Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_position End_position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_file Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID Genome_Change Annotation_Transcript Transcript_Strand Transcript_Exon Transcript_Position cDNA_Change Codon_Change Protein_Change Other_Transcripts Refseq_mRNA_Id Refseq_prot_Id SwissProt_acc_Id SwissProt_entry_Id Description COSMIC_overlapping_mutations COSMIC_fusion_genes COSMIC_total_alterations_in_gene Tumorscape_Amplification_Peaks Tumorscape_Deletion_Peaks TCGAscape_Amplification_Peaks DrugBank ref_context gc_content CCLE_ONCOMAP_overlapping_mutations CCLE_ONCOMAP_total_mutations_in_gene CGC_Mutation_Type CGC_Translocation_Partner CGC_Tumor_Types_Somatic CGC_Tumor_Types_Germline CGC_Other_Diseases DNARepairGenes_Role FamilialCancerDatabase_Syndromes MUTSIG_Published_Results OREGANNO_ID OREGANNO_Values ACHILLES_Lineage_Results_Top_Genes CGC_CancerGermlineMut CGC_CancerMolecularGenetics CGC_CancerSomaticMut CGC_CancerSyndrome CGC_Chr CGC_ChrBand CGC_GeneID CGC_Name CGC_OtherGermlineMut CGC_TissueType COSMIC_n_overlapping_mutations COSMIC_overlapping_mutation_descriptions ClinVar_ASSEMBLY ClinVar_HGMD_ID ClinVar_SYM ClinVar_TYPE ClinVar_rs Ensembl_so_accession Ensembl_so_term Familial_Cancer_Genes_Reference Familial_Cancer_Genes_Synonym annotation_transcript bcgsc broad build ccds_id dbNSFP_1000Gp1_AC dbNSFP_1000Gp1_AF dbNSFP_1000Gp1_AFR_AC dbNSFP_1000Gp1_AFR_AF dbNSFP_1000Gp1_AMR_AC dbNSFP_1000Gp1_AMR_AF dbNSFP_1000Gp1_ASN_AC dbNSFP_1000Gp1_ASN_AF dbNSFP_1000Gp1_EUR_AC dbNSFP_1000Gp1_EUR_AF dbNSFP_Ancestral_allele dbNSFP_CADD_phred dbNSFP_CADD_raw dbNSFP_CADD_raw_rankscore dbNSFP_ESP6500_AA_AF dbNSFP_ESP6500_EA_AF dbNSFP_Ensembl_geneid dbNSFP_Ensembl_transcriptid dbNSFP_FATHMM_pred dbNSFP_FATHMM_rankscore dbNSFP_FATHMM_score dbNSFP_GERP_NR dbNSFP_GERP_RS dbNSFP_GERP_RS_rankscore dbNSFP_Interpro_domain dbNSFP_LRT_Omega dbNSFP_LRT_converted_rankscore dbNSFP_LRT_pred dbNSFP_LRT_score dbNSFP_LR_pred dbNSFP_LR_rankscore dbNSFP_LR_score dbNSFP_MutationAssessor_pred dbNSFP_MutationAssessor_rankscore dbNSFP_MutationAssessor_score dbNSFP_MutationTaster_converted_rankscore dbNSFP_MutationTaster_pred dbNSFP_MutationTaster_score dbNSFP_Polyphen2_HDIV_pred dbNSFP_Polyphen2_HDIV_rankscore dbNSFP_Polyphen2_HDIV_score dbNSFP_Polyphen2_HVAR_pred dbNSFP_Polyphen2_HVAR_rankscore dbNSFP_Polyphen2_HVAR_score dbNSFP_RadialSVM_pred dbNSFP_RadialSVM_rankscore dbNSFP_RadialSVM_score dbNSFP_Reliability_index dbNSFP_SIFT_converted_rankscore dbNSFP_SIFT_pred dbNSFP_SIFT_score dbNSFP_SLR_test_statistic dbNSFP_SiPhy_29way_logOdds dbNSFP_SiPhy_29way_logOdds_rankscore dbNSFP_SiPhy_29way_pi dbNSFP_UniSNP_ids dbNSFP_Uniprot_aapos dbNSFP_Uniprot_acc dbNSFP_Uniprot_id dbNSFP_aaalt dbNSFP_aapos dbNSFP_aapos_FATHMM dbNSFP_aapos_SIFT dbNSFP_aaref dbNSFP_cds_strand dbNSFP_codonpos dbNSFP_folddegenerate dbNSFP_genename dbNSFP_hg18_pos1coor dbNSFP_phastCons100way_vertebrate dbNSFP_phastCons100way_vertebrate_rankscore dbNSFP_phastCons46way_placental dbNSFP_phastCons46way_placental_rankscore dbNSFP_phastCons46way_primate dbNSFP_phastCons46way_primate_rankscore dbNSFP_phyloP100way_vertebrate dbNSFP_phyloP100way_vertebrate_rankscore dbNSFP_phyloP46way_placental dbNSFP_phyloP46way_placental_rankscore dbNSFP_phyloP46way_primate dbNSFP_phyloP46way_primate_rankscore dbNSFP_refcodon entrez_gene_id external_id_capture gencode_transcript_name gencode_transcript_status gencode_transcript_tags gencode_transcript_type gene_type havana_transcript hgsc igv_bad ucsc t_alt_count t_ref_count n_alt_count n_ref_count validation_judgement_rna validation_power_rna validation_tumor_alt_count_rna validation_tumor_ref_count_rna validation_normal_alt_count_rna validation_normal_ref_count_rna min_val_count_rna validation_judgement_targeted validation_power_targeted validation_tumor_alt_count_targeted validation_tumor_ref_count_targeted validation_normal_alt_count_targeted validation_normal_ref_count_targeted min_val_count_targeted validation_judgement_localAssembly validation_power_localAssembly t_alt_count_localAssembly t_ref_count_localAssembly n_alt_count_localAssembly n_ref_count_localAssembly min_val_count_localAssembly validation_judgement_KRAS validation_power_KRAS t_alt_count_KRAS t_ref_count_KRAS n_alt_count_KRAS n_ref_count_KRAS min_val_count_KRAS pon_loglike pon_pass_loglike localAssembly_detected ExAC_AN ExAC_AC ExAC_LQ passExAC SCNA_NA SCNA_NB SCNA_q_hat SCNA_tau IS_SCNA purity ploidy dna_fraction_in_tumor CCF_hat CCF_CI95_low CCF_CI95_high CCF_mode CCF_mean CCF_median clonal CCF_CI_low CCF_CI_high TP53 7157 broad.mit.edu 37 17 7577558 7577558 + Frame_Shift_Del DEL G G - TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 G - G G Valid Somatic Phase_I WXS targeted Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr17:7577558delG ENST00000269305.4 - 7 912 c.723delC c.(721-723)tccfs p.S241fs TP53_ENST00000445888.2_Frame_Shift_Del_p.S241fs|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Frame_Shift_Del_p.S241fs|TP53_ENST00000420246.2_Frame_Shift_Del_p.S241fs|TP53_ENST00000359597.4_Frame_Shift_Del_p.S241fs|TP53_ENST00000413465.2_Frame_Shift_Del_p.S241fs 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.C242fs*5(9)|p.0?(8)|p.?(5)|p.S241del(5)|p.S241F(5)|p.N239_C242delNSSC(3)|p.S241S(3)|p.N239_C242>S(1)|p.S241_C242insX(1)|p.C238fs*21(1)|p.C242fs*20(1)|p.C242fs*23(1)|p.S241fs*22(1)|p.N239_C242del(1)|p.Y236_M243delYMCNSSCM(1)|p.S241_G245delSCMGG(1)|p.N239fs*4(1)|p.C238_M246delCNSSCMGGM(1)|p.H233_C242del10(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) CGCCCATGCAGGAACTGTTAC 0.577000 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 50 Deletion - In frame(13)|Deletion - Frameshift(13)|Whole gene deletion(8)|Unknown(5)|Substitution - Missense(5)|Substitution - coding silent(3)|Insertion - Frameshift(1)|Insertion - In frame(1)|Complex - deletion inframe(1) SO:0001589 frameshift_variant Familial Cancer Database Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma; ENST00000269305.4 0 1 hg19 CCDS11118.1 TCGA-FB-AAPY-01A-11D-A40W-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 0 30 294 0 54 0 8.549890e-01 0 36 0 54 2 1 1 56 603 0 620 2 1 0.957408 32 287 1 53 19 -3.142702 1 1 0 0 1 0 1 1 1.766681 1 0.260000 1.920000 0.149425 0.610000 0.420000 0.830000 0.610000 0.624867 0.610000 0 5.100000e-01 7.300000e-01 CPXM2 119587 broad.mit.edu 37 10 125539748 125539748 + Missense_Mutation SNP G G A TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr10:125539748G>A ENST00000241305.3 - 7 1067 c.913C>T c.(913-915)Cgg>Tgg p.R305W CPXM2_ENST00000368854.3_5'UTR|RP11-391M7.3_ENST00000446888.1_RNA NM_198148.2 NP_937791.2 Q8N436 CPXM2_HUMAN carboxypeptidase X (M14 family), member 2 47 all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233) ATCTCGTTCCGGCGGTGATAA 0.448000 0 SO:0001583 missense ENST00000241305.3 1 1 hg19 CCDS7637.1 . . . . . . . . . . G 14.50 2.555273 0.45487 0.0 1.16E-4 ENSG00000121898 ENST00000241305;ENST00000540123;ENST00000418782 D 0.96459 -4.02 4.62 2.6 0.31112 . 0.059335 0.64402 D 0.000003 D 0.95996 0.8696 L 0.44542 1.39 0.80722 D 1 D 0.76494 0.999 D 0.68765 0.96 D 0.94907 0.8061 10 0.87932 D 0 -16.204 7.5893 0.28012 0.0955:0.0:0.684:0.2205 . 305 Q8N436 CPXM2_HUMAN W 305;138;305 ENSP00000241305:R305W ENSP00000241305:R305W R - 1 2 CPXM2 125529738 1.000000 0.71417 0.998000 0.56505 0.342000 0.28953 2.618000 0.46393 1.169000 0.42739 -0.136000 0.14681 CGG TCGA-FB-AAPY-01A-11D-A40W-08 CPXM2-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050853.1 1 0 0 59 547 0 115 0 3.714629e-01 0 13 0 115 2 0 0 0 0 0 2 1 1.000000 59 545 0 112 2 -3.221883 1 1 121412 6 41 1 1 2 3 2.059041 0 0.260000 1.920000 0.268558 0.760000 0.580000 1.000000 0.750000 0.781340 0.760000 0 6.700000e-01 8.900000e-01 PARD3 56288 broad.mit.edu 37 10 34663823 34663823 + Silent SNP G G A TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr10:34663823G>A ENST00000374789.3 - 11 1972 c.1647C>T c.(1645-1647)gaC>gaT p.D549D PARD3_ENST00000374773.1_Silent_p.D549D|PARD3_ENST00000545693.1_Silent_p.D549D|PARD3_ENST00000545260.1_Silent_p.D505D|PARD3_ENST00000374794.3_Silent_p.D505D|PARD3_ENST00000374788.3_Silent_p.D549D|PARD3_ENST00000544292.1_Silent_p.D279D|PARD3_ENST00000374768.1_5'Flank|PARD3_ENST00000374776.1_Silent_p.D549D|PARD3_ENST00000346874.4_Silent_p.D549D|PARD3_ENST00000374790.3_Silent_p.D505D|PARD3_ENST00000350537.4_Silent_p.D549D|PARD3_ENST00000340077.5_Silent_p.D549D NM_019619.3 NP_062565.2 Q8TEW0 PARD3_HUMAN par-3 family cell polarity regulator 63 Breast(68;0.0707) GGTGGAAGGCGTCTTCCTGGC 0.478000 0 SO:0001819 synonymous_variant ENST00000374789.3 1 1 hg19 CCDS7178.1 TCGA-FB-AAPY-01A-11D-A40W-08 PARD3-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000047527.1 0 0 1 138 788 1 158 1 9.421334e-01 8 21 1 158 2 0 0 0 0 0 2 1 1.000000 136 784 1 156 20 -20.000000 1 1 121410 1 39 1 1 2 3 2.039750 0 0.260000 1.920000 0.264779 0.990000 0.980000 1.000000 1.000000 0.998779 0.990000 1 9.900000e-01 1 OR4D5 219875 broad.mit.edu 37 11 123810641 123810641 + Missense_Mutation SNP C C A TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr11:123810641C>A ENST00000307033.2 + 1 392 c.318C>A c.(316-318)ttC>ttA p.F106L NM_001001965.1 NP_001001965.1 Q8NGN0 OR4D5_HUMAN olfactory receptor, family 4, subfamily D, member 5 41 Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22) TCTTCCACTTCATTGGAGGCA 0.498000 0 SO:0001583 missense ENST00000307033.2 1 1 hg19 CCDS31699.1 . . . . . . . . . . C 14.59 2.580034 0.46006 . . ENSG00000171014 ENST00000307033 T 0.00408 7.54 5.5 4.58 0.56647 GPCR, rhodopsin-like superfamily (1); 0.132917 0.34386 N 0.004004 T 0.00178 0.0005 N 0.04063 -0.285 0.32942 D 0.518614 B 0.17038 0.02 B 0.18871 0.023 T 0.33111 -0.9881 10 0.13470 T 0.59 -18.5794 8.7808 0.34789 0.0:0.8248:0.0:0.1752 . 106 Q8NGN0 OR4D5_HUMAN L 106 ENSP00000305970:F106L ENSP00000305970:F106L F + 3 2 OR4D5 123315851 0.000000 0.05858 1.000000 0.80357 0.996000 0.88848 0.448000 0.21726 2.575000 0.86900 0.655000 0.94253 TTC TCGA-FB-AAPY-01A-11D-A40W-08 OR4D5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000387263.1 1 0 1 57 320 0 80 0 0 0 0 80 2 0 0 0 0 0 2 1 1.000000 56 315 0 80 2 -20.000000 1 1 0 0 1 1 2 3 2.039641 0 0.260000 1.920000 0.264779 0.990000 0.900000 1.000000 1.000000 0.994015 0.990000 1 9.900000e-01 1 OR8B12 219858 broad.mit.edu 37 11 124412927 124412927 + Missense_Mutation SNP C C A TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr11:124412927C>A ENST00000306842.2 - 1 648 c.624G>T c.(622-624)atG>atT p.M208I NM_001005195.1 NP_001005195.1 Q8NGG6 OR8BC_HUMAN olfactory receptor, family 8, subfamily B, member 12 31 Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224) TGACAATGGGCATTCCAACGT 0.453000 0 SO:0001583 missense ENST00000306842.2 1 1 hg19 CCDS31711.1 . . . . . . . . . . C 0.960 -0.703660 0.03255 . . ENSG00000170953 ENST00000306842 T 0.30981 1.51 3.89 -0.137 0.13469 GPCR, rhodopsin-like superfamily (1); 1.388370 0.04278 N 0.343265 T 0.09247 0.0228 N 0.00436 -1.5 0.09310 N 1 B 0.06786 0.001 B 0.11329 0.006 T 0.17198 -1.0377 10 0.39692 T 0.17 . 4.7775 0.13187 0.0:0.4882:0.1521:0.3598 . 208 Q8NGG6 OR8BC_HUMAN I 208 ENSP00000307159:M208I ENSP00000307159:M208I M - 3 0 OR8B12 123918137 0.000000 0.05858 0.002000 0.10522 0.015000 0.08874 -2.035000 0.01423 -0.013000 0.14199 -0.145000 0.13849 ATG TCGA-FB-AAPY-01A-11D-A40W-08 OR8B12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000387061.1 1 0 1 24 147 0 36 0 0 0 0 36 2 0 0 0 0 0 2 1 1.000000 24 147 0 36 2 -20.000000 1 1 0 0 1 1 2 3 2.039641 0 0.260000 1.920000 0.264779 0.990000 0.730000 1.000000 1.000000 0.963158 0.990000 1 8.900000e-01 1 NTM 50863 broad.mit.edu 37 11 132177680 132177680 + Silent SNP C C T TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr11:132177680C>T ENST00000374786.1 + 4 1103 c.624C>T c.(622-624)gcC>gcT p.A208A NTM_ENST00000539799.1_Silent_p.A208A|NTM_ENST00000425719.2_Silent_p.A208A|NTM_ENST00000474900.1_3'UTR|NTM_ENST00000374784.1_Silent_p.A208A|NTM_ENST00000374791.3_Silent_p.A208A|NTM_ENST00000427481.2_Silent_p.A199A NM_001144058.1|NM_016522.2 NP_001137530.1|NP_057606.1 Q9P121 NTRI_HUMAN neurotrimin 56 ATGACGTGGCCGCGCCCGTGG 0.582000 0 SO:0001819 synonymous_variant ENST00000374786.1 1 1 hg19 CCDS8491.1 TCGA-FB-AAPY-01A-11D-A40W-08 NTM-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000141937.1 1 0 1 26 154 0 41 0 9.744702e-01 0 38 0 41 2 0 0 0 0 0 2 1 1.000000 26 151 0 40 2 -20.000000 1 1 121412 1 27 1 1 2 3 2.039641 0 0.260000 1.920000 0.264779 0.990000 0.760000 1.000000 1.000000 0.972472 0.990000 1 9.300000e-01 1 C11orf40 143501 broad.mit.edu 37 11 4594586 4594586 + Missense_Mutation SNP A A T rs143067877 TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr11:4594586A>T ENST00000307616.1 - 2 257 c.258T>A c.(256-258)gaT>gaA p.D86E NM_144663.1 NP_653264.1 Q8WZ69 CK040_HUMAN chromosome 11 open reading frame 40 7 Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577) TGTGGCCGTTATCACCCATCA 0.473000 0 SO:0001583 missense ENST00000307616.1 1 1 hg19 CCDS31354.1 . . . . . . . . . . A 8.861 0.946988 0.18356 . . ENSG00000171987 ENST00000307616 T 0.54866 0.55 1.45 -1.1 0.09872 . . . . . T 0.26304 0.0642 N 0.08118 0 0.09310 N 1 B 0.09022 0.002 B 0.04013 0.001 T 0.16808 -1.0390 9 0.87932 D 0 . 2.2405 0.04018 0.4644:0.3189:0.2167:0.0 . 86 Q8WZ69 CK040_HUMAN E 86 ENSP00000302918:D86E ENSP00000302918:D86E D - 3 2 C11orf40 4551162 0.000000 0.05858 0.000000 0.03702 0.002000 0.02628 -1.039000 0.03550 -0.336000 0.08438 0.338000 0.21704 GAT TCGA-FB-AAPY-01A-11D-A40W-08 C11orf40-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000383529.1 1 0 0 26 383 0 80 0 0 0 0 80 2 0 0 0 0 0 2 1 1.000000 26 378 0 79 2 -20.000000 1 1 121412 2 37 1 1 2 3 2.049718 0 0.260000 1.920000 0.266673 0.500000 0.330000 1.000000 0.500000 0.534024 0.500000 0 4.100000e-01 6.200000e-01 AGBL2 79841 broad.mit.edu 37 11 47681762 47681762 + Missense_Mutation SNP G G A rs138759912 byFrequency TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr11:47681762G>A ENST00000525123.1 - 19 2957 c.2672C>T c.(2671-2673)gCg>gTg p.A891V AGBL2_ENST00000298861.4_Missense_Mutation_p.A891V|AGBL2_ENST00000357610.3_Missense_Mutation_p.A893V NM_024783.3 NP_079059.2 Q5U5Z8 CBPC2_HUMAN ATP/GTP binding protein-like 2 34 TGGGTATGCCGCCATGGCAGC 0.507000 0 SO:0001583 missense ENST00000525123.1 1 1 hg19 CCDS7944.1 7 0.003205128205128205 7 0.014227642276422764 0 0.0 0 0.0 0 0.0 G 3.229 -0.157929 0.06544 0.002045 0.0 ENSG00000165923 ENST00000528609;ENST00000525123;ENST00000357610;ENST00000298861 T;T;T 0.09538 2.97;2.97;2.97 4.79 0.562 0.17290 . 0.950318 0.08662 N 0.912279 T 0.03915 0.0110 N 0.16478 0.41 0.09310 N 1 B 0.10296 0.003 B 0.04013 0.001 T 0.46555 -0.9183 10 0.13108 T 0.6 2.8316 6.4798 0.22057 0.4834:0.0:0.5166:0.0 . 891 Q5U5Z8 CBPC2_HUMAN V 274;891;893;891 ENSP00000435582:A891V;ENSP00000350228:A893V;ENSP00000298861:A891V ENSP00000298861:A891V A - 2 0 AGBL2 47638338 0.000000 0.05858 0.000000 0.03702 0.105000 0.19272 -0.127000 0.10547 0.017000 0.15025 -0.384000 0.06662 GCG TCGA-FB-AAPY-01A-11D-A40W-08 AGBL2-001 KNOWN non_canonical_conserved|basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000383726.2 1 0 1 44 335 0 69 0 7.202794e-02 1 3 0 69 2 0 0 0 0 0 2 1 1.000000 42 334 0 68 2 -2.966615 1 1 121412 25 48 1 1 2 3 2.049718 0 0.260000 1.920000 0.266673 0.900000 0.670000 1.000000 1.000000 0.897157 0.900000 1 7.800000e-01 1 NRXN2 9379 broad.mit.edu 37 11 64375284 64375284 + Missense_Mutation SNP G G A TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr11:64375284G>A ENST00000377551.1 - 22 4734 c.4523C>T c.(4522-4524)aCg>aTg p.T1508M NRXN2_ENST00000301894.2_Missense_Mutation_p.T462M|NRXN2_ENST00000265459.6_Missense_Mutation_p.T1508M|NRXN2_ENST00000377559.3_Missense_Mutation_p.T1438M|NRXN2_ENST00000409571.1_Missense_Mutation_p.T1501M Q9P2S2 NRX2A_HUMAN neurexin 2 71 CTCGTCGTCCGTGGGGGGGAG 0.687000 0 SO:0001583 missense ENST00000377551.1 0 1 hg19 CCDS8077.1 . . . . . . . . . . G 17.28 3.350585 0.61183 . . ENSG00000110076 ENST00000301894;ENST00000377551;ENST00000377559;ENST00000265459;ENST00000345863;ENST00000409571 T;T;T;T;T 0.65549 0.35;-0.15;-0.16;-0.15;-0.04 3.9 3.9 0.45041 . . . . . T 0.66790 0.2825 N 0.24115 0.695 0.50313 D 0.99986 D;D;D;D 0.89917 0.999;0.979;0.989;1.0 P;P;P;D 0.87578 0.83;0.582;0.63;0.998 T 0.71500 -0.4574 9 0.72032 D 0.01 . 13.7387 0.62833 0.0:0.0:1.0:0.0 . 1438;1508;1254;462 Q9P2S2-2;Q9P2S2;E7EV67;P58401 .;NRX2A_HUMAN;.;NRX2B_HUMAN M 462;1508;1438;1508;1438;1501 ENSP00000301894:T462M;ENSP00000366774:T1508M;ENSP00000366782:T1438M;ENSP00000265459:T1508M;ENSP00000386416:T1501M ENSP00000265459:T1508M T - 2 0 NRXN2 64131860 1.000000 0.71417 1.000000 0.80357 0.793000 0.44817 5.307000 0.65762 1.899000 0.54978 0.313000 0.20887 ACG TCGA-FB-AAPY-01A-11D-A40W-08 NRXN2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000104967.3 0 0 0 6 48 0 12 0 6.872679e-01 0 20 0 12 2 0 0 0 0 0 2 1 0.963891 6 46 0 12 2 -11.896020 1 1 0 0 1 1 2 3 2.039641 0 0.260000 1.920000 0.264779 0.890000 0.380000 1.000000 1.000000 0.832069 0.890000 1 6.000000e-01 1 MAP4K2 5871 broad.mit.edu 37 11 64566932 64566932 + Silent SNP G G A TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr11:64566932G>A ENST00000294066.2 - 14 1105 c.1014C>T c.(1012-1014)ggC>ggT p.G338G MAP4K2_ENST00000468062.1_5'Flank|MAP4K2_ENST00000377350.3_Silent_p.G338G NM_004579.3 NP_004570.2 Q12851 M4K2_HUMAN mitogen-activated protein kinase kinase kinase kinase 2 8 TGCGTGGGGCGCCAAATTTCA 0.597000 0 SO:0001819 synonymous_variant ENST00000294066.2 0 1 hg19 CCDS8082.1 TCGA-FB-AAPY-01A-11D-A40W-08 MAP4K2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000105239.1 0 0 0 7 394 0 64 0 6.266901e-02 0 20 0 64 2 0 0 0 0 0 2 1 0.979934 6 390 0 62 2 -2.129064 0 1 0 0 1 1 2 3 2.039641 0 0.260000 1.920000 0.264779 0.140000 0.060000 1.000000 0.140000 0.184809 0.140000 0 9.000000e-02 2.100000e-01 RBM19 9904 broad.mit.edu 37 12 114377796 114377796 + Missense_Mutation SNP C C T TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr12:114377796C>T ENST00000545145.2 - 15 1985 c.1907G>A c.(1906-1908)cGc>cAc p.R636H RP11-780K2.1_ENST00000550206.1_RNA|RBM19_ENST00000261741.5_Missense_Mutation_p.R636H|RBM19_ENST00000392561.3_Missense_Mutation_p.R636H NM_001146699.1 NP_001140171.1 Q9Y4C8 RBM19_HUMAN RNA binding motif protein 19 55 Medulloblastoma(191;0.163)|all_neural(191;0.178) GAAGGCCTTGCGGGCCTCCAG 0.622000 0 SO:0001583 missense ENST00000545145.2 0 1 hg19 CCDS9172.1 . . . . . . . . . . C 19.02 3.745338 0.69418 0.0 1.16E-4 ENSG00000122965 ENST00000545145;ENST00000392561;ENST00000261741 T;T;T 0.09073 3.02;3.02;3.02 4.3 2.42 0.29668 Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2); 0.185022 0.44483 N 0.000448 T 0.19805 0.0476 M 0.65320 2 0.39781 D 0.972299 D 0.71674 0.998 D 0.68353 0.957 T 0.01146 -1.1437 10 0.87932 D 0 -11.8564 6.7325 0.23390 0.0:0.5626:0.0:0.4373 . 636 Q9Y4C8 RBM19_HUMAN H 636 ENSP00000442053:R636H;ENSP00000376344:R636H;ENSP00000261741:R636H ENSP00000261741:R636H R - 2 0 RBM19 112862179 1.000000 0.71417 1.000000 0.80357 0.978000 0.69477 5.445000 0.66594 0.820000 0.34516 0.561000 0.74099 CGC TCGA-FB-AAPY-01A-11D-A40W-08 RBM19-003 KNOWN alternative_3_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000405251.1 0 0 0 6 354 0 54 0 3.624288e-02 0 15 0 54 2 0 0 0 0 0 2 1 0.963120 6 347 0 54 2 -1.927406 0 1 0 0 1 0 1 1 1.816916 1 0.260000 1.920000 0.151960 0.110000 0.040000 0.230000 0.110000 0.127789 0.110000 0 7.000000e-02 1.700000e-01 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr12:25398284C>T ENST00000256078.4 - 2 98 c.35G>A c.(34-36)gGt>gAt p.G12D KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 0 0 hg19 CCDS8703.1 . . . . . . . . . . C 23.4 4.409094 0.83340 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.85919 0.5809 M 0.91818 3.245 0.80722 D 1 B;P 0.35714 0.385;0.517 B;B 0.41619 0.257;0.361 D 0.87870 0.2670 10 0.87932 D 0 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN D 12 ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D ENSP00000256078:G12D G - 2 0 KRAS 25289551 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-FB-AAPY-01A-11D-A40W-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 22 190 1 61 0 2.110806e-01 1 6 1 61 2 1 1 29 255 0 273 2 1 0.958067 22 188 1 58 13 -10.133150 1 1 121404 2 44 1 1 2 3 2.104873 0 0.260000 1.920000 0.276920 0.850000 0.540000 1.000000 1.000000 0.844974 0.850000 1 6.800000e-01 1 LRP1 4035 broad.mit.edu 37 12 57578958 57578958 + Missense_Mutation SNP A A G TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr12:57578958A>G ENST00000243077.3 + 40 6899 c.6433A>G c.(6433-6435)Atc>Gtc p.I2145V NM_002332.2 NP_002323.2 Q07954 LRP1_HUMAN low density lipoprotein receptor-related protein 1 184 Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031) GCTTAAAGACATCAAAGTCTT 0.627000 0 SO:0001583 missense ENST00000243077.3 1 1 hg19 CCDS8932.1 . . . . . . . . . . A 12.65 2.002798 0.35320 . . ENSG00000123384 ENST00000243077 D 0.91180 -2.8 5.31 5.31 0.75309 Six-bladed beta-propeller, TolB-like (1); 0.000000 0.64402 D 0.000001 D 0.88683 0.6503 N 0.14661 0.345 0.80722 D 1 P 0.48640 0.913 P 0.61592 0.891 D 0.85470 0.1172 10 0.12103 T 0.63 . 14.2419 0.65963 1.0:0.0:0.0:0.0 . 2145 Q07954 LRP1_HUMAN V 2145 ENSP00000243077:I2145V ENSP00000243077:I2145V I + 1 0 LRP1 55865225 1.000000 0.71417 1.000000 0.80357 0.660000 0.38997 5.392000 0.66272 2.014000 0.59158 0.402000 0.26972 ATC TCGA-FB-AAPY-01A-11D-A40W-08 LRP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000412772.2 1 0 0 38 422 0 88 0 5.594590e-01 0 22 0 88 2 0 0 0 0 0 2 1 1.000000 37 411 0 86 2 -20.000000 1 1 0 0 1 1 2 3 2.104873 0 0.260000 1.920000 0.276920 0.670000 0.470000 1.000000 0.650000 0.707914 0.670000 0 5.600000e-01 8.700000e-01 MDM1 56890 broad.mit.edu 37 12 68720759 68720759 + Missense_Mutation SNP G G A TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr12:68720759G>A ENST00000303145.7 - 3 262 c.176C>T c.(175-177)cCt>cTt p.P59L MDM1_ENST00000545724.1_5'UTR|MDM1_ENST00000540418.1_Intron|MDM1_ENST00000430606.2_Missense_Mutation_p.P59L|MDM1_ENST00000393543.3_3'UTR|MDM1_ENST00000411698.2_Missense_Mutation_p.P59L NM_017440.4 NP_059136.2 Q8TC05 MDM1_HUMAN Mdm1 nuclear protein homolog (mouse) 33 Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018) GTCATGGTAAGGGACTCTTCT 0.413000 0 SO:0001583 missense ENST00000303145.7 1 1 hg19 CCDS8983.1 . . . . . . . . . . G 21.2 4.110659 0.77210 . . ENSG00000111554 ENST00000303145;ENST00000411698;ENST00000541686;ENST00000430606 T;T;T;T 0.26957 1.7;1.7;1.7;1.7 5.1 5.1 0.69264 . 0.115685 0.56097 D 0.000021 T 0.52141 0.1716 M 0.74881 2.28 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.91635 0.999;0.999;0.999 T 0.51395 -0.8711 9 . . . -18.3387 17.0854 0.86610 0.0:0.0:1.0:0.0 . 59;59;59 E7EPQ3;Q8TC05-2;Q8TC05 .;.;MDM1_HUMAN L 59;59;54;59 ENSP00000302537:P59L;ENSP00000391006:P59L;ENSP00000446000:P54L;ENSP00000408694:P59L . P - 2 0 MDM1 67007026 1.000000 0.71417 0.997000 0.53966 0.997000 0.91878 6.242000 0.72376 2.532000 0.85374 0.561000 0.74099 CCT TCGA-FB-AAPY-01A-11D-A40W-08 MDM1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000402402.1 1 0 1 44 297 0 78 0 3.344040e-01 1 8 0 78 2 0 0 0 0 0 2 1 1.000000 44 293 0 77 2 -2.807064 1 1 121410 1 34 1 0 1 1 1.819842 1 0.260000 1.920000 0.150694 0.830000 0.630000 1.000000 0.850000 0.837529 0.830000 0 7.300000e-01 9.400000e-01 LCP1 3936 broad.mit.edu 37 13 46730641 46730641 + Silent SNP C C T TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr13:46730641C>T ENST00000398576.2 - 8 811 c.423G>A c.(421-423)cgG>cgA p.R141R LCP1_ENST00000460190.1_5'Flank|LCP1_ENST00000323076.2_Silent_p.R141R P13796 PLSL_HUMAN lymphocyte cytosolic protein 1 (L-plastin) p.R141R(1) 34 Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262) KIRC - Kidney renal clear cell carcinoma(16;0.234) GGATGACATGCCGACAATCAG 0.383000 T BCL6 NHL Dom yes 13 13q14.1-q14.3 3936 lymphocyte cytosolic protein 1 (L-plastin) L 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000398576.2 0 1 hg19 CCDS9403.1 TCGA-FB-AAPY-01A-11D-A40W-08 LCP1-006 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044800.3 0 0 0 6 709 0 103 0 1.346060e-01 0 63 0 103 2 0 0 0 0 0 2 1 0.963989 8 700 0 103 2 -1.751656 0 1 0 0 1 1 2 3 2.050384 0 0.260000 1.920000 0.266673 0.060000 0.020000 1.000000 0.060000 0.127049 0.060000 0 4.000000e-02 1.100000e-01 ESR2 2100 broad.mit.edu 37 14 64735549 64735549 + Missense_Mutation SNP G G T TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr14:64735549G>T ENST00000341099.4 - 4 1033 c.616C>A c.(616-618)Ctt>Att p.L206I ESR2_ENST00000357782.2_Missense_Mutation_p.L206I|ESR2_ENST00000557772.1_Missense_Mutation_p.L206I|ESR2_ENST00000267525.6_Missense_Mutation_p.L206I|ESR2_ENST00000353772.3_Missense_Mutation_p.L206I|ESR2_ENST00000542956.1_Missense_Mutation_p.L206I|ESR2_ENST00000555278.1_Missense_Mutation_p.L206I|ESR2_ENST00000553796.1_Missense_Mutation_p.L206I|ESR2_ENST00000555483.1_5'UTR|ESR2_ENST00000358599.5_Missense_Mutation_p.L206I|ESR2_ENST00000554572.1_Missense_Mutation_p.L206I NM_001437.2 NP_001428.1 Q92731 ESR2_HUMAN estrogen receptor 2 (ER beta) 23 Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estropipate(DB04574)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Trilostane(DB01108) CACTTCCGAAGTCGGCAGGCC 0.478000 0 SO:0001583 missense ENST00000341099.4 1 1 hg19 CCDS9762.1 . . . . . . . . . . G 35 5.413647 0.96072 . . ENSG00000140009 ENST00000556275;ENST00000542956;ENST00000554572;ENST00000353772;ENST00000358599;ENST00000555278;ENST00000553796;ENST00000357782;ENST00000557772;ENST00000341099;ENST00000267525 D;D;D;D;D;D;D;D;D;D;D 0.97994 -4.65;-4.65;-4.65;-4.65;-4.65;-4.65;-4.65;-4.65;-4.65;-4.65;-4.65 5.67 5.67 0.87782 Zinc finger, NHR/GATA-type (1);Nuclear hormone receptor, ligand-binding (1);Zinc finger, nuclear hormone receptor-type (5); 0.059913 0.64402 D 0.000002 D 0.98820 0.9602 M 0.82923 2.615 0.80722 D 1 D;D;D;D;D 0.89917 0.999;1.0;1.0;1.0;1.0 D;D;D;D;D 0.91635 0.996;0.999;0.997;0.997;0.996 D 0.99758 1.1020 10 0.87932 D 0 . 19.7793 0.96412 0.0:0.0:1.0:0.0 . 206;206;206;206;206 Q92731-7;Q92731;Q92731-6;Q92731-5;F1D8N3 .;ESR2_HUMAN;.;.;. I 206 ENSP00000452485:L206I;ENSP00000441792:L206I;ENSP00000450699:L206I;ENSP00000335551:L206I;ENSP00000351412:L206I;ENSP00000450488:L206I;ENSP00000452426:L206I;ENSP00000350427:L206I;ENSP00000451582:L206I;ENSP00000343925:L206I;ENSP00000267525:L206I ENSP00000267525:L206I L - 1 0 ESR2 63805302 1.000000 0.71417 1.000000 0.80357 0.994000 0.84299 9.756000 0.98918 2.678000 0.91216 0.555000 0.69702 CTT TCGA-FB-AAPY-01A-11D-A40W-08 ESR2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000280621.1 1 0 0 87 487 0 87 0 0 0 1 0 87 2 0 0 0 0 0 2 1 1.000000 85 478 0 87 2 -20.000000 1 1 0 0 1 1 2 3 2.030151 0 0.260000 1.920000 0.263828 0.990000 0.950000 1.000000 1.000000 0.997447 0.990000 1 9.900000e-01 1 ATP10A 57194 broad.mit.edu 37 15 25953443 25953443 + Silent SNP G G A TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr15:25953443G>A ENST00000356865.6 - 11 2460 c.2349C>T c.(2347-2349)gaC>gaT p.D783D 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) TCCCTCTGGCGTCAACTAGGT 0.502000 0 SO:0001819 synonymous_variant ENST00000356865.6 1 1 hg19 CCDS32178.1 TCGA-FB-AAPY-01A-11D-A40W-08 ATP10A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000414830.1 1 0 0 44 320 0 55 0 5.618492e-01 0 15 0 55 2 0 0 0 0 0 2 1 1.000000 44 318 0 51 2 -17.880320 1 1 121412 2 36 1 1 2 3 2.036004 0 0.260000 1.920000 0.264779 0.940000 0.690000 1.000000 1.000000 0.917706 0.940000 1 8.100000e-01 1 ATP10A 57194 broad.mit.edu 37 15 26026228 26026228 + Missense_Mutation SNP C C T TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr15:26026228C>T ENST00000356865.6 - 2 703 c.592G>A c.(592-594)Gcc>Acc p.A198T 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) TCCAGGTTGGCGGTCTCGATG 0.602000 0 SO:0001583 missense ENST00000356865.6 1 1 hg19 CCDS32178.1 . . . . . . . . . . C 35 5.527017 0.96431 . . ENSG00000206190 ENST00000356865 D 0.91996 -2.95 4.67 4.67 0.58626 ATPase, P-type, ATPase-associated domain (1);ATPase, P-type, cytoplasmic transduction domain A (1); 0.000000 0.85682 D 0.000000 D 0.96163 0.8749 M 0.88775 2.98 0.58432 D 0.999998 D 0.60160 0.987 P 0.62491 0.903 D 0.96807 0.9594 10 0.66056 D 0.02 -27.9289 16.7413 0.85460 0.0:1.0:0.0:0.0 . 198 O60312 AT10A_HUMAN T 198 ENSP00000349325:A198T ENSP00000349325:A198T A - 1 0 ATP10A 23577321 1.000000 0.71417 0.948000 0.38648 0.963000 0.63663 5.657000 0.67996 2.428000 0.82296 0.561000 0.74099 GCC TCGA-FB-AAPY-01A-11D-A40W-08 ATP10A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000414830.1 1 0 1 45 351 0 88 0 4.102712e-01 0 12 0 88 2 0 0 0 0 0 2 1 1.000000 41 338 0 85 2 -3.075757 1 1 121412 1 31 1 1 2 3 2.036004 0 0.260000 1.920000 0.264779 0.880000 0.650000 1.000000 1.000000 0.879937 0.880000 1 7.600000e-01 1 CCDC102A 92922 broad.mit.edu 37 16 57559977 57559977 + Silent SNP C C T TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr16:57559977C>T ENST00000258214.2 - 3 894 c.648G>A c.(646-648)gaG>gaA p.E216E NM_033212.3 NP_149989.2 Q96A19 C102A_HUMAN coiled-coil domain containing 102A 8 GGCTGCGCGCCTCCCAGCAGT 0.716000 0 SO:0001819 synonymous_variant ENST00000258214.2 0 1 hg19 CCDS10784.1 TCGA-FB-AAPY-01A-11D-A40W-08 CCDC102A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257348.1 1 0 1 7 42 0 10 0 1.837844e-01 0 5 0 10 2 0 0 0 0 0 2 1 0.983355 7 42 0 10 2 -14.577000 1 1 0 0 1 1 2 3 2.042215 0 0.260000 1.920000 0.265727 0.990000 0.520000 1.000000 1.000000 0.924819 0.990000 1 7.800000e-01 1 MAP2K4 6416 broad.mit.edu 37 17 11998898 11998898 + Missense_Mutation SNP C C T TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr17:11998898C>T ENST00000353533.5 + 4 463 c.400C>T c.(400-402)Cgg>Tgg p.R134W MAP2K4_ENST00000581941.1_3'UTR|MAP2K4_ENST00000415385.3_Missense_Mutation_p.R145W NM_003010.2 NP_003001.1 P45985 MP2K4_HUMAN mitogen-activated protein kinase kinase 4 p.0?(10)|p.R134W(2)|p.?(1) 100 all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163) CCAGAGAATTCGGTCAACAGT 0.338000 D, Mis, N pancreatic, breast, colorectal Rec yes 17 17p11.2 6416 mitogen-activated protein kinase kinase 4 E 13 Whole gene deletion(10)|Substitution - Missense(2)|Unknown(1) SO:0001583 missense ENST00000353533.5 1 1 hg19 CCDS11162.1 . . . . . . . . . . C 14.66 2.600257 0.46423 . . ENSG00000065559 ENST00000353533;ENST00000415385;ENST00000538465;ENST00000536413 T;T 0.66815 -0.23;-0.23 5.97 4.94 0.65067 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 D 0.83454 0.5258 M 0.87456 2.885 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.87578 0.998;0.997;0.997 D 0.85848 0.1402 10 0.87932 D 0 . 14.9277 0.70893 0.1438:0.8562:0.0:0.0 . 6;145;134 B7ZA62;P45985-2;P45985 .;.;MP2K4_HUMAN W 134;145;111;6 ENSP00000262445:R134W;ENSP00000410402:R145W ENSP00000262445:R134W R + 1 2 MAP2K4 11939623 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 4.735000 0.62051 2.835000 0.97688 0.591000 0.81541 CGG TCGA-FB-AAPY-01A-11D-A40W-08 MAP2K4-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000441226.1 1 0 1 34 231 0 58 0 2.818035e-01 1 7 0 58 2 1 9.999999e-01 33 151 0 211 2 1 1.000000 34 229 0 57 2 -2.967195 1 1 0 0 1 0 1 1 1.766681 1 0.260000 1.920000 0.149425 0.820000 0.600000 0.990000 0.840000 0.821104 0.820000 0 7.000000e-01 9.300000e-01 KRTAP4-2 85291 broad.mit.edu 37 17 39334112 39334112 + Missense_Mutation SNP C C T TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr17:39334112C>T ENST00000377726.2 - 1 348 c.305G>A c.(304-306)cGc>cAc p.R102H NM_033062.3 NP_149051 Q9BYR5 KRA42_HUMAN keratin associated protein 4-2 p.R102H(1) 7 Breast(137;0.000496) STAD - Stomach adenocarcinoma(17;0.000449) ACAGCTGGGGCGGCAGCAGGT 0.657000 1 Substitution - Missense(1) SO:0001583 missense ENST00000377726.2 1 1 hg19 CCDS11384.1 . . . . . . . . . . . 15.62 2.886123 0.51908 . . ENSG00000244537 ENST00000377726;ENST00000458321 T 0.01505 4.82 4.21 0.00697 0.14069 . 5.476650 0.00783 U 0.001287 T 0.04634 0.0126 M 0.74467 2.265 0.09310 N 1 D 0.53885 0.963 P 0.46389 0.515 T 0.42999 -0.9418 10 0.33141 T 0.24 . 6.1825 0.20480 0.5372:0.303:0.1599:0.0 . 102 Q9BYR5 KRA42_HUMAN H 102;219 ENSP00000366955:R102H ENSP00000366955:R102H R - 2 0 KRTAP4-2 36587638 0.000000 0.05858 0.005000 0.12908 0.538000 0.34931 -2.424000 0.01029 0.251000 0.21505 0.609000 0.83330 CGC TCGA-FB-AAPY-01A-11D-A40W-08 KRTAP4-2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257305.1 1 0 1 78 434 1 84 0 0 0 1 84 2 0 0 0 0 0 2 1 1.000000 75 428 0 83 2 -20.000000 1 1 121392 5 40 1 1 2 3 2.030134 0 0.260000 1.920000 0.263828 0.990000 0.940000 1.000000 1.000000 0.997079 0.990000 1 9.900000e-01 1 GJC1 10052 broad.mit.edu 37 17 42882797 42882797 + Missense_Mutation SNP G G A TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr17:42882797G>A ENST00000426548.1 - 3 658 c.389C>T c.(388-390)aCg>aTg p.T130M GJC1_ENST00000592524.1_Missense_Mutation_p.T130M|GJC1_ENST00000330514.4_Missense_Mutation_p.T130M|GJC1_ENST00000590758.1_Missense_Mutation_p.T130M NM_001080383.1|NM_005497.3 NP_001073852.1|NP_005488.2 P36383 CXG1_HUMAN gap junction protein, gamma 1, 45kDa 19 Prostate(33;0.0959) GTCCTCCTCCGTTTCTTCCAG 0.483000 0 SO:0001583 missense ENST00000426548.1 1 1 hg19 CCDS11487.1 . . . . . . . . . . G 12.25 1.883056 0.33255 . . ENSG00000182963 ENST00000426548;ENST00000330514 D;D 0.97976 -4.64;-4.64 5.27 5.27 0.74061 . 0.449024 0.23777 N 0.044678 D 0.96160 0.8748 L 0.29908 0.895 0.40774 D 0.983116 P 0.47484 0.896 P 0.47044 0.535 D 0.96891 0.9653 10 0.54805 T 0.06 . 17.8983 0.88896 0.0:0.0:1.0:0.0 . 130 P36383 CXG1_HUMAN M 130 ENSP00000411528:T130M;ENSP00000333193:T130M ENSP00000333193:T130M T - 2 0 GJC1 40238323 1.000000 0.71417 0.995000 0.50966 0.210000 0.24377 7.686000 0.84128 2.462000 0.83206 0.462000 0.41574 ACG TCGA-FB-AAPY-01A-11D-A40W-08 GJC1-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000448661.1 1 0 1 78 516 0 93 0 2.349599e-01 0 7 0 93 2 0 0 0 0 0 2 1 1.000000 79 508 0 90 2 -2.690408 1 1 121412 6 40 1 1 2 3 2.030134 0 0.260000 1.920000 0.263828 0.990000 0.810000 1.000000 1.000000 0.967820 0.990000 1 9.100000e-01 1 KCNH6 81033 broad.mit.edu 37 17 61611293 61611293 + Missense_Mutation SNP C C T TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr17:61611293C>T ENST00000583023.1 + 5 733 c.722C>T c.(721-723)gCg>gTg p.A241V KCNH6_ENST00000581784.1_Missense_Mutation_p.A241V|KCNH6_ENST00000580652.1_Missense_Mutation_p.A241V|KCNH6_ENST00000314672.5_Missense_Mutation_p.A241V|KCNH6_ENST00000456941.2_Missense_Mutation_p.A241V NM_030779.2 NP_110406.1 Q9H252 KCNH6_HUMAN potassium voltage-gated channel, subfamily H (eag-related), member 6 p.A241V(1) 54 Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162) AAGCTGCAGGCGCCGCGCATC 0.672000 1 Substitution - Missense(1) SO:0001583 missense ENST00000583023.1 1 1 hg19 CCDS11638.1 1 4.578754578754579E-4 1 0.0020325203252032522 0 0.0 0 0.0 0 0.0 C 10.97 1.501304 0.26861 2.27E-4 0.0 ENSG00000173826 ENST00000314672;ENST00000456941 D;D 0.94650 -3.48;-3.48 3.9 2.93 0.34026 . 0.064020 0.64402 D 0.000008 D 0.92645 0.7663 M 0.68952 2.095 0.50039 D 0.999849 B;B;P;B;B 0.47841 0.004;0.001;0.901;0.003;0.006 B;B;B;B;B 0.42319 0.007;0.004;0.383;0.002;0.005 D 0.91303 0.5068 10 0.49607 T 0.09 . 11.9936 0.53189 0.0:0.9134:0.0:0.0866 . 118;241;241;241;241 B4DPJ3;B4DKC0;Q9H252-2;Q9H252;Q9H252-3 .;.;.;KCNH6_HUMAN;. V 241 ENSP00000318212:A241V;ENSP00000396900:A241V ENSP00000318212:A241V A + 2 0 KCNH6 58965025 1.000000 0.71417 0.842000 0.33263 0.406000 0.30931 5.929000 0.70096 0.969000 0.38237 -0.657000 0.03884 GCG TCGA-FB-AAPY-01A-11D-A40W-08 KCNH6-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000443853.1 1 0 1 79 385 0 73 0 7.857973e-02 0 3 0 73 2 0 0 0 0 0 2 1 1.000000 78 380 0 68 2 -4.565590 1 1 121410 16 43 1 1 2 3 2.030134 0 0.260000 1.920000 0.263828 0.990000 0.990000 1.000000 1.000000 0.999799 0.990000 1 9.900000e-01 1 LRRC37A3 374819 broad.mit.edu 37 17 62893346 62893346 + Silent SNP C C A TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr17:62893346C>A ENST00000584306.1 - 3 560 c.30G>T c.(28-30)gcG>gcT p.A10A RP11-927P21.1_ENST00000584131.1_RNA|LRRC37A3_ENST00000319651.5_Silent_p.A10A|RP11-927P21.1_ENST00000577938.1_RNA|LRRC37A3_ENST00000577487.1_5'Flank|RP11-927P21.1_ENST00000584959.1_RNA|RP11-927P21.2_ENST00000581622.1_RNA|LRRC37A3_ENST00000400877.3_Intron|LRRC37A3_ENST00000339474.5_Intron NM_199340.2 NP_955372.2 O60309 L37A3_HUMAN leucine rich repeat containing 37, member A3 40 ACATGACACACGCTAGTGCCG 0.572000 0 SO:0001819 synonymous_variant ENST00000584306.1 0 1 hg19 CCDS32708.1 TCGA-FB-AAPY-01A-11D-A40W-08 LRRC37A3-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000445377.1 0 0 0 10 926 1 241 0 2.157438e-03 0 6 1 241 2 0 0 0 0 0 2 0 0.241578 9 896 1 240 14 -2.841452 1 1 0 0 1 1 2 3 2.030134 0 0.260000 1.920000 0.263828 0.080000 0.030000 1.000000 0.080000 0.116584 0.080000 0 5.000000e-02 1.200000e-01 APCDD1 147495 broad.mit.edu 37 18 10471951 10471951 + Missense_Mutation SNP C C T TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr18:10471951C>T ENST00000355285.5 + 3 1021 c.667C>T c.(667-669)Ctc>Ttc p.L223F APCDD1_ENST00000578882.1_Intron NM_153000.4 NP_694545.1 adenomatosis polyposis coli down-regulated 1 22 TCACCACAACCTCGACCACCT 0.572000 0 SO:0001583 missense ENST00000355285.5 1 1 hg19 CCDS11849.1 . . . . . . . . . . C 5.558 0.287867 0.10513 . . ENSG00000154856 ENST00000355285;ENST00000423585 T 0.18174 2.23 5.3 1.14 0.20703 . 0.067248 0.64402 D 0.000011 T 0.15825 0.0381 M 0.69823 2.125 0.80722 D 1 B 0.06786 0.001 B 0.11329 0.006 T 0.08743 -1.0707 10 0.14656 T 0.56 -22.2921 7.5727 0.27918 0.0:0.4399:0.0:0.5601 . 223 Q8J025 APCD1_HUMAN F 223;274 ENSP00000347433:L223F ENSP00000347433:L223F L + 1 0 APCDD1 10461951 1.000000 0.71417 0.931000 0.37212 0.062000 0.15995 1.147000 0.31602 0.329000 0.23460 0.655000 0.94253 CTC TCGA-FB-AAPY-01A-11D-A40W-08 APCDD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254529.2 1 0 1 123 578 0 114 0 9.995072e-01 0 54 0 114 2 0 0 0 0 0 2 1 1.000000 123 568 1 111 20 -3.342749 1 1 0 0 1 1 2 3 2.111398 0 0.260000 1.920000 0.277837 0.990000 0.990000 1.000000 1.000000 0.999998 0.990000 1 9.900000e-01 1 ROCK1 6093 broad.mit.edu 37 18 18562785 18562785 + Missense_Mutation SNP C C T TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr18:18562785C>T ENST00000399799.2 - 21 3438 c.2498G>A c.(2497-2499)aGa>aAa p.R833K NM_005406.2 NP_005397.1 Q13464 ROCK1_HUMAN Rho-associated, coiled-coil containing protein kinase 1 16 Melanoma(1;0.165) TTCATTTCCTCTATACTGTCT 0.333000 0 SO:0001583 missense ENST00000399799.2 1 1 hg19 CCDS11870.2 . . . . . . . . . . C 16.46 3.130305 0.56721 . . ENSG00000067900 ENST00000399799 T 0.12879 2.64 5.17 5.17 0.71159 . 0.000000 0.85682 D 0.000000 T 0.14787 0.0357 L 0.47716 1.5 0.58432 D 0.999991 B 0.06786 0.001 B 0.04013 0.001 T 0.09707 -1.0662 10 0.14252 T 0.57 . 18.8588 0.92264 0.0:1.0:0.0:0.0 . 833 Q13464 ROCK1_HUMAN K 833 ENSP00000382697:R833K ENSP00000382697:R833K R - 2 0 ROCK1 16816783 1.000000 0.71417 1.000000 0.80357 0.894000 0.52154 5.210000 0.65214 2.699000 0.92147 0.591000 0.81541 AGA TCGA-FB-AAPY-01A-11D-A40W-08 ROCK1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254641.2 1 0 0 52 351 0 55 0 9.939542e-01 1 54 0 55 2 0 0 0 0 0 2 1 1.000000 52 347 0 55 2 -2.744810 1 1 0 0 1 0.260000 1.920000 0 0 SMAD4 4089 broad.mit.edu 37 18 48581229 48581229 + Nonsense_Mutation SNP C C A TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 C A C C Valid Somatic Phase_I WXS targeted Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr18:48581229C>A ENST00000342988.3 + 5 1071 c.533C>A c.(532-534)tCa>tAa p.S178* SMAD4_ENST00000452201.2_3'UTR|SMAD4_ENST00000588745.1_Nonsense_Mutation_p.S178*|RP11-729L2.2_ENST00000590722.2_3'UTR|SMAD4_ENST00000398417.2_Nonsense_Mutation_p.S178* NM_005359.5 NP_005350.1 Q13485 SMAD4_HUMAN SMAD family member 4 p.0?(36)|p.?(3) 454 all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336) GAAGGACATTCAATTCAAACC 0.438000 39 Whole gene deletion(36)|Unknown(3) GRCh37 CM994756 SMAD4 M SO:0001587 stop_gained ENST00000342988.3 0 1 hg19 CCDS11950.1 . . . . . . . . . . C 42 9.219139 0.99105 . . ENSG00000141646 ENST00000342988;ENST00000544926;ENST00000398417 . . . 5.86 5.86 0.93980 . 0.282373 0.35378 N 0.003258 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.05525 T 0.97 . 19.3335 0.94306 0.0:1.0:0.0:0.0 . . . . X 178 . ENSP00000341551:S178X S + 2 0 SMAD4 46835227 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 3.952000 0.56691 2.937000 0.99478 0.650000 0.86243 TCA TCGA-FB-AAPY-01A-11D-A40W-08 SMAD4-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255993.3 1 0 1 68 332 0 79 1 9.472578e-01 3 23 0 79 2 1 1 83 516 0 580 2 1 1.000000 67 328 0 77 2 -3.253371 1 1 0 0 1 0 1 1 1.766790 1 0.260000 1.920000 0.149425 0.950000 0.810000 1.000000 0.990000 0.946001 0.950000 1 8.900000e-01 9.900000e-01 AKT2 208 broad.mit.edu 37 19 40762881 40762881 + Missense_Mutation SNP C C T TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr19:40762881C>T ENST00000392038.2 - 3 425 c.127G>A c.(127-129)Gag>Aag p.E43K AKT2_ENST00000311278.6_Missense_Mutation_p.E43K|AKT2_ENST00000424901.1_Missense_Mutation_p.E43K|AKT2_ENST00000579047.1_5'UTR NM_001243027.1|NM_001243028.1|NM_001626.4 NP_001229956.1|NP_001229957.1|NP_001617.1 P31751 AKT2_HUMAN v-akt murine thymoma viral oncogene homolog 2 27 Lung(22;0.000499) TCAGGGGCCTCGGGCCTCTCC 0.562000 A ovarian, pancreatic Dom yes 19 19q13.1-q13.2 208 v-akt murine thymoma viral oncogene homolog 2 E 0 SO:0001583 missense ENST00000392038.2 0 1 hg19 CCDS12552.1 . . . . . . . . . . C 15.56 2.868462 0.51588 . . ENSG00000105221 ENST00000392038;ENST00000358335;ENST00000424901;ENST00000311278;ENST00000537834;ENST00000452077;ENST00000392037;ENST00000416362;ENST00000423127;ENST00000456441;ENST00000416994;ENST00000427375;ENST00000441941 T;T;T;T;T;T;T;T;T;T;T 0.41400 1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0 5.27 5.27 0.74061 Pleckstrin homology-type (1);Pleckstrin homology domain (3); 0.093111 0.64402 D 0.000001 T 0.23688 0.0573 N 0.10733 0.035 0.49798 D 0.999823 B;B;B 0.22480 0.07;0.027;0.008 B;B;B 0.19666 0.026;0.015;0.004 T 0.09596 -1.0667 10 0.07482 T 0.82 . 17.8288 0.88674 0.0:1.0:0.0:0.0 . 43;43;43 B7Z8Z9;Q0VAN0;P31751 .;.;AKT2_HUMAN K 43;42;43;43;43;43;43;43;43;43;43;43;43 ENSP00000375892:E43K;ENSP00000399532:E43K;ENSP00000309428:E43K;ENSP00000404083:E43K;ENSP00000375891:E43K;ENSP00000407999:E43K;ENSP00000403842:E43K;ENSP00000396532:E43K;ENSP00000392458:E43K;ENSP00000403890:E43K;ENSP00000396968:E43K ENSP00000309428:E43K E - 1 0 AKT2 45454721 0.888000 0.30383 0.953000 0.39169 0.965000 0.64279 1.770000 0.38532 2.758000 0.94735 0.561000 0.74099 GAG TCGA-FB-AAPY-01A-11D-A40W-08 AKT2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268029.1 0 0 0 6 337 0 60 0 5.061951e-01 1 87 0 60 2 0 0 0 0 0 2 1 0.963042 6 330 0 58 2 -2.312410 0 1 0 0 1 1 2 3 2.291445 1 0.260000 1.920000 0.345133 0.160000 0.060000 0.310000 0.150000 0.175389 0.160000 0 1.000000e-01 2.400000e-01 ZNF114 163071 broad.mit.edu 37 19 48789965 48789965 + Missense_Mutation SNP G G A TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr19:48789965G>A ENST00000595607.1 + 6 1578 c.1084G>A c.(1084-1086)Gaa>Aaa p.E362K ZNF114_ENST00000315849.1_Missense_Mutation_p.E362K|ZNF114_ENST00000597695.1_Missense_Mutation_p.E328K|ZNF114_ENST00000600687.1_Missense_Mutation_p.E362K Q8NC26 ZN114_HUMAN zinc finger protein 114 18 all_epithelial(76;8.01e-05)|all_lung(116;0.000112)|Lung NSC(112;0.000192)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113) GAAGCCCTACGAATGTGAAGA 0.388000 0 SO:0001583 missense ENST00000595607.1 1 1 hg19 CCDS12713.1 . . . . . . . . . . G 5.803 0.332407 0.10956 . . ENSG00000178150 ENST00000315849 T 0.19250 2.16 2.35 -1.76 0.08006 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.05777 0.0151 N 0.01576 -0.805 0.09310 N 1 B 0.24882 0.113 B 0.16289 0.015 T 0.41627 -0.9498 9 0.16420 T 0.52 . 6.9118 0.24338 0.6724:0.0:0.3276:0.0 . 362 Q8NC26 ZN114_HUMAN K 362 ENSP00000318898:E362K ENSP00000318898:E362K E + 1 0 ZNF114 53481777 0.000000 0.05858 0.000000 0.03702 0.021000 0.10359 -1.780000 0.01775 -0.303000 0.08856 0.205000 0.17691 GAA TCGA-FB-AAPY-01A-11D-A40W-08 ZNF114-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000465601.1 0 0 1 229 662 0 132 0 0 0 1 0 132 2 0 0 0 0 0 2 1 1.000000 224 649 0 129 2 -8.001620 1 1 0 0 1 1 2 3 2.291445 1 0.260000 1.920000 0.345133 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 9.900000e-01 1 CNOT3 4849 broad.mit.edu 37 19 54649652 54649652 + Missense_Mutation SNP C C T TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr19:54649652C>T ENST00000406403.1 + 8 2313 c.710C>T c.(709-711)gCg>gTg p.A237V CNOT3_ENST00000221232.5_Missense_Mutation_p.A237V|CNOT3_ENST00000358389.3_Missense_Mutation_p.A56V O75175 CNOT3_HUMAN CCR4-NOT transcription complex, subunit 3 28 all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19) ACAGCACAGGCGCTGGTCGCC 0.632000 0 SO:0001583 missense ENST00000406403.1 1 1 hg19 CCDS12880.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 32|32 5.172407|5.172407 0.94807|0.94807 .|. .|. ENSG00000088038|ENSG00000088038 ENST00000221232;ENST00000358389;ENST00000406403|ENST00000440571 T;T;T|. 0.61510|. 0.89;0.1;0.89|. 4.79|4.79 4.79|4.79 0.61399|0.61399 .|. 0.179711|. 0.48767|. D|. 0.000163|. T|T 0.58047|0.58047 0.2095|0.2095 L|L 0.34521|0.34521 1.04|1.04 0.52099|0.52099 D|D 0.999947|0.999947 D;P;D|. 0.67145|. 0.978;0.886;0.996|. B;B;P|. 0.47786|. 0.313;0.206;0.557|. T|T 0.52968|0.52968 -0.8504|-0.8504 10|5 0.41790|. T|. 0.15|. -26.6693|-26.6693 17.1265|17.1265 0.86715|0.86715 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. 237;237;161|. B7Z6J7;O75175;Q6ZMJ6|. .;CNOT3_HUMAN;.|. V|C 237;56;237|159 ENSP00000221232:A237V;ENSP00000351159:A56V;ENSP00000383954:A237V|. ENSP00000221232:A237V|. A|R +|+ 2|1 0|0 CNOT3|CNOT3 59341464|59341464 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.999000|0.999000 0.98932|0.98932 6.923000|6.923000 0.75817|0.75817 2.663000|2.663000 0.90544|0.90544 0.655000|0.655000 0.94253|0.94253 GCG|CGC TCGA-FB-AAPY-01A-11D-A40W-08 CNOT3-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000142130.3 1 0 0 20 361 0 48 1 7.085765e-01 5 41 0 48 2 0 0 0 0 0 2 1 0.999993 18 346 0 45 2 -19.984690 1 1 121412 2 34 1 1 2 3 2.303890 1 0.260000 1.920000 0.345133 0.460000 0.280000 0.670000 0.450000 0.474233 0.460000 0 3.600000e-01 5.700000e-01 C1orf127 148345 broad.mit.edu 37 1 11007918 11007918 + Silent SNP C C T TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr1:11007918C>T ENST00000377008.4 - 11 2219 c.1773G>A c.(1771-1773)acG>acA p.T591T C1orf127_ENST00000377004.4_Silent_p.T758T Q8N9H9 CA127_HUMAN chromosome 1 open reading frame 127 32 Ovarian(185;0.249) Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731) STAD - Stomach adenocarcinoma(5;0.0224) TCAGGGTTTGCGTGGATGGAG 0.672000 0 SO:0001819 synonymous_variant ENST00000377008.4 0 1 hg19 . . . . . . . . . . c 2.475 -0.321065 0.05386 . . ENSG00000175262 ENST00000418570;ENST00000520253 . . . 3.59 -6.14 0.02111 . . . . . T 0.20495 0.0493 . . . 0.09310 N 1 . . . . . . T 0.30592 -0.9973 4 . . . 0.8678 5.6596 0.17662 0.0:0.2003:0.281:0.5187 . . . . H 593;710 . . R - 2 0 C1orf127 10930505 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 -0.158000 0.10070 -1.131000 0.02910 -0.930000 0.02707 CGC TCGA-FB-AAPY-01A-11D-A40W-08 C1orf127-202 KNOWN basic protein_coding protein_coding 1 0 1 16 135 0 20 0 7.777647e-01 0 26 0 20 2 0 0 0 0 0 2 1 0.999941 15 133 0 20 2 -3.222465 1 1 121400 1 28 1 1 2 3 2.049694 0 0.260000 1.920000 0.266673 0.840000 0.500000 1.000000 1.000000 0.830815 0.840000 0 6.500000e-01 1 VPS13D 55187 broad.mit.edu 37 1 12516159 12516159 + Missense_Mutation SNP G G A TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr1:12516159G>A ENST00000358136.3 + 66 12569 c.12439G>A c.(12439-12441)Gta>Ata p.V4147I VPS13D_ENST00000543766.1_Missense_Mutation_p.V145I|VPS13D_ENST00000356315.4_Missense_Mutation_p.V4122I|VPS13D_ENST00000496628.1_Intron NM_015378.2 NP_056193.2 vacuolar protein sorting 13 homolog D (S. cerevisiae) 130 Ovarian(185;0.249) Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255) TGAACACCTTGTAGCCGGCAT 0.532000 0 SO:0001583 missense ENST00000358136.3 0 1 hg19 CCDS30588.1 . . . . . . . . . . G 36 5.629524 0.96671 . . ENSG00000048707 ENST00000356315;ENST00000358136;ENST00000543766 T;T;T 0.78003 0.59;0.59;-1.14 5.84 5.84 0.93424 . 0.109616 0.64402 D 0.000009 D 0.86806 0.6021 M 0.71581 2.175 0.80722 D 1 P;D;D 0.67145 0.724;0.99;0.996 B;P;P 0.61940 0.372;0.896;0.889 D 0.85069 0.0939 10 0.40728 T 0.16 . 20.1454 0.98074 0.0:0.0:1.0:0.0 . 145;4122;4146 F5GX56;Q5THJ4-2;Q5THJ4 .;.;VP13D_HUMAN I 4122;4147;145 ENSP00000348666:V4122I;ENSP00000350854:V4147I;ENSP00000441122:V145I ENSP00000348666:V4122I V + 1 0 VPS13D 12438746 1.000000 0.71417 0.694000 0.30210 0.991000 0.79684 7.571000 0.82399 2.748000 0.94277 0.650000 0.86243 GTA TCGA-FB-AAPY-01A-11D-A40W-08 VPS13D-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000036897.2 0 0 0 5 377 1 56 0 1.919548e-03 0 46 1 56 5 0 0 0 0 0 2 0 0.000920 5 372 1 55 21 -3.307309 1 1 0 0 1 1 2 3 2.049694 0 0.260000 1.920000 0.266673 0.110000 0.030000 1.000000 0.100000 0.169453 0.110000 0 6.000000e-02 1.800000e-01 DCAF8 50717 broad.mit.edu 37 1 160213756 160213756 + Missense_Mutation SNP C C T TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr1:160213756C>T ENST00000368073.3 - 3 477 c.43G>A c.(43-45)Gct>Act p.A15T DCAF8_ENST00000610139.1_Missense_Mutation_p.A15T|DCAF8_ENST00000326837.2_Missense_Mutation_p.A15T|DCAF8_ENST00000608310.1_Missense_Mutation_p.A169T|DCAF8_ENST00000475733.1_Missense_Mutation_p.A15T|DCAF8_ENST00000556710.1_Missense_Mutation_p.A169T|DCAF8_ENST00000368074.1_Missense_Mutation_p.A15T Q5TAQ9 DCAF8_HUMAN DDB1 and CUL4 associated factor 8 33 TTACCATTAGCTAAGTCTGTT 0.463000 0 SO:0001583 missense ENST00000368073.3 1 1 hg19 CCDS1200.1 . . . . . . . . . . C 17.46 3.395161 0.62066 . . ENSG00000132716;ENSG00000132716;ENSG00000132716;ENSG00000132716;ENSG00000132716;ENSG00000132716;ENSG00000132716;ENSG00000132716;ENSG00000132716;ENSG00000258465 ENST00000368073;ENST00000326837;ENST00000368074;ENST00000555195;ENST00000540855;ENST00000447377;ENST00000440682;ENST00000407642;ENST00000419626;ENST00000556710 T;T;T;T;T 0.67171 -0.25;-0.25;-0.25;-0.13;-0.13 5.48 5.48 0.80851 . 0.098728 0.39020 U 0.001496 T 0.36552 0.0971 N 0.22421 0.69 0.38321 D 0.943512 P;B;B 0.37330 0.59;0.006;0.0 B;B;B 0.37304 0.246;0.007;0.0 T 0.33163 -0.9879 10 0.13108 T 0.6 . 14.4304 0.67246 0.0:0.8517:0.1483:0.0 . 169;15;15 G3V3G9;Q5TAQ9-2;Q5TAQ9 .;.;DCAF8_HUMAN T 15;15;15;169;15;15;15;15;15;169 ENSP00000357052:A15T;ENSP00000318227:A15T;ENSP00000357053:A15T;ENSP00000451989:A169T;ENSP00000451235:A169T ENSP00000318227:A15T A - 1 0 RP11-574F21.3;DCAF8 158480380 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 2.360000 0.44151 2.575000 0.86900 0.655000 0.94253 GCT TCGA-FB-AAPY-01A-11D-A40W-08 DCAF8-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000077402.2 1 0 1 112 771 0 191 1 9.644134e-01 7 32 0 191 2 0 0 0 0 0 2 1 1.000000 112 760 0 187 2 -20.000000 1 1 0 0 1 1 2 3 2.039386 0 0.260000 1.920000 0.264779 0.980000 0.810000 1.000000 1.000000 0.959085 0.980000 1 8.900000e-01 1 UBR4 23352 broad.mit.edu 37 1 19439055 19439055 + Missense_Mutation SNP G G A TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr1:19439055G>A ENST00000375254.3 - 78 11791 c.11764C>T c.(11764-11766)Cgg>Tgg p.R3922W UBR4_ENST00000375217.2_Missense_Mutation_p.R3915W|UBR4_ENST00000375267.2_Missense_Mutation_p.R3922W|UBR4_ENST00000375226.2_Missense_Mutation_p.R3898W|UBR4_ENST00000375218.3_3'UTR NM_020765.2 NP_065816.2 Q5T4S7 UBR4_HUMAN ubiquitin protein ligase E3 component n-recognin 4 171 Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256) ACCTCCTCCCGCATGGCCGCA 0.602000 0 SO:0001583 missense ENST00000375254.3 0 1 hg19 CCDS189.1 . . . . . . . . . . G 21.7 4.187593 0.78789 . . ENSG00000127481 ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226 T;T;T;T 0.76316 -1.01;-1.01;-1.01;-1.01 5.85 2.67 0.31697 . 0.000000 0.85682 D 0.000000 D 0.84437 0.5472 L 0.58810 1.83 0.80722 D 1 D 0.89917 1.0 D 0.74023 0.982 D 0.85499 0.1190 10 0.87932 D 0 . 13.6518 0.62314 0.0:0.0:0.5163:0.4837 . 3922 Q5T4S7 UBR4_HUMAN W 3922;3922;3915;3898 ENSP00000364403:R3922W;ENSP00000364416:R3922W;ENSP00000364365:R3915W;ENSP00000364374:R3898W ENSP00000364365:R3915W R - 1 2 UBR4 19311642 1.000000 0.71417 1.000000 0.80357 0.960000 0.62799 1.609000 0.36858 0.734000 0.32515 0.655000 0.94253 CGG TCGA-FB-AAPY-01A-11D-A40W-08 UBR4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000007085.1 0 0 0 5 407 0 65 0 3.058344e-02 0 18 0 65 2 0 0 0 0 0 2 1 0.936290 6 402 0 61 2 -2.642146 1 1 0 0 1 1 2 3 2.051659 0 0.260000 1.920000 0.267617 0.100000 0.030000 1.000000 0.100000 0.169033 0.100000 0 6.000000e-02 1.700000e-01 ADSS 159 broad.mit.edu 37 1 244574656 244574656 + Silent SNP C C T TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr1:244574656C>T ENST00000366535.3 - 12 1567 c.1251G>A c.(1249-1251)gcG>gcA p.A417A RP11-518L10.5_ENST00000417765.1_RNA NM_001126.3 NP_001117.2 adenylosuccinate synthase 12 all_cancers(71;2.17e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121) all_cancers(173;0.0896)|all_epithelial(177;0.172) all cancers(7;9.71e-08)|GBM - Glioblastoma multiforme(7;1.28e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.0014) GTTCTTTAAACGCCCTTGCAT 0.333000 0 SO:0001819 synonymous_variant ENST00000366535.3 1 1 hg19 CCDS1624.1 TCGA-FB-AAPY-01A-11D-A40W-08 ADSS-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000096697.1 1 0 1 65 335 0 84 1 9.999951e-01 9 85 0 84 2 0 0 0 0 0 2 1 1.000000 66 333 0 84 2 -20.000000 1 1 121408 4 35 1 1 2 3 2.046262 0 0.260000 1.920000 0.266673 0.990000 0.990000 1.000000 1.000000 0.998896 0.990000 1 9.900000e-01 1 GRIK3 2899 broad.mit.edu 37 1 37307495 37307495 + Missense_Mutation SNP C C T TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr1:37307495C>T ENST00000373091.3 - 10 1388 c.1372G>A c.(1372-1374)Ggg>Agg p.G458R GRIK3_ENST00000373093.4_Missense_Mutation_p.G458R NM_000831.3 NP_000822.2 Q13003 GRIK3_HUMAN glutamate receptor, ionotropic, kainate 3 89 Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169) CGGTCATTCCCGTATAGCGTC 0.572000 0 SO:0001583 missense ENST00000373091.3 1 1 hg19 CCDS416.1 . . . . . . . . . . C 19.19 3.779833 0.70222 2.27E-4 0.0 ENSG00000163873 ENST00000373091;ENST00000373093 T;T 0.80123 -1.34;-1.34 4.95 4.95 0.65309 Glutamate receptor, L-glutamate/glycine-binding (2);Ionotropic glutamate receptor (1); 0.000000 0.85682 D 0.000000 D 0.93485 0.7921 H 0.97051 3.93 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 D 0.95656 0.8711 10 0.87932 D 0 . 18.5686 0.91126 0.0:1.0:0.0:0.0 . 458;458 A9Z1Z8;Q13003 .;GRIK3_HUMAN R 458 ENSP00000362183:G458R;ENSP00000362185:G458R ENSP00000362183:G458R G - 1 0 GRIK3 37080082 1.000000 0.71417 0.904000 0.35570 0.167000 0.22549 5.959000 0.70339 2.446000 0.82766 0.655000 0.94253 GGG TCGA-FB-AAPY-01A-11D-A40W-08 GRIK3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000012053.1 1 0 1 81 610 0 111 0 0 0 0 111 2 0 0 0 0 0 2 1 1.000000 79 602 0 107 2 -2.213283 0 1 121412 2 39 1 1 2 3 2.051659 0 0.260000 1.920000 0.267617 0.910000 0.730000 1.000000 1.000000 0.911585 0.910000 1 8.200000e-01 1 KRTAP19-3 337970 broad.mit.edu 37 21 31864178 31864178 + Missense_Mutation SNP C C T TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr21:31864178C>T ENST00000334063.4 - 1 97 c.98G>A c.(97-99)cGc>cAc p.R33H NM_181609.3 NP_853640.1 Q7Z4W3 KR193_HUMAN keratin associated protein 19-3 9 ACCCAGTCTGCGGAAGCTGCC 0.582000 0 SO:0001583 missense ENST00000334063.4 1 1 hg19 CCDS13596.1 . . . . . . . . . . C 9.864 1.197214 0.22037 0.0 1.16E-4 ENSG00000244025 ENST00000334063 T 0.10668 2.85 4.72 -4.85 0.03142 . . . . . T 0.07324 0.0185 . . . 0.09310 N 1 B 0.02656 0.0 B 0.04013 0.001 T 0.37033 -0.9723 8 0.87932 D 0 . 6.2846 0.21027 0.0:0.2226:0.3779:0.3996 . 33 Q7Z4W3 KR193_HUMAN H 33 ENSP00000386376:R33H ENSP00000386376:R33H R - 2 0 KRTAP19-3 30786049 0.000000 0.05858 0.000000 0.03702 0.062000 0.15995 -0.462000 0.06704 -1.247000 0.02507 -0.218000 0.12543 CGC TCGA-FB-AAPY-01A-11D-A40W-08 KRTAP19-3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000128234.2 1 0 1 143 990 0 185 0 0 0 0 185 2 0 0 0 0 0 2 1 1.000000 141 958 0 183 2 -3.318794 1 1 121412 11 45 1 0 1 1 1.903979 0 0.260000 1.920000 0.209655 0.900000 0.770000 1.000000 1.000000 0.906844 0.900000 1 8.300000e-01 9.800000e-01 KIF1A 547 broad.mit.edu 37 2 241712602 241712602 + Missense_Mutation SNP C C T TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr2:241712602C>T ENST00000320389.7 - 13 1267 c.1109G>A c.(1108-1110)cGc>cAc p.R370H KIF1A_ENST00000498729.2_Missense_Mutation_p.R370H NM_004321.6 NP_004312.2 Q12756 KIF1A_HUMAN kinesin family member 1A 66 all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244) CTTCAGCTCGCGGATCAGCTT 0.617000 0 SO:0001583 missense ENST00000320389.7 1 1 hg19 CCDS46561.1 . . . . . . . . . . C 26.8 4.777059 0.90195 . . ENSG00000130294 ENST00000320389;ENST00000498729;ENST00000373308;ENST00000404283 T;T;T 0.76186 -0.89;-0.92;-1.0 3.83 3.83 0.44106 . 0.000000 0.85682 U 0.000000 D 0.90225 0.6944 H 0.95850 3.73 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.97110 1.0;0.997;0.999 D 0.93733 0.7043 10 0.87932 D 0 . 15.7385 0.77866 0.0:1.0:0.0:0.0 . 370;370;370 F5H045;Q12756-2;Q12756 .;.;KIF1A_HUMAN H 370 ENSP00000322791:R370H;ENSP00000438388:R370H;ENSP00000384231:R370H ENSP00000322791:R370H R - 2 0 KIF1A 241361275 1.000000 0.71417 0.853000 0.33588 0.956000 0.61745 7.626000 0.83164 1.688000 0.51068 0.491000 0.48974 CGC TCGA-FB-AAPY-01A-11D-A40W-08 KIF1A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000324536.3 1 0 1 39 219 0 44 0 0 0 0 44 2 0 0 0 0 0 2 1 1.000000 38 216 0 44 2 -19.480280 1 1 0 0 1 0 1 1 2.014424 0 0.260000 1.920000 0.258071 0.990000 0.840000 1.000000 1.000000 0.987272 0.990000 1 9.900000e-01 1 KLF15 28999 broad.mit.edu 37 3 126070729 126070729 + Missense_Mutation SNP G G A TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr3:126070729G>A ENST00000296233.3 - 2 1267 c.1037C>T c.(1036-1038)aCg>aTg p.T346M KLF15_ENST00000509675.1_5'Flank NM_014079.3 NP_054798.1 Q9UIH9 KLF15_HUMAN Kruppel-like factor 15 12 CTTCTCACCCGTGTGCCGGCG 0.592000 0 SO:0001583 missense ENST00000296233.3 0 1 hg19 CCDS3036.1 . . . . . . . . . . G 23.6 4.439084 0.83885 . . ENSG00000163884 ENST00000296233 T 0.26373 1.74 5.37 5.37 0.77165 Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.000000 0.85682 D 0.000000 T 0.55878 0.1948 M 0.83012 2.62 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 T 0.60520 -0.7247 10 0.72032 D 0.01 . 16.9708 0.86298 0.0:0.0:1.0:0.0 . 346 Q9UIH9 KLF15_HUMAN M 346 ENSP00000296233:T346M ENSP00000296233:T346M T - 2 0 KLF15 127553419 1.000000 0.71417 0.991000 0.47740 0.972000 0.66771 9.792000 0.99085 2.688000 0.91661 0.491000 0.48974 ACG TCGA-FB-AAPY-01A-11D-A40W-08 KLF15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000370096.1 1 0 0 5 117 0 15 0 8.744613e-02 0 10 0 15 2 0 0 0 0 0 2 1 0.936144 6 114 0 14 2 -3.397408 1 1 121382 1 31 1 0 1 1 1.924892 0 0.260000 1.920000 0.221544 0.320000 0.120000 0.630000 0.290000 0.343698 0.320000 0 2.000000e-01 4.700000e-01 EIF2B5 8893 broad.mit.edu 37 3 183854501 183854501 + Silent SNP T T A TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr3:183854501T>A ENST00000273783.3 + 2 419 c.297T>A c.(295-297)gcT>gcA p.A99A EIF2B5_ENST00000498831.1_3'UTR|RP11-778D9.12_ENST00000608232.1_RNA|RP11-778D9.12_ENST00000608135.1_RNA|EIF2B5_ENST00000432569.1_Silent_p.A99A|EIF2B5_ENST00000444495.1_Silent_p.A99A NM_003907.2 NP_003898.2 Q13144 EI2BE_HUMAN eukaryotic translation initiation factor 2B, subunit 5 epsilon, 82kDa 27 all_cancers(143;7.59e-11)|Ovarian(172;0.0303) Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22) GCTGGAAAGCTGCTCAAATCA 0.423000 0 SO:0001819 synonymous_variant ENST00000273783.3 0 1 hg19 CCDS3252.1 TCGA-FB-AAPY-01A-11D-A40W-08 EIF2B5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000346168.1 0 0 0 7 903 0 168 0 1.276068e-01 1 68 0 168 2 0 0 0 0 0 2 1 0.979514 7 889 0 167 2 -4.899695 1 1 0 0 1 0 1 1 1.924892 0 0.260000 1.920000 0.221544 0.050000 0.010000 0.110000 0.060000 0.063907 0.050000 0 3.000000e-02 9.000000e-02 TP63 8626 broad.mit.edu 37 3 189582120 189582120 + Missense_Mutation SNP G G A TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr3:189582120G>A ENST00000264731.3 + 5 768 c.679G>A c.(679-681)Gcc>Acc p.A227T TP63_ENST00000437221.1_Missense_Mutation_p.A133T|TP63_ENST00000392461.3_Missense_Mutation_p.A133T|TP63_ENST00000440651.2_Missense_Mutation_p.A227T|TP63_ENST00000449992.1_Missense_Mutation_p.A48T|TP63_ENST00000456148.1_Missense_Mutation_p.A133T|TP63_ENST00000382063.4_Missense_Mutation_p.A142T|TP63_ENST00000418709.2_Missense_Mutation_p.A227T|TP63_ENST00000392460.3_Missense_Mutation_p.A227T|TP63_ENST00000320472.5_Missense_Mutation_p.A227T|TP63_ENST00000392463.2_Missense_Mutation_p.A133T|TP63_ENST00000354600.5_Missense_Mutation_p.A133T NM_001114978.1|NM_003722.4 NP_001108450.1|NP_003713.3 Q9H3D4 P63_HUMAN tumor protein p63 61 all_cancers(143;3.35e-10)|Ovarian(172;0.0925) Lung(62;3.33e-05) TGTTATCCGCGCCATGCCTGT 0.517000 HNSCC(45;0.13) 0 SO:0001583 missense ENST00000264731.3 0 1 hg19 CCDS3293.1 . . . . . . . . . . G 29.9 5.046830 0.93740 . . ENSG00000073282 ENST00000264731;ENST00000418709;ENST00000320472;ENST00000392460;ENST00000440651;ENST00000382063;ENST00000354600;ENST00000437221;ENST00000392463;ENST00000392461;ENST00000449992;ENST00000456148 D;D;D;D;D;D;D;D;D;D;D;D 0.99857 -7.22;-7.22;-7.22;-7.22;-7.22;-7.22;-7.22;-7.22;-7.22;-7.22;-7.22;-7.22 5.85 4.97 0.65823 p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1); 0.000000 0.85682 D 0.000000 D 0.99802 0.9915 M 0.75264 2.295 0.58432 D 0.999999 D;D;D;D;D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0 D;D;D;D;D;D;D;D;D;D 0.97110 0.995;0.999;0.999;0.999;0.999;0.999;1.0;0.995;1.0;0.999 D 0.96749 0.9552 9 . . . -13.4834 14.4917 0.67654 0.0715:0.0:0.9285:0.0 . 48;227;227;133;133;133;133;227;227;227 Q9H3D4-10;Q9H3D4-7;Q9H3D4-11;Q9H3D4-4;Q9H3D4-2;Q9H3D4-6;C9D7C9;Q9H3D4-3;Q9H3D4;Q9H3D4-5 .;.;.;.;.;.;.;.;P63_HUMAN;. T 227;227;227;227;227;142;133;133;133;133;48;133 ENSP00000264731:A227T;ENSP00000407144:A227T;ENSP00000317510:A227T;ENSP00000376253:A227T;ENSP00000394337:A227T;ENSP00000371495:A142T;ENSP00000346614:A133T;ENSP00000392488:A133T;ENSP00000376256:A133T;ENSP00000376254:A133T;ENSP00000387839:A48T;ENSP00000389485:A133T . A + 1 0 TP63 191064814 1.000000 0.71417 1.000000 0.80357 0.830000 0.47004 8.013000 0.88655 2.768000 0.95171 0.655000 0.94253 GCC TCGA-FB-AAPY-01A-11D-A40W-08 TP63-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000343865.1 0 0 0 5 499 0 80 0 0 0 1 0 80 2 0 0 0 0 0 2 1 0.934826 6 489 0 79 2 -2.270054 0 1 0 0 1 0 1 1 1.924892 0 0.260000 1.920000 0.221544 0.070000 0.020000 0.160000 0.070000 0.086106 0.070000 0 4.000000e-02 1.200000e-01 FLNB 2317 broad.mit.edu 37 3 58120468 58120468 + Missense_Mutation SNP C C T TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr3:58120468C>T ENST00000295956.4 + 27 4805 c.4640C>T c.(4639-4641)gCc>gTc p.A1547V FLNB_ENST00000493452.1_Missense_Mutation_p.A1378V|FLNB_ENST00000357272.4_Missense_Mutation_p.A1547V|FLNB_ENST00000429972.2_Missense_Mutation_p.A1547V|FLNB_ENST00000490882.1_Missense_Mutation_p.A1578V|FLNB_ENST00000358537.3_Missense_Mutation_p.A1547V|FLNB_ENST00000419752.2_Missense_Mutation_p.A1378V|FLNB_ENST00000348383.5_Missense_Mutation_p.A1547V NM_001457.3 NP_001448.2 O75369 FLNB_HUMAN filamin B, beta 120 GCCCGAGATGCCGGGGAAGGC 0.483000 0 GRCh37 CM061773 FLNB M SO:0001583 missense ENST00000295956.4 0 1 hg19 CCDS2885.1 . . . . . . . . . . C 35 5.522694 0.96431 . . ENSG00000136068 ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752 D;D;D;D;D;D;D;D 0.87256 -2.23;-2.23;-2.23;-2.23;-2.23;-2.23;-2.23;-2.23 5.68 5.68 0.88126 Immunoglobulin E-set (1);Immunoglobulin-like fold (1); 0.000000 0.85682 D 0.000000 D 0.95010 0.8385 M 0.90595 3.13 0.80722 D 1 P;D;P;D;P;P 0.71674 0.832;0.998;0.879;0.977;0.917;0.917 P;D;P;P;P;P 0.77557 0.55;0.99;0.67;0.809;0.863;0.863 D 0.95415 0.8502 10 0.87932 D 0 . 19.7958 0.96481 0.0:1.0:0.0:0.0 . 1547;1578;1378;1378;1547;1547 O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369 .;.;.;.;.;FLNB_HUMAN V 1547;1578;1547;1547;1547;1547;1378;1378 ENSP00000295956:A1547V;ENSP00000420213:A1578V;ENSP00000351339:A1547V;ENSP00000415599:A1547V;ENSP00000232447:A1547V;ENSP00000349819:A1547V;ENSP00000418510:A1378V;ENSP00000414532:A1378V ENSP00000295956:A1547V A + 2 0 FLNB 58095508 1.000000 0.71417 0.958000 0.39756 0.982000 0.71751 7.764000 0.85297 2.669000 0.90835 0.563000 0.77884 GCC TCGA-FB-AAPY-01A-11D-A40W-08 FLNB-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000353569.1 0 0 0 6 709 0 127 0 2.417209e-01 0 96 0 127 2 0 0 0 0 0 2 1 0.961540 6 688 0 122 2 -1.924228 0 1 0 0 1 0 1 1 1.924892 0 0.260000 1.920000 0.221544 0.060000 0.020000 0.130000 0.060000 0.071047 0.060000 0 3.000000e-02 1.000000e-01 PPIP5K2 23262 broad.mit.edu 37 5 102509562 102509562 + Splice_Site SNP G G A TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr5:102509562G>A ENST00000358359.3 + 21 2924 c.2415G>A c.(2413-2415)gtG>gtA p.V805V PPIP5K2_ENST00000414217.1_Splice_Site_p.V805V|PPIP5K2_ENST00000321521.9_Splice_Site_p.V805V|PPIP5K2_ENST00000513500.1_3'UTR NM_001276277.1 NP_001263206.1 O43314 VIP2_HUMAN diphosphoinositol pentakisphosphate kinase 2 42 CTAATTTTAGGTATTCTAGAG 0.303000 0 SO:0001630 splice_region_variant ENST00000358359.3 1 0 hg19 TCGA-FB-AAPY-01A-11D-A40W-08 PPIP5K2-003 KNOWN basic protein_coding protein_coding OTTHUMT00000370487.1 1 0 1 36 215 0 29 0 4.898907e-01 1 10 0 29 2 0 0 0 0 0 2 1 1.000000 36 212 0 29 2 -20.000000 1 1 0 0 1 1 2 3 2.044124 0 0.260000 1.920000 0.265727 0.990000 0.800000 1.000000 1.000000 0.978998 0.990000 1 9.500000e-01 1 PCDHA2 56146 broad.mit.edu 37 5 140176342 140176342 + Missense_Mutation SNP A A G TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr5:140176342A>G ENST00000526136.1 + 1 1793 c.1793A>G c.(1792-1794)gAc>gGc p.D598G PCDHA2_ENST00000520672.2_Missense_Mutation_p.D598G|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000378132.1_Missense_Mutation_p.D598G|PCDHA1_ENST00000394633.3_Intron NM_018905.2 NP_061728.1 Q9Y5H9 PCDA2_HUMAN protocadherin alpha 2 71 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) CGCGCAGTGGACGCTGACTCA 0.662000 0 SO:0001583 missense ENST00000526136.1 1 1 hg19 CCDS54914.1 . . . . . . . . . . a 14.62 2.588873 0.46110 . . ENSG00000204969 ENST00000520672;ENST00000378132;ENST00000526136 T;T;T 0.61627 0.09;0.09;0.09 3.91 3.91 0.45181 Cadherin (4);Cadherin-like (1); 0.000000 0.41194 U 0.000923 D 0.84433 0.5471 H 0.99261 4.49 0.46222 D 0.998935 D;D;D 0.62365 0.967;0.991;0.967 P;D;D 0.68039 0.799;0.923;0.955 D 0.90120 0.4198 10 0.87932 D 0 . 12.7909 0.57533 1.0:0.0:0.0:0.0 . 598;598;598 Q9Y5H9-3;Q9Y5H9;Q9Y5H9-2 .;PCDA2_HUMAN;. G 598 ENSP00000430584:D598G;ENSP00000367372:D598G;ENSP00000431748:D598G ENSP00000367372:D598G D + 2 0 PCDHA2 140156526 1.000000 0.71417 0.959000 0.39883 0.110000 0.19582 8.674000 0.91191 1.563000 0.49615 0.449000 0.29647 GAC TCGA-FB-AAPY-01A-11D-A40W-08 PCDHA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000372877.3 1 0 1 58 388 0 90 0 0 0 0 90 2 0 0 0 0 0 2 1 1.000000 55 382 0 89 2 -20.000000 1 1 0 0 1 1 2 3 2.044124 0 0.260000 1.920000 0.265727 0.990000 0.780000 1.000000 1.000000 0.960066 0.990000 1 8.900000e-01 1 PCSK1 5122 broad.mit.edu 37 5 95757592 95757592 + Silent SNP G G A rs6231 byFrequency TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr5:95757592G>A ENST00000311106.3 - 5 849 c.612C>T c.(610-612)aaC>aaT p.N204N PCSK1_ENST00000508626.1_Silent_p.N157N|CTD-2337A12.1_ENST00000502645.2_RNA NM_000439.4|NM_001177876.1 NP_000430.3|NP_001171347.1 P29120 NEC1_HUMAN proprotein convertase subtilisin/kexin type 1 36 all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244) """Insulin(DB00071)|Insulin Regular(DB00030)" ACTTGTTCTCGTTTGTGGGAT 0.333000 0 SO:0001819 synonymous_variant ENST00000311106.3 1 0 hg19 CCDS4081.1 TCGA-FB-AAPY-01A-11D-A40W-08 PCSK1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000242851.1 0 0 1 85 644 0 178 0 1.955121e-01 0 7 0 178 2 0 0 0 0 0 2 1 1.000000 80 612 0 177 2 -10.387400 1 1 121412 2126 68 1 1 2 3 2.044124 0 0.260000 1.920000 0.265727 0.900000 0.730000 1.000000 1.000000 0.904831 0.900000 1 8.100000e-01 1 MAK 4117 broad.mit.edu 37 6 10764813 10764813 + Missense_Mutation SNP G G A TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr6:10764813G>A ENST00000313243.2 - 14 2126 c.1744C>T c.(1744-1746)Cgg>Tgg p.R582W MAK_ENST00000538030.1_3'UTR|SYCP2L_ENST00000543878.1_Intron|MAK_ENST00000474039.1_Missense_Mutation_p.R582W|MAK_ENST00000354489.2_Missense_Mutation_p.R582W|RP11-637O19.3_ENST00000480294.1_Intron P20794 MAK_HUMAN male germ cell-associated kinase p.R582R(1) 22 Breast(50;0.107)|Ovarian(93;0.107) all_hematologic(90;0.117) AACTGCCCCCGACCAGTTTTT 0.398000 1 Substitution - coding silent(1) SO:0001583 missense ENST00000313243.2 1 1 hg19 CCDS4516.1 1 4.578754578754579E-4 0 0.0 0 0.0 0 0.0 1 0.0013192612137203166 G 25.7 4.660715 0.88154 . . ENSG00000111837 ENST00000313243;ENST00000354489 T;T 0.74002 -0.8;-0.8 5.66 5.66 0.87406 . 0.265585 0.36932 N 0.002337 D 0.83704 0.5312 M 0.77103 2.36 0.80722 D 1 D 0.76494 0.999 P 0.62382 0.901 D 0.85294 0.1069 10 0.87932 D 0 . 19.3453 0.94361 0.0:0.0:1.0:0.0 . 582 P20794 MAK_HUMAN W 582 ENSP00000313021:R582W;ENSP00000346484:R582W ENSP00000313021:R582W R - 1 2 MAK 10872799 1.000000 0.71417 0.963000 0.40424 0.994000 0.84299 6.187000 0.72039 2.648000 0.89879 0.655000 0.94253 CGG TCGA-FB-AAPY-01A-11D-A40W-08 MAK-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000039841.1 1 0 0 87 512 0 152 0 0 0 1 0 152 2 0 0 0 0 0 2 1 1.000000 86 505 0 147 2 -3.075884 1 1 121408 17 46 1 0 1 1 1.907629 0 0.260000 1.920000 0.220478 0.990000 0.860000 1.000000 1.000000 0.982986 0.990000 1 9.500000e-01 1 XPO5 57510 broad.mit.edu 37 6 43540277 43540277 + Missense_Mutation SNP T T C TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr6:43540277T>C ENST00000265351.7 - 3 476 c.266A>G c.(265-267)tAt>tGt p.Y89C NM_020750.2 NP_065801.1 Q9HAV4 XPO5_HUMAN exportin 5 34 all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243) all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524) GTTCTTCAGATACACCTTCTC 0.423000 0 SO:0001583 missense ENST00000265351.7 0 1 hg19 CCDS47430.1 . . . . . . . . . . T 13.05 2.122120 0.37436 . . ENSG00000124571 ENST00000265351 T 0.67523 -0.27 4.88 0.572 0.17357 Armadillo-like helical (1);Armadillo-type fold (1);Importin-beta, N-terminal (1); 0.296130 0.34411 N 0.003997 T 0.27169 0.0666 N 0.20986 0.625 0.47374 D 0.999402 B 0.02656 0.0 B 0.01281 0.0 T 0.07309 -1.0779 10 0.39692 T 0.17 -8.5042 5.3596 0.16081 0.3917:0.0735:0.0:0.5348 . 89 Q9HAV4 XPO5_HUMAN C 89 ENSP00000265351:Y89C ENSP00000265351:Y89C Y - 2 0 XPO5 43648255 0.998000 0.40836 0.987000 0.45799 0.975000 0.68041 2.130000 0.42064 0.258000 0.21686 -0.336000 0.08194 TAT TCGA-FB-AAPY-01A-11D-A40W-08 XPO5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040657.2 0 0 0 8 340 0 71 0 1.810591e-02 0 8 0 71 2 0 0 0 0 0 2 1 0.989196 8 337 0 70 2 -8.442419 1 1 0 0 1 0 1 1 1.899097 1 0.260000 1.920000 0.211844 0.170000 0.070000 0.310000 0.170000 0.183736 0.170000 0 1.100000e-01 2.400000e-01 CDYL 9425 broad.mit.edu 37 6 4892101 4892101 + Missense_Mutation SNP C C T TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr6:4892101C>T ENST00000328908.5 + 4 472 c.341C>T c.(340-342)aCg>aTg p.T114M CDYL_ENST00000343762.5_5'UTR|CDYL_ENST00000449732.2_5'UTR|CDYL_ENST00000472453.1_Intron|CDYL_ENST00000397588.3_Missense_Mutation_p.T60M Q9Y232 CDYL1_HUMAN chromodomain protein, Y-like 30 Ovarian(93;0.11) all_hematologic(90;0.0901)|Lung NSC(90;0.244) AGACGCCACACGGAGAAGCAG 0.507000 0 SO:0001583 missense ENST00000328908.5 0 1 hg19 . . . . . . . . . . C 8.820 0.937390 0.18206 . . ENSG00000153046 ENST00000328908;ENST00000397588 T;T 0.55930 0.97;0.49 5.79 1.46 0.22682 Chromo domain-like (1);Chromo domain/shadow (2); 0.437153 0.26029 N 0.026769 T 0.19127 0.0459 L 0.57536 1.79 0.09310 N 0.999993 B;B 0.27140 0.037;0.169 B;B 0.20577 0.025;0.03 T 0.13176 -1.0519 10 0.28530 T 0.3 . 2.7961 0.05401 0.3942:0.3057:0.2149:0.0852 . 60;114 Q9Y232-2;Q9Y232 .;CDYL1_HUMAN M 114;60 ENSP00000330512:T114M;ENSP00000380718:T60M ENSP00000330512:T114M T + 2 0 CDYL 4837100 0.057000 0.20700 0.224000 0.23877 0.400000 0.30750 0.442000 0.21628 0.327000 0.23409 0.650000 0.86243 ACG TCGA-FB-AAPY-01A-11D-A40W-08 CDYL-001 KNOWN basic protein_coding protein_coding OTTHUMT00000039736.1 0 0 0 5 258 0 50 0 4.257413e-02 0 14 0 50 2 0 0 0 0 0 2 1 0.934947 5 254 0 48 2 -3.014201 1 1 121412 1 35 1 0 1 1 1.907629 0 0.260000 1.920000 0.220478 0.140000 0.050000 0.300000 0.140000 0.163121 0.140000 0 9.000000e-02 2.200000e-01 PARP12 64761 broad.mit.edu 37 7 139756817 139756817 + Missense_Mutation SNP T T A TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr7:139756817T>A ENST00000263549.3 - 3 1472 c.599A>T c.(598-600)gAt>gTt p.D200V NM_022750.2 NP_073587.1 Q9H0J9 PAR12_HUMAN poly (ADP-ribose) polymerase family, member 12 19 Melanoma(164;0.0142) ATTAGAGAAATCATGGGATCT 0.438000 0 SO:0001583 missense ENST00000263549.3 1 1 hg19 CCDS5857.1 . . . . . . . . . . T 13.07 2.127084 0.37533 . . ENSG00000059378 ENST00000263549 T 0.40756 1.02 5.31 2.88 0.33553 Zinc finger, CCCH-type (3); 0.829138 0.11297 N 0.578676 T 0.41558 0.1164 M 0.69358 2.11 0.22581 N 0.998967 B 0.14438 0.01 B 0.19946 0.027 T 0.41484 -0.9506 10 0.72032 D 0.01 . 7.4741 0.27365 0.1274:0.0701:0.0:0.8025 . 200 Q9H0J9 PAR12_HUMAN V 200 ENSP00000263549:D200V ENSP00000263549:D200V D - 2 0 PARP12 139403286 0.998000 0.40836 0.644000 0.29465 0.955000 0.61496 2.199000 0.42715 0.393000 0.25203 0.445000 0.29226 GAT TCGA-FB-AAPY-01A-11D-A40W-08 PARP12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000348413.1 1 0 1 71 477 0 94 1 6.983821e-01 3 15 0 94 2 0 0 0 0 0 2 1 1.000000 71 476 0 93 2 -20.000000 1 1 0 0 1 1 2 3 2.052201 0 0.260000 1.920000 0.267617 0.990000 0.800000 1.000000 1.000000 0.964149 0.990000 1 9.000000e-01 1 DMRT3 58524 broad.mit.edu 37 9 990483 990483 + Silent SNP C C T rs145231691 byFrequency TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chr9:990483C>T ENST00000190165.2 + 2 935 c.897C>T c.(895-897)tcC>tcT p.S299S NM_021240.2 NP_067063.1 Q9NQL9 DMRT3_HUMAN doublesex and mab-3 related transcription factor 3 26 all_lung(10;1.39e-08)|Lung NSC(10;1.42e-08) AGCGAACTTCCGCAGAACCTG 0.577000 0 SO:0001819 synonymous_variant ENST00000190165.2 1 1 hg19 CCDS6443.1 TCGA-FB-AAPY-01A-11D-A40W-08 DMRT3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000051490.1 1 0 1 65 255 0 44 0 0 0 0 44 2 0 0 0 0 0 2 1 1.000000 64 251 0 40 2 -2.948555 1 1 121412 60 51 1 0 1 1 1.766215 1 0.260000 1.920000 0.149425 0.960000 0.860000 1.000000 0.990000 0.964234 0.960000 1 9.200000e-01 1 AFF2 2334 broad.mit.edu 37 X 148072839 148072839 + Missense_Mutation SNP C C T TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chrX:148072839C>T ENST00000370460.2 + 21 4392 c.3913C>T c.(3913-3915)Cgc>Tgc p.R1305C AFF2_ENST00000370457.5_Missense_Mutation_p.R1270C|AFF2_ENST00000342251.3_Missense_Mutation_p.R1272C|AFF2_ENST00000286437.5_Missense_Mutation_p.R946C NM_001169123.1|NM_002025.3 NP_001162594.1|NP_002016.2 P51816 AFF2_HUMAN AF4/FMR2 family, member 2 109 Acute lymphoblastic leukemia(192;6.56e-05) GTGTTGGCTGCGCATCGATGC 0.542000 0 SO:0001583 missense ENST00000370460.2 1 1 hg19 CCDS14684.1 . . . . . . . . . . C 25.8 4.676515 0.88445 . . ENSG00000155966 ENST00000370460;ENST00000370457;ENST00000342251;ENST00000286437 T;T;T;T 0.70869 -0.52;-0.52;-0.52;-0.52 5.46 5.46 0.80206 . 0.000000 0.85682 D 0.000000 D 0.85890 0.5802 M 0.82193 2.58 0.80722 D 1 D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0;1.0 D;D;D;D;D;D 0.85130 0.997;0.995;0.995;0.979;0.979;0.988 D 0.88026 0.2772 10 0.87932 D 0 . 18.3752 0.90433 0.0:1.0:0.0:0.0 . 946;1270;1270;1266;1295;1305 B4DXD5;P51816-6;P51816-3;P51816-2;P51816-5;P51816 .;.;.;.;.;AFF2_HUMAN C 1305;1270;1272;946 ENSP00000359489:R1305C;ENSP00000359486:R1270C;ENSP00000345459:R1272C;ENSP00000286437:R946C ENSP00000286437:R946C R + 1 0 AFF2 147880545 1.000000 0.71417 1.000000 0.80357 0.954000 0.61252 7.696000 0.84270 2.279000 0.76181 0.594000 0.82650 CGC TCGA-FB-AAPY-01A-11D-A40W-08 AFF2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000058673.2 1 0 1 112 362 0 82 0 0 0 0 82 2 0 0 0 0 0 2 1 1.000000 112 360 0 82 2 -20.000000 1 1 121404 1 31 1 0 1 1 0.260000 1.920000 0.260000 0.890000 0.750000 0.990000 0.900000 0.892045 0.890000 1 8.200000e-01 9.600000e-01 KDM6A 7403 broad.mit.edu 37 X 44833922 44833922 + Missense_Mutation SNP T T C TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chrX:44833922T>C ENST00000377967.4 + 4 387 c.346T>C c.(346-348)Tac>Cac p.Y116H KDM6A_ENST00000536777.1_Missense_Mutation_p.Y116H|KDM6A_ENST00000382899.4_Missense_Mutation_p.Y116H|KDM6A_ENST00000543216.1_Missense_Mutation_p.Y116H NM_021140.2 NP_066963.2 O15550 KDM6A_HUMAN lysine (K)-specific demethylase 6A p.0(14)|p.0?(6)|p.?(1) 170 ATTATCTGCATACCAGAGGTA 0.348000 D, N, F, S renal, oesophageal SCC, MM Colon(129;1273 1667 15230 27352 52914) Rec yes X Xp11.2 7403 lysine (K)-specific demethylase 6A, UTX E, L 21 No detectable mRNA/protein(14)|Whole gene deletion(6)|Unknown(1) SO:0001583 missense ENST00000377967.4 0 1 hg19 CCDS14265.1 . . . . . . . . . . T 18.32 3.597277 0.66332 . . ENSG00000147050 ENST00000377967;ENST00000536777;ENST00000382899;ENST00000543216;ENST00000542299 T;T;T;T 0.76709 2.23;2.23;-1.04;2.23 4.75 4.75 0.60458 Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1); 0.116882 0.64402 D 0.000012 D 0.87402 0.6168 M 0.82823 2.61 0.51233 D 0.999919 D;D;D;D;D 0.76494 0.997;0.998;0.999;0.995;0.997 D;D;D;D;D 0.79784 0.991;0.983;0.993;0.969;0.961 D 0.88806 0.3288 10 0.87932 D 0 -7.0249 10.9422 0.47281 0.0:0.0:0.0:1.0 . 116;116;116;116;116 F8W8R6;F5H6S1;B7ZKN5;B4E253;O15550 .;.;.;.;KDM6A_HUMAN H 116 ENSP00000367203:Y116H;ENSP00000437405:Y116H;ENSP00000372355:Y116H;ENSP00000443078:Y116H ENSP00000367203:Y116H Y + 1 0 KDM6A 44718866 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 5.968000 0.70413 1.853000 0.53794 0.441000 0.28932 TAC TCGA-FB-AAPY-01A-11D-A40W-08 KDM6A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000056324.1 0 0 0 4 230 0 41 0 5.055988e-03 0 5 0 41 2 0 5.055988e-03 0 5 0 4 2 1 0.891132 4 230 0 41 2 -5.974334 1 1 0 0 1 0 1 1 0.260000 1.920000 0.260000 0.070000 0.020000 0.160000 0.070000 0.080490 0.070000 0 4.000000e-02 1.100000e-01 FAM104B 90736 broad.mit.edu 37 X 55172659 55172659 + Missense_Mutation SNP A A G rs5018687 by1000genomes TCGA-FB-AAPY-01A-11D-A40W-08 TCGA-FB-AAPY-11A-11D-A40W-08 Untested Somatic Phase_I WXS none Illumina GAIIx c5708a05-d6ea-45e7-95b3-396cb55160cb 1df543cd-3c9f-4509-bcee-0ce063aa435c g.chrX:55172659A>G ENST00000358460.4 - 3 359 c.206T>C c.(205-207)aTt>aCt p.I69T FAM104B_ENST00000478918.1_5'Flank|FAM104B_ENST00000477847.2_Missense_Mutation_p.I66T|FAM104B_ENST00000332132.4_Missense_Mutation_p.I70T|FAM104B_ENST00000472571.2_3'UTR|FAM104B_ENST00000489298.1_Missense_Mutation_p.I68T|FAM104B_ENST00000425133.2_Missense_Mutation_p.I70T Q5XKR9 F104B_HUMAN family with sequence similarity 104, member B p.I70T(2) 8 TTCAGTAACAATCTGGTTTAA 0.458000 2 Substitution - Missense(2) SO:0001583 missense ENST00000358460.4 0 1 hg19 CCDS35305.2 . . . . . . . . . . a 7.632 0.678969 0.14841 . . ENSG00000182518 ENST00000358460;ENST00000332132;ENST00000425133;ENST00000477847;ENST00000489298 T;T;T;T;T 0.43294 0.95;0.95;0.95;0.95;0.95 1.6 -0.877 0.10621 . 0.273281 0.24341 N 0.039374 T 0.34424 0.0897 N 0.20685 0.6 0.09310 N 1 B;B;B 0.33000 0.007;0.393;0.393 B;P;B 0.51701 0.003;0.677;0.291 T 0.41215 -0.9521 10 0.21014 T 0.42 -1.7781 4.1887 0.10411 0.5262:0.0:0.4738:0.0 rs5018687;rs5018687 70;69;70 Q5XKR9-3;Q5XKR9;Q5XKR9-2 .;F104B_HUMAN;. T 69;70;70;66;68 ENSP00000364101:I69T;ENSP00000333394:I70T;ENSP00000397188:I70T;ENSP00000421161:I66T;ENSP00000423164:I68T ENSP00000333394:I70T I - 2 0 FAM104B 55189384 0.000000 0.05858 0.000000 0.03702 0.238000 0.25445 -0.374000 0.07484 -0.346000 0.08312 0.356000 0.21956 ATT TCGA-FB-AAPY-01A-11D-A40W-08 FAM104B-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000056851.1 0 0 0 6 290 0 55 0 5.848170e-01 0 89 0 55 2 0 0 0 0 0 2 0 0.012911 5 283 1 58 17 -2.129250 0 1 0 0 1 0 1 1 0.260000 1.920000 0.260000 0.080000 0.030000 0.160000 0.080000 0.089472 0.080000 0 5.000000e-02 1.200000e-01