0.640000 1.940000 0.644550 0.860000 0.700000 1.000000 1.000000 0.870026 0.860000 1 0.780000 0.960000 BCR 613 broad.mit.edu 37 22 23596046 23596046 + Missense_Mutation SNP G G A TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr22:23596046G>A ENST00000305877.8 + 2 2091 c.1340G>A c.(1339-1341)cGc>cAc p.R447H BCR_ENST00000359540.3_Missense_Mutation_p.R447H NM_004327.3 NP_004318.3 P11274 BCR_HUMAN breakpoint cluster region BCR/JAK2(6) 35 Bosutinib(DB06616)|Ponatinib(DB08901) GAGGAGCAGCGCCGGCACCAA 0.622000 T ABL1, FGFR1, JAK2 CML, ALL, AML Dom yes 22 22q11.21 613 breakpoint cluster region L 0 SO:0001583 missense ENST00000305877.8 1 1 hg19 CCDS13806.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 31|31 5.104628|5.104628 0.94245|0.94245 .|. .|. ENSG00000186716|ENSG00000186716 ENST00000334149|ENST00000305877;ENST00000359540 .|T;T .|0.30714 .|1.55;1.52 5.37|5.37 5.37|5.37 0.77165|0.77165 .|. .|0.139385 .|0.47852 .|D .|0.000211 T|T 0.33147|0.33147 0.0853|0.0853 L|L 0.29908|0.29908 0.895|0.895 0.80722|0.80722 D|D 1|1 .|P;D;D .|0.61080 .|0.873;0.989;0.981 .|B;P;P .|0.51974 .|0.256;0.686;0.488 T|T 0.04593|0.04593 -1.0940|-1.0940 6|10 0.13470|0.72032 T|D 0.59|0.01 .|. 12.4859|12.4859 0.55872|0.55872 0.0818:0.0:0.9182:0.0|0.0818:0.0:0.9182:0.0 .|. .|36;447;447 .|B4E065;P11274-2;P11274 .|.;.;BCR_HUMAN T|H 112|447 .|ENSP00000303507:R447H;ENSP00000352535:R447H ENSP00000335450:A112T|ENSP00000303507:R447H A|R +|+ 1|2 0|0 BCR|BCR 21926046|21926046 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.991000|0.991000 0.79684|0.79684 2.513000|2.513000 0.45494|0.45494 2.688000|2.688000 0.91661|0.91661 0.591000|0.591000 0.81541|0.81541 GCC|CGC TCGA-HV-A5A6-01A-11D-A26I-08 BCR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000075819.1 1 0 1 82 196 0 49 1 9.992319e-01 9 19 0 49 2 0 0 0 0 0 2 1 1.000000 82 195 0 48 2 0 0 0 0 49 2 -20.000000 1 1 0 0 1 2 2 4 2.171594 0 0.640000 1.940000 0.661654 0.980000 0.800000 1.000000 1.000000 0.958621 0.980000 1 0.890000 1.000000 MOV10L1 54456 broad.mit.edu 37 22 50589311 50589311 + Missense_Mutation SNP G G A TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr22:50589311G>A ENST00000262794.5 + 21 2958 c.2875G>A c.(2875-2877)Gca>Aca p.A959T MOV10L1_ENST00000395852.1_Missense_Mutation_p.A86T|MOV10L1_ENST00000540615.1_Missense_Mutation_p.A939T|MOV10L1_ENST00000395858.3_Missense_Mutation_p.A959T|MOV10L1_ENST00000395843.1_Intron|MOV10L1_ENST00000545383.1_Missense_Mutation_p.A959T|MOV10L1_ENST00000354853.2_Intron NM_018995.2 NP_061868.1 Q9BXT6 M10L1_HUMAN Mov10 RISC complex RNA helicase like 1 67 all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114) TGCTTGTGGCGCACATAATCC 0.577000 0 SO:0001583 missense ENST00000262794.5 1 1 hg19 CCDS14084.1 . . . . . . . . . . . 9.423 1.083604 0.20309 0.0 1.16E-4 ENSG00000073146 ENST00000545383;ENST00000262794;ENST00000395858;ENST00000540615;ENST00000395852 D;D;T;D;D 0.92752 -1.86;-1.86;-1.44;-2.06;-3.1 5.47 2.05 0.26809 . 0.372221 0.26106 N 0.026316 D 0.84906 0.5576 L 0.27053 0.805 0.21220 N 0.999751 P;B;P;P 0.46987 0.863;0.019;0.587;0.888 B;B;B;P 0.44561 0.324;0.016;0.181;0.453 T 0.76099 -0.3083 10 0.33141 T 0.24 -14.1676 6.3649 0.21449 0.1608:0.0:0.4837:0.3554 . 939;86;959;959 F5H403;Q9BXT6-2;A8MXC6;Q9BXT6 .;.;.;M10L1_HUMAN T 959;959;959;939;86 ENSP00000438978:A959T;ENSP00000262794:A959T;ENSP00000379199:A959T;ENSP00000438542:A939T;ENSP00000379193:A86T ENSP00000262794:A959T A + 1 0 MOV10L1 48931438 0.899000 0.30636 0.334000 0.25495 0.053000 0.15095 1.890000 0.39728 0.670000 0.31165 -0.136000 0.14681 GCA TCGA-HV-A5A6-01A-11D-A26I-08 MOV10L1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000075009.2 1 0 1 33 51 0 31 0 0 0 1 0 31 2 0 0 0 0 0 2 1 1.000000 31 51 0 31 2 0 0 0 0 31 2 -20.000000 1 1 121412 8 38 1 0 1 1 1.430720 1 0.640000 1.940000 0.475524 0.820000 0.610000 0.990000 0.830000 0.824307 0.820000 0 0.710000 0.930000 NCKAP5 344148 broad.mit.edu 37 2 133542913 133542913 + Missense_Mutation SNP C C A TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr2:133542913C>A ENST00000409261.1 - 14 1844 c.1471G>T c.(1471-1473)Gtt>Ttt p.V491F NCKAP5_ENST00000317721.6_Missense_Mutation_p.V491F|NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000409213.1_Intron NM_207363.2 NP_997246.2 O14513 NCKP5_HUMAN NCK-associated protein 5 118 TGGTTTGGAACTGCTTGGAGC 0.502000 0 SO:0001583 missense ENST00000409261.1 1 1 hg19 CCDS46418.1 . . . . . . . . . . c 2.579 -0.297922 0.05532 . . ENSG00000176771 ENST00000409261;ENST00000317721 T;T 0.12039 2.72;2.72 5.11 -3.94 0.04130 . 1.465370 0.05533 U 0.564360 T 0.07593 0.0191 N 0.19112 0.55 0.09310 N 1 B 0.18610 0.029 B 0.16289 0.015 T 0.40040 -0.9584 10 0.66056 D 0.02 . 2.5501 0.04747 0.1056:0.2809:0.3501:0.2633 . 491 O14513 NCKP5_HUMAN F 491 ENSP00000387128:V491F;ENSP00000380603:V491F ENSP00000380603:V491F V - 1 0 NCKAP5 133259383 0.000000 0.05858 0.000000 0.03702 0.012000 0.07955 -0.038000 0.12144 -0.609000 0.05724 -0.162000 0.13425 GTT TCGA-HV-A5A6-01A-11D-A26I-08 NCKAP5-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000331663.1 0 0 0 14 473 0 67 0 0 0 0 67 2 0 0 0 0 0 2 1 0.999743 14 468 0 66 2 0 0 0 0 67 2 -3.378445 1 1 0 0 1 1 2 3 2.131913 0 0.640000 1.940000 0.647887 0.090000 0.040000 1.000000 0.090000 0.148187 0.090000 0 0.060000 0.130000 B3GALT1 8708 broad.mit.edu 37 2 168726199 168726199 + Missense_Mutation SNP G G A rs148250645 by1000genomes TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr2:168726199G>A ENST00000392690.3 + 1 742 c.650G>A c.(649-651)cGc>cAc p.R217H AC016723.4_ENST00000430546.1_RNA|B3GALT1_ENST00000305861.1_Missense_Mutation_p.R217H|AC016723.4_ENST00000436982.2_RNA Q9Y5Z6 B3GT1_HUMAN UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 1 18 CGGGATGTCCGCAGTAAGTGG 0.453000 0 SO:0001583 missense ENST00000392690.3 1 1 hg19 CCDS2227.1 2 9.157509157509158E-4 0 0.0 0 0.0 2 0.0034965034965034965 0 0.0 G 13.23 2.174355 0.38413 0.0 1.16E-4 ENSG00000172318 ENST00000305861;ENST00000392690 D;D 0.85258 -1.96;-1.96 6.02 5.12 0.69794 . 0.000000 0.85682 D 0.000000 T 0.78342 0.4268 L 0.28274 0.84 0.58432 D 0.99999 B 0.20671 0.047 B 0.19946 0.027 T 0.72827 -0.4175 10 0.39692 T 0.17 -16.8954 16.7521 0.85488 0.0:0.0:0.8704:0.1295 . 217 Q9Y5Z6 B3GT1_HUMAN H 217 ENSP00000303740:R217H;ENSP00000376456:R217H ENSP00000303740:R217H R + 2 0 B3GALT1 168434445 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 7.976000 0.88070 2.865000 0.98341 0.655000 0.94253 CGC TCGA-HV-A5A6-01A-11D-A26I-08 B3GALT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255211.2 1 0 1 94 200 0 36 0 0 0 0 36 2 0 0 0 0 0 2 1 1.000000 93 198 0 35 2 0 0 0 0 36 2 -9.285806 1 1 121412 21 44 1 1 2 3 2.131913 0 0.640000 1.940000 0.647887 0.990000 0.850000 1.000000 1.000000 0.977349 0.990000 1 0.930000 1.000000 C2orf44 80304 broad.mit.edu 37 2 24262175 24262175 + Missense_Mutation SNP A A G TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr2:24262175A>G ENST00000295148.4 - 2 247 c.190T>C c.(190-192)Tcc>Ccc p.S64P C2orf44_ENST00000406895.3_Missense_Mutation_p.S64P NM_025203.2 NP_079479.1 Q9H6R7 CB044_HUMAN chromosome 2 open reading frame 44 C2orf44/ALK(2) 24 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) GGGGCCCAGGACAACCCACAG 0.517000 T ALK NSCLC Dom yes 2 2p23.3 80304 chromosome 2 open reading frame 44 E 0 SO:0001583 missense ENST00000295148.4 1 1 hg19 CCDS1705.1 . . . . . . . . . . A 18.33 3.599470 0.66332 . . ENSG00000163026 ENST00000295148;ENST00000406895;ENST00000443232 T;T;T 0.54071 3.31;3.31;0.59 5.24 5.24 0.73138 . 0.230586 0.47455 D 0.000236 T 0.66117 0.2757 M 0.62723 1.935 0.30894 N 0.730021 D;D 0.63880 0.993;0.993 P;P 0.61132 0.884;0.884 T 0.68236 -0.5462 10 0.36615 T 0.2 -4.878 15.4386 0.75165 1.0:0.0:0.0:0.0 . 64;64 Q9H6R7-2;Q9H6R7 .;CB044_HUMAN P 64 ENSP00000295148:S64P;ENSP00000385816:S64P;ENSP00000413426:S64P ENSP00000295148:S64P S - 1 0 C2orf44 24115679 1.000000 0.71417 0.935000 0.37517 0.714000 0.41099 7.490000 0.81461 2.115000 0.64714 0.533000 0.62120 TCC TCGA-HV-A5A6-01A-11D-A26I-08 C2orf44-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000246825.1 1 0 1 82 204 0 59 0 2.021935e-01 0 3 0 59 2 0 0 0 0 0 2 1 1.000000 82 202 0 59 2 0 0 0 0 59 2 -20.000000 1 1 0 0 1 1 2 3 2.127734 0 0.640000 1.940000 0.647887 0.910000 0.750000 1.000000 1.000000 0.915815 0.910000 1 0.830000 1.000000 CAD 790 broad.mit.edu 37 2 27449518 27449518 + Splice_Site SNP G G A TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr2:27449518G>A ENST00000403525.1 + 13 2111 c.e13+1 CAD_ENST00000264705.4_Splice_Site O76075 DFFB_HUMAN carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase 92 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) CTGAGCTCAGGTACGAGGATG 0.542000 0 SO:0001630 splice_region_variant ENST00000403525.1 1 1 hg19 . . . . . . . . . . G 19.44 3.828761 0.71258 . . ENSG00000084774 ENST00000264705;ENST00000403525 . . . 5.06 5.06 0.68205 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 17.0413 0.86490 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . CAD 27303022 1.000000 0.71417 1.000000 0.80357 0.725000 0.41563 8.942000 0.92970 2.358000 0.79984 0.485000 0.47835 . TCGA-HV-A5A6-01A-11D-A26I-08 CAD-002 NOVEL basic|exp_conf protein_coding protein_coding OTTHUMT00000324970.1 1 0 1 55 119 0 17 0 0 1 0 0 17 2 0 0 0 0 0 2 1 1.000000 55 118 0 16 2 0 0 0 0 17 2 -20.000000 1 1 0 0 1 1 2 3 2.127734 0 0.640000 1.940000 0.647887 0.990000 0.790000 1.000000 1.000000 0.963996 0.990000 1 0.900000 1.000000 ECT2 1894 broad.mit.edu 37 3 172534509 172534509 + Missense_Mutation SNP C C T TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr3:172534509C>T ENST00000392692.3 + 24 2713 c.2537C>T c.(2536-2538)aCt>aTt p.T846I ECT2_ENST00000417960.1_Missense_Mutation_p.T814I|ECT2_ENST00000232458.5_Missense_Mutation_p.T815I|ECT2_ENST00000427830.1_Missense_Mutation_p.T815I|ECT2_ENST00000441497.2_Missense_Mutation_p.T815I|ECT2_ENST00000540509.1_Missense_Mutation_p.T846I NM_001258315.1 NP_001245244.1 Q9H8V3 ECT2_HUMAN epithelial cell transforming 2 37 Ovarian(172;0.00197)|Breast(254;0.158) Lung(28;1.33e-14)|LUSC - Lung squamous cell carcinoma(14;1.48e-14) TTCTCCAAAACTCCAAAAAGA 0.378000 0 SO:0001583 missense ENST00000392692.3 1 1 hg19 CCDS58860.1 . . . . . . . . . . C 24.4 4.523463 0.85600 . . ENSG00000114346 ENST00000232458;ENST00000392692;ENST00000427830;ENST00000417960;ENST00000441497;ENST00000540509 T;T;T;T;T;T 0.75260 -0.8;-0.86;-0.92;-0.8;-0.8;-0.86 5.58 5.58 0.84498 . 0.129180 0.64402 D 0.000001 D 0.84465 0.5478 M 0.73217 2.22 0.80722 D 1 P;D;D;D;B 0.63880 0.867;0.967;0.966;0.993;0.134 P;P;P;P;B 0.61003 0.533;0.823;0.744;0.882;0.041 D 0.85923 0.1447 10 0.87932 D 0 -7.6751 18.3345 0.90283 0.0:1.0:0.0:0.0 . 846;291;846;815;814 Q9H8V3;Q96SJ9;Q9H8V3-3;G5E9L8;Q9H8V3-2 ECT2_HUMAN;.;.;.;. I 815;846;815;814;815;846 ENSP00000232458:T815I;ENSP00000376457:T846I;ENSP00000401910:T815I;ENSP00000415876:T814I;ENSP00000412259:T815I;ENSP00000443160:T846I ENSP00000232458:T815I T + 2 0 ECT2 174017203 1.000000 0.71417 1.000000 0.80357 0.988000 0.76386 5.978000 0.70501 2.630000 0.89119 0.561000 0.74099 ACT TCGA-HV-A5A6-01A-11D-A26I-08 ECT2-003 NOVEL basic|CCDS protein_coding protein_coding OTTHUMT00000345994.2 1 0 1 77 185 0 21 1 1 33 48 0 21 2 0 0 0 0 0 2 1 1.000000 77 184 0 21 2 0 0 0 0 21 2 -20.000000 1 1 0 0 1 1 2 3 2.129753 0 0.640000 1.940000 0.647887 0.940000 0.760000 1.000000 1.000000 0.931692 0.940000 1 0.850000 1.000000 LRIT3 345193 broad.mit.edu 37 4 110791281 110791281 + Missense_Mutation SNP G G A TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr4:110791281G>A ENST00000594814.1 + 4 1376 c.1376G>A c.(1375-1377)aGt>aAt p.S459N LRIT3_ENST00000327908.3_Missense_Mutation_p.S276N|LRIT3_ENST00000379920.3_Missense_Mutation_p.S414N|LRIT3_ENST00000409621.2_Missense_Mutation_p.S276N NM_198506.3 NP_940908.3 Q3SXY7 LRIT3_HUMAN leucine-rich repeat, immunoglobulin-like and transmembrane domains 3 16 AAGAATGGAAGTAAGCTTCCT 0.468000 0 SO:0001583 missense ENST00000594814.1 1 1 hg19 CCDS3688.3 . . . . . . . . . . G 0.339 -0.951342 0.02285 . . ENSG00000183423 ENST00000327908;ENST00000379920;ENST00000409621 T;T;T 0.58358 0.34;0.52;0.34 5.06 0.19 0.15125 . 0.885835 0.09711 N 0.765695 T 0.31009 0.0783 N 0.24115 0.695 0.09310 N 1 B;B 0.13594 0.001;0.008 B;B 0.12156 0.001;0.007 T 0.22836 -1.0205 10 0.13470 T 0.59 . 4.3391 0.11101 0.4444:0.1716:0.384:0.0 . 414;276 Q3SXY7;Q3SXY7-2 LRIT3_HUMAN;. N 276;414;276 ENSP00000328222:S276N;ENSP00000369252:S414N;ENSP00000386734:S276N ENSP00000328222:S276N S + 2 0 LRIT3 111010730 0.000000 0.05858 0.001000 0.08648 0.043000 0.13939 0.091000 0.15046 0.160000 0.19432 -0.123000 0.14984 AGT TCGA-HV-A5A6-01A-11D-A26I-08 LRIT3-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000335270.2 0 0 0 10 253 0 30 0 0 0 0 30 2 0 0 0 0 0 2 1 0.996797 10 249 0 30 2 0 0 0 0 30 2 -11.774240 1 1 0 0 1 0 1 1 1.861229 1 0.640000 1.940000 0.587156 0.100000 0.050000 0.180000 0.100000 0.112815 0.100000 0 0.070000 0.140000 C4orf21 0 broad.mit.edu 37 4 113511003 113511003 + Missense_Mutation SNP T T A TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr4:113511003T>A ENST00000505019.1 - 11 3129 c.3004A>T c.(3004-3006)Aca>Tca p.T1002S C4orf21_ENST00000309071.5_Missense_Mutation_p.T1002S NM_018392.4 NP_060862.3 Q86YA3 ZGRF1_HUMAN 45 Ovarian(17;0.156) GGGCTCAATGTAGAGATGTTT 0.358000 0 SO:0001583 missense ENST00000505019.1 1 1 hg19 . . . . . . . . . . T 8.042 0.764003 0.15914 . . ENSG00000138658 ENST00000505019;ENST00000309071 D;T 0.82984 -1.67;1.92 5.23 1.42 0.22433 . 0.154469 0.30584 N 0.009308 T 0.81283 0.4790 L 0.57536 1.79 0.23298 N 0.997957 D;P 0.52996 0.957;0.95 P;P 0.52856 0.711;0.684 T 0.70044 -0.4980 10 0.20046 T 0.44 -3.4573 6.8286 0.23897 0.0:0.2906:0.0:0.7094 . 1002;1002 Q86YA3;G5EA02 CD021_HUMAN;. S 1002 ENSP00000424737:T1002S;ENSP00000309095:T1002S ENSP00000309095:T1002S T - 1 0 C4orf21 113730452 0.001000 0.12720 0.002000 0.10522 0.064000 0.16182 -0.294000 0.08309 0.073000 0.16731 0.477000 0.44152 ACA TCGA-HV-A5A6-01A-11D-A26I-08 C4orf21-003 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000256413.1 1 0 0 104 151 0 32 0 0 1 0 0 32 2 0 0 0 0 0 2 1 1.000000 103 149 0 32 2 0 0 0 0 32 2 -20.000000 1 1 0 0 1 0 1 1 1.861229 1 0.640000 1.940000 0.587156 0.990000 0.940000 1.000000 1.000000 0.996542 0.990000 1 0.990000 1.000000 KLHL5 51088 broad.mit.edu 37 4 39083623 39083623 + Missense_Mutation SNP A A T TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr4:39083623A>T ENST00000504108.1 + 4 1165 c.882A>T c.(880-882)ttA>ttT p.L294F KLHL5_ENST00000508137.2_Missense_Mutation_p.L107F|KLHL5_ENST00000359687.2_Missense_Mutation_p.L294F|KLHL5_ENST00000381930.3_Missense_Mutation_p.L294F|KLHL5_ENST00000261425.3_Missense_Mutation_p.L248F|KLHL5_ENST00000261426.5_Missense_Mutation_p.L233F NM_015990.4 NP_057074.3 Q96PQ7 KLHL5_HUMAN kelch-like family member 5 29 AGTGCCTGTTATCTACAGCTT 0.343000 0 SO:0001583 missense ENST00000504108.1 0 1 hg19 CCDS33974.1 . . . . . . . . . . A 20.8 4.046001 0.75846 . . ENSG00000109790 ENST00000544221;ENST00000261425;ENST00000508137;ENST00000504108;ENST00000359687;ENST00000381930;ENST00000261426 T;T;T;T;T;T 0.81163 -1.46;-1.46;-1.46;-1.46;-1.46;-1.46 5.45 -3.8 0.04307 BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2); 0.000000 0.85682 D 0.000000 D 0.86961 0.6059 M 0.80616 2.505 0.58432 D 0.999998 D;D;D 0.89917 0.985;1.0;1.0 P;D;D 0.87578 0.868;0.998;0.996 D 0.85649 0.1281 10 0.87932 D 0 . 12.1229 0.53902 0.267:0.1183:0.6147:0.0 . 233;294;294 F8WAE7;Q96PQ7;Q96PQ7-2 .;KLHL5_HUMAN;. F 328;248;107;294;294;294;233 ENSP00000261425:L248F;ENSP00000423080:L107F;ENSP00000423897:L294F;ENSP00000352716:L294F;ENSP00000371355:L294F;ENSP00000261426:L233F ENSP00000261425:L248F L + 3 2 KLHL5 38760018 0.997000 0.39634 0.918000 0.36340 0.982000 0.71751 0.453000 0.21811 -0.821000 0.04312 -0.561000 0.04177 TTA TCGA-HV-A5A6-01A-11D-A26I-08 KLHL5-006 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000360604.1 0 0 0 10 419 0 34 0 6.460234e-02 0 16 0 34 2 0 0 0 0 0 2 1 0.996808 10 415 0 34 2 0 0 0 0 34 2 -9.656365 1 1 0 0 1 1 2 3 2.127070 0 0.640000 1.940000 0.647887 0.070000 0.030000 1.000000 0.080000 0.132640 0.070000 0 0.050000 0.110000 PCDHA7 56141 broad.mit.edu 37 5 140215907 140215907 + Missense_Mutation SNP C C T TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr5:140215907C>T ENST00000525929.1 + 1 1939 c.1939C>T c.(1939-1941)Ctt>Ttt p.L647F PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA7_ENST00000378125.3_Missense_Mutation_p.L647F|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529619.1_Intron NM_018910.2 NP_061733.1 Q9UN72 PCDA7_HUMAN protocadherin alpha 7 63 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) GCGCCACCGCCTTCTGGTGCT 0.672000 NSCLC(160;258 2013 5070 22440 28951) 0 SO:0001583 missense ENST00000525929.1 0 1 hg19 CCDS54918.1 . . . . . . . . . . C 15.46 2.839491 0.51057 0.0 1.16E-4 ENSG00000204963 ENST00000525929;ENST00000378125 T;T 0.56776 0.44;0.44 3.57 2.67 0.31697 Cadherin (4);Cadherin-like (1); 0.000000 0.26373 U 0.024756 T 0.67924 0.2945 M 0.70275 2.135 0.37052 D 0.897663 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.998 T 0.73566 -0.3942 10 0.87932 D 0 . 10.3044 0.43672 0.0:0.899:0.0:0.101 . 647;647 Q9UN72-2;Q9UN72 .;PCDA7_HUMAN F 647 ENSP00000436426:L647F;ENSP00000367365:L647F ENSP00000367365:L647F L + 1 0 PCDHA7 140196091 0.008000 0.16893 0.997000 0.53966 0.436000 0.31835 0.148000 0.16224 0.787000 0.33731 0.462000 0.41574 CTT TCGA-HV-A5A6-01A-11D-A26I-08 PCDHA7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000372887.2 0 0 0 6 261 0 60 0 0 0 1 0 60 2 0 0 0 0 0 2 1 0.964641 6 259 0 59 2 0 0 0 0 60 2 -7.124412 1 0 121400 4 40 1 0 1 1 1.467848 1 0.640000 1.940000 0.475524 0.040000 0.010000 0.100000 0.050000 0.055590 0.040000 0 0.020000 0.080000 PCDHGB7 56099 broad.mit.edu 37 5 140798705 140798705 + Missense_Mutation SNP A A G TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr5:140798705A>G ENST00000398594.2 + 1 1279 c.1279A>G c.(1279-1281)Agg>Ggg p.R427G PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA11_ENST00000398587.2_5'Flank|PCDHGA5_ENST00000518069.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000518882.1_5'Flank NM_018927.3 NP_061750.1 Q9Y5F8 PCDGJ_HUMAN protocadherin gamma subfamily B, 7 56 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) AGCCACAGACAGGGGCAAGCC 0.512000 0 SO:0001583 missense ENST00000398594.2 0 1 hg19 CCDS47293.1 . . . . . . . . . . a 0.022 -1.406676 0.01155 . . ENSG00000254122 ENST00000398594 T 0.01665 4.7 5.48 2.98 0.34508 Cadherin (4);Cadherin-like (1); 0.246709 0.20343 U 0.094184 T 0.01092 0.0036 N 0.12611 0.24 0.09310 N 1 B;B 0.17038 0.02;0.009 B;B 0.20384 0.029;0.018 T 0.49504 -0.8933 10 0.19590 T 0.45 . 4.0845 0.09940 0.5796:0.2387:0.0668:0.1149 . 427;427 Q9Y5F8;Q9Y5F8-2 PCDGJ_HUMAN;. G 427 ENSP00000381594:R427G ENSP00000381594:R427G R + 1 2 PCDHGB7 140778889 0.000000 0.05858 0.933000 0.37362 0.268000 0.26511 0.449000 0.21744 0.338000 0.23692 0.402000 0.26972 AGG TCGA-HV-A5A6-01A-11D-A26I-08 PCDHGB7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000376973.1 0 0 0 5 175 0 39 0 1.261034e-03 0 2 0 39 2 0 0 0 0 0 2 1 0.935641 5 172 0 39 2 0 0 0 0 39 2 -7.413249 1 0 0 0 1 0 1 1 1.467848 1 0.640000 1.940000 0.475524 0.060000 0.020000 0.130000 0.060000 0.070284 0.060000 0 0.030000 0.100000 KIF4B 285643 broad.mit.edu 37 5 154394186 154394186 + Missense_Mutation SNP G G A TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr5:154394186G>A ENST00000435029.4 + 1 927 c.767G>A c.(766-768)cGt>cAt p.R256H NM_001099293.1 NP_001092763.1 Q2VIQ3 KIF4B_HUMAN kinesin family member 4B 58 Renal(175;0.00488) Medulloblastoma(196;0.0523) KIRC - Kidney renal clear cell carcinoma(527;0.00112) GAAGGGGATCGTCTAAAAGAG 0.438000 0 SO:0001583 missense ENST00000435029.4 1 1 hg19 CCDS47324.1 . . . . . . . . . . g 15.48 2.846628 0.51164 . . ENSG00000226650 ENST00000435029 T 0.75704 -0.96 1.73 -0.196 0.13232 Kinesin, motor domain (4); . . . . D 0.85796 0.5780 M 0.92880 3.355 0.54753 D 0.999988 D 0.89917 1.0 D 0.97110 1.0 T 0.82358 -0.0497 9 0.87932 D 0 . 5.6824 0.17784 0.3387:0.0:0.6613:0.0 . 256 Q2VIQ3 KIF4B_HUMAN H 256 ENSP00000387875:R256H ENSP00000387875:R256H R + 2 0 KIF4B 154374379 0.928000 0.31464 0.987000 0.45799 0.991000 0.79684 3.002000 0.49496 -0.068000 0.12953 -0.137000 0.14449 CGT TCGA-HV-A5A6-01A-11D-A26I-08 KIF4B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000377478.1 1 0 1 174 183 0 57 0 0 0 0 57 2 0 0 0 0 0 2 1 1.000000 170 180 0 57 2 0 0 0 0 57 2 -20.000000 1 1 121412 3 37 1 0 1 1 1.467848 1 0.640000 1.940000 0.475524 0.980000 0.900000 1.000000 1.000000 0.980439 0.980000 1 0.940000 1.000000 CDH9 1007 broad.mit.edu 37 5 26889954 26889954 + Silent SNP T T C TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr5:26889954T>C ENST00000231021.4 - 9 1675 c.1503A>G c.(1501-1503)aaA>aaG p.K501K NM_016279.3 NP_057363.3 Q9ULB4 CADH9_HUMAN cadherin 9, type 2 (T1-cadherin) 137 CCTGCCCAGGTTTTGCATTTT 0.308000 Melanoma(8;187 585 15745 40864 52829) 0 SO:0001819 synonymous_variant ENST00000231021.4 1 1 hg19 CCDS3893.1 TCGA-HV-A5A6-01A-11D-A26I-08 CDH9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207352.1 1 0 0 181 200 0 19 0 0 0 0 19 2 0 0 0 0 0 2 1 1.000000 181 198 0 19 2 0 0 0 0 19 2 -20.000000 1 1 0 0 1 1 3 4 2.829217 1 0.640000 1.940000 0.738676 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 AHRR 57491 broad.mit.edu 37 5 434610 434610 + Silent SNP G G A TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr5:434610G>A ENST00000505113.1 + 11 1811 c.1767G>A c.(1765-1767)tcG>tcA p.S589S AHRR_ENST00000316418.5_Silent_p.S607S|AHRR_ENST00000512529.1_Silent_p.S435S|AHRR_ENST00000506456.1_Silent_p.S445S NM_001242412.1 NP_001229341.1 A9YTQ3 AHRR_HUMAN aryl-hydrocarbon receptor repressor 20 Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863) TGTACATCTCGCACCTGGGGC 0.667000 0 SO:0001819 synonymous_variant ENST00000505113.1 1 1 hg19 CCDS56355.1 TCGA-HV-A5A6-01A-11D-A26I-08 AHRR-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000367720.1 1 0 1 60 119 0 16 1 2.653755e-01 2 1 0 16 2 0 0 0 0 0 2 1 1.000000 59 119 0 15 2 0 0 0 0 16 2 -20.000000 1 1 121012 3 30 1 1 3 4 2.766949 1 0.640000 1.940000 0.751381 0.990000 0.990000 1.000000 1.000000 0.999994 0.990000 1 0.990000 1.000000 JARID2 3720 broad.mit.edu 37 6 15497190 15497190 + Silent SNP C C T TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr6:15497190C>T ENST00000341776.2 + 7 1978 c.1734C>T c.(1732-1734)cgC>cgT p.R578R JARID2_ENST00000541660.1_Silent_p.R540R|JARID2_ENST00000397311.3_Silent_p.R406R NM_004973.3 NP_004964.2 Q92833 JARD2_HUMAN jumonji, AT rich interactive domain 2 59 Breast(50;0.0142)|Ovarian(93;0.103) all_hematologic(90;0.00612) AGTCGGTCCGCGCTCAGGTGG 0.652000 0 SO:0001819 synonymous_variant ENST00000341776.2 1 1 hg19 CCDS4533.1 TCGA-HV-A5A6-01A-11D-A26I-08 JARID2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000039926.1 1 0 1 23 87 0 12 0 2.934624e-01 0 5 0 12 2 0 0 0 0 0 2 1 1.000000 23 87 0 12 2 0 0 0 0 12 2 -20.000000 1 1 121408 2 29 1 0 1 1 1.785526 1 0.640000 1.940000 0.579439 0.550000 0.370000 0.770000 0.560000 0.569464 0.550000 0 0.460000 0.670000 TTBK1 84630 broad.mit.edu 37 6 43251409 43251409 + Silent SNP G G A TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr6:43251409G>A ENST00000259750.4 + 14 3014 c.2931G>A c.(2929-2931)gcG>gcA p.A977A NM_032538.1 NP_115927.1 Q5TCY1 TTBK1_HUMAN tau tubulin kinase 1 53 Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399) GGGCCCGAGCGCCCCTGGAGA 0.697000 0 SO:0001819 synonymous_variant ENST00000259750.4 1 1 hg19 CCDS34455.1 TCGA-HV-A5A6-01A-11D-A26I-08 TTBK1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040584.3 1 0 1 46 194 0 41 0 0 0 0 41 2 0 0 0 0 0 2 1 1.000000 45 193 0 41 2 0 0 0 0 41 2 -3.539157 1 1 121356 15 40 1 0 1 1 1.790127 1 0.640000 1.940000 0.576271 0.500000 0.380000 0.640000 0.510000 0.514067 0.500000 0 0.440000 0.580000 MTO1 25821 broad.mit.edu 37 6 74210401 74210401 + Silent SNP A A G TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr6:74210401A>G ENST00000370300.4 + 13 2187 c.2097A>G c.(2095-2097)tcA>tcG p.S699S MTO1_ENST00000370305.1_Silent_p.S625S|MTO1_ENST00000415954.2_Silent_p.S714S|MTO1_ENST00000498286.1_Silent_p.S674S NM_012123.3|NM_133645.2 NP_036255.2|NP_598400.1 Q9Y2Z2 MTO1_HUMAN mitochondrial tRNA translation optimization 1 27 TGAATGAATCATCCAAGACTG 0.398000 0 SO:0001819 synonymous_variant ENST00000370300.4 0 1 hg19 CCDS4979.1 TCGA-HV-A5A6-01A-11D-A26I-08 MTO1-003 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000041215.2 0 0 0 7 324 0 29 0 2.421131e-01 0 39 0 29 2 0 0 0 0 0 2 1 0.980471 7 322 0 29 2 0 0 0 0 29 2 -3.426537 1 1 0 0 1 1 2 3 2.074786 0 0.640000 1.940000 0.642289 0.060000 0.020000 0.140000 0.060000 0.084500 0.060000 0 0.040000 0.100000 OR2A14 135941 broad.mit.edu 37 7 143826995 143826995 + Missense_Mutation SNP C C T TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr7:143826995C>T ENST00000408899.2 + 1 845 c.790C>T c.(790-792)Cgc>Tgc p.R264C NM_001001659.1 NP_001001659.1 Q96R47 O2A14_HUMAN olfactory receptor, family 2, subfamily A, member 14 22 Melanoma(164;0.0783) CCCCAAGTCCCGCCATCCTGA 0.542000 0 SO:0001583 missense ENST00000408899.2 1 1 hg19 CCDS43672.1 . . . . . . . . . . C 4.537 0.099753 0.08681 . . ENSG00000221938 ENST00000408899 T 0.00130 8.69 4.18 -5.49 0.02584 GPCR, rhodopsin-like superfamily (1); 2.119410 0.03153 U 0.168207 T 0.00144 0.0004 L 0.35414 1.06 0.09310 N 1 B 0.19817 0.039 B 0.21546 0.035 T 0.33904 -0.9850 10 0.72032 D 0.01 0.4492 11.4184 0.49967 0.7699:0.1508:0.0:0.0792 . 264 Q96R47 O2A14_HUMAN C 264 ENSP00000386137:R264C ENSP00000386137:R264C R + 1 0 OR2A14 143457928 0.000000 0.05858 0.001000 0.08648 0.001000 0.01503 -2.560000 0.00921 -0.882000 0.03987 -0.310000 0.09108 CGC TCGA-HV-A5A6-01A-11D-A26I-08 OR2A14-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000349980.1 1 0 1 147 450 0 132 0 0 0 0 132 2 0 0 0 0 0 2 1 1.000000 144 444 0 132 2 0 0 0 0 132 2 -5.033565 1 1 0 0 1 0 1 1 1.455483 1 0.640000 1.940000 0.475524 0.520000 0.450000 0.600000 0.530000 0.529005 0.520000 0 0.480000 0.570000 FAM126A 84668 broad.mit.edu 37 7 23000935 23000935 + Silent SNP A A G TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr7:23000935A>G ENST00000432176.2 - 9 982 c.750T>C c.(748-750)aaT>aaC p.N250N FAM126A_ENST00000498833.1_5'UTR|FAM126A_ENST00000409923.1_Silent_p.N250N NM_032581.3 NP_115970.2 Q9BYI3 HYCCI_HUMAN family with sequence similarity 126, member A 23 CCCATTCTCCATTATAACTAT 0.294000 0 SO:0001819 synonymous_variant ENST00000432176.2 1 1 hg19 CCDS5377.1 . . . . . . . . . . A 7.238 0.600710 0.13939 . . ENSG00000122591 ENST00000440481 . . . 5.29 5.29 0.74685 . . . . . T 0.71239 0.3316 . . . 0.80722 D 1 . . . . . . T 0.70722 -0.4794 4 . . . -20.4149 15.2237 0.73333 1.0:0.0:0.0:0.0 . . . . T 302 . . M - 2 0 FAM126A 22967460 1.000000 0.71417 1.000000 0.80357 0.900000 0.52787 3.815000 0.55651 2.008000 0.58898 0.528000 0.53228 ATG TCGA-HV-A5A6-01A-11D-A26I-08 FAM126A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250230.1 1 0 0 48 601 0 38 0 1.714472e-01 1 9 0 38 2 0 0 0 0 0 2 1 1.000000 48 593 0 38 2 0 0 0 0 38 2 -11.272510 1 1 0 0 1 1 3 4 3.140805 1 0.640000 1.940000 0.763903 0.360000 0.260000 1.000000 0.360000 0.447703 0.360000 0 0.300000 0.460000 CHST12 55501 broad.mit.edu 37 7 2473140 2473140 + Missense_Mutation SNP G G A TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr7:2473140G>A ENST00000258711.6 + 2 1001 c.866G>A c.(865-867)cGc>cAc p.R289H NM_001243794.1|NM_001243795.1|NM_018641.4 NP_001230723.1|NP_001230724.1|NP_061111.1 Q9NRB3 CHSTC_HUMAN carbohydrate (chondroitin 4) sulfotransferase 12 21 Ovarian(82;0.0253) GCCTCGGCGCGCGAGGCCTTC 0.652000 0 SO:0001583 missense ENST00000258711.6 1 1 hg19 CCDS5333.1 . . . . . . . . . . G 9.812 1.183472 0.21870 . . ENSG00000136213 ENST00000258711 T 0.74106 -0.81 5.27 4.38 0.52667 . 1.737820 0.03407 N 0.204206 T 0.66626 0.2808 L 0.32530 0.975 0.23673 N 0.997141 P 0.34615 0.459 B 0.19666 0.026 T 0.57825 -0.7744 10 0.48119 T 0.1 -6.0021 13.4009 0.60883 0.0759:0.0:0.9241:0.0 . 289 Q9NRB3 CHSTC_HUMAN H 289 ENSP00000258711:R289H ENSP00000258711:R289H R + 2 0 CHST12 2439666 0.995000 0.38212 0.794000 0.32065 0.913000 0.54294 2.682000 0.46934 1.221000 0.43506 0.462000 0.41574 CGC TCGA-HV-A5A6-01A-11D-A26I-08 CHST12-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000060170.3 1 0 1 104 464 0 74 1 1 28 89 0 74 2 0 0 0 0 0 2 1 1.000000 100 448 0 72 2 0 0 0 0 74 2 -20.000000 1 1 0 0 1 1 3 4 3.140805 1 0.640000 1.940000 0.763903 0.880000 0.720000 1.000000 1.000000 0.892362 0.880000 1 0.800000 1.000000 TECPR1 25851 broad.mit.edu 37 7 97863071 97863071 + Missense_Mutation SNP G G T rs113639233 TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr7:97863071G>T ENST00000447648.2 - 11 1633 c.1334C>A c.(1333-1335)gCc>gAc p.A445D TECPR1_ENST00000542604.1_Missense_Mutation_p.A375D|TECPR1_ENST00000379795.3_Missense_Mutation_p.A445D Q7Z6L1 TCPR1_HUMAN tectonin beta-propeller repeat containing 1 26 CAGGCCTGAGGCTGAGTTCCC 0.647000 0 SO:0001583 missense ENST00000447648.2 0 0 hg19 CCDS47648.1 . . . . . . . . . . G 5.957 0.360476 0.11296 . . ENSG00000205356 ENST00000447648;ENST00000379795;ENST00000542604 T;T;T 0.31247 1.5;1.5;1.5 3.73 3.73 0.42828 . 1.167180 0.06148 N 0.673577 T 0.19846 0.0477 N 0.08118 0 0.09310 N 0.999998 B;B 0.29341 0.216;0.242 B;B 0.31191 0.125;0.068 T 0.08066 -1.0740 10 0.12430 T 0.62 -14.1381 14.8693 0.70444 0.0:0.0:1.0:0.0 . 375;445 F5GX57;Q7Z6L1 .;TCPR1_HUMAN D 445;445;375 ENSP00000404923:A445D;ENSP00000369121:A445D;ENSP00000441121:A375D ENSP00000369121:A445D A - 2 0 TECPR1 97701007 0.059000 0.20769 0.081000 0.20488 0.039000 0.13416 2.694000 0.47035 1.826000 0.53198 0.462000 0.41574 GCC TCGA-HV-A5A6-01A-11D-A26I-08 TECPR1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000334661.1 1 0 1 14 120 0 13 1 8.835639e-01 19 16 0 13 2 0 0 0 0 0 2 1 0.999798 14 119 0 13 2 0 0 0 0 13 2 -8.149257 1 0 0 0 1 1 2 3 2.508307 1 0.640000 1.940000 0.699599 0.430000 0.230000 1.000000 0.390000 0.545835 0.430000 0 0.320000 1.000000 AP3M2 10947 broad.mit.edu 37 8 42023053 42023053 + Silent SNP C C T TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chr8:42023053C>T ENST00000518421.1 + 7 1069 c.778C>T c.(778-780)Ctg>Ttg p.L260L AP3M2_ENST00000396926.3_Silent_p.L260L|AP3M2_ENST00000174653.3_Silent_p.L260L|AP3M2_ENST00000517922.1_Silent_p.L260L|AP3M2_ENST00000520685.1_Intron NM_001134296.1 NP_001127768.1 P53677 AP3M2_HUMAN adaptor-related protein complex 3, mu 2 subunit 17 all_cancers(6;8.14e-25)|all_epithelial(6;2.41e-27)|all_lung(13;5.09e-13)|Lung NSC(13;8.38e-12)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211) all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983) BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|Colorectal(10;0.00165)|OV - Ovarian serous cystadenocarcinoma(14;0.00346)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024) CTTCCGCCTGCTGTCTTACCA 0.453000 0 SO:0001819 synonymous_variant ENST00000518421.1 1 1 hg19 CCDS6125.1 TCGA-HV-A5A6-01A-11D-A26I-08 AP3M2-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000376996.1 0 0 0 18 767 0 91 0 1.235539e-01 0 25 0 91 2 0 0 0 0 0 2 1 0.999979 18 755 0 91 2 0 0 0 0 91 2 -2.732411 1 1 0 0 1 1 2 3 2.335731 1 0.640000 1.940000 0.688797 0.090000 0.040000 1.000000 0.080000 0.308508 0.090000 0 0.060000 1.000000 COL4A5 1287 broad.mit.edu 37 X 107849999 107849999 + Missense_Mutation SNP C C A TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chrX:107849999C>A ENST00000361603.2 + 29 2516 c.2272C>A c.(2272-2274)Cca>Aca p.P758T COL4A5_ENST00000328300.6_Missense_Mutation_p.P758T NM_000495.4 NP_000486.1 P29400 CO4A5_HUMAN collagen, type IV, alpha 5 99 ATTACCTGGGCCACCTGGGCC 0.507000 Alport syndrome with Diffuse Leiomyomatosis 0 SO:0001583 missense Familial Cancer Database ENST00000361603.2 0 1 hg19 CCDS14543.1 . . . . . . . . . . C 17.45 3.392716 0.62066 . . ENSG00000188153 ENST00000328300;ENST00000361603;ENST00000508186 D;D 0.97710 -4.5;-4.5 5.61 5.61 0.85477 . 0.121540 0.56097 D 0.000027 D 0.98071 0.9364 M 0.66506 2.035 0.53688 D 0.999976 D;D;D 0.69078 0.982;0.997;0.982 P;D;P 0.63113 0.812;0.911;0.812 D 0.97820 1.0256 10 0.14656 T 0.56 . 18.6523 0.91435 0.0:1.0:0.0:0.0 . 758;366;758 E7EVY4;Q49AM6;P29400 .;.;CO4A5_HUMAN T 758 ENSP00000331902:P758T;ENSP00000354505:P758T ENSP00000331902:P758T P + 1 0 COL4A5 107736655 1.000000 0.71417 1.000000 0.80357 0.902000 0.53008 7.456000 0.80751 2.348000 0.79779 0.600000 0.82982 CCA TCGA-HV-A5A6-01A-11D-A26I-08 COL4A5-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000057880.2 0 0 0 11 545 0 65 0 2.901728e-03 0 4 0 65 2 0 0 0 0 0 2 1 0.998291 11 541 0 64 2 0 0 0 0 65 2 -3.117730 1 1 0 0 1 0 1 1 0.640000 1.940000 0.640000 0.060000 0.020000 0.110000 0.060000 0.067096 0.060000 0 0.040000 0.090000 ARHGAP6 395 broad.mit.edu 37 X 11187680 11187680 + Missense_Mutation SNP G G A TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chrX:11187680G>A ENST00000337414.4 - 9 2626 c.1754C>T c.(1753-1755)aCg>aTg p.T585M ARHGAP6_ENST00000380732.3_Missense_Mutation_p.T617M|ARHGAP6_ENST00000413512.3_Missense_Mutation_p.T394M|ARHGAP6_ENST00000534860.1_Missense_Mutation_p.T410M|ARHGAP6_ENST00000303025.6_Missense_Mutation_p.T382M|ARHGAP6_ENST00000491514.1_5'UTR|ARHGAP6_ENST00000380718.1_Missense_Mutation_p.T585M|ARHGAP6_ENST00000380736.1_Missense_Mutation_p.T382M NM_013427.2 NP_038286.2 O43182 RHG06_HUMAN Rho GTPase activating protein 6 38 GATGATGGCCGTGCTCTCCTC 0.483000 0 SO:0001583 missense ENST00000337414.4 1 1 hg19 CCDS14140.1 . . . . . . . . . . G 18.43 3.622793 0.66787 2.61E-4 0.0 ENSG00000047648 ENST00000534860;ENST00000380736;ENST00000303025;ENST00000337414;ENST00000380717;ENST00000380718;ENST00000413512;ENST00000380732 T;T;T;T;T;T;T;T 0.42900 0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96 5.57 5.57 0.84162 Rho GTPase-activating protein domain (3);Rho GTPase activation protein (1); 0.000000 0.53938 D 0.000044 T 0.55641 0.1933 L 0.45051 1.395 0.58432 D 0.999995 D;D;D;D;D 0.89917 0.999;0.996;1.0;0.998;1.0 P;P;D;D;D 0.69824 0.791;0.813;0.966;0.917;0.964 T 0.55829 -0.8079 10 0.54805 T 0.06 . 14.2504 0.66016 0.0:0.0:0.8507:0.1493 . 394;382;585;585;585 B7Z8H7;O43182-5;O43182-2;O43182;A8KAL3 .;.;.;RHG06_HUMAN;. M 410;382;382;585;421;585;394;617 ENSP00000438135:T410M;ENSP00000370112:T382M;ENSP00000302312:T382M;ENSP00000338967:T585M;ENSP00000370093:T421M;ENSP00000370094:T585M;ENSP00000389394:T394M;ENSP00000370108:T617M ENSP00000302312:T382M T - 2 0 ARHGAP6 11097601 1.000000 0.71417 0.975000 0.42487 0.717000 0.41224 6.141000 0.71744 2.344000 0.79699 0.544000 0.68410 ACG TCGA-HV-A5A6-01A-11D-A26I-08 ARHGAP6-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000055760.2 1 0 1 86 426 0 56 1 5.749979e-01 5 6 0 56 2 0 0 0 0 0 2 1 1.000000 85 424 0 56 2 0 0 0 0 56 2 -20.000000 1 1 121412 1 36 1 0 1 1 0.640000 1.940000 0.640000 0.520000 0.420000 0.630000 0.520000 0.528350 0.520000 0 0.470000 0.580000 SLC7A3 84889 broad.mit.edu 37 X 70149579 70149579 + Missense_Mutation SNP C C T TCGA-HV-A5A6-01A-11D-A26I-08 TCGA-HV-A5A6-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx cef48024-e351-4de9-a83b-f3c10fe9e0f7 bc5bef8e-3ef9-4f30-9ed9-5b861c924522 g.chrX:70149579C>T ENST00000374299.3 - 2 413 c.269G>A c.(268-270)cGg>cAg p.R90Q SLC7A3_ENST00000298085.4_Missense_Mutation_p.R90Q Q8WY07 CTR3_HUMAN solute carrier family 7 (cationic amino acid transporter, y+ system), member 3 31 Renal(35;0.156) L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129) ACGGGGAACCCGGGCACCAAA 0.542000 0 SO:0001583 missense ENST00000374299.3 1 1 hg19 CCDS14404.1 . . . . . . . . . . C 28.8 4.954560 0.92726 . . ENSG00000165349 ENST00000374299;ENST00000298085 D;D 0.89875 -2.58;-2.58 4.7 4.7 0.59300 Amino acid permease domain (1); 0.000000 0.85682 D 0.000000 D 0.94145 0.8122 M 0.87269 2.87 0.80722 D 1 D 0.62365 0.991 P 0.60012 0.867 D 0.95016 0.8156 10 0.62326 D 0.03 . 15.7504 0.77980 0.0:1.0:0.0:0.0 . 90 Q8WY07 CTR3_HUMAN Q 90 ENSP00000363417:R90Q;ENSP00000298085:R90Q ENSP00000298085:R90Q R - 2 0 SLC7A3 70066304 1.000000 0.71417 0.961000 0.40146 0.906000 0.53458 7.511000 0.81718 2.168000 0.68352 0.529000 0.55759 CGG TCGA-HV-A5A6-01A-11D-A26I-08 SLC7A3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057080.1 1 0 1 33 95 0 22 0 0 0 0 22 2 0 0 0 0 0 2 1 1.000000 33 95 0 22 2 0 0 0 0 22 2 -20.000000 1 1 121410 1 21 1 0 1 1 0.640000 1.940000 0.640000 0.800000 0.580000 1.000000 1.000000 0.810000 0.800000 0 0.680000 0.930000