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 PACS2 23241 broad.mit.edu 37 14 105818795 105818797 + In_Frame_Del DEL CTC CTC - TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 CTC - CTC CTC Valid Somatic Phase_I WXS RNA Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr14:105818795_105818797delCTC ENST00000325438.8 + 3 792_794 c.288_290delCTC c.(286-291)ttctcc>ttc p.S97del PACS2_ENST00000447393.1_In_Frame_Del_p.S97del|PACS2_ENST00000430725.2_In_Frame_Del_p.S30del|PACS2_ENST00000458164.2_In_Frame_Del_p.S97del|PACS2_ENST00000547217.1_Intron Q86VP3 PACS2_HUMAN phosphofurin acidic cluster sorting protein 2 21 all_cancers(154;0.0351)|all_epithelial(191;0.153)|Melanoma(154;0.155) OV - Ovarian serous cystadenocarcinoma(23;0.0145)|Epithelial(46;0.036) CCCTGACCTTCTCCTTGCAGGTG 0.616000 OREG0022968 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001651 inframe_deletion ENST00000325438.8 1 1 hg19 CCDS32168.1 TCGA-FB-A5VM-01A-11D-A32N-08 PACS2-003 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000409209.1 1 0 0 72 437 0 115 1 1 14 733 0 115 2 0 0 0 0 1 0.999735 103 453 6 119 43 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 1 1 1.824587 1 0.280000 1.920000 0.162791 0.850000 0.680000 0.990000 0.860000 0.852248 0.850000 1 0.760000 0.940000 TP53 7157 broad.mit.edu 37 17 7579585 7579585 + Frame_Shift_Del DEL G G - rs11575998 TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 G - G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr17:7579585delG ENST00000269305.4 - 4 291 c.102delC c.(100-102)cccfs p.P34fs TP53_ENST00000445888.2_Frame_Shift_Del_p.P34fs|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000455263.2_Frame_Shift_Del_p.P34fs|TP53_ENST00000420246.2_Frame_Shift_Del_p.P34fs|TP53_ENST00000359597.4_Frame_Shift_Del_p.P34fs|TP53_ENST00000413465.2_Frame_Shift_Del_p.P34fs 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.0?(8)|p.L35fs*9(2)|p.?(1)|p.S33fs*23(1)|p.P34fs*8(1)|p.P36fs*7(1)|p.P13fs*18(1)|p.S33fs*6(1) 24185 all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081) Acetylsalicylic acid(DB00945) GGGACGGCAAGGGGGACTGTA 0.597000 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 16 Whole gene deletion(8)|Deletion - Frameshift(6)|Unknown(1)|Insertion - Frameshift(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 1 0 hg19 CCDS11118.1 TCGA-FB-A5VM-01A-11D-A32N-08 TP53-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367397.1 1 0 0 122 963 0 272 1 9.417375e-01 7 32 0 272 2 1 1 106 704 0 316 2 1 0.980472 157 948 19 268 96 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 1 1 1.767176 1 0.280000 1.920000 0.172223 0.690000 0.580000 0.810000 0.690000 0.699908 0.690000 0 0.630000 0.760000 ZNF470 388566 broad.mit.edu 37 19 57089013 57089014 + In_Frame_Ins INS - - TAA TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr19:57089013_57089014insTAA ENST00000330619.8 + 6 1902_1903 c.1216_1217insTAA c.(1216-1218)ttc>tTAAtc p.406_406F>LI ZNF470_ENST00000601902.1_Intron|ZNF470_ENST00000391709.3_In_Frame_Ins_p.406_406F>LI NM_001001668.3 NP_001001668.3 Q6ECI4 ZN470_HUMAN zinc finger protein 470 41 Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157) TGGGAAGGCTTTCACTGATCAC 0.426000 0 SO:0001652 inframe_insertion ENST00000330619.8 0 1 hg19 CCDS33122.1 TCGA-FB-A5VM-01A-11D-A32N-08 ZNF470-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000459707.2 1 0 0 29 416 0 85 0 1.327021e-02 0 3 0 85 2 0 0 0 0 1 1.000000 40 413 0 83 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 1 2 3 2.065357 0 0.280000 1.920000 0.288959 0.480000 0.320000 1.000000 0.470000 0.520363 0.480000 0 0.390000 0.600000 DUPD1 338599 broad.mit.edu 37 10 76797813 76797813 + Silent SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr10:76797813G>A ENST00000338487.5 - 3 443 c.444C>T c.(442-444)gtC>gtT p.V148V NM_001003892.1 NP_001003892.1 Q68J44 DUPD1_HUMAN dual specificity phosphatase and pro isomerase domain containing 1 11 all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348) TGCGGCCCATGACGCAGTGAA 0.617000 0 SO:0001819 synonymous_variant ENST00000338487.5 1 1 hg19 CCDS31223.1 TCGA-FB-A5VM-01A-11D-A32N-08 DUPD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000048777.2 1 0 1 41 285 0 58 0 0 0 0 58 2 0 0 0 0 0 2 1 1.000000 40 283 0 58 2 0 0 0 0 58 2 -20.000000 1 1 0 0 1 0 0 0 1.993227 0 0.280000 1.920000 0.267697 0.870000 0.650000 1.000000 1.000000 0.876315 0.870000 1 0.750000 1.000000 IGSF22 283284 broad.mit.edu 37 11 18736985 18736985 + Missense_Mutation SNP C C G TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr11:18736985C>G ENST00000513874.1 - 11 1664 c.1525G>C c.(1525-1527)Gtg>Ctg p.V509L RP11-1081L13.4_ENST00000527285.1_RNA NM_173588.3 NP_775859 Q8N9C0 IGS22_HUMAN immunoglobulin superfamily, member 22 56 TTACCCTCCACAGTGACGATG 0.547000 0 SO:0001583 missense ENST00000513874.1 1 1 hg19 CCDS41625.2 . . . . . . . . . . C 1.041 -0.678902 0.03378 . . ENSG00000179057 ENST00000513874 T 0.13307 2.6 4.92 2.03 0.26663 . 0.203922 0.24126 N 0.041315 T 0.11110 0.0271 L 0.50333 1.59 0.19945 N 0.999945 B 0.34015 0.435 B 0.24974 0.057 T 0.14615 -1.0466 10 0.62326 D 0.03 . 8.4726 0.32995 0.0:0.7586:0.0:0.2414 . 509 D6RGV7 . L 509 ENSP00000421191:V509L ENSP00000322422:V509L V - 1 0 IGSF22 18693561 0.998000 0.40836 0.291000 0.24904 0.028000 0.11728 2.788000 0.47806 0.143000 0.18926 0.555000 0.69702 GTG TCGA-FB-A5VM-01A-11D-A32N-08 IGSF22-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000360850.2 1 0 1 69 463 0 125 0 0 0 0 125 2 0 0 0 0 0 2 1 1.000000 69 447 0 124 2 0 0 0 0 125 2 -20.000000 1 1 0 0 1 1 2 3 2.044068 0 0.280000 1.920000 0.285005 0.930000 0.730000 1.000000 1.000000 0.922873 0.930000 1 0.830000 1.000000 ANO5 203859 broad.mit.edu 37 11 22281145 22281145 + Silent SNP A A G TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr11:22281145A>G ENST00000324559.8 + 15 1805 c.1488A>G c.(1486-1488)gaA>gaG p.E496E CTD-3064C13.1_ENST00000526935.1_RNA NM_001142649.1|NM_213599.2 NP_001136121.1|NP_998764.1 Q75V66 ANO5_HUMAN anoctamin 5 63 GTTTCATGGAAAGTGATGCAT 0.413000 0 SO:0001819 synonymous_variant ENST00000324559.8 1 1 hg19 CCDS31444.1 TCGA-FB-A5VM-01A-11D-A32N-08 ANO5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000387615.1 1 0 0 37 291 0 58 0 0 0 0 58 2 0 0 0 0 0 2 1 1.000000 38 287 0 57 2 0 0 0 0 58 2 -14.955220 1 1 0 0 1 1 2 3 2.044068 0 0.280000 1.920000 0.285005 0.810000 0.580000 1.000000 1.000000 0.823427 0.810000 0 0.690000 0.970000 FBXO3 26273 broad.mit.edu 37 11 33763529 33763529 + Silent SNP T T C TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr11:33763529T>C ENST00000265651.3 - 11 1359 c.1341A>G c.(1339-1341)gaA>gaG p.E447E FBXO3_ENST00000530401.1_3'UTR|FBXO3_ENST00000526785.1_Silent_p.E334E|FBXO3_ENST00000532057.1_Silent_p.E134E|FBXO3_ENST00000531080.1_Silent_p.E134E NM_012175.3 NP_036307.2 Q9UK99 FBX3_HUMAN F-box protein 3 13 Lung NSC(402;0.0804) CTTCATCATCTTCATCTGATT 0.478000 0 SO:0001819 synonymous_variant ENST00000265651.3 1 1 hg19 CCDS7887.1 TCGA-FB-A5VM-01A-11D-A32N-08 FBXO3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000388665.1 1 0 1 29 184 0 36 1 9.737808e-01 11 29 0 36 2 0 0 0 0 0 2 1 1.000000 29 179 0 35 2 0 0 0 0 36 2 -14.692590 1 1 0 0 1 1 2 3 2.044068 0 0.280000 1.920000 0.285005 0.980000 0.680000 1.000000 1.000000 0.931675 0.980000 1 0.820000 1.000000 FBXO3 26273 broad.mit.edu 37 11 33763531 33763531 + Missense_Mutation SNP C C T TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr11:33763531C>T ENST00000265651.3 - 11 1357 c.1339G>A c.(1339-1341)Gaa>Aaa p.E447K FBXO3_ENST00000530401.1_3'UTR|FBXO3_ENST00000526785.1_Missense_Mutation_p.E334K|FBXO3_ENST00000532057.1_Missense_Mutation_p.E134K|FBXO3_ENST00000531080.1_Missense_Mutation_p.E134K NM_012175.3 NP_036307.2 Q9UK99 FBX3_HUMAN F-box protein 3 13 Lung NSC(402;0.0804) TCATCATCTTCATCTGATTCA 0.483000 0 SO:0001583 missense ENST00000265651.3 1 1 hg19 CCDS7887.1 . . . . . . . . . . C 17.79 3.476081 0.63737 . . ENSG00000110429 ENST00000526785;ENST00000265651;ENST00000531080;ENST00000532057 T;T;T;T 0.70282 -0.47;-0.47;-0.47;-0.47 4.78 4.78 0.61160 . 0.143577 0.32372 N 0.006184 T 0.71609 0.3360 N 0.14661 0.345 0.80722 D 1 P 0.46578 0.88 P 0.62184 0.899 T 0.76759 -0.2841 10 0.66056 D 0.02 -6.8063 15.9536 0.79861 0.0:1.0:0.0:0.0 . 447 Q9UK99 FBX3_HUMAN K 334;447;134;134 ENSP00000435680:E334K;ENSP00000265651:E447K;ENSP00000435165:E134K;ENSP00000434001:E134K ENSP00000265651:E447K E - 1 0 FBXO3 33720107 0.999000 0.42202 0.999000 0.59377 0.978000 0.69477 4.196000 0.58407 2.339000 0.79563 0.561000 0.74099 GAA TCGA-FB-A5VM-01A-11D-A32N-08 FBXO3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000388665.1 1 0 1 28 177 0 37 1 9.739817e-01 11 29 0 37 2 0 0 0 0 0 2 1 1.000000 28 172 0 35 2 0 0 0 0 37 2 -20.000000 1 1 0 0 1 1 2 3 2.044068 0 0.280000 1.920000 0.285005 0.990000 0.680000 1.000000 1.000000 0.932196 0.990000 1 0.820000 1.000000 OR5M3 219482 broad.mit.edu 37 11 56237570 56237570 + Nonsense_Mutation SNP G G C TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr11:56237570G>C ENST00000312240.2 - 1 444 c.404C>G c.(403-405)tCa>tGa p.S135* NM_001004742.2 NP_001004742.2 Q8NGP4 OR5M3_HUMAN olfactory receptor, family 5, subfamily M, member 3 37 Esophageal squamous(21;0.00448) GACAACCCTTGACATTTTACT 0.408000 0 SO:0001587 stop_gained ENST00000312240.2 0 1 hg19 CCDS31532.1 . . . . . . . . . . G 17.90 3.502469 0.64298 . . ENSG00000174937 ENST00000312240 . . . 5.13 4.15 0.48705 . 0.000000 0.40064 N 0.001184 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.87932 D 0 -11.6464 11.3494 0.49579 0.0:0.0:0.692:0.308 . . . . X 135 . ENSP00000312208:S135X S - 2 0 OR5M3 55994146 0.250000 0.23951 0.977000 0.42913 0.808000 0.45660 0.644000 0.24766 2.381000 0.81170 0.478000 0.44815 TCA TCGA-FB-A5VM-01A-11D-A32N-08 OR5M3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391639.1 0 0 0 8 614 0 131 0 0 0 0 131 2 0 0 0 0 0 2 1 0.988786 8 605 0 131 2 0 0 0 0 131 2 -3.144007 1 1 0 0 1 1 2 3 2.044068 0 0.280000 1.920000 0.285005 0.090000 0.040000 1.000000 0.090000 0.137372 0.090000 0 0.060000 0.140000 GIF 2694 broad.mit.edu 37 11 59599213 59599213 + Missense_Mutation SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr11:59599213G>A ENST00000257248.2 - 8 1177 c.1130C>T c.(1129-1131)gCg>gTg p.A377V GIF_ENST00000541311.1_Missense_Mutation_p.A352V NM_005142.2 NP_005133.2 P27352 IF_HUMAN gastric intrinsic factor (vitamin B synthesis) p.A377V(1) 17 Cyanocobalamin(DB00115) AACATTTTCCGCGATATTGTT 0.368000 NSCLC(53;1139 1245 16872 38474 42853) 1 Substitution - Missense(1) SO:0001583 missense ENST00000257248.2 1 1 hg19 CCDS7977.1 . . . . . . . . . . G 9.534 1.111534 0.20714 2.27E-4 2.33E-4 ENSG00000134812 ENST00000257248;ENST00000541311 T;T 0.42131 1.09;0.98 5.41 4.41 0.53225 . 0.412532 0.22845 N 0.054935 T 0.28234 0.0697 L 0.53249 1.67 0.20821 N 0.999847 P 0.43909 0.821 B 0.17098 0.017 T 0.35076 -0.9803 10 0.25751 T 0.34 -10.6094 12.1115 0.53842 0.0:0.0:0.8172:0.1828 . 377 P27352 IF_HUMAN V 377;352 ENSP00000257248:A377V;ENSP00000440427:A352V ENSP00000257248:A377V A - 2 0 GIF 59355789 0.563000 0.26594 0.980000 0.43619 0.764000 0.43329 1.685000 0.37659 2.532000 0.85374 0.655000 0.94253 GCG TCGA-FB-A5VM-01A-11D-A32N-08 GIF-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000394497.1 1 0 1 40 327 0 66 0 0 0 0 66 2 0 0 0 0 0 2 1 1.000000 37 323 0 65 2 0 0 0 0 66 2 -14.895970 1 1 121410 11 44 1 1 2 3 2.044068 0 0.280000 1.920000 0.285005 0.780000 0.570000 1.000000 1.000000 0.799121 0.780000 0 0.670000 0.930000 PLCB3 5331 broad.mit.edu 37 11 64026576 64026576 + Missense_Mutation SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr11:64026576G>A ENST00000540288.1 + 13 1488 c.1385G>A c.(1384-1386)cGt>cAt p.R462H PLCB3_ENST00000325234.5_Missense_Mutation_p.R395H|PLCB3_ENST00000279230.6_Missense_Mutation_p.R462H NM_000932.2 NP_000923.1 Q01970 PLCB3_HUMAN phospholipase C, beta 3 (phosphatidylinositol-specific) 33 CTGATGGGCCGTATCCTGGTG 0.706000 0 SO:0001583 missense ENST00000540288.1 0 1 hg19 CCDS8064.1 . . . . . . . . . . G 21.8 4.196608 0.79015 . . ENSG00000149782 ENST00000279230;ENST00000540288;ENST00000325234 T;T;T 0.66995 -0.24;-0.24;-0.24 4.58 4.58 0.56647 PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3); 0.123452 0.53938 D 0.000042 T 0.74230 0.3689 M 0.77486 2.375 0.45464 D 0.998435 D;D 0.63880 0.993;0.979 P;P 0.53593 0.73;0.697 T 0.78178 -0.2305 10 0.87932 D 0 . 9.9241 0.41481 0.0964:0.0:0.9036:0.0 . 395;462 G5E960;Q01970 .;PLCB3_HUMAN H 462;462;395 ENSP00000279230:R462H;ENSP00000443631:R462H;ENSP00000324660:R395H ENSP00000279230:R462H R + 2 0 PLCB3 63783152 0.998000 0.40836 1.000000 0.80357 0.968000 0.65278 4.876000 0.63079 2.111000 0.64477 0.561000 0.74099 CGT TCGA-FB-A5VM-01A-11D-A32N-08 PLCB3-002 KNOWN alternative_3_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000396405.1 0 0 0 4 133 0 36 0 2.668729e-01 0 28 0 36 2 0 0 0 0 0 2 1 0.891499 4 133 0 36 2 0 0 0 0 36 2 -3.538875 1 1 0 0 1 1 2 3 2.044068 0 0.280000 1.920000 0.285005 0.230000 0.070000 1.000000 0.210000 0.282359 0.230000 0 0.140000 0.380000 RBM19 9904 broad.mit.edu 37 12 114377796 114377796 + Missense_Mutation SNP C C T TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 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-A5VM-01A-11D-A32N-08 RBM19-003 KNOWN alternative_3_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000405251.1 0 0 0 8 532 0 112 0 1.080334e-01 0 33 0 112 2 0 0 0 0 0 2 1 0.989299 8 530 0 111 2 0 0 0 0 112 2 -1.905563 0 1 0 0 1 0 0 0 2.006247 0 0.280000 1.920000 0.271845 0.100000 0.040000 0.200000 0.100000 0.116699 0.100000 0 0.070000 0.150000 KRAS 3845 broad.mit.edu 37 12 25380275 25380275 + Missense_Mutation SNP T T G rs17851045 TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 T G T T Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr12:25380275T>G ENST00000256078.4 - 3 246 c.183A>C c.(181-183)caA>caC p.Q61H KRAS_ENST00000557334.1_Intron|AC087239.1_ENST00000594112.1_5'Flank|KRAS_ENST00000311936.3_Missense_Mutation_p.Q61H NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.Q61H(153) 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) TGTACTCCTCTTGACCTGCTG 0.423000 Q61H(CL11_LARGE_INTESTINE)|Q61H(HS766T_PANCREAS)|Q61H(NCIH1155_LUNG)|Q61H(NCIH460_LUNG)|Q61H(T3M4_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 153 Substitution - Missense(153) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . T 21.3 4.133750 0.77662 . . ENSG00000133703 ENST00000311936;ENST00000256078 D;D 0.84146 -1.81;-1.81 5.77 5.77 0.91146 Small GTP-binding protein domain (1); 0.049057 0.85682 D 0.000000 D 0.87265 0.6134 M 0.91140 3.18 0.80722 D 1 B;B 0.33413 0.411;0.09 B;B 0.32724 0.092;0.151 D 0.87829 0.2643 10 0.72032 D 0.01 . 9.9836 0.41828 0.0:0.0752:0.0:0.9248 . 61;61 P01116-2;P01116 .;RASK_HUMAN H 61 ENSP00000308495:Q61H;ENSP00000256078:Q61H ENSP00000256078:Q61H Q - 3 2 KRAS 25271542 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 2.240000 0.43088 2.326000 0.78906 0.533000 0.62120 CAA TCGA-FB-A5VM-01A-11D-A32N-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 35 235 0 57 1 5.646846e-01 6 8 0 57 2 1 1 32 301 0 610 2 1 1.000000 35 230 0 57 2 1 1 1302 6692 0 57 2 -20.000000 1 1 0 0 1 0 0 0 2.006247 0 0.280000 1.920000 0.271845 0.910000 0.650000 1.000000 1.000000 0.896985 0.910000 1 0.770000 1.000000 RGMA 56963 broad.mit.edu 37 15 93595475 93595475 + Silent SNP C C T TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr15:93595475C>T ENST00000329082.7 - 3 664 c.393G>A c.(391-393)ccG>ccA p.P131P RGMA_ENST00000555584.1_5'Flank|RGMA_ENST00000425933.2_Silent_p.P115P|RGMA_ENST00000542321.2_Silent_p.P115P|RGMA_ENST00000557301.1_Silent_p.P139P|RGMA_ENST00000556658.1_Silent_p.P22P|RGMA_ENST00000538818.1_Silent_p.P22P|RGMA_ENST00000543599.1_Silent_p.P115P|RGMA_ENST00000556087.1_Silent_p.P115P|RGMA_ENST00000557420.1_Intron NM_020211.2 NP_064596 Q96B86 RGMA_HUMAN repulsive guidance molecule family member a 9 Lung NSC(78;0.0542)|all_lung(78;0.0786) BRCA - Breast invasive adenocarcinoma(143;0.0312)|OV - Ovarian serous cystadenocarcinoma(32;0.108) TGTCTCCGGCCGGTGGGAGCG 0.647000 0 SO:0001819 synonymous_variant ENST00000329082.7 1 1 hg19 CCDS45357.1 TCGA-FB-A5VM-01A-11D-A32N-08 RGMA-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000415091.1 1 0 1 47 328 0 97 0 1.650457e-02 0 2 0 97 2 0 0 0 0 0 2 1 1.000000 47 322 0 96 2 0 0 0 0 97 2 -3.221921 1 1 121328 2 37 1 1 2 3 2.039741 0 0.280000 1.920000 0.285005 0.900000 0.670000 1.000000 1.000000 0.896329 0.900000 1 0.780000 1.000000 FLYWCH1 84256 broad.mit.edu 37 16 2979735 2979735 + Missense_Mutation SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr16:2979735G>A ENST00000253928.9 + 3 454 c.49G>A c.(49-51)Ggc>Agc p.G17S FLYWCH1_ENST00000399667.2_Missense_Mutation_p.G17S|FLYWCH1_ENST00000416288.2_Missense_Mutation_p.G17S Q4VC44 FWCH1_HUMAN FLYWCH-type zinc finger 1 4 TGTGAAGGCCGGCCAGGAGCC 0.692000 0 SO:0001583 missense ENST00000253928.9 0 1 hg19 . . . . . . . . . . G 10.36 1.329821 0.24167 . . ENSG00000059122 ENST00000399667;ENST00000253928;ENST00000416288 . . . 3.01 2.04 0.26737 . . . . . T 0.15609 0.0376 N 0.19112 0.55 0.24293 N 0.995159 B;P 0.39060 0.105;0.657 B;B 0.32677 0.018;0.15 T 0.10042 -1.0647 8 0.38643 T 0.18 . 6.03 0.19675 0.1435:0.0:0.8565:0.0 . 17;17 Q4VC44;Q4VC44-2 FWCH1_HUMAN;. S 17 . ENSP00000253928:G17S G + 1 0 FLYWCH1 2919736 0.537000 0.26386 0.679000 0.29978 0.109000 0.19521 0.577000 0.23758 0.844000 0.35094 0.456000 0.33151 GGC TCGA-FB-A5VM-01A-11D-A32N-08 FLYWCH1-001 KNOWN basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000436479.1 0 0 0 4 126 0 34 0 6.917223e-02 0 11 0 34 2 0 0 0 0 0 2 1 0.887878 4 124 0 34 2 0 0 0 0 34 2 -6.741605 1 1 121390 14 43 1 0 1 1 1.751874 1 0.280000 1.920000 0.162791 0.200000 0.060000 0.430000 0.180000 0.223543 0.200000 0 0.120000 0.310000 SEPHS2 22928 broad.mit.edu 37 16 30455811 30455811 + Missense_Mutation SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr16:30455811G>A ENST00000478753.2 - 1 1691 c.1238C>T c.(1237-1239)aCg>aTg p.T413M SEPHS2_ENST00000500504.2_Missense_Mutation_p.T413M|SEPHS2_ENST00000542752.1_Missense_Mutation_p.T356M Q99611 SPS2_HUMAN selenophosphate synthetase 2 10 GATCCGGGCCGTTCGGTTTCC 0.537000 Esophageal Squamous(81;1142 1261 11202 24614 35697) 0 SO:0001583 missense ENST00000478753.2 0 1 hg19 . . . . . . . . . . G 7.619 0.676333 0.14841 . . ENSG00000179918 ENST00000478753;ENST00000542752;ENST00000418751;ENST00000500504 T;T;T 0.18174 2.23;2.23;2.23 5.28 4.32 0.51571 AIR synthase-related protein, C-terminal (2); 0.239370 0.39834 N 0.001245 T 0.18882 0.0453 L 0.61387 1.9 0.80722 D 1 P;B 0.42039 0.769;0.091 B;B 0.36186 0.219;0.082 T 0.03268 -1.1054 10 0.48119 T 0.1 -14.479 14.0137 0.64513 0.0:0.1527:0.8473:0.0 . 413;356 Q99611;F5H8F9 SPS2_HUMAN;. M 413;356;364;413 ENSP00000418669:T413M;ENSP00000443601:T356M;ENSP00000426234:T413M ENSP00000390233:T364M T - 2 0 SEPHS2 30363312 1.000000 0.71417 0.880000 0.34516 0.045000 0.14185 4.815000 0.62634 1.361000 0.45981 -0.176000 0.13171 ACG TCGA-FB-A5VM-01A-11D-A32N-08 SEPHS2-001 KNOWN basic|seleno protein_coding protein_coding OTTHUMT00000109640.11 0 0 0 5 357 0 67 0 9.342221e-01 0 354 0 67 2 0 7.709763e-01 0 741 1 455 8 1 0.934703 6 349 0 67 2 0 0 0 0 67 2 -5.034304 1 0 0 0 1 1 2 3 2.039724 0 0.280000 1.920000 0.285005 0.100000 0.030000 1.000000 0.100000 0.151247 0.100000 0 0.060000 0.170000 PHKB 5257 broad.mit.edu 37 16 47683068 47683068 + Missense_Mutation SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr16:47683068G>A ENST00000323584.5 + 18 1774 c.1750G>A c.(1750-1752)Gat>Aat p.D584N PHKB_ENST00000566044.1_Missense_Mutation_p.D577N|PHKB_ENST00000299167.8_Missense_Mutation_p.D584N|PHKB_ENST00000455779.1_Missense_Mutation_p.D577N NM_000293.2 NP_000284.1 Q93100 KPBB_HUMAN phosphorylase kinase, beta 41 all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203) CGACCTAAGTGATTTCTACAT 0.343000 0 SO:0001583 missense ENST00000323584.5 1 1 hg19 CCDS10729.1 . . . . . . . . . . G 35 5.512079 0.96402 . . ENSG00000102893 ENST00000299167;ENST00000455779;ENST00000323584 D;D 0.91180 -2.8;-2.8 5.89 5.89 0.94794 Glycoside hydrolase 15-related (1); 0.000000 0.85682 D 0.000000 D 0.95717 0.8607 M 0.79805 2.47 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.91635 0.998;0.999 D 0.95278 0.8383 10 0.59425 D 0.04 -29.7077 19.8459 0.96707 0.0:0.0:1.0:0.0 . 584;577 Q93100;Q93100-4 KPBB_HUMAN;. N 577;577;584 ENSP00000414345:D577N;ENSP00000313504:D584N ENSP00000299167:D577N D + 1 0 PHKB 46240569 1.000000 0.71417 1.000000 0.80357 0.925000 0.55904 9.037000 0.93765 2.788000 0.95919 0.585000 0.79938 GAT TCGA-FB-A5VM-01A-11D-A32N-08 PHKB-002 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000430413.1 1 0 1 53 338 0 63 1 3.548848e-01 3 6 0 63 2 0 0 0 0 0 2 1 1.000000 54 337 0 63 2 0 0 0 0 63 2 -3.319021 1 1 0 0 1 1 2 3 2.039724 0 0.280000 1.920000 0.285005 0.970000 0.740000 1.000000 1.000000 0.943014 0.970000 1 0.850000 1.000000 PARD6A 50855 broad.mit.edu 37 16 67695975 67695975 + Nonsense_Mutation SNP C C T TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr16:67695975C>T ENST00000219255.3 + 3 546 c.466C>T c.(466-468)Cga>Tga p.R156* ENKD1_ENST00000602409.1_5'Flank|ACD_ENST00000393919.4_5'Flank|PARD6A_ENST00000602551.1_Nonsense_Mutation_p.R126*|ACD_ENST00000219251.8_5'Flank|PARD6A_ENST00000458121.2_Nonsense_Mutation_p.R155* Q9NPB6 PAR6A_HUMAN par-6 family cell polarity regulator alpha 6 Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563) TGAGACCCACCGACGGGTGCG 0.647000 0 SO:0001587 stop_gained ENST00000219255.3 0 1 hg19 CCDS10843.1 . . . . . . . . . . C 22.8 4.342839 0.82022 . . ENSG00000102981 ENST00000458121;ENST00000219255 . . . 5.07 4.1 0.47936 . 0.073470 0.53938 D 0.000047 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.02654 T 1 -6.4892 11.7101 0.51620 0.3209:0.6791:0.0:0.0 . . . . X 155;156 . ENSP00000219255:R156X R + 1 2 PARD6A 66253476 1.000000 0.71417 0.998000 0.56505 0.991000 0.79684 2.149000 0.42244 1.091000 0.41335 0.563000 0.77884 CGA TCGA-FB-A5VM-01A-11D-A32N-08 PARD6A-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000268863.2 1 0 1 62 420 0 109 1 6.946017e-01 3 15 0 109 2 0 0 0 0 0 2 1 1.000000 62 415 0 108 2 0 0 0 0 109 2 -3.075766 1 1 0 0 1 1 2 3 2.057540 0 0.280000 1.920000 0.287975 0.930000 0.720000 1.000000 1.000000 0.921165 0.930000 1 0.820000 1.000000 LLGL1 3996 broad.mit.edu 37 17 18138848 18138848 + Missense_Mutation SNP C C T rs141275484 TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr17:18138848C>T ENST00000316843.4 + 11 1445 c.1349C>T c.(1348-1350)aCg>aTg p.T450M NM_004140.3 NP_004131 Q15334 L2GL1_HUMAN lethal giant larvae homolog 1 (Drosophila) 21 all_neural(463;0.228) CTGCTGCTGACGGGGTAGGTG 0.652000 0 SO:0001583 missense ENST00000316843.4 0 1 hg19 CCDS32586.1 . . . . . . . . . . C 21.1 4.090348 0.76756 0.0 1.16E-4 ENSG00000131899 ENST00000316843 T 0.33216 1.42 5.01 5.01 0.66863 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1); 0.090164 0.85682 D 0.000000 T 0.66867 0.2833 M 0.93720 3.45 0.80722 D 1 D 0.89917 1.0 D 0.85130 0.997 T 0.76094 -0.3085 10 0.87932 D 0 -27.9792 17.6696 0.88213 0.0:1.0:0.0:0.0 . 450 Q15334 L2GL1_HUMAN M 450 ENSP00000321537:T450M ENSP00000321537:T450M T + 2 0 LLGL1 18079573 1.000000 0.71417 0.963000 0.40424 0.227000 0.25037 7.487000 0.81328 2.776000 0.95493 0.650000 0.86243 ACG TCGA-FB-A5VM-01A-11D-A32N-08 LLGL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000132067.3 0 0 0 4 247 0 67 0 1.171722e-02 0 8 0 67 2 0 0 0 0 0 2 1 0.886315 4 242 0 67 2 0 0 0 0 67 2 -5.130001 1 1 121404 2 32 1 0 1 1 1.780231 1 0.280000 1.920000 0.162791 0.100000 0.030000 0.230000 0.100000 0.118915 0.100000 0 0.060000 0.170000 TAOK1 57551 broad.mit.edu 37 17 27807459 27807459 + Missense_Mutation SNP A A T TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr17:27807459A>T ENST00000261716.3 + 7 1042 c.523A>T c.(523-525)Atg>Ttg p.M175L TAOK1_ENST00000536202.1_Missense_Mutation_p.M175L NM_020791.2 NP_065842.1 Q7L7X3 TAOK1_HUMAN TAO kinase 1 28 Colorectal(6;0.198) CTCTGCTTCCATGGCATCACC 0.418000 0 SO:0001583 missense ENST00000261716.3 0 1 hg19 CCDS32601.1 . . . . . . . . . . A 14.69 2.610191 0.46527 . . ENSG00000160551 ENST00000261716;ENST00000536202 T;T 0.63417 -0.04;-0.04 5.21 5.21 0.72293 Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); 0.081007 0.85682 D 0.000000 T 0.39226 0.1070 N 0.02973 -0.45 0.42825 D 0.994006 B;B;B 0.02656 0.0;0.0;0.0 B;B;B 0.10450 0.005;0.001;0.001 T 0.27640 -1.0068 10 0.31617 T 0.26 . 15.3559 0.74425 1.0:0.0:0.0:0.0 . 175;1;175 B7ZLV6;Q7L7X3-2;Q7L7X3 .;.;TAOK1_HUMAN L 175 ENSP00000261716:M175L;ENSP00000438819:M175L ENSP00000261716:M175L M + 1 0 TAOK1 24831585 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 7.169000 0.77578 2.100000 0.63781 0.477000 0.44152 ATG TCGA-FB-A5VM-01A-11D-A32N-08 TAOK1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000447790.1 0 0 0 4 169 0 35 0 0 0 0 35 2 0 0 0 0 0 2 0 0.887186 1 169 0 34 2 0 0 0 0 35 2 -6.453829 1 0 0 0 1 1 2 3 2.067579 0 0.280000 1.920000 0.288959 0.190000 0.060000 1.000000 0.170000 0.261635 0.190000 0 0.110000 0.330000 XYLT2 64132 broad.mit.edu 37 17 48431870 48431870 + Missense_Mutation SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr17:48431870G>A ENST00000017003.2 + 3 779 c.730G>A c.(730-732)Gcc>Acc p.A244T XYLT2_ENST00000507602.1_Missense_Mutation_p.A244T NM_022167.2 NP_071450.2 Q9H1B5 XYLT2_HUMAN xylosyltransferase II 12 Breast(11;7.18e-19) TCACGGCCGCGCCATCCGCCA 0.612000 0 SO:0001583 missense ENST00000017003.2 0 1 hg19 CCDS11563.1 . . . . . . . . . . G 27.2 4.813933 0.90790 . . ENSG00000015532 ENST00000017003;ENST00000507602 T;T 0.11169 2.8;2.8 4.62 4.62 0.57501 . 0.000000 0.85682 D 0.000000 T 0.37293 0.0998 M 0.82630 2.6 0.80722 D 1 D 0.89917 1.0 D 0.77557 0.99 T 0.31081 -0.9956 10 0.54805 T 0.06 -17.8105 17.6496 0.88159 0.0:0.0:1.0:0.0 . 244 Q9H1B5 XYLT2_HUMAN T 244 ENSP00000017003:A244T;ENSP00000426501:A244T ENSP00000017003:A244T A + 1 0 XYLT2 45786869 1.000000 0.71417 0.919000 0.36401 0.568000 0.35870 9.411000 0.97342 2.403000 0.81681 0.313000 0.20887 GCC TCGA-FB-A5VM-01A-11D-A32N-08 XYLT2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000367046.1 0 0 0 5 226 0 47 0 6.786375e-02 0 16 0 47 2 0 0 0 0 0 2 1 0.938216 5 226 0 46 2 0 0 0 0 47 2 -6.312877 1 1 0 0 1 1 2 3 2.063493 0 0.280000 1.920000 0.288959 0.170000 0.060000 1.000000 0.150000 0.243598 0.170000 0 0.100000 0.290000 WSCD1 23302 broad.mit.edu 37 17 5984019 5984019 + Missense_Mutation SNP G G A rs148296936 TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr17:5984019G>A ENST00000574946.1 + 2 431 c.41G>A c.(40-42)cGa>cAa p.R14Q WSCD1_ENST00000573634.1_Intron|WSCD1_ENST00000539421.1_Missense_Mutation_p.R14Q|WSCD1_ENST00000317744.5_Missense_Mutation_p.R14Q|WSCD1_ENST00000574232.1_Missense_Mutation_p.R14Q Q658N2 WSCD1_HUMAN WSC domain containing 1 35 TTTCTCCGCCGAACACAGTTC 0.672000 0 SO:0001583 missense ENST00000574946.1 0 1 hg19 CCDS32538.1 . . . . . . . . . . g 31 5.082163 0.94050 0.0 2.43E-4 ENSG00000179314 ENST00000317744;ENST00000539421 D;D 0.85955 -2.05;-2.05 4.78 4.78 0.61160 . 0.000000 0.64402 D 0.000008 D 0.89550 0.6747 L 0.47190 1.495 0.36291 D 0.856398 D 0.89917 1.0 D 0.76575 0.988 D 0.92691 0.6166 10 0.87932 D 0 -12.0492 15.3569 0.74434 0.0:0.0:1.0:0.0 . 14 Q658N2 WSCD1_HUMAN Q 14 ENSP00000323087:R14Q;ENSP00000446032:R14Q ENSP00000323087:R14Q R + 2 0 WSCD1 5924743 1.000000 0.71417 0.976000 0.42696 0.972000 0.66771 6.190000 0.72057 2.203000 0.70933 0.552000 0.68991 CGA TCGA-FB-A5VM-01A-11D-A32N-08 WSCD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000438965.4 0 0 0 4 224 1 52 0 0 0 1 1 52 2 0 0 0 0 0 2 0 0.007987 4 223 1 52 15 0 0 0 1 52 2 -3.858104 1 1 121070 25 45 1 0 1 1 1.767176 1 0.280000 1.920000 0.172223 0.110000 0.030000 0.260000 0.110000 0.132228 0.110000 0 0.070000 0.190000 ABCA10 10349 broad.mit.edu 37 17 67183986 67183986 + Silent SNP C C A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr17:67183986C>A ENST00000269081.4 - 20 3075 c.2166G>T c.(2164-2166)gtG>gtT p.V722V ABCA10_ENST00000416101.2_3'UTR NM_080282.3 NP_525021.3 Q8WWZ4 ABCAA_HUMAN ATP-binding cassette, sub-family A (ABC1), member 10 81 Breast(10;6.95e-12) TATTTCTTGTCACATGTATTT 0.348000 0 SO:0001819 synonymous_variant ENST00000269081.4 1 1 hg19 CCDS11684.1 TCGA-FB-A5VM-01A-11D-A32N-08 ABCA10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000379881.4 1 0 1 30 178 0 32 0 0 0 0 32 2 0 0 0 0 0 2 1 1.000000 29 176 0 32 2 0 0 0 0 32 2 -20.000000 1 1 0 0 1 1 2 3 2.063493 0 0.280000 1.920000 0.288959 0.990000 0.730000 1.000000 1.000000 0.958802 0.990000 1 0.880000 1.000000 DSG4 147409 broad.mit.edu 37 18 28991322 28991322 + Missense_Mutation SNP G G A rs145949758 TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr18:28991322G>A ENST00000308128.4 + 15 2401 c.2266G>A c.(2266-2268)Gca>Aca p.A756T RP11-534N16.1_ENST00000581856.1_RNA|RP11-534N16.1_ENST00000578477.1_RNA|DSG4_ENST00000359747.4_Missense_Mutation_p.A775T NM_177986.3 NP_817123.1 Q86SJ6 DSG4_HUMAN desmoglein 4 70 OV - Ovarian serous cystadenocarcinoma(10;0.00504) ctcaggggccgcaAGGAAGAG 0.617000 0 SO:0001583 missense ENST00000308128.4 0 1 hg19 CCDS11897.1 . . . . . . . . . . G 4.141 0.024420 0.08054 . . ENSG00000175065 ENST00000308128;ENST00000359747 T;T 0.54479 0.57;0.57 5.87 -11.7 0.00046 . . . . . T 0.18341 0.0440 N 0.08118 0 0.09310 N 1 B;B 0.10296 0.0;0.003 B;B 0.04013 0.001;0.001 T 0.09640 -1.0665 9 0.17369 T 0.5 . 0.3831 0.00398 0.351:0.2389:0.1437:0.2663 . 775;756 Q86SJ6-2;Q86SJ6 .;DSG4_HUMAN T 756;775 ENSP00000311859:A756T;ENSP00000352785:A775T ENSP00000311859:A756T A + 1 0 DSG4 27245320 0.000000 0.05858 0.000000 0.03702 0.008000 0.06430 -0.460000 0.06720 -2.897000 0.00313 -0.905000 0.02835 GCA TCGA-FB-A5VM-01A-11D-A32N-08 DSG4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254941.1 0 0 0 5 288 0 79 0 0 0 0 79 2 0 0 0 0 0 2 1 0.936938 5 286 0 77 2 0 0 0 0 79 2 -3.132460 1 1 0 0 1 0 1 1 1.765013 1 0.280000 1.920000 0.162791 0.110000 0.030000 0.230000 0.100000 0.122746 0.110000 0 0.060000 0.170000 GALNT1 2589 broad.mit.edu 37 18 33289706 33289706 + Missense_Mutation SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr18:33289706G>A ENST00000269195.5 + 11 1755 c.1652G>A c.(1651-1653)cGa>cAa p.R551Q GALNT1_ENST00000537549.1_Missense_Mutation_p.R491Q NM_020474.3 NP_065207.2 Q10472 GALT1_HUMAN polypeptide N-acetylgalactosaminyltransferase 1 21 TGGCTTCTTCGAAACGTCACC 0.453000 0 SO:0001583 missense ENST00000269195.5 1 1 hg19 CCDS11915.1 . . . . . . . . . . G 15.21 2.767083 0.49574 0.0 1.16E-4 ENSG00000141429 ENST00000537748;ENST00000269195;ENST00000537549 T;T 0.78003 -1.14;-1.14 5.59 5.59 0.84812 Ricin B-related lectin (1);Ricin B lectin (2); 0.000000 0.85682 D 0.000000 T 0.64034 0.2562 N 0.12182 0.205 0.80722 D 1 B 0.18166 0.026 B 0.06405 0.002 T 0.59558 -0.7432 10 0.41790 T 0.15 . 17.0846 0.86608 0.0:0.0:1.0:0.0 . 551 Q10472 GALT1_HUMAN Q 551;551;491 ENSP00000269195:R551Q;ENSP00000440910:R491Q ENSP00000269195:R551Q R + 2 0 GALNT1 31543704 1.000000 0.71417 0.999000 0.59377 0.990000 0.78478 9.556000 0.98127 2.622000 0.88805 0.637000 0.83480 CGA TCGA-FB-A5VM-01A-11D-A32N-08 GALNT1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255771.2 1 0 1 29 153 0 40 1 9.996585e-01 33 36 0 40 2 0 0 0 0 0 2 1 1.000000 30 153 0 40 2 0 0 0 0 40 2 -20.000000 1 1 121412 8 36 1 0 1 1 1.765013 1 0.280000 1.920000 0.162791 0.870000 0.640000 1.000000 0.950000 0.866561 0.870000 1 0.760000 0.960000 COL5A3 50509 broad.mit.edu 37 19 10071228 10071228 + Silent SNP C C T TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr19:10071228C>T ENST00000264828.3 - 67 5182 c.5097G>A c.(5095-5097)cgG>cgA p.R1699R NM_015719.3 NP_056534.2 P25940 CO5A3_HUMAN collagen, type V, alpha 3 116 Epithelial(33;7.11e-05) TCTGTCCTTTCCGGAGCTGTC 0.587000 0 SO:0001819 synonymous_variant ENST00000264828.3 1 1 hg19 CCDS12222.1 TCGA-FB-A5VM-01A-11D-A32N-08 COL5A3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000315788.1 1 0 1 95 550 0 128 0 1 1 147 0 128 2 0 0 0 0 0 2 1 1.000000 95 544 0 127 2 0 0 0 0 128 2 -20.000000 1 1 0 0 1 1 2 3 2.072738 0 0.280000 1.920000 0.289941 0.990000 0.870000 1.000000 1.000000 0.987248 0.990000 1 0.970000 1.000000 CIC 23152 broad.mit.edu 37 19 42799006 42799006 + Missense_Mutation SNP A A G TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr19:42799006A>G ENST00000575354.2 + 20 4530 c.4490A>G c.(4489-4491)tAt>tGt p.Y1497C CIC_ENST00000160740.3_Missense_Mutation_p.Y1495C|CIC_ENST00000572681.2_Missense_Mutation_p.Y2403C NM_015125.3 NP_055940.3 Q96RK0 CIC_HUMAN capicua transcriptional repressor 82 Prostate(69;0.00682) CAGGCCCGCTATGCAGACATC 0.587000 Mis, F, S oligodendroglioma Rec yes 19 19q13.2 23152 capicua homolog O 0 SO:0001583 missense ENST00000575354.2 1 1 hg19 CCDS12601.1 . . . . . . . . . . A 16.55 3.155719 0.57259 . . ENSG00000079432 ENST00000160740 . . . 4.49 3.45 0.39498 . . . . . T 0.56543 0.1992 L 0.29908 0.895 0.42414 D 0.992613 D 0.69078 0.997 D 0.66847 0.947 T 0.58476 -0.7630 8 0.87932 D 0 -2.7629 9.5983 0.39587 0.8231:0.1768:0.0:0.0 . 1497 Q96RK0 CIC_HUMAN C 1497 . ENSP00000160740:Y1497C Y + 2 0 CIC 47490846 1.000000 0.71417 0.965000 0.40720 0.996000 0.88848 4.776000 0.62354 0.845000 0.35118 0.402000 0.26972 TAT TCGA-FB-A5VM-01A-11D-A32N-08 CIC-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000438532.2 1 0 1 55 487 0 140 1 9.999964e-01 52 108 0 140 2 0 0 0 0 0 2 1 1.000000 54 480 0 140 2 0 0 0 0 140 2 -20.000000 1 1 121408 2 31 1 1 2 3 2.054689 0 0.280000 1.920000 0.286988 0.730000 0.560000 1.000000 0.720000 0.753481 0.730000 0 0.640000 0.860000 KCNN4 3783 broad.mit.edu 37 19 44280710 44280710 + Missense_Mutation SNP G G C TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr19:44280710G>C ENST00000262888.3 - 2 633 c.238C>G c.(238-240)Cat>Gat p.H80D NM_002250.2 NP_002241.1 O15554 KCNN4_HUMAN potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4 15 Prostate(69;0.0352) Clotrimazole(DB00257)|Enflurane(DB00228)|Halothane(DB01159)|Miconazole(DB01110)|Procaine(DB00721)|Quinine(DB00468) TCTTTGGCATGAAAGGCCACG 0.592000 0 SO:0001583 missense ENST00000262888.3 1 1 hg19 CCDS12630.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 17.48|17.48 3.400039|3.400039 0.62177|0.62177 .|. .|. ENSG00000104783|ENSG00000104783 ENST00000262888|ENST00000407385 D|. 0.99907|. -7.79|. 2.95|2.95 2.95|2.95 0.34219|0.34219 Potassium channel, calcium-activated, SK, conserved region (1);|. 0.000000|. 0.85682|. D|. 0.000000|. T|. 0.72269|. 0.3439|. M|M 0.73962|0.73962 2.25|2.25 0.54753|0.54753 D|D 0.999989|0.999989 D|. 0.61697|. 0.99|. P|. 0.62089|. 0.898|. T|. 0.75969|. -0.3130|. 10|. 0.87932|0.62326 D|D 0|0.03 -18.4681|-18.4681 11.8767|11.8767 0.52552|0.52552 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. 80|. O15554|. KCNN4_HUMAN|. D|X 80|18 ENSP00000262888:H80D|. ENSP00000262888:H80D|ENSP00000384427:S18X H|S -|- 1|2 0|0 KCNN4|KCNN4 48972550|48972550 1.000000|1.000000 0.71417|0.71417 0.998000|0.998000 0.56505|0.56505 0.782000|0.782000 0.44232|0.44232 8.720000|8.720000 0.91442|0.91442 1.711000|1.711000 0.51337|0.51337 0.549000|0.549000 0.68633|0.68633 CAT|TCA TCGA-FB-A5VM-01A-11D-A32N-08 KCNN4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000463598.1 1 0 1 32 227 0 53 1 9.999506e-01 52 59 0 53 2 0 0 0 0 0 2 1 1.000000 31 224 0 51 2 0 0 0 0 53 2 -20.000000 1 1 0 0 1 1 2 3 2.072191 0 0.280000 1.920000 0.289941 0.910000 0.630000 1.000000 1.000000 0.891716 0.910000 1 0.760000 1.000000 LAIR1 3903 broad.mit.edu 37 19 54872731 54872731 + Silent SNP C C T rs140141368 byFrequency TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr19:54872731C>T ENST00000391742.2 - 3 308 c.156G>A c.(154-156)ccG>ccA p.P52P LAIR1_ENST00000474878.1_Silent_p.P51P|LAIR1_ENST00000313038.6_Silent_p.P45P|LAIR1_ENST00000434277.2_Silent_p.P51P|LAIR1_ENST00000348231.4_Silent_p.P52P|LAIR1_ENST00000463489.1_5'UTR|LAIR1_ENST00000391743.3_Silent_p.P34P Q6GTX8 LAIR1_HUMAN leukocyte-associated immunoglobulin-like receptor 1 26 Ovarian(34;0.19) GAACCCCAACCGGGCCCCGGC 0.567000 0 SO:0001819 synonymous_variant ENST00000391742.2 1 0 hg19 CCDS12891.1 TCGA-FB-A5VM-01A-11D-A32N-08 LAIR1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000140506.1 1 0 1 103 565 0 134 0 9.971734e-01 0 50 0 134 2 0 0 0 0 0 2 1 1.000000 102 556 0 134 2 0 0 0 0 134 2 -2.967176 1 1 121412 56 52 1 1 2 3 2.065357 0 0.280000 1.920000 0.288959 0.990000 0.920000 1.000000 1.000000 0.995009 0.990000 1 0.990000 1.000000 PEG3 5178 broad.mit.edu 37 19 57335031 57335031 + Silent SNP G G A rs146592671 byFrequency TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr19:57335031G>A ENST00000326441.9 - 5 774 c.411C>T c.(409-411)gaC>gaT p.D137D PEG3_ENST00000598410.1_Silent_p.D11D|PEG3_ENST00000594706.1_5'Flank|PEG3_ENST00000423103.2_Silent_p.D137D|ZIM2_ENST00000599935.1_Silent_p.D11D|ZIM2_ENST00000593931.1_Silent_p.D11D|ZIM2_ENST00000593711.1_Silent_p.D11D|PEG3_ENST00000593695.1_Silent_p.D11D|ZIM2_ENST00000601070.1_Silent_p.D11D|ZIM2_ENST00000391708.3_Silent_p.D11D|ZIM2_ENST00000221722.5_Silent_p.D11D NM_006210.2 NP_006201.1 Q9GZU2 PEG3_HUMAN paternally expressed 3 170 Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243) CGCTGGTCACGTCACTGTTGT 0.552000 0 SO:0001819 synonymous_variant ENST00000326441.9 1 0 hg19 CCDS12948.1 TCGA-FB-A5VM-01A-11D-A32N-08 PEG3-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000416099.2 1 0 0 50 348 0 85 0 0 0 0 85 2 0 0 0 0 0 2 1 1.000000 50 336 0 84 2 0 0 0 0 85 2 -7.261781 1 1 121412 63 51 1 1 2 3 2.065357 0 0.280000 1.920000 0.288959 0.910000 0.690000 1.000000 1.000000 0.905747 0.910000 1 0.790000 1.000000 INTS3 65123 broad.mit.edu 37 1 153723618 153723618 + Missense_Mutation SNP C C T TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr1:153723618C>T ENST00000318967.2 + 7 1200 c.632C>T c.(631-633)aCg>aTg p.T211M INTS3_ENST00000456435.1_Missense_Mutation_p.T5M|INTS3_ENST00000476843.1_3'UTR|RP11-216N14.9_ENST00000434575.1_RNA|snoU13_ENST00000458994.1_RNA|INTS3_ENST00000435409.2_Missense_Mutation_p.T211M|INTS3_ENST00000512605.1_Missense_Mutation_p.T5M|RP11-216N14.8_ENST00000453778.1_RNA NM_023015.3 NP_075391.3 Q68E01 INT3_HUMAN integrator complex subunit 3 38 all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199) LUSC - Lung squamous cell carcinoma(543;0.151) GCTGTTTACACGTACCTCCGC 0.567000 0 SO:0001583 missense ENST00000318967.2 1 1 hg19 CCDS1052.1 . . . . . . . . . . C 27.6 4.844025 0.91197 . . ENSG00000143624 ENST00000318967;ENST00000456435;ENST00000435409;ENST00000512605 . . . 4.95 4.95 0.65309 . 0.000000 0.85682 D 0.000000 T 0.76414 0.3984 M 0.81341 2.54 0.58432 D 0.999999 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.85130 0.997;0.985;0.994 T 0.79783 -0.1658 9 0.87932 D 0 . 15.7443 0.77926 0.0:1.0:0.0:0.0 . 5;212;211 Q68E01-3;Q68E01;Q68E01-2 .;INT3_HUMAN;. M 211;5;211;5 . ENSP00000318641:T211M T + 2 0 INTS3 151990242 1.000000 0.71417 0.986000 0.45419 0.968000 0.65278 7.039000 0.76544 2.570000 0.86706 0.555000 0.69702 ACG TCGA-FB-A5VM-01A-11D-A32N-08 INTS3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000090045.2 1 0 0 12 154 0 40 0 3.371862e-02 1 3 0 40 2 0 0 0 0 0 2 1 0.999228 12 154 0 40 2 0 0 0 0 40 2 -3.222033 1 1 121412 2 30 1 1 2 3 2.046586 0 0.280000 1.920000 0.285998 0.540000 0.290000 1.000000 0.510000 0.569947 0.540000 0 0.400000 0.720000 RAB25 57111 broad.mit.edu 37 1 156038083 156038083 + Missense_Mutation SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr1:156038083G>A ENST00000361084.5 + 3 503 c.262G>A c.(262-264)Gcc>Acc p.A88T RAB25_ENST00000487325.1_3'UTR NM_020387.2 NP_065120.2 P57735 RAB25_HUMAN RAB25, member RAS oncogene family 5 Hepatocellular(266;0.158)|all_neural(408;0.195) TGCAGTGGGGGCCCTCCTGGT 0.557000 0 SO:0001583 missense ENST00000361084.5 1 1 hg19 CCDS41413.1 . . . . . . . . . . G 35 5.595812 0.96602 . . ENSG00000132698 ENST00000361084 T 0.81163 -1.46 5.19 5.19 0.71726 Small GTP-binding protein domain (1); 0.106823 0.64402 D 0.000006 D 0.92851 0.7726 H 0.97131 3.945 0.80722 D 1 D 0.89917 1.0 D 0.87578 0.998 D 0.94704 0.7886 10 0.87932 D 0 . 17.4443 0.87574 0.0:0.0:1.0:0.0 . 88 P57735 RAB25_HUMAN T 88 ENSP00000354376:A88T ENSP00000354376:A88T A + 1 0 RAB25 154304707 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 9.520000 0.98027 2.686000 0.91538 0.655000 0.94253 GCC TCGA-FB-A5VM-01A-11D-A32N-08 RAB25-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000046185.1 1 0 1 96 501 0 121 1 1 146 207 0 121 2 0 0 0 0 0 2 1 1.000000 96 497 0 120 2 0 0 0 0 121 2 -20.000000 1 1 0 0 1 1 2 3 2.046586 0 0.280000 1.920000 0.285998 0.990000 0.950000 1.000000 1.000000 0.997448 0.990000 1 0.990000 1.000000 OLFML2B 25903 broad.mit.edu 37 1 161953822 161953822 + Silent SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 G A G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr1:161953822G>A ENST00000294794.3 - 8 2319 c.1896C>T c.(1894-1896)atC>atT p.I632I OLFML2B_ENST00000367938.1_Silent_p.I115I|OLFML2B_ENST00000367940.2_Silent_p.I633I NM_015441.1 NP_056256.1 Q68BL8 OLM2B_HUMAN olfactomedin-like 2B 48 all_hematologic(112;0.156) BRCA - Breast invasive adenocarcinoma(70;0.0172) GGGCCGGGTAGATGAGCCATA 0.617000 0 SO:0001819 synonymous_variant ENST00000294794.3 1 1 hg19 CCDS1236.1 TCGA-FB-A5VM-01A-11D-A32N-08 OLFML2B-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000060552.2 1 0 1 52 262 0 69 0 1 0 207 0 69 2 0 0 0 0 0 2 1 1.000000 50 258 0 68 2 0 0 0 0 69 2 -20.000000 1 1 0 0 1 1 2 3 2.046641 0 0.280000 1.920000 0.285998 0.990000 0.910000 1.000000 1.000000 0.994890 0.990000 1 0.990000 1.000000 PLA2G4A 5321 broad.mit.edu 37 1 186916023 186916023 + Silent SNP C C A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr1:186916023C>A ENST00000367466.3 + 12 1346 c.1194C>A c.(1192-1194)tcC>tcA p.S398S PLA2G4A_ENST00000442353.2_Silent_p.S338S NM_024420.2 NP_077734 P47712 PA24A_HUMAN phospholipase A2, group IVA (cytosolic, calcium-dependent) 53 Aldesleukin(DB00041)|Carbachol(DB00411)|Carbenicillin(DB00578)|Epirubicin(DB00445)|Fluocinolone Acetonide(DB00591)|Fluticasone Propionate(DB00588)|Niflumic Acid(DB04552)|Orlistat(DB01083)|Quinacrine(DB01103)|Streptokinase(DB00086)|Suramin(DB04786) GTGCCTTTTCCATATTGTTCA 0.358000 0 SO:0001819 synonymous_variant ENST00000367466.3 1 1 hg19 CCDS1372.1 TCGA-FB-A5VM-01A-11D-A32N-08 PLA2G4A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000086236.1 1 0 1 45 367 0 77 0 9.927503e-02 1 4 0 77 2 0 0 0 0 0 2 1 1.000000 44 363 0 75 2 0 0 0 0 77 2 -3.017764 1 1 0 0 1 1 2 3 2.046641 0 0.280000 1.920000 0.285998 0.790000 0.580000 1.000000 1.000000 0.803177 0.790000 0 0.680000 0.930000 B3GALT2 8707 broad.mit.edu 37 1 193149903 193149903 + Missense_Mutation SNP T T C TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr1:193149903T>C ENST00000367434.4 - 2 1545 c.790A>G c.(790-792)Aat>Gat p.N264D CDC73_ENST00000367435.3_Intron NM_003783.3 NP_003774.1 O43825 B3GT2_HUMAN UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2 16 AGTAACTTATTGATTAAATAT 0.388000 0 SO:0001583 missense ENST00000367434.4 0 1 hg19 CCDS1383.1 . . . . . . . . . . T 12.60 1.985401 0.35036 . . ENSG00000162630 ENST00000367434 T 0.42513 0.97 5.42 4.5 0.54988 . 0.104621 0.64402 D 0.000003 T 0.24470 0.0593 N 0.04297 -0.235 0.25600 N 0.98661 B 0.14012 0.009 B 0.24848 0.056 T 0.13953 -1.0490 10 0.24483 T 0.36 . 15.5666 0.76298 0.0:0.0:0.8593:0.1407 . 264 O43825 B3GT2_HUMAN D 264 ENSP00000356404:N264D ENSP00000356404:N264D N - 1 0 B3GALT2 191416526 1.000000 0.71417 1.000000 0.80357 0.979000 0.70002 2.987000 0.49378 1.266000 0.44231 -0.173000 0.13275 AAT TCGA-FB-A5VM-01A-11D-A32N-08 B3GALT2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000086759.1 0 0 0 5 227 0 44 0 0 0 1 0 44 2 0 0 0 0 0 2 1 0.936790 5 225 0 44 2 0 0 0 0 44 2 -3.472347 1 1 0 0 1 1 2 3 2.046641 0 0.280000 1.920000 0.285998 0.170000 0.060000 1.000000 0.150000 0.221094 0.170000 0 0.100000 0.270000 CSMD2 114784 broad.mit.edu 37 1 34401481 34401481 + Missense_Mutation SNP C C T TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr1:34401481C>T ENST00000373381.4 - 4 768 c.592G>A c.(592-594)Ggt>Agt p.G198S NM_001281956.1|NM_052896.3 NP_001268885.1|NP_443128.2 Q7Z408 CSMD2_HUMAN CUB and Sushi multiple domains 2 246 Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249) ACCTTGTCACCGAGGTTGAAG 0.597000 0 SO:0001583 missense ENST00000373381.4 1 1 hg19 . . . . . . . . . . C 22.8 4.337261 0.81911 . . ENSG00000121904 ENST00000373381 T 0.72394 -0.65 5.27 5.27 0.74061 Complement control module (2);Sushi/SCR/CCP (3); 0.000000 0.64402 D 0.000001 D 0.85579 0.5729 M 0.87971 2.92 0.80722 D 1 B;D 0.89917 0.241;1.0 B;D 0.65010 0.094;0.931 D 0.88169 0.2863 10 0.72032 D 0.01 . 17.8728 0.88816 0.0:1.0:0.0:0.0 . 158;198 Q7Z408;E7EUA6 CSMD2_HUMAN;. S 198 ENSP00000362479:G198S ENSP00000241312:G158S G - 1 0 CSMD2 34174068 1.000000 0.71417 0.575000 0.28536 0.940000 0.58332 7.733000 0.84916 2.439000 0.82584 0.563000 0.77884 GGT TCGA-FB-A5VM-01A-11D-A32N-08 CSMD2-201 KNOWN basic|appris_principal protein_coding protein_coding 1 0 1 66 521 0 134 0 0 0 0 134 2 0 0 0 0 0 2 1 1.000000 66 520 0 134 2 0 0 0 0 134 2 -2.559126 1 1 121412 1 30 1 1 2 3 2.059604 0 0.280000 1.920000 0.287975 0.810000 0.630000 1.000000 0.810000 0.828594 0.810000 0 0.720000 0.940000 PTPRF 5792 broad.mit.edu 37 1 44069850 44069850 + Silent SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr1:44069850G>A ENST00000359947.4 + 16 3367 c.3027G>A c.(3025-3027)ccG>ccA p.P1009P PTPRF_ENST00000438120.1_Silent_p.P1000P|PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000372414.3_Silent_p.P1009P|PTPRF_ENST00000372413.3_Silent_p.P1000P|PTPRF_ENST00000422171.2_Silent_p.P357P NM_002840.3 NP_002831.2 P10586 PTPRF_HUMAN protein tyrosine phosphatase, receptor type, F p.P999P(1) 72 all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0333) GGACCATGCCGGTGGAGCAAG 0.622000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000359947.4 0 1 hg19 CCDS489.2 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. g|g 0.011|0.011 -1.698940|-1.698940 0.00725|0.00725 .|. .|. ENSG00000142949|ENSG00000142949 ENST00000414879|ENST00000429895 .|. .|. .|. 4.92|4.92 -9.55|-9.55 0.00569|0.00569 .|. .|. .|. .|. .|. T|T 0.32164|0.32164 0.0820|0.0820 .|. .|. .|. 0.80722|0.80722 D|D 1|1 .|. .|. .|. .|. .|. .|. T|T 0.39292|0.39292 -0.9621|-0.9621 4|4 .|. .|. .|. .|. 1.4878|1.4878 0.02451|0.02451 0.3792:0.1043:0.1405:0.376|0.3792:0.1043:0.1405:0.376 .|. .|. .|. .|. S|Q 423|655 .|. .|. G|R +|+ 1|2 0|0 PTPRF|PTPRF 43842437|43842437 0.000000|0.000000 0.05858|0.05858 0.000000|0.000000 0.03702|0.03702 0.123000|0.123000 0.20343|0.20343 -3.041000|-3.041000 0.00632|0.00632 -1.978000|-1.978000 0.00993|0.00993 -4.209000|-4.209000 0.00009|0.00009 GGT|CGG TCGA-FB-A5VM-01A-11D-A32N-08 PTPRF-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000019710.1 0 0 0 5 304 0 63 0 1.782789e-01 0 39 0 63 2 0 0 0 0 0 2 1 0.935879 5 300 0 63 2 0 0 0 0 63 2 -2.985697 1 1 121406 5 39 1 1 2 3 2.059604 0 0.280000 1.920000 0.287975 0.130000 0.040000 1.000000 0.120000 0.193679 0.130000 0 0.080000 0.210000 RAD54L 8438 broad.mit.edu 37 1 46739341 46739341 + Missense_Mutation SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr1:46739341G>A ENST00000371975.4 + 14 2206 c.1532G>A c.(1531-1533)cGt>cAt p.R511H RAD54L_ENST00000442598.1_Missense_Mutation_p.R511H NM_003579.3 NP_003570.2 Q92698 RAD54_HUMAN RAD54-like (S. cerevisiae) 25 Acute lymphoblastic leukemia(166;0.155) Breast(1374;0.0634) ACCCGAAGCCGTAGCAGTGAC 0.542000 Direct reversal of damage;Homologous recombination 0 SO:0001583 missense ENST00000371975.4 0 1 hg19 CCDS532.1 . . . . . . . . . . G 15.64 2.893653 0.52121 0.0 1.16E-4 ENSG00000085999 ENST00000442598;ENST00000371975;ENST00000535499 T;T 0.75367 -0.93;-0.93 4.94 2.99 0.34606 Helicase, C-terminal (1); 0.260402 0.43260 D 0.000586 T 0.55033 0.1895 N 0.17564 0.495 0.80722 D 1 B;B 0.06786 0.001;0.001 B;B 0.08055 0.003;0.0 T 0.52328 -0.8590 10 0.45353 T 0.12 0.0048 7.8659 0.29537 0.0986:0.3489:0.5525:0.0 . 331;511 G3V1N0;Q92698 .;RAD54_HUMAN H 511;511;331 ENSP00000396113:R511H;ENSP00000361043:R511H ENSP00000361043:R511H R + 2 0 RAD54L 46511928 1.000000 0.71417 0.888000 0.34837 0.852000 0.48524 4.373000 0.59537 1.341000 0.45600 -0.259000 0.10710 CGT TCGA-FB-A5VM-01A-11D-A32N-08 RAD54L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000021272.1 0 0 0 4 159 0 23 0 3.542871e-01 0 41 0 23 2 0 0 0 0 0 2 1 0.886949 4 156 0 23 2 0 0 0 0 23 2 -3.661016 1 1 121412 6 37 1 1 2 3 2.059604 0 0.280000 1.920000 0.287975 0.200000 0.060000 1.000000 0.180000 0.266042 0.200000 0 0.120000 0.340000 LRRC40 55631 broad.mit.edu 37 1 70641617 70641617 + Missense_Mutation SNP G G C TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr1:70641617G>C ENST00000370952.3 - 7 932 c.853C>G c.(853-855)Ctt>Gtt p.L285V NM_017768.4 NP_060238.3 Q9H9A6 LRC40_HUMAN leucine rich repeat containing 40 27 AGATGTTTAAGATGTTCTGCC 0.348000 0 SO:0001583 missense ENST00000370952.3 1 1 hg19 CCDS646.1 . . . . . . . . . . G 17.28 3.350555 0.61183 . . ENSG00000066557 ENST00000370952 T 0.61510 0.1 5.46 5.46 0.80206 . 0.000000 0.85682 D 0.000000 T 0.63271 0.2497 L 0.55481 1.735 0.53688 D 0.999978 D 0.67145 0.996 D 0.65573 0.936 T 0.56056 -0.8042 10 0.22706 T 0.39 . 18.9046 0.92455 0.0:0.0:1.0:0.0 . 285 Q9H9A6 LRC40_HUMAN V 285 ENSP00000359990:L285V ENSP00000359990:L285V L - 1 0 LRRC40 70414205 1.000000 0.71417 1.000000 0.80357 0.728000 0.41692 6.021000 0.70832 2.567000 0.86603 0.585000 0.79938 CTT TCGA-FB-A5VM-01A-11D-A32N-08 LRRC40-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000025914.1 1 0 0 15 229 0 40 1 9.308925e-02 2 6 0 40 2 0 0 0 0 0 2 1 0.999871 15 225 0 40 2 0 0 0 0 40 2 -5.705470 1 1 0 0 1 1 2 3 2.059604 0 0.280000 1.920000 0.287975 0.460000 0.260000 1.000000 0.440000 0.499453 0.460000 0 0.350000 0.610000 NEGR1 257194 broad.mit.edu 37 1 71873147 71873147 + Silent SNP C C T TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr1:71873147C>T ENST00000357731.5 - 7 1286 c.1047G>A c.(1045-1047)aaG>aaA p.K349K NEGR1_ENST00000306821.3_Silent_p.K221K|ZRANB2-AS2_ENST00000590186.1_RNA|ZRANB2-AS2_ENST00000430605.1_RNA|ZRANB2-AS2_ENST00000608579.1_RNA|ZRANB2-AS2_ENST00000587306.1_RNA|ZRANB2-AS2_ENST00000585499.1_RNA|ZRANB2-AS2_ENST00000587066.1_RNA|ZRANB2-AS2_ENST00000585415.1_RNA|ZRANB2-AS2_ENST00000586006.1_RNA|NEGR1_ENST00000434200.1_Silent_p.K303K NM_173808.2 NP_776169.2 Q7Z3B1 NEGR1_HUMAN neuronal growth regulator 1 32 all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117) GAATGGCATTCTTCAGGTAGA 0.428000 0 SO:0001819 synonymous_variant ENST00000357731.5 1 1 hg19 CCDS661.1 TCGA-FB-A5VM-01A-11D-A32N-08 NEGR1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000026722.4 1 0 1 30 176 0 33 0 6.128608e-02 0 3 0 33 2 0 0 0 0 0 2 1 1.000000 29 174 0 32 2 0 0 0 0 33 2 -20.000000 1 1 0 0 1 1 2 3 2.059604 0 0.280000 1.920000 0.287975 0.990000 0.740000 1.000000 1.000000 0.961030 0.990000 1 0.890000 1.000000 CASS4 57091 broad.mit.edu 37 20 55012332 55012332 + Missense_Mutation SNP G G T TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr20:55012332G>T ENST00000360314.3 + 3 374 c.149G>T c.(148-150)gGt>gTt p.G50V CASS4_ENST00000371336.3_Missense_Mutation_p.G50V|CASS4_ENST00000434344.1_Missense_Mutation_p.G50V NM_001164116.1 NP_001157588.1 Q9NQ75 CASS4_HUMAN Cas scaffolding protein family member 4 54 GAAAGCGAGGGTTGGTGGAAG 0.602000 0 SO:0001583 missense ENST00000360314.3 1 1 hg19 CCDS33492.1 . . . . . . . . . . G 22.3 4.274043 0.80580 . . ENSG00000087589 ENST00000360314;ENST00000371336;ENST00000434344 T;T;T 0.74737 -0.87;-0.87;-0.87 5.71 5.71 0.89125 Src homology-3 domain (4); 0.051653 0.85682 D 0.000000 D 0.91586 0.7342 H 0.96604 3.85 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.97110 1.0;0.998;0.999;0.999 D 0.93821 0.7119 10 0.87932 D 0 -42.9102 19.8625 0.96789 0.0:0.0:1.0:0.0 . 50;50;50;50 B4DII4;Q9NQ75-3;Q9NQ75-2;Q9NQ75 .;.;.;CASS4_HUMAN V 50 ENSP00000353462:G50V;ENSP00000360387:G50V;ENSP00000410027:G50V ENSP00000353462:G50V G + 2 0 CASS4 54445739 1.000000 0.71417 1.000000 0.80357 0.701000 0.40568 7.431000 0.80335 2.689000 0.91719 0.655000 0.94253 GGT TCGA-FB-A5VM-01A-11D-A32N-08 CASS4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000079789.2 1 0 0 44 408 0 75 0 0 0 0 75 2 0 0 0 0 0 2 1 1.000000 44 406 0 73 2 0 0 0 0 75 2 -20.000000 1 1 0 0 1 1 2 3 2.320304 1 0.280000 1.920000 0.368421 0.790000 0.580000 1.000000 1.000000 0.801303 0.790000 0 0.680000 0.910000 ZBP1 81030 broad.mit.edu 37 20 56186849 56186849 + Missense_Mutation SNP T T G TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr20:56186849T>G ENST00000371173.3 - 6 985 c.808A>C c.(808-810)Aat>Cat p.N270H ZBP1_ENST00000340462.4_Missense_Mutation_p.N247H|ZBP1_ENST00000343535.4_Missense_Mutation_p.N270H|ZBP1_ENST00000395822.3_Missense_Mutation_p.N195H NM_001160417.1|NM_030776.2 NP_001153889.1|NP_110403.2 Q9H171 ZBP1_HUMAN Z-DNA binding protein 1 27 Lung NSC(12;0.000545)|all_lung(29;0.00195)|Melanoma(10;0.242) BRCA - Breast invasive adenocarcinoma(13;7.87e-13)|Epithelial(14;3.26e-09)|all cancers(14;3.62e-08) CTCATCTCATTGCTGTGTCCC 0.632000 0 SO:0001583 missense ENST00000371173.3 1 1 hg19 CCDS13461.1 . . . . . . . . . . T 13.37 2.216027 0.39201 . . ENSG00000124256 ENST00000371173;ENST00000395822;ENST00000340462;ENST00000357677;ENST00000343535 T;T;T;T 0.23348 2.29;1.91;2.29;2.26 3.25 2.09 0.27110 . 0.365705 0.19940 N 0.102675 T 0.38904 0.1058 L 0.52573 1.65 0.09310 N 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.91635 0.999;0.999;0.999 T 0.07233 -1.0783 10 0.87932 D 0 -23.1631 6.3696 0.21473 0.0:0.0:0.2548:0.7452 . 270;195;270 A2RRL9;A2A2F7;Q9H171 .;.;ZBP1_HUMAN H 270;195;247;270;270 ENSP00000360215:N270H;ENSP00000379167:N195H;ENSP00000344954:N247H;ENSP00000340584:N270H ENSP00000344954:N247H N - 1 0 ZBP1 55620255 0.552000 0.26505 0.002000 0.10522 0.036000 0.12997 1.422000 0.34826 0.592000 0.29728 0.454000 0.30748 AAT TCGA-FB-A5VM-01A-11D-A32N-08 ZBP1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000079849.1 1 0 1 16 113 0 27 0 2.296670e-01 1 6 0 27 2 0 0 0 0 0 2 1 0.999943 16 110 0 27 2 0 0 0 0 27 2 -20.000000 1 1 0 0 1 1 2 3 2.320304 1 0.280000 1.920000 0.368421 0.990000 0.620000 1.000000 1.000000 0.927307 0.990000 1 0.800000 1.000000 LRRN4 164312 broad.mit.edu 37 20 6021941 6021941 + Silent SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr20:6021941G>A ENST00000378858.4 - 5 2174 c.1950C>T c.(1948-1950)tgC>tgT p.C650C NM_152611.4 NP_689824.2 Q8WUT4 LRRN4_HUMAN leucine rich repeat neuronal 4 27 CCGCCAGCACGCACACGCGGT 0.721000 0 SO:0001819 synonymous_variant ENST00000378858.4 0 1 hg19 CCDS13097.1 TCGA-FB-A5VM-01A-11D-A32N-08 LRRN4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000077907.2 0 0 0 4 184 0 40 0 0 0 1 0 40 2 0 0 0 0 0 2 1 0.888735 4 182 0 39 2 0 0 0 0 40 2 -6.023351 1 1 119864 1 26 1 1 2 3 2.046593 0 0.280000 1.920000 0.285998 0.170000 0.050000 1.000000 0.150000 0.225224 0.170000 0 0.100000 0.290000 LAMA5 3911 broad.mit.edu 37 20 60921843 60921843 + Silent SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr20:60921843G>A ENST00000252999.3 - 8 1152 c.1086C>T c.(1084-1086)taC>taT p.Y362Y LAMA5_ENST00000370692.3_Silent_p.Y362Y|LAMA5_ENST00000370677.3_Silent_p.Y362Y NM_005560.3 NP_005551.3 O15230 LAMA5_HUMAN laminin, alpha 5 81 Breast(26;1.57e-08) BRCA - Breast invasive adenocarcinoma(19;4.36e-06) TGGCATGGCCGTAGCAGTTAC 0.667000 0 SO:0001819 synonymous_variant ENST00000252999.3 0 1 hg19 CCDS33502.1 TCGA-FB-A5VM-01A-11D-A32N-08 LAMA5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000080014.2 0 0 0 4 143 0 34 0 0 0 0 34 2 0 0 0 0 0 2 1 0.889833 4 142 0 32 2 0 0 0 0 34 2 -6.333987 1 1 120876 1 25 1 1 2 3 2.320304 1 0.280000 1.920000 0.368421 0.240000 0.080000 0.520000 0.210000 0.270078 0.240000 0 0.140000 0.380000 SUMO3 6612 broad.mit.edu 37 21 46229016 46229016 + Silent SNP C C T TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr21:46229016C>T ENST00000397898.3 - 3 250 c.168G>A c.(166-168)caG>caA p.Q56Q SUMO3_ENST00000411651.2_Silent_p.Q94Q|SUMO3_ENST00000479153.1_5'UTR|SUMO3_ENST00000332859.6_Silent_p.Q56Q|SUMO3_ENST00000397893.3_Silent_p.Q56Q small ubiquitin-like modifier 3 1 TGAATCTGATCTGCCTCATTG 0.532000 0 SO:0001819 synonymous_variant ENST00000397898.3 1 1 hg19 TCGA-FB-A5VM-01A-11D-A32N-08 SUMO3-002 NOVEL basic|exp_conf protein_coding protein_coding OTTHUMT00000206561.1 1 0 1 31 217 0 59 1 1 119 278 0 59 2 0 0 0 0 0 2 1 1.000000 29 212 0 58 2 0 0 0 0 59 2 -14.372590 1 1 0 0 1 1 2 3 2.039265 0 0.280000 1.920000 0.284010 0.900000 0.630000 1.000000 1.000000 0.886855 0.900000 1 0.750000 1.000000 TNRC6B 23112 broad.mit.edu 37 22 40662850 40662850 + Silent SNP C C T TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr22:40662850C>T ENST00000454349.2 + 5 2827 c.2616C>T c.(2614-2616)ccC>ccT p.P872P TNRC6B_ENST00000402203.1_Intron|TNRC6B_ENST00000335727.9_Silent_p.P872P|TNRC6B_ENST00000301923.9_Intron NM_001162501.1 NP_001155973.1 Q9UPQ9 TNR6B_HUMAN trinucleotide repeat containing 6B 1 ATGAGGAACCCAGTGGTTGGG 0.552000 0 SO:0001819 synonymous_variant ENST00000454349.2 1 1 hg19 CCDS54533.1 . . . . . . . . . . C 9.556 1.117318 0.20795 . . ENSG00000100354 ENST00000446273 T 0.24538 1.85 5.46 5.46 0.80206 . 0.052766 0.85682 D 0.000000 T 0.34919 0.0914 . . . 0.80722 D 1 . . . . . . T 0.16217 -1.0410 7 0.72032 D 0.01 -4.2812 6.4872 0.22095 0.3133:0.6:0.0:0.0866 . . . . L 615 ENSP00000409429:P615L ENSP00000409429:P615L P + 2 0 TNRC6B 38992796 0.993000 0.37304 1.000000 0.80357 0.998000 0.95712 0.325000 0.19628 2.561000 0.86390 0.561000 0.74099 CCA TCGA-FB-A5VM-01A-11D-A32N-08 TNRC6B-202 KNOWN basic|CCDS protein_coding protein_coding 1 0 1 27 135 0 30 0 0 0 0 30 2 0 0 0 0 0 2 1 1.000000 27 135 0 30 2 0 0 0 0 30 2 -3.393926 1 1 0 0 1 1 2 3 2.067918 0 0.280000 1.920000 0.289941 0.990000 0.830000 1.000000 1.000000 0.987568 0.990000 1 0.990000 1.000000 ACOXL 55289 broad.mit.edu 37 2 111556628 111556628 + Silent SNP C C T TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr2:111556628C>T ENST00000389811.4 + 7 722 c.498C>T c.(496-498)aaC>aaT p.N166N ACOXL_ENST00000340561.4_Silent_p.N166N|ACOXL_ENST00000439055.1_Silent_p.N166N Q9NUZ1 ACOXL_HUMAN acyl-CoA oxidase-like 21 GGGATGAAAACGGAAGCTTGT 0.502000 0 SO:0001819 synonymous_variant ENST00000389811.4 1 1 hg19 . . . . . . . . . . C 8.179 0.793474 0.16327 0.0 1.16E-4 ENSG00000153093 ENST00000422487 . . . 5.35 -10.7 0.00240 . . . . . T 0.61085 0.2319 . . . 0.45662 D 0.998582 . . . . . . T 0.77075 -0.2722 5 0.87932 D 0 -22.6667 9.5339 0.39211 0.0906:0.5713:0.0924:0.2458 . . . . M 18 . ENSP00000404255:T18M T + 2 0 ACOXL 111273099 0.078000 0.21339 0.094000 0.20943 0.932000 0.56968 -1.471000 0.02344 -2.880000 0.00319 -0.961000 0.02630 ACG TCGA-FB-A5VM-01A-11D-A32N-08 ACOXL-001 NOVEL basic|appris_principal protein_coding protein_coding OTTHUMT00000254024.2 0 0 0 71 455 1 106 1 1.874666e-02 2 0 1 106 2 0 0 0 0 0 2 1 1.000000 71 451 1 105 17 0 0 0 1 106 2 -7.257158 1 1 121412 28 48 1 1 2 3 2.033904 0 0.280000 1.920000 0.284010 0.970000 0.770000 1.000000 1.000000 0.944940 0.970000 1 0.860000 1.000000 GPD2 2820 broad.mit.edu 37 2 157435503 157435503 + Missense_Mutation SNP G G T TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr2:157435503G>T ENST00000310454.6 + 14 2242 c.1870G>T c.(1870-1872)Gac>Tac p.D624Y GPD2_ENST00000438166.2_Missense_Mutation_p.D624Y|GPD2_ENST00000409674.1_Missense_Mutation_p.D624Y|GPD2_ENST00000540309.1_Intron|GPD2_ENST00000409125.4_Missense_Mutation_p.D397Y NM_001083112.2 NP_001076581.2 P43304 GPDM_HUMAN glycerol-3-phosphate dehydrogenase 2 (mitochondrial) 22 ACTGCCTTCAGACATTGACAG 0.333000 0 SO:0001583 missense ENST00000310454.6 1 1 hg19 CCDS2202.1 . . . . . . . . . . G 25.7 4.669779 0.88348 . . ENSG00000115159 ENST00000310454;ENST00000409125;ENST00000438166;ENST00000409674 T;T;T;T 0.63913 -0.07;-0.07;-0.07;-0.07 5.79 5.79 0.91817 EF-hand-like domain (1); 0.042575 0.85682 D 0.000000 T 0.70876 0.3274 M 0.68593 2.085 0.80722 D 1 P 0.40398 0.716 P 0.45946 0.498 T 0.73212 -0.4054 10 0.87932 D 0 . 20.0308 0.97536 0.0:0.0:1.0:0.0 . 624 P43304 GPDM_HUMAN Y 624;397;624;624 ENSP00000308610:D624Y;ENSP00000386484:D397Y;ENSP00000409708:D624Y;ENSP00000386425:D624Y ENSP00000308610:D624Y D + 1 0 GPD2 157143749 1.000000 0.71417 1.000000 0.80357 0.992000 0.81027 9.845000 0.99498 2.732000 0.93576 0.585000 0.79938 GAC TCGA-FB-A5VM-01A-11D-A32N-08 GPD2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254910.3 1 0 0 35 400 0 94 1 1.375752e-01 2 6 0 94 2 0 0 0 0 0 2 1 1.000000 35 398 0 94 2 0 0 0 0 94 2 -10.278150 1 1 0 0 1 1 2 3 2.033904 0 0.280000 1.920000 0.284010 0.580000 0.410000 1.000000 0.570000 0.600148 0.580000 0 0.490000 0.690000 SCN3A 6328 broad.mit.edu 37 2 165953881 165953881 + Missense_Mutation SNP C C A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr2:165953881C>A ENST00000360093.3 - 23 4611 c.4120G>T c.(4120-4122)Gac>Tac p.D1374Y SCN3A_ENST00000283254.7_Missense_Mutation_p.D1374Y|SCN3A_ENST00000409101.3_Missense_Mutation_p.D1325Y NM_001081677.1 NP_001075146.1 Q9NY46 SCN3A_HUMAN sodium channel, voltage-gated, type III, alpha subunit 120 Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909) TCACTAATGTCAAACATGTTA 0.423000 0 SO:0001583 missense ENST00000360093.3 1 1 hg19 . . . . . . . . . . C 15.01 2.705927 0.48412 . . ENSG00000153253 ENST00000360093;ENST00000283254;ENST00000409101;ENST00000440431 D;D;D;D 0.96522 -4.04;-4.04;-3.98;-3.8 5.72 1.94 0.25998 Ion transport (1); 0.992515 0.08199 N 0.982552 D 0.97470 0.9172 M 0.80332 2.49 0.80722 D 1 P;P;B;B;P 0.41910 0.764;0.642;0.25;0.25;0.722 P;B;B;B;P 0.58130 0.833;0.353;0.173;0.173;0.743 D 0.92897 0.6336 10 0.72032 D 0.01 . 6.9439 0.24508 0.0:0.6271:0.1154:0.2575 . 1374;1325;1325;1325;1374 Q9NY46;E7EUE6;Q9NY46-2;Q9NY46-4;Q9NY46-3 SCN3A_HUMAN;.;.;.;. Y 1374;1374;1325;1325 ENSP00000353206:D1374Y;ENSP00000283254:D1374Y;ENSP00000386726:D1325Y;ENSP00000403348:D1325Y ENSP00000283254:D1374Y D - 1 0 SCN3A 165662127 1.000000 0.71417 0.488000 0.27440 0.504000 0.33889 1.422000 0.34826 0.149000 0.19098 -0.812000 0.03155 GAC TCGA-FB-A5VM-01A-11D-A32N-08 SCN3A-201 KNOWN basic|appris_candidate_longest protein_coding protein_coding 1 0 1 39 247 0 51 0 0 0 0 51 2 0 0 0 0 0 2 1 1.000000 38 242 0 51 2 0 0 0 0 51 2 -17.805170 1 1 0 0 1 1 2 3 2.033904 0 0.280000 1.920000 0.284010 0.980000 0.710000 1.000000 1.000000 0.938172 0.980000 1 0.840000 1.000000 AMOTL2 51421 broad.mit.edu 37 3 134090033 134090033 + Silent SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr3:134090033G>A ENST00000422605.2 - 2 409 c.243C>T c.(241-243)ggC>ggT p.G81G AMOTL2_ENST00000511759.1_5'UTR|AMOTL2_ENST00000514516.1_Silent_p.G139G|AMOTL2_ENST00000513145.1_Silent_p.G81G|AMOTL2_ENST00000249883.5_Silent_p.G81G Q9Y2J4 AMOL2_HUMAN angiomotin like 2 19 GGTTCTCACCGCCCTGGTGCT 0.677000 0 SO:0001819 synonymous_variant ENST00000422605.2 0 1 hg19 TCGA-FB-A5VM-01A-11D-A32N-08 AMOTL2-014 KNOWN basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000358149.1 0 0 0 4 258 0 45 0 1.081150e-02 0 8 0 45 2 0 0 0 0 0 2 1 0.890180 4 257 0 45 2 0 0 0 0 45 2 -5.022657 1 1 121408 1 27 1 1 2 3 2.319513 1 0.280000 1.920000 0.368421 0.130000 0.040000 0.300000 0.120000 0.153189 0.130000 0 0.080000 0.220000 TRIM42 287015 broad.mit.edu 37 3 140401600 140401600 + Missense_Mutation SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 G A G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr3:140401600G>A ENST00000286349.3 + 2 829 c.638G>A c.(637-639)cGt>cAt p.R213H NM_152616.4 NP_689829.3 Q8IWZ5 TRI42_HUMAN tripartite motif containing 42 p.R213H(1) 69 CTGCACGGGCGTCTCACCAAG 0.612000 1 Substitution - Missense(1) SO:0001583 missense ENST00000286349.3 1 1 hg19 CCDS3113.1 . . . . . . . . . . G 21.9 4.215216 0.79352 . . ENSG00000155890 ENST00000286349 T 0.38722 1.12 5.2 4.32 0.51571 Zinc finger, RING/FYVE/PHD-type (1); 0.117429 0.35349 N 0.003274 T 0.46347 0.1388 L 0.52905 1.665 0.30123 N 0.805474 D 0.71674 0.998 P 0.54140 0.743 T 0.45366 -0.9266 10 0.35671 T 0.21 -16.8257 8.6972 0.34303 0.1016:0.0:0.8984:0.0 . 213 Q8IWZ5 TRI42_HUMAN H 213 ENSP00000286349:R213H ENSP00000286349:R213H R + 2 0 TRIM42 141884290 1.000000 0.71417 0.999000 0.59377 0.973000 0.67179 2.158000 0.42329 2.435000 0.82474 0.561000 0.74099 CGT TCGA-FB-A5VM-01A-11D-A32N-08 TRIM42-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000359531.2 1 0 1 76 569 0 91 0 0 0 0 91 2 1 1 97 639 1 634 6 1 1.000000 76 566 0 91 2 0 0 0 0 91 2 -20.000000 1 1 0 0 1 1 2 3 2.319513 1 0.280000 1.920000 0.368421 0.950000 0.760000 1.000000 1.000000 0.939293 0.950000 1 0.850000 1.000000 SPATA16 83893 broad.mit.edu 37 3 172643179 172643179 + Missense_Mutation SNP T T G TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr3:172643179T>G ENST00000351008.3 - 7 1368 c.1185A>C c.(1183-1185)aaA>aaC p.K395N NM_031955.5 NP_114161.3 Q9BXB7 SPT16_HUMAN spermatogenesis associated 16 43 Ovarian(172;0.00319)|Breast(254;0.197) LUSC - Lung squamous cell carcinoma(14;1.48e-14)|Lung(28;6.63e-14) TTTCCAAAAATTTTCCATCAT 0.408000 0 SO:0001583 missense ENST00000351008.3 1 0 hg19 CCDS3221.1 . . . . . . . . . . T 16.94 3.261858 0.59431 . . ENSG00000144962 ENST00000351008 T 0.24350 1.86 5.3 1.47 0.22746 . 0.075584 0.56097 D 0.000029 T 0.28234 0.0697 L 0.32530 0.975 0.27421 N 0.954285 D 0.54964 0.969 P 0.55455 0.776 T 0.09079 -1.0691 10 0.72032 D 0.01 -12.8705 8.3366 0.32219 0.0:0.2297:0.0:0.7703 . 395 Q9BXB7 SPT16_HUMAN N 395 ENSP00000341765:K395N ENSP00000341765:K395N K - 3 2 SPATA16 174125873 1.000000 0.71417 0.985000 0.45067 0.788000 0.44548 0.492000 0.22435 0.059000 0.16252 -0.371000 0.07208 AAA TCGA-FB-A5VM-01A-11D-A32N-08 SPATA16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000346322.1 1 0 1 26 204 0 41 0 0 0 0 41 2 0 0 0 0 0 2 1 1.000000 26 201 0 40 2 0 0 0 0 41 2 -11.834820 1 1 0 0 1 1 2 3 2.319513 1 0.280000 1.920000 0.368421 0.920000 0.620000 1.000000 1.000000 0.897307 0.920000 1 0.760000 1.000000 OR5K3 403277 broad.mit.edu 37 3 98109887 98109887 + Missense_Mutation SNP A A G TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr3:98109887A>G ENST00000383695.1 + 1 378 c.378A>G c.(376-378)atA>atG p.I126M RP11-325B23.2_ENST00000508616.1_lincRNA NM_001005516.1 NP_001005516.1 A6NET4 OR5K3_HUMAN olfactory receptor, family 5, subfamily K, member 3 27 ATGTGGCCATATGCAACCCAC 0.478000 0 SO:0001583 missense ENST00000383695.1 1 1 hg19 CCDS33803.1 . . . . . . . . . . A 16.20 3.056919 0.55325 . . ENSG00000206536 ENST00000383695 T 0.59083 0.29 5.15 -2.93 0.05598 GPCR, rhodopsin-like superfamily (1); 0.331813 0.21303 N 0.076767 T 0.80082 0.4558 H 0.98238 4.18 0.25262 N 0.98958 D 0.89917 1.0 D 0.97110 1.0 T 0.70894 -0.4748 10 0.87932 D 0 -61.4606 8.1546 0.31160 0.2367:0.5363:0.0:0.2271 . 126 A6NET4 OR5K3_HUMAN M 126 ENSP00000373194:I126M ENSP00000373194:I126M I + 3 3 OR5K3 99592577 0.004000 0.15560 0.808000 0.32385 0.947000 0.59692 -1.359000 0.02602 -0.708000 0.05015 0.491000 0.48974 ATA TCGA-FB-A5VM-01A-11D-A32N-08 OR5K3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000359110.1 1 0 1 144 500 0 94 0 0 0 0 94 2 0 0 0 0 0 2 1 1.000000 144 495 0 92 2 0 0 0 0 94 2 -20.000000 1 1 121412 5 41 1 1 2 3 2.319513 1 0.280000 1.920000 0.368421 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 KIAA0922 23240 broad.mit.edu 37 4 154542991 154542991 + Missense_Mutation SNP G G T TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr4:154542991G>T ENST00000409663.3 + 28 3898 c.3846G>T c.(3844-3846)caG>caT p.Q1282H KIAA0922_ENST00000440693.1_Missense_Mutation_p.Q1199H|KIAA0922_ENST00000409959.3_Missense_Mutation_p.Q1283H NM_015196.3 NP_056011.3 A2VDJ0 T131L_HUMAN KIAA0922 63 all_hematologic(180;0.093) Renal(120;0.118) CTGCTGCCCAGAGAGAGGCAG 0.423000 0 SO:0001583 missense ENST00000409663.3 1 1 hg19 CCDS3783.2 . . . . . . . . . . G 10.72 1.431059 0.25726 . . ENSG00000121210 ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487 T;T;T;T 0.19394 2.42;2.15;2.42;2.15 5.16 3.08 0.35506 . 0.507289 0.20653 N 0.088171 T 0.28962 0.0719 L 0.43152 1.355 0.24200 N 0.995515 D;P;P 0.71674 0.998;0.925;0.877 P;P;P 0.62560 0.904;0.667;0.467 T 0.04053 -1.0981 10 0.31617 T 0.26 -3.8639 7.293 0.26376 0.1656:0.0:0.6948:0.1396 . 1199;1283;1282 A2VDJ0-3;A2VDJ0-5;A2VDJ0 .;.;T131L_HUMAN H 1282;1199;1283;1060 ENSP00000386574:Q1282H;ENSP00000409663:Q1199H;ENSP00000386787:Q1283H;ENSP00000240487:Q1060H ENSP00000240487:Q1060H Q + 3 2 KIAA0922 154762441 1.000000 0.71417 0.947000 0.38551 0.251000 0.25915 1.834000 0.39171 1.173000 0.42796 0.655000 0.94253 CAG TCGA-FB-A5VM-01A-11D-A32N-08 KIAA0922-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000330370.1 1 0 1 21 156 0 38 1 7.546089e-01 4 18 0 38 2 0 0 0 0 0 2 1 0.999998 21 154 0 38 2 0 0 0 0 38 2 -20.000000 1 1 0 0 1 0 1 1 1.796882 1 0.280000 1.920000 0.174880 0.720000 0.470000 1.000000 1.000000 0.737916 0.720000 0 0.590000 0.880000 GABRB1 2560 broad.mit.edu 37 4 47163392 47163392 + Missense_Mutation SNP T T C TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr4:47163392T>C ENST00000295454.3 + 4 659 c.367T>C c.(367-369)Ttt>Ctt p.F123L GABRB1_ENST00000538619.1_Missense_Mutation_p.F53L NM_000812.3 NP_000803.2 P18505 GBRB1_HUMAN gamma-aminobutyric acid (GABA) A receptor, beta 1 44 Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Gamma Hydroxybutyric Acid(DB01440)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lindane(DB00431)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897) AGACACCTACTTTCTGAATGA 0.443000 0 SO:0001583 missense ENST00000295454.3 1 1 hg19 CCDS3474.1 . . . . . . . . . . T 26.5 4.740563 0.89573 . . ENSG00000163288 ENST00000513567;ENST00000295454;ENST00000538619 T;T;T 0.73363 -0.74;-0.74;-0.74 5.01 5.01 0.66863 Neurotransmitter-gated ion-channel ligand-binding (3); 0.000000 0.64402 D 0.000001 D 0.86163 0.5867 M 0.82193 2.58 0.58432 D 0.999997 D;D 0.62365 0.991;0.979 P;D 0.74023 0.86;0.982 D 0.87603 0.2498 10 0.54805 T 0.06 -13.1774 14.0523 0.64745 0.0:0.0:0.0:1.0 . 53;123 F5GXV5;P18505 .;GBRB1_HUMAN L 90;123;53 ENSP00000426753:F90L;ENSP00000295454:F123L;ENSP00000440330:F53L ENSP00000295454:F123L F + 1 0 GABRB1 46858149 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.868000 0.87116 2.109000 0.64355 0.528000 0.53228 TTT TCGA-FB-A5VM-01A-11D-A32N-08 GABRB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000216896.1 1 0 1 71 501 0 124 0 0 0 1 0 124 2 0 0 0 0 0 2 1 1.000000 70 497 0 123 2 0 0 0 0 124 2 -20.000000 1 1 0 0 1 1 2 3 2.032823 0 0.280000 1.920000 0.282010 0.880000 0.700000 1.000000 1.000000 0.887677 0.880000 1 0.790000 1.000000 LRRC66 339977 broad.mit.edu 37 4 52860732 52860732 + Missense_Mutation SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr4:52860732G>A ENST00000343457.3 - 4 2462 c.2456C>T c.(2455-2457)cCg>cTg p.P819L NM_001024611.1 NP_001019782.1 Q68CR7 LRC66_HUMAN leucine rich repeat containing 66 58 GAACATGCCCGGAAACTCATC 0.463000 0 SO:0001583 missense ENST00000343457.3 0 1 hg19 CCDS43229.1 . . . . . . . . . . G 1.908 -0.451422 0.04572 . . ENSG00000188993 ENST00000343457 T 0.33216 1.42 4.67 1.01 0.19927 . 0.968471 0.08482 N 0.939308 T 0.17066 0.0410 N 0.16656 0.425 0.09310 N 1 B 0.20550 0.046 B 0.13407 0.009 T 0.33163 -0.9879 10 0.18276 T 0.48 -0.8776 7.5126 0.27583 0.3337:0.0:0.6663:0.0 . 819 Q68CR7 LRC66_HUMAN L 819 ENSP00000341944:P819L ENSP00000341944:P819L P - 2 0 LRRC66 52555489 0.001000 0.12720 0.000000 0.03702 0.000000 0.00434 0.670000 0.25157 0.038000 0.15604 -1.556000 0.00890 CCG TCGA-FB-A5VM-01A-11D-A32N-08 LRRC66-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000361473.1 0 0 0 5 254 0 40 0 0 0 0 40 2 0 0 0 0 0 2 1 0.938138 5 254 0 40 2 0 0 0 0 40 2 -2.719341 1 1 120832 168 51 1 1 2 3 2.032823 0 0.280000 1.920000 0.282010 0.150000 0.050000 0.340000 0.140000 0.171248 0.150000 0 0.090000 0.230000 EVC 2121 broad.mit.edu 37 4 5798842 5798842 + Silent SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr4:5798842G>A ENST00000264956.6 + 14 2164 c.1980G>A c.(1978-1980)acG>acA p.T660T EVC_ENST00000515113.1_3'UTR|EVC_ENST00000382674.2_Silent_p.T660T NM_153717.2 NP_714928.1 P57679 EVC_HUMAN Ellis van Creveld syndrome 28 Myeloproliferative disorder(84;0.117) CCACCCTGACGCAGATGCGGC 0.672000 0 SO:0001819 synonymous_variant ENST00000264956.6 1 1 hg19 CCDS3383.1 TCGA-FB-A5VM-01A-11D-A32N-08 EVC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000206859.1 1 0 1 41 258 0 55 0 0 0 0 55 2 0 0 0 0 0 2 1 1.000000 41 257 0 55 2 0 0 0 0 55 2 -20.000000 1 1 121382 6 35 1 1 2 3 2.032823 0 0.280000 1.920000 0.282010 0.980000 0.720000 1.000000 1.000000 0.939380 0.980000 1 0.840000 1.000000 MTHFD2L 441024 broad.mit.edu 37 4 75041057 75041057 + Missense_Mutation SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr4:75041057G>A ENST00000395759.2 + 3 415 c.388G>A c.(388-390)Gta>Ata p.V130I MTHFD2L_ENST00000331145.6_Missense_Mutation_p.V72I|MTHFD2L_ENST00000325278.6_Missense_Mutation_p.V72I|MTHFD2L_ENST00000433372.1_5'UTR NM_001144978.1 NP_001138450.1 Q9H903 MTD2L_HUMAN methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like 8 all cancers(17;0.0101)|Lung(101;0.196) ACTTTTGGACGTAACTGATCA 0.368000 0 SO:0001583 missense ENST00000395759.2 0 1 hg19 CCDS47075.1 . . . . . . . . . . A 7.970 0.748962 0.15710 . . ENSG00000163738 ENST00000395759;ENST00000331145;ENST00000359107;ENST00000325278 T;T;T;T 0.29917 1.97;1.56;1.55;1.98 5.36 5.36 0.76844 Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain (1);NAD(P)-binding domain (1); 0.213853 0.50627 N 0.000109 T 0.16642 0.0400 N 0.16201 0.385 0.80722 D 1 B;B 0.06786 0.001;0.001 B;B 0.09377 0.004;0.001 T 0.08973 -1.0696 10 0.28530 T 0.3 -29.7782 6.9337 0.24455 0.8268:0.0:0.1732:0.0 . 130;72 Q9H903;Q9H903-3 MTD2L_HUMAN;. I 130;72;72;72 ENSP00000379108:V130I;ENSP00000330982:V72I;ENSP00000352012:V72I;ENSP00000321984:V72I ENSP00000321984:V72I V + 1 0 MTHFD2L 75259921 0.039000 0.19947 0.997000 0.53966 0.849000 0.48306 0.068000 0.14531 1.067000 0.40740 -0.268000 0.10319 GTA TCGA-FB-A5VM-01A-11D-A32N-08 MTHFD2L-202 KNOWN basic|appris_principal|CCDS protein_coding protein_coding 0 0 0 5 303 0 65 0 0 0 1 0 65 2 0 0 0 0 0 2 1 0.938036 5 303 0 63 2 0 0 0 0 65 2 -2.818194 1 1 121402 3 37 1 1 2 3 2.032823 0 0.280000 1.920000 0.282010 0.120000 0.040000 0.280000 0.120000 0.145941 0.120000 0 0.070000 0.190000 IBSP 3381 broad.mit.edu 37 4 88732603 88732603 + Silent SNP C C T TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr4:88732603C>T ENST00000226284.5 + 7 562 c.495C>T c.(493-495)agC>agT p.S165S NM_004967.3 NP_004958.2 P21815 SIAL_HUMAN integrin-binding sialoprotein p.S165S(1) 21 Hepatocellular(203;0.114) acgaagaaagcgaagcagaag 0.458000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000226284.5 1 1 hg19 CCDS3624.1 TCGA-FB-A5VM-01A-11D-A32N-08 IBSP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253050.2 1 0 0 17 105 0 25 0 1.046122e-01 0 4 0 25 2 0 0 0 0 0 2 1 0.999968 16 102 0 25 2 0 0 0 0 25 2 -10.221070 1 1 0 0 1 1 2 3 2.032823 0 0.280000 1.920000 0.282010 0.990000 0.620000 1.000000 1.000000 0.922257 0.990000 1 0.790000 1.000000 KLHL3 26249 broad.mit.edu 37 5 136997650 136997650 + Missense_Mutation SNP A A G TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr5:136997650A>G ENST00000309755.4 - 7 1150 c.707T>C c.(706-708)aTg>aCg p.M236T KLHL3_ENST00000508657.1_Missense_Mutation_p.M204T|KLHL3_ENST00000541417.1_Missense_Mutation_p.M116T|KLHL3_ENST00000394937.3_Missense_Mutation_p.M236T|KLHL3_ENST00000506873.1_5'UTR|KLHL3_ENST00000506491.1_Missense_Mutation_p.M154T NM_017415.2 NP_059111.2 Q9UH77 KLHL3_HUMAN kelch-like family member 3 21 all_hematologic(541;3.67e-07)|Breast(839;7.61e-05)|Prostate(281;0.000825)|Ovarian(839;0.0481)|all_lung(232;0.198) KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233) GACATGTTCCATCAGCTTTGC 0.443000 0 SO:0001583 missense ENST00000309755.4 1 1 hg19 CCDS4192.1 . . . . . . . . . . A 22.8 4.343183 0.82022 . . ENSG00000146021 ENST00000506491;ENST00000508657;ENST00000309755;ENST00000541417;ENST00000505853;ENST00000394937 T;T;T;T;T;T 0.70164 -0.46;-0.46;-0.46;-0.46;-0.46;-0.46 4.99 4.99 0.66335 BTB/Kelch-associated (2); 0.000000 0.85682 D 0.000000 D 0.84037 0.5384 M 0.90650 3.135 0.80722 D 1 P;D;P;D;D 0.67145 0.858;0.996;0.848;0.996;0.976 B;D;P;D;D 0.68621 0.412;0.944;0.511;0.959;0.932 D 0.87765 0.2601 10 0.87932 D 0 . 15.1492 0.72684 1.0:0.0:0.0:0.0 . 5;196;204;236;236 B7Z6E2;D6RH21;Q9UH77-2;Q9UH77;Q8N4I8 .;.;.;KLHL3_HUMAN;. T 154;204;236;116;196;236 ENSP00000424828:M154T;ENSP00000422099:M204T;ENSP00000312397:M236T;ENSP00000440319:M116T;ENSP00000426173:M196T;ENSP00000378395:M236T ENSP00000312397:M236T M - 2 0 KLHL3 137025549 1.000000 0.71417 1.000000 0.80357 0.995000 0.86356 9.036000 0.93758 2.234000 0.73211 0.533000 0.62120 ATG TCGA-FB-A5VM-01A-11D-A32N-08 KLHL3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251220.2 1 0 1 46 214 0 54 0 0 0 0 54 2 0 0 0 0 0 2 1 1.000000 46 212 0 54 2 0 0 0 0 54 2 -20.000000 1 1 0 0 1 0 1 1 1.750197 1 0.280000 1.920000 0.162791 0.930000 0.750000 1.000000 0.990000 0.920271 0.930000 1 0.840000 0.980000 FAM105A 54491 broad.mit.edu 37 5 14610393 14610393 + Silent SNP C C T TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr5:14610393C>T ENST00000274217.3 + 8 1161 c.1041C>T c.(1039-1041)aaC>aaT p.N347N NM_019018.2 NP_061891.1 Q9NUU6 F105A_HUMAN family with sequence similarity 105, member A p.N347N(1) 11 Lung NSC(4;0.00592) TGACCGAGAACGACCGCCACT 0.532000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000274217.3 1 1 hg19 CCDS3884.1 TCGA-FB-A5VM-01A-11D-A32N-08 FAM105A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253710.1 1 0 0 37 390 0 57 0 7.474746e-01 1 29 0 57 2 0 0 0 0 0 2 1 1.000000 36 380 0 55 2 0 0 0 0 57 2 -3.318794 1 1 121410 2 30 1 1 2 3 2.325338 1 0.280000 1.920000 0.368421 0.700000 0.500000 0.930000 0.700000 0.717923 0.700000 0 0.600000 0.830000 ADAMTS16 170690 broad.mit.edu 37 5 5235183 5235183 + Missense_Mutation SNP A A G TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr5:5235183A>G ENST00000274181.7 + 13 2045 c.1907A>G c.(1906-1908)aAc>aGc p.N636S ADAMTS16_ENST00000513709.1_3'UTR NM_139056.2 NP_620687.2 Q8TE57 ATS16_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 16 107 AAGCTCTGCAACAGTCAGAAA 0.502000 0 SO:0001583 missense ENST00000274181.7 1 1 hg19 CCDS43299.1 . . . . . . . . . . A 18.31 3.595341 0.66219 . . ENSG00000145536 ENST00000274181;ENST00000536857 T 0.05319 3.46 4.67 2.19 0.27852 . 0.000000 0.85682 D 0.000000 T 0.16557 0.0398 M 0.80422 2.495 0.58432 D 0.999993 P;P 0.50528 0.805;0.936 P;P 0.55713 0.492;0.782 T 0.00423 -1.1748 10 0.56958 D 0.05 . 6.7912 0.23701 0.7648:0.1522:0.083:0.0 . 636;636 Q8TE57;Q8TE57-2 ATS16_HUMAN;. S 636 ENSP00000274181:N636S ENSP00000274181:N636S N + 2 0 ADAMTS16 5288183 1.000000 0.71417 0.986000 0.45419 0.793000 0.44817 4.860000 0.62961 0.243000 0.21327 0.533000 0.62120 AAC TCGA-FB-A5VM-01A-11D-A32N-08 ADAMTS16-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000365657.1 1 0 0 39 393 0 70 0 0 0 0 70 2 0 0 0 0 0 2 1 1.000000 39 388 0 70 2 0 0 0 0 70 2 -12.541270 1 1 0 0 1 1 2 3 2.325338 1 0.280000 1.920000 0.368421 0.730000 0.530000 0.960000 0.730000 0.746613 0.730000 0 0.620000 0.860000 SLC16A10 117247 broad.mit.edu 37 6 111493921 111493921 + Missense_Mutation SNP G G T TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr6:111493921G>T ENST00000368851.5 + 2 542 c.367G>T c.(367-369)Ggg>Tgg p.G123W SLC16A10_ENST00000465319.1_3'UTR NM_018593.4 NP_061063.2 Q8TF71 MOT10_HUMAN solute carrier family 16 (aromatic amino acid transporter), member 10 12 all_cancers(87;0.00172)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0313)|Colorectal(196;0.0466) Droxidopa(DB06262)|Glycine(DB00145)|L-Alanine(DB00160)|L-Arginine(DB00125)|L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)|L-Cysteine(DB00151)|L-Cystine(DB00138)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Histidine(DB00117)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Lysine(DB00123)|L-Methionine(DB00134)|L-Phenylalanine(DB00120)|L-Proline(DB00172)|L-Serine(DB00133)|L-Threonine(DB00156)|L-Tryptophan(DB00150)|L-Tyrosine(DB00135)|L-Valine(DB00161)|Liothyronine(DB00279)|Liotrix(DB01583)|Pyruvic acid(DB00119) TCTCTCCATGGGGATGATTTT 0.428000 0 SO:0001583 missense ENST00000368851.5 1 1 hg19 CCDS5089.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 26.5|26.5 4.741282|4.741282 0.89573|0.89573 .|. .|. ENSG00000112394|ENSG00000112394 ENST00000535637;ENST00000368851;ENST00000368853|ENST00000419619;ENST00000439288 T|. 0.56103|. 0.48|. 5.65|5.65 5.65|5.65 0.86999|0.86999 Major facilitator superfamily domain, general substrate transporter (1);|. 0.092388|. 0.85682|. D|. 0.000000|. D|D 0.85344|0.85344 0.5675|0.5675 M|M 0.92649|0.92649 3.33|3.33 0.80722|0.80722 D|D 1|1 D;D|. 0.89917|. 1.0;1.0|. D;D|. 0.97110|. 1.0;1.0|. D|D 0.88182|0.88182 0.2871|0.2871 10|5 0.87932|. D|. 0|. .|. 19.7204|19.7204 0.96139|0.96139 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. 123;123|. Q8TF71;Q05BR4|. MOT10_HUMAN;.|. W|C 123;123;14|8 ENSP00000357844:G123W|. ENSP00000357844:G123W|. G|W +|+ 1|3 0|0 SLC16A10|SLC16A10 111600614|111600614 1.000000|1.000000 0.71417|0.71417 1.000000|1.000000 0.80357|0.80357 0.993000|0.993000 0.82548|0.82548 9.414000|9.414000 0.97362|0.97362 2.662000|2.662000 0.90505|0.90505 0.491000|0.491000 0.48974|0.48974 GGG|TGG TCGA-FB-A5VM-01A-11D-A32N-08 SLC16A10-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041822.2 1 0 0 22 360 0 80 0 2.051674e-02 0 4 0 80 2 0 0 0 0 0 2 1 0.999999 23 355 0 80 2 0 0 0 0 80 2 -2.389317 0 1 0 0 1 1 2 3 2.035096 0 0.280000 1.920000 0.284010 0.420000 0.260000 1.000000 0.410000 0.443874 0.420000 0 0.330000 0.520000 HIVEP1 3096 broad.mit.edu 37 6 12121002 12121002 + Missense_Mutation SNP T T C TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 T C T T Valid Somatic Phase_I WXS targeted Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr6:12121002T>C ENST00000379388.2 + 4 1306 c.974T>C c.(973-975)gTt>gCt p.V325A NM_002114.2 NP_002105.2 P15822 ZEP1_HUMAN human immunodeficiency virus type I enhancer binding protein 1 90 Breast(50;0.0639)|Ovarian(93;0.0816) all_hematologic(90;0.117) CTTGAACAGGTTTATAATATA 0.423000 0 SO:0001583 missense ENST00000379388.2 1 1 hg19 CCDS43426.1 . . . . . . . . . . T 11.85 1.762438 0.31228 . . ENSG00000095951 ENST00000379388 T 0.08370 3.1 5.69 5.69 0.88448 . 0.511841 0.14674 N 0.305158 T 0.03434 0.0099 L 0.31926 0.97 0.80722 D 1 B 0.16166 0.016 B 0.15484 0.013 T 0.41893 -0.9483 9 . . . -8.7034 15.942 0.79763 0.0:0.0:0.0:1.0 . 325 P15822 ZEP1_HUMAN A 325 ENSP00000368698:V325A . V + 2 0 HIVEP1 12228988 0.950000 0.32346 0.071000 0.20095 0.594000 0.36715 2.109000 0.41863 2.162000 0.67917 0.533000 0.62120 GTT TCGA-FB-A5VM-01A-11D-A32N-08 HIVEP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000039870.2 1 0 1 91 478 0 104 0 0 0 0 104 2 1 1 71 247 0 366 2 1 1.000000 90 474 0 104 2 0 0 0 0 104 2 -20.000000 1 1 0 0 1 0 0 0 2.002174 0 0.280000 1.920000 0.271845 0.990000 0.920000 1.000000 1.000000 0.994896 0.990000 1 0.990000 1.000000 BTN3A1 11119 broad.mit.edu 37 6 26413540 26413540 + Missense_Mutation SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr6:26413540G>A ENST00000289361.6 + 10 1530 c.1162G>A c.(1162-1164)Gag>Aag p.E388K BTN3A1_ENST00000414912.2_Missense_Mutation_p.E336K NM_001145008.1|NM_001145009.1|NM_007048.5 NP_001138480.1|NP_001138481.1|NP_008979.3 O00481 BT3A1_HUMAN butyrophilin, subfamily 3, member A1 28 TCTCGGCTGTGAGAGCTTCAT 0.512000 0 SO:0001583 missense ENST00000289361.6 1 1 hg19 CCDS4608.1 . . . . . . . . . . . 12.68 2.010049 0.35415 . . ENSG00000026950 ENST00000289361;ENST00000414912 T;T 0.15017 2.46;2.46 2.96 1.08 0.20341 Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1); . . . . T 0.03520 0.0101 N 0.25992 0.78 0.19300 N 0.999971 B;B 0.18461 0.028;0.028 B;B 0.17722 0.019;0.012 T 0.42949 -0.9421 9 0.44086 T 0.13 . 6.0568 0.19816 0.3689:0.0:0.6311:0.0 . 336;388 E9PGB4;O00481 .;BT3A1_HUMAN K 388;336 ENSP00000289361:E388K;ENSP00000406667:E336K ENSP00000289361:E388K E + 1 0 BTN3A1 26521519 0.131000 0.22433 0.000000 0.03702 0.003000 0.03518 0.910000 0.28571 0.080000 0.16959 0.609000 0.83330 GAG TCGA-FB-A5VM-01A-11D-A32N-08 BTN3A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040112.3 1 0 1 69 507 0 117 0 2.518982e-01 0 8 0 117 2 0 0 0 0 0 2 1 1.000000 69 499 0 117 2 0 0 0 0 117 2 -19.999990 1 1 0 0 1 0 0 0 2.002174 0 0.280000 1.920000 0.271845 0.840000 0.660000 1.000000 1.000000 0.848374 0.840000 0 0.750000 0.940000 KIFC1 3833 broad.mit.edu 37 6 33374225 33374225 + Missense_Mutation SNP T T C TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr6:33374225T>C ENST00000428849.2 + 8 2239 c.1789T>C c.(1789-1791)Tcc>Ccc p.S597P NM_002263.3 NP_002254.2 Q9BW19 KIFC1_HUMAN kinesin family member C1 13 CAGCAGCCTGTCCACGCTGGG 0.637000 0 SO:0001583 missense ENST00000428849.2 1 1 hg19 CCDS34430.1 . . . . . . . . . . t 21.4 4.145930 0.77888 . . ENSG00000237649 ENST00000428849 T 0.76839 -1.05 5.22 5.22 0.72569 Kinesin, motor domain (3); 0.057178 0.64402 D 0.000001 D 0.90133 0.6917 H 0.96333 3.805 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.85130 0.997;0.993 D 0.92850 0.6296 10 0.87932 D 0 -1.8945 13.1064 0.59249 0.0:0.0:0.0:1.0 . 589;597 B4E063;Q9BW19 .;KIFC1_HUMAN P 597 ENSP00000393963:S597P ENSP00000393963:S597P S + 1 0 KIFC1 33482203 1.000000 0.71417 1.000000 0.80357 0.888000 0.51559 3.048000 0.49862 2.189000 0.69895 0.456000 0.33151 TCC TCGA-FB-A5VM-01A-11D-A32N-08 KIFC1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000076417.1 1 0 1 44 307 0 91 1 9.999787e-01 38 75 0 91 2 0 0 0 0 0 2 1 1.000000 43 305 0 90 2 0 0 0 0 91 2 -20.000000 1 1 0 0 1 1 2 3 2.035096 0 0.280000 1.920000 0.284010 0.900000 0.670000 1.000000 1.000000 0.893697 0.900000 1 0.780000 1.000000 MDN1 23195 broad.mit.edu 37 6 90422465 90422465 + Missense_Mutation SNP C C T TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr6:90422465C>T ENST00000369393.3 - 48 7374 c.7259G>A c.(7258-7260)cGa>cAa p.R2420Q MDN1_ENST00000428876.1_Missense_Mutation_p.R2420Q Q9NU22 MDN1_HUMAN MDN1, midasin homolog (yeast) 218 all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246) TTCATGTGCTCGCAAAGAAGA 0.448000 0 SO:0001583 missense ENST00000369393.3 1 1 hg19 CCDS5024.1 . . . . . . . . . . C 9.464 1.093904 0.20471 . . ENSG00000112159 ENST00000369393;ENST00000428876 T;T 0.02837 4.14;4.14 5.62 -6.75 0.01738 . 1.628850 0.03584 N 0.230613 T 0.00524 0.0017 N 0.19112 0.55 0.09310 N 1 B 0.13145 0.007 B 0.04013 0.001 T 0.47649 -0.9101 10 0.13108 T 0.6 . 6.2293 0.20726 0.0757:0.219:0.127:0.5784 . 2420 Q9NU22 MDN1_HUMAN Q 2420 ENSP00000358400:R2420Q;ENSP00000413970:R2420Q ENSP00000358400:R2420Q R - 2 0 MDN1 90479186 0.000000 0.05858 0.005000 0.12908 0.504000 0.33889 -1.025000 0.03600 -0.943000 0.03691 0.467000 0.42956 CGA TCGA-FB-A5VM-01A-11D-A32N-08 MDN1-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041514.2 0 0 1 37 271 0 45 0 0 0 0 45 2 0 0 0 0 0 2 1 1.000000 37 269 0 44 2 0 0 0 0 45 2 -2.841729 1 1 121412 4 36 1 1 2 3 2.035096 0 0.280000 1.920000 0.284010 0.860000 0.620000 1.000000 1.000000 0.864014 0.860000 1 0.730000 1.000000 SLC12A9 56996 broad.mit.edu 37 7 100460407 100460407 + Missense_Mutation SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr7:100460407G>A ENST00000354161.3 + 13 1941 c.1816G>A c.(1816-1818)Gtg>Atg p.V606M SLC12A9_ENST00000540482.1_Missense_Mutation_p.V606M|SLC12A9_ENST00000275729.3_Missense_Mutation_p.V517M|SLC12A9_ENST00000415287.1_Missense_Mutation_p.V517M|SLC12A9_ENST00000428758.1_Missense_Mutation_p.V606M NM_020246.3 NP_064631.2 Q9BXP2 S12A9_HUMAN solute carrier family 12, member 9 41 Lung NSC(181;0.041)|all_lung(186;0.0581) CTCACCCTCCGTGCGCCAGGG 0.637000 0 SO:0001583 missense ENST00000354161.3 1 1 hg19 CCDS5707.1 . . . . . . . . . . G 27.0 4.787707 0.90367 . . ENSG00000146828 ENST00000540482;ENST00000428758;ENST00000275729;ENST00000415287;ENST00000354161;ENST00000539308 D;D;D;D;D 0.93953 -2.61;-2.61;-2.24;-2.24;-3.32 5.16 5.16 0.70880 . 0.000000 0.85682 D 0.000000 D 0.96315 0.8798 M 0.75884 2.315 0.80722 D 1 D;D 0.89917 1.0;0.999 D;D 0.77557 0.99;0.968 D 0.96645 0.9477 10 0.66056 D 0.02 . 16.1082 0.81241 0.0:0.0:1.0:0.0 . 517;606 Q9BXP2-2;Q9BXP2 .;S12A9_HUMAN M 606;606;517;517;606;232 ENSP00000443702:V606M;ENSP00000408301:V606M;ENSP00000275729:V517M;ENSP00000413796:V517M;ENSP00000275730:V606M ENSP00000275729:V517M V + 1 0 SLC12A9 100298343 1.000000 0.71417 0.950000 0.38849 0.891000 0.51852 7.581000 0.82535 2.404000 0.81709 0.491000 0.48974 GTG TCGA-FB-A5VM-01A-11D-A32N-08 SLC12A9-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000342837.1 1 0 1 101 613 0 129 1 9.999937e-01 38 65 0 129 2 0 0 0 0 0 2 1 1.000000 100 600 0 127 2 0 0 0 0 129 2 -3.318805 1 1 121412 2 36 1 1 2 3 2.047593 0 0.280000 1.920000 0.285998 0.990000 0.840000 1.000000 1.000000 0.974204 0.990000 1 0.920000 1.000000 CTTNBP2 83992 broad.mit.edu 37 7 117432633 117432633 + Missense_Mutation SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr7:117432633G>A ENST00000160373.3 - 4 708 c.617C>T c.(616-618)aCg>aTg p.T206M CTTNBP2_ENST00000487820.1_5'Flank NM_033427.2 NP_219499.1 Q8WZ74 CTTB2_HUMAN cortactin binding protein 2 83 Lung NSC(10;0.0018)|all_lung(10;0.002) TAATTCATTCGTCTTTTTCTT 0.463000 0 SO:0001583 missense ENST00000160373.3 1 1 hg19 CCDS5774.1 . . . . . . . . . . G 6.153 0.396356 0.11638 . . ENSG00000077063 ENST00000160373 T 0.64260 -0.09 5.77 3.96 0.45880 . 0.457226 0.27139 N 0.020745 T 0.59945 0.2231 M 0.71581 2.175 0.25918 N 0.983145 B 0.19445 0.036 B 0.20384 0.029 T 0.56553 -0.7960 10 0.54805 T 0.06 -14.2498 10.3555 0.43960 0.0669:0.2536:0.6795:0.0 . 206 Q8WZ74 CTTB2_HUMAN M 206 ENSP00000160373:T206M ENSP00000160373:T206M T - 2 0 CTTNBP2 117219869 0.591000 0.26824 0.005000 0.12908 0.249000 0.25844 2.379000 0.44318 0.899000 0.36444 0.650000 0.86243 ACG TCGA-FB-A5VM-01A-11D-A32N-08 CTTNBP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000059201.4 1 0 1 51 279 0 60 0 0 0 0 60 2 0 0 0 0 0 2 1 1.000000 51 276 0 59 2 0 0 0 0 60 2 -19.999970 1 1 121412 2 38 1 1 2 3 2.047593 0 0.280000 1.920000 0.285998 0.990000 0.850000 1.000000 1.000000 0.985956 0.990000 1 0.970000 1.000000 ELMO1 9844 broad.mit.edu 37 7 36917614 36917614 + Splice_Site SNP C C T TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr7:36917614C>T ENST00000310758.4 - 19 2470 c.e19+1 ELMO1_ENST00000396040.2_Splice_Site|ELMO1_ENST00000442504.1_Splice_Site|ELMO1_ENST00000448602.1_Splice_Site|ELMO1_ENST00000341056.3_Splice_Site|ELMO1_ENST00000396045.3_Splice_Site NM_001206480.1|NM_014800.10 NP_001193409.1|NP_055615.8 Q92556 ELMO1_HUMAN engulfment and cell motility 1 58 GAGCTACTTACGTTTGTCCTG 0.488000 0 SO:0001630 splice_region_variant ENST00000310758.4 1 1 hg19 CCDS5449.1 . . . . . . . . . . C 32 5.112821 0.94339 . . ENSG00000155849 ENST00000341056;ENST00000396045;ENST00000310758;ENST00000361912;ENST00000396040;ENST00000442504;ENST00000448602 . . . 5.81 5.81 0.92471 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 20.0833 0.97789 0.0:1.0:0.0:0.0 . . . . . -1 . . . - . . ELMO1 36884139 1.000000 0.71417 0.986000 0.45419 0.981000 0.71138 7.399000 0.79935 2.756000 0.94617 0.655000 0.94253 . TCGA-FB-A5VM-01A-11D-A32N-08 ELMO1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000219830.4 1 0 1 17 138 0 32 0 0 0 0 32 2 0 0 0 0 0 2 1 0.999964 16 133 0 32 2 0 0 0 0 32 2 -19.999990 1 1 0 0 1 1 2 3 2.026740 0 0.280000 1.920000 0.282010 0.790000 0.480000 1.000000 1.000000 0.794529 0.790000 0 0.620000 0.990000 ABCA13 154664 broad.mit.edu 37 7 48315041 48315041 + Silent SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr7:48315041G>A ENST00000435803.1 + 17 5802 c.5778G>A c.(5776-5778)ccG>ccA p.P1926P NM_152701.3 NP_689914.2 Q86UQ4 ABCAD_HUMAN ATP-binding cassette, sub-family A (ABC1), member 13 270 AGATATTACCGTTTGTCCCAC 0.373000 0 SO:0001819 synonymous_variant ENST00000435803.1 1 0 hg19 CCDS47584.1 TCGA-FB-A5VM-01A-11D-A32N-08 ABCA13-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000341964.2 0 0 1 98 521 1 141 0 0 0 1 141 2 0 0 0 0 0 2 1 1.000000 97 518 1 140 16 0 0 0 1 141 2 -4.804042 1 1 120802 231 59 1 1 2 3 2.038903 0 0.280000 1.920000 0.284010 0.990000 0.930000 1.000000 1.000000 0.996243 0.990000 1 0.990000 1.000000 GJC3 349149 broad.mit.edu 37 7 99521174 99521174 + Missense_Mutation SNP A A T TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr7:99521174A>T ENST00000312891.2 - 2 833 c.834T>A c.(832-834)gaT>gaA p.D278E NM_181538.2 NP_853516.1 Q8NFK1 CXG3_HUMAN gap junction protein, gamma 3, 30.2kDa 9 Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323) caactcaggcatctctgggtc 0.388000 0 SO:0001583 missense ENST00000312891.2 1 1 hg19 CCDS34697.1 . . . . . . . . . . A 14.02 2.409331 0.42715 . . ENSG00000176402 ENST00000312891 D 0.97850 -4.57 0.235 -0.47 0.12131 . . . . . D 0.91928 0.7444 N 0.08118 0 0.19575 N 0.999967 P 0.38711 0.643 B 0.43360 0.417 D 0.87092 0.2173 8 0.21540 T 0.41 . . . . . 278 Q8NFK1 CXG3_HUMAN E 278 ENSP00000325775:D278E ENSP00000325775:D278E D - 3 2 GJC3 99359110 0.157000 0.22836 0.581000 0.28614 0.590000 0.36582 -0.593000 0.05740 -0.738000 0.04817 -0.736000 0.03550 GAT TCGA-FB-A5VM-01A-11D-A32N-08 GJC3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000345052.1 1 0 1 39 266 0 63 1 3.312274e-01 4 5 0 63 2 0 0 0 0 0 2 1 1.000000 39 260 0 62 2 0 0 0 0 63 2 -20.000000 1 1 0 0 1 1 2 3 2.047593 0 0.280000 1.920000 0.285998 0.920000 0.670000 1.000000 1.000000 0.907519 0.920000 1 0.790000 1.000000 RP1L1 94137 broad.mit.edu 37 8 10470231 10470231 + Silent SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr8:10470231G>A ENST00000382483.3 - 4 1600 c.1377C>T c.(1375-1377)acC>acT p.T459T NM_178857.5 NP_849188.4 Q8IWN7 RP1L1_HUMAN retinitis pigmentosa 1-like 1 148 CGGGGAGGCCGGTGCTGGAGG 0.726000 0 SO:0001819 synonymous_variant ENST00000382483.3 1 1 hg19 CCDS43708.1 TCGA-FB-A5VM-01A-11D-A32N-08 RP1L1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000375673.1 1 0 1 71 445 0 111 0 0 0 0 111 2 0 0 0 0 0 2 1 1.000000 70 439 0 111 2 0 0 0 0 111 2 -2.841728 1 1 0 0 1 1 2 3 2.079777 0 0.280000 1.920000 0.291896 0.990000 0.790000 1.000000 1.000000 0.962547 0.990000 1 0.890000 1.000000 RIMS2 9699 broad.mit.edu 37 8 105026802 105026802 + Missense_Mutation SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr8:105026802G>A ENST00000436393.2 + 17 2754 c.2513G>A c.(2512-2514)cGa>cAa p.R838Q RIMS2_ENST00000507740.1_Missense_Mutation_p.R912Q|RIMS2_ENST00000406091.3_Missense_Mutation_p.R1098Q|RIMS2_ENST00000262231.10_Missense_Mutation_p.R937Q Q9UQ26 RIMS2_HUMAN regulating synaptic membrane exocytosis 2 144 OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229) CGAAGGGGCCGACAGCTTCCA 0.443000 HNSCC(12;0.0054) 0 SO:0001583 missense ENST00000436393.2 1 1 hg19 . . . . . . . . . . G 26.3 4.726423 0.89298 . . ENSG00000176406 ENST00000504942;ENST00000329869;ENST00000406091;ENST00000402998;ENST00000262231;ENST00000507740;ENST00000408894;ENST00000436393 T;T;T;T;T;T 0.57273 0.41;2.37;2.07;1.98;0.65;1.18 5.63 5.63 0.86233 . . . . . T 0.68155 0.2970 L 0.42245 1.32 0.80722 D 1 D;D;D;D;D 0.89917 1.0;0.997;1.0;0.999;1.0 D;D;D;D;D 0.85130 0.997;0.974;0.996;0.993;0.996 T 0.69258 -0.5192 9 0.72032 D 0.01 . 19.6846 0.95976 0.0:0.0:1.0:0.0 . 1160;838;937;912;1098 Q9UQ26;D6RA03;Q9UQ26-1;Q9UQ26-3;F8WD47 RIMS2_HUMAN;.;.;.;. Q 1098;1135;1098;1160;937;912;912;838 ENSP00000427018:R1098Q;ENSP00000384892:R1098Q;ENSP00000262231:R937Q;ENSP00000423559:R912Q;ENSP00000386228:R912Q;ENSP00000390665:R838Q ENSP00000262231:R937Q R + 2 0 RIMS2 105095978 1.000000 0.71417 0.998000 0.56505 0.998000 0.95712 9.175000 0.94831 2.652000 0.90054 0.591000 0.81541 CGA TCGA-FB-A5VM-01A-11D-A32N-08 RIMS2-007 NOVEL basic|exp_conf protein_coding protein_coding OTTHUMT00000367217.1 1 0 1 25 178 0 44 0 0 0 0 44 2 0 0 0 0 0 2 1 1.000000 24 176 0 43 2 0 0 0 0 44 2 -3.222953 1 1 0 0 1 0 1 1 2.014413 0 0.280000 1.920000 0.277978 0.870000 0.590000 1.000000 1.000000 0.865491 0.870000 1 0.720000 1.000000 KCNQ3 3786 broad.mit.edu 37 8 133142050 133142050 + Missense_Mutation SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr8:133142050G>A ENST00000388996.4 - 15 2498 c.2078C>T c.(2077-2079)cCg>cTg p.P693L KCNQ3_ENST00000521134.1_Missense_Mutation_p.P573L|KCNQ3_ENST00000519445.1_Missense_Mutation_p.P681L NM_004519.3 NP_004510.1 O43525 KCNQ3_HUMAN potassium voltage-gated channel, KQT-like subfamily, member 3 p.E694fs*12(1) 70 Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155) BRCA - Breast invasive adenocarcinoma(115;0.000311) Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939) GGGTGGTTCCGGGGGGCCTGT 0.547000 1 Insertion - Frameshift(1) SO:0001583 missense ENST00000388996.4 1 1 hg19 CCDS34943.1 . . . . . . . . . . G 9.836 1.189602 0.21954 . . ENSG00000184156 ENST00000388996;ENST00000521134;ENST00000519445;ENST00000542679;ENST00000423790 D;D;D 0.98901 -5.21;-5.17;-5.22 5.49 3.51 0.40186 . 0.504521 0.23192 N 0.050897 D 0.91872 0.7427 N 0.08118 0 0.47737 D 0.999504 P;B 0.35328 0.495;0.178 B;B 0.17722 0.019;0.012 D 0.88843 0.3314 10 0.37606 T 0.19 -9.8678 3.0642 0.06209 0.0918:0.1206:0.4274:0.3601 . 681;693 E7ET42;O43525 .;KCNQ3_HUMAN L 693;573;681;670;572 ENSP00000373648:P693L;ENSP00000429799:P573L;ENSP00000428790:P681L ENSP00000373648:P693L P - 2 0 KCNQ3 133211232 0.989000 0.36119 0.712000 0.30502 0.718000 0.41266 2.135000 0.42112 1.330000 0.45394 0.549000 0.68633 CCG TCGA-FB-A5VM-01A-11D-A32N-08 KCNQ3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268621.2 0 0 0 42 522 0 84 0 0 0 0 84 2 0 0 0 0 0 2 1 1.000000 41 514 0 82 2 0 0 0 0 84 2 -2.239612 0 1 121412 4 38 1 1 3 4 2.592854 1 0.280000 1.920000 0.436267 0.680000 0.490000 0.900000 0.670000 0.691371 0.680000 0 0.580000 0.790000 KCNQ3 3786 broad.mit.edu 37 8 133153411 133153411 + Missense_Mutation SNP C C T rs141821338 TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr8:133153411C>T ENST00000388996.4 - 10 1850 c.1430G>A c.(1429-1431)cGc>cAc p.R477H KCNQ3_ENST00000521134.1_Missense_Mutation_p.R357H|KCNQ3_ENST00000519445.1_Missense_Mutation_p.R477H NM_004519.3 NP_004510.1 O43525 KCNQ3_HUMAN potassium voltage-gated channel, KQT-like subfamily, member 3 p.R477H(1) 70 Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155) BRCA - Breast invasive adenocarcinoma(115;0.000311) Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939) GGCTTTCATGCGGAAGGCCGT 0.473000 1 Substitution - Missense(1) SO:0001583 missense ENST00000388996.4 1 1 hg19 CCDS34943.1 . . . . . . . . . . C 29.5 5.011674 0.93346 . . ENSG00000184156 ENST00000388996;ENST00000521134;ENST00000519445;ENST00000542679;ENST00000423790 D;D;D 0.99735 -6.58;-6.58;-6.58 5.63 5.63 0.86233 Potassium channel, voltage dependent, KCNQ, C-terminal (1); 0.118141 0.56097 D 0.000027 D 0.99600 0.9855 M 0.64170 1.965 0.52099 D 0.999943 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.999 D 0.98327 1.0531 10 0.87932 D 0 -16.6136 18.6978 0.91607 0.0:1.0:0.0:0.0 . 477;477 E7ET42;O43525 .;KCNQ3_HUMAN H 477;357;477;466;356 ENSP00000373648:R477H;ENSP00000429799:R357H;ENSP00000428790:R477H ENSP00000373648:R477H R - 2 0 KCNQ3 133222593 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 4.524000 0.60552 2.652000 0.90054 0.655000 0.94253 CGC TCGA-FB-A5VM-01A-11D-A32N-08 KCNQ3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268621.2 1 0 1 60 527 0 63 0 0 0 1 0 63 2 0 0 0 0 0 2 1 1.000000 60 515 0 63 2 0 0 0 0 63 2 -3.221883 1 1 0 0 1 1 3 4 2.592854 1 0.280000 1.920000 0.436267 0.930000 0.720000 1.000000 1.000000 0.919150 0.930000 1 0.820000 1.000000 COMMD5 28991 broad.mit.edu 37 8 146076505 146076505 + Silent SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chr8:146076505G>A ENST00000305103.3 - 2 471 c.219C>T c.(217-219)gtC>gtT p.V73V COMMD5_ENST00000402718.3_Silent_p.V73V|AF235103.1_ENST00000578937.1_RNA|COMMD5_ENST00000450361.2_Silent_p.V73V NM_014066.3 NP_054785.2 Q9GZQ3 COMD5_HUMAN COMM domain containing 5 11 all_cancers(97;1.14e-11)|all_epithelial(106;7.74e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155) Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055) GGTTGGCGCTGACCCCAAGAC 0.647000 0 SO:0001819 synonymous_variant ENST00000305103.3 1 1 hg19 CCDS6436.1 TCGA-FB-A5VM-01A-11D-A32N-08 COMMD5-004 PUTATIVE alternative_5_UTR|basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000382962.1 1 0 1 33 188 0 36 1 9.999999e-01 52 102 0 36 2 0 0 0 0 0 2 1 1.000000 33 185 0 36 2 0 0 0 0 36 2 -20.000000 1 1 0 0 1 1 2 3 2.075471 0 0.280000 1.920000 0.290920 0.990000 0.770000 1.000000 1.000000 0.972388 0.990000 1 0.920000 1.000000 ATP2B3 492 broad.mit.edu 37 X 152806983 152806983 + Silent SNP G G T TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chrX:152806983G>T ENST00000349466.2 + 3 701 c.375G>T c.(373-375)tcG>tcT p.S125S ATP2B3_ENST00000263519.4_Silent_p.S125S|ATP2B3_ENST00000370181.2_Silent_p.S125S|ATP2B3_ENST00000370186.1_Silent_p.S125S|ATP2B3_ENST00000359149.3_Silent_p.S125S|ATP2B3_ENST00000393842.1_Silent_p.S125S Q16720 AT2B3_HUMAN ATPase, Ca++ transporting, plasma membrane 3 50 all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05) TGGGCCTCTCGTTCTATGCGC 0.622000 0 SO:0001819 synonymous_variant ENST00000349466.2 1 1 hg19 CCDS35440.1 TCGA-FB-A5VM-01A-11D-A32N-08 ATP2B3-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000060957.1 1 0 1 49 112 0 35 0 0 0 0 35 2 0 0 0 0 0 2 1 1.000000 49 111 0 34 2 0 0 0 0 35 2 -20.000000 1 1 0 0 1 0 1 1 0.280000 1.920000 0.280000 0.930000 0.770000 1.000000 0.990000 0.929529 0.930000 1 0.860000 0.990000 BRWD3 254065 broad.mit.edu 37 X 79932804 79932804 + Silent SNP G G A TCGA-FB-A5VM-01A-11D-A32N-08 TCGA-FB-A5VM-10A-01D-A32N-08 Untested Somatic Phase_I WXS none Illumina GAIIx 64face78-864d-4f47-9be1-d9c2d6ad6fe1 533e52da-782c-4274-afbe-e017bb6b0286 g.chrX:79932804G>A ENST00000373275.4 - 41 4929 c.4713C>T c.(4711-4713)atC>atT p.I1571I BRWD3_ENST00000473691.1_5'UTR NM_153252.4 NP_694984 Q6RI45 BRWD3_HUMAN bromodomain and WD repeat domain containing 3 87 GTTTTCTCTTGATTCCTGTCC 0.368000 0 SO:0001819 synonymous_variant ENST00000373275.4 1 1 hg19 CCDS14447.1 TCGA-FB-A5VM-01A-11D-A32N-08 BRWD3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057344.1 1 0 1 34 87 0 28 1 4.386202e-01 5 0 0 28 2 0 0 0 0 0 2 1 1.000000 34 86 0 28 2 0 0 0 0 28 2 -20.000000 1 1 0 0 1 0 1 1 0.280000 1.920000 0.280000 0.890000 0.690000 1.000000 0.980000 0.890049 0.890000 1 0.800000 0.970000