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 HTRA1 5654 broad.mit.edu 37 10 124266340 124266340 + Missense_Mutation SNP G G A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr10:124266340G>A ENST00000368984.3 + 4 1039 c.911G>A c.(910-912)gGc>gAc p.G304D NM_002775.4 NP_002766.1 Q92743 HTRA1_HUMAN HtrA serine peptidase 1 17 all_neural(114;0.0765)|Lung NSC(174;0.133)|all_lung(145;0.163)|Breast(234;0.238) CAGCGAGGCGGCAAAGAGCTG 0.617000 0 SO:0001583 missense ENST00000368984.3 0 1 hg19 CCDS7630.1 . . . . . . . . . . G 33 5.241471 0.95272 . . ENSG00000166033 ENST00000368984;ENST00000435263;ENST00000420892 D;D 0.88201 -2.35;-2.34 5.24 5.24 0.73138 Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1); 0.000000 0.85682 D 0.000000 D 0.91556 0.7333 L 0.31065 0.9 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 D 0.92821 0.6272 10 0.87932 D 0 -14.1768 18.8615 0.92273 0.0:0.0:1.0:0.0 . 304 Q92743 HTRA1_HUMAN D 304;271;45 ENSP00000357980:G304D;ENSP00000412676:G45D ENSP00000357980:G304D G + 2 0 HTRA1 124256330 1.000000 0.71417 0.998000 0.56505 0.972000 0.66771 9.613000 0.98350 2.456000 0.83038 0.655000 0.94253 GGC TCGA-FB-AAPZ-01A-11D-A40W-08 HTRA1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000128327.1 0 0 0 6 289 0 65 0 8.951188e-01 0 197 0 65 2 0 0 0 0 0 2 1 9.642824e-01 6 286 0 65 2 -2.823622 1 1 0 0 1 1 3 4 2.062720 1 0.680000 3.130000 0.770511 1.000000e-01 3.000000e-02 1.000000 0.090000 0.309835 1.000000e-01 0 5.000000e-02 1 MKI67 4288 broad.mit.edu 37 10 129906577 129906577 + Missense_Mutation SNP G G A rs117795868 by1000genomes TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr10:129906577G>A ENST00000368654.3 - 13 3902 c.3527C>T c.(3526-3528)aCg>aTg p.T1176M MKI67_ENST00000368653.3_Missense_Mutation_p.T816M NM_002417.4 NP_002408.3 P46013 KI67_HUMAN marker of proliferation Ki-67 159 all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203) TGGTTTGGGCGTAAGCATGGC 0.463000 0 SO:0001583 missense ENST00000368654.3 0 1 hg19 CCDS7659.1 1 4.578754578754579E-4 0 0.0 0 0.0 1 0.0017482517482517483 0 0.0 G 12.05 1.822665 0.32237 . . ENSG00000148773 ENST00000368654;ENST00000368653;ENST00000537609 T;T 0.03301 3.98;3.98 2.74 1.83 0.25207 . 1.848640 0.03443 N 0.209516 T 0.15998 0.0385 M 0.72118 2.19 0.09310 N 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.78314 0.96;0.991;0.989 T 0.06058 -1.0848 10 0.52906 T 0.07 . 5.4955 0.16799 0.1565:0.0:0.8435:0.0 . 1175;816;1176 F5H4V4;P46013-2;P46013 .;.;KI67_HUMAN M 1176;816;1175 ENSP00000357643:T1176M;ENSP00000357642:T816M ENSP00000357642:T816M T - 2 0 MKI67 129796567 0.005000 0.15991 0.002000 0.10522 0.005000 0.04900 0.110000 0.15437 0.740000 0.32651 0.462000 0.41574 ACG TCGA-FB-AAPZ-01A-11D-A40W-08 MKI67-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000050999.1 0 0 0 7 1189 1 233 0 5.012524e-05 0 2 1 233 2 0 0 0 0 0 2 0 1.935142e-02 7 1173 1 229 18 -2.031104 0 1 121412 29 52 1 1 3 4 2.079943 1 0.680000 3.130000 0.769386 3.000000e-02 0 1.000000 0.030000 0.261777 3.000000e-02 0 1.000000e-02 1 GLYAT 10249 broad.mit.edu 37 11 58477299 58477299 + Nonsense_Mutation SNP G G T TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr11:58477299G>T ENST00000344743.3 - 6 972 c.831C>A c.(829-831)taC>taA p.Y277* GLYAT_ENST00000529732.1_Nonsense_Mutation_p.Y277* NM_201648.2 NP_964011.2 Q6IB77 GLYAT_HUMAN glycine-N-acyltransferase 16 Breast(21;0.0044)|all_epithelial(135;0.0157) Glycine(DB00145) GTTGCAGTGTGTAACTCATTT 0.463000 0 SO:0001587 stop_gained ENST00000344743.3 0 1 hg19 CCDS7970.1 . . . . . . . . . . G 12.86 2.064053 0.36373 . . ENSG00000149124 ENST00000344743;ENST00000529732 . . . 6.06 -0.557 0.11800 . 2.072040 0.02028 N 0.048337 . . . . . . 0.09310 N 1 . . . . . . . . . . 0.02654 T 1 0.6363 1.6509 0.02771 0.2466:0.3236:0.3044:0.1255 . . . . X 277 . ENSP00000340200:Y277X Y - 3 2 GLYAT 58233875 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 -0.083000 0.11286 -0.048000 0.13401 -0.912000 0.02778 TAC TCGA-FB-AAPZ-01A-11D-A40W-08 GLYAT-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000394593.1 0 0 0 5 245 1 60 0 0 0 1 60 2 0 0 0 0 0 2 0 1.710635e-02 5 242 1 59 15 -3.336917 1 1 0 0 1 0 2 2 1.488230 1 0.680000 3.130000 0.680000 6.000000e-02 1.000000e-02 0.130000 0.060000 0.069868 6.000000e-02 0 3.000000e-02 1.000000e-01 ANO1 55107 broad.mit.edu 37 11 69978186 69978186 + Splice_Site SNP G G A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr11:69978186G>A ENST00000355303.5 + 11 1563 c.e11+1 ANO1_ENST00000316296.5_Splice_Site|ANO1_ENST00000398543.2_Splice_Site|ANO1_ENST00000530676.1_Splice_Site|RP11-805J14.3_ENST00000530525.1_RNA|ANO1_ENST00000531349.1_Splice_Site|ANO1_ENST00000538023.1_Splice_Site NM_018043.5 NP_060513.5 Q5XXA6 ANO1_HUMAN anoctamin 1, calcium activated chloride channel 29 Crofelemer(DB04941) GCCCTCTGGGGTAAGCAGGGC 0.597000 0 SO:0001630 splice_region_variant ENST00000355303.5 1 1 hg19 CCDS44663.1 . . . . . . . . . . G 20.4 3.981281 0.74474 . . ENSG00000131620 ENST00000355303;ENST00000538023;ENST00000398543;ENST00000546327;ENST00000316296;ENST00000530676;ENST00000531349 . . . 4.77 3.85 0.44370 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 14.3645 0.66795 0.0:0.0:0.8509:0.1491 . . . . . -1 . . . + . . ANO1 69655834 1.000000 0.71417 1.000000 0.80357 0.958000 0.62258 7.683000 0.84093 0.995000 0.38917 0.555000 0.69702 . TCGA-FB-AAPZ-01A-11D-A40W-08 ANO1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000393685.1 1 0 1 19 55 0 15 0 0 0 0 15 2 0 0 0 0 0 2 1 9.999944e-01 18 52 0 15 2 -20.000000 1 1 0 0 1 2 3 5 2.180428 1 0.680000 3.130000 0.789501 9.900000e-01 7.700000e-01 1.000000 1.000000 0.980110 9.900000e-01 1 9.800000e-01 1 CLEC1B 51266 broad.mit.edu 37 12 10147796 10147796 + Missense_Mutation SNP C C A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr12:10147796C>A ENST00000298527.6 - 5 667 c.488G>T c.(487-489)cGc>cTc p.R163L CLEC1B_ENST00000348658.4_Missense_Mutation_p.R130L|CLEC1B_ENST00000428126.2_Missense_Mutation_p.R130L NM_016509.3 NP_057593.3 Q9P126 CLC1B_HUMAN C-type lectin domain family 1, member B 19 CGACTTCTGGCGAGATAATCC 0.433000 0 SO:0001583 missense ENST00000298527.6 1 1 hg19 CCDS41752.1 . . . . . . . . . . C 16.85 3.236215 0.58886 . . ENSG00000165682 ENST00000398937;ENST00000428126;ENST00000298527;ENST00000348658;ENST00000398939 T;T;T;T 0.19532 2.14;2.14;2.14;2.14 3.83 3.83 0.44106 C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3); 0.000000 0.49305 D 0.000156 T 0.42539 0.1207 M 0.80332 2.49 0.44268 D 0.997128 D;D 0.89917 0.999;1.0 D;D 0.85130 0.99;0.997 T 0.39583 -0.9607 10 0.13853 T 0.58 . 11.1397 0.48396 0.0:1.0:0.0:0.0 . 130;163 Q9P126-2;Q9P126 .;CLC1B_HUMAN L 70;130;163;130;70 ENSP00000381910:R70L;ENSP00000406338:R130L;ENSP00000298527:R163L;ENSP00000327169:R130L ENSP00000298527:R163L R - 2 0 CLEC1B 10039063 0.991000 0.36638 0.902000 0.35471 0.685000 0.39939 2.087000 0.41653 1.954000 0.56735 0.298000 0.19748 CGC TCGA-FB-AAPZ-01A-11D-A40W-08 CLEC1B-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000399922.1 1 0 0 92 1996 0 355 0 0 0 0 355 2 0 0 0 0 0 2 1 1 92 1968 1 347 20 -6.101907 1 1 0 0 1 2 2 4 2.317841 1 0.680000 3.130000 0.800648 2.000000e-01 1.500000e-01 1.000000 0.220000 0.280063 2.000000e-01 0 1.700000e-01 2.500000e-01 KRAS 3845 broad.mit.edu 37 12 25398285 25398285 + Missense_Mutation SNP C C G rs121913530 TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 C G C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr12:25398285C>G ENST00000256078.4 - 2 97 c.34G>C c.(34-36)Ggt>Cgt p.G12R KRAS_ENST00000556131.1_Missense_Mutation_p.G12R|KRAS_ENST00000557334.1_Missense_Mutation_p.G12R|KRAS_ENST00000311936.3_Missense_Mutation_p.G12R NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|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) CCTACGCCACCAGCTCCAACT 0.348000 G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE) 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 5144 Substitution - Missense(5142)|Insertion - In frame(2) GRCh37 CM076251 KRAS M rs121913530 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 28.6 4.930538 0.92389 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78246 -1.16;-1.16;-1.16;-1.16 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.84893 0.5573 M 0.84082 2.675 0.80722 D 1 P;P 0.43287 0.802;0.741 B;P 0.47941 0.36;0.562 D 0.86658 0.1902 10 0.66056 D 0.02 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN R 12 ENSP00000308495:G12R;ENSP00000452512:G12R;ENSP00000256078:G12R;ENSP00000451856:G12R ENSP00000256078:G12R G - 1 0 KRAS 25289552 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-FB-AAPZ-01A-11D-A40W-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 79 154 0 76 1 9.803785e-01 3 12 0 76 2 1 1 112 196 0 283 2 1 1 80 151 0 73 2 -20.000000 1 1 0 0 1 2 2 4 2.372814 1 0.680000 3.130000 0.805589 9.900000e-01 9.900000e-01 1.000000 1.000000 1.000000 9.900000e-01 1 9.900000e-01 1 NTF3 4908 broad.mit.edu 37 12 5603793 5603793 + Missense_Mutation SNP G G A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr12:5603793G>A ENST00000331010.6 + 1 496 c.413G>A c.(412-414)cGg>cAg p.R138Q NTF3_ENST00000535299.1_Intron|NTF3_ENST00000423158.3_Missense_Mutation_p.R151Q NM_002527.4 NP_002518.1 P20783 NTF3_HUMAN neurotrophin 3 p.R138Q(1) 22 CGGCGGAAACGGTACGCGGAG 0.602000 GBM(194;1104 2182 8339 9578 18493) 1 Substitution - Missense(1) SO:0001583 missense ENST00000331010.6 1 1 hg19 CCDS8538.1 . . . . . . . . . . G 22.3 4.265075 0.80358 . . ENSG00000185652 ENST00000423158;ENST00000331010 T;T 0.70516 -0.49;-0.49 5.52 3.71 0.42584 . 0.000000 0.85682 D 0.000000 T 0.70824 0.3268 M 0.89601 3.045 0.47214 D 0.999355 P;D 0.54601 0.892;0.967 B;B 0.35859 0.212;0.212 T 0.76143 -0.3067 10 0.87932 D 0 -11.5385 11.2247 0.48877 0.1475:0.0:0.8525:0.0 . 138;151 P20783;B7Z1T5 NTF3_HUMAN;. Q 151;138 ENSP00000397297:R151Q;ENSP00000328738:R138Q ENSP00000328738:R138Q R + 2 0 NTF3 5474054 1.000000 0.71417 0.997000 0.53966 0.953000 0.61014 9.869000 0.99810 0.724000 0.32296 0.591000 0.81541 CGG TCGA-FB-AAPZ-01A-11D-A40W-08 NTF3-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000400486.1 1 0 1 225 286 1 64 0 0 0 1 1 64 2 0 0 0 0 0 2 1 1 221 285 1 61 25 -20.000000 1 1 0 0 1 2 2 4 2.317841 1 0.680000 3.130000 0.800648 9.900000e-01 9.900000e-01 1.000000 1.000000 1.000000 9.900000e-01 1 9.900000e-01 1 VWF 7450 broad.mit.edu 37 12 6105363 6105363 + Silent SNP C C T TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr12:6105363C>T ENST00000261405.5 - 35 6122 c.5868G>A c.(5866-5868)cgG>cgA p.R1956R NM_000552.3 NP_000543 P04275 VWF_HUMAN von Willebrand factor 129 Antihemophilic Factor(DB00025) TCACGATGTGCCGAGTGGAGC 0.522000 0 SO:0001819 synonymous_variant ENST00000261405.5 0 1 hg19 CCDS8539.1 TCGA-FB-AAPZ-01A-11D-A40W-08 VWF-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000399020.1 0 0 0 4 162 0 41 0 6.840568e-01 0 90 0 41 2 0 0 0 0 0 2 1 8.870172e-01 4 159 0 41 2 -5.942028 1 1 0 0 1 2 2 4 2.317841 1 0.680000 3.130000 0.800648 1.300000e-01 3.000000e-02 1.000000 0.110000 0.216619 1.300000e-01 0 7.000000e-02 2.400000e-01 SKA3 221150 broad.mit.edu 37 13 21742393 21742393 + Silent SNP T T A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr13:21742393T>A ENST00000314759.5 - 4 601 c.477A>T c.(475-477)tcA>tcT p.S159S SKA3_ENST00000400018.3_Silent_p.S159S NM_145061.5 NP_659498.4 Q8IX90 SKA3_HUMAN spindle and kinetochore associated complex subunit 3 19 GTCCAAAATCTGAAAGTTGTG 0.438000 0 SO:0001819 synonymous_variant ENST00000314759.5 0 1 hg19 CCDS31946.1 TCGA-FB-AAPZ-01A-11D-A40W-08 SKA3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000272912.1 0 0 0 5 576 0 100 0 2.475119e-03 0 7 0 100 2 0 0 0 0 0 2 0 9.345952e-01 1 569 0 99 2 -4.628092 1 0 0 0 1 2 4 6 2.072044 1 0.680000 3.130000 0.779128 4.000000e-02 0 1.000000 0.030000 0.247000 4.000000e-02 0 1.000000e-02 1 BEGAIN 57596 broad.mit.edu 37 14 101004539 101004539 + Missense_Mutation SNP C C T TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr14:101004539C>T ENST00000355173.2 - 7 1620 c.1549G>A c.(1549-1551)Gag>Aag p.E517K BEGAIN_ENST00000443071.2_Missense_Mutation_p.E517K|BEGAIN_ENST00000556751.1_Missense_Mutation_p.E453K|CTD-2062F14.3_ENST00000553301.1_lincRNA NM_020836.3 NP_065887.1 Q9BUH8 BEGIN_HUMAN brain-enriched guanylate kinase-associated 14 Melanoma(154;0.212) TCCCCCCCCTCGCTGGGTGCA 0.731000 NSCLC(159;1889 2010 9965 27479 40101) 0 SO:0001583 missense ENST00000355173.2 0 1 hg19 CCDS9962.1 . . . . . . . . . . c 12.23 1.875165 0.33162 . . ENSG00000183092 ENST00000355173;ENST00000556751;ENST00000443071 . . . 4.72 3.83 0.44106 . 0.564050 0.18819 N 0.130300 T 0.56031 0.1958 L 0.54323 1.7 0.42735 D 0.993725 B 0.28971 0.229 B 0.24269 0.052 T 0.52238 -0.8602 9 0.28530 T 0.3 . 14.6592 0.68858 0.0:0.8449:0.1551:0.0 . 517 Q9BUH8 BEGIN_HUMAN K 517;453;517 . ENSP00000347301:E517K E - 1 0 BEGAIN 100074292 1.000000 0.71417 0.893000 0.35052 0.164000 0.22412 3.288000 0.51739 0.948000 0.37687 0.450000 0.29827 GAG TCGA-FB-AAPZ-01A-11D-A40W-08 BEGAIN-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000414329.1 1 0 0 21 21 0 14 1 8.753438e-01 5 1 0 14 2 0 0 0 0 0 2 1 9.999989e-01 18 17 0 12 2 -20.000000 1 1 0 0 1 2 6 8 2.304479 1 0.680000 3.130000 0.798944 9.900000e-01 9.900000e-01 1.000000 1.000000 0.999999 9.900000e-01 1 9.900000e-01 1 OR4Q3 441669 broad.mit.edu 37 14 20215715 20215715 + Silent SNP C C A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr14:20215715C>A ENST00000331723.1 + 1 129 c.129C>A c.(127-129)ctC>ctA p.L43L NM_172194.1 NP_751944.1 Q8NH05 OR4Q3_HUMAN olfactory receptor, family 4, subfamily Q, member 3 47 all_cancers(95;0.00108) Epithelial(56;9.96e-07)|all cancers(55;2.95e-06) TGGGAAACCTCTTGATAGTGG 0.408000 0 SO:0001819 synonymous_variant ENST00000331723.1 1 1 hg19 CCDS32020.1 TCGA-FB-AAPZ-01A-11D-A40W-08 OR4Q3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000409818.2 1 0 0 438 436 1 169 0 0 0 1 169 2 0 0 0 0 0 2 1 1 426 427 1 167 18 -20.000000 1 1 0 0 1 0.680000 3.130000 0 0 SYNE2 23224 broad.mit.edu 37 14 64681074 64681074 + Missense_Mutation SNP G G A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr14:64681074G>A ENST00000344113.4 + 106 19431 c.19219G>A c.(19219-19221)Gag>Aag p.E6407K SYNE2_ENST00000357395.3_Missense_Mutation_p.E2792K|SYNE2_ENST00000358025.3_Missense_Mutation_p.E6407K|SYNE2_ENST00000555002.1_Missense_Mutation_p.E3041K|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555022.1_Missense_Mutation_p.E285K|SYNE2_ENST00000554584.1_Missense_Mutation_p.E6349K|SYNE2_ENST00000441438.2_5'Flank|SYNE2_ENST00000394768.2_Missense_Mutation_p.E2792K|SYNE2_ENST00000458046.2_Missense_Mutation_p.E41K|SYNE2_ENST00000554805.1_Missense_Mutation_p.E190K NM_015180.4 NP_055995.4 Q8WXH0 SYNE2_HUMAN spectrin repeat containing, nuclear envelope 2 224 GTCTGGCTGCGAGACCCCTGT 0.632000 0 SO:0001583 missense ENST00000344113.4 1 1 hg19 CCDS41963.1 . . . . . . . . . . G 19.96 3.923682 0.73213 . . ENSG00000054654 ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768;ENST00000555022;ENST00000554805;ENST00000458046 T;T;T;T;T;T;T;T;T 0.65549 0.24;3.64;0.23;-0.16;3.64;3.64;3.47;2.98;2.5 5.27 5.27 0.74061 . 0.000000 0.50627 D 0.000114 T 0.78220 0.4249 M 0.61703 1.905 0.80722 D 1 D;D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0;0.998;1.0 D;D;D;D;D;D;D 0.91635 0.998;0.991;0.999;0.973;0.989;0.975;0.997 T 0.79374 -0.1830 10 0.72032 D 0.01 . 19.0978 0.93260 0.0:0.0:1.0:0.0 . 41;2792;41;795;6349;6407;6407 B4DND7;Q8WXH0-7;Q8WXH0-5;Q7Z362;G3V5X4;Q8WXH0;Q8WXH0-2 .;.;.;.;.;SYNE2_HUMAN;. K 6407;2792;6407;6349;6355;3041;2792;285;190;41 ENSP00000350719:E6407K;ENSP00000349969:E2792K;ENSP00000341781:E6407K;ENSP00000452570:E6349K;ENSP00000450831:E3041K;ENSP00000378249:E2792K;ENSP00000451009:E285K;ENSP00000450605:E190K;ENSP00000391937:E41K ENSP00000261678:E6355K E + 1 0 SYNE2 63750827 1.000000 0.71417 0.998000 0.56505 0.861000 0.49209 9.411000 0.97342 2.735000 0.93741 0.655000 0.94253 GAG TCGA-FB-AAPZ-01A-11D-A40W-08 SYNE2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000276994.2 1 0 1 216 230 0 81 1 1 31 57 0 81 2 0 0 0 0 0 2 1 1 215 225 0 79 2 -20.000000 1 1 0 0 1 2 6 8 2.304479 1 0.680000 3.130000 0.798944 9.900000e-01 9.900000e-01 1.000000 1.000000 1.000000 9.900000e-01 1 9.900000e-01 1 NRXN3 9369 broad.mit.edu 37 14 79175640 79175640 + Silent SNP C C T TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr14:79175640C>T ENST00000554719.1 + 4 674 c.183C>T c.(181-183)ggC>ggT p.G61G NRXN3_ENST00000335750.5_Silent_p.G61G|RP11-232C2.2_ENST00000555680.1_RNA NM_004796.4 NP_004787.2 Q9HDB5 NRX3B_HUMAN neurexin 3 p.G61G(2) 104 Renal(4;0.00876) AAATCTATGGCGAAGTTGTGT 0.468000 2 Substitution - coding silent(2) SO:0001819 synonymous_variant ENST00000554719.1 1 1 hg19 CCDS9870.1 TCGA-FB-AAPZ-01A-11D-A40W-08 NRXN3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000413787.1 1 0 1 209 201 0 71 0 0 0 0 71 2 0 0 0 0 0 2 1 1 206 199 0 69 2 -20.000000 1 1 121410 2 33 1 2 6 8 2.304479 1 0.680000 3.130000 0.798944 9.900000e-01 9.900000e-01 1.000000 1.000000 1.000000 9.900000e-01 1 9.900000e-01 1 ATP10A 57194 broad.mit.edu 37 15 25924552 25924552 + Missense_Mutation SNP C C T TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr15:25924552C>T ENST00000356865.6 - 21 4547 c.4436G>A c.(4435-4437)cGa>cAa p.R1479Q NM_024490.3 NP_077816.1 O60312 AT10A_HUMAN ATPase, class V, type 10A 103 all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125) AAGTCCTGATCGGCCTGAGTG 0.512000 0 SO:0001583 missense ENST00000356865.6 1 1 hg19 CCDS32178.1 . . . . . . . . . . C 10.32 1.318296 0.23994 . . ENSG00000206190 ENST00000356865 T 0.10382 2.88 5.12 3.19 0.36642 . 6.590700 0.00166 N 0.000007 T 0.05090 0.0136 N 0.08118 0 0.09310 N 1 P 0.44006 0.824 B 0.28011 0.085 T 0.32955 -0.9887 10 0.25751 T 0.34 11.1915 6.8241 0.23872 0.0:0.7845:0.0:0.2155 . 1479 O60312 AT10A_HUMAN Q 1479 ENSP00000349325:R1479Q ENSP00000349325:R1479Q R - 2 0 ATP10A 23475645 0.021000 0.18746 0.001000 0.08648 0.005000 0.04900 0.520000 0.22878 0.688000 0.31529 0.655000 0.94253 CGA TCGA-FB-AAPZ-01A-11D-A40W-08 ATP10A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000414830.1 1 0 0 19 272 0 71 0 3.239395e-01 0 17 0 71 2 0 0 0 0 0 2 1 9.999909e-01 19 268 0 68 2 -3.017663 1 1 0 0 1 0 2 2 1.519396 1 0.680000 3.130000 0.680000 1.900000e-01 1.100000e-01 0.290000 0.190000 0.200423 1.900000e-01 0 1.500000e-01 2.400000e-01 FEM1B 10116 broad.mit.edu 37 15 68570843 68570843 + Missense_Mutation SNP A A G TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 A G A A Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr15:68570843A>G ENST00000306917.4 + 1 703 c.88A>G c.(88-90)Agc>Ggc p.S30G RP11-315D16.4_ENST00000563057.1_lincRNA NM_015322.4 NP_056137.1 Q9UK73 FEM1B_HUMAN fem-1 homolog b (C. elegans) 9 CCGGTCTGAAAGCGACATCCG 0.632000 0 SO:0001583 missense ENST00000306917.4 1 1 hg19 CCDS10228.1 . . . . . . . . . . A 12.78 2.041286 0.35989 . . ENSG00000169018 ENST00000306917 T 0.53640 0.61 4.29 4.29 0.51040 Ankyrin repeat-containing domain (1); 0.316936 0.33854 N 0.004490 T 0.24736 0.0600 N 0.08118 0 0.27961 N 0.936787 B 0.15473 0.013 B 0.14023 0.01 T 0.11203 -1.0597 10 0.23302 T 0.38 -27.3124 8.8849 0.35398 0.8112:0.1887:0.0:0.0 . 30 Q9UK73 FEM1B_HUMAN G 30 ENSP00000307298:S30G ENSP00000307298:S30G S + 1 0 FEM1B 66357897 1.000000 0.71417 0.997000 0.53966 0.998000 0.95712 3.542000 0.53625 1.812000 0.52913 0.454000 0.30748 AGC TCGA-FB-AAPZ-01A-11D-A40W-08 FEM1B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257065.1 1 0 0 127 62 0 52 0 9.995515e-01 1 9 0 52 2 0 0 0 0 0 2 1 1 125 61 0 50 2 -20.000000 1 1 0 0 1 0 2 2 1.519396 1 0.680000 3.130000 0.680000 9.900000e-01 9.900000e-01 1.000000 1.000000 1.000000 9.900000e-01 1 9.900000e-01 1 ACSM3 6296 broad.mit.edu 37 16 20781387 20781387 + Missense_Mutation SNP C C T TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr16:20781387C>T ENST00000289416.5 + 2 506 c.31C>T c.(31-33)Cgt>Tgt p.R11C ACSM3_ENST00000450120.2_5'Flank|ACSM3_ENST00000440284.2_Missense_Mutation_p.R11C NM_005622.3 NP_005613.2 Q53FZ2 ACSM3_HUMAN acyl-CoA synthetase medium-chain family member 3 21 GAAGATGCTACGTCATGCCAA 0.438000 0 SO:0001583 missense ENST00000289416.5 1 1 hg19 CCDS10589.1 . . . . . . . . . . C 5.071 0.198692 0.09652 . . ENSG00000005187 ENST00000289416;ENST00000440284 T;T 0.44083 0.93;1.68 5.91 0.758 0.18432 . 0.674484 0.14670 N 0.305411 T 0.23014 0.0556 N 0.14661 0.345 0.09310 N 1 B;B 0.02656 0.0;0.0 B;B 0.01281 0.0;0.0 T 0.16335 -1.0406 10 0.37606 T 0.19 -2.0692 8.0878 0.30782 0.0:0.5219:0.0:0.4781 . 11;11 Q53FZ2;Q53FZ2-2 ACSM3_HUMAN;. C 11 ENSP00000289416:R11C;ENSP00000394565:R11C ENSP00000289416:R11C R + 1 0 ACSM3 20688888 0.003000 0.15002 0.002000 0.10522 0.003000 0.03518 0.634000 0.24614 0.132000 0.18615 -0.137000 0.14449 CGT TCGA-FB-AAPZ-01A-11D-A40W-08 ACSM3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254414.2 1 0 1 174 112 0 81 0 9.168836e-01 1 4 0 81 2 0 0 0 0 0 2 1 1 169 106 0 79 2 -20.000000 1 1 0 0 1 0 2 2 1.473083 1 0.680000 3.130000 0.680000 9.900000e-01 9.900000e-01 1.000000 1.000000 1.000000 9.900000e-01 1 9.900000e-01 1 CDIPT 10423 broad.mit.edu 37 16 29872467 29872467 + Missense_Mutation SNP T T C TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr16:29872467T>C ENST00000219789.6 - 3 1170 c.292A>G c.(292-294)Atg>Gtg p.M98V CDIPT_ENST00000569956.1_Missense_Mutation_p.M98V|CDIPT-AS1_ENST00000398859.3_RNA|CDIPT-AS1_ENST00000565014.1_RNA|CDIPT_ENST00000567459.1_5'Flank|CDIPT_ENST00000566113.1_Missense_Mutation_p.M53V|CDIPT_ENST00000570016.1_Missense_Mutation_p.M98V|CDIPT_ENST00000563415.1_Missense_Mutation_p.M98V|CDIPT_ENST00000561555.1_Missense_Mutation_p.M122V NM_006319.3 NP_006310.1 O14735 CDIPT_HUMAN CDP-diacylglycerol--inositol 3-phosphatidyltransferase 4 TCCAAACTCATGCTGATTTGG 0.607000 0 SO:0001583 missense ENST00000219789.6 1 1 hg19 CCDS10657.1 . . . . . . . . . . T 13.17 2.156835 0.38119 . . ENSG00000103502 ENST00000219789;ENST00000403894 T 0.39056 1.1 5.78 5.78 0.91487 . 0.000000 0.85682 D 0.000000 T 0.33352 0.0860 N 0.21142 0.635 0.58432 D 0.999994 B;B;P 0.50943 0.104;0.048;0.94 B;B;P 0.44946 0.051;0.086;0.465 T 0.05989 -1.0852 10 0.24483 T 0.36 -15.9386 14.0659 0.64828 0.0:0.0:0.0:1.0 . 53;98;122 B4DUV0;O14735;B3KY94 .;CDIPT_HUMAN;. V 98;151 ENSP00000219789:M98V ENSP00000219789:M98V M - 1 0 CDIPT 29779968 1.000000 0.71417 1.000000 0.80357 0.972000 0.66771 6.797000 0.75150 2.220000 0.72140 0.533000 0.62120 ATG TCGA-FB-AAPZ-01A-11D-A40W-08 CDIPT-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255147.3 1 0 1 81 99 0 28 1 1 4 80 0 28 2 0 0 0 0 0 2 1 1 76 99 0 28 2 -20.000000 1 1 0 0 1 3 4 7 2.188718 1 0.680000 3.130000 0.788079 9.900000e-01 9.900000e-01 1.000000 1.000000 1.000000 9.900000e-01 1 9.900000e-01 1 ZNF48 197407 broad.mit.edu 37 16 30410328 30410328 + Missense_Mutation SNP G G A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr16:30410328G>A ENST00000320159.2 + 2 2133 c.1757G>A c.(1756-1758)cGc>cAc p.R586H NM_001214906.1|NM_001214907.1|NM_001214909.1|NM_152652.2 NP_001201835.1|NP_001201836.1|NP_001201838.1|NP_689865.2 Q96MX3 ZNF48_HUMAN zinc finger protein 48 21 AGTTCTGCCCGCATCAAGCAC 0.592000 0 SO:0001583 missense ENST00000320159.2 0 1 hg19 CCDS10679.1 . . . . . . . . . . G 11.68 1.709960 0.30322 . . ENSG00000180035 ENST00000495929;ENST00000320159 T 0.28454 1.61 4.6 4.6 0.57074 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.000000 0.34507 N 0.003901 T 0.19765 0.0475 N 0.24115 0.695 0.27017 N 0.964547 B 0.26363 0.147 B 0.13407 0.009 T 0.14896 -1.0456 10 0.87932 D 0 -16.7957 10.3576 0.43974 0.0:0.0:0.8042:0.1958 . 586 Q96MX3 ZNF48_HUMAN H 711;586 ENSP00000324056:R586H ENSP00000324056:R586H R + 2 0 ZNF48 30317829 0.193000 0.23313 0.954000 0.39281 0.780000 0.44128 1.880000 0.39628 2.556000 0.86216 0.557000 0.71058 CGC TCGA-FB-AAPZ-01A-11D-A40W-08 ZNF48-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255549.2 0 0 0 6 570 0 87 0 1.740175e-02 0 16 0 87 2 0 0 0 0 0 2 1 9.639753e-01 6 564 0 86 2 -1.813077 0 1 0 0 1 3 4 7 2.188718 1 0.680000 3.130000 0.788079 5.000000e-02 0 1.000000 0.040000 0.243486 5.000000e-02 0 2.000000e-02 1 ADAMTS18 170692 broad.mit.edu 37 16 77327045 77327045 + Silent SNP C C T TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr16:77327045C>T ENST00000282849.5 - 20 3535 c.3117G>A c.(3115-3117)ctG>ctA p.L1039L RP11-538I12.3_ENST00000561672.1_RNA NM_199355.2 NP_955387.1 Q8TE60 ATS18_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 18 118 AGCCCTCCTGCAGCTCAGGTC 0.607000 0 SO:0001819 synonymous_variant ENST00000282849.5 1 1 hg19 CCDS10926.1 TCGA-FB-AAPZ-01A-11D-A40W-08 ADAMTS18-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000269037.1 1 0 1 154 288 0 82 0 0 0 0 82 2 0 0 0 0 0 2 1 1 152 285 0 80 2 -20.000000 1 1 0 0 1 2 2 4 2.341113 1 0.680000 3.130000 0.803150 9.900000e-01 9.900000e-01 1.000000 1.000000 1.000000 9.900000e-01 1 9.900000e-01 1 TP53 7157 broad.mit.edu 37 17 7578212 7578212 + Nonsense_Mutation SNP G G A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr17:7578212G>A ENST00000269305.4 - 6 826 c.637C>T c.(637-639)Cga>Tga p.R213* TP53_ENST00000445888.2_Nonsense_Mutation_p.R213*|TP53_ENST00000574684.1_Intron|TP53_ENST00000455263.2_Nonsense_Mutation_p.R213*|TP53_ENST00000420246.2_Nonsense_Mutation_p.R213*|TP53_ENST00000359597.4_Nonsense_Mutation_p.R213*|TP53_ENST00000413465.2_Nonsense_Mutation_p.R213* 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.R213*(250)|p.R81*(21)|p.R120*(21)|p.0?(8)|p.?(5)|p.R213G(5)|p.R213fs*35(3)|p.R213fs*34(3)|p.D208_V216delDRNTFRHSV(1)|p.R120G(1)|p.D207_R213delDDRNTFR(1)|p.T211_S215delTFRHS(1)|p.R81fs*>11(1)|p.D208fs*1(1)|p.R120fs*35(1)|p.R81G(1)|p.R209_R213delRNTFR(1)|p.R213fs*2(1)|p.T211fs*28(1)|p.R213_S215>X(1)|p.D207_V216del10(1)|p.R213R(1)|p.R213fs*32(1)|p.R209fs*6(1)|p.R213W(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) ACACTATGTCGAAAAGTGTTT 0.532000 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 333 Substitution - Nonsense(292)|Deletion - Frameshift(8)|Whole gene deletion(8)|Substitution - Missense(8)|Deletion - In frame(5)|Insertion - Frameshift(5)|Unknown(5)|Complex - deletion inframe(1)|Substitution - coding silent(1) GRCh37 CM951226 TP53 M SO:0001587 stop_gained 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 0 1 hg19 CCDS11118.1 . . . . . . . . . . G 37 6.039727 0.97226 . . ENSG00000141510 ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315 . . . 5.28 3.25 0.37280 . 0.057335 0.64402 D 0.000003 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 -7.5444 12.7263 0.57173 0.0:0.0:0.701:0.299 . . . . X 213;213;213;213;213;213;202;120;81;120;81 . ENSP00000269305:R213X R - 1 2 TP53 7518937 0.971000 0.33674 0.123000 0.21794 0.957000 0.61999 1.659000 0.37387 0.702000 0.31825 0.563000 0.77884 CGA TCGA-FB-AAPZ-01A-11D-A40W-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 0 117 54 0 30 1 1 3 22 0 30 2 1 1 641 287 2 1068 7 1 1 116 52 0 29 2 -20.000000 1 1 121412 1 30 1 0 3 3 1.690177 1 0.680000 3.130000 0.748428 9.900000e-01 9.900000e-01 1.000000 1.000000 1.000000 9.900000e-01 1 9.900000e-01 1 ROCK1 6093 broad.mit.edu 37 18 18625398 18625398 + Missense_Mutation SNP G G A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr18:18625398G>A ENST00000399799.2 - 5 1385 c.445C>T c.(445-447)Ctc>Ttc p.L149F NM_005406.2 NP_005397.1 Q13464 ROCK1_HUMAN Rho-associated, coiled-coil containing protein kinase 1 16 Melanoma(1;0.165) ACCATGTAGAGATAACGATCA 0.328000 0 SO:0001583 missense ENST00000399799.2 1 1 hg19 CCDS11870.2 . . . . . . . . . . G 26.0 4.699139 0.88830 . . ENSG00000067900 ENST00000399799 T 0.69175 -0.38 5.36 4.49 0.54785 Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); 0.000000 0.85682 D 0.000000 T 0.78413 0.4279 L 0.58969 1.84 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 T 0.80892 -0.1179 10 0.87932 D 0 . 14.1018 0.65062 0.0719:0.0:0.9281:0.0 . 149 Q13464 ROCK1_HUMAN F 149 ENSP00000382697:L149F ENSP00000382697:L149F L - 1 0 ROCK1 16879396 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 4.561000 0.60809 1.485000 0.48380 0.655000 0.94253 CTC TCGA-FB-AAPZ-01A-11D-A40W-08 ROCK1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254641.2 1 0 1 23 208 0 32 1 6.644365e-01 2 20 0 32 2 0 0 0 0 0 2 1 9.999995e-01 23 208 0 32 2 -20.000000 1 1 0 0 1 1 4 5 2.954331 1 0.680000 3.130000 0.839968 5.900000e-01 3.800000e-01 0.880000 0.590000 0.609078 5.900000e-01 0 4.800000e-01 7.300000e-01 RNF165 494470 broad.mit.edu 37 18 44030346 44030346 + Missense_Mutation SNP G G A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr18:44030346G>A ENST00000269439.7 + 5 754 c.703G>A c.(703-705)Gta>Ata p.V235I RNF165_ENST00000543885.1_Missense_Mutation_p.V43I NM_152470.2 NP_689683.2 Q6ZSG1 RN165_HUMAN ring finger protein 165 11 CACCTCCGCCGTACGGGAGAG 0.522000 0 SO:0001583 missense ENST00000269439.7 1 1 hg19 CCDS32823.1 . . . . . . . . . . G 18.57 3.653556 0.67472 2.27E-4 0.0 ENSG00000141622 ENST00000269439;ENST00000543885 T;T 0.22945 2.18;1.93 5.28 5.28 0.74379 . 0.067191 0.64402 D 0.000015 T 0.35913 0.0948 L 0.60455 1.87 0.58432 D 0.999999 D 0.61080 0.989 P 0.49421 0.61 T 0.03852 -1.0998 10 0.20519 T 0.43 . 19.277 0.94036 0.0:0.0:1.0:0.0 . 235 Q6ZSG1 RN165_HUMAN I 235;43 ENSP00000269439:V235I;ENSP00000444285:V43I ENSP00000269439:V235I V + 1 0 RNF165 42284344 1.000000 0.71417 0.746000 0.31095 0.873000 0.50193 9.420000 0.97426 2.647000 0.89833 0.467000 0.42956 GTA TCGA-FB-AAPZ-01A-11D-A40W-08 RNF165-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000445358.1 1 0 1 76 59 0 47 0 0 0 0 47 2 0 0 0 0 0 2 1 1 76 56 0 47 2 -20.000000 1 1 121412 10 39 1 0 1 1 1.033301 1 0.680000 3.130000 0.517636 9.700000e-01 8.600000e-01 1.000000 1.000000 0.967699 9.700000e-01 1 9.200000e-01 1 ZNF546 339327 broad.mit.edu 37 19 40520572 40520572 + Silent SNP T T C TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr19:40520572T>C ENST00000347077.4 + 7 1611 c.1395T>C c.(1393-1395)ggT>ggC p.G465G ZNF546_ENST00000596894.1_Intron|ZNF546_ENST00000600094.1_Silent_p.G439G NM_178544.3 NP_848639.2 Q86UE3 ZN546_HUMAN zinc finger protein 546 34 all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925) CTCATACTGGTGAGAAACCCT 0.403000 0 SO:0001819 synonymous_variant ENST00000347077.4 1 1 hg19 CCDS12548.1 TCGA-FB-AAPZ-01A-11D-A40W-08 ZNF546-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000462495.2 1 0 1 206 312 0 83 0 0 0 1 0 83 2 0 0 0 0 0 2 1 1 205 311 0 78 2 -20.000000 1 1 0 0 1 2 2 4 2.327377 1 0.680000 3.130000 0.801489 9.900000e-01 9.900000e-01 1.000000 1.000000 1.000000 9.900000e-01 1 9.900000e-01 1 PSG8 440533 broad.mit.edu 37 19 43259170 43259170 + Missense_Mutation SNP G G A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr19:43259170G>A ENST00000306511.4 - 4 1055 c.958C>T c.(958-960)Cgc>Tgc p.R320C PSG8_ENST00000600709.1_Intron|PSG8_ENST00000404209.4_Missense_Mutation_p.R320C|PSG8_ENST00000406636.3_Missense_Mutation_p.R198C|PSG8_ENST00000401467.2_Missense_Mutation_p.R227C NM_182707.2 NP_874366.1 Q9UQ74 PSG8_HUMAN pregnancy specific beta-1-glycoprotein 8 p.R320C(2) 40 Prostate(69;0.00899) GGGTAACTGCGGATGCCACCA 0.483000 2 Substitution - Missense(2) SO:0001583 missense ENST00000306511.4 1 1 hg19 CCDS33037.1 . . . . . . . . . . N 4.888 0.164951 0.09287 0.0 1.16E-4 ENSG00000124467 ENST00000404209;ENST00000406636;ENST00000401467;ENST00000426252;ENST00000407488;ENST00000306511 T;T;T;T 0.12774 2.65;2.65;2.65;2.65 1.38 -1.99 0.07457 Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); . . . . T 0.25494 0.0620 M 0.78285 2.405 0.09310 N 1 D;P;B;B;B;B 0.69078 0.997;0.594;0.02;0.005;0.005;0.006 P;B;B;B;B;B 0.61397 0.888;0.284;0.009;0.07;0.005;0.009 T 0.13737 -1.0498 9 0.51188 T 0.08 . 2.0334 0.03534 0.2288:0.0:0.475:0.2962 . 198;227;320;227;320;320 Q9UQ74-2;B5MCQ0;Q9UQ74;E7ENH0;Q9UQ74-3;A5PKV3 .;.;PSG8_HUMAN;.;.;. C 320;198;227;132;227;320 ENSP00000385869:R320C;ENSP00000385081:R198C;ENSP00000386090:R227C;ENSP00000305005:R320C ENSP00000305005:R320C R - 1 0 PSG8 47951010 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -1.436000 0.02421 -0.117000 0.11872 -1.261000 0.01458 CGC TCGA-FB-AAPZ-01A-11D-A40W-08 PSG8-008 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000464526.1 1 0 1 303 475 0 121 0 0 0 0 121 2 0 0 0 0 0 2 1 1 296 465 0 134 2 -20.000000 1 1 121404 12 44 1 2 2 4 2.327377 1 0.680000 3.130000 0.801489 9.900000e-01 9.900000e-01 1.000000 1.000000 1.000000 9.900000e-01 1 9.900000e-01 1 PSG11 5680 broad.mit.edu 37 19 43523094 43523094 + Silent SNP C C T TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr19:43523094C>T ENST00000401740.1 - 3 640 c.537G>A c.(535-537)ctG>ctA p.L179L PSG11_ENST00000595312.1_5'UTR|PSG11_ENST00000320078.7_Silent_p.L179L|PSG11_ENST00000403486.1_Silent_p.L57L|PSG11_ENST00000306322.7_Silent_p.L57L Q00887 PSG9_HUMAN pregnancy specific beta-1-glycoprotein 11 26 Prostate(69;0.00682) TCATCCACCACAGGTAGCTTG 0.512000 0 SO:0001819 synonymous_variant ENST00000401740.1 1 1 hg19 CCDS12614.2 TCGA-FB-AAPZ-01A-11D-A40W-08 PSG11-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000323079.1 1 0 1 768 1165 0 320 0 0 0 0 320 2 0 0 0 0 0 2 1 1 759 1147 0 308 2 -20.000000 1 1 0 0 1 2 2 4 2.327377 1 0.680000 3.130000 0.801489 9.900000e-01 9.900000e-01 1.000000 1.000000 1.000000 9.900000e-01 1 9.900000e-01 1 TNNI3 7137 broad.mit.edu 37 19 55665406 55665406 + Missense_Mutation SNP T T G TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr19:55665406T>G ENST00000344887.5 - 7 683 c.541A>C c.(541-543)Acc>Ccc p.T181P TNNI3_ENST00000588882.1_Missense_Mutation_p.T156P|TNNI3_ENST00000590463.1_5'Flank NM_000363.4 NP_000354.4 P19429 TNNI3_HUMAN troponin I type 3 (cardiac) 12 BRCA - Breast invasive adenocarcinoma(297;0.209) ACCTTCTCGGTGTCCTCCTTC 0.627000 0 SO:0001583 missense ENST00000344887.5 1 1 hg19 CCDS42628.1 . . . . . . . . . . T 13.78 2.337852 0.41398 . . ENSG00000129991 ENST00000344887 D 0.94723 -3.5 4.72 2.5 0.30297 . 0.581099 0.16498 N 0.211800 D 0.90079 0.6901 L 0.52573 1.65 0.35660 D 0.81242 B 0.02656 0.0 B 0.01281 0.0 D 0.86432 0.1761 10 0.54805 T 0.06 -21.4095 4.2672 0.10769 0.0:0.1778:0.1798:0.6424 . 181 P19429 TNNI3_HUMAN P 181 ENSP00000341838:T181P ENSP00000341838:T181P T - 1 0 TNNI3 60357218 1.000000 0.71417 0.968000 0.41197 0.989000 0.77384 3.726000 0.54977 0.714000 0.32081 0.477000 0.44152 ACC TCGA-FB-AAPZ-01A-11D-A40W-08 TNNI3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000452098.1 0 0 1 254 382 0 96 0 3.508749e-01 1 2 0 96 2 0 0 0 0 0 2 1 1 247 373 0 91 2 -20.000000 1 1 0 0 1 2 2 4 2.455654 1 0.680000 3.130000 0.809524 9.900000e-01 9.900000e-01 1.000000 1.000000 1.000000 9.900000e-01 1 9.900000e-01 1 ZNF132 7691 broad.mit.edu 37 19 58944797 58944797 + Missense_Mutation SNP G G A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr19:58944797G>A ENST00000254166.3 - 3 2414 c.2014C>T c.(2014-2016)Cgg>Tgg p.R672W CTD-2619J13.17_ENST00000594816.1_lincRNA NM_003433.3 NP_003424.3 P52740 ZN132_HUMAN zinc finger protein 132 19 all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184) TTCTGGTGCCGAACAAGTGTA 0.448000 0 SO:0001583 missense ENST00000254166.3 0 1 hg19 CCDS12980.1 . . . . . . . . . . G 14.03 2.412314 0.42817 . . ENSG00000131849 ENST00000254166;ENST00000391695 T 0.26660 1.72 3.05 1.76 0.24704 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.44519 0.1297 M 0.75884 2.315 0.09310 N 1 D 0.76494 0.999 D 0.65773 0.938 T 0.11991 -1.0565 9 0.62326 D 0.03 . 7.4495 0.27229 0.0:0.0:0.4465:0.5535 . 672 P52740 ZN132_HUMAN W 672;387 ENSP00000254166:R672W ENSP00000254166:R672W R - 1 2 ZNF132 63636609 0.000000 0.05858 0.998000 0.56505 0.965000 0.64279 -4.163000 0.00282 1.419000 0.47118 0.650000 0.86243 CGG TCGA-FB-AAPZ-01A-11D-A40W-08 ZNF132-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000467035.1 0 0 0 6 423 0 67 0 3.007648e-04 0 2 0 67 2 0 0 0 0 0 2 1 9.641985e-01 6 419 0 65 2 -2.579007 1 1 121412 7 39 1 2 2 4 2.455654 1 0.680000 3.130000 0.809524 7.000000e-02 1.000000e-02 0.150000 0.080000 0.079554 7.000000e-02 0 3.000000e-02 1.100000e-01 GBA 2629 broad.mit.edu 37 1 155209725 155209725 + Missense_Mutation SNP G G A rs1141814 TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr1:155209725G>A ENST00000327247.5 - 4 491 c.259C>T c.(259-261)Cgg>Tgg p.R87W GBA_ENST00000536770.1_Intron|GBA_ENST00000427500.3_Missense_Mutation_p.R87W|GBA_ENST00000493842.1_5'UTR|GBA_ENST00000428024.3_De_novo_Start_OutOfFrame|GBA_ENST00000368373.3_Missense_Mutation_p.R87W NM_001005741.2|NM_001005742.2 NP_001005741.1|NP_001005742.1 P04062 GLCM_HUMAN glucosidase, beta, acid 26 all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088) Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193) Velaglucerase alfa(DB06720) AGCTCCATCCGTCGCCCACTG 0.592000 Gaucher disease type I 0 GRCh37 CM950561 GBA M rs1141814 SO:0001583 missense Familial Cancer Database glucocerebrosidase insufficiency ENST00000327247.5 1 0 hg19 CCDS1102.1 . . . . . . . . . . G 12.33 1.906424 0.33628 . . ENSG00000177628 ENST00000427500;ENST00000368373;ENST00000327247;ENST00000536555;ENST00000402928 D;D;D 0.99652 -4.04;-6.3;-6.3 3.46 1.33 0.21861 . 0.081577 0.45867 N 0.000328 D 0.99278 0.9748 M 0.82323 2.585 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;0.973 D 0.99107 1.0845 10 0.87932 D 0 . 3.8119 0.08801 0.1327:0.0:0.6312:0.2361 rs1141814;rs3205618;rs17401365 87;87 B7Z5G2;P04062 .;GLCM_HUMAN W 87;87;87;44;87 ENSP00000402577:R87W;ENSP00000357357:R87W;ENSP00000314508:R87W ENSP00000314508:R87W R - 1 2 GBA 153476349 1.000000 0.71417 0.240000 0.24138 0.020000 0.10135 2.947000 0.49058 0.802000 0.34089 -0.356000 0.07607 CGG TCGA-FB-AAPZ-01A-11D-A40W-08 GBA-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000087204.1 1 0 0 13 127 0 26 1 9.005170e-01 2 40 0 26 2 0 0 0 0 0 2 1 9.995996e-01 13 126 0 26 2 -18.808840 1 1 121412 2 32 1 2 3 5 1.933017 0 0.680000 3.130000 0.762400 4.100000e-01 2.100000e-01 1.000000 0.360000 0.521899 4.100000e-01 0 3.000000e-01 1 TAS1R2 80834 broad.mit.edu 37 1 19183978 19183978 + Silent SNP C C T TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr1:19183978C>T ENST00000375371.3 - 2 351 c.330G>A c.(328-330)ccG>ccA p.P110P RP13-279N23.2_ENST00000494072.3_3'UTR NM_152232.2 NP_689418.2 Q8TE23 TS1R2_HUMAN taste receptor, type 1, member 2 45 Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255) Aspartame(DB00168) AGTAGAGCACCGGCTGGACAT 0.542000 0 SO:0001819 synonymous_variant ENST00000375371.3 1 1 hg19 CCDS187.1 TCGA-FB-AAPZ-01A-11D-A40W-08 TAS1R2-001 NOVEL basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000006953.1 1 0 0 28 379 0 78 0 0 0 0 78 2 0 0 0 0 0 2 1 1 27 376 0 78 2 -2.473695 0 1 121412 3 38 1 2 3 5 2.022724 1 0.680000 3.130000 0.772727 3.000000e-01 1.900000e-01 1.000000 0.290000 0.457632 3.000000e-01 0 2.400000e-01 1 EPHA8 2046 broad.mit.edu 37 1 22924191 22924191 + Silent SNP C C T TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr1:22924191C>T ENST00000166244.3 + 11 2025 c.1953C>T c.(1951-1953)taC>taT p.Y651Y NM_020526.3 NP_065387.1 P29322 EPHA8_HUMAN EPH receptor A8 61 Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255) AAGTCTGCTACGGGAGGCTGC 0.692000 0 SO:0001819 synonymous_variant ENST00000166244.3 1 1 hg19 CCDS225.1 TCGA-FB-AAPZ-01A-11D-A40W-08 EPHA8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000008085.1 1 0 1 51 147 0 31 0 0 0 0 31 2 0 0 0 0 0 2 1 1 50 146 0 31 2 -20.000000 1 1 0 0 1 2 3 5 2.022724 1 0.680000 3.130000 0.772727 9.900000e-01 8.400000e-01 1.000000 1.000000 0.983414 9.900000e-01 1 9.600000e-01 1 THRAP3 9967 broad.mit.edu 37 1 36752394 36752394 + Missense_Mutation SNP G G A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr1:36752394G>A ENST00000354618.5 + 4 787 c.563G>A c.(562-564)cGg>cAg p.R188Q THRAP3_ENST00000469141.2_Missense_Mutation_p.R188Q NM_005119.3 NP_005110.2 Q9Y2W1 TR150_HUMAN thyroid hormone receptor associated protein 3 37 Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164) AAGGATAGCCGGCCATCTCAG 0.527000 T USP6 aneurysmal bone cysts Pancreas(129;785 1795 20938 23278 32581) Dom yes 1 1p34.3 9967 thyroid hormone receptor associated protein 3 (TRAP150) M 0 SO:0001583 missense ENST00000354618.5 0 1 hg19 CCDS405.1 . . . . . . . . . . G 16.88 3.245450 0.59103 . . ENSG00000054118 ENST00000354618;ENST00000469141 T;T 0.13089 2.62;2.62 5.72 5.72 0.89469 . 0.000000 0.64402 D 0.000004 T 0.18173 0.0436 L 0.41236 1.265 0.51233 D 0.999918 D 0.63046 0.992 P 0.45753 0.492 T 0.00273 -1.1858 10 0.54805 T 0.06 -2.4011 18.8828 0.92364 0.0:0.0:1.0:0.0 . 188 Q9Y2W1 TR150_HUMAN Q 188 ENSP00000346634:R188Q;ENSP00000433825:R188Q ENSP00000346634:R188Q R + 2 0 THRAP3 36524981 1.000000 0.71417 1.000000 0.80357 0.886000 0.51366 6.476000 0.73587 2.711000 0.92665 0.655000 0.94253 CGG TCGA-FB-AAPZ-01A-11D-A40W-08 THRAP3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000021688.2 0 0 0 6 789 0 164 0 1.084992e-01 0 62 0 164 2 0 0 0 0 0 2 1 9.639347e-01 7 780 0 161 2 -2.129839 0 1 0 0 1 2 3 5 2.042750 1 0.680000 3.130000 0.774362 3.000000e-02 0 1.000000 0.030000 0.262045 3.000000e-02 0 1.000000e-02 1 PHACTR3 116154 broad.mit.edu 37 20 58381152 58381152 + Missense_Mutation SNP C C T TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr20:58381152C>T ENST00000371015.1 + 8 1698 c.1231C>T c.(1231-1233)Cca>Tca p.P411S PHACTR3_ENST00000395639.4_Missense_Mutation_p.P300S|PHACTR3_ENST00000355648.4_Missense_Mutation_p.P370S|PHACTR3_ENST00000361300.4_Missense_Mutation_p.P300S|PHACTR3_ENST00000359926.3_Missense_Mutation_p.P408S|PHACTR3_ENST00000541461.1_Missense_Mutation_p.P370S|PHACTR3_ENST00000395636.2_Missense_Mutation_p.P370S NM_001281507.1|NM_080672.3 NP_001268436.1|NP_542403.1 Q96KR7 PHAR3_HUMAN phosphatase and actin regulator 3 59 all_lung(29;0.00344) BRCA - Breast invasive adenocarcinoma(7;2.76e-09) AAGGAACCGGCCAAGCAAACA 0.512000 0 SO:0001583 missense ENST00000371015.1 1 1 hg19 CCDS13480.1 . . . . . . . . . . C 23.7 4.446091 0.84101 . . ENSG00000087495 ENST00000359926;ENST00000371015;ENST00000395639;ENST00000541461;ENST00000355648;ENST00000395636;ENST00000361300 T;T;T;T;T;T;T 0.43688 1.21;1.25;0.94;1.25;1.25;1.25;0.94 5.25 5.25 0.73442 . 0.000000 0.85682 D 0.000000 T 0.68686 0.3028 M 0.83012 2.62 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.97110 0.999;1.0;1.0 T 0.73467 -0.3973 10 0.66056 D 0.02 -16.2549 17.8596 0.88777 0.0:1.0:0.0:0.0 . 300;411;408 Q96KR7-3;Q96KR7;B1AKX0 .;PHAR3_HUMAN;. S 408;411;300;370;370;370;300 ENSP00000353002:P408S;ENSP00000360054:P411S;ENSP00000379001:P300S;ENSP00000442483:P370S;ENSP00000347866:P370S;ENSP00000378998:P370S;ENSP00000354555:P300S ENSP00000347866:P370S P + 1 0 PHACTR3 57814547 1.000000 0.71417 0.999000 0.59377 0.625000 0.37756 7.818000 0.86416 2.460000 0.83146 0.650000 0.86243 CCA TCGA-FB-AAPZ-01A-11D-A40W-08 PHACTR3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079923.3 0 0 1 459 598 1 143 0 0 0 1 143 2 0 0 0 0 0 2 1 1 457 589 1 139 24 -20.000000 1 1 0 0 1 2 2 4 2.294843 1 0.680000 3.130000 0.798944 9.900000e-01 9.900000e-01 1.000000 1.000000 1.000000 9.900000e-01 1 9.900000e-01 1 DSCAM 1826 broad.mit.edu 37 21 42080519 42080519 + Silent SNP G G A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr21:42080519G>A ENST00000400454.1 - 2 699 c.222C>T c.(220-222)caC>caT p.H74H NM_001271534.1|NM_001389.3 NP_001258463.1|NP_001380.2 O60469 DSCAM_HUMAN Down syndrome cell adhesion molecule 142 all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103) TGGGGTGGACGTGGCGGATCC 0.542000 Melanoma(134;970 1778 1785 21664 32388) 0 SO:0001819 synonymous_variant ENST00000400454.1 1 1 hg19 CCDS42929.1 TCGA-FB-AAPZ-01A-11D-A40W-08 DSCAM-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000195029.1 1 0 1 52 366 0 80 0 0 0 0 80 2 0 0 0 0 0 2 1 9.999942e-01 52 360 1 77 18 -19.895370 1 1 120894 1 31 1 2 4 6 2.030803 1 0.680000 3.130000 0.770511 5.300000e-01 3.900000e-01 1.000000 0.510000 0.612745 5.300000e-01 0 4.500000e-01 1 MX2 4600 broad.mit.edu 37 21 42749046 42749046 + Missense_Mutation SNP G G T rs142593261 TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr21:42749046G>T ENST00000330714.3 + 2 397 c.213G>T c.(211-213)caG>caT p.Q71H MX2_ENST00000543692.1_Missense_Mutation_p.Q71H NM_002463.1 NP_002454.1 P20592 MX2_HUMAN MX dynamin-like GTPase 2 34 Prostate(19;1.57e-07)|all_epithelial(19;0.0222) TGAACAATCAGCCACCACCAG 0.552000 0 SO:0001583 missense ENST00000330714.3 1 1 hg19 CCDS13672.1 . . . . . . . . . . G 12.39 1.923572 0.33908 . . ENSG00000183486 ENST00000330714;ENST00000436410;ENST00000435611;ENST00000543692;ENST00000418103 D;D 0.92397 -2.58;-3.03 2.47 1.58 0.23477 . 4.843280 0.00597 N 0.000371 D 0.90407 0.6997 L 0.50333 1.59 0.09310 N 1 P 0.49961 0.93 P 0.44732 0.459 T 0.78957 -0.1999 10 0.59425 D 0.04 . 5.0852 0.14678 0.1707:0.0:0.8293:0.0 . 71 P20592 MX2_HUMAN H 71 ENSP00000333657:Q71H;ENSP00000446017:Q71H ENSP00000333657:Q71H Q + 3 2 MX2 41670916 0.005000 0.15991 0.002000 0.10522 0.018000 0.09664 1.088000 0.30877 0.614000 0.30107 0.561000 0.74099 CAG TCGA-FB-AAPZ-01A-11D-A40W-08 MX2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000195147.1 0 0 1 303 416 1 113 0 9.774018e-01 0 11 1 113 2 0 0 0 0 0 2 1 1 300 404 1 113 21 -20.000000 1 1 0 0 1 2 4 6 2.030803 1 0.680000 3.130000 0.770511 9.900000e-01 9.900000e-01 1.000000 1.000000 1.000000 9.900000e-01 1 9.900000e-01 1 RBM45 129831 broad.mit.edu 37 2 178990889 178990889 + Missense_Mutation SNP C C G TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr2:178990889C>G ENST00000286070.5 + 9 1503 c.1411C>G c.(1411-1413)Caa>Gaa p.Q471E RBM45_ENST00000464647.1_3'UTR NM_152945.2 NP_694453.2 Q8IUH3 RBM45_HUMAN RNA binding motif protein 45 27 OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.00957)|all cancers(119;0.037) TAACAAACGGCAAAGAACTTA 0.348000 0 SO:0001583 missense ENST00000286070.5 1 1 hg19 CCDS33335.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 19.03|19.03 3.747532|3.747532 0.69533|0.69533 .|. .|. ENSG00000155636|ENSG00000155636 ENST00000424099|ENST00000286070 .|T .|0.05081 .|3.5 5.78|5.78 5.78|5.78 0.91487|0.91487 .|. .|0.113073 .|0.64402 .|D .|0.000007 T|T 0.10252|0.10252 0.0251|0.0251 L|L 0.47716|0.47716 1.5|1.5 0.58432|0.58432 D|D 0.999999|0.999999 .|P .|0.46859 .|0.885 .|B .|0.42593 .|0.392 T|T 0.02705|0.02705 -1.1121|-1.1121 5|10 .|0.44086 .|T .|0.13 -14.8272|-14.8272 18.9873|18.9873 0.92777|0.92777 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. .|471 .|Q8IUH3-3 .|. G|E 69|471 .|ENSP00000286070:Q471E .|ENSP00000286070:Q471E A|Q +|+ 2|1 0|0 RBM45|RBM45 178699135|178699135 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.999000|0.999000 0.98932|0.98932 5.796000|5.796000 0.69080|0.69080 2.724000|2.724000 0.93272|0.93272 0.655000|0.655000 0.94253|0.94253 GCA|CAA TCGA-FB-AAPZ-01A-11D-A40W-08 RBM45-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000334375.2 1 0 1 112 185 0 61 1 9.996035e-01 6 17 0 61 2 0 0 0 0 0 2 1 1 112 182 0 61 2 -20.000000 1 1 0 0 1 1 2 3 2.002322 0 0.680000 3.130000 0.732710 9.900000e-01 9.900000e-01 1.000000 1.000000 0.999995 9.900000e-01 1 9.900000e-01 1 DNAH7 56171 broad.mit.edu 37 2 196825327 196825327 + Missense_Mutation SNP G G A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr2:196825327G>A ENST00000312428.6 - 18 2648 c.2548C>T c.(2548-2550)Cgc>Tgc p.R850C NM_018897.2 NP_061720.2 Q8WXX0 DYH7_HUMAN dynein, axonemal, heavy chain 7 p.R850C(1) 205 TGCCTGGGGCGCAAACCAGGA 0.453000 1 Substitution - Missense(1) SO:0001583 missense ENST00000312428.6 0 1 hg19 CCDS42794.1 . . . . . . . . . . G 15.84 2.952760 0.53293 . . ENSG00000118997 ENST00000312428 T 0.63417 -0.04 5.74 5.74 0.90152 Dynein heavy chain, domain-2 (1); 0.125121 0.53938 D 0.000044 D 0.84392 0.5462 M 0.93375 3.41 0.80722 D 1 D 0.76494 0.999 D 0.64877 0.93 D 0.87323 0.2319 10 0.59425 D 0.04 . 19.9196 0.97082 0.0:0.0:1.0:0.0 . 850 Q8WXX0 DYH7_HUMAN C 850 ENSP00000311273:R850C ENSP00000311273:R850C R - 1 0 DNAH7 196533572 1.000000 0.71417 1.000000 0.80357 0.963000 0.63663 4.626000 0.61269 2.708000 0.92522 0.650000 0.86243 CGC TCGA-FB-AAPZ-01A-11D-A40W-08 DNAH7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000335202.3 0 0 0 6 741 0 63 0 0 0 1 0 63 2 0 0 0 0 0 2 1 9.634199e-01 5 731 0 61 2 -1.779367 0 1 120856 4 40 1 2 4 6 2.804002 1 0.680000 3.130000 0.833749 5.000000e-02 0 1.000000 0.050000 0.251326 5.000000e-02 0 2.000000e-02 1 EHBP1 23301 broad.mit.edu 37 2 63223823 63223823 + Missense_Mutation SNP G G A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr2:63223823G>A ENST00000263991.5 + 21 3720 c.3238G>A c.(3238-3240)Gca>Aca p.A1080T EHBP1_ENST00000354487.3_Missense_Mutation_p.A1045T|EHBP1_ENST00000496857.1_3'UTR|EHBP1_ENST00000431489.1_Missense_Mutation_p.A1009T|EHBP1_ENST00000405289.1_Missense_Mutation_p.A1045T|EHBP1_ENST00000405015.3_Missense_Mutation_p.A1009T NM_015252.3 NP_056067.2 Q8NDI1 EHBP1_HUMAN EH domain binding protein 1 47 Lung NSC(7;0.0951)|all_lung(7;0.169) LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189) AGAATTGGCAGCACTAGAGAA 0.443000 0 SO:0001583 missense ENST00000263991.5 0 1 hg19 CCDS1872.1 . . . . . . . . . . G 25.6 4.657246 0.88154 . . ENSG00000115504 ENST00000405015;ENST00000431489;ENST00000263991;ENST00000354487;ENST00000405289;ENST00000545092 T;T;T;T;T 0.44881 0.91;0.91;0.91;0.91;0.91 5.19 5.19 0.71726 Domain of unknown function DUF3585 (1); 0.000000 0.85682 D 0.000000 T 0.61788 0.2375 L 0.60455 1.87 0.80722 D 1 D;D;D 0.89917 0.999;1.0;1.0 D;D;D 0.91635 0.997;0.998;0.999 T 0.57435 -0.7812 10 0.32370 T 0.25 . 18.7221 0.91698 0.0:0.0:1.0:0.0 . 1045;1009;1080 Q8NDI1-2;Q8NDI1-3;Q8NDI1 .;.;EHBP1_HUMAN T 1009;1009;1080;1045;1045;51 ENSP00000384143:A1009T;ENSP00000403783:A1009T;ENSP00000263991:A1080T;ENSP00000346482:A1045T;ENSP00000385524:A1045T ENSP00000263991:A1080T A + 1 0 EHBP1 63077327 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 9.869000 0.99810 2.438000 0.82558 0.650000 0.86243 GCA TCGA-FB-AAPZ-01A-11D-A40W-08 EHBP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251616.1 0 0 0 5 427 0 69 0 8.579740e-02 0 34 0 69 2 0 0 0 0 0 2 1 9.363465e-01 5 423 0 69 2 -2.908839 1 1 0 0 1 2 2 4 2.335306 1 0.680000 3.130000 0.802323 6.000000e-02 0 1.000000 0.060000 0.132475 6.000000e-02 0 2.000000e-02 1.100000e-01 TCF7L1 83439 broad.mit.edu 37 2 85532397 85532397 + Missense_Mutation SNP G G A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr2:85532397G>A ENST00000282111.3 + 8 1135 c.860G>A c.(859-861)cGg>cAg p.R287Q NM_031283.2 NP_112573.1 Q9HCS4 TF7L1_HUMAN transcription factor 7-like 1 (T-cell specific, HMG-box) 18 GTCTCCAGTCGGTTCTCTCCT 0.627000 0 SO:0001583 missense ENST00000282111.3 1 1 hg19 CCDS1971.1 . . . . . . . . . . G 23.2 4.381282 0.82792 . . ENSG00000152284 ENST00000282111 D 0.98617 -5.03 5.18 5.18 0.71444 . 0.057692 0.64402 D 0.000001 D 0.99001 0.9659 M 0.77820 2.39 0.45183 D 0.99819 D 0.76494 0.999 D 0.72625 0.978 D 0.99785 1.1029 10 0.72032 D 0.01 . 16.1893 0.81975 0.0:0.0:1.0:0.0 . 287 Q9HCS4 TF7L1_HUMAN Q 287 ENSP00000282111:R287Q ENSP00000282111:R287Q R + 2 0 TCF7L1 85385908 1.000000 0.71417 1.000000 0.80357 0.338000 0.28826 9.782000 0.99034 2.401000 0.81631 0.591000 0.81541 CGG TCGA-FB-AAPZ-01A-11D-A40W-08 TCF7L1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252301.2 1 0 1 147 450 0 87 0 3.601788e-01 0 5 0 87 2 0 0 0 0 0 2 1 1 146 443 0 85 2 -5.416782 1 1 121412 3 38 1 2 2 4 2.308637 1 0.680000 3.130000 0.799800 9.900000e-01 9.900000e-01 1.000000 1.000000 0.999336 9.900000e-01 1 9.900000e-01 1 CD8B 926 broad.mit.edu 37 2 87085431 87085431 + Missense_Mutation SNP C C T TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr2:87085431C>T ENST00000390655.6 - 2 210 c.152G>A c.(151-153)cGc>cAc p.R51H CD8B_ENST00000349455.3_Missense_Mutation_p.R51H|CD8B_ENST00000393761.2_Missense_Mutation_p.R51H|CD8B_ENST00000431506.2_Intron|CD8B_ENST00000393759.2_Missense_Mutation_p.R51H|CD8B_ENST00000331469.2_Missense_Mutation_p.R51H NM_004931.4 NP_004922.1 P10966 CD8B_HUMAN CD8b molecule 13 CCAGTAGATGCGCATGTTACT 0.552000 0 SO:0001583 missense ENST00000390655.6 1 1 hg19 CCDS1997.1 . . . . . . . . . . C 15.31 2.796172 0.50208 . . ENSG00000172116 ENST00000393761;ENST00000393759;ENST00000349455;ENST00000331469;ENST00000390655;ENST00000445248 T;T;T;T;T 0.66460 -0.21;-0.21;-0.21;-0.21;-0.21 4.49 0.103 0.14526 Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 1.342240 0.04418 N 0.367173 T 0.63283 0.2498 N 0.08118 0 0.09310 N 1 D;D;D;D;D;D 0.89917 1.0;1.0;0.999;0.999;0.999;1.0 D;D;D;P;D;D 0.68943 0.961;0.961;0.93;0.899;0.91;0.934 T 0.56860 -0.7909 10 0.35671 T 0.21 -3.9365 7.4646 0.27314 0.0:0.3982:0.5015:0.1003 . 51;51;51;51;51;51 Q496E2;Q53QL8;P10966;P10966-3;P10966-2;P10966-6 .;.;CD8B_HUMAN;.;.;. H 51 ENSP00000377358:R51H;ENSP00000377356:R51H;ENSP00000340592:R51H;ENSP00000331172:R51H;ENSP00000375070:R51H ENSP00000331172:R51H R - 2 0 CD8B 86938942 0.000000 0.05858 0.001000 0.08648 0.111000 0.19643 -0.174000 0.09839 0.009000 0.14813 -0.140000 0.14226 CGC TCGA-FB-AAPZ-01A-11D-A40W-08 CD8B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000330402.1 1 0 1 118 228 0 65 0 4.226639e-01 0 4 0 65 2 0 0 0 0 0 2 1 1 116 223 0 66 2 -20.000000 1 1 121412 3 37 1 2 2 4 2.308637 1 0.680000 3.130000 0.799800 9.900000e-01 9.900000e-01 1.000000 1.000000 1.000000 9.900000e-01 1 9.900000e-01 1 TRAT1 50852 broad.mit.edu 37 3 108572493 108572493 + Nonsense_Mutation SNP C C A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr3:108572493C>A ENST00000295756.6 + 6 560 c.330C>A c.(328-330)taC>taA p.Y110* TRAT1_ENST00000426646.1_Nonsense_Mutation_p.Y73* NM_016388.2 NP_057472.2 Q6PIZ9 TRAT1_HUMAN T cell receptor associated transmembrane adaptor 1 28 AGATGTGCTACGCCTCACTTG 0.413000 0 SO:0001587 stop_gained ENST00000295756.6 0 1 hg19 CCDS33813.1 . . . . . . . . . . C 11.78 1.740523 0.30865 . . ENSG00000163519 ENST00000295756;ENST00000426646 . . . 5.63 -9.83 0.00482 . 0.110144 0.41001 D 0.000963 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 -0.2088 16.9584 0.86266 0.0:0.7349:0.0:0.2651 . . . . X 110;73 . ENSP00000295756:Y110X Y + 3 2 TRAT1 110055183 0.373000 0.25073 0.002000 0.10522 0.054000 0.15201 -0.978000 0.03778 -2.084000 0.00866 -0.140000 0.14226 TAC TCGA-FB-AAPZ-01A-11D-A40W-08 TRAT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000353794.1 1 0 1 58 414 0 93 0 4.493298e-01 0 12 0 93 2 0 0 0 0 0 2 1 1 57 409 0 92 2 -19.997640 1 1 0 0 1 3 4 7 2.348910 1 0.680000 3.130000 0.803560 6.100000e-01 4.500000e-01 1.000000 0.580000 0.687122 6.100000e-01 0 5.200000e-01 1 RHOA 387 broad.mit.edu 37 3 49412957 49412957 + Silent SNP G G A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr3:49412957G>A ENST00000418115.1 - 2 450 c.66C>T c.(64-66)ctC>ctT p.L22L RHOA_ENST00000422781.1_Silent_p.L22L|RHOA_ENST00000454011.2_Silent_p.L22L NM_001664.2 NP_001655.1 P61586 RHOA_HUMAN ras homolog family member A 12 TGAAGACTATGAGCAAGCATG 0.473000 0 SO:0001819 synonymous_variant ENST00000418115.1 1 1 hg19 CCDS2795.1 TCGA-FB-AAPZ-01A-11D-A40W-08 RHOA-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000346157.3 1 0 1 142 290 0 120 1 1 150 606 0 120 2 0 0 0 0 0 2 1 1 142 288 0 117 2 -13.078020 1 1 0 0 1 0 3 3 1.696043 1 0.680000 3.130000 0.749765 9.900000e-01 9.900000e-01 1.000000 1.000000 0.999961 9.900000e-01 1 9.900000e-01 1 HS3ST1 9957 broad.mit.edu 37 4 11401393 11401393 + Silent SNP G G A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr4:11401393G>A ENST00000002596.5 - 2 1411 c.237C>T c.(235-237)gaC>gaT p.D79D NM_005114.2 NP_005105.1 O14792 HS3S1_HUMAN heparan sulfate (glucosamine) 3-O-sulfotransferase 1 p.D79D(1) 15 CGGCCGCCACGTCGGGGTGCA 0.662000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000002596.5 0 1 hg19 CCDS3408.1 TCGA-FB-AAPZ-01A-11D-A40W-08 HS3ST1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207073.3 0 0 0 8 322 0 74 1 3.408764e-01 4 41 0 74 2 0 0 0 0 0 2 1 9.884920e-01 8 314 0 73 2 -8.533830 1 1 121402 1 30 1 1 2 3 1.953323 1 0.680000 3.130000 0.761194 9.000000e-02 3.000000e-02 0.180000 0.090000 0.106745 9.000000e-02 0 6.000000e-02 1.400000e-01 PROL1 58503 broad.mit.edu 37 4 71275677 71275677 + Missense_Mutation SNP G G A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr4:71275677G>A ENST00000399575.2 + 3 806 c.632G>A c.(631-633)cGt>cAt p.R211H NM_021225.4 NP_067048.4 Q99935 PROL1_HUMAN proline rich, lacrimal 1 15 all_hematologic(202;0.196) CTCGCCAACCGTCCTCACACA 0.448000 0 SO:0001583 missense ENST00000399575.2 1 1 hg19 CCDS43235.1 . . . . . . . . . . C 13.85 2.361243 0.41801 0.0 2.39E-4 ENSG00000171199 ENST00000399575 T 0.42131 0.98 3.08 1.33 0.21861 . . . . . T 0.18718 0.0449 N 0.08118 0 0.09310 N 1 B 0.24368 0.102 B 0.08055 0.003 T 0.15206 -1.0445 9 0.44086 T 0.13 . 3.3539 0.07162 0.0:0.5226:0.2206:0.2569 . 211 Q99935 PROL1_HUMAN H 211 ENSP00000382485:R211H ENSP00000382485:R211H R + 2 0 PROL1 71310266 0.000000 0.05858 0.001000 0.08648 0.036000 0.12997 -0.417000 0.07088 0.045000 0.15804 -0.187000 0.12897 CGT TCGA-FB-AAPZ-01A-11D-A40W-08 PROL1-001 PUTATIVE basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000362639.1 0 0 1 101 290 0 93 0 0 0 1 0 93 2 0 0 0 0 0 2 1 1 99 284 0 92 2 -3.222083 1 1 121002 17 45 1 1 2 3 1.953323 1 0.680000 3.130000 0.761194 9.900000e-01 8.400000e-01 1.000000 1.000000 0.975066 9.900000e-01 1 9.200000e-01 1 ADAMTS19 171019 broad.mit.edu 37 5 129039960 129039960 + Missense_Mutation SNP G G A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr5:129039960G>A ENST00000274487.4 + 21 3315 c.3170G>A c.(3169-3171)cGt>cAt p.R1057H ADAMTS19_ENST00000509467.1_3'UTR|CTC-575N7.1_ENST00000503616.1_RNA NM_133638.3 NP_598377.3 Q8TE59 ATS19_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 19 91 all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238) KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365) AAAGGCATACGTCATCGGACC 0.423000 0 SO:0001583 missense ENST00000274487.4 1 1 hg19 CCDS4146.1 . . . . . . . . . . G 10.62 1.401303 0.25291 . . ENSG00000145808 ENST00000274487 T 0.57907 0.37 4.45 4.45 0.53987 . 0.078589 0.51477 D 0.000088 T 0.49864 0.1582 M 0.63169 1.94 0.50813 D 0.99989 B 0.30211 0.273 B 0.23275 0.045 T 0.49428 -0.8941 9 . . . . 18.3946 0.90494 0.0:0.0:1.0:0.0 . 1057 Q8TE59 ATS19_HUMAN H 1057 ENSP00000274487:R1057H . R + 2 0 ADAMTS19 129067859 0.988000 0.35896 0.419000 0.26584 0.023000 0.10783 3.651000 0.54431 2.758000 0.94735 0.655000 0.94253 CGT TCGA-FB-AAPZ-01A-11D-A40W-08 ADAMTS19-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250979.2 1 0 0 46 688 0 135 0 0 0 0 135 2 0 0 0 0 0 2 1 1 46 682 0 128 2 -8.494014 1 1 121412 8 44 1 2 2 4 2.380632 1 0.680000 3.130000 0.806389 3.000000e-01 2.100000e-01 1.000000 0.310000 0.330177 3.000000e-01 0 2.500000e-01 3.600000e-01 KCTD16 57528 broad.mit.edu 37 5 143853641 143853641 + Silent SNP T T C TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr5:143853641T>C ENST00000507359.3 + 3 2342 c.1251T>C c.(1249-1251)ccT>ccC p.P417P KCTD16_ENST00000512467.1_Silent_p.P417P NM_020768.3 NP_065819.1 Q68DU8 KCD16_HUMAN potassium channel tetramerization domain containing 16 21 all_hematologic(541;0.118) KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176) GAAAACATCCTTGGCAATCTG 0.378000 0 SO:0001819 synonymous_variant ENST00000507359.3 1 1 hg19 CCDS34260.1 TCGA-FB-AAPZ-01A-11D-A40W-08 KCTD16-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000371898.3 1 0 1 169 331 0 75 0 0 0 0 75 2 0 0 0 0 0 2 1 1 168 322 0 73 2 -20.000000 1 1 0 0 1 3 4 7 2.282443 1 0.680000 3.130000 0.797212 9.900000e-01 9.900000e-01 1.000000 1.000000 1.000000 9.900000e-01 1 9.900000e-01 1 C5orf34 375444 broad.mit.edu 37 5 43508741 43508741 + Nonsense_Mutation SNP G G A rs143336043 TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr5:43508741G>A ENST00000306862.2 - 3 598 c.223C>T c.(223-225)Cga>Tga p.R75* RP11-159F24.3_ENST00000505645.1_RNA|RP11-159F24.6_ENST00000512498.1_RNA NM_198566.2 NP_940968 Q96MH7 CE034_HUMAN chromosome 5 open reading frame 34 p.R75*(1) 21 Lung NSC(6;2.07e-05) GAAGAGTTTCGAAAATCTAGG 0.289000 1 Substitution - Nonsense(1) SO:0001587 stop_gained ENST00000306862.2 0 1 hg19 CCDS3946.1 . . . . . . . . . . G 37 6.582089 0.97680 0.0 1.16E-4 ENSG00000172244 ENST00000306862 . . . 5.35 3.27 0.37495 . 0.000000 0.85682 D 0.000000 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.02654 T 1 -7.7736 13.9037 0.63821 0.0:0.0:0.7113:0.2887 . . . . X 75 . ENSP00000303490:R75X R - 1 2 C5orf34 43544498 1.000000 0.71417 1.000000 0.80357 0.976000 0.68499 1.350000 0.34010 1.184000 0.42957 0.655000 0.94253 CGA TCGA-FB-AAPZ-01A-11D-A40W-08 C5orf34-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253843.1 1 0 1 179 307 0 85 1 4.701862e-01 2 2 0 85 2 0 0 0 0 0 2 1 1 178 306 0 81 2 -20.000000 1 1 121408 24 47 1 2 2 4 2.392500 1 0.680000 3.130000 0.807969 9.900000e-01 9.900000e-01 1.000000 1.000000 1.000000 9.900000e-01 1 9.900000e-01 1 MEF2C 4208 broad.mit.edu 37 5 88027589 88027589 + Missense_Mutation SNP C C T TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr5:88027589C>T ENST00000437473.2 - 7 1184 c.767G>A c.(766-768)cGa>cAa p.R256Q MEF2C_ENST00000510942.1_Missense_Mutation_p.R256Q|MEF2C_ENST00000504921.2_Missense_Mutation_p.R256Q|MEF2C_ENST00000340208.5_Missense_Mutation_p.R274Q|MEF2C_ENST00000508569.1_Missense_Mutation_p.R256Q|MEF2C_ENST00000503554.1_5'Flank|MEF2C_ENST00000514028.1_Missense_Mutation_p.R256Q|MEF2C_ENST00000539796.1_Missense_Mutation_p.R208Q|MEF2C_ENST00000424173.2_Missense_Mutation_p.R254Q|MEF2C_ENST00000514015.1_Missense_Mutation_p.R256Q|MEF2C_ENST00000506554.1_Missense_Mutation_p.R256Q NM_001193350.1|NM_002397.4 NP_001180279.1|NP_002388.2 Q06413 MEF2C_HUMAN myocyte enhancer factor 2C p.R256L(2)|p.R254L(1) 40 all_cancers(142;6.67e-05)|all_epithelial(76;7.77e-07)|Lung NSC(167;0.00566)|all_lung(232;0.00732)|Colorectal(57;0.0959)|Ovarian(174;0.1) AATAAGAACTCGGAGATCTGG 0.378000 HNSCC(66;0.2) 3 Substitution - Missense(3) SO:0001583 missense ENST00000437473.2 1 1 hg19 CCDS47245.1 . . . . . . . . . . C 37 6.088843 0.97271 . . ENSG00000081189 ENST00000340208;ENST00000424173;ENST00000504921;ENST00000514028;ENST00000437473;ENST00000510942;ENST00000506554;ENST00000508569;ENST00000514015;ENST00000539796 T;T;T;T;T;T;T;T;T;T 0.38240 1.15;1.15;1.15;1.15;1.15;1.15;1.15;1.15;1.15;1.15 6.03 6.03 0.97812 . 0.000000 0.85682 D 0.000000 T 0.66056 0.2751 M 0.80616 2.505 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;0.999;1.0 D;D;D;D 0.91635 0.994;0.998;0.974;0.999 T 0.67465 -0.5664 10 0.87932 D 0 -4.0687 20.5666 0.99351 0.0:1.0:0.0:0.0 . 254;274;256;256 C9JMZ0;F8W7V7;Q06413;Q06413-2 .;.;MEF2C_HUMAN;. Q 274;254;256;256;256;256;256;256;256;208 ENSP00000340874:R274Q;ENSP00000389610:R254Q;ENSP00000421925:R256Q;ENSP00000426665:R256Q;ENSP00000396219:R256Q;ENSP00000422390:R256Q;ENSP00000425636:R256Q;ENSP00000423597:R256Q;ENSP00000424606:R256Q;ENSP00000441153:R208Q ENSP00000340874:R274Q R - 2 0 MEF2C 88063345 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 7.487000 0.81328 2.854000 0.98071 0.655000 0.94253 CGA TCGA-FB-AAPZ-01A-11D-A40W-08 MEF2C-003 KNOWN alternative_5_UTR|basic|CCDS protein_coding protein_coding OTTHUMT00000369817.1 1 0 1 88 144 0 41 0 8.102472e-01 0 7 0 41 2 0 0 0 0 0 2 1 1 85 144 0 41 2 -12.800020 1 1 0 0 1 2 2 4 2.338893 1 0.680000 3.130000 0.802323 9.900000e-01 9.900000e-01 1.000000 1.000000 1.000000 9.900000e-01 1 9.900000e-01 1 IYD 389434 broad.mit.edu 37 6 150715311 150715311 + Missense_Mutation SNP G G A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr6:150715311G>A ENST00000344419.3 + 4 747 c.607G>A c.(607-609)Gca>Aca p.A203T IYD_ENST00000500320.3_Missense_Mutation_p.A203T|IYD_ENST00000392255.3_Missense_Mutation_p.A203T|IYD_ENST00000392256.2_Missense_Mutation_p.A203T|IYD_ENST00000229447.5_Missense_Mutation_p.A203T|IYD_ENST00000425615.3_Missense_Mutation_p.A148T NM_203395.2 NP_981932.1 Q6PHW0 IYD1_HUMAN iodotyrosine deiodinase 15 Ovarian(120;0.028) BRCA - Breast invasive adenocarcinoma(37;0.215) TGGTTTCGCCGCAAATGGCAA 0.433000 0 SO:0001583 missense ENST00000344419.3 0 1 hg19 CCDS5227.1 . . . . . . . . . . g 5.689 0.311597 0.10789 2.27E-4 0.0 ENSG00000009765 ENST00000229447;ENST00000344419;ENST00000392256;ENST00000392255;ENST00000500320;ENST00000425615 T;T;T;T;T;T 0.76578 -1.03;-1.03;-1.03;-1.03;-1.03;-1.03 6.17 2.1 0.27182 Nitroreductase-like (3); 0.509560 0.22264 N 0.062376 T 0.43055 0.1230 L 0.46885 1.475 0.09310 N 1 B;B;B;B 0.20261 0.004;0.043;0.001;0.002 B;B;B;B 0.18561 0.003;0.022;0.001;0.005 T 0.24548 -1.0157 10 0.27785 T 0.31 -23.7178 1.2452 0.01971 0.2372:0.2256:0.3896:0.1475 . 121;203;203;203 Q2VPV9;C9JFW2;Q6PHW0-3;Q6PHW0 .;.;.;IYD1_HUMAN T 203;203;203;203;203;148 ENSP00000229447:A203T;ENSP00000343763:A203T;ENSP00000376085:A203T;ENSP00000376084:A203T;ENSP00000441276:A203T;ENSP00000390081:A148T ENSP00000229447:A203T A + 1 0 IYD 150757004 0.019000 0.18553 0.001000 0.08648 0.174000 0.22865 0.255000 0.18333 0.496000 0.27904 -0.119000 0.15052 GCA TCGA-FB-AAPZ-01A-11D-A40W-08 IYD-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000043754.3 0 0 0 6 359 0 96 0 4.146428e-04 0 2 0 96 2 0 0 0 0 0 2 1 9.649964e-01 6 358 0 95 2 -1.992233 0 1 121412 3 38 1 0 2 2 1.519410 1 0.680000 3.130000 0.680000 4.000000e-02 1.000000e-02 0.100000 0.050000 0.056024 4.000000e-02 0 2.000000e-02 8.000000e-02 ENPP4 22875 broad.mit.edu 37 6 46108833 46108833 + Missense_Mutation SNP A A C TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr6:46108833A>C ENST00000321037.4 + 3 1101 c.871A>C c.(871-873)Atg>Ctg p.M291L NM_014936.4 NP_055751.1 Q9Y6X5 ENPP4_HUMAN ectonucleotide pyrophosphatase/phosphodiesterase 4 (putative) 18 TAGCCCTCATATGAATGTTTA 0.323000 0 SO:0001583 missense ENST00000321037.4 1 1 hg19 CCDS34468.1 . . . . . . . . . . A 9.051 0.992094 0.18966 . . ENSG00000001561 ENST00000321037;ENST00000371401 T 0.74002 -0.8 6.16 0.723 0.18231 Alkaline-phosphatase-like, core domain (1); 0.189676 0.64402 N 0.000004 T 0.28830 0.0715 N 0.16307 0.4 0.49798 D 0.999825 B 0.11235 0.004 B 0.17979 0.02 T 0.38542 -0.9656 10 0.02654 T 1 -10.9395 9.624 0.39739 0.5348:0.3528:0.0:0.1124 . 291 Q9Y6X5 ENPP4_HUMAN L 291 ENSP00000318066:M291L ENSP00000318066:M291L M + 1 0 ENPP4 46216792 1.000000 0.71417 0.996000 0.52242 0.785000 0.44390 2.205000 0.42770 -0.084000 0.12595 0.528000 0.53228 ATG TCGA-FB-AAPZ-01A-11D-A40W-08 ENPP4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040777.2 1 0 1 137 303 0 93 0 8.995325e-01 0 11 0 93 2 0 0 0 0 0 2 1 1 134 300 0 92 2 -20.000000 1 1 0 0 1 2 3 5 2.245979 1 0.680000 3.130000 0.793655 9.900000e-01 9.900000e-01 1.000000 1.000000 1.000000 9.900000e-01 1 9.900000e-01 1 SEPT7 989 broad.mit.edu 37 7 35923505 35923505 + Missense_Mutation SNP G G A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr7:35923505G>A ENST00000435235.1 + 8 1001 c.569G>A c.(568-570)cGt>cAt p.R190H SEPT7_ENST00000494488.2_Missense_Mutation_p.R229H|SEPT7_ENST00000350320.6_Missense_Mutation_p.R242H|SEPT7_ENST00000399035.3_Missense_Mutation_p.R242H|SEPT7_ENST00000469679.2_Intron|SEPT7_ENST00000399034.2_Missense_Mutation_p.R244H|SEPT7_ENST00000432293.2_Intron Q16181 SEPT7_HUMAN septin 7 14 TTATAGGACCGTTTACCTCTT 0.358000 0 SO:0001583 missense ENST00000435235.1 1 1 hg19 . . . . . . . . . . G 15.05 2.716738 0.48622 . . ENSG00000122545 ENST00000435235;ENST00000399034;ENST00000350320;ENST00000399035;ENST00000537785;ENST00000493670;ENST00000494488 T;T;T;T;T 0.79749 -1.3;1.4;1.4;1.4;1.4 4.88 4.88 0.63580 . 0.243404 0.30890 U 0.008678 T 0.72447 0.3461 L 0.37800 1.135 0.80722 D 1 B;B;B 0.16166 0.01;0.016;0.016 B;B;B 0.19391 0.024;0.025;0.025 T 0.67329 -0.5698 10 0.08599 T 0.76 . 18.4417 0.90669 0.0:0.0:1.0:0.0 . 188;242;243 B4DNE4;E7EPK1;Q16181 .;.;SEPT7_HUMAN H 190;244;242;242;188;190;229 ENSP00000413507:R190H;ENSP00000381992:R244H;ENSP00000344868:R242H;ENSP00000381993:R242H;ENSP00000438395:R229H ENSP00000344868:R242H R + 2 0 SEPT7 35890030 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 7.596000 0.82721 2.422000 0.82143 0.558000 0.71614 CGT TCGA-FB-AAPZ-01A-11D-A40W-08 SEPT7-001 NOVEL basic protein_coding protein_coding OTTHUMT00000338285.1 1 0 0 13 281 0 41 1 9.395397e-01 2 104 0 41 2 0 0 0 0 0 2 1 9.995338e-01 13 278 0 40 2 -14.409580 1 1 0 0 1 3 3 6 2.684319 1 0.680000 3.130000 0.827660 2.700000e-01 1.300000e-01 1.000000 0.230000 0.425362 2.700000e-01 0 1.900000e-01 1 PKD1L1 168507 broad.mit.edu 37 7 47933504 47933504 + Silent SNP G G A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr7:47933504G>A ENST00000289672.2 - 15 2474 c.2424C>T c.(2422-2424)ttC>ttT p.F808F NM_138295.3 NP_612152.1 Q8TDX9 PK1L1_HUMAN polycystic kidney disease 1 like 1 BBS9/PKD1L1(2) 142 CGTCAGGGTCGAAGGACTGGG 0.617000 0 SO:0001819 synonymous_variant ENST00000289672.2 1 1 hg19 CCDS34633.1 TCGA-FB-AAPZ-01A-11D-A40W-08 PKD1L1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000340974.1 1 0 0 57 91 0 22 0 0 0 0 22 2 0 0 0 0 0 2 1 1 56 89 0 22 2 -20.000000 1 1 121412 4 34 1 3 3 6 2.674979 1 0.680000 3.130000 0.827660 9.900000e-01 9.900000e-01 1.000000 1.000000 1.000000 9.900000e-01 1 9.900000e-01 1 SUMF2 25870 broad.mit.edu 37 7 56142409 56142409 + Missense_Mutation SNP C C T TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr7:56142409C>T ENST00000413756.1 + 5 538 c.515C>T c.(514-516)gCc>gTc p.A172V SUMF2_ENST00000434526.2_Missense_Mutation_p.A191V|SUMF2_ENST00000437307.2_Intron|SUMF2_ENST00000395435.2_Intron|SUMF2_ENST00000395436.2_Missense_Mutation_p.A176V|SUMF2_ENST00000342190.6_Missense_Mutation_p.A191V|SUMF2_ENST00000275607.9_Missense_Mutation_p.A84V Q8NBJ7 SUMF2_HUMAN sulfatase modifying factor 2 14 Breast(14;0.214) Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099) TGGGAGTTTGCCGCCCGAGGG 0.567000 OREG0018081 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000413756.1 0 1 hg19 . . . . . . . . . . C 36 5.686691 0.96784 . . ENSG00000129103 ENST00000395436;ENST00000434526;ENST00000275607;ENST00000413952;ENST00000342190;ENST00000413756;ENST00000451338 D;D;D;D;D;D;D 0.98968 -5.28;-5.28;-5.28;-5.28;-5.28;-5.28;-5.28 5.53 5.53 0.82687 C-type lectin fold (1);Formylglycine-generating sulphatase enzyme domain (2); 0.000000 0.85682 D 0.000000 D 0.99309 0.9758 M 0.90198 3.095 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.97110 1.0;1.0;0.951 D 0.99226 1.0880 10 0.87932 D 0 -11.665 18.8414 0.92186 0.0:1.0:0.0:0.0 . 176;172;191 A8MXB9;Q8NBJ7;F8WA42 .;SUMF2_HUMAN;. V 176;191;84;194;191;172;189 ENSP00000378824:A176V;ENSP00000400922:A191V;ENSP00000275607:A84V;ENSP00000414434:A194V;ENSP00000341938:A191V;ENSP00000406445:A172V;ENSP00000410796:A189V ENSP00000275607:A84V A + 2 0 SUMF2 56109903 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 7.607000 0.82883 2.777000 0.95525 0.591000 0.81541 GCC TCGA-FB-AAPZ-01A-11D-A40W-08 SUMF2-013 NOVEL basic|exp_conf protein_coding protein_coding OTTHUMT00000341457.2 0 0 0 6 694 0 85 0 4.302332e-01 0 152 0 85 2 0 0 0 0 0 2 0 0 0 0 0 2 -1.901312 0 1 0 0 1 3 3 6 2.674979 1 0.680000 3.130000 0.827660 5.000000e-02 0 1.000000 0.050000 0.266377 5.000000e-02 0 2.000000e-02 1 ADAM28 10863 broad.mit.edu 37 8 24193065 24193065 + Missense_Mutation SNP A A G rs7001647 byFrequency TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chr8:24193065A>G ENST00000265769.4 + 14 1588 c.1478A>G c.(1477-1479)aAt>aGt p.N493S RP11-624C23.1_ENST00000518988.1_RNA|RP11-624C23.1_ENST00000523700.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAM28_ENST00000397649.3_Missense_Mutation_p.N240S|RP11-624C23.1_ENST00000519689.1_RNA|ADAM28_ENST00000437154.2_Missense_Mutation_p.N493S|ADAM28_ENST00000540823.1_Missense_Mutation_p.N260S NM_014265.4 NP_055080.2 Q9UKQ2 ADA28_HUMAN ADAM metallopeptidase domain 28 42 Prostate(55;0.0959) TTCCAAGTCAATGGCTTCCCT 0.532000 NSCLC(193;488 2149 22258 34798 40734) 0 SO:0001583 missense ENST00000265769.4 1 0 hg19 CCDS34865.1 31 0.014194139194139194 31 0.06300813008130081 0 0.0 0 0.0 0 0.0 A 16.74 3.208031 0.58343 0.041307 1.16E-4 ENSG00000042980 ENST00000265769;ENST00000397649;ENST00000540823;ENST00000437154 T;T;T;T 0.26810 1.71;1.71;1.71;1.71 5.69 5.69 0.88448 ADAM, cysteine-rich (2);Blood coagulation inhibitor, Disintegrin (1); . . . . T 0.13713 0.0332 M 0.90650 3.135 0.58432 D 0.999999 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.91635 0.999;0.998;0.998;0.999 T 0.51317 -0.8721 9 0.87932 D 0 . 13.8927 0.63750 1.0:0.0:0.0:0.0 rs7001647;rs52800840;rs7001647 260;493;493;493 B4DDY3;B2RMV5;Q9UKQ2;Q9UKQ2-2 .;.;ADA28_HUMAN;. S 493;240;260;493 ENSP00000265769:N493S;ENSP00000380770:N240S;ENSP00000443743:N260S;ENSP00000393699:N493S ENSP00000265769:N493S N + 2 0 ADAM28 24249010 1.000000 0.71417 0.998000 0.56505 0.207000 0.24258 7.932000 0.87634 2.156000 0.67533 0.528000 0.53228 AAT TCGA-FB-AAPZ-01A-11D-A40W-08 ADAM28-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000375441.2 1 0 1 15 64 0 29 0 9.526916e-01 0 25 0 29 2 0 0 0 0 0 2 1 9.999274e-01 15 64 0 29 2 -2.298601 0 1 121406 533 58 1 0 2 2 1.484975 1 0.680000 3.130000 0.680000 5.600000e-01 3.400000e-01 0.830000 0.560000 0.577463 5.600000e-01 0 4.400000e-01 7.000000e-01 ZIC3 7547 broad.mit.edu 37 X 136651124 136651124 + Missense_Mutation SNP G G A TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chrX:136651124G>A ENST00000287538.5 + 2 1674 c.1124G>A c.(1123-1125)cGt>cAt p.R375H ZIC3_ENST00000478471.1_3'UTR|ZIC3_ENST00000370606.3_Missense_Mutation_p.R375H NM_003413.3 NP_003404.1 O60481 ZIC3_HUMAN Zic family member 3 37 Acute lymphoblastic leukemia(192;0.000127) AGCAGCGACCGTAAGAAGCAC 0.502000 0 SO:0001583 missense ENST00000287538.5 0 1 hg19 CCDS14663.1 . . . . . . . . . . G 34 5.308427 0.95629 . . ENSG00000156925 ENST00000287538;ENST00000370606 T;T 0.07567 3.18;3.18 5.74 5.74 0.90152 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.000000 0.85682 D 0.000000 T 0.23133 0.0559 L 0.39898 1.24 0.80722 D 1 D 0.89917 1.0 D 0.83275 0.996 T 0.00316 -1.1823 10 0.87932 D 0 . 17.7298 0.88374 0.0:0.0:1.0:0.0 . 375 O60481 ZIC3_HUMAN H 375 ENSP00000287538:R375H;ENSP00000359638:R375H ENSP00000287538:R375H R + 2 0 ZIC3 136478790 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 9.796000 0.99103 2.405000 0.81733 0.600000 0.82982 CGT TCGA-FB-AAPZ-01A-11D-A40W-08 ZIC3-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000058526.1 0 0 0 6 839 0 142 0 0 0 0 142 2 0 0 0 0 0 2 1 9.645181e-01 5 836 0 140 2 -2.331330 0 1 0 0 1 0 1 1 0.680000 3.130000 0.680000 0 0 0.020000 0.010000 0.011765 0 0 0 2.000000e-02 CYBB 1536 broad.mit.edu 37 X 37653065 37653065 + Splice_Site SNP T T C TCGA-FB-AAPZ-01A-11D-A40W-08 TCGA-FB-AAPZ-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 2feaf6e8-f76a-4c02-9536-689e3ad149de 3b27aea6-7bdb-48d4-9fef-c5748fef457d g.chrX:37653065T>C ENST00000378588.4 + 5 550 c.e5+2 CYBB_ENST00000536160.1_Intron|TM4SF2_ENST00000465127.1_Intron|CYBB_ENST00000545017.1_Splice_Site NM_000397.3 NP_000388.2 P04839 CY24B_HUMAN cytochrome b-245, beta polypeptide 32 Dextromethorphan(DB00514) AGAATAAAGGTAAGCCTCTCA 0.373000 0 GRCh37 CS961541 CYBB S SO:0001630 splice_region_variant ENST00000378588.4 1 1 hg19 CCDS14242.1 . . . . . . . . . . T 17.31 3.357925 0.61403 . . ENSG00000165168 ENST00000378588;ENST00000545017 . . . 5.67 5.67 0.87782 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 14.9689 0.71217 0.0:0.0:0.0:1.0 . . . . . -1 . . . + . . CYBB 37538005 1.000000 0.71417 1.000000 0.80357 0.702000 0.40608 4.466000 0.60148 1.917000 0.55516 0.483000 0.47432 . TCGA-FB-AAPZ-01A-11D-A40W-08 CYBB-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000080881.1 1 0 1 26 169 0 45 0 0 0 0 45 2 0 0 0 0 0 2 1 9.999999e-01 26 166 0 42 2 -20.000000 1 1 0 0 1 0 1 1 0.680000 3.130000 0.680000 1.900000e-01 1.300000e-01 0.270000 0.200000 0.201063 1.900000e-01 0 1.600000e-01 2.400000e-01