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 DIP2C 22982 broad.mit.edu 37 10 395301 395301 + Missense_Mutation SNP C C T TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr10:395301C>T ENST00000280886.6 - 25 3166 c.3079G>A c.(3079-3081)Ggc>Agc p.G1027S NM_014974.2 NP_055789.1 Q9Y2E4 DIP2C_HUMAN DIP2 disco-interacting protein 2 homolog C (Drosophila) 81 all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235) OV - Ovarian serous cystadenocarcinoma(33;0.136) ACGTGGTCGCCGTCCTGAAGG 0.652000 0 SO:0001583 missense ENST00000280886.6 0 1 hg19 CCDS7054.1 . . . . . . . . . . C 24.200000 4.501679 0.851760 . . ENSG00000151240 ENST00000280886 T 0.19532 2.14 5.180000 5.180000 0.714440 AMP-dependent synthetase/ligase (1); 0.000000 0.85682 D 0.000000 T 0.52451 0.1735 M 0.83774 2.66 0.807220 D 1.000000 D 0.89917 1.0 D 0.97110 1.0 T 0.59606 -0.7423 10 0.87932 D 0 -23.0966 18.710900 0.916560 0.0:1.0:0.0:0.0 . 1027 Q9Y2E4 DIP2C_HUMAN S 1027 ENSP00000280886:G1027S ENSP00000280886:G1027S G - 1 0 DIP2C 385301 1 0.714170 4.210000e-01 0.266090 0.302000 0.276580 7.811000 0.860920 2.409000 0.818220 0.563000 0.778840 GGC TCGA-FB-A4P5-01A-11D-A26I-08 DIP2C-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000046389.1 0 0 0 5 175 0 40 0 1.155322e-02 0 5 0 40 2 0 0 0 0 0 2 1 0.938422 5 175 0 40 2 0 0 0 0 40 2 -6.941940 1 0 121398 1 30 1 1 2 3 2.004724 0 0.130000 2 0.135060 0.480000 0.180000 1.000000 0.400000 0.527398 0.480000 0 0.300000 0.760000 TCN1 6947 broad.mit.edu 37 11 59629067 59629067 + Silent SNP G G A TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr11:59629067G>A ENST00000257264.3 - 4 593 c.489C>T c.(487-489)acC>acT p.T163T TCN1_ENST00000532419.1_5'UTR NM_001062.3 NP_001053.2 P20061 TCO1_HUMAN transcobalamin I (vitamin B12 binding protein, R binder family) 29 all_epithelial(135;0.198) Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200) CAACTTCGGCGGTTGAGTAGT 0.448000 0 SO:0001819 synonymous_variant ENST00000257264.3 0 1 hg19 CCDS7978.1 TCGA-FB-A4P5-01A-11D-A26I-08 TCN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000394503.1 0 0 0 12 577 0 72 1 6.595281e-01 14 93 0 72 2 0 0 0 0 0 2 1 0.999099 12 574 0 69 2 0 0 0 0 72 2 -2.406236 0 1 121412 58 51 1 1 2 3 2.009813 0 0.130000 2 0.136176 0.330000 0.170000 1.000000 0.310000 0.396079 0.330000 0 0.240000 0.480000 CCDC87 55231 broad.mit.edu 37 11 66360267 66360267 + Missense_Mutation SNP C C T TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr11:66360267C>T ENST00000333861.3 - 1 287 c.220G>A c.(220-222)Gga>Aga p.G74R CCS_ENST00000310190.4_5'Flank|CCS_ENST00000533244.1_5'Flank NM_018219.2 NP_060689.2 Q9NVE4 CCD87_HUMAN coiled-coil domain containing 87 28 GGAGGCACTCCCGCTGCTATC 0.657000 OREG0021111 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000333861.3 1 1 hg19 CCDS8145.1 . . . . . . . . . . G 4.935000 0.173708 0.093910 . . ENSG00000182791 ENST00000333861 T 0.27890 1.64 5.390000 2.330000 0.289320 . 1.311630 0.05373 N 0.535892 T 0.08492 0.0211 N 0.00237 -1.79 0.093100 N 1.000000 B 0.02656 0.0 B 0.01281 0.0 T 0.26950 -1.0088 10 0.11485 T 0.65 -0.9844 8.499300 0.331480 0.0872:0.4903:0.4226:0.0 . 74 Q9NVE4 CCD87_HUMAN R 74 ENSP00000328487:G74R ENSP00000328487:G74R G - 1 0 CCDC87 66116843 4.000000e-03 0.155600 0 0.037020 0.003000 0.035180 1.494000 0.356160 0.405000 0.255320 -0.120000 0.150300 GGA TCGA-FB-A4P5-01A-11D-A26I-08 CCDC87-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000393825.1 1 0 0 9 234 0 48 0 0 0 0 48 2 0 0 0 0 0 2 1 0.994143 9 231 0 48 2 0 0 0 0 48 2 -3.319084 1 1 0 0 1 1 2 3 2.009813 0 0.130000 2 0.136176 0.610000 0.290000 1.000000 1.000000 0.646764 0.610000 0 0.430000 0.900000 LRP5 4041 broad.mit.edu 37 11 68115353 68115353 + Missense_Mutation SNP C C T TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr11:68115353C>T ENST00000294304.7 + 2 236 c.130C>T c.(130-132)Cgg>Tgg p.R44W NM_002335.2 NP_002326.2 O75197 LRP5_HUMAN low density lipoprotein receptor-related protein 5 63 CCGGGACGTACGGCTGGTGGA 0.647000 0 SO:0001583 missense ENST00000294304.7 1 1 hg19 CCDS8181.1 . . . . . . . . . . C 13.790000 2.342253 0.414980 0.0 1.19E-4 ENSG00000162337 ENST00000294304 D 0.91792 -2.91 4.230000 2.220000 0.280830 Six-bladed beta-propeller, TolB-like (1); 0.000000 0.38436 U 0.001695 D 0.96513 0.8862 H 0.95079 3.62 0.494830 D 0.999798 D 0.89917 1.0 D 0.97110 1.0 D 0.95702 0.8750 10 0.87932 D 0 . 8.593600 0.337010 0.2119:0.7033:0.0:0.0848 . 44 O75197 LRP5_HUMAN W 44 ENSP00000294304:R44W ENSP00000294304:R44W R + 1 2 LRP5 67871929 9.480000e-01 0.322510 9.640000e-01 0.405700 0.037000 0.131400 2.186000 0.425930 1.148000 0.423850 -0.215000 0.126440 CGG TCGA-FB-A4P5-01A-11D-A26I-08 LRP5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000395088.1 0 0 0 13 390 0 76 0 4.665106e-02 0 10 0 76 2 0 0 0 0 0 2 1 0.999461 12 380 0 75 2 0 0 0 0 76 2 -3.703704 1 1 121000 1 27 1 1 2 3 2.009813 0 0.130000 2 0.136176 0.520000 0.280000 1.000000 0.490000 0.569099 0.520000 0 0.390000 0.730000 CCDC60 160777 broad.mit.edu 37 12 119773039 119773039 + Missense_Mutation SNP C C T TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr12:119773039C>T ENST00000327554.2 + 1 523 c.58C>T c.(58-60)Cgg>Tgg p.R20W CCDC60_ENST00000546345.1_3'UTR|CCDC60_ENST00000539847.1_Missense_Mutation_p.R20W|CCDC60_ENST00000536742.1_Missense_Mutation_p.R20W NM_178499.3 NP_848594.2 Q8IWA6 CCD60_HUMAN coiled-coil domain containing 60 40 all_neural(191;0.0804)|Medulloblastoma(191;0.0922) GGGGGCTGTCCGGCCCTTTTA 0.502000 0 SO:0001583 missense ENST00000327554.2 1 1 hg19 CCDS9190.1 . . . . . . . . . . C 6.197000 0.404573 0.117540 . . ENSG00000183273 ENST00000536742;ENST00000327554;ENST00000539847 T;T;T 0.48836 0.8;1.83;0.95 4.420000 -3.660000 0.044890 . 1.591660 0.03532 N 0.222527 T 0.17492 0.0420 N 0.01874 -0.695 0.093100 N 1.000000 B 0.02656 0.0 B 0.01281 0.0 T 0.09773 -1.0659 9 . . . 0.016 3.287800 0.069370 0.3849:0.3158:0.0:0.2993 . 20 Q8IWA6 CCD60_HUMAN W 20 ENSP00000445505:R20W;ENSP00000333374:R20W;ENSP00000443403:R20W . R + 1 2 CCDC60 118257422 0 0.058580 1.000000e-03 0.086480 0.056000 0.154070 -0.894000 0.041230 -0.330000 0.085140 -0.377000 0.069320 CGG TCGA-FB-A4P5-01A-11D-A26I-08 CCDC60-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000401680.1 0 0 0 12 359 0 61 0 0 0 0 61 2 0 0 0 0 0 2 1 0.999014 11 351 0 61 2 0 0 0 0 61 2 -2.748327 1 1 121410 4 38 1 1 2 3 2.001364 0 0.130000 2 0.134501 0.520000 0.280000 1.000000 0.490000 0.559715 0.520000 0 0.380000 0.720000 KRAS 3845 broad.mit.edu 37 12 25398284 25398284 + Missense_Mutation SNP C C T rs121913529 TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 C T C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr12:25398284C>T ENST00000256078.4 - 2 98 c.35G>A c.(34-36)gGt>gAt p.G12D KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) GCCTACGCCACCAGCTCCAAC 0.348000 G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 15813 Substitution - Missense(15812)|Deletion - Frameshift(1) SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 hg19 CCDS8703.1 . . . . . . . . . . C 23.400000 4.409094 0.833400 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78595 -1.19;-1.19;-1.19;-1.19 5.680000 5.680000 0.881260 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.85919 0.5809 M 0.91818 3.245 0.807220 D 1.000000 B;P 0.35714 0.385;0.517 B;B 0.41619 0.257;0.361 D 0.87870 0.2670 10 0.87932 D 0 . 18.371900 0.904090 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN D 12 ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D ENSP00000256078:G12D G - 2 0 KRAS 25289551 1 0.714170 1 0.803570 0.998000 0.957120 7.743000 0.850200 2.668000 0.907890 0.563000 0.778840 GGT TCGA-FB-A4P5-01A-11D-A26I-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 0 2 91 0 15 0 7.364601e-03 1 3 0 15 2 1 9.683217e-01 7 341 0 180 2 1 0.681391 2 90 0 15 2 1 9.999940e-01 353 7668 0 15 2 -3.568862 1 1 121404 2 44 1 1 2 3 2.009941 0 0.130000 2 0.136176 0.430000 0.090000 1.000000 1.000000 0.498729 0.430000 0 0.210000 0.850000 FREM2 341640 broad.mit.edu 37 13 39357268 39357268 + Missense_Mutation SNP C C A TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr13:39357268C>A ENST00000280481.7 + 5 5919 c.5703C>A c.(5701-5703)ttC>ttA p.F1901L NM_207361.4 NP_997244.3 Q5SZK8 FREM2_HUMAN FRAS1 related extracellular matrix protein 2 148 Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114) GTGAGCTGTTCATTCCCATCA 0.448000 0 SO:0001583 missense ENST00000280481.7 0 1 hg19 CCDS31960.1 . . . . . . . . . . C 0.016000 -1.513669 0.009750 . . ENSG00000150893 ENST00000280481 T 0.28454 1.61 5.840000 3.090000 0.356070 Na-Ca exchanger/integrin-beta4 (2); 0.154739 0.64402 N 0.000015 T 0.09555 0.0235 N 0.03177 -0.4 0.410290 D 0.985147 B 0.02656 0.0 B 0.09377 0.004 T 0.22487 -1.0215 10 0.05620 T 0.96 . 4.307300 0.109530 0.1488:0.4504:0.0:0.4008 . 1901 Q5SZK8 FREM2_HUMAN L 1901 ENSP00000280481:F1901L ENSP00000280481:F1901L F + 3 2 FREM2 38255268 4.160000e-01 0.254240 8.260000e-01 0.328280 0.043000 0.139390 -0.373000 0.074940 0.334000 0.235900 0.514000 0.502590 TTC TCGA-FB-A4P5-01A-11D-A26I-08 FREM2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044599.2 0 0 0 17 597 0 64 0 0 0 0 64 2 0 0 0 0 0 2 1 0.999963 17 593 0 64 2 0 0 0 0 64 2 -2.882516 1 1 0 0 1 1 2 3 2.007468 0 0.130000 2 0.135618 0.440000 0.260000 1.000000 0.420000 0.492457 0.440000 0 0.340000 0.600000 DGKH 160851 broad.mit.edu 37 13 42774011 42774011 + Missense_Mutation SNP C C T TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr13:42774011C>T ENST00000337343.4 + 20 2480 c.2459C>T c.(2458-2460)tCg>tTg p.S820L DGKH_ENST00000540693.1_Missense_Mutation_p.S820L|DGKH_ENST00000261491.5_Missense_Mutation_p.S820L|DGKH_ENST00000379274.2_Missense_Mutation_p.S684L|DGKH_ENST00000536612.1_Missense_Mutation_p.S684L|DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000538674.1_Missense_Mutation_p.S575L NM_178009.3 NP_821077.1 Q86XP1 DGKH_HUMAN diacylglycerol kinase, eta 43 Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114) TTACAGAGATCGTACAAGAAT 0.333000 0 SO:0001583 missense ENST00000337343.4 0 1 hg19 CCDS9381.1 . . . . . . . . . . C 21.700000 4.184618 0.786770 . . ENSG00000102780 ENST00000540693;ENST00000337343;ENST00000261491;ENST00000379274;ENST00000536612;ENST00000538674 T;T;T;T;T;T 0.44083 0.93;0.93;0.93;0.93;0.93;0.93 5.690000 5.690000 0.884480 Diacylglycerol kinase, accessory domain (2); 0.059562 0.64402 D 0.000004 T 0.49304 0.1549 M 0.75615 2.305 0.584320 D 0.999998 P;P;P;P 0.46952 0.874;0.644;0.887;0.824 B;B;B;B 0.40375 0.3;0.22;0.22;0.327 T 0.58869 -0.7560 10 0.87932 D 0 . 19.801300 0.965090 0.0:1.0:0.0:0.0 . 575;684;820;820 F5GYP2;Q86XP1-3;Q86XP1-2;Q86XP1 .;.;.;DGKH_HUMAN L 820;820;820;684;684;575 ENSP00000440823:S820L;ENSP00000337572:S820L;ENSP00000261491:S820L;ENSP00000368576:S684L;ENSP00000445114:S684L;ENSP00000441308:S575L ENSP00000261491:S820L S + 2 0 DGKH 41672011 1 0.714170 9.630000e-01 0.404240 0.825000 0.466860 7.818000 0.864160 2.670000 0.908740 0.591000 0.815410 TCG TCGA-FB-A4P5-01A-11D-A26I-08 DGKH-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044699.2 0 0 0 6 161 0 14 0 0 0 0 14 2 0 0 0 0 0 2 1 0.964522 6 159 0 14 2 0 0 0 0 14 2 -2.787793 1 1 0 0 1 1 2 3 2.007468 0 0.130000 2 0.135618 0.610000 0.250000 1.000000 1.000000 0.640236 0.610000 0 0.400000 0.940000 SPSB3 90864 broad.mit.edu 37 16 1828584 1828584 + Silent SNP G G A TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr16:1828584G>A ENST00000566339.1 - 3 486 c.156C>T c.(154-156)taC>taT p.Y52Y SPSB3_ENST00000301717.4_Silent_p.Y52Y NM_080861.3 NP_543137.2 Q6PJ21 SPSB3_HUMAN splA/ryanodine receptor domain and SOCS box containing 3 10 GCAGCGTGGAGTACTCGGGGT 0.652000 0 SO:0001819 synonymous_variant ENST00000566339.1 1 1 hg19 CCDS32365.1 TCGA-FB-A4P5-01A-11D-A26I-08 SPSB3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000433512.1 0 0 0 12 344 0 115 1 8.226456e-01 5 88 0 115 2 0 0 0 0 0 2 1 0.999093 12 340 0 115 2 0 0 0 0 115 2 -12.158340 1 1 0 0 1 1 2 3 2.019557 0 0.130000 2 0.138401 0.560000 0.290000 1.000000 0.520000 0.606832 0.560000 0 0.410000 0.830000 CACNB1 782 broad.mit.edu 37 17 37339981 37339981 + Silent SNP C C T TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr17:37339981C>T ENST00000394303.3 - 11 1242 c.1035G>A c.(1033-1035)aaG>aaA p.K345K CACNB1_ENST00000344140.5_Silent_p.K390K|CACNB1_ENST00000582877.1_5'Flank|CACNB1_ENST00000394310.3_Silent_p.K345K NM_000723.4 NP_000714.3 Q02641 CACB1_HUMAN calcium channel, voltage-dependent, beta 1 subunit p.K390N(1) 16 Dronedarone(DB04855)|Ibutilide(DB00308)|Magnesium Sulfate(DB00653)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661) GAGAGGTGATCTTGATGTAAA 0.567000 Esophageal Squamous(5;100 366 38393 41452 45827) 1 Substitution - Missense(1) SO:0001819 synonymous_variant ENST00000394303.3 0 1 hg19 CCDS42311.1 TCGA-FB-A4P5-01A-11D-A26I-08 CACNB1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000256945.3 0 0 0 4 66 0 11 1 1.819839e-01 3 8 0 11 2 0 0 0 0 0 2 1 0.885455 4 64 0 11 2 0 0 0 0 11 2 -8.518474 1 1 0 0 1 0 1 1 1.989980 0 0.130000 2 0.123735 0.880000 0.310000 1.000000 1.000000 0.813457 0.880000 1 0.550000 1.000000 CA10 56934 broad.mit.edu 37 17 50008436 50008436 + Missense_Mutation SNP G G A TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr17:50008436G>A ENST00000285273.4 - 4 1304 c.193C>T c.(193-195)Cgg>Tgg p.R65W CA10_ENST00000442502.2_Missense_Mutation_p.R65W|CA10_ENST00000570565.1_De_novo_Start_OutOfFrame|CA10_ENST00000451037.2_Missense_Mutation_p.R65W|CA10_ENST00000340813.6_Missense_Mutation_p.R71W NM_001082533.1 NP_001076002.1 Q9NS85 CAH10_HUMAN carbonic anhydrase X 41 BRCA - Breast invasive adenocarcinoma(22;4.74e-06) Zonisamide(DB00909) GGCGACTGCCGTTTCCCCACA 0.473000 0 SO:0001583 missense ENST00000285273.4 0 1 hg19 CCDS32684.1 . . . . . . . . . . G 26.300000 4.725381 0.892980 . . ENSG00000154975 ENST00000442502;ENST00000285273;ENST00000451037;ENST00000340813 T;T;T;T 0.70986 -0.53;-0.53;-0.53;-0.53 5.930000 4.930000 0.648220 Carbonic anhydrase, alpha-class, catalytic domain (4); 0.000000 0.64402 D 0.000001 D 0.84875 0.5569 M 0.86502 2.82 0.460610 D 0.998844 D;D 0.89917 1.0;1.0 D;D 0.76575 0.988;0.988 D 0.86086 0.1547 9 . . . . 13.520500 0.615660 0.0:0.0:0.6936:0.3064 . 65;71 Q9NS85;Q68D28 CAH10_HUMAN;. W 65;65;65;71 ENSP00000390666:R65W;ENSP00000285273:R65W;ENSP00000405388:R65W;ENSP00000340363:R71W . R - 1 2 CA10 47363435 1 0.714170 1 0.803570 0.973000 0.671790 4.008000 0.571030 2.826000 0.973560 0.655000 0.942530 CGG TCGA-FB-A4P5-01A-11D-A26I-08 CA10-003 NOVEL basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000437480.1 0 0 0 21 678 0 93 0 0 0 0 93 2 0 0 0 0 0 2 1 0.999997 21 675 0 93 2 0 0 0 0 93 2 -2.468949 0 1 121410 3 38 1 0 1 1 1.989980 0 0.130000 2 0.123735 0.460000 0.290000 0.670000 0.450000 0.474524 0.460000 0 0.370000 0.570000 KCTD11 147040 broad.mit.edu 37 17 7256580 7256580 + Missense_Mutation SNP C C T rs35280612 TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr17:7256580C>T ENST00000333751.3 + 1 1373 c.319C>T c.(319-321)Cgg>Tgg p.R107W RP11-542C16.1_ENST00000572417.1_RNA|TMEM95_ENST00000330767.4_5'Flank|TMEM95_ENST00000576060.1_5'Flank|TMEM95_ENST00000389982.4_5'Flank NM_001002914.2 NP_001002914.1 Q693B1 KCD11_HUMAN potassium channel tetramerization domain containing 11 4 Prostate(122;0.157) CTCTGCTCGCCGGGGACCCCA 0.642000 0 SO:0001583 missense ENST00000333751.3 1 1 hg19 CCDS32545.1 . . . . . . . . . . C 17.410000 3.382499 0.618450 . . ENSG00000213859 ENST00000333751 T 0.71698 -0.59 5.380000 -3.060000 0.053790 . 0.158994 0.26979 U 0.021525 T 0.47002 0.1422 N 0.19112 0.55 0.093100 N 1.000000 P 0.51537 0.946 B 0.33521 0.165 T 0.55471 -0.8136 10 0.72032 D 0.01 . 15.056400 0.719170 0.774:0.226:0.0:0.0 . 107 Q693B1 KCD11_HUMAN W 107 ENSP00000328352:R107W ENSP00000328352:R107W R + 1 2 KCTD11 7197304 6.460000e-01 0.272950 8.730000e-01 0.342540 0.874000 0.502790 0.512000 0.227550 -0.389000 0.077860 0.462000 0.415740 CGG TCGA-FB-A4P5-01A-11D-A26I-08 KCTD11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255084.2 1 0 0 11 299 0 61 0 1.941789e-01 1 20 0 61 2 0 0 0 0 0 2 1 0.998382 11 298 0 61 2 0 0 0 0 61 2 -3.149275 1 1 0 0 1 0 0 0 1.967944 0 0.130000 2 0.111520 0.540000 0.280000 0.880000 0.520000 0.563833 0.540000 0 0.400000 0.710000 ITGB4 3691 broad.mit.edu 37 17 73748594 73748594 + Missense_Mutation SNP G G A TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr17:73748594G>A ENST00000200181.3 + 32 4231 c.4044G>A c.(4042-4044)atG>atA p.M1348I ITGB4_ENST00000579662.1_Missense_Mutation_p.M1348I|ITGB4_ENST00000339591.3_Missense_Mutation_p.M1348I|GALK1_ENST00000225614.2_Intron|ITGB4_ENST00000450894.3_Missense_Mutation_p.M1348I|ITGB4_ENST00000449880.2_Missense_Mutation_p.M1348I NM_000213.3 NP_000204.3 P16144 ITB4_HUMAN integrin, beta 4 43 all_cancers(13;1.5e-07) all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154) GCTTCCTTATGTACAGCGATG 0.627000 0 SO:0001583 missense ENST00000200181.3 1 1 hg19 CCDS11727.1 . . . . . . . . . . G 14.880000 2.667504 0.476770 . . ENSG00000132470 ENST00000200181;ENST00000339591;ENST00000449880 T;T;T 0.75938 -0.98;-0.94;-0.94 4.310000 4.310000 0.513920 . 0.000000 0.85682 D 0.000000 T 0.80449 0.4625 L 0.36672 1.1 0.807220 D 1.000000 D;D;D 0.69078 0.997;0.995;0.995 D;D;D 0.80764 0.994;0.987;0.987 T 0.81342 -0.0976 10 0.46703 T 0.11 . 16.957500 0.862630 0.0:0.0:1.0:0.0 . 1348;1348;1348 P16144-3;A0AVL6;P16144 .;.;ITB4_HUMAN I 1348 ENSP00000200181:M1348I;ENSP00000344079:M1348I;ENSP00000400217:M1348I ENSP00000200181:M1348I M + 3 0 ITGB4 71260189 1 0.714170 1 0.803570 0.730000 0.417780 9.571000 0.981760 2.207000 0.712020 0.561000 0.740990 ATG TCGA-FB-A4P5-01A-11D-A26I-08 ITGB4-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000448334.1 0 0 1 18 573 0 129 1 9.885349e-01 124 107 0 129 2 0 0 0 0 0 2 1 0.999979 18 562 0 128 2 0 0 0 0 129 2 -3.524704 1 1 0 0 1 0 1 1 1.989980 0 0.130000 2 0.123735 0.460000 0.280000 0.700000 0.470000 0.483548 0.460000 0 0.370000 0.590000 SEPT9 10801 broad.mit.edu 37 17 75398245 75398245 + Nonsense_Mutation SNP C C T TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr17:75398245C>T ENST00000427177.1 + 3 307 c.181C>T c.(181-183)Cag>Tag p.Q61* SEPT9_ENST00000449803.2_5'UTR|SEPT9_ENST00000588690.1_5'UTR|SEPT9_ENST00000590294.1_Nonsense_Mutation_p.Q43*|SEPT9_ENST00000592420.1_5'UTR|SEPT9_ENST00000431235.2_5'UTR|SEPT9_ENST00000585930.1_5'Flank|SEPT9_ENST00000423034.2_Nonsense_Mutation_p.Q54*|SEPT9_ENST00000427674.2_5'UTR|SEPT9_ENST00000591198.1_Nonsense_Mutation_p.Q42*|SEPT9_ENST00000329047.8_Nonsense_Mutation_p.Q43* NM_001113491.1 NP_001106963.1 Q9UHD8 SEPT9_HUMAN septin 9 16 BRCA - Breast invasive adenocarcinoma(99;0.153) CAGCTCCACCCAGAAATTCCA 0.627000 0 SO:0001587 stop_gained ENST00000427177.1 0 1 hg19 CCDS45790.1 . . . . . . . . . . C 45.000000 11.389194 0.995550 . . ENSG00000184640 ENST00000427177;ENST00000329047;ENST00000423034 . . . 4.890000 4.890000 0.638310 . 2.942800 0.01335 U 0.011366 . . . . . . 0.807220 D 1.000000 . . . . . . . . . . 0.59425 D 0.04 . 17.043500 0.864960 0.0:1.0:0.0:0.0 . . . . X 61;43;54 . ENSP00000329161:Q43X Q + 1 0 SEPT9 72909840 1 0.714170 1 0.803570 0.997000 0.918780 4.105000 0.577970 2.262000 0.750190 0.555000 0.697020 CAG TCGA-FB-A4P5-01A-11D-A26I-08 SEPT9-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000436304.2 1 0 0 11 221 0 46 0 8.677940e-01 0 75 0 46 2 0 0 0 0 0 2 1 0.998250 11 216 0 46 2 0 0 0 0 46 2 -2.943210 1 1 0 0 1 0 1 1 1.989980 0 0.130000 2 0.123735 0.730000 0.390000 1.000000 1.000000 0.741941 0.730000 0 0.540000 0.960000 RCVRN 5957 broad.mit.edu 37 17 9808122 9808122 + Missense_Mutation SNP C C T TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr17:9808122C>T ENST00000226193.5 - 1 816 c.376G>A c.(376-378)Gtc>Atc p.V126I NM_002903.2 NP_002894.1 P35243 RECO_HUMAN recoverin 12 CTGACCATGACGATCTCCAGC 0.642000 0 SO:0001583 missense ENST00000226193.5 1 1 hg19 CCDS11151.1 . . . . . . . . . . C 8.226000 0.803586 0.164670 . . ENSG00000109047 ENST00000226193 T 0.66280 -0.2 4.860000 1.660000 0.240080 EF-hand-like domain (1); 0.252761 0.39909 N 0.001225 T 0.41282 0.1152 N 0.21508 0.67 0.807220 D 1.000000 B 0.11235 0.004 B 0.04013 0.001 T 0.11542 -1.0583 10 0.26408 T 0.33 . 7.045500 0.250420 0.0:0.6107:0.0:0.3893 . 126 P35243 RECO_HUMAN I 126 ENSP00000226193:V126I ENSP00000226193:V126I V - 1 0 RCVRN 9748847 5.200000e-02 0.205160 9.970000e-01 0.539660 0.306000 0.277900 0.015000 0.133550 0.554000 0.290610 0.655000 0.942530 GTC TCGA-FB-A4P5-01A-11D-A26I-08 RCVRN-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252600.2 0 0 0 17 453 0 112 0 8.611770e-03 0 4 0 112 2 0 0 0 0 0 2 1 0.999964 17 449 0 112 2 0 0 0 0 112 2 -3.764973 1 1 0 0 1 0 0 0 1.967944 0 0.130000 2 0.111520 0.540000 0.330000 0.820000 0.540000 0.564653 0.540000 0 0.430000 0.690000 SERPINB11 89778 broad.mit.edu 37 18 61377522 61377522 + RNA SNP C C T TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr18:61377522C>T ENST00000382749.5 + 0 340 SERPINB11_ENST00000536691.1_RNA|SERPINB11_ENST00000544088.1_RNA|SERPINB11_ENST00000489748.1_RNA|SERPINB11_ENST00000538847.1_RNA Q96P15 SPB11_HUMAN serpin peptidase inhibitor, clade B (ovalbumin), member 11 (gene/pseudogene) 6 Esophageal squamous(42;0.129) TTCTTTTCTTCGCTGAGTCTG 0.428000 Ovarian(27;496 784 5942 8975 23930) 0 ENST00000382749.5 0 1 hg19 . . . . . . . . . . C 9.959000 1.222256 0.224570 2.61E-4 0.0 ENSG00000206072 ENST00000544088;ENST00000538847 D;D 0.82526 -1.62;-1.62 5.140000 4.270000 0.506960 Serpin domain (3); 0.266677 0.26734 N 0.022770 T 0.73329 0.3573 L 0.28649 0.875 0.807220 D 1.000000 B;B 0.31611 0.098;0.331 B;B 0.28385 0.033;0.089 T 0.73920 -0.3830 10 0.87932 D 0 . 11.743800 0.518090 0.0:0.9128:0.0:0.0872 . 32;32 F5GY69;Q96P15 .;SPB11_HUMAN L 32 ENSP00000441497:S32L;ENSP00000440795:S32L ENSP00000421854:S32L S + 2 0 SERPINB11 59528502 7.170000e-01 0.279660 1.100000e-01 0.214370 0.034000 0.127010 3.569000 0.538270 1.284000 0.445310 0.655000 0.942530 TCG TCGA-FB-A4P5-01A-11D-A26I-08 SERPINB11-002 KNOWN basic polymorphic_pseudogene polymorphic_pseudogene OTTHUMT00000207392.3 0 0 0 6 170 0 21 0 0 0 0 21 2 0 0 0 0 0 2 1 0.965782 6 170 0 21 2 0 0 0 0 21 2 -8.067376 1 1 120850 4 35 1 0 1 1 1.997298 0 0.130000 2 0.125452 0.540000 0.230000 1.000000 1.000000 0.573279 0.540000 0 0.360000 0.780000 ZNF430 80264 broad.mit.edu 37 19 21239860 21239860 + Missense_Mutation SNP C C T TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr19:21239860C>T ENST00000261560.5 + 5 927 c.746C>T c.(745-747)aCt>aTt p.T249I AC012627.1_ENST00000578233.1_RNA NM_001172671.1|NM_025189.3 NP_001166142.1|NP_079465.3 Q9H8G1 ZN430_HUMAN zinc finger protein 430 23 TCAACCCTTACTAGACACAGA 0.348000 0 SO:0001583 missense ENST00000261560.5 1 1 hg19 CCDS32978.1 . . . . . . . . . . . 3.684000 -0.064825 0.072730 . . ENSG00000118620 ENST00000261560 T 0.33865 1.39 1.040000 -0.123000 0.135270 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.26195 0.0639 N 0.12471 0.22 0.093100 N 1.000000 D;P 0.56968 0.978;0.723 P;B 0.53760 0.734;0.41 T 0.12915 -1.0529 9 0.38643 T 0.18 . 4.590700 0.123060 0.0:0.5789:0.0:0.4211 . 248;249 Q2NKJ9;Q9H8G1 .;ZN430_HUMAN I 249 ENSP00000261560:T249I ENSP00000261560:T249I T + 2 0 ZNF430 21031700 0 0.058580 1.500000e-02 0.157900 0.014000 0.085840 -3.561000 0.004300 0.452000 0.268300 0.455000 0.322230 ACT TCGA-FB-A4P5-01A-11D-A26I-08 ZNF430-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000463539.1 0 0 0 9 290 0 30 0 3.534434e-03 0 3 0 30 2 0 0 0 0 0 2 1 0.994233 9 288 0 29 2 0 0 0 0 30 2 -9.985004 1 1 0 0 1 1 2 3 2.014925 0 0.130000 2 0.137290 0.500000 0.240000 1.000000 0.460000 0.555958 0.500000 0 0.350000 0.760000 ZNF208 7757 broad.mit.edu 37 19 22171675 22171675 + Missense_Mutation SNP A A T TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr19:22171675A>T ENST00000397126.4 - 2 188 c.40T>A c.(40-42)Tct>Act p.S14T ZNF208_ENST00000601773.1_Missense_Mutation_p.S14T|ZNF208_ENST00000599916.1_Missense_Mutation_p.S14T|ZNF208_ENST00000597040.1_5'UTR NM_007153.3 NP_009084.2 O43345 ZN208_HUMAN zinc finger protein 208 113 all_lung(12;0.0961)|Lung NSC(12;0.103) TCCTCCAGAGAGAATTCTATG 0.403000 0 SO:0001583 missense ENST00000397126.4 1 1 hg19 CCDS54240.1 . . . . . . . . . . A 3.819000 -0.038200 0.074970 . . ENSG00000160321 ENST00000397126;ENST00000428290 T 0.01484 4.84 1.320000 -0.168000 0.133430 Krueppel-associated box (4); . . . . T 0.02304 0.0071 . . . 0.093100 N 1.000000 D;P 0.63046 0.992;0.876 P;P 0.60012 0.867;0.652 T 0.27640 -1.0068 8 0.07175 T 0.84 . 3.607000 0.080460 0.3597:0.0:0.0:0.6403 . 14;14 O43345;F8WEA0 ZN208_HUMAN;. T 14 ENSP00000380315:S14T ENSP00000380315:S14T S - 1 0 ZNF208 21963515 2.000000e-03 0.142020 9.000000e-03 0.144450 0.641000 0.383120 -0.021000 0.125040 -0.610000 0.057160 0.234000 0.178320 TCT TCGA-FB-A4P5-01A-11D-A26I-08 ZNF208-001 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000464302.1 0 0 0 16 748 0 87 0 0 0 1 0 87 2 0 0 0 0 0 2 1 0.999929 16 744 0 87 2 0 0 0 0 87 2 -3.179099 1 1 0 0 1 1 2 3 2.014925 0 0.130000 2 0.137290 0.340000 0.190000 1.000000 0.320000 0.410127 0.340000 0 0.260000 0.480000 ZNF616 90317 broad.mit.edu 37 19 52619638 52619638 + Missense_Mutation SNP T T C TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr19:52619638T>C ENST00000600228.1 - 4 1040 c.779A>G c.(778-780)cAa>cGa p.Q260R ZNF616_ENST00000330123.5_3'UTR NM_178523.3 NP_848618.2 Q08AN1 ZN616_HUMAN zinc finger protein 616 48 GTGACTCCTTTGGTGTCTTAC 0.383000 0 SO:0001583 missense ENST00000600228.1 1 1 hg19 CCDS33090.1 . . . . . . . . . . T 9.538000 1.112700 0.207950 . . ENSG00000204611 ENST00000330123 . . . 0.954000 -0.118000 0.135470 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.25457 0.0619 L 0.28344 0.845 0.093100 N 1.000000 B 0.27594 0.182 B 0.28638 0.092 T 0.20874 -1.0262 8 0.35671 T 0.21 . 4.225900 0.105800 0.0:0.2336:0.0:0.7664 . 260 Q08AN1 ZN616_HUMAN R 260 . ENSP00000328722:Q260R Q - 2 0 ZNF616 57311450 0 0.058580 4.000000e-03 0.123270 0.858000 0.489760 -0.069000 0.115420 -0.101000 0.122190 0.254000 0.183690 CAA TCGA-FB-A4P5-01A-11D-A26I-08 ZNF616-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000462451.1 0 0 0 19 500 0 35 0 4.503075e-03 0 3 0 35 2 0 0 0 0 0 2 1 0.999990 19 495 0 34 2 0 0 0 0 35 2 -4.024561 1 1 0 0 1 1 2 3 2.022814 0 0.130000 2 0.138955 0.590000 0.360000 1.000000 0.570000 0.641063 0.590000 0 0.460000 0.830000 ZNF561 93134 broad.mit.edu 37 19 9721440 9721440 + Silent SNP G G A TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr19:9721440G>A ENST00000302851.3 - 6 1260 c.897C>T c.(895-897)caC>caT p.H299H ZNF561_ENST00000424629.1_Silent_p.H230H|ZNF561_ENST00000354661.4_Silent_p.H163H|ZNF561_ENST00000495503.1_5'Flank|ZNF561_ENST00000326044.5_3'UTR NM_152289.2 NP_689502.2 Q8N587 ZN561_HUMAN zinc finger protein 561 14 GAATTTGAATGTGATCATTAA 0.373000 0 SO:0001819 synonymous_variant ENST00000302851.3 1 1 hg19 CCDS12216.2 TCGA-FB-A4P5-01A-11D-A26I-08 ZNF561-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347272.2 0 0 0 25 646 0 57 0 1.137424e-01 1 14 0 57 2 0 0 0 0 0 2 1 1.000000 25 641 0 57 2 0 0 0 0 57 2 -3.901997 1 1 121412 1 34 1 1 2 3 2.009114 0 0.130000 2 0.136176 0.590000 0.380000 1.000000 0.570000 0.629087 0.590000 0 0.480000 0.760000 HMCN1 83872 broad.mit.edu 37 1 186057376 186057376 + Missense_Mutation SNP C C T TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr1:186057376C>T ENST00000271588.4 + 62 9774 c.9545C>T c.(9544-9546)aCg>aTg p.T3182M HMCN1_ENST00000367492.2_Missense_Mutation_p.T3182M NM_031935.2 NP_114141.2 Q96RW7 HMCN1_HUMAN hemicentin 1 308 CCACCTCCCACGATAGCATGG 0.443000 0 SO:0001583 missense ENST00000271588.4 0 1 hg19 CCDS30956.1 . . . . . . . . . . C 11.090000 1.535093 0.274750 . . ENSG00000143341 ENST00000271588;ENST00000367492 T;T 0.68479 -0.33;-0.33 5.630000 -1.850000 0.077840 Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); 0.735216 0.13487 N 0.384223 T 0.62925 0.2468 M 0.78456 2.415 0.093100 N 1.000000 B 0.27791 0.189 B 0.24155 0.051 T 0.54234 -0.8324 10 0.48119 T 0.1 . 11.213300 0.488130 0.0:0.5779:0.0:0.4221 . 3182 Q96RW7 HMCN1_HUMAN M 3182 ENSP00000271588:T3182M;ENSP00000356462:T3182M ENSP00000271588:T3182M T + 2 0 HMCN1 184323999 2.000000e-03 0.142020 0 0.037020 0.741000 0.422610 0.371000 0.204500 -0.692000 0.051280 -0.471000 0.050190 ACG TCGA-FB-A4P5-01A-11D-A26I-08 HMCN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000131848.1 0 0 0 7 232 0 27 0 1.234526e-03 0 2 0 27 2 0 0 0 0 0 2 1 0.979869 6 229 0 27 2 0 0 0 0 27 2 -3.586890 1 1 121398 3 32 1 1 2 3 2.010868 0 0.130000 2 0.136733 0.500000 0.210000 1.000000 0.440000 0.548638 0.500000 0 0.330000 0.780000 PRG4 10216 broad.mit.edu 37 1 186281436 186281436 + Missense_Mutation SNP T T A TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr1:186281436T>A ENST00000445192.2 + 11 3968 c.3923T>A c.(3922-3924)aTa>aAa p.I1308K PRG4_ENST00000367485.4_Missense_Mutation_p.I1215K|PRG4_ENST00000367483.4_Missense_Mutation_p.I1267K|PRG4_ENST00000367486.3_Missense_Mutation_p.I1265K|TPR_ENST00000367478.4_3'UTR|RNU6-1240P_ENST00000365155.1_RNA|PRG4_ENST00000367484.3_Missense_Mutation_p.I837K NM_005807.3 NP_005798.2 Q92954 PRG4_HUMAN proteoglycan 4 102 GAACGTGCTATAGGACCTTCT 0.418000 0 SO:0001583 missense ENST00000445192.2 1 1 hg19 CCDS1369.1 . . . . . . . . . . T 11.110000 1.543642 0.275630 . . ENSG00000116690 ENST00000367486;ENST00000367484;ENST00000367483;ENST00000367485;ENST00000445192 T;T;T;T;T 0.07688 3.17;3.29;3.27;3.18;3.27 5.480000 1.860000 0.254190 Hemopexin/matrixin (1); 0.514144 0.16080 N 0.230549 T 0.15652 0.0377 L 0.47716 1.5 0.093100 N 1.000000 D;D;D;D 0.71674 0.988;0.988;0.998;0.988 P;P;P;P 0.62014 0.851;0.851;0.897;0.851 T 0.08534 -1.0717 10 0.87932 D 0 -2.0141 5.775400 0.182770 0.0:0.1475:0.1412:0.7113 . 1174;1215;1308;1267 Q92954-4;Q92954-3;Q92954;Q92954-2 .;.;PRG4_HUMAN;. K 1265;837;1267;1215;1308 ENSP00000356456:I1265K;ENSP00000356454:I837K;ENSP00000356453:I1267K;ENSP00000356455:I1215K;ENSP00000399679:I1308K ENSP00000356453:I1267K I + 2 0 PRG4 184548059 7.000000e-03 0.166370 1.000000e-03 0.086480 0.291000 0.272940 1.709000 0.379090 0.121000 0.182840 0.477000 0.441520 ATA TCGA-FB-A4P5-01A-11D-A26I-08 PRG4-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000086346.1 0 0 0 20 674 0 78 0 1.330862e-01 0 21 0 78 2 0 0 0 0 0 2 1 0.999995 20 666 0 77 2 0 0 0 0 78 2 -16.596960 1 1 0 0 1 1 2 3 2.010868 0 0.130000 2 0.136733 0.460000 0.280000 1.000000 0.440000 0.515411 0.460000 0 0.360000 0.620000 EPHA8 2046 broad.mit.edu 37 1 22923888 22923888 + Missense_Mutation SNP G G A TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr1:22923888G>A ENST00000166244.3 + 10 1921 c.1849G>A c.(1849-1851)Gag>Aag p.E617K NM_020526.3 NP_065387.1 P29322 EPHA8_HUMAN EPH receptor A8 61 Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255) CCACACCTACGAGGAGCCAGG 0.637000 0 SO:0001583 missense ENST00000166244.3 0 1 hg19 CCDS225.1 . . . . . . . . . . G 20.400000 3.987973 0.745890 0.0 1.16E-4 ENSG00000070886 ENST00000166244 T 0.23754 1.89 4.630000 4.630000 0.577260 Protein kinase-like domain (1); 0.000000 0.85682 D 0.000000 T 0.53094 0.1775 M 0.82716 2.605 0.807220 D 1.000000 D 0.71674 0.998 D 0.65987 0.94 T 0.61407 -0.7069 10 0.87932 D 0 . 16.210100 0.821500 0.0:0.0:1.0:0.0 . 617 P29322 EPHA8_HUMAN K 617 ENSP00000166244:E617K ENSP00000166244:E617K E + 1 0 EPHA8 22796475 1 0.714170 9.780000e-01 0.431390 0.105000 0.192720 9.657000 0.985540 2.412000 0.818960 0.491000 0.489740 GAG TCGA-FB-A4P5-01A-11D-A26I-08 EPHA8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000008085.1 0 0 0 18 817 0 138 0 3.143196e-03 0 4 0 138 2 0 0 0 0 0 2 1 0.999979 16 807 0 136 2 0 0 0 0 138 2 -2.302281 0 1 121412 9 44 1 0 1 1 1.999275 0 0.130000 2 0.125452 0.330000 0.200000 0.500000 0.330000 0.344520 0.330000 0 0.260000 0.420000 EPHA8 2046 broad.mit.edu 37 1 22927844 22927844 + Silent SNP C C T TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr1:22927844C>T ENST00000166244.3 + 16 2853 c.2781C>T c.(2779-2781)agC>agT p.S927S NM_020526.3 NP_065387.1 P29322 EPHA8_HUMAN EPH receptor A8 61 Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255) GAGGGGGCAGCGGTGGCGGTG 0.692000 0 SO:0001819 synonymous_variant ENST00000166244.3 0 1 hg19 CCDS225.1 TCGA-FB-A4P5-01A-11D-A26I-08 EPHA8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000008085.1 0 0 0 10 443 0 76 0 0 0 1 0 76 2 0 0 0 0 0 2 1 0.996623 10 434 0 73 2 0 0 0 0 76 2 -3.016787 1 1 121136 1 38 1 0 1 1 1.999275 0 0.130000 2 0.125452 0.340000 0.170000 0.580000 0.330000 0.364320 0.340000 0 0.250000 0.470000 CHD5 26038 broad.mit.edu 37 1 6202252 6202252 + Missense_Mutation SNP C C T TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr1:6202252C>T ENST00000262450.3 - 15 2471 c.2372G>A c.(2371-2373)cGg>cAg p.R791Q CHD5_ENST00000378021.1_5'UTR NM_015557.2 NP_056372.1 O00258 WRB_HUMAN chromodomain helicase DNA binding protein 5 16 Ovarian(185;0.0634) all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15) CTCGTTCTCCCGAATCACCGA 0.557000 0 SO:0001583 missense ENST00000262450.3 1 1 hg19 CCDS57.1 . . . . . . . . . . C 32.000000 5.152028 0.946450 . . ENSG00000116254 ENST00000262450;ENST00000378006;ENST00000536802;ENST00000538279 D 0.93712 -3.27 4.070000 4.070000 0.474770 DEAD-like helicase (2);SNF2-related (1); 0.076633 0.49305 D 0.000151 D 0.95475 0.8530 L 0.56769 1.78 0.807220 D 1.000000 D 0.71674 0.998 D 0.76575 0.988 D 0.94752 0.7928 10 0.35671 T 0.21 -22.1812 16.621800 0.849320 0.0:1.0:0.0:0.0 . 791 Q8TDI0 CHD5_HUMAN Q 791;307;199;199 ENSP00000262450:R791Q ENSP00000262450:R791Q R - 2 0 CHD5 6124839 1 0.714170 9.960000e-01 0.522420 0.952000 0.607820 7.693000 0.842140 1.977000 0.576050 0.561000 0.740990 CGG TCGA-FB-A4P5-01A-11D-A26I-08 CHD5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000002823.2 0 0 0 24 827 0 152 0 0 0 0 152 2 0 0 0 0 0 2 1 1.000000 24 820 0 152 2 0 0 0 0 152 2 -1.968955 0 1 121412 1 34 1 1 2 3 2.013303 0 0.130000 2 0.137290 0.450000 0.290000 1.000000 0.430000 0.508542 0.450000 0 0.360000 0.600000 APOB 338 broad.mit.edu 37 2 21251239 21251239 + Missense_Mutation SNP T T C TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr2:21251239T>C ENST00000233242.1 - 13 1916 c.1789A>G c.(1789-1791)Att>Gtt p.I597V APOB_ENST00000399256.4_Missense_Mutation_p.I597V NM_000384.2 NP_000375 P04114 APOB_HUMAN apolipoprotein B 305 Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215) ATATTGGCAATATGGGAAGCC 0.418000 0 SO:0001583 missense ENST00000233242.1 0 1 hg19 CCDS1703.1 . . . . . . . . . . T 14.510000 2.558392 0.455900 . . ENSG00000084674 ENST00000233242;ENST00000535079;ENST00000399256 T;T 0.57436 0.4;0.4 5.690000 3.170000 0.364340 Lipid transport protein, N-terminal (3);Vitellinogen, superhelical (2); 0.352961 0.27764 N 0.017944 T 0.47229 0.1434 L 0.56769 1.78 0.369090 D 0.890822 P 0.42908 0.793 B 0.38655 0.278 T 0.57757 -0.7756 10 0.42905 T 0.14 . 12.434100 0.555900 0.0:0.0:0.2866:0.7134 . 597 P04114 APOB_HUMAN V 597 ENSP00000233242:I597V;ENSP00000382200:I597V ENSP00000233242:I597V I - 1 0 APOB 21104744 1 0.714170 1 0.803570 0.971000 0.663760 0.596000 0.240440 1.098000 0.414790 0.533000 0.621200 ATT TCGA-FB-A4P5-01A-11D-A26I-08 APOB-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207571.1 0 0 0 20 399 1 35 0 0 0 1 35 2 0 0 0 0 0 2 0 0.052275 20 395 1 35 32 0 0 0 1 35 2 -19.987640 1 1 0 0 1 0 1 1 1.997827 0 0.130000 2 0.125452 0.730000 0.460000 1.000000 1.000000 0.744823 0.730000 0 0.580000 0.900000 CNGA3 1261 broad.mit.edu 37 2 99013339 99013339 + Missense_Mutation SNP G G A TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr2:99013339G>A ENST00000272602.2 + 7 1745 c.1706G>A c.(1705-1707)cGc>cAc p.R569H CNGA3_ENST00000393504.1_Missense_Mutation_p.R569H|CNGA3_ENST00000409937.1_Missense_Mutation_p.R573H|CNGA3_ENST00000436404.2_Missense_Mutation_p.R551H Q16281 CNGA3_HUMAN cyclic nucleotide gated channel alpha 3 49 GCCAACATCCGCAGCATTGGC 0.582000 0 GRCh37 CM014559 CNGA3 M SO:0001583 missense ENST00000272602.2 1 1 hg19 CCDS2034.1 . . . . . . . . . . G 19.460000 3.832457 0.712580 0.0 1.16E-4 ENSG00000144191 ENST00000393504;ENST00000436404;ENST00000272602;ENST00000409937 D;D;D;D 0.97161 -4.27;-4.27;-4.27;-4.27 5.420000 5.420000 0.788660 Cyclic nucleotide-binding, conserved site (1);Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3); 0.000000 0.85682 D 0.000000 D 0.98833 0.9606 H 0.96208 3.785 0.807220 D 1.000000 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.78314 0.988;0.988;0.991 D 0.98965 1.0799 10 0.87932 D 0 . 12.119600 0.538830 0.0815:0.0:0.9185:0.0 . 573;551;569 E9PF93;Q4VAP7;Q16281 .;.;CNGA3_HUMAN H 569;551;569;573 ENSP00000377140:R569H;ENSP00000410070:R551H;ENSP00000272602:R569H;ENSP00000386761:R573H ENSP00000272602:R569H R + 2 0 CNGA3 98379771 9.870000e-01 0.356910 1 0.803570 0.697000 0.404080 4.514000 0.604820 2.826000 0.973560 0.563000 0.778840 CGC TCGA-FB-A4P5-01A-11D-A26I-08 CNGA3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000252986.1 0 0 0 31 682 1 111 0 0 0 1 1 111 2 0 0 0 0 0 2 1 0.937179 31 678 1 111 21 0 0 0 1 111 2 -4.165749 1 1 121412 3 41 1 1 2 3 2.015221 0 0.130000 2 0.137290 0.690000 0.470000 1.000000 0.670000 0.720339 0.690000 0 0.570000 0.880000 DCBLD2 131566 broad.mit.edu 37 3 98518461 98518461 + Nonsense_Mutation SNP G G A TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr3:98518461G>A ENST00000326840.6 - 16 2445 c.2083C>T c.(2083-2085)Cag>Tag p.Q695* DCBLD2_ENST00000326857.9_Nonsense_Mutation_p.Q709* NM_080927.3 NP_563615.3 Q96PD2 DCBD2_HUMAN discoidin, CUB and LCCL domain containing 2 25 GTGGAGGGCTGACCAACTGAA 0.527000 0 SO:0001587 stop_gained ENST00000326840.6 0 1 hg19 CCDS46878.1 . . . . . . . . . . G 37.000000 6.627228 0.977180 . . ENSG00000057019 ENST00000326840;ENST00000326857 . . . 5.650000 2.790000 0.327310 . 0.592892 0.15545 N 0.256738 . . . . . . 0.807220 D 1.000000 . . . . . . . . . . 0.52906 T 0.07 -6.2138 1.824800 0.031180 0.1818:0.169:0.4938:0.1554 . . . . X 695;709 . ENSP00000321573:Q695X Q - 1 0 DCBLD2 100001151 2.500000e-02 0.190820 7.030000e-01 0.303540 0.563000 0.357120 1.076000 0.307290 1.393000 0.466050 0.655000 0.942530 CAG TCGA-FB-A4P5-01A-11D-A26I-08 DCBLD2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000324675.2 0 0 0 13 462 0 70 1 1.376979e-01 3 19 0 70 2 0 0 0 0 0 2 1 0.999532 13 461 0 70 2 0 0 0 0 70 2 -3.088139 1 1 0 0 1 1 2 3 2.009434 0 0.130000 2 0.136176 0.440000 0.240000 1.000000 0.420000 0.497699 0.440000 0 0.330000 0.620000 PCDHGB3 56102 broad.mit.edu 37 5 140751764 140751764 + Silent SNP C C T rs57763341 TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr5:140751764C>T ENST00000576222.1 + 1 1934 c.1803C>T c.(1801-1803)aaC>aaT p.N601N PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_5'Flank NM_018924.2|NM_032097.1 NP_061747.1|NP_115268.1 Q9Y5G1 PCDGF_HUMAN protocadherin gamma subfamily B, 3 5 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) CGGGATACAACGCCTGGCTGT 0.672000 0 SO:0001819 synonymous_variant ENST00000576222.1 0 1 hg19 CCDS58980.1 TCGA-FB-A4P5-01A-11D-A26I-08 PCDHGB3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000437094.1 0 0 0 8 455 0 114 0 0 0 0 114 2 0 0 0 0 0 2 1 0.988919 8 449 0 112 2 0 0 0 0 114 2 -6.967111 1 1 121404 50 50 1 1 2 3 2.010250 0 0.130000 2 0.136176 0.290000 0.130000 1.000000 0.270000 0.358387 0.290000 0 0.190000 0.440000 PCDHGB4 8641 broad.mit.edu 37 5 140769030 140769030 + Missense_Mutation SNP G G A TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr5:140769030G>A ENST00000519479.1 + 1 1579 c.1579G>A c.(1579-1581)Gaa>Aaa p.E527K PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron NM_003736.2|NM_018925.2|NM_032098.1 NP_003727.1|NP_061748.1|NP_115269.1 Q9UN71 PCDGG_HUMAN protocadherin gamma subfamily B, 4 37 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) GCGCGCCTTCGAACTCACACT 0.677000 0 SO:0001583 missense ENST00000519479.1 1 1 hg19 CCDS54928.1 . . . . . . . . . . . 8.696000 0.908490 0.178330 . . ENSG00000253953 ENST00000519479 T 0.54071 0.59 4.950000 -1.960000 0.075250 Cadherin (5);Cadherin-like (1); . . . . T 0.43831 0.1265 L 0.46947 1.48 0.093100 N 1.000000 P;P 0.44478 0.836;0.697 B;B 0.38458 0.261;0.274 T 0.29336 -1.0015 9 0.33940 T 0.23 . 15.777100 0.782320 0.1245:0.6211:0.2544:0.0 . 527;527 Q9UN71-2;Q9UN71 .;PCDGG_HUMAN K 527 ENSP00000428288:E527K ENSP00000428288:E527K E + 1 0 PCDHGB4 140749214 0 0.058580 6.880000e-01 0.301170 0.248000 0.258090 -2.903000 0.007030 -1.088000 0.030770 -2.589000 0.001650 GAA TCGA-FB-A4P5-01A-11D-A26I-08 PCDHGB4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000374745.1 0 0 0 8 304 0 59 0 9.099181e-04 0 2 0 59 2 0 0 0 0 0 2 1 0.989189 8 301 0 59 2 0 0 0 0 59 2 -8.433194 1 1 0 0 1 1 2 3 2.010250 0 0.130000 2 0.136176 0.430000 0.190000 1.000000 0.390000 0.485255 0.430000 0 0.290000 0.650000 SLC6A7 6534 broad.mit.edu 37 5 149576606 149576606 + Splice_Site SNP C C T TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr5:149576606C>T ENST00000230671.2 + 4 722 c.351C>T c.(349-351)ggC>ggT p.G117G SLC6A7_ENST00000524041.1_Splice_Site_p.G117G NM_014228.3 NP_055043.2 Q99884 SC6A7_HUMAN solute carrier family 6 (neurotransmitter transporter), member 7 16 all_hematologic(541;0.224) KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101) L-Proline(DB00172) CCACACCAGGCGCCGGCGCAG 0.637000 0 SO:0001630 splice_region_variant ENST00000230671.2 1 0 hg19 CCDS4305.1 TCGA-FB-A4P5-01A-11D-A26I-08 SLC6A7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252325.1 1 0 0 5 133 0 36 0 0 0 0 36 2 0 0 0 0 0 2 1 0.936303 5 131 0 36 2 0 0 0 0 36 2 -7.986053 1 0 121398 3 35 1 1 2 3 2.010250 0 0.130000 2 0.136176 0.620000 0.230000 1.000000 1.000000 0.653703 0.620000 0 0.390000 1.000000 GRM6 2916 broad.mit.edu 37 5 178410024 178410024 + Missense_Mutation SNP C C T TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr5:178410024C>T ENST00000517717.1 - 10 2361 c.2323G>A c.(2323-2325)Gtg>Atg p.V775M RP11-281O15.4_ENST00000519491.1_RNA|GRM6_ENST00000231188.5_Missense_Mutation_p.V775M O15303 GRM6_HUMAN glutamate receptor, metabotropic 6 p.V775M(2) 55 all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351) all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21) Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178) GTCTCGGGCACGCCACGGGCC 0.597000 2 Substitution - Missense(2) SO:0001583 missense ENST00000517717.1 0 1 hg19 CCDS4442.1 . . . . . . . . . . C 17.400000 3.379871 0.618450 . . ENSG00000113262 ENST00000231188;ENST00000517717 D;D 0.89485 -2.52;-2.52 5.180000 5.180000 0.714440 GPCR, family 3, C-terminal (2); . . . . D 0.94823 0.8328 M 0.84683 2.71 0.547530 D 0.999987 D;D 0.76494 0.999;0.998 D;D 0.77557 0.99;0.967 D 0.95314 0.8414 9 0.72032 D 0.01 . 16.553400 0.844780 0.0:1.0:0.0:0.0 . 775;69 O15303;Q5HYM4 GRM6_HUMAN;. M 775 ENSP00000231188:V775M;ENSP00000430767:V775M ENSP00000231188:V775M V - 1 0 GRM6 178342630 1 0.714170 7.670000e-01 0.314950 0.036000 0.129970 7.658000 0.837550 2.591000 0.875370 0.313000 0.208870 GTG TCGA-FB-A4P5-01A-11D-A26I-08 GRM6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253474.2 0 0 0 10 371 0 70 0 0 0 0 70 2 0 0 0 0 0 2 1 0.996806 10 367 0 69 2 0 0 0 0 70 2 -9.742636 1 1 121412 5 41 1 1 2 3 2.010250 0 0.130000 2 0.136176 0.430000 0.210000 1.000000 0.400000 0.487587 0.430000 0 0.310000 0.630000 SEMA5A 9037 broad.mit.edu 37 5 9066644 9066644 + Nonsense_Mutation SNP G G A TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr5:9066644G>A ENST00000382496.5 - 17 2853 c.2188C>T c.(2188-2190)Cga>Tga p.R730* NM_003966.2 NP_003957.2 Q13591 SEM5A_HUMAN sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A 81 CATGTGTATCGGAATCGTTGC 0.557000 0 SO:0001587 stop_gained ENST00000382496.5 0 1 hg19 CCDS3875.1 . . . . . . . . . . G 44.000000 10.876622 0.994820 . . ENSG00000112902 ENST00000382496 . . . 5.520000 4.650000 0.581690 . 0.000000 0.85682 D 0.000000 . . . . . . 0.807220 A 1.000000 . . . . . . . . . . 0.02654 T 1 . 13.937300 0.640320 0.0:0.0:0.8468:0.1532 . . . . X 730 . ENSP00000371936:R730X R - 1 2 SEMA5A 9119644 1 0.714170 9.610000e-01 0.401460 0.351000 0.292360 2.938000 0.489870 1.468000 0.480640 -0.230000 0.122520 CGA TCGA-FB-A4P5-01A-11D-A26I-08 SEMA5A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000206989.2 0 0 0 26 773 0 89 0 2.184866e-02 0 7 0 89 2 0 0 0 0 0 2 1 1.000000 26 767 0 87 2 0 0 0 0 89 2 -2.391692 0 1 0 0 1 1 2 3 2.010809 0 0.130000 2 0.136733 0.520000 0.340000 1.000000 0.500000 0.565041 0.520000 0 0.420000 0.670000 SP4 6671 broad.mit.edu 37 7 21516727 21516727 + Missense_Mutation SNP T T C TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr7:21516727T>C ENST00000222584.3 + 4 1927 c.1709T>C c.(1708-1710)gTc>gCc p.V570A NM_003112.3 NP_003103.2 Q02446 SP4_HUMAN Sp4 transcription factor 35 GGAGTAAAAGTCCAGCAAGCT 0.378000 0 SO:0001583 missense ENST00000222584.3 0 1 hg19 CCDS5373.1 . . . . . . . . . . T 17.250000 3.341432 0.609630 . . ENSG00000105866 ENST00000222584;ENST00000432066 T 0.10099 2.91 6.170000 6.170000 0.997090 . 0.000000 0.85682 D 0.000000 T 0.26195 0.0639 L 0.49126 1.545 0.807220 D 1.000000 D 0.58970 0.984 D 0.68192 0.956 T 0.01858 -1.1259 10 0.18276 T 0.48 . 16.822200 0.858350 0.0:0.0:0.0:1.0 . 570 Q02446 SP4_HUMAN A 570;13 ENSP00000222584:V570A ENSP00000222584:V570A V + 2 0 SP4 21483252 1 0.714170 1 0.803570 0.998000 0.957120 7.611000 0.829620 2.371000 0.807100 0.533000 0.621200 GTC TCGA-FB-A4P5-01A-11D-A26I-08 SP4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000211617.2 0 0 0 5 187 0 28 0 1.110230e-03 0 2 0 28 2 0 0 0 0 0 2 1 0.933953 5 182 0 28 2 0 0 0 0 28 2 -7.234855 1 1 0 0 1 1 2 3 2.012047 0 0.130000 2 0.136733 0.460000 0.170000 1.000000 0.390000 0.514766 0.460000 0 0.280000 0.760000 RADIL 55698 broad.mit.edu 37 7 4917630 4917630 + Silent SNP G G A TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr7:4917630G>A ENST00000399583.3 - 2 328 c.141C>T c.(139-141)ggC>ggT p.G47G RADIL_ENST00000536091.1_Silent_p.G47G NM_018059.4 NP_060529.4 Q96JH8 RADIL_HUMAN Ras association and DIL domains 41 Ovarian(82;0.0175) CATCGCTGGCGCCCAGGCTGG 0.627000 0 SO:0001819 synonymous_variant ENST00000399583.3 0 1 hg19 CCDS43544.1 TCGA-FB-A4P5-01A-11D-A26I-08 RADIL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000323769.2 1 0 0 6 106 0 20 0 0 0 1 0 20 2 0 0 0 0 0 2 1 0.964368 5 105 0 20 2 0 0 0 0 20 2 -9.908031 1 1 120894 7 34 1 1 2 3 2.012047 0 0.130000 2 0.136733 0.900000 0.370000 1.000000 1.000000 0.828945 0.900000 1 0.590000 1.000000 HAS2 3037 broad.mit.edu 37 8 122641537 122641537 + Missense_Mutation SNP G G T TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr8:122641537G>T ENST00000303924.4 - 2 581 c.44C>A c.(43-45)aCc>aAc p.T15N NM_005328.2 NP_005319.1 Q92819 HYAS2_HUMAN hyaluronan synthase 2 HAS2/PLAG1(10) 38 Lung NSC(37;3.12e-08)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)|all_neural(195;0.142) STAD - Stomach adenocarcinoma(47;0.00503) AAAGAGTGTGGTTCCAATTAT 0.378000 0 SO:0001583 missense ENST00000303924.4 0 1 hg19 CCDS6335.1 . . . . . . . . . . G 23.100000 4.369297 0.824630 . . ENSG00000170961 ENST00000303924;ENST00000443194 T 0.57107 0.42 6.170000 6.170000 0.997090 . 0.000000 0.85682 D 0.000000 T 0.70780 0.3263 M 0.79123 2.44 0.807220 D 1.000000 D 0.56035 0.974 P 0.55615 0.78 T 0.69495 -0.5130 10 0.49607 T 0.09 -22.0036 20.879400 0.998670 0.0:0.0:1.0:0.0 . 15 Q92819 HAS2_HUMAN N 15 ENSP00000306991:T15N ENSP00000306991:T15N T - 2 0 HAS2 122710718 1 0.714170 1 0.803570 0.991000 0.796840 9.800000 0.991240 2.941000 0.997820 0.655000 0.942530 ACC TCGA-FB-A4P5-01A-11D-A26I-08 HAS2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000381150.2 0 0 0 8 328 0 26 0 0 0 0 26 2 0 0 0 0 0 2 1 0.989325 8 326 0 26 2 0 0 0 0 26 2 -8.452718 1 1 0 0 1 0 1 1 1.991578 0 0.130000 2 0.123735 0.370000 0.170000 0.660000 0.360000 0.398157 0.370000 0 0.260000 0.520000 TRAPPC9 83696 broad.mit.edu 37 8 141461429 141461429 + Missense_Mutation SNP G G A rs142839408 TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr8:141461429G>A ENST00000438773.2 - 2 177 c.44C>T c.(43-45)aCg>aTg p.T15M TRAPPC9_ENST00000389327.3_Missense_Mutation_p.T15M|TRAPPC9_ENST00000389328.4_Missense_Mutation_p.T113M NM_001160372.1 NP_001153844.1 Q96Q05 TPPC9_HUMAN trafficking protein particle complex 9 47 CACGAGCAGCGTCTGGTGGTC 0.537000 0 SO:0001583 missense ENST00000438773.2 1 1 hg19 CCDS55278.1 . . . . . . . . . . G 19.950000 3.921045 0.732130 0.001136 2.33E-4 ENSG00000167632 ENST00000389328;ENST00000389327;ENST00000438773 . . . 5.260000 4.390000 0.528550 . 0.046901 0.85682 D 0.000000 T 0.70369 0.3216 L 0.54323 1.7 0.442210 D 0.997050 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.76071 0.987;0.967;0.967 T 0.71474 -0.4582 9 0.51188 T 0.08 . 13.901700 0.638090 0.0735:0.0:0.9265:0.0 . 15;15;113 Q96Q05;Q96Q05-3;Q96Q05-2 TPPC9_HUMAN;.;. M 113;15;15 . ENSP00000373978:T15M T - 2 0 TRAPPC9 141530611 1 0.714170 9.240000e-01 0.367210 0.956000 0.617450 9.640000 0.984530 1.210000 0.433360 0.650000 0.862430 ACG TCGA-FB-A4P5-01A-11D-A26I-08 TRAPPC9-002 PUTATIVE basic|CCDS protein_coding protein_coding OTTHUMT00000377749.1 0 0 0 9 191 0 35 0 8.851073e-02 0 10 0 35 2 0 0 0 0 0 2 1 0.994411 9 190 0 35 2 0 0 0 0 35 2 -11.483710 1 1 121346 28 44 1 0 1 1 1.991578 0 0.130000 2 0.123735 0.700000 0.350000 1.000000 1.000000 0.712860 0.700000 0 0.500000 0.940000 PPAPDC3 84814 broad.mit.edu 37 9 134165668 134165668 + Missense_Mutation SNP G G A TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr9:134165668G>A ENST00000372264.3 + 1 588 c.284G>A c.(283-285)cGg>cAg p.R95Q PPAPDC3_ENST00000372261.1_Missense_Mutation_p.R95Q NM_032728.3 NP_116117.3 Q8NBV4 PPAC3_HUMAN phosphatidic acid phosphatase type 2 domain containing 3 16 all_hematologic(7;0.0119) ATGTCCAAGCGGCTGGGGGTG 0.652000 0 SO:0001583 missense ENST00000372264.3 0 1 hg19 CCDS6942.1 . . . . . . . . . . G 37.000000 6.011501 0.972000 . . ENSG00000160539 ENST00000372264;ENST00000372261 T;T 0.50548 1.8;0.74 5.690000 5.690000 0.884480 . 0.000000 0.85682 D 0.000000 T 0.68961 0.3058 M 0.71581 2.175 0.807220 D 1.000000 D 0.69078 0.997 D 0.70227 0.968 T 0.70174 -0.4944 10 0.62326 D 0.03 -40.1758 18.802000 0.920220 0.0:0.0:1.0:0.0 . 95 Q8NBV4 PPAC3_HUMAN Q 95 ENSP00000361338:R95Q;ENSP00000361335:R95Q ENSP00000361335:R95Q R + 2 0 PPAPDC3 133155489 1 0.714170 1 0.803570 0.978000 0.694770 7.608000 0.828980 2.682000 0.913650 0.561000 0.740990 CGG TCGA-FB-A4P5-01A-11D-A26I-08 PPAPDC3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054724.1 0 0 0 11 536 0 119 0 5.166418e-04 0 2 0 119 2 0 0 0 0 0 2 1 0.998256 11 530 0 118 2 0 0 0 0 119 2 -3.034886 1 1 0 0 1 1 2 3 2.005945 0 0.130000 2 0.135618 0.330000 0.170000 1.000000 0.300000 0.388362 0.330000 0 0.230000 0.470000 TRPM6 140803 broad.mit.edu 37 9 77386696 77386696 + Silent SNP G G A TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chr9:77386696G>A ENST00000360774.1 - 25 3696 c.3459C>T c.(3457-3459)tgC>tgT p.C1153C TRPM6_ENST00000451710.3_Silent_p.C1153C|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000376864.4_Silent_p.C1153C|TRPM6_ENST00000361255.3_Silent_p.C1148C|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000449912.2_Silent_p.C1148C NM_017662.4 NP_060132.3 Q9BX84 TRPM6_HUMAN transient receptor potential cation channel, subfamily M, member 6 126 ATTTTTCCACGCACTGCTCCT 0.358000 0 SO:0001819 synonymous_variant ENST00000360774.1 0 1 hg19 CCDS6647.1 TCGA-FB-A4P5-01A-11D-A26I-08 TRPM6-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000052693.1 1 0 0 10 213 0 20 0 0 0 0 20 2 0 0 0 0 0 2 1 0.996865 9 211 0 20 2 0 0 0 0 20 2 -2.978244 1 1 121410 4 34 1 0 0 0 1.965775 0 0.130000 2 0.110338 0.680000 0.350000 1.000000 1.000000 0.697920 0.680000 0 0.490000 0.900000 DCAF12L2 340578 broad.mit.edu 37 X 125299285 125299285 + Missense_Mutation SNP G G C TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chrX:125299285G>C ENST00000360028.2 - 1 649 c.623C>G c.(622-624)gCt>gGt p.A208G DCAF12L2_ENST00000538699.1_Missense_Mutation_p.A208G Q5VW00 DC122_HUMAN DDB1 and CUL4 associated factor 12-like 2 64 GCCGCTCACAGCTACGGTGTC 0.647000 0 SO:0001583 missense ENST00000360028.2 1 1 hg19 CCDS43991.1 . . . . . . . . . . G 11.110000 1.543243 0.275630 . . ENSG00000198354 ENST00000538699;ENST00000360028 T;T 0.60171 0.21;0.21 3.870000 0.855000 0.190130 WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1); 0.817806 0.10000 N 0.728605 T 0.56702 0.2003 L 0.51422 1.61 0.308150 N 0.738405 P 0.44659 0.84 P 0.48552 0.581 T 0.57717 -0.7763 10 0.87932 D 0 . 6.754900 0.235070 0.4053:0.0:0.5947:0.0 . 208 Q5VW00 DC122_HUMAN G 208 ENSP00000441489:A208G;ENSP00000353128:A208G ENSP00000353128:A208G A - 2 0 DCAF12L2 125126966 9.980000e-01 0.408360 2.000000e-03 0.105220 0.010000 0.072450 2.707000 0.471430 0.042000 0.157170 0.544000 0.684100 GCT TCGA-FB-A4P5-01A-11D-A26I-08 DCAF12L2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000058181.1 0 0 0 10 361 0 68 0 0 0 0 68 2 0 0 0 0 0 2 1 0.996805 10 357 0 67 2 0 0 0 0 68 2 -9.829924 1 1 0 0 1 0 1 1 0.130000 2 0.130000 0.420000 0.210000 0.710000 0.410000 0.445498 0.420000 0 0.300000 0.570000 FRMD7 90167 broad.mit.edu 37 X 131216469 131216469 + Missense_Mutation SNP G G A TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chrX:131216469G>A ENST00000298542.4 - 9 1002 c.827C>T c.(826-828)gCt>gTt p.A276V FRMD7_ENST00000370879.1_Missense_Mutation_p.A156V|FRMD7_ENST00000464296.1_Missense_Mutation_p.A261V NM_194277.2 NP_919253.1 Q6ZUT3 FRMD7_HUMAN FERM domain containing 7 24 Acute lymphoblastic leukemia(192;0.000127) CCTGAAGAAAGCATGGTATTC 0.468000 0 SO:0001583 missense ENST00000298542.4 1 1 hg19 CCDS35397.1 . . . . . . . . . . G 32.000000 5.112065 0.943390 . . ENSG00000165694 ENST00000370879;ENST00000298542;ENST00000464296 D;D;D 0.87650 -2.28;-2.28;-2.28 5.200000 5.200000 0.720130 FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1); 0.116646 0.56097 D 0.000024 D 0.94686 0.8286 M 0.90019 3.08 0.807220 D 1.000000 D;D 0.89917 1.0;1.0 D;D 0.85130 0.997;0.996 D 0.95702 0.8750 10 0.87932 D 0 . 16.979300 0.863230 0.0:0.0:1.0:0.0 . 261;276 Q6ZUT3-2;Q6ZUT3 .;FRMD7_HUMAN V 156;276;261 ENSP00000359916:A156V;ENSP00000298542:A276V;ENSP00000417996:A261V ENSP00000298542:A276V A - 2 0 FRMD7 131044150 1 0.714170 1 0.803570 0.913000 0.542940 9.813000 0.992860 2.305000 0.776050 0.544000 0.684100 GCT TCGA-FB-A4P5-01A-11D-A26I-08 FRMD7-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000355031.1 0 0 0 41 1459 0 175 0 0 0 0 175 2 0 0 0 0 0 2 1 1.000000 41 1447 0 175 2 0 0 0 0 175 2 -3.378389 1 1 0 0 1 0 1 1 0.130000 2 0.130000 0.410000 0.300000 0.550000 0.420000 0.428266 0.410000 0 0.350000 0.490000 MED14 9282 broad.mit.edu 37 X 40573077 40573077 + Missense_Mutation SNP C C T TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chrX:40573077C>T ENST00000324817.1 - 5 723 c.605G>A c.(604-606)cGg>cAg p.R202Q NM_004229.3 NP_004220.2 O60244 MED14_HUMAN mediator complex subunit 14 39 GGTTACAAGCCGATGTCTAAG 0.383000 0 SO:0001583 missense ENST00000324817.1 0 1 hg19 CCDS14254.1 . . . . . . . . . . C 36.000000 5.665183 0.967450 . . ENSG00000180182 ENST00000324817 . . . 5.170000 5.170000 0.711590 . 0.000000 0.85682 D 0.000000 T 0.74756 0.3758 M 0.88105 2.93 0.807220 D 1.000000 D 0.54397 0.966 P 0.47645 0.553 T 0.82108 -0.0620 9 0.72032 D 0.01 . 18.065800 0.893900 0.0:1.0:0.0:0.0 . 202 O60244 MED14_HUMAN Q 202 . ENSP00000323720:R202Q R - 2 0 MED14 40458021 1 0.714170 1 0.803570 0.998000 0.957120 7.400000 0.799490 2.290000 0.770570 0.544000 0.684100 CGG TCGA-FB-A4P5-01A-11D-A26I-08 MED14-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000060692.1 0 0 0 16 502 1 42 0 6.986228e-03 0 12 1 42 3 0 0 0 0 0 2 0 0.007580 16 493 1 41 33 0 0 0 1 42 2 -2.679387 1 1 0 0 1 0 1 1 0.130000 2 0.130000 0.480000 0.280000 0.730000 0.470000 0.496449 0.480000 0 0.370000 0.610000 TBC1D25 4943 broad.mit.edu 37 X 48418156 48418156 + Missense_Mutation SNP C C T TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chrX:48418156C>T ENST00000376771.4 + 6 1201 c.860C>T c.(859-861)aCg>aTg p.T287M snoU13_ENST00000459609.1_RNA|TBC1D25_ENST00000537536.1_Missense_Mutation_p.T33M NM_002536.2 NP_002527.1 Q3MII6 TBC25_HUMAN TBC1 domain family, member 25 4 ATCCGCAGCACGGTCCTCAAG 0.627000 0 SO:0001583 missense ENST00000376771.4 1 1 hg19 CCDS35242.1 . . . . . . . . . . C 10.150000 1.272312 0.232210 . . ENSG00000068354 ENST00000376771;ENST00000537536 T;T 0.12361 2.69;2.69 5.890000 4.950000 0.653090 Rab-GAP/TBC domain (4); 0.053790 0.64402 D 0.000001 T 0.03178 0.0093 N 0.00765 -1.205 0.345690 D 0.713181 B;B;B 0.25441 0.126;0.023;0.013 B;B;B 0.14023 0.01;0.01;0.01 T 0.28996 -1.0026 10 0.02654 T 1 -2.3984 9.728700 0.403480 0.3521:0.6479:0.0:0.0 . 291;229;287 B4DF03;B4DGU3;Q3MII6 .;.;TBC25_HUMAN M 287;33 ENSP00000365962:T287M;ENSP00000444091:T33M ENSP00000365962:T287M T + 2 0 TBC1D25 48303100 9.980000e-01 0.408360 9.670000e-01 0.410340 0.807000 0.456020 3.928000 0.565060 2.499000 0.843000 0.529000 0.557590 ACG TCGA-FB-A4P5-01A-11D-A26I-08 TBC1D25-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000060764.2 0 0 0 7 193 0 36 0 2.188141e-01 0 22 0 36 2 0 0 0 0 0 2 1 0.980828 7 192 0 36 2 0 0 0 0 36 2 -9.311809 1 1 0 0 1 0 1 1 0.130000 2 0.130000 0.550000 0.250000 1.000000 1.000000 0.584820 0.550000 0 0.380000 0.780000 TFE3 7030 broad.mit.edu 37 X 48896768 48896768 + Missense_Mutation SNP C C T TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chrX:48896768C>T ENST00000315869.7 - 3 657 c.398G>A c.(397-399)cGt>cAt p.R133H TFE3_ENST00000487451.1_5'UTR NM_006521.4 NP_006512.2 P19532 TFE3_HUMAN transcription factor binding to IGHM enhancer 3 NONO/TFE3(2)|PRCC/TFE3(25)|SFPQ/TFE3(6)|CLTC/TFE3(2)|ASPSCR1/TFE3(167) 1 CTGTTCCCGACGCTCACGCCT 0.662000 T SFPQ, ASPSCR1, PRCC, NONO, CLTC papillary renal, alveolar soft part sarcoma, renal Dom yes X Xp11.22 7030 transcription factor binding to IGHM enhancer 3 E 0 SO:0001583 missense ENST00000315869.7 0 1 hg19 CCDS14315.3 . . . . . . . . . . C 15.440000 2.834420 0.509510 . . ENSG00000068323 ENST00000315869 T 0.17370 2.28 5.360000 4.490000 0.547850 . 0.207799 0.40554 N 0.001077 T 0.12646 0.0307 L 0.52011 1.625 0.305570 N 0.764871 P 0.49783 0.928 B 0.35813 0.211 T 0.23797 -1.0178 10 0.72032 D 0.01 -7.8369 6.423900 0.217580 0.0:0.8025:0.0:0.1975 . 133 P19532 TFE3_HUMAN H 133 ENSP00000314129:R133H ENSP00000314129:R133H R - 2 0 TFE3 48783712 2.530000e-01 0.239820 9.980000e-01 0.565050 0.716000 0.411820 0.777000 0.267180 2.224000 0.724170 0.513000 0.501650 CGT TCGA-FB-A4P5-01A-11D-A26I-08 TFE3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000058872.2 0 0 0 4 87 0 13 0 4.734416e-01 0 31 0 13 2 0 0 0 0 0 2 1 0.881091 4 83 0 13 2 0 0 0 0 13 2 -8.189270 1 1 0 0 1 0 1 1 0.130000 2 0.130000 0.710000 0.250000 1.000000 1.000000 0.713265 0.710000 0 0.440000 1.000000 SLC7A3 84889 broad.mit.edu 37 X 70146745 70146745 + Missense_Mutation SNP T T C TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chrX:70146745T>C ENST00000374299.3 - 9 1577 c.1433A>G c.(1432-1434)tAt>tGt p.Y478C SLC7A3_ENST00000298085.4_Missense_Mutation_p.Y478C Q8WY07 CTR3_HUMAN solute carrier family 7 (cationic amino acid transporter, y+ system), member 3 31 Renal(35;0.156) L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129) GGAACAAACATAGACAATTTG 0.488000 0 SO:0001583 missense ENST00000374299.3 0 1 hg19 CCDS14404.1 . . . . . . . . . . T 13.070000 2.126783 0.375330 . . ENSG00000165349 ENST00000374299;ENST00000298085 D;D 0.88431 -2.38;-2.38 5.310000 5.310000 0.753090 . 0.111999 0.64402 D 0.000006 D 0.89626 0.6769 M 0.86028 2.79 0.520990 D 0.999945 B 0.26081 0.141 B 0.25759 0.063 D 0.88089 0.2812 10 0.51188 T 0.08 . 13.061000 0.590080 0.0:0.0:0.0:1.0 . 478 Q8WY07 CTR3_HUMAN C 478 ENSP00000363417:Y478C;ENSP00000298085:Y478C ENSP00000298085:Y478C Y - 2 0 SLC7A3 70063470 1 0.714170 1 0.803570 0.951000 0.605550 5.912000 0.699480 1.968000 0.572510 0.430000 0.284900 TAT TCGA-FB-A4P5-01A-11D-A26I-08 SLC7A3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057080.1 0 0 0 7 208 0 18 0 0 0 0 18 2 0 0 0 0 0 2 1 0.980475 7 206 0 18 2 0 0 0 0 18 2 -9.330272 1 1 0 0 1 0 1 1 0.130000 2 0.130000 0.520000 0.230000 0.940000 0.480000 0.547459 0.520000 0 0.350000 0.730000 TGIF2LX 90316 broad.mit.edu 37 X 89177404 89177404 + Missense_Mutation SNP G G A TCGA-FB-A4P5-01A-11D-A26I-08 TCGA-FB-A4P5-10A-01D-A26I-08 Untested Somatic Phase_I WXS none Illumina GAIIx 3c284834-b0e8-490a-a7c7-e7b880122282 e9984562-78e0-444d-92ca-64a3135fb628 g.chrX:89177404G>A ENST00000561129.2 + 1 450 c.320G>A c.(319-321)cGc>cAc p.R107H TGIF2LX_ENST00000283891.5_Missense_Mutation_p.R107H Q8IUE1 TF2LX_HUMAN TGFB-induced factor homeobox 2-like, X-linked 40 GCTCGCAGACGCATTCTCCCG 0.493000 0 SO:0001583 missense ENST00000561129.2 0 1 hg19 CCDS14459.1 . . . . . . . . . . G 16.150000 3.041557 0.550030 . . ENSG00000153779 ENST00000283891 D 0.98617 -5.03 3.080000 2.180000 0.277750 Homeodomain-related (1);Homeobox (2);Homeobox KN domain (1);Homeodomain-like (1); . . . . D 0.99245 0.9737 H 0.96048 3.76 0.188730 N 0.999989 D 0.76494 0.999 D 0.70227 0.968 D 0.95720 0.8765 8 . . . -22.4853 8.104400 0.308770 0.1341:0.0:0.8659:0.0 . 107 Q8IUE1 TF2LX_HUMAN H 107 ENSP00000355119:R107H . R + 2 0 TGIF2LX 89064060 2.320000e-01 0.237620 1.000000e-03 0.086480 0.285000 0.270930 3.495000 0.532800 0.663000 0.310270 0.513000 0.501650 CGC TCGA-FB-A4P5-01A-11D-A26I-08 TGIF2LX-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000417911.2 0 0 0 20 859 0 108 0 0 0 0 108 2 0 0 0 0 0 2 1 0.999992 18 822 0 126 2 0 0 0 0 108 2 -2.560905 1 1 0 0 1 0 1 1 0.130000 2 0.130000 0.350000 0.220000 0.520000 0.350000 0.363915 0.350000 0 0.280000 0.440000