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 ZNF658 26149 broad.mit.edu 37 9 40772411 40772411 + Frame_Shift_Del DEL A A - TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr9:40772411delA ENST00000602553.1 - 5 3158 c.2864delT c.(2863-2865)gtafs p.V955fs ZNF658_ENST00000377626.3_Frame_Shift_Del_p.V955fs|ZNF658_ENST00000441795.1_Intron Q5TYW1 ZN658_HUMAN zinc finger protein 658 46 TCTTTGATGTACTCTGAGGGT 0.423000 0 SO:0001589 frameshift_variant ENST00000602553.1 0 1 hg19 CCDS35023.1 TCGA-RB-A7B8-01A-12D-A33T-08 ZNF658-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000467800.1 1 0 0 143 1156 0 180 0 2.194645e-01 0 8 0 180 2 0 0 0 0 0 0 1 1 41 182 0 180 2 0 0 0 0 0 0 -20.000000 1 1 0 0 1 0 0 0 1.770920 1 0.270000 2.180000 0.145399 0.690000 5.800000e-01 0.800000 0.690000 0.697158 0.690000 0 0.630000 0.750000 CTNNA3 29119 broad.mit.edu 37 10 67680252 67680252 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr10:67680252G>A ENST00000433211.2 - 18 2698 c.2524C>T c.(2524-2526)Cgg>Tgg p.R842W CTNNA3_ENST00000373735.1_5'UTR|CTNNA3_ENST00000373744.4_Missense_Mutation_p.R842W NM_013266.2 NP_037398.2 catenin (cadherin-associated protein), alpha 3 95 ACTGGGTGCCGGGGCCCAGCA 0.478000 0 SO:0001583 missense ENST00000433211.2 0 1 hg19 CCDS7269.1 . . . . . . . . . . G 18.84 3.709574 0.68730 2.27E-4 0.0 ENSG00000183230 ENST00000433211;ENST00000373744;ENST00000373735 T;T;T 0.37235 1.21;1.21;1.21 5.92 2.87 0.33458 . 0.000000 0.52532 D 0.000080 T 0.43875 0.1267 N 0.22421 0.69 0.80722 D 1 D 0.89917 1.0 D 0.73708 0.981 T 0.44513 -0.9323 10 0.72032 D 0.01 -12.5285 13.3618 0.60661 0.0:0.0:0.423:0.577 . 842 Q9UI47 CTNA3_HUMAN W 842;842;181 ENSP00000389714:R842W;ENSP00000362849:R842W;ENSP00000362840:R181W ENSP00000362840:R181W R - 1 2 CTNNA3 67350258 1.000000 0.71417 0.980000 0.43619 0.984000 0.73092 2.574000 0.46016 0.779000 0.33543 -0.169000 0.13324 CGG TCGA-RB-A7B8-01A-12D-A33T-08 CTNNA3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000048282.2 0 0 0 8 639 0 101 0 0 0 0 101 2 0 0 0 0 0 2 1 9.890169e-01 8 633 0 101 2 0 0 0 0 101 2 -1.986958 0 1 121412 8 46 1 0 0 0 1.924992 0 0.270000 2.180000 0.257979 0.090000 3.000000e-02 0.170000 0.090000 0.100610 0.090000 0 0.060000 0.130000 EIF4EBP2 1979 broad.mit.edu 37 10 72179709 72179709 + Missense_Mutation SNP G G C TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr10:72179709G>C ENST00000373218.4 + 2 208 c.185G>C c.(184-186)cGt>cCt p.R62P NM_004096.4 NP_004087.1 Q13542 4EBP2_HUMAN eukaryotic translation initiation factor 4E binding protein 2 1 CTGTTGGATCGTCGCAATTCT 0.433000 0 SO:0001583 missense ENST00000373218.4 1 1 hg19 CCDS7303.1 . . . . . . . . . . G 25.3 4.628140 0.87560 . . ENSG00000148730 ENST00000373218 . . . 5.56 4.66 0.58398 . 0.047741 0.85682 D 0.000000 T 0.68274 0.2983 L 0.56769 1.78 0.58432 D 0.999999 D 0.61697 0.99 P 0.59357 0.856 T 0.71258 -0.4646 9 0.59425 D 0.04 -6.3829 13.7427 0.62857 0.0756:0.0:0.9244:0.0 . 62 Q13542 4EBP2_HUMAN P 62 . ENSP00000362314:R62P R + 2 0 EIF4EBP2 71849715 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 9.117000 0.94347 1.498000 0.48600 0.650000 0.86243 CGT TCGA-RB-A7B8-01A-12D-A33T-08 EIF4EBP2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000048513.1 1 0 1 63 399 0 63 1 9.992112e-01 14 55 0 63 2 0 0 0 0 0 2 1 1 63 389 0 62 2 0 0 0 0 63 2 -20.000000 1 1 0 0 1 0 0 0 1.924992 0 0.270000 2.180000 0.257979 0.980000 7.700000e-01 1.000000 1.000000 0.953232 0.980000 1 0.870000 1.000000 ZC3H12C 85463 broad.mit.edu 37 11 110036119 110036119 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr11:110036119G>A ENST00000278590.3 + 6 2360 c.2309G>A c.(2308-2310)cGc>cAc p.R770H ZC3H12C_ENST00000453089.2_Missense_Mutation_p.R739H|ZC3H12C_ENST00000528673.1_Missense_Mutation_p.R771H NM_033390.1 NP_203748.1 Q9C0D7 ZC12C_HUMAN zinc finger CCCH-type containing 12C 37 all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544) CCTTATTCCCGCCAGGAAGGC 0.552000 0 SO:0001583 missense ENST00000278590.3 0 1 hg19 CCDS44727.1 . . . . . . . . . . G 10.83 1.459973 0.26248 . . ENSG00000149289 ENST00000278590;ENST00000528673;ENST00000453089 T;T;T 0.31769 1.48;1.48;1.48 5.92 5.92 0.95590 . 0.526358 0.22068 N 0.065080 T 0.26231 0.0640 L 0.29908 0.895 0.36328 D 0.858707 B;B;B 0.02656 0.0;0.0;0.0 B;B;B 0.04013 0.001;0.0;0.001 T 0.16778 -1.0391 10 0.14656 T 0.56 -14.1476 20.3206 0.98668 0.0:0.0:1.0:0.0 . 771;770;770 B4DR47;B4DI65;Q9C0D7 .;.;ZC12C_HUMAN H 770;771;739 ENSP00000278590:R770H;ENSP00000431821:R771H;ENSP00000413094:R739H ENSP00000278590:R770H R + 2 0 ZC3H12C 109541329 0.997000 0.39634 0.996000 0.52242 0.081000 0.17604 2.472000 0.45136 2.809000 0.96659 0.655000 0.94253 CGC TCGA-RB-A7B8-01A-12D-A33T-08 ZC3H12C-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000390491.1 0 0 0 10 487 1 110 0 3.065673e-03 0 4 1 110 2 0 0 0 0 0 2 1 9.966758e-01 10 479 0 110 2 0 0 0 1 110 2 -2.493307 0 1 120920 1 37 1 0 0 0 1.939489 0 0.270000 2.180000 0.266037 0.150000 7.000000e-02 0.260000 0.150000 0.161509 0.150000 0 0.100000 0.210000 SCN3B 55800 broad.mit.edu 37 11 123516310 123516310 + Silent SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr11:123516310G>A ENST00000392770.2 - 2 1006 c.204C>T c.(202-204)ggC>ggT p.G68G SCN3B_ENST00000299333.3_Silent_p.G68G|SCN3B_ENST00000530277.1_Silent_p.G68G NM_018400.3 NP_060870.1 Q9NY72 SCN3B_HUMAN sodium channel, voltage-gated, type III, beta subunit 26 Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) Valproic Acid(DB00313)|Zonisamide(DB00909) AATCTTTACCGCCCTCGGGCC 0.592000 0 SO:0001819 synonymous_variant ENST00000392770.2 1 1 hg19 CCDS8442.1 TCGA-RB-A7B8-01A-12D-A33T-08 SCN3B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000387412.1 1 0 1 109 525 0 84 0 0 0 0 84 2 0 0 0 0 0 2 1 1 109 521 0 84 2 0 0 0 0 84 2 -20.000000 1 1 121412 2 33 1 0 0 0 1.939489 0 0.270000 2.180000 0.266037 0.990000 9.900000e-01 1.000000 1.000000 0.999848 0.990000 1 0.990000 1.000000 NUP160 23279 broad.mit.edu 37 11 47861533 47861533 + Missense_Mutation SNP T T C TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr11:47861533T>C ENST00000378460.2 - 4 656 c.610A>G c.(610-612)Att>Gtt p.I204V NUP160_ENST00000530326.1_Missense_Mutation_p.I90V|NUP160_ENST00000528071.1_Missense_Mutation_p.I90V|NUP160_ENST00000532747.1_Intron|NUP160_ENST00000526870.1_3'UTR NM_015231.1 NP_056046.1 Q12769 NU160_HUMAN nucleoporin 160kDa 53 ACTGCTGGAATTAACTGATAG 0.458000 0 SO:0001583 missense ENST00000378460.2 1 1 hg19 CCDS31484.1 . . . . . . . . . . T 22.0 4.236417 0.79800 . . ENSG00000030066 ENST00000378460;ENST00000530326;ENST00000528071 T;T;T 0.44881 0.91;0.91;0.91 5.44 5.44 0.79542 . 0.052986 0.64402 D 0.000001 T 0.54029 0.1833 M 0.65975 2.015 0.80722 D 1 P 0.45126 0.851 P 0.51055 0.657 T 0.53563 -0.8421 10 0.39692 T 0.17 . 15.4885 0.75587 0.0:0.0:0.0:1.0 . 204 Q12769 NU160_HUMAN V 204;90;90 ENSP00000367721:I204V;ENSP00000433590:I90V;ENSP00000432367:I90V ENSP00000367721:I204V I - 1 0 NUP160 47818109 1.000000 0.71417 0.992000 0.48379 0.917000 0.54804 5.079000 0.64431 2.063000 0.61619 0.533000 0.62120 ATT TCGA-RB-A7B8-01A-12D-A33T-08 NUP160-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000390239.2 1 0 1 81 443 0 61 1 5.281107e-01 2 9 0 61 2 0 0 0 0 0 2 1 1 81 438 0 61 2 0 0 0 0 61 2 -20.000000 1 1 0 0 1 0 0 0 1.943762 0 0.270000 2.180000 0.266037 0.990000 9.100000e-01 1.000000 1.000000 0.994626 0.990000 1 0.990000 1.000000 OR51A2 401667 broad.mit.edu 37 11 4976163 4976163 + Missense_Mutation SNP C C T rs75797492 byFrequency TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr11:4976163C>T ENST00000380371.1 - 1 780 c.781G>A c.(781-783)Gtt>Att p.V261I MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron NM_001004748.1 NP_001004748.1 Q8NGJ7 O51A2_HUMAN olfactory receptor, family 51, subfamily A, member 2 17 Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086) CGGTGGACAACGGCCAGGTTG 0.468000 0 SO:0001583 missense ENST00000380371.1 1 1 hg19 CCDS31368.1 3 0.0013736263736263737 3 0.006097560975609756 0 0.0 0 0.0 0 0.0 - 1.405 -0.577068 0.03854 0.007315 1.27E-4 ENSG00000205496 ENST00000380371 T 0.34667 1.35 3.26 -2.5 0.06384 GPCR, rhodopsin-like superfamily (1); . . . . T 0.09113 0.0225 N 0.03608 -0.345 0.09310 N 1 B 0.09022 0.002 B 0.09377 0.004 T 0.23762 -1.0179 9 0.25106 T 0.35 . 4.7352 0.12984 0.1471:0.3962:0.0:0.4567 . 261 Q8NGJ7 O51A2_HUMAN I 261 ENSP00000369729:V261I ENSP00000369729:V261I V - 1 0 OR51A2 4932739 0.000000 0.05858 0.000000 0.03702 0.002000 0.02628 -6.751000 0.00055 -0.397000 0.07691 -0.367000 0.07326 GTT TCGA-RB-A7B8-01A-12D-A33T-08 OR51A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000142809.1 1 0 1 92 273 0 55 0 0 0 0 55 2 0 0 0 0 0 2 1 1 91 266 0 60 2 0 0 0 0 55 2 -2.844697 1 1 107788 65 53 1 0 0 0 1.943762 0 0.270000 2.180000 0.266037 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 OR8H2 390151 broad.mit.edu 37 11 55872750 55872750 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr11:55872750G>A ENST00000313503.1 + 1 232 c.232G>A c.(232-234)Gtc>Atc p.V78I NM_001005200.1 NP_001005200.1 Q8N162 OR8H2_HUMAN olfactory receptor, family 8, subfamily H, member 2 61 Esophageal squamous(21;0.00693) CTCAACTGTCGTCACACCTAA 0.438000 HNSCC(53;0.14) 0 SO:0001583 missense ENST00000313503.1 0 1 hg19 CCDS31518.1 . . . . . . . . . . g 0.053 -1.245473 0.01481 . . ENSG00000181767 ENST00000313503 T 0.01406 4.93 3.58 1.05 0.20165 GPCR, rhodopsin-like superfamily (1); 0.117869 0.38959 N 0.001502 T 0.00608 0.0020 N 0.03016 -0.435 0.09310 N 1 B 0.02656 0.0 B 0.04013 0.001 T 0.49123 -0.8972 10 0.02654 T 1 . 8.3388 0.32230 0.8257:0.0:0.1743:0.0 . 78 Q8N162 OR8H2_HUMAN I 78 ENSP00000323982:V78I ENSP00000323982:V78I V + 1 0 OR8H2 55629326 0.004000 0.15560 0.989000 0.46669 0.646000 0.38490 2.210000 0.42816 0.080000 0.16959 -0.573000 0.04149 GTC TCGA-RB-A7B8-01A-12D-A33T-08 OR8H2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391540.1 0 0 0 15 1523 0 310 0 0 0 0 310 2 0 0 0 0 0 2 1 9.997491e-01 13 1399 0 339 2 0 0 0 0 310 2 -2.619821 1 1 121412 2 39 1 0 0 0 1.943762 0 0.270000 2.180000 0.266037 0.070000 3.000000e-02 0.120000 0.080000 0.076412 0.070000 0 0.050000 0.100000 OR5T3 390154 broad.mit.edu 37 11 56020051 56020051 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr11:56020051G>A ENST00000303059.3 + 1 376 c.376G>A c.(376-378)Gga>Aga p.G126R NM_001004747.1 NP_001004747.1 Q8NGG3 OR5T3_HUMAN olfactory receptor, family 5, subfamily T, member 3 39 Esophageal squamous(21;0.00448) TTCATTTATCGGATGTGCAAC 0.363000 0 SO:0001583 missense ENST00000303059.3 0 1 hg19 CCDS31524.1 . . . . . . . . . . g 10.80 1.452159 0.26074 . . ENSG00000172489 ENST00000303059 T 0.09817 2.94 4.55 2.59 0.31030 GPCR, rhodopsin-like superfamily (1); 0.542212 0.15279 U 0.270784 T 0.24812 0.0602 M 0.69358 2.11 0.09310 N 1 D 0.62365 0.991 P 0.58660 0.843 T 0.04216 -1.0968 10 0.87932 D 0 . 11.1733 0.48584 0.0:0.1392:0.716:0.1448 . 126 Q8NGG3 OR5T3_HUMAN R 126 ENSP00000305403:G126R ENSP00000305403:G126R G + 1 0 OR5T3 55776627 0.000000 0.05858 0.001000 0.08648 0.028000 0.11728 0.613000 0.24299 0.603000 0.29913 -0.189000 0.12847 GGA TCGA-RB-A7B8-01A-12D-A33T-08 OR5T3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391599.1 0 0 0 5 779 0 142 0 0 0 0 142 2 0 0 0 0 0 2 1 9.366554e-01 5 774 0 142 2 0 0 0 0 142 2 -1.839087 0 1 121410 13 46 1 0 0 0 1.943762 0 0.270000 2.180000 0.266037 0.040000 0 0.110000 0.050000 0.055980 0.040000 0 0.020000 0.080000 TNKS1BP1 85456 broad.mit.edu 37 11 57077417 57077417 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr11:57077417G>A ENST00000532437.1 - 5 3079 c.2768C>T c.(2767-2769)gCc>gTc p.A923V TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.A923V|TNKS1BP1_ENST00000530920.1_5'UTR Q9C0C2 TB182_HUMAN tankyrase 1 binding protein 1, 182kDa p.A923V(1) 64 all_epithelial(135;0.21) CTGCTCATCGGCATCCTGGCT 0.572000 1 Substitution - Missense(1) SO:0001583 missense ENST00000532437.1 0 1 hg19 CCDS7951.1 . . . . . . . . . . G 13.35 2.209903 0.39003 . . ENSG00000149115 ENST00000358252;ENST00000532437 T;T 0.34472 1.36;1.36 5.47 1.3 0.21679 . 0.803739 0.10698 N 0.644437 T 0.42223 0.1193 L 0.59436 1.845 0.09310 N 1 D 0.54964 0.969 P 0.55011 0.766 T 0.22977 -1.0201 10 0.46703 T 0.11 -0.6792 3.1082 0.06348 0.1593:0.1452:0.5597:0.1357 . 923 Q9C0C2 TB182_HUMAN V 923 ENSP00000350990:A923V;ENSP00000437271:A923V ENSP00000350990:A923V A - 2 0 TNKS1BP1 56833993 0.000000 0.05858 0.002000 0.10522 0.117000 0.20001 0.116000 0.15561 0.245000 0.21373 0.462000 0.41574 GCC TCGA-RB-A7B8-01A-12D-A33T-08 TNKS1BP1-003 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000392455.1 0 0 0 8 964 1 166 0 1.463471e-02 0 184 1 166 6 0 0 0 0 0 2 0 1.584165e-02 8 953 1 164 20 0 0 0 1 166 2 -1.695440 0 1 0 0 1 0 0 0 1.943762 0 0.270000 2.180000 0.266037 0.060000 2.000000e-02 0.120000 0.060000 0.067897 0.060000 0 0.030000 0.090000 RARRES3 5920 broad.mit.edu 37 11 63312120 63312120 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr11:63312120G>A ENST00000255688.3 + 3 194 c.146G>A c.(145-147)aGt>aAt p.S49N RARRES3_ENST00000439013.2_Missense_Mutation_p.S49N|RARRES3_ENST00000537871.1_3'UTR|RARRES3_ENST00000354445.2_Missense_Mutation_p.S49N NM_004585.3 NP_004576.2 Q9UL19 HRSL4_HUMAN retinoic acid receptor responder (tazarotene induced) 3 6 GGCTCCTCCAGTGTCTTCTCA 0.567000 0 SO:0001583 missense ENST00000255688.3 0 1 hg19 CCDS41662.1 . . . . . . . . . . G 13.93 2.385443 0.42308 . . ENSG00000133321 ENST00000439013;ENST00000255688;ENST00000354445 T;T;T 0.24908 1.83;1.83;1.83 4.29 -3.33 0.04958 . 0.677062 0.13847 N 0.358591 T 0.26159 0.0638 M 0.87547 2.89 0.09310 N 1 B 0.25206 0.12 B 0.26094 0.066 T 0.40572 -0.9556 10 0.62326 D 0.03 . 1.3662 0.02202 0.301:0.276:0.2986:0.1245 . 49 Q9UL19 TIG3_HUMAN N 49 ENSP00000402943:S49N;ENSP00000255688:S49N;ENSP00000346431:S49N ENSP00000255688:S49N S + 2 0 RARRES3 63068696 0.977000 0.34250 0.000000 0.03702 0.008000 0.06430 1.927000 0.40094 -0.643000 0.05473 0.655000 0.94253 AGT TCGA-RB-A7B8-01A-12D-A33T-08 RARRES3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000396629.1 0 0 0 27 1096 0 158 1 9.337539e-01 3 182 0 158 2 0 0 0 0 0 2 1 9.999999e-01 27 1077 0 153 2 0 0 0 0 158 2 -2.943408 1 1 0 0 1 0 1 1 1.944752 0 0.270000 2.180000 0.268024 0.170000 1.100000e-01 0.250000 0.180000 0.183419 0.170000 0 0.140000 0.220000 NAA40 79829 broad.mit.edu 37 11 63721522 63721522 + Splice_Site SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr11:63721522G>A ENST00000377793.4 + 7 673 c.e7+1 NAA40_ENST00000539656.1_Splice_Site|NAA40_ENST00000542163.1_Splice_Site|NAA40_ENST00000456907.2_Splice_Site NM_024771.2 NP_079047.2 Q86UY6 NAA40_HUMAN N(alpha)-acetyltransferase 40, NatD catalytic subunit 5 AAGCGTTGCAGTAAGGAGCTG 0.512000 0 SO:0001630 splice_region_variant ENST00000377793.4 0 1 hg19 CCDS8053.1 . . . . . . . . . . G 25.0 4.596843 0.86953 . . ENSG00000110583 ENST00000377793;ENST00000456907;ENST00000539656;ENST00000542163 . . . 5.28 5.28 0.74379 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 17.6823 0.88247 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . NAA40 63478098 1.000000 0.71417 1.000000 0.80357 0.983000 0.72400 9.436000 0.97532 2.474000 0.83562 0.462000 0.41574 . TCGA-RB-A7B8-01A-12D-A33T-08 NAA40-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000396266.1 0 0 0 5 598 0 103 0 3.406511e-04 0 3 0 103 2 0 0 0 0 0 2 1 9.369527e-01 5 595 0 103 2 0 0 0 0 103 2 -2.540337 1 1 0 0 1 0 1 1 1.644030 1 0.270000 2.180000 0.156069 0.050000 1.000000e-02 0.120000 0.050000 0.062968 0.050000 0 0.030000 0.090000 CCDC88B 283234 broad.mit.edu 37 11 64120219 64120219 + Silent SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr11:64120219C>T ENST00000356786.5 + 20 3404 c.3360C>T c.(3358-3360)caC>caT p.H1120H CCDC88B_ENST00000301897.4_5'UTR|CCDC88B_ENST00000463837.1_3'UTR|CCDC88B_ENST00000359902.2_Silent_p.H272H NM_032251.5 NP_115627.6 A6NC98 CC88B_HUMAN coiled-coil domain containing 88B p.H1120H(1) 27 ATCCCAGGCACGAGCAGCTGC 0.677000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000356786.5 1 1 hg19 CCDS8072.2 TCGA-RB-A7B8-01A-12D-A33T-08 CCDC88B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000104845.1 1 0 1 36 233 0 27 1 9.577772e-01 6 30 0 27 2 0 0 0 0 0 2 1 1 36 231 0 26 2 0 0 0 0 27 2 -16.957830 1 1 121318 2 32 1 0 0 0 1.939489 0 0.270000 2.180000 0.266037 0.980000 7.100000e-01 1.000000 1.000000 0.937229 0.980000 1 0.830000 1.000000 SCYL1 57410 broad.mit.edu 37 11 65299135 65299135 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr11:65299135G>A ENST00000270176.5 + 8 1174 c.1097G>A c.(1096-1098)cGc>cAc p.R366H SCYL1_ENST00000524944.1_Missense_Mutation_p.R366H|SCYL1_ENST00000279270.6_Missense_Mutation_p.R366H|SCYL1_ENST00000527009.1_Missense_Mutation_p.R223H|SCYL1_ENST00000420247.2_Missense_Mutation_p.R366H|SCYL1_ENST00000525364.1_Missense_Mutation_p.R366H|SCYL1_ENST00000533862.1_Missense_Mutation_p.R366H NM_020680.3 NP_065731.3 Q96KG9 NTKL_HUMAN SCY1-like 1 (S. cerevisiae) 2 CGGGCCATGCGCATCCGCCTC 0.617000 0 SO:0001583 missense ENST00000270176.5 0 1 hg19 CCDS41672.1 . . . . . . . . . . G 28.5 4.925405 0.92319 . . ENSG00000142186 ENST00000270176;ENST00000525364;ENST00000420247;ENST00000533862;ENST00000527630;ENST00000349495;ENST00000279270;ENST00000524944;ENST00000527009 T;T;T;T;T;T;T;T 0.52295 0.67;0.67;0.67;0.67;0.67;0.67;0.67;0.67 5.17 5.17 0.71159 Armadillo-like helical (1);Armadillo-type fold (1); 0.179297 0.45361 D 0.000375 T 0.74473 0.3721 M 0.90595 3.13 0.80722 D 1 D;D;D;D;D 0.89917 0.999;1.0;1.0;0.997;0.998 D;D;D;D;P 0.75484 0.949;0.986;0.981;0.928;0.85 T 0.80327 -0.1429 10 0.87932 D 0 -8.8898 16.593 0.84772 0.0:0.0:1.0:0.0 . 366;366;366;366;366 E9PS17;Q96KG9-4;Q96KG9-6;Q96KG9-2;Q96KG9 .;.;.;.;NTKL_HUMAN H 366;366;366;366;366;366;366;366;223 ENSP00000270176:R366H;ENSP00000431635:R366H;ENSP00000408192:R366H;ENSP00000437254:R366H;ENSP00000433450:R366H;ENSP00000279270:R366H;ENSP00000432175:R366H;ENSP00000436993:R223H ENSP00000270176:R366H R + 2 0 SCYL1 65055711 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 8.515000 0.90548 2.609000 0.88269 0.650000 0.86243 CGC TCGA-RB-A7B8-01A-12D-A33T-08 SCYL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000389159.2 0 0 0 5 230 0 26 0 7.861242e-01 0 133 0 26 2 0 0 0 0 0 2 1 9.360826e-01 5 227 0 26 2 0 0 0 0 26 2 -3.762525 1 1 121188 2 36 1 0 0 0 1.939489 0 0.270000 2.180000 0.266037 0.160000 6.000000e-02 0.340000 0.160000 0.184337 0.160000 0 0.100000 0.250000 MYEOV 26579 broad.mit.edu 37 11 69063478 69063478 + Silent SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr11:69063478G>A ENST00000308946.3 + 3 1011 c.561G>A c.(559-561)cgG>cgA p.R187R MYEOV_ENST00000535407.1_Silent_p.R129R|MYEOV_ENST00000441339.2_Silent_p.R187R NM_138768.2 NP_620123.2 Q96EZ4 MYEOV_HUMAN myeloma overexpressed 24 all_lung(4;2.21e-19)|Lung NSC(4;6.13e-19)|Melanoma(5;0.00128) LUSC - Lung squamous cell carcinoma(11;3.33e-11)|STAD - Stomach adenocarcinoma(18;0.00654)|LUAD - Lung adenocarcinoma(13;0.0713) TGCATGGGCGGCATGGGCTCT 0.627000 0 SO:0001819 synonymous_variant ENST00000308946.3 0 1 hg19 CCDS8190.1 TCGA-RB-A7B8-01A-12D-A33T-08 MYEOV-004 KNOWN alternative_5_UTR|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000396548.1 0 0 0 6 816 0 137 0 3.168449e-01 0 136 0 137 2 0 0 0 0 0 2 1 9.645090e-01 7 811 0 134 2 0 0 0 0 137 2 -1.887318 0 1 0 0 1 0 0 0 1.939489 0 0.270000 2.180000 0.266037 0.050000 1.000000e-02 0.110000 0.060000 0.062401 0.050000 0 0.030000 0.090000 ATP2A2 488 broad.mit.edu 37 12 110778541 110778541 + Silent SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr12:110778541C>T ENST00000539276.2 + 14 1948 c.1839C>T c.(1837-1839)tgC>tgT p.C613C ATP2A2_ENST00000395494.2_Silent_p.C586C|ATP2A2_ENST00000308664.6_Silent_p.C613C P16615 AT2A2_HUMAN ATPase, Ca++ transporting, cardiac muscle, slow twitch 2 38 TGAAGCTGTGCCGGCAAGCAG 0.572000 0 GRCh37 CM014166 ATP2A2 M SO:0001819 synonymous_variant ENST00000539276.2 0 1 hg19 CCDS9144.1 . . . . . . . . . . C 9.993 1.231362 0.22626 . . ENSG00000174437 ENST00000548169 . . . 5.93 -0.83 0.10792 . . . . . T 0.63954 0.2555 . . . 0.80722 D 1 . . . . . . T 0.61178 -0.7115 4 . . . . 12.8976 0.58108 0.0:0.5245:0.0:0.4755 . . . . S 504 . . P + 1 0 ATP2A2 109262924 0.928000 0.31464 0.994000 0.49952 0.973000 0.67179 0.080000 0.14802 -0.056000 0.13221 -0.126000 0.14955 CCG TCGA-RB-A7B8-01A-12D-A33T-08 ATP2A2-003 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000403539.1 0 0 0 5 554 1 65 0 2.619409e-04 0 189 1 65 11 0 0 0 0 0 2 0 7.149995e-05 5 550 1 64 26 0 0 0 1 65 2 -2.051129 0 1 0 0 1 1 2 3 1.996640 0 0.270000 2.180000 0.279724 0.070000 2.000000e-02 1.000000 0.070000 0.154353 0.070000 0 0.040000 0.130000 TMEM132D 121256 broad.mit.edu 37 12 129558549 129558549 + Silent SNP G G A rs74724941 by1000genomes TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr12:129558549G>A ENST00000422113.2 - 9 3497 c.3171C>T c.(3169-3171)gaC>gaT p.D1057D TMEM132D_ENST00000389441.4_Silent_p.D595D NM_133448.2 NP_597705.2 Q14C87 T132D_HUMAN transmembrane protein 132D p.D1057E(1) 152 all_neural(191;0.101)|Medulloblastoma(191;0.163) all_epithelial(31;0.0934)|Breast(359;0.133) TGGGGTACTCGTCGTCTGAGG 0.512000 1 Substitution - Missense(1) SO:0001819 synonymous_variant ENST00000422113.2 1 0 hg19 CCDS9266.1 TCGA-RB-A7B8-01A-12D-A33T-08 TMEM132D-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000399592.1 1 0 1 57 506 0 99 0 0 0 0 99 2 0 0 0 0 0 2 1 1 57 503 0 98 2 0 0 0 0 99 2 -12.552980 1 1 121412 82 52 1 1 2 3 1.996640 0 0.270000 2.180000 0.279724 0.760000 5.800000e-01 1.000000 0.760000 0.785594 0.760000 0 0.670000 0.900000 PGAM5 192111 broad.mit.edu 37 12 133294121 133294121 + Missense_Mutation SNP C C A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr12:133294121C>A ENST00000498926.2 + 3 525 c.467C>A c.(466-468)aCc>aAc p.T156N PXMP2_ENST00000545677.1_3'UTR|PGAM5_ENST00000543955.1_Missense_Mutation_p.T7N|PGAM5_ENST00000317555.2_Missense_Mutation_p.T156N|PGAM5_ENST00000454808.2_Missense_Mutation_p.T7N NM_001170543.1|NM_001170544.1 NP_001164014.1|NP_001164015.1 Q96HS1 PGAM5_HUMAN phosphoglycerate mutase family member 5 5 all_neural(191;0.0982)|Medulloblastoma(191;0.163) GCCATAGAGACCACCGATATC 0.632000 0 SO:0001583 missense ENST00000498926.2 1 1 hg19 CCDS53845.1 . . . . . . . . . . C 20.6 4.019366 0.75275 . . ENSG00000247077 ENST00000317555;ENST00000498926;ENST00000543955;ENST00000454808 T;D 0.88896 -0.78;-2.44 5.6 5.6 0.85130 Histidine phosphatase superfamily, clade-1 (2); 0.000000 0.85682 D 0.000000 D 0.97225 0.9093 H 0.99042 4.41 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.997 D 0.98593 1.0655 10 0.87932 D 0 -3.1057 19.6338 0.95721 0.0:1.0:0.0:0.0 . 156;156 Q96HS1;Q96HS1-2 PGAM5_HUMAN;. N 156;156;7;7 ENSP00000321503:T156N;ENSP00000438465:T156N ENSP00000321503:T156N T + 2 0 PGAM5 131804194 1.000000 0.71417 0.978000 0.43139 0.113000 0.19764 7.255000 0.78338 2.636000 0.89361 0.591000 0.81541 ACC TCGA-RB-A7B8-01A-12D-A33T-08 PGAM5-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000397562.1 1 0 0 28 203 0 28 1 9.156384e-01 7 25 0 28 2 0 0 0 0 0 2 1 1 28 202 0 27 2 0 0 0 0 28 2 -20.000000 1 1 0 0 1 1 2 3 1.996640 0 0.270000 2.180000 0.279724 0.920000 6.300000e-01 1.000000 1.000000 0.898751 0.920000 1 0.760000 1.000000 KRAS 3845 broad.mit.edu 37 12 25398285 25398285 + Missense_Mutation SNP C C G rs121913530 TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 C G C C Valid Somatic Phase_I WXS KRAS_deep Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr12:25398285C>G ENST00000256078.4 - 2 97 c.34G>C c.(34-36)Ggt>Cgt p.G12R KRAS_ENST00000556131.1_Missense_Mutation_p.G12R|KRAS_ENST00000557334.1_Missense_Mutation_p.G12R|KRAS_ENST00000311936.3_Missense_Mutation_p.G12R NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) CCTACGCCACCAGCTCCAACT 0.348000 G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 5144 Substitution - Missense(5142)|Insertion - In frame(2) GRCh37 CM076251 KRAS M rs121913530 SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 0 1 hg19 CCDS8703.1 . . . . . . . . . . C 28.6 4.930538 0.92389 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78246 -1.16;-1.16;-1.16;-1.16 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.84893 0.5573 M 0.84082 2.675 0.80722 D 1 P;P 0.43287 0.802;0.741 B;P 0.47941 0.36;0.562 D 0.86658 0.1902 10 0.66056 D 0.02 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN R 12 ENSP00000308495:G12R;ENSP00000452512:G12R;ENSP00000256078:G12R;ENSP00000451856:G12R ENSP00000256078:G12R G - 1 0 KRAS 25289552 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-RB-A7B8-01A-12D-A33T-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 11 100 0 11 1 4.031158e-01 4 8 0 11 2 1 9.999997e-01 41 302 0 285 2 1 9.982984e-01 11 96 0 11 2 1 1 1667 6368 0 11 2 -7.059248 1 1 0 0 1 1 2 3 1.990823 0 0.270000 2.180000 0.278763 0.770000 4.100000e-01 1.000000 1.000000 0.775878 0.770000 0 0.570000 1.000000 DENND5B 160518 broad.mit.edu 37 12 31577541 31577541 + Silent SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr12:31577541C>T ENST00000389082.5 - 10 2583 c.2319G>A c.(2317-2319)gaG>gaA p.E773E DENND5B_ENST00000536562.1_Silent_p.E808E|DENND5B_ENST00000306833.6_Silent_p.E808E NM_144973.3 NP_659410.3 Q6ZUT9 DEN5B_HUMAN DENN/MADD domain containing 5B 38 AGGTGTTCTCCTCCAGGCCGG 0.517000 0 SO:0001819 synonymous_variant ENST00000389082.5 1 1 hg19 CCDS44857.1 TCGA-RB-A7B8-01A-12D-A33T-08 DENND5B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000402040.1 1 0 0 30 606 0 107 0 1.361586e-02 0 4 0 107 2 0 0 0 0 0 2 1 1 30 601 0 107 2 0 0 0 0 107 2 -3.295405 1 1 0 0 1 1 2 3 1.990823 0 0.270000 2.180000 0.278763 0.360000 2.400000e-01 1.000000 0.350000 0.409151 0.360000 0 0.290000 0.450000 SLC6A13 6540 broad.mit.edu 37 12 346453 346453 + Silent SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr12:346453C>T ENST00000343164.4 - 6 619 c.567G>A c.(565-567)cgG>cgA p.R189R SLC6A13_ENST00000445055.2_Silent_p.R97R NM_016615.4 NP_057699.2 Q9NSD5 S6A13_HUMAN solute carrier family 6 (neurotransmitter transporter), member 13 28 all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142) OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239) TCAAGACCCGCCGCCTGGGGA 0.622000 0 SO:0001819 synonymous_variant ENST00000343164.4 0 1 hg19 CCDS8502.1 TCGA-RB-A7B8-01A-12D-A33T-08 SLC6A13-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000397801.1 0 0 0 5 436 0 69 0 0 0 0 69 2 0 0 0 0 0 2 1 9.356030e-01 5 430 0 66 2 0 0 0 0 69 2 -3.217084 1 1 0 0 1 1 2 3 1.977682 0 0.270000 2.180000 0.276834 0.090000 2.000000e-02 1.000000 0.080000 0.150814 0.090000 0 0.050000 0.150000 CNTN1 1272 broad.mit.edu 37 12 41422975 41422975 + Silent SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr12:41422975G>A ENST00000551295.2 + 23 3051 c.2934G>A c.(2932-2934)gcG>gcA p.A978A CNTN1_ENST00000347616.1_Silent_p.A978A|CNTN1_ENST00000348761.2_Silent_p.A967A NM_001843.3 NP_001834.2 Q12860 CNTN1_HUMAN contactin 1 90 all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716) Lung NSC(34;0.0211)|all_lung(34;0.0294) AGGTTCGCGCGCACAGTGATG 0.458000 0 SO:0001819 synonymous_variant ENST00000551295.2 0 1 hg19 CCDS8737.1 TCGA-RB-A7B8-01A-12D-A33T-08 CNTN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000403692.2 0 0 0 7 840 0 130 0 4.382955e-02 0 34 0 130 2 0 0 0 0 0 2 1 9.803857e-01 9 835 0 130 2 0 0 0 0 130 2 -1.777108 0 1 121412 2 36 1 1 2 3 1.990823 0 0.270000 2.180000 0.278763 0.060000 2.000000e-02 1.000000 0.060000 0.138051 0.060000 0 0.040000 0.110000 ADAMTS20 80070 broad.mit.edu 37 12 43860592 43860592 + Silent SNP A A G TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr12:43860592A>G ENST00000389420.3 - 9 1229 c.1230T>C c.(1228-1230)ggT>ggC p.G410G ADAMTS20_ENST00000553158.1_Silent_p.G410G NM_025003.3 NP_079279.3 P59510 ATS20_HUMAN ADAM metallopeptidase with thrombospondin type 1 motif, 20 95 all_cancers(12;2.6e-05)|Lung SC(27;0.184) Lung NSC(34;0.0569)|all_lung(34;0.129) CATGTTGAACACCAAGTCTAA 0.294000 0 SO:0001819 synonymous_variant ENST00000389420.3 1 1 hg19 CCDS31778.2 TCGA-RB-A7B8-01A-12D-A33T-08 ADAMTS20-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000403643.1 1 0 0 22 201 0 47 0 0 0 0 47 2 0 0 0 0 0 2 1 9.999990e-01 23 199 0 47 2 0 0 0 0 47 2 -20.000000 1 1 0 0 1 1 2 3 1.990823 0 0.270000 2.180000 0.278763 0.750000 4.800000e-01 1.000000 1.000000 0.770766 0.750000 0 0.610000 0.960000 COQ10A 93058 broad.mit.edu 37 12 56662938 56662938 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr12:56662938G>A ENST00000308197.5 + 3 638 c.377G>A c.(376-378)cGt>cAt p.R126H RP11-977G19.14_ENST00000546464.1_RNA|COQ10A_ENST00000546544.1_Missense_Mutation_p.R109H|COQ10A_ENST00000433805.2_Missense_Mutation_p.R94H NM_144576.3 NP_653177.3 Q96MF6 CQ10A_HUMAN coenzyme Q10 homolog A (S. cerevisiae) 8 GTATCCAGCCGTAAGGGTCAT 0.512000 0 SO:0001583 missense ENST00000308197.5 0 1 hg19 CCDS41796.1 . . . . . . . . . . G 35 5.436623 0.96168 . . ENSG00000135469 ENST00000308197;ENST00000433805;ENST00000546544 T;T;T 0.26810 1.71;1.73;1.73 5.33 5.33 0.75918 START-like domain (1); 0.000000 0.85682 D 0.000000 T 0.30166 0.0756 L 0.54965 1.715 0.80722 D 1 P;P;P 0.47350 0.87;0.894;0.894 B;B;B 0.41571 0.245;0.258;0.36 T 0.06643 -1.0815 10 0.54805 T 0.06 . 18.1779 0.89767 0.0:0.0:1.0:0.0 . 109;131;126 Q96MF6-2;Q8TAL2;Q96MF6 .;.;CQ10A_HUMAN H 126;94;109 ENSP00000312587:R126H;ENSP00000407843:R94H;ENSP00000446723:R109H ENSP00000312587:R126H R + 2 0 COQ10A 54949205 1.000000 0.71417 0.999000 0.59377 0.993000 0.82548 7.651000 0.83577 2.665000 0.90641 0.561000 0.74099 CGT TCGA-RB-A7B8-01A-12D-A33T-08 COQ10A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000408332.1 0 0 0 7 627 1 92 0 1.845335e-02 0 16 1 92 2 0 0 0 0 0 2 0 3.580266e-03 8 624 1 90 22 0 0 0 1 92 2 -2.221341 0 1 120890 1 36 1 1 2 3 1.990823 0 0.270000 2.180000 0.278763 0.080000 3.000000e-02 1.000000 0.080000 0.159810 0.080000 0 0.050000 0.140000 ZNF384 171017 broad.mit.edu 37 12 6782390 6782390 + Silent SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr12:6782390C>T ENST00000396801.3 - 7 1110 c.903G>A c.(901-903)caG>caA p.Q301Q ZNF384_ENST00000361959.3_Silent_p.Q301Q|ZNF384_ENST00000396799.2_Silent_p.Q301Q|RP4-761J14.8_ENST00000586338.1_RNA|ZNF384_ENST00000355772.4_Silent_p.Q246Q|ZNF384_ENST00000396795.1_Silent_p.Q301Q|ZNF384_ENST00000319770.3_Silent_p.Q285Q NM_001135734.2 NP_001129206.1 Q8TF68 ZN384_HUMAN zinc finger protein 384 EWSR1/ZNF384(4) 18 ACCGGGTGTGCTGCTGAAGGT 0.542000 T EWSR1, TAF15 ALL Dom yes 12 12p13 171017 zinc finger protein 384 (CIZ/NMP4) L 0 SO:0001819 synonymous_variant ENST00000396801.3 0 1 hg19 CCDS44817.1 TCGA-RB-A7B8-01A-12D-A33T-08 ZNF384-001 NOVEL basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000400712.1 0 0 0 4 159 0 21 0 4.942079e-01 0 58 0 21 2 0 0 0 0 0 2 1 8.913573e-01 4 159 0 20 2 0 0 0 0 21 2 -6.060673 1 1 0 0 1 1 2 3 1.977682 0 0.270000 2.180000 0.276834 0.210000 6.000000e-02 1.000000 0.190000 0.266299 0.210000 0 0.120000 0.350000 CD163L1 283316 broad.mit.edu 37 12 7559219 7559219 + Silent SNP G G A rs143012538 TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr12:7559219G>A ENST00000313599.3 - 5 1053 c.996C>T c.(994-996)tcC>tcT p.S332S CD163L1_ENST00000396630.1_Silent_p.S332S|CD163L1_ENST00000416109.2_Silent_p.S342S Q9NR16 C163B_HUMAN CD163 molecule-like 1 96 ATTCATTACCGGAGCAGGAGA 0.473000 0 SO:0001819 synonymous_variant ENST00000313599.3 0 1 hg19 CCDS8577.1 TCGA-RB-A7B8-01A-12D-A33T-08 CD163L1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000399329.1 0 0 0 6 436 0 70 0 0 0 0 70 2 0 0 0 0 0 2 1 9.649694e-01 6 434 0 69 2 0 0 0 0 70 2 -2.708902 1 1 121412 6 40 1 1 2 3 1.977682 0 0.270000 2.180000 0.276834 0.110000 4.000000e-02 1.000000 0.100000 0.166409 0.110000 0 0.070000 0.170000 SAP18 10284 broad.mit.edu 37 13 21721345 21721345 + Missense_Mutation SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr13:21721345C>T ENST00000607003.1 + 4 358 c.326C>T c.(325-327)aCc>aTc p.T109I SAP18_ENST00000382533.4_Missense_Mutation_p.T128I O00422 SAP18_HUMAN Sin3A-associated protein, 18kDa 6 all_cancers(29;2.16e-20)|all_epithelial(30;2.97e-18)|all_lung(29;4.58e-16)|Lung SC(185;0.0262)|Breast(139;0.147) ATTGGCAGCACCATGTCTGGC 0.433000 0 SO:0001583 missense ENST00000607003.1 0 1 hg19 . . . . . . . . . . C 19.36 3.813017 0.70912 . . ENSG00000150459 ENST00000382533 . . . 5.87 5.87 0.94306 . 0.000000 0.85682 D 0.000000 T 0.75110 0.3805 M 0.69185 2.1 0.80722 D 1 B 0.27823 0.19 B 0.41666 0.363 T 0.70572 -0.4835 9 0.40728 T 0.16 -22.1376 20.2033 0.98269 0.0:1.0:0.0:0.0 . 109 O00422 SAP18_HUMAN I 128 . ENSP00000371973:T128I T + 2 0 SAP18 20619345 1.000000 0.71417 1.000000 0.80357 0.999000 0.98932 7.640000 0.83355 2.779000 0.95612 0.655000 0.94253 ACC TCGA-RB-A7B8-01A-12D-A33T-08 SAP18-009 PUTATIVE basic|appris_candidate protein_coding protein_coding OTTHUMT00000470725.1 0 0 0 6 601 0 94 1 9.838105e-01 13 750 0 94 2 0 0 0 0 0 2 1 9.647541e-01 7 598 0 94 2 0 0 0 0 94 2 -2.915686 1 1 0 0 1 0 0 0 1.939761 0 0.270000 2.180000 0.266037 0.070000 2.000000e-02 0.150000 0.080000 0.084307 0.070000 0 0.040000 0.110000 CCNA1 8900 broad.mit.edu 37 13 37007204 37007204 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr13:37007204G>A ENST00000255465.4 + 2 407 c.143G>A c.(142-144)aGc>aAc p.S48N CCNA1_ENST00000440264.1_Missense_Mutation_p.S4N|CCNA1_ENST00000449823.1_Missense_Mutation_p.S4N|CCNA1_ENST00000463403.1_3'UTR|CCNA1_ENST00000418263.1_Missense_Mutation_p.S47N P78396 CCNA1_HUMAN cyclin A1 35 Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174) KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169) ATGCACTGCAGCAACCCCAAG 0.602000 0 SO:0001583 missense ENST00000255465.4 1 1 hg19 CCDS9357.1 . . . . . . . . . . G 13.69 2.311316 0.40895 . . ENSG00000133101 ENST00000440264;ENST00000449823;ENST00000418263;ENST00000255465 T;T;T;T 0.17370 2.43;2.43;2.28;2.29 4.63 2.86 0.33363 . 0.954771 0.08588 N 0.923463 T 0.18173 0.0436 L 0.54323 1.7 0.09310 N 1 B;B 0.11235 0.004;0.002 B;B 0.10450 0.005;0.002 T 0.27839 -1.0062 10 0.40728 T 0.16 . 7.931 0.29901 0.1899:0.0:0.8101:0.0 . 47;48 P78396-2;P78396 .;CCNA1_HUMAN N 4;4;47;48 ENSP00000400666:S4N;ENSP00000409873:S4N;ENSP00000396479:S47N;ENSP00000255465:S48N ENSP00000255465:S48N S + 2 0 CCNA1 35905204 0.291000 0.24352 0.014000 0.15608 0.121000 0.20230 0.587000 0.23909 0.466000 0.27193 0.555000 0.69702 AGC TCGA-RB-A7B8-01A-12D-A33T-08 CCNA1-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000044514.2 0 0 0 11 517 0 67 0 0 0 1 0 67 2 0 0 0 0 0 2 1 9.982546e-01 11 511 0 66 2 0 0 0 0 67 2 -2.902034 1 1 0 0 1 0 0 0 1.939761 0 0.270000 2.180000 0.266037 0.150000 7.000000e-02 0.260000 0.150000 0.165940 0.150000 0 0.110000 0.210000 POSTN 10631 broad.mit.edu 37 13 38145544 38145544 + Missense_Mutation SNP A A T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 A T A A Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr13:38145544A>T ENST00000379747.4 - 18 2258 c.2141T>A c.(2140-2142)aTt>aAt p.I714N POSTN_ENST00000541179.1_Missense_Mutation_p.I687N|POSTN_ENST00000379742.4_Intron|POSTN_ENST00000497145.1_5'UTR|POSTN_ENST00000541481.1_Intron|POSTN_ENST00000379749.4_Missense_Mutation_p.I714N|POSTN_ENST00000379743.4_Missense_Mutation_p.I687N NM_006475.2 NP_006466.2 Q15063 POSTN_HUMAN periostin, osteoblast specific factor 59 Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743) ACCTTCTTTAATCAGTCTGAA 0.383000 0 SO:0001583 missense ENST00000379747.4 1 1 hg19 CCDS9364.1 . . . . . . . . . . A 17.66 3.444763 0.63178 . . ENSG00000133110 ENST00000541179;ENST00000379749;ENST00000379747;ENST00000379743 D;D;D;D 0.93712 -3.26;-3.13;-3.16;-3.27 5.49 1.61 0.23674 . 0.628327 0.15902 N 0.239022 D 0.91533 0.7326 L 0.36672 1.1 0.38885 D 0.956994 P;P;P 0.52692 0.523;0.955;0.93 B;P;P 0.54312 0.248;0.748;0.629 D 0.88467 0.3059 10 0.72032 D 0.01 -1.7243 6.9327 0.24449 0.74:0.1263:0.1337:0.0 . 687;687;714 B1ALD8;Q15063-3;Q15063 .;.;POSTN_HUMAN N 687;714;714;687 ENSP00000437959:I687N;ENSP00000369073:I714N;ENSP00000369071:I714N;ENSP00000369067:I687N ENSP00000369067:I687N I - 2 0 POSTN 37043544 0.980000 0.34600 0.107000 0.21349 0.993000 0.82548 2.741000 0.47426 0.108000 0.17862 0.477000 0.44152 ATT TCGA-RB-A7B8-01A-12D-A33T-08 POSTN-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000044566.2 1 0 1 61 391 0 72 0 1 0 523 0 72 2 0 0 0 0 0 2 1 1 61 390 0 71 2 0 0 0 0 72 2 -20.000000 1 1 0 0 1 0 0 0 1.939761 0 0.270000 2.180000 0.266037 0.980000 7.700000e-01 1.000000 1.000000 0.952952 0.980000 1 0.870000 1.000000 PCDH17 27253 broad.mit.edu 37 13 58208306 58208306 + Silent SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr13:58208306C>T ENST00000377918.3 + 1 1652 c.1626C>T c.(1624-1626)ttC>ttT p.F542F NM_001040429.2 NP_001035519.1 O14917 PCD17_HUMAN protocadherin 17 120 Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132) CCTTTAACTTCGAGCAGACCA 0.582000 Melanoma(72;952 1291 1619 12849 33676) 0 SO:0001819 synonymous_variant ENST00000377918.3 1 1 hg19 CCDS31986.1 TCGA-RB-A7B8-01A-12D-A33T-08 PCDH17-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000045139.1 0 0 0 10 311 0 56 0 1.699687e-02 0 6 0 56 2 0 0 0 0 0 2 1 9.968018e-01 10 307 0 54 2 0 0 0 0 56 2 -10.470270 1 1 0 0 1 0 0 0 1.939761 0 0.270000 2.180000 0.266037 0.230000 1.100000e-01 0.400000 0.230000 0.248752 0.230000 0 0.170000 0.320000 SGPP1 81537 broad.mit.edu 37 14 64152974 64152974 + Missense_Mutation SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr14:64152974C>T ENST00000247225.6 - 3 1269 c.1175G>A c.(1174-1176)tGc>tAc p.C392Y NM_030791.2 NP_110418.1 Q9BX95 SGPP1_HUMAN sphingosine-1-phosphate phosphatase 1 10 GAAGATTTTGCAGGCTAAAGG 0.378000 0 SO:0001583 missense ENST00000247225.6 0 1 hg19 CCDS9760.1 . . . . . . . . . . C 14.66 2.600744 0.46423 . . ENSG00000126821 ENST00000247225 . . . 6.07 6.07 0.98685 . 0.000000 0.85682 D 0.000000 T 0.75817 0.3901 M 0.65975 2.015 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 T 0.67581 -0.5634 9 0.02654 T 1 -10.149 20.6593 0.99626 0.0:1.0:0.0:0.0 . 392 Q9BX95 SGPP1_HUMAN Y 392 . ENSP00000247225:C392Y C - 2 0 SGPP1 63222727 1.000000 0.71417 1.000000 0.80357 0.961000 0.63080 7.416000 0.80143 2.885000 0.99019 0.655000 0.94253 TGC TCGA-RB-A7B8-01A-12D-A33T-08 SGPP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000072626.3 0 0 0 5 469 0 85 0 4.633913e-02 0 26 0 85 2 0 0 0 0 0 2 1 9.368026e-01 5 466 0 85 2 0 0 0 0 85 2 -2.011348 0 1 0 0 1 0 0 0 1.943466 0 0.270000 2.180000 0.266037 0.080000 2.000000e-02 0.170000 0.080000 0.092330 0.080000 0 0.050000 0.130000 SYNE2 23224 broad.mit.edu 37 14 64685207 64685207 + Missense_Mutation SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr14:64685207C>T ENST00000344113.4 + 108 19777 c.19565C>T c.(19564-19566)gCc>gTc p.A6522V SYNE2_ENST00000357395.3_Missense_Mutation_p.A2907V|SYNE2_ENST00000358025.3_Missense_Mutation_p.A6545V|SYNE2_ENST00000555002.1_Missense_Mutation_p.A3179V|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555022.1_Missense_Mutation_p.A400V|SYNE2_ENST00000554584.1_Intron|SYNE2_ENST00000441438.2_Missense_Mutation_p.A53V|SYNE2_ENST00000394768.2_Missense_Mutation_p.A2907V|SYNE2_ENST00000458046.2_Missense_Mutation_p.A179V|SYNE2_ENST00000554805.1_Missense_Mutation_p.A305V NM_015180.4 NP_055995.4 Q8WXH0 SYNE2_HUMAN spectrin repeat containing, nuclear envelope 2 224 GGGGGACTGGCCGGTATCACA 0.527000 0 SO:0001583 missense ENST00000344113.4 0 1 hg19 CCDS41963.1 . . . . . . . . . . C 12.74 2.028348 0.35797 . . ENSG00000054654 ENST00000358025;ENST00000357395;ENST00000344113;ENST00000555002;ENST00000394768;ENST00000555022;ENST00000554805;ENST00000458046;ENST00000441438 T;T;T;T;T;T;T;T;T 0.47177 0.86;4.09;0.85;4.15;4.09;3.72;3.25;2.92;2.74 4.83 4.83 0.62350 . 0.300803 0.23782 N 0.044608 T 0.42743 0.1216 L 0.55481 1.735 0.80722 D 1 B;B;B;B;B;B;P 0.38048 0.03;0.03;0.107;0.107;0.009;0.192;0.616 B;B;B;B;B;B;B 0.34824 0.01;0.033;0.061;0.023;0.01;0.082;0.19 T 0.45833 -0.9234 10 0.51188 T 0.08 . 13.2847 0.60237 0.0:1.0:0.0:0.0 . 179;2907;53;179;910;6522;6545 B4DND7;Q8WXH0-7;Q8WXH0-6;Q8WXH0-5;Q7Z362;Q8WXH0;Q8WXH0-2 .;.;.;.;.;SYNE2_HUMAN;. V 6545;2907;6522;3179;2907;400;305;179;53 ENSP00000350719:A6545V;ENSP00000349969:A2907V;ENSP00000341781:A6522V;ENSP00000450831:A3179V;ENSP00000378249:A2907V;ENSP00000451009:A400V;ENSP00000450605:A305V;ENSP00000391937:A179V;ENSP00000396794:A53V ENSP00000341781:A6522V A + 2 0 SYNE2 63754960 0.417000 0.25432 0.013000 0.15412 0.004000 0.04260 1.003000 0.29809 2.489000 0.83994 0.561000 0.74099 GCC TCGA-RB-A7B8-01A-12D-A33T-08 SYNE2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000276994.2 0 0 0 5 198 0 39 0 6.332597e-01 0 80 0 39 2 0 0 0 0 0 2 1 9.366879e-01 5 195 0 38 2 0 0 0 0 39 2 -3.153617 1 1 121410 3 34 1 0 0 0 1.943466 0 0.270000 2.180000 0.266037 0.190000 7.000000e-02 0.390000 0.180000 0.212716 0.190000 0 0.120000 0.290000 CCDC88C 440193 broad.mit.edu 37 14 91760540 91760540 + Silent SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr14:91760540G>A ENST00000389857.6 - 23 4175 c.4089C>T c.(4087-4089)taC>taT p.Y1363Y NM_001080414.3 NP_001073883.2 Q9P219 DAPLE_HUMAN coiled-coil domain containing 88C 24 all_cancers(154;0.0468) GCTCCTCATGGTACTGCTCCT 0.542000 0 SO:0001819 synonymous_variant ENST00000389857.6 1 1 hg19 CCDS45151.1 TCGA-RB-A7B8-01A-12D-A33T-08 CCDC88C-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000411650.1 1 0 1 146 737 0 127 0 4.548277e-01 0 9 0 127 2 0 0 0 0 0 2 1 1 146 731 0 127 2 0 0 0 0 127 2 -20.000000 1 1 0 0 1 0 0 0 1.943466 0 0.270000 2.180000 0.266037 0.990000 9.900000e-01 1.000000 1.000000 0.999834 0.990000 1 0.990000 1.000000 IGDCC3 9543 broad.mit.edu 37 15 65622967 65622967 + Silent SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr15:65622967G>A ENST00000327987.4 - 10 1925 c.1674C>T c.(1672-1674)taC>taT p.Y558Y IGDCC3_ENST00000559231.1_5'Flank NM_004884.3 NP_004875.2 Q8IVU1 IGDC3_HUMAN immunoglobulin superfamily, DCC subclass, member 3 30 TTGCTGGGCGGTAAAACAGCT 0.652000 0 SO:0001819 synonymous_variant ENST00000327987.4 0 1 hg19 CCDS10205.1 TCGA-RB-A7B8-01A-12D-A33T-08 IGDCC3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000256826.1 0 0 0 5 417 0 58 0 0 0 0 58 2 0 0 0 0 0 2 1 9.375019e-01 5 416 0 58 2 0 0 0 0 58 2 -2.953612 1 1 121410 1 30 1 1 2 3 2.085874 1 0.270000 2.180000 0.319601 0.120000 3.000000e-02 1.000000 0.100000 0.325830 0.120000 0 0.060000 1.000000 LRRC28 123355 broad.mit.edu 37 15 99874263 99874263 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr15:99874263G>A ENST00000301981.3 + 6 761 c.521G>A c.(520-522)cGc>cAc p.R174H LRRC28_ENST00000447360.2_Missense_Mutation_p.R174H|LRRC28_ENST00000442993.2_Silent_p.A142A|LRRC28_ENST00000422500.2_Intron|LRRC28_ENST00000558879.1_Intron|LRRC28_ENST00000331450.5_Intron|LRRC28_ENST00000559399.1_3'UTR NM_144598.2 NP_653199.2 Q86X40 LRC28_HUMAN leucine rich repeat containing 28 12 Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163) OV - Ovarian serous cystadenocarcinoma(32;0.00106) TATGTGCCGCGCCATCTCTGC 0.488000 0 SO:0001583 missense ENST00000301981.3 0 1 hg19 CCDS10380.1 . . . . . . . . . . G 29.9 5.047388 0.93740 . . ENSG00000168904 ENST00000301981;ENST00000447360 T;T 0.29655 1.56;1.56 5.83 4.91 0.64330 . 0.000000 0.85682 D 0.000000 T 0.50497 0.1619 L 0.59436 1.845 0.80722 D 1 D;B 0.89917 1.0;0.027 D;B 0.79784 0.993;0.007 T 0.42172 -0.9467 10 0.48119 T 0.1 . 14.4478 0.67364 0.0716:0.0:0.9284:0.0 . 174;174 Q86X40-2;Q86X40 .;LRC28_HUMAN H 174 ENSP00000304923:R174H;ENSP00000404520:R174H ENSP00000304923:R174H R + 2 0 LRRC28 97691786 1.000000 0.71417 0.992000 0.48379 0.998000 0.95712 7.304000 0.78882 2.775000 0.95449 0.585000 0.79938 CGC TCGA-RB-A7B8-01A-12D-A33T-08 LRRC28-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000313546.1 0 0 0 7 526 0 57 0 7.368039e-02 0 29 0 57 2 0 0 0 0 0 2 1 9.800675e-01 7 521 0 56 2 0 0 0 0 57 2 -2.392077 0 1 121412 2 34 1 1 2 3 2.092368 0 0.270000 2.180000 0.310052 0.120000 4.000000e-02 1.000000 0.100000 0.326534 0.120000 0 0.070000 1.000000 SMG1 23049 broad.mit.edu 37 16 18841673 18841673 + Silent SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr16:18841673G>A ENST00000446231.2 - 52 9223 c.8811C>T c.(8809-8811)taC>taT p.Y2937Y SMG1_ENST00000389467.3_Silent_p.Y2937Y Q96Q15 SMG1_HUMAN SMG1 phosphatidylinositol 3-kinase-related kinase 92 TTAATTCACCGTACTGAGCAT 0.413000 0 SO:0001819 synonymous_variant ENST00000446231.2 0 1 hg19 CCDS45430.1 TCGA-RB-A7B8-01A-12D-A33T-08 SMG1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000391817.1 0 0 0 4 182 0 39 0 2.041713e-02 0 8 0 39 2 0 0 0 0 0 2 1 8.887143e-01 4 180 0 39 2 0 0 0 0 39 2 -3.141551 1 1 120822 7 39 1 1 2 3 1.969257 0 0.270000 2.180000 0.274894 0.180000 5.000000e-02 1.000000 0.160000 0.226085 0.180000 0 0.100000 0.300000 PRSS21 10942 broad.mit.edu 37 16 2871460 2871460 + Missense_Mutation SNP C C T rs146520280 byFrequency TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr16:2871460C>T ENST00000005995.3 + 6 841 c.799C>T c.(799-801)Cgg>Tgg p.R267W PRSS21_ENST00000575739.1_Intron|PRSS21_ENST00000450020.3_Missense_Mutation_p.R253W|PRSS21_ENST00000455114.1_Missense_Mutation_p.R265W Q9Y6M0 TEST_HUMAN protease, serine, 21 (testisin) 15 TCGGCCCAATCGGCCCGGTGT 0.592000 0 SO:0001583 missense ENST00000005995.3 1 0 hg19 CCDS10478.1 14 0.00641025641025641 14 0.028455284552845527 0 0.0 0 0.0 0 0.0 c 12.48 1.950839 0.34471 0.012284 0.0 ENSG00000007038 ENST00000455114;ENST00000450020;ENST00000005995 D;D;D 0.89746 -2.56;-2.56;-2.56 3.96 1.92 0.25849 Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3); . . . . T 0.81992 0.4940 L 0.51853 1.615 0.19775 N 0.999955 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.81914 0.995;0.991;0.991 T 0.77043 -0.2734 9 0.72032 D 0.01 . 10.2025 0.43094 0.3607:0.6393:0.0:0.0 . 267;265;253 Q9Y6M0;Q9Y6M0-2;Q9Y6M0-3 TEST_HUMAN;.;. W 265;253;267 ENSP00000400632:R265W;ENSP00000407741:R253W;ENSP00000005995:R267W ENSP00000005995:R267W R + 1 2 PRSS21 2811461 0.000000 0.05858 0.627000 0.29227 0.396000 0.30629 0.525000 0.22956 0.327000 0.23409 -0.333000 0.08304 CGG TCGA-RB-A7B8-01A-12D-A33T-08 PRSS21-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000250910.1 1 0 0 11 272 0 52 1 2.074124e-01 2 18 0 52 2 0 0 0 0 0 2 1 9.982575e-01 11 267 0 50 2 0 0 0 0 52 2 -12.202280 1 1 121412 147 52 1 1 2 3 1.985305 0 0.270000 2.180000 0.277800 0.300000 1.500000e-01 1.000000 0.290000 0.356613 0.300000 0 0.220000 0.430000 C16orf93 90835 broad.mit.edu 37 16 30768893 30768893 + Silent SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr16:30768893C>T ENST00000543610.1 - 9 1861 c.900G>A c.(898-900)cgG>cgA p.R300R C16orf93_ENST00000541260.1_Silent_p.R365R|PHKG2_ENST00000563588.1_3'UTR|PHKG2_ENST00000424889.3_Intron NM_001014979.2 NP_001014979.2 A1A4V9 CP093_HUMAN chromosome 16 open reading frame 93 11 TGGCCTTGAGCCGCTCCTCCA 0.607000 0 SO:0001819 synonymous_variant ENST00000543610.1 0 1 hg19 CCDS32434.2 . . . . . . . . . . C 4.971 0.180321 0.09443 . . ENSG00000196118 ENST00000535476 . . . 5.97 2.97 0.34412 . . . . . T 0.54447 0.1859 . . . 0.53688 D 0.999971 . . . . . . T 0.45071 -0.9286 4 . . . -7.5983 6.1942 0.20540 0.0:0.6832:0.1532:0.1635 . . . . D 167 . . G - 2 0 C16orf93 30676394 0.922000 0.31269 0.134000 0.22075 0.562000 0.35680 0.541000 0.23207 0.421000 0.25980 0.655000 0.94253 GGC TCGA-RB-A7B8-01A-12D-A33T-08 C16orf93-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000397089.1 0 0 0 5 689 0 107 0 6.211975e-03 0 13 0 107 2 0 0 0 0 0 2 1 9.363032e-01 6 682 0 106 2 0 0 0 0 107 2 -2.762985 1 1 0 0 1 0 0 0 1.944391 0 0.270000 2.180000 0.266037 0.050000 1.000000e-02 0.120000 0.060000 0.063236 0.050000 0 0.030000 0.090000 ZNF646 9726 broad.mit.edu 37 16 31089682 31089682 + Silent SNP C C T rs145751871 TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr16:31089682C>T ENST00000394979.2 + 1 2460 c.2037C>T c.(2035-2037)ggC>ggT p.G679G ZNF646_ENST00000300850.5_Silent_p.G679G O15015 ZN646_HUMAN zinc finger protein 646 49 AGCGGGCTGGCGGTGCCAGCG 0.652000 0 SO:0001819 synonymous_variant ENST00000394979.2 0 1 hg19 TCGA-RB-A7B8-01A-12D-A33T-08 ZNF646-003 KNOWN basic protein_coding protein_coding OTTHUMT00000108510.2 0 0 0 5 351 0 66 0 1.044397e-02 0 9 0 66 2 0 0 0 0 0 2 0 2.377141e-03 5 346 1 62 19 0 0 0 0 66 2 -3.120263 1 1 121294 5 37 1 0 0 0 1.944391 0 0.270000 2.180000 0.266037 0.110000 3.000000e-02 0.230000 0.100000 0.122524 0.110000 0 0.060000 0.170000 PRPF8 10594 broad.mit.edu 37 17 1585571 1585571 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr17:1585571G>A ENST00000572621.1 - 3 551 c.286C>T c.(286-288)Ccc>Tcc p.P96S PRPF8_ENST00000304992.6_Missense_Mutation_p.P96S Q6P2Q9 PRP8_HUMAN pre-mRNA processing factor 8 77 ACTGCGTGGGGCATGTACTTT 0.507000 0 SO:0001583 missense ENST00000572621.1 0 1 hg19 CCDS11010.1 . . . . . . . . . . G 25.6 4.656010 0.88056 . . ENSG00000174231 ENST00000304992 T 0.67698 -0.28 5.6 5.6 0.85130 Pre-mRNA-processing-splicing factor 8 (2); 0.000000 0.85682 D 0.000000 D 0.86859 0.6034 M 0.92555 3.32 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.89501 0.3764 10 0.87932 D 0 . 19.616 0.95634 0.0:0.0:1.0:0.0 . 96 Q6P2Q9 PRP8_HUMAN S 96 ENSP00000304350:P96S ENSP00000304350:P96S P - 1 0 PRPF8 1532321 1.000000 0.71417 1.000000 0.80357 0.811000 0.45836 9.314000 0.96306 2.642000 0.89623 0.555000 0.69702 CCC TCGA-RB-A7B8-01A-12D-A33T-08 PRPF8-002 NOVEL alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000438412.2 0 0 0 5 462 0 69 0 5.754962e-02 0 29 0 69 2 0 0 0 0 0 2 1 9.367921e-01 5 459 0 68 2 0 0 0 0 69 2 -2.358297 0 1 0 0 1 0 0 0 1.929070 0 0.270000 2.180000 0.260010 0.080000 2.000000e-02 0.170000 0.080000 0.092919 0.080000 0 0.050000 0.130000 FAM83G 644815 broad.mit.edu 37 17 18874844 18874844 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr17:18874844G>A ENST00000388995.6 - 6 2523 c.2300C>T c.(2299-2301)gCc>gTc p.A767V FAM83G_ENST00000585154.2_Missense_Mutation_p.A767V|SLC5A10_ENST00000395645.3_Intron|SLC5A10_ENST00000395642.1_Intron|SLC5A10_ENST00000395643.2_Intron|FAM83G_ENST00000345041.4_Missense_Mutation_p.A767V|SLC5A10_ENST00000317977.6_Intron|SLC5A10_ENST00000417251.2_Intron|SLC5A10_ENST00000395647.2_Intron A6ND36 FA83G_HUMAN family with sequence similarity 83, member G 22 CATGGGGCGGGCATTTTGGGC 0.652000 0 SO:0001583 missense ENST00000388995.6 0 1 hg19 CCDS42276.1 . . . . . . . . . . G 7.947 0.743933 0.15642 . . ENSG00000188522 ENST00000388995;ENST00000345041 T;T 0.12039 2.72;2.72 5.04 2.98 0.34508 . 1.318120 0.05124 N 0.491337 T 0.15219 0.0367 L 0.51422 1.61 0.09310 N 1 B 0.20261 0.043 B 0.19946 0.027 T 0.33085 -0.9882 10 0.23891 T 0.37 -5.5706 8.3552 0.32327 0.089:0.1598:0.7512:0.0 . 767 A6ND36 FA83G_HUMAN V 767 ENSP00000373647:A767V;ENSP00000343279:A767V ENSP00000343279:A767V A - 2 0 FAM83G 18815569 0.002000 0.14202 0.001000 0.08648 0.069000 0.16628 1.162000 0.31786 1.209000 0.43321 0.561000 0.74099 GCC TCGA-RB-A7B8-01A-12D-A33T-08 FAM83G-002 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253108.4 0 0 0 6 841 0 134 0 1.427627e-02 0 21 0 134 2 0 0 0 0 0 2 1 9.642563e-01 7 834 0 132 2 0 0 0 0 134 2 -2.439846 0 1 0 0 1 0 0 0 1.929070 0 0.270000 2.180000 0.260010 0.050000 1.000000e-02 0.110000 0.060000 0.060074 0.050000 0 0.030000 0.080000 HAP1 9001 broad.mit.edu 37 17 39881124 39881124 + Silent SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr17:39881124G>A ENST00000310778.5 - 12 1854 c.1845C>T c.(1843-1845)agC>agT p.S615S JUP_ENST00000540235.1_Intron|HAP1_ENST00000393939.2_Silent_p.S538S|HAP1_ENST00000347901.4_Silent_p.S563S|HAP1_ENST00000341193.5_Silent_p.S546S P54257 HAP1_HUMAN huntingtin-associated protein 1 21 Breast(137;0.000162) BRCA - Breast invasive adenocarcinoma(4;0.0677) GGCCCAAGCCGCTGGCCTCCA 0.607000 0 SO:0001819 synonymous_variant ENST00000310778.5 0 1 hg19 TCGA-RB-A7B8-01A-12D-A33T-08 HAP1-006 KNOWN basic|appris_principal protein_coding protein_coding OTTHUMT00000389619.1 0 0 0 7 1198 0 182 0 0 0 0 182 2 0 0 0 0 0 2 1 9.797549e-01 7 1184 0 174 2 0 0 0 0 182 2 -2.363744 0 1 121412 3 42 1 1 2 3 2.003532 0 0.270000 2.180000 0.280682 0.040000 0 1.000000 0.040000 0.134225 0.040000 0 0.020000 0.080000 EZH1 2145 broad.mit.edu 37 17 40865346 40865346 + Missense_Mutation SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr17:40865346C>T ENST00000428826.2 - 11 1206 c.1085G>A c.(1084-1086)cGg>cAg p.R362Q EZH1_ENST00000585893.1_Missense_Mutation_p.R322Q|EZH1_ENST00000435174.1_Missense_Mutation_p.R223Q|EZH1_ENST00000590078.1_Missense_Mutation_p.R292Q|EZH1_ENST00000592743.1_Missense_Mutation_p.R362Q|EZH1_ENST00000415827.2_Missense_Mutation_p.R353Q Q92800 EZH1_HUMAN enhancer of zeste 1 polycomb repressive complex 2 subunit 27 Breast(137;0.00104) GTGCCTTCTCCGGCGACGACC 0.552000 0 SO:0001583 missense ENST00000428826.2 0 1 hg19 CCDS32659.1 . . . . . . . . . . C 20.5 4.008400 0.75046 . . ENSG00000108799 ENST00000264646;ENST00000428826;ENST00000415827;ENST00000435174 D;D 0.86030 -2.06;-2.06 5.26 5.26 0.73747 . 0.000000 0.85682 D 0.000000 T 0.79718 0.4494 L 0.46157 1.445 0.58432 D 0.999998 P;P;P;P;P 0.46656 0.764;0.882;0.882;0.72;0.812 B;B;B;B;B 0.35859 0.212;0.209;0.209;0.209;0.149 T 0.78558 -0.2158 10 0.22706 T 0.39 . 19.0657 0.93108 0.0:1.0:0.0:0.0 . 223;322;368;292;362 Q92800-5;Q92800-3;Q92800-2;Q92800-4;Q92800 .;.;.;.;EZH1_HUMAN Q 365;362;322;223 ENSP00000404658:R362Q;ENSP00000404071:R223Q ENSP00000264646:R365Q R - 2 0 EZH1 38118872 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 6.590000 0.74085 2.734000 0.93682 0.555000 0.69702 CGG TCGA-RB-A7B8-01A-12D-A33T-08 EZH1-004 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000452347.1 0 0 0 5 522 0 73 0 1.377477e-02 0 15 0 73 2 0 0 0 0 0 2 1 9.371887e-01 5 521 0 73 2 0 0 0 0 73 2 -2.547753 1 1 121412 1 32 1 1 2 3 2.008247 0 0.270000 2.180000 0.282591 0.080000 2.000000e-02 1.000000 0.070000 0.180439 0.080000 0 0.040000 0.140000 NFE2L1 4779 broad.mit.edu 37 17 46136986 46136986 + Missense_Mutation SNP A A G TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 A G A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr17:46136986A>G ENST00000362042.3 + 6 2918 c.2302A>G c.(2302-2304)Aag>Gag p.K768E RP5-890E16.4_ENST00000583349.1_RNA|NFE2L1_ENST00000582155.1_Missense_Mutation_p.K580E|NFE2L1_ENST00000361665.3_Missense_Mutation_p.K757E|NFE2L1_ENST00000357480.5_Missense_Mutation_p.K738E|NFE2L1_ENST00000583378.1_Missense_Mutation_p.K569E|NFE2L1_ENST00000536222.1_Missense_Mutation_p.K612E|NFE2L1_ENST00000585291.1_Missense_Mutation_p.K738E NM_003204.2 NP_003195.1 Q14494 NF2L1_HUMAN nuclear factor, erythroid 2-like 1 32 GAGGAAGCCAAAGGACCGGAG 0.647000 0 SO:0001583 missense ENST00000362042.3 1 1 hg19 CCDS11524.1 . . . . . . . . . . A 18.91 3.723743 0.68959 . . ENSG00000082641 ENST00000362042;ENST00000361665;ENST00000357480;ENST00000536222 T;T 0.29142 1.9;1.58 5.89 5.89 0.94794 . 0.220853 0.48767 D 0.000174 T 0.47655 0.1457 L 0.43923 1.385 0.54753 D 0.999983 D;D;D;D 0.71674 0.994;0.989;0.958;0.998 P;P;P;D 0.75484 0.885;0.709;0.827;0.986 T 0.44847 -0.9301 10 0.66056 D 0.02 -12.13 13.8341 0.63400 1.0:0.0:0.0:0.0 . 612;580;738;768 F5H1B7;B4DYE1;Q14494-2;Q14494 .;.;.;NF2L1_HUMAN E 787;768;738;612 ENSP00000350072:K738E;ENSP00000445811:K612E ENSP00000350072:K738E K + 1 0 NFE2L1 43491985 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.390000 0.79816 2.257000 0.74773 0.460000 0.39030 AAG TCGA-RB-A7B8-01A-12D-A33T-08 NFE2L1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000443019.1 1 0 0 15 187 0 28 1 9.999821e-01 17 235 0 28 2 0 0 0 0 0 2 1 9.998870e-01 15 186 0 28 2 0 0 0 0 28 2 -19.876170 1 1 0 0 1 1 2 3 2.005347 0 0.270000 2.180000 0.281637 0.580000 3.300000e-01 1.000000 0.560000 0.623008 0.580000 0 0.440000 0.800000 TRIM37 4591 broad.mit.edu 37 17 57093004 57093004 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr17:57093004G>A ENST00000262294.7 - 21 2802 c.2543C>T c.(2542-2544)gCg>gTg p.A848V TRIM37_ENST00000376149.3_Missense_Mutation_p.A726V|TRIM37_ENST00000393065.2_Missense_Mutation_p.A814V|TRIM37_ENST00000393066.3_Missense_Mutation_p.A848V NM_015294.3 NP_056109.1 O94972 TRI37_HUMAN tripartite motif containing 37 p.A848V(1) 37 Medulloblastoma(34;0.0922)|all_neural(34;0.101) TTTCTCAACCGCAGGCAAGCC 0.398000 Mulibrey Nanism 1 Substitution - Missense(1) SO:0001583 missense Familial Cancer Database Perheentupa syndrome ENST00000262294.7 0 1 hg19 CCDS32694.1 . . . . . . . . . . G 11.52 1.661961 0.29515 . . ENSG00000108395 ENST00000393066;ENST00000262294;ENST00000376149;ENST00000393065 T;T;T;T 0.31247 1.5;1.5;1.5;1.5 4.93 2.9 0.33743 . 0.843050 0.10578 N 0.658234 T 0.21267 0.0512 N 0.24115 0.695 0.09310 N 1 B;B;B 0.09022 0.002;0.001;0.0 B;B;B 0.06405 0.002;0.001;0.0 T 0.17531 -1.0366 10 0.48119 T 0.1 -0.0368 9.163 0.37035 0.1801:0.0:0.8199:0.0 . 814;726;848 F8WEE6;O94972-2;O94972 .;.;TRI37_HUMAN V 848;848;726;814 ENSP00000376785:A848V;ENSP00000262294:A848V;ENSP00000365319:A726V;ENSP00000376784:A814V ENSP00000262294:A848V A - 2 0 TRIM37 54447786 0.197000 0.23362 0.437000 0.26809 0.721000 0.41392 1.507000 0.35758 1.082000 0.41137 0.313000 0.20887 GCG TCGA-RB-A7B8-01A-12D-A33T-08 TRIM37-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000445930.1 0 0 0 7 798 1 114 0 2.168257e-02 0 22 1 114 2 0 0 0 0 0 2 0 2.052756e-03 6 785 1 113 23 0 0 0 1 114 2 -1.937388 0 1 121412 7 43 1 1 2 3 2.005347 0 0.270000 2.180000 0.281637 0.070000 2.000000e-02 1.000000 0.070000 0.163868 0.070000 0 0.040000 0.120000 CDH2 1000 broad.mit.edu 37 18 25572669 25572669 + Missense_Mutation SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr18:25572669C>T ENST00000269141.3 - 9 1717 c.1294G>A c.(1294-1296)Gcc>Acc p.A432T CDH2_ENST00000399380.3_Missense_Mutation_p.A401T NM_001792.3 NP_001783.2 P19022 CADH2_HUMAN cadherin 2, type 1, N-cadherin (neuronal) 82 GTCTGGATGGCGAACCGTCCA 0.532000 0 SO:0001583 missense ENST00000269141.3 1 1 hg19 CCDS11891.1 . . . . . . . . . . C 3.023 -0.201263 0.06219 . . ENSG00000170558 ENST00000269141;ENST00000399380 T;T 0.49139 0.79;0.79 5.39 4.51 0.55191 Cadherin (4);Cadherin-like (1); 0.160521 0.56097 D 0.000022 T 0.25975 0.0633 N 0.13140 0.3 0.46222 D 0.998936 B;B 0.13594 0.001;0.008 B;B 0.11329 0.003;0.006 T 0.09122 -1.0689 10 0.08381 T 0.77 . 10.1311 0.42680 0.0:0.8447:0.0:0.1553 . 401;432 A8MWK3;P19022 .;CADH2_HUMAN T 432;401 ENSP00000269141:A432T;ENSP00000382312:A401T ENSP00000269141:A432T A - 1 0 CDH2 23826667 1.000000 0.71417 0.993000 0.49108 0.455000 0.32408 3.907000 0.56348 2.674000 0.91012 0.655000 0.94253 GCC TCGA-RB-A7B8-01A-12D-A33T-08 CDH2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000133246.3 1 0 1 62 321 0 58 0 7.247729e-01 1 14 0 58 2 0 0 0 0 0 2 1 1 62 315 0 58 2 0 0 0 0 58 2 -2.934807 1 1 0 0 1 0 0 0 1.925972 0 0.270000 2.180000 0.257979 0.990000 9.200000e-01 1.000000 1.000000 0.995337 0.990000 1 0.990000 1.000000 HMHA1 23526 broad.mit.edu 37 19 1073163 1073163 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr19:1073163G>A ENST00000313093.2 + 3 668 c.437G>A c.(436-438)cGc>cAc p.R146H HMHA1_ENST00000590214.1_Missense_Mutation_p.R173H|HMHA1_ENST00000539243.2_Missense_Mutation_p.R162H|HMHA1_ENST00000592335.1_Missense_Mutation_p.A27T|HMHA1_ENST00000543365.1_Missense_Mutation_p.R29H|HMHA1_ENST00000536472.1_5'UTR|HMHA1_ENST00000586866.1_Missense_Mutation_p.R150H NM_012292.3 NP_036424.2 Q92619 HMHA1_HUMAN histocompatibility (minor) HA-1 16 Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137) CTTGAGGCCCGCCGCCCGCGG 0.642000 0 SO:0001583 missense ENST00000313093.2 0 1 hg19 CCDS32863.1 . . . . . . . . . . G 13.40 2.225757 0.39300 . . ENSG00000180448 ENST00000539243;ENST00000313093;ENST00000544746;ENST00000412039;ENST00000543365 T;T;T 0.25085 1.96;1.96;1.82 4.16 4.16 0.48862 . 0.068586 0.64402 D 0.000017 T 0.43100 0.1232 M 0.64997 1.995 0.80722 D 1 D;D;D 0.89917 0.999;1.0;0.998 P;D;P 0.68765 0.878;0.96;0.862 T 0.27054 -1.0085 10 0.45353 T 0.12 -29.6413 9.9138 0.41421 0.1043:0.0:0.8957:0.0 . 162;29;146 F6QP70;F5H1R4;Q92619 .;.;HMHA1_HUMAN H 162;146;146;140;29 ENSP00000439601:R162H;ENSP00000316772:R146H;ENSP00000438979:R29H ENSP00000316772:R146H R + 2 0 HMHA1 1024163 1.000000 0.71417 0.997000 0.53966 0.498000 0.33706 3.603000 0.54074 1.855000 0.53841 0.491000 0.48974 CGC TCGA-RB-A7B8-01A-12D-A33T-08 HMHA1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000458026.1 0 0 0 7 624 0 82 0 3.574831e-03 0 7 0 82 2 0 0 0 0 0 2 1 9.802442e-01 7 620 0 81 2 0 0 0 0 82 2 -2.442455 0 1 121228 1 33 1 1 2 3 1.996663 0 0.270000 2.180000 0.279724 0.080000 3.000000e-02 1.000000 0.080000 0.167752 0.080000 0 0.050000 0.140000 SARS2 54938 broad.mit.edu 37 19 39421234 39421234 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr19:39421234G>A ENST00000221431.6 - 1 302 c.143C>T c.(142-144)gCg>gTg p.A48V MRPS12_ENST00000308018.4_5'UTR|MRPS12_ENST00000402029.3_5'Flank|SARS2_ENST00000600042.1_Missense_Mutation_p.A48V|SARS2_ENST00000430193.3_Missense_Mutation_p.A48V|MRPS12_ENST00000407800.2_5'Flank|SARS2_ENST00000448145.2_Intron|CTC-360G5.8_ENST00000599996.1_Intron|SARS2_ENST00000594171.1_5'Flank NM_017827.3 NP_060297.1 Q9NP81 SYSM_HUMAN seryl-tRNA synthetase 2, mitochondrial 15 all_cancers(60;2.74e-06)|all_epithelial(25;4.36e-06)|Ovarian(47;0.0454) Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554) GCCCTCGCGCGCATACTCGTA 0.627000 OREG0025455 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000221431.6 0 1 hg19 CCDS33017.1 . . . . . . . . . . G 14.36 2.512002 0.44660 . . ENSG00000104835 ENST00000430193;ENST00000221431;ENST00000455102 T;T;T 0.55588 0.51;0.51;1.49 5.65 4.57 0.56435 . 0.122893 0.53938 D 0.000045 T 0.40979 0.1139 L 0.43923 1.385 . . . D;B;B 0.56746 0.977;0.206;0.257 B;B;B 0.43623 0.425;0.014;0.007 T 0.44952 -0.9294 9 0.16896 T 0.51 . 8.6175 0.33840 0.1027:0.0:0.8973:0.0 . 48;48;48 B4DJP6;B4DE10;Q9NP81 .;.;SYSM_HUMAN V 48 ENSP00000406754:A48V;ENSP00000221431:A48V;ENSP00000414954:A48V ENSP00000221431:A48V A - 2 0 FBXO17 44113074 1.000000 0.71417 1.000000 0.80357 0.672000 0.39443 3.764000 0.55264 2.941000 0.99782 0.655000 0.94253 GCG TCGA-RB-A7B8-01A-12D-A33T-08 SARS2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000463139.1 0 0 0 7 701 1 112 0 4.441061e-03 0 27 1 112 3 0 0 0 0 0 2 0 5.429036e-03 7 695 1 112 21 0 0 0 1 112 2 -1.741208 0 1 121412 2 37 1 1 2 3 1.972107 0 0.270000 2.180000 0.275865 0.070000 2.000000e-02 1.000000 0.080000 0.126863 0.070000 0 0.040000 0.120000 ZNF606 80095 broad.mit.edu 37 19 58490664 58490664 + Missense_Mutation SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr19:58490664C>T ENST00000341164.4 - 7 2004 c.1384G>A c.(1384-1386)Gga>Aga p.G462R ZNF606_ENST00000536132.1_Missense_Mutation_p.G372R NM_025027.3 NP_079303.2 Q8WXB4 ZN606_HUMAN zinc finger protein 606 26 Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157) AAGGCTTTTCCACATTTATTA 0.358000 0 SO:0001583 missense ENST00000341164.4 1 1 hg19 CCDS12968.1 . . . . . . . . . . C 16.80 3.223390 0.58668 . . ENSG00000166704 ENST00000341164;ENST00000536132;ENST00000551380 T;T;T 0.01484 4.84;4.84;4.84 4.55 4.55 0.56014 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); 0.000000 0.45361 D 0.000365 T 0.08935 0.0221 M 0.67517 2.055 0.53688 D 0.999976 D 0.89917 1.0 D 0.68483 0.958 T 0.01648 -1.1304 10 0.66056 D 0.02 . 16.585 0.84725 0.0:1.0:0.0:0.0 . 462 Q8WXB4 ZN606_HUMAN R 462;372;462 ENSP00000343617:G462R;ENSP00000445624:G372R;ENSP00000446972:G462R ENSP00000343617:G462R G - 1 0 ZNF606 63182476 0.976000 0.34144 1.000000 0.80357 0.997000 0.91878 2.375000 0.44283 2.515000 0.84797 0.655000 0.94253 GGA TCGA-RB-A7B8-01A-12D-A33T-08 ZNF606-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000405961.1 1 0 1 39 220 0 42 0 2.929391e-01 0 7 0 42 2 0 0 0 0 0 2 1 1 39 218 0 41 2 0 0 0 0 42 2 -3.153007 1 1 0 0 1 1 2 3 1.991890 0 0.270000 2.180000 0.278763 0.990000 8.300000e-01 1.000000 1.000000 0.984146 0.990000 1 0.970000 1.000000 COL11A1 1301 broad.mit.edu 37 1 103483426 103483426 + Missense_Mutation SNP G G T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 G T G G Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr1:103483426G>T ENST00000370096.3 - 11 1675 c.1363C>A c.(1363-1365)Cct>Act p.P455T COL11A1_ENST00000512756.1_Missense_Mutation_p.P339T|COL11A1_ENST00000358392.2_Missense_Mutation_p.P467T|COL11A1_ENST00000353414.4_Missense_Mutation_p.P416T NM_001854.3 NP_001845.3 P12107 COBA1_HUMAN collagen, type XI, alpha 1 258 all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181) AGACCTGGAGGACCCATAATA 0.418000 0 SO:0001583 missense ENST00000370096.3 1 1 hg19 CCDS778.1 . . . . . . . . . . G 17.17 3.322302 0.60634 . . ENSG00000060718 ENST00000370096;ENST00000358392;ENST00000353414;ENST00000512756;ENST00000427239 D;D;D;D;D 0.94828 -3.53;-3.53;-3.53;-2.43;-2.43 5.38 5.38 0.77491 . 0.110223 0.64402 D 0.000005 D 0.96935 0.8999 M 0.79475 2.455 0.80722 D 1 D;D;D;D 0.76494 0.999;0.999;0.999;0.999 D;D;D;D 0.85130 0.995;0.991;0.994;0.997 D 0.95999 0.8992 10 0.44086 T 0.13 . 19.111 0.93317 0.0:0.0:1.0:0.0 . 339;416;467;455 E9PCU0;P12107-3;P12107-2;P12107 .;.;.;COBA1_HUMAN T 455;467;416;339;467 ENSP00000359114:P455T;ENSP00000351163:P467T;ENSP00000302551:P416T;ENSP00000426533:P339T;ENSP00000408640:P467T ENSP00000302551:P416T P - 1 0 COL11A1 103256014 1.000000 0.71417 1.000000 0.80357 0.978000 0.69477 8.281000 0.89905 2.673000 0.90976 0.650000 0.86243 CCT TCGA-RB-A7B8-01A-12D-A33T-08 COL11A1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000029997.1 1 0 1 75 473 0 69 0 9.999969e-01 0 115 0 69 2 0 0 0 0 0 2 1 1 73 467 0 69 2 0 0 0 0 69 2 -20.000000 1 1 0 0 1 1 2 3 2.068492 0 0.270000 2.180000 0.294754 0.990000 8.400000e-01 1.000000 1.000000 0.981990 0.990000 1 0.950000 1.000000 ALX3 257 broad.mit.edu 37 1 110607330 110607330 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr1:110607330G>A ENST00000369792.4 - 2 560 c.473C>T c.(472-474)aCg>aTg p.T158M RP4-773N10.4_ENST00000554749.1_RNA NM_006492.2 NP_006483.2 O95076 ALX3_HUMAN ALX homeobox 3 6 all_cancers(81;2.35e-05)|all_epithelial(167;7.69e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233) GCTGAAGGTCGTGCGGTTACG 0.597000 0 SO:0001583 missense ENST00000369792.4 1 1 hg19 CCDS819.1 . . . . . . . . . . G 21.0 4.087698 0.76642 . . ENSG00000156150 ENST00000369792 D 0.97352 -4.35 4.18 4.18 0.49190 Homeodomain-related (1);Homeobox (3);Homeodomain-like (1); 0.000000 0.64402 D 0.000001 D 0.98960 0.9646 H 0.97682 4.055 0.80722 D 1 D 0.89917 1.0 D 0.87578 0.998 D 0.99316 1.0905 10 0.87932 D 0 . 14.3494 0.66691 0.0:0.0:1.0:0.0 . 158 O95076 ALX3_HUMAN M 158 ENSP00000358807:T158M ENSP00000358807:T158M T - 2 0 ALX3 110408853 1.000000 0.71417 0.907000 0.35723 0.987000 0.75469 9.813000 0.99286 2.022000 0.59522 0.462000 0.41574 ACG TCGA-RB-A7B8-01A-12D-A33T-08 ALX3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000032232.2 0 0 1 112 350 1 65 0 0 0 1 65 2 0 0 0 0 0 2 1 1 112 349 1 65 22 0 0 0 1 65 2 -20.000000 1 1 0 0 1 1 2 3 2.068492 0 0.270000 2.180000 0.294754 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 FLG 2312 broad.mit.edu 37 1 152277587 152277587 + Missense_Mutation SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr1:152277587C>T ENST00000368799.1 - 3 9810 c.9775G>A c.(9775-9777)Gaa>Aaa p.E3259K FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA NM_002016.1 NP_002007.1 P20930 FILA_HUMAN filaggrin 424 Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127) LUSC - Lung squamous cell carcinoma(543;0.206) GCTCTGTCTTCGTGATGGGAC 0.582000 Ichthyosis 0 SO:0001583 missense Familial Cancer Database X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris ENST00000368799.1 1 1 hg19 CCDS30860.1 . . . . . . . . . . C 10.70 1.424271 0.25639 . . ENSG00000143631 ENST00000368799;ENST00000368796 T 0.02103 4.45 1.52 -3.04 0.05412 . . . . . T 0.01287 0.0042 M 0.68317 2.08 0.09310 N 1 D 0.56287 0.975 P 0.55713 0.782 T 0.30416 -0.9979 9 0.07644 T 0.81 -0.6633 3.8186 0.08825 0.0:0.3025:0.4847:0.2128 . 3259 P20930 FILA_HUMAN K 3259;197 ENSP00000357789:E3259K ENSP00000357786:E197K E - 1 0 FLG 150544211 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -1.047000 0.03521 -0.855000 0.04125 -0.535000 0.04281 GAA TCGA-RB-A7B8-01A-12D-A33T-08 FLG-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000033742.1 0 0 1 290 2141 0 345 0 0 0 1 0 345 2 0 0 0 0 0 2 1 1 288 2115 0 343 2 0 0 0 0 345 2 -20.000000 1 1 121408 3 40 1 1 3 4 2.417547 1 0.270000 2.180000 0.413984 0.990000 9.700000e-01 1.000000 1.000000 0.998934 0.990000 1 0.990000 1.000000 AQP10 89872 broad.mit.edu 37 1 154295786 154295786 + Missense_Mutation SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr1:154295786C>T ENST00000324978.3 + 4 480 c.440C>T c.(439-441)gCc>gTc p.A147V ATP8B2_ENST00000368487.3_5'Flank|AQP10_ENST00000484864.1_Missense_Mutation_p.A147V|AQP10_ENST00000355197.4_3'UTR NM_080429.2 NP_536354.2 Q96PS8 AQP10_HUMAN aquaporin 10 23 all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877) LUSC - Lung squamous cell carcinoma(543;0.185) TCCATTTTTGCCACCTATCCT 0.557000 0 SO:0001583 missense ENST00000324978.3 0 1 hg19 CCDS1065.1 . . . . . . . . . . C 24.0 4.484892 0.84854 . . ENSG00000143595 ENST00000324978;ENST00000484864 T;T 0.11930 2.73;2.73 5.04 4.12 0.48240 Aquaporin-like (2); 0.332186 0.32503 N 0.006010 T 0.19406 0.0466 M 0.83312 2.635 0.33617 D 0.604262 D;P 0.54047 0.964;0.912 P;P 0.56127 0.792;0.756 T 0.08722 -1.0708 10 0.87932 D 0 . 8.5573 0.33489 0.0:0.7645:0.1526:0.0828 . 147;147 Q96PS8-2;Q96PS8 .;AQP10_HUMAN V 147 ENSP00000318355:A147V;ENSP00000420341:A147V ENSP00000318355:A147V A + 2 0 AQP10 152562410 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 3.810000 0.55613 1.364000 0.46038 0.555000 0.69702 GCC TCGA-RB-A7B8-01A-12D-A33T-08 AQP10-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000087661.1 0 0 0 7 753 1 113 0 0 0 1 113 2 0 0 0 0 0 2 0 3.504678e-03 7 747 1 112 22 0 0 0 1 113 2 -2.147296 0 1 0 0 1 1 3 4 2.394335 1 0.270000 2.180000 0.408859 0.090000 2.000000e-02 1.000000 0.080000 0.190216 0.090000 0 0.050000 0.160000 CELA2A 63036 broad.mit.edu 37 1 15783633 15783633 + Silent SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr1:15783633C>T ENST00000359621.4 + 2 118 c.93C>T c.(91-93)ggC>ggT p.G31G CELA2A_ENST00000497590.1_3'UTR NM_033440.2 NP_254275.1 P08217 CEL2A_HUMAN chymotrypsin-like elastase family, member 2A 16 GGGTGGTTGGCGGTGAAGAAG 0.577000 0 SO:0001819 synonymous_variant ENST00000359621.4 0 1 hg19 CCDS157.1 TCGA-RB-A7B8-01A-12D-A33T-08 CELA2A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000006445.1 0 0 0 4 256 0 31 0 0 0 0 31 2 0 0 0 0 0 2 1 8.826125e-01 4 247 0 31 2 0 0 0 0 31 2 -2.811549 1 1 121412 4 36 1 0 1 1 1.649643 1 0.270000 2.180000 0.156069 0.100000 3.000000e-02 0.230000 0.100000 0.119738 0.100000 0 0.060000 0.170000 MYOC 4653 broad.mit.edu 37 1 171605766 171605766 + Nonsense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr1:171605766G>A ENST00000037502.6 - 3 885 c.814C>T c.(814-816)Cga>Tga p.R272* NM_000261.1 NP_000252.1 Q99972 MYOC_HUMAN myocilin, trabecular meshwork inducible glucocorticoid response p.R272*(1) 28 all_cancers(6;5.47e-10)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181) TTGGGGTCTCGCATCCACACA 0.512000 1 Substitution - Nonsense(1) GRCh37 CM005409 MYOC M SO:0001587 stop_gained ENST00000037502.6 0 1 hg19 CCDS1297.1 . . . . . . . . . . G 28.3 4.908515 0.92107 0.0 1.16E-4 ENSG00000034971 ENST00000037502;ENST00000357746;ENST00000536591;ENST00000537133 . . . 5.76 -1.13 0.09775 . 0.139314 0.64402 D 0.000004 . . . . . . 0.80722 D 1 . . . . . . . . . . 0.05620 T 0.96 . 16.4257 0.83814 0.0:0.0:0.6471:0.3529 . . . . X 272;225;205;272 . ENSP00000037502:R272X R - 1 2 MYOC 169872389 1.000000 0.71417 0.991000 0.47740 0.951000 0.60555 1.127000 0.31357 -0.445000 0.07159 0.555000 0.69702 CGA TCGA-RB-A7B8-01A-12D-A33T-08 MYOC-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000084178.2 0 0 0 7 553 0 67 0 0 0 0 67 2 0 0 0 0 0 2 1 9.804696e-01 7 551 0 67 2 0 0 0 0 67 2 -2.353732 0 1 121412 1 34 1 1 3 4 2.394335 1 0.270000 2.180000 0.408859 0.120000 4.000000e-02 1.000000 0.110000 0.220607 0.120000 0 0.080000 0.210000 CACNA1E 777 broad.mit.edu 37 1 181690939 181690939 + Missense_Mutation SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr1:181690939C>T ENST00000367573.2 + 16 2002 c.2002C>T c.(2002-2004)Cgc>Tgc p.R668C CACNA1E_ENST00000367567.4_Missense_Mutation_p.R275C|CACNA1E_ENST00000526775.1_Missense_Mutation_p.R668C|CACNA1E_ENST00000360108.3_Missense_Mutation_p.R668C|CACNA1E_ENST00000358338.5_Missense_Mutation_p.R619C|CACNA1E_ENST00000357570.5_Missense_Mutation_p.R619C|CACNA1E_ENST00000367570.1_Missense_Mutation_p.R668C NM_001205293.1 NP_001192222.1 Q15878 CAC1E_HUMAN calcium channel, voltage-dependent, R type, alpha 1E subunit p.R668C(2) 204 CAATGGGATCCGCTCCCAGGG 0.507000 2 Substitution - Missense(2) SO:0001583 missense ENST00000367573.2 1 1 hg19 CCDS55664.1 . . . . . . . . . . C 24.5 4.535986 0.85812 . . ENSG00000198216 ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573 D;D;D;D;D;D;D 0.97430 -4.38;-4.38;-4.38;-4.38;-4.38;-4.38;-4.38 5.33 5.33 0.75918 . 0.048724 0.85682 N 0.000000 D 0.98413 0.9472 M 0.79805 2.47 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.72338 0.977;0.977 D 0.99482 1.0948 10 0.72032 D 0.01 . 18.6084 0.91275 0.0:1.0:0.0:0.0 . 668;668 Q15878-2;Q15878-3 .;. C 668;668;619;619;275;668;668 ENSP00000356542:R668C;ENSP00000434814:R668C;ENSP00000350183:R619C;ENSP00000351101:R619C;ENSP00000356539:R275C;ENSP00000353222:R668C;ENSP00000356545:R668C ENSP00000350183:R619C R + 1 0 CACNA1E 179957562 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 4.705000 0.61838 2.465000 0.83290 0.563000 0.77884 CGC TCGA-RB-A7B8-01A-12D-A33T-08 CACNA1E-003 KNOWN non_canonical_U12|basic|CCDS protein_coding protein_coding OTTHUMT00000090793.2 1 0 1 150 693 0 96 0 0 0 0 96 2 0 0 0 0 0 2 1 1 150 679 0 96 2 0 0 0 0 96 2 -2.991684 1 1 0 0 1 1 3 4 2.394335 1 0.270000 2.180000 0.408859 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 KLHDC8A 55220 broad.mit.edu 37 1 205307704 205307704 + Nonsense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr1:205307704G>A ENST00000367156.3 - 8 1594 c.778C>T c.(778-780)Cga>Tga p.R260* KLHDC8A_ENST00000367155.3_Nonsense_Mutation_p.R260*|KLHDC8A_ENST00000537168.1_Nonsense_Mutation_p.R147*|KLHDC8A_ENST00000539253.1_Nonsense_Mutation_p.R260*|KLHDC8A_ENST00000460687.1_Nonsense_Mutation_p.R126* NM_001271863.1 NP_001258792.1 Q8IYD2 KLD8A_HUMAN kelch domain containing 8A 14 Breast(84;0.23) BRCA - Breast invasive adenocarcinoma(75;0.117) AAGAACGATCGTTCCATCTTC 0.517000 0 SO:0001587 stop_gained ENST00000367156.3 0 1 hg19 CCDS30985.1 . . . . . . . . . . G 38 6.698759 0.97772 . . ENSG00000162873 ENST00000367155;ENST00000367156;ENST00000539253;ENST00000537168 . . . 5.62 5.62 0.85841 . 0.216018 0.49305 D 0.000149 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.06365 T 0.9 -19.0544 19.2423 0.93888 0.0:0.0:1.0:0.0 . . . . X 260;260;260;147 . ENSP00000356123:R260X R - 1 2 KLHDC8A 203574327 1.000000 0.71417 0.992000 0.48379 0.950000 0.60333 5.085000 0.64468 2.642000 0.89623 0.655000 0.94253 CGA TCGA-RB-A7B8-01A-12D-A33T-08 KLHDC8A-002 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000090397.1 1 0 1 85 414 0 63 0 7.883851e-02 0 3 0 63 2 0 0 0 0 0 2 1 1 69 361 0 54 2 0 0 0 0 63 2 -20.000000 1 1 0 0 1 1 3 4 2.395465 1 0.270000 2.180000 0.408859 0.990000 9.900000e-01 1.000000 1.000000 0.999999 0.990000 1 0.990000 1.000000 HIST3H2BB 128312 broad.mit.edu 37 1 228646127 228646127 + Silent SNP T T G rs145799075 byFrequency TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr1:228646127T>G ENST00000369160.2 + 1 320 c.297T>G c.(295-297)gtT>gtG p.V99V HIST3H2A_ENST00000366695.2_5'Flank NM_175055.2 NP_778225.1 Q8N257 H2B3B_HUMAN histone cluster 3, H2bb 1 Prostate(94;0.183) AGACGGCCGTTCGCCTGCTGC 0.652000 0 SO:0001819 synonymous_variant ENST00000369160.2 0 1 hg19 CCDS1574.1 TCGA-RB-A7B8-01A-12D-A33T-08 HIST3H2BB-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000096597.1 0 0 0 7 489 0 71 0 0 0 1 0 71 2 0 0 0 0 0 2 1 9.800372e-01 7 484 0 70 2 0 0 0 0 71 2 -6.444935 1 1 121402 33 46 1 1 3 4 2.395465 1 0.270000 2.180000 0.408859 0.140000 5.000000e-02 1.000000 0.120000 0.235493 0.140000 0 0.090000 0.240000 SLC6A9 6536 broad.mit.edu 37 1 44468618 44468618 + Silent SNP A A G TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr1:44468618A>G ENST00000360584.2 - 6 1040 c.849T>C c.(847-849)ttT>ttC p.F283F SLC6A9_ENST00000475075.2_Silent_p.F99F|SLC6A9_ENST00000357730.2_Silent_p.F229F|SLC6A9_ENST00000372306.3_Silent_p.F210F|SLC6A9_ENST00000372310.3_Silent_p.F210F|SLC6A9_ENST00000537678.1_Silent_p.F145F|SLC6A9_ENST00000372307.3_Silent_p.F145F NM_201649.3 NP_964012.2 P48067 SC6A9_HUMAN solute carrier family 6 (neurotransmitter transporter, glycine), member 9 22 Acute lymphoblastic leukemia(166;0.155) Myeloproliferative disorder(586;0.0511) Glycine(DB00145) GCACCTCCCCAAAGTTCCCAA 0.592000 0 SO:0001819 synonymous_variant ENST00000360584.2 1 1 hg19 CCDS41317.1 TCGA-RB-A7B8-01A-12D-A33T-08 SLC6A9-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000022825.2 0 0 1 142 803 1 130 0 1.112019e-01 1 3 1 130 2 0 0 0 0 0 2 1 1 141 799 1 128 23 0 0 0 1 130 2 -20.000000 1 1 0 0 1 1 2 3 2.082796 1 0.270000 2.180000 0.317023 0.990000 9.900000e-01 1.000000 1.000000 0.999663 0.990000 1 0.990000 1.000000 JAG1 182 broad.mit.edu 37 20 10621878 10621878 + Silent SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr20:10621878C>T ENST00000254958.5 - 24 3446 c.2931G>A c.(2929-2931)gaG>gaA p.E977E JAG1_ENST00000423891.2_Silent_p.E818E NM_000214.2 NP_000205.1 P78504 JAG1_HUMAN jagged 1 44 TGCAAATGTGCTCCGTAGTAA 0.408000 Alagille Syndrome 0 SO:0001819 synonymous_variant Familial Cancer Database ALGS1, ALGS2.Alagille-Watson syndrome ENST00000254958.5 1 1 hg19 CCDS13112.1 TCGA-RB-A7B8-01A-12D-A33T-08 JAG1-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding 1 0 1 40 281 0 41 1 9.999668e-01 18 92 0 41 2 0 0 0 0 0 2 1 1 40 277 0 41 2 0 0 0 0 41 2 -20.000000 1 1 0 0 1 1 2 3 1.954423 0 0.270000 2.180000 0.270984 0.920000 6.700000e-01 1.000000 1.000000 0.905318 0.920000 1 0.790000 1.000000 RBM12 10137 broad.mit.edu 37 20 34241168 34241168 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr20:34241168G>A ENST00000374114.3 - 3 2340 c.2077C>T c.(2077-2079)Ccc>Tcc p.P693S CPNE1_ENST00000397442.1_Intron|CPNE1_ENST00000317619.3_Intron|CPNE1_ENST00000397446.1_Intron|CPNE1_ENST00000317677.5_Intron|CPNE1_ENST00000352393.4_Intron|CPNE1_ENST00000397443.1_Intron|RP1-309K20.6_ENST00000541176.2_Intron|RBM12_ENST00000374104.3_Missense_Mutation_p.P693S|RBM12_ENST00000359646.1_Missense_Mutation_p.P693S|CPNE1_ENST00000397445.1_Intron NM_001198838.1|NM_001198840.1|NM_006047.5 NP_001185767.1|NP_001185769.1|NP_006038.2 Q9NTZ6 RBM12_HUMAN RNA binding motif protein 12 36 Lung NSC(9;0.00608)|all_lung(11;0.00918) BRCA - Breast invasive adenocarcinoma(18;0.00953) CCTGCACTGGGCATTCCCGCA 0.557000 0 SO:0001583 missense ENST00000374114.3 0 1 hg19 CCDS13261.1 . . . . . . . . . . G 36 5.653504 0.96724 . . ENSG00000244462 ENST00000374114;ENST00000359646;ENST00000374104;ENST00000349942 T;T;T 0.22336 1.96;1.96;1.96 4.03 4.03 0.46877 . 0.000000 0.64402 D 0.000018 T 0.27663 0.0680 N 0.19112 0.55 0.80722 D 1 D 0.63880 0.993 D 0.70227 0.968 T 0.02365 -1.1170 10 0.19590 T 0.45 -3.377 14.4866 0.67622 0.0:0.0:1.0:0.0 . 693 Q9NTZ6 RBM12_HUMAN S 693;693;693;492 ENSP00000363228:P693S;ENSP00000352668:P693S;ENSP00000363217:P693S ENSP00000339879:P492S P - 1 0 RBM12 33704582 0.002000 0.14202 0.997000 0.53966 0.903000 0.53119 -0.160000 0.10041 2.528000 0.85240 0.563000 0.77884 CCC TCGA-RB-A7B8-01A-12D-A33T-08 RBM12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000078894.1 0 0 0 5 387 0 55 0 1.605901e-01 1 45 0 55 2 0 0 0 0 0 2 1 9.375022e-01 5 386 0 55 2 0 0 0 0 55 2 -2.184585 0 1 0 0 1 1 2 3 1.954264 0 0.270000 2.180000 0.270984 0.100000 3.000000e-02 0.220000 0.100000 0.112186 0.100000 0 0.060000 0.160000 EPB41L1 2036 broad.mit.edu 37 20 34773105 34773105 + Silent SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr20:34773105G>A ENST00000338074.2 + 7 794 c.633G>A c.(631-633)acG>acA p.T211T EPB41L1_ENST00000441639.1_Silent_p.T149T|EPB41L1_ENST00000373950.2_Silent_p.T114T|EPB41L1_ENST00000373946.3_Silent_p.T180T|EPB41L1_ENST00000373941.1_Silent_p.T211T|EPB41L1_ENST00000202028.5_Silent_p.T149T NM_001258329.1|NM_012156.2 NP_001245258.1|NP_036288.2 Q9H4G0 E41L1_HUMAN erythrocyte membrane protein band 4.1-like 1 37 Breast(12;0.0239) CCTTTGTCACGCATGCCCTAC 0.612000 0 SO:0001819 synonymous_variant ENST00000338074.2 0 1 hg19 CCDS13271.1 TCGA-RB-A7B8-01A-12D-A33T-08 EPB41L1-008 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000078978.3 0 0 0 5 423 0 76 0 2.654994e-01 0 72 0 76 2 0 0 0 0 0 2 1 9.355442e-01 5 417 0 75 2 0 0 0 0 76 2 -2.400102 0 1 121412 2 38 1 1 2 3 1.954264 0 0.270000 2.180000 0.270984 0.090000 3.000000e-02 0.200000 0.080000 0.102854 0.090000 0 0.050000 0.140000 GNAS 2778 broad.mit.edu 37 20 57430245 57430245 + Missense_Mutation SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 C T C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr20:57430245C>T ENST00000371100.4 + 1 2477 c.1925C>T c.(1924-1926)gCg>gTg p.A642V GNAS_ENST00000371098.2_Intron|GNAS_ENST00000371099.2_Missense_Mutation_p.A642V|GNAS_ENST00000313949.7_Intron|GNAS_ENST00000306120.3_Missense_Mutation_p.R579W|GNAS_ENST00000371075.3_Intron|GNAS_ENST00000371102.4_Missense_Mutation_p.A642V|GNAS_ENST00000464624.2_3'UTR NM_001077490.1|NM_080425.2 NP_001070958.1|NP_536350.2 P63092 GNAS2_HUMAN GNAS complex locus 441 all_lung(29;0.0104) BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109) GTACCCCTGGCGGAGAAGCGC 0.592000 Mis pituitary adenoma McCune-Albright syndrome; pseudohypoparathyroidism, type IA TSP Lung(22;0.16) Colon(117;935 1597 6045 8307 46442) Dom yes 20 20q13.2 2778 guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1 yes E 0 SO:0001583 missense ENST00000371100.4 1 0 hg19 CCDS46622.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 3.632|3.632 -0.075297|-0.075297 0.07184|0.07184 .|. .|. ENSG00000087460|ENSG00000087460 ENST00000371099;ENST00000371100;ENST00000371102;ENST00000349036|ENST00000306120;ENST00000423897 D;D;D|. 0.89810|. -2.41;-2.41;-2.57|. 3.84|3.84 -3.82|-3.82 0.04281|0.04281 .|. 11.375600|. 0.00166|. N|. 0.000002|. T|T 0.16981|0.16981 0.0408|0.0408 N|N 0.08118|0.08118 0|0 0.24069|0.24069 N|N 0.995984|0.995984 B|. 0.28178|. 0.202|. B|. 0.17433|. 0.018|. T|T 0.28332|0.28332 -1.0047|-1.0047 10|6 0.44086|0.87932 T|D 0.13|0 .|. 4.5295|4.5295 0.11997|0.11997 0.5251:0.2857:0.0:0.1892|0.5251:0.2857:0.0:0.1892 .|. 642|. Q5JWF2|. GNAS1_HUMAN|. V|W 642;642;642;15|579;5 ENSP00000360141:A642V;ENSP00000360143:A642V;ENSP00000265621:A15V|. ENSP00000265621:A15V|ENSP00000302237:R579W A|R +|+ 2|1 0|2 GNAS|GNAS 56863640|56863640 0.002000|0.002000 0.14202|0.14202 0.204000|0.204000 0.23530|0.23530 0.101000|0.101000 0.19017|0.19017 -0.367000|-0.367000 0.07553|0.07553 -0.810000|-0.810000 0.04375|0.04375 -0.362000|-0.362000 0.07510|0.07510 GCG|CGG TCGA-RB-A7B8-01A-12D-A33T-08 GNAS-001 PUTATIVE basic|CCDS protein_coding protein_coding OTTHUMT00000080417.3 1 0 0 15 60 0 14 0 5.751016e-01 0 9 0 14 2 1 1 86 339 1 364 6 1 9.999135e-01 15 58 0 14 2 0 0 0 0 14 2 -20.000000 1 1 0 0 1 1 2 3 1.954264 0 0.270000 2.180000 0.270984 0.990000 8.800000e-01 1.000000 1.000000 0.993482 0.990000 1 0.990000 1.000000 TPTE 7179 broad.mit.edu 37 21 10970018 10970018 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr21:10970018G>A ENST00000361285.4 - 6 439 c.110C>T c.(109-111)gCg>gTg p.A37V TPTE_ENST00000298232.7_Missense_Mutation_p.A37V|TPTE_ENST00000342420.5_Missense_Mutation_p.A37V|TPTE_ENST00000415664.2_5'UTR NM_199261.2 NP_954870 P56180 TPTE_HUMAN transmembrane phosphatase with tensin homology 130 Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723) CCTTTCTTTCGCAGGTGCCTC 0.413000 0 SO:0001583 missense ENST00000361285.4 0 1 hg19 CCDS13560.2 . . . . . . . . . . G 3.609 -0.080010 0.07141 0.0 1.16E-4 ENSG00000166157 ENST00000298232;ENST00000361285;ENST00000342420 D;D;D 0.95137 -3.43;-3.62;-3.51 0.725 -1.45 0.08828 . 0.367802 0.19873 U 0.104151 T 0.82135 0.4971 N 0.14661 0.345 0.09310 N 1 B;B;B 0.18610 0.009;0.001;0.029 B;B;B 0.10450 0.003;0.0;0.005 T 0.70342 -0.4898 10 0.02654 T 1 . 4.7832 0.13213 0.0:0.0:0.5421:0.4579 . 37;37;37 P56180-3;P56180-2;P56180 .;.;TPTE_HUMAN V 37 ENSP00000298232:A37V;ENSP00000355208:A37V;ENSP00000344441:A37V ENSP00000298232:A37V A - 2 0 TPTE 9991889 0.000000 0.05858 0.000000 0.03702 0.004000 0.04260 -1.742000 0.01835 -1.132000 0.02907 0.194000 0.17425 GCG TCGA-RB-A7B8-01A-12D-A33T-08 TPTE-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000157413.1 0 0 0 13 706 0 113 0 0 0 0 113 2 0 0 0 0 0 2 1 9.995118e-01 13 701 0 113 2 0 0 0 0 113 2 -2.612478 1 1 121412 11 42 1 0 0 0 1.940250 0 0.270000 2.180000 0.266037 0.130000 7.000000e-02 0.220000 0.140000 0.142510 0.130000 0 0.090000 0.180000 ERG 2078 broad.mit.edu 37 21 39755612 39755612 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr21:39755612G>A ENST00000417133.2 - 12 1359 c.1174C>T c.(1174-1176)Cgc>Tgc p.R392C ERG_ENST00000442448.1_Missense_Mutation_p.R368C|ERG_ENST00000398919.2_Missense_Mutation_p.R392C|ERG_ENST00000398905.1_Missense_Mutation_p.R361C|ERG_ENST00000453032.2_Missense_Mutation_p.R293C|ERG_ENST00000398911.1_Missense_Mutation_p.R368C|ERG_ENST00000398897.1_Missense_Mutation_p.R269C|ERG_ENST00000288319.7_Missense_Mutation_p.R385C|ERG_ENST00000398910.1_Missense_Mutation_p.R369C|ERG_ENST00000398907.1_Missense_Mutation_p.R362C NM_001136154.1|NM_001243432.1 NP_001129626.1|NP_001230361.1 Q12809 KCNH2_HUMAN v-ets avian erythroblastosis virus E26 oncogene homolog EWSR1/ERG(178)|NDRG1/ERG(5)|TMPRSS2/ERG(3582)|FUS/ERG(167)|SLC45A3/ERG(50) 4 Prostate(19;3.6e-06) Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661) TAGGCGTAGCGCTTCCCATGG 0.572000 T EWSR1, TMPRSS2, ELF4, FUS, HERPUD1, NDRG1 Ewing sarcoma, prostate, AML Esophageal Squamous(130;336 1700 3010 3083 40589) Dom yes 21 21q22.3 2078 v-ets erythroblastosis virus E26 oncogene like (avian) M, E, L 0 SO:0001583 missense ENST00000417133.2 1 1 hg19 CCDS46648.1 . . . . . . . . . . G 26.3 4.728867 0.89390 . . ENSG00000157554 ENST00000398905;ENST00000398907;ENST00000288319;ENST00000398897;ENST00000398911;ENST00000417133;ENST00000398910;ENST00000442448;ENST00000453032;ENST00000398919 T;T;T;T;T;T;T;T;T;T 0.31247 1.5;1.5;1.5;1.5;1.5;1.5;1.5;1.5;1.5;1.5 5.2 5.2 0.72013 Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (4); 0.000000 0.85682 D 0.000000 T 0.63319 0.2501 M 0.87758 2.905 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;0.999 D;D;D;D 0.97110 0.992;1.0;1.0;0.957 T 0.70905 -0.4745 10 0.87932 D 0 . 18.7596 0.91845 0.0:0.0:1.0:0.0 . 392;361;368;385 P11308;B5MDW0;P11308-1;P11308-4 ERG_HUMAN;.;.;. C 361;362;385;269;368;392;369;368;293;392 ENSP00000381877:R361C;ENSP00000381879:R362C;ENSP00000288319:R385C;ENSP00000381871:R269C;ENSP00000381882:R368C;ENSP00000414150:R392C;ENSP00000381881:R369C;ENSP00000394694:R368C;ENSP00000396268:R293C;ENSP00000381891:R392C ENSP00000288319:R385C R - 1 0 ERG 38677482 1.000000 0.71417 1.000000 0.80357 0.980000 0.70556 9.869000 0.99810 2.404000 0.81709 0.655000 0.94253 CGC TCGA-RB-A7B8-01A-12D-A33T-08 ERG-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000207532.2 0 0 0 17 609 0 82 0 6.128642e-02 0 14 0 82 2 0 0 0 0 0 2 1 9.999603e-01 17 599 0 82 2 0 0 0 0 82 2 -3.004264 1 1 121412 1 33 1 0 0 0 1.940250 0 0.270000 2.180000 0.266037 0.200000 1.100000e-01 0.310000 0.200000 0.210239 0.200000 0 0.150000 0.260000 PCNT 5116 broad.mit.edu 37 21 47786815 47786815 + Missense_Mutation SNP C C A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr21:47786815C>A ENST00000359568.5 + 15 3033 c.2926C>A c.(2926-2928)Ctc>Atc p.L976I PCNT_ENST00000480896.1_3'UTR NM_006031.5 NP_006022.3 O95613 PCNT_HUMAN pericentrin 104 Breast(49;0.112) ATCCTGTTACCTCTCTGAATT 0.537000 0 SO:0001583 missense ENST00000359568.5 0 1 hg19 CCDS33592.1 . . . . . . . . . . C 13.58 2.280740 0.40294 . . ENSG00000160299 ENST00000359568 T 0.24908 1.83 5.36 3.45 0.39498 . 0.744958 0.10484 N 0.669220 T 0.40322 0.1112 M 0.64997 1.995 0.23700 N 0.99707 D;P 0.55800 0.973;0.954 P;P 0.53593 0.73;0.541 T 0.20840 -1.0263 10 0.36615 T 0.2 . 13.0171 0.58764 0.0:0.677:0.323:0.0 . 858;976 O95613-2;O95613 .;PCNT_HUMAN I 976 ENSP00000352572:L976I ENSP00000352572:L976I L + 1 0 PCNT 46611243 0.997000 0.39634 0.748000 0.31131 0.011000 0.07611 0.383000 0.20651 0.567000 0.29293 0.561000 0.74099 CTC TCGA-RB-A7B8-01A-12D-A33T-08 PCNT-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207336.1 0 0 0 5 647 1 123 0 5.787602e-04 0 4 1 123 2 0 0 0 0 0 2 0 4.724497e-03 5 643 1 122 18 0 0 0 1 123 2 -2.403309 0 1 0 0 1 0 0 0 1.940250 0 0.270000 2.180000 0.266037 0.050000 1.000000e-02 0.130000 0.060000 0.067292 0.050000 0 0.030000 0.090000 ZNRF3 84133 broad.mit.edu 37 22 29439358 29439358 + Silent SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr22:29439358G>A ENST00000544604.2 + 4 748 c.573G>A c.(571-573)ctG>ctA p.L191L ZNRF3_ENST00000406323.3_Silent_p.L91L|ZNRF3_ENST00000402174.1_Silent_p.L91L|ZNRF3_ENST00000332811.4_Silent_p.L91L NM_001206998.1 NP_001193927.1 Q9ULT6 ZNRF3_HUMAN zinc and ring finger 3 28 CCATTAAGCTGATGAACATCG 0.562000 0 SO:0001819 synonymous_variant ENST00000544604.2 0 1 hg19 CCDS56225.1 TCGA-RB-A7B8-01A-12D-A33T-08 ZNRF3-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000320943.2 0 0 0 6 431 0 55 0 4.118005e-03 0 6 0 55 2 0 0 0 0 0 2 1 9.629015e-01 6 422 0 54 2 0 0 0 0 55 2 -3.325609 1 1 0 0 1 1 3 4 2.261605 1 0.270000 2.180000 0.368840 0.140000 4.000000e-02 1.000000 0.120000 0.340006 0.140000 0 0.080000 1.000000 SLC5A1 6523 broad.mit.edu 37 22 32481008 32481008 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr22:32481008G>A ENST00000266088.4 + 9 1257 c.1007G>A c.(1006-1008)cGc>cAc p.R336H SLC5A1_ENST00000543737.1_Missense_Mutation_p.R209H NM_000343.3 NP_000334.1 P13866 SC5A1_HUMAN solute carrier family 5 (sodium/glucose cotransporter), member 1 p.R336H(1) 37 Canagliflozin(DB08907) ATGATCAGCCGCATTCTGTAC 0.483000 1 Substitution - Missense(1) SO:0001583 missense ENST00000266088.4 0 1 hg19 CCDS13902.1 . . . . . . . . . . G 19.87 3.907312 0.72868 . . ENSG00000100170 ENST00000266088;ENST00000543737 D;D 0.89123 -2.47;-2.47 4.92 2.8 0.32819 . 0.051673 0.85682 N 0.000000 D 0.95370 0.8497 H 0.95574 3.69 0.58432 D 0.999999 D 0.89917 1.0 D 0.91635 0.999 D 0.94570 0.7770 10 0.87932 D 0 . 9.6601 0.39950 0.078:0.142:0.78:0.0 . 336 P13866 SC5A1_HUMAN H 336;209 ENSP00000266088:R336H;ENSP00000444898:R209H ENSP00000266088:R336H R + 2 0 SLC5A1 30811008 1.000000 0.71417 0.996000 0.52242 0.796000 0.44982 9.582000 0.98214 0.589000 0.29677 -0.229000 0.12294 CGC TCGA-RB-A7B8-01A-12D-A33T-08 SLC5A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000075656.3 0 0 0 7 852 1 103 0 3.607382e-03 0 59 1 103 4 0 0 0 0 0 2 0 8.460456e-04 7 842 1 103 25 0 0 0 1 103 2 -1.732319 0 1 121412 1 37 1 1 3 4 2.261605 1 0.270000 2.180000 0.368840 0.080000 2.000000e-02 1.000000 0.070000 0.296820 0.080000 0 0.050000 1.000000 CACNG2 10369 broad.mit.edu 37 22 36960745 36960745 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr22:36960745G>A ENST00000300105.6 - 4 1606 c.625C>T c.(625-627)Cgg>Tgg p.R209W RP5-1119A7.17_ENST00000562756.1_RNA NM_006078.3 NP_006069.1 Q9Y698 CCG2_HUMAN calcium channel, voltage-dependent, gamma subunit 2 18 GCCGTGGCCCGCAGCTGTTTG 0.667000 0 SO:0001583 missense ENST00000300105.6 1 1 hg19 CCDS13931.1 . . . . . . . . . . G 21.2 4.119367 0.77323 . . ENSG00000166862 ENST00000300105 T 0.40756 1.02 5.62 5.62 0.85841 . 0.000000 0.85682 D 0.000000 T 0.64305 0.2586 M 0.75615 2.305 0.80722 D 1 D 0.89917 1.0 D 0.77557 0.99 T 0.66590 -0.5885 10 0.66056 D 0.02 -7.8981 14.4754 0.67541 0.0:0.0:0.8529:0.1471 . 209 Q9Y698 CCG2_HUMAN W 209 ENSP00000300105:R209W ENSP00000300105:R209W R - 1 2 CACNG2 35290691 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.456000 0.80751 2.656000 0.90262 0.655000 0.94253 CGG TCGA-RB-A7B8-01A-12D-A33T-08 CACNG2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000075500.2 1 0 0 68 1382 0 209 0 0 0 0 209 2 0 0 0 0 0 2 1 1 69 1364 0 205 2 0 0 0 0 209 2 -5.857161 1 1 0 0 1 1 3 4 2.261605 1 0.270000 2.180000 0.368840 0.410000 3.100000e-01 1.000000 0.410000 0.546701 0.410000 0 0.360000 1.000000 NPAS2 4862 broad.mit.edu 37 2 101592029 101592029 + Splice_Site SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr2:101592029G>A ENST00000335681.5 + 14 1677 c.1392G>A c.(1390-1392)ccG>ccA p.P464P AC016738.3_ENST00000433012.1_RNA|NPAS2_ENST00000542504.1_Splice_Site_p.P529P|AC016738.3_ENST00000439150.1_RNA|AC016738.3_ENST00000446644.1_RNA NM_002518.3 NP_002509.2 Q99743 NPAS2_HUMAN neuronal PAS domain protein 2 29 CCACCATGCCGGTAAGTGTGT 0.622000 0 SO:0001630 splice_region_variant ENST00000335681.5 0 1 hg19 CCDS2048.1 TCGA-RB-A7B8-01A-12D-A33T-08 NPAS2-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000253168.3 0 0 0 6 503 0 84 0 2.829292e-01 0 77 0 84 2 0 0 0 0 0 2 1 9.645197e-01 6 500 0 83 2 0 0 0 0 84 2 -2.713821 1 1 121404 7 41 1 0 0 0 1.939708 0 0.270000 2.180000 0.266037 0.090000 3.000000e-02 0.180000 0.080000 0.100382 0.090000 0 0.050000 0.140000 CKAP2L 150468 broad.mit.edu 37 2 113514269 113514269 + Missense_Mutation SNP A A C TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr2:113514269A>C ENST00000302450.6 - 4 757 c.679T>G c.(679-681)Ttg>Gtg p.L227V CKAP2L_ENST00000541405.1_Missense_Mutation_p.L62V|CKAP2L_ENST00000481732.1_5'Flank NM_152515.3 NP_689728.3 Q8IYA6 CKP2L_HUMAN cytoskeleton associated protein 2-like 28 CTTTTGCCCAAGGCTTGTTTA 0.373000 0 SO:0001583 missense ENST00000302450.6 1 1 hg19 CCDS2100.1 . . . . . . . . . . A 10.37 1.330842 0.24167 . . ENSG00000169607 ENST00000541405;ENST00000302450 T;T 0.12879 2.64;3.29 5.0 0.984 0.19773 . 0.914293 0.09252 N 0.827794 T 0.14874 0.0359 M 0.64997 1.995 0.25552 N 0.987079 B 0.23540 0.087 B 0.26202 0.067 T 0.32929 -0.9888 10 0.42905 T 0.14 0.472 5.4096 0.16341 0.5372:0.1583:0.0:0.3044 . 227 Q8IYA6 CKP2L_HUMAN V 62;227 ENSP00000438763:L62V;ENSP00000305204:L227V ENSP00000305204:L227V L - 1 2 CKAP2L 113230740 0.000000 0.05858 0.169000 0.22859 0.861000 0.49209 -0.261000 0.08694 0.062000 0.16340 0.477000 0.44152 TTG TCGA-RB-A7B8-01A-12D-A33T-08 CKAP2L-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254082.2 1 0 0 25 414 0 74 0 0 1 0 0 74 2 0 0 0 0 0 2 1 9.999998e-01 25 413 0 74 2 0 0 0 0 74 2 -6.149242 1 1 0 0 1 0 0 0 1.939708 0 0.270000 2.180000 0.266037 0.420000 2.700000e-01 0.590000 0.420000 0.431636 0.420000 0 0.340000 0.510000 LCT 3938 broad.mit.edu 37 2 136575286 136575286 + Silent SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr2:136575286G>A ENST00000264162.2 - 6 1342 c.1332C>T c.(1330-1332)tgC>tgT p.C444C AC011893.3_ENST00000437007.1_RNA NM_002299.2 NP_002290.2 P09848 LPH_HUMAN lactase 124 Vitamin C(DB00126) CCCGGAGGCCGCAAAGCAGGG 0.647000 0 SO:0001819 synonymous_variant ENST00000264162.2 0 1 hg19 CCDS2178.1 TCGA-RB-A7B8-01A-12D-A33T-08 LCT-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254657.1 0 0 0 8 491 0 81 0 0 0 0 81 2 0 0 0 0 0 2 1 9.891249e-01 7 488 0 80 2 0 0 0 0 81 2 -2.342122 0 1 121412 7 40 1 0 0 0 1.939708 0 0.270000 2.180000 0.266037 0.120000 5.000000e-02 0.220000 0.120000 0.131620 0.120000 0 0.080000 0.170000 SCN1A 6323 broad.mit.edu 37 2 166901827 166901827 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr2:166901827G>A ENST00000303395.4 - 10 1387 c.1388C>T c.(1387-1389)aCg>aTg p.T463M AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000375405.3_Missense_Mutation_p.T463M|SCN1A_ENST00000409050.1_Missense_Mutation_p.T463M|SCN1A_ENST00000423058.2_Missense_Mutation_p.T463M|AC010127.3_ENST00000599041.1_RNA|AC010127.3_ENST00000595268.1_RNA P35498 SCN1A_HUMAN sodium channel, voltage-gated, type I, alpha subunit 200 Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909) GGCAGTTGCCGTTGCTGCCTG 0.443000 0 SO:0001583 missense ENST00000303395.4 0 1 hg19 CCDS54413.1 . . . . . . . . . . G 10.99 1.507602 0.27036 . . ENSG00000144285 ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050 T;T;T;T 0.26223 1.75;1.75;1.75;1.75 5.37 4.49 0.54785 . 0.572471 0.15627 N 0.252583 T 0.13286 0.0322 N 0.04203 -0.255 0.24301 N 0.99512 B;B;B 0.30021 0.265;0.173;0.173 B;B;B 0.25759 0.063;0.029;0.029 T 0.16305 -1.0407 10 0.37606 T 0.19 . 14.4281 0.67230 0.0709:0.0:0.9291:0.0 . 463;463;463 P35498-2;E9PG49;P35498 .;.;SCN1A_HUMAN M 463 ENSP00000407030:T463M;ENSP00000303540:T463M;ENSP00000364554:T463M;ENSP00000386312:T463M ENSP00000303540:T463M T - 2 0 SCN1A 166610073 0.963000 0.33076 0.098000 0.21074 0.070000 0.16714 3.561000 0.53770 1.411000 0.46957 0.655000 0.94253 ACG TCGA-RB-A7B8-01A-12D-A33T-08 SCN1A-001 KNOWN non_canonical_U12|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000102661.1 0 0 0 6 498 0 90 0 0 0 0 90 2 0 0 0 0 0 2 1 9.640746e-01 6 494 0 90 2 0 0 0 0 90 2 -2.716045 1 1 121408 4 37 1 0 0 0 1.939708 0 0.270000 2.180000 0.266037 0.090000 3.000000e-02 0.180000 0.090000 0.101368 0.090000 0 0.050000 0.140000 TTN 7273 broad.mit.edu 37 2 179418445 179418445 + Missense_Mutation SNP C C A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr2:179418445C>A ENST00000591111.1 - 284 84588 c.84364G>T c.(84364-84366)Ggc>Tgc p.G28122C TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.G27195C|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.G20698C|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.G29763C|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.G20890C|TTN_ENST00000359218.5_Missense_Mutation_p.G20823C|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592600.1_RNA Q8WZ42 TITIN_HUMAN titin 1448 OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134) ACAGCACTGCCCCCATCATAG 0.483000 0 SO:0001583 missense ENST00000591111.1 0 1 hg19 . . . . . . . . . . C 20.1 3.939712 0.73557 . . ENSG00000155657 ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127 T;T;T;T 0.61510 0.1;0.1;0.1;0.1 5.6 5.6 0.85130 Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1); . . . . D 0.84297 0.5441 H 0.95079 3.62 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;1.0;1.0;1.0 D 0.88293 0.2944 9 0.87932 D 0 . 19.9823 0.97331 0.0:1.0:0.0:0.0 . 20698;20823;20890;28122 D3DPF9;E7EQE6;E7ET18;Q8WZ42 .;.;.;TITIN_HUMAN C 27195;20698;20890;20823;20695 ENSP00000343764:G27195C;ENSP00000434586:G20698C;ENSP00000340554:G20890C;ENSP00000352154:G20823C ENSP00000340554:G20890C G - 1 0 TTN 179126691 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 7.818000 0.86416 2.788000 0.95919 0.650000 0.86243 GGC TCGA-RB-A7B8-01A-12D-A33T-08 TTN-019 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460310.1 0 0 0 6 306 0 46 0 0 0 1 0 46 2 0 0 0 0 0 2 1 9.653717e-01 6 306 0 45 2 0 0 0 0 46 2 -6.508263 1 1 0 0 1 0 0 0 1.939708 0 0.270000 2.180000 0.266037 0.140000 5.000000e-02 0.290000 0.140000 0.162795 0.140000 0 0.090000 0.220000 ITGA4 3676 broad.mit.edu 37 2 182360534 182360534 + Silent SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr2:182360534C>T ENST00000397033.2 + 14 1840 c.1410C>T c.(1408-1410)gaC>gaT p.D470D NM_000885.4 NP_000876.3 P13612 ITA4_HUMAN integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor) 58 OV - Ovarian serous cystadenocarcinoma(117;0.0593) Natalizumab(DB00108)|Tinzaparin(DB06822) TAATTGTTGACGCTTCTTTAA 0.358000 0 SO:0001819 synonymous_variant ENST00000397033.2 1 1 hg19 CCDS42788.1 TCGA-RB-A7B8-01A-12D-A33T-08 ITGA4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000334427.1 1 0 1 55 339 0 63 0 1.501614e-01 0 5 0 63 2 0 0 0 0 0 2 1 1 54 338 0 63 2 0 0 0 0 63 2 -19.999970 1 1 120818 4 37 1 0 0 0 1.939708 0 0.270000 2.180000 0.266037 0.990000 7.900000e-01 1.000000 1.000000 0.964861 0.990000 1 0.900000 1.000000 COL6A3 1293 broad.mit.edu 37 2 238253001 238253001 + Missense_Mutation SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr2:238253001C>T ENST00000295550.4 - 36 8112 c.7660G>A c.(7660-7662)Gct>Act p.A2554T COL6A3_ENST00000472056.1_Missense_Mutation_p.A1947T|COL6A3_ENST00000409809.1_Missense_Mutation_p.A2348T|COL6A3_ENST00000353578.4_Missense_Mutation_p.A2348T|COL6A3_ENST00000346358.4_Missense_Mutation_p.A2354T|COL6A3_ENST00000347401.3_Missense_Mutation_p.A2353T NM_004369.3 NP_004360.2 P12111 CO6A3_HUMAN collagen, type VI, alpha 3 217 Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203) ACCTGCAAAGCGTTGATGAGC 0.557000 0 SO:0001583 missense ENST00000295550.4 0 1 hg19 CCDS33412.1 . . . . . . . . . . C 15.60 2.881687 0.51908 . . ENSG00000163359 ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358 D;D;D;D;D;D 0.82984 -1.67;-1.67;-1.67;-1.67;-1.67;-1.67 5.08 5.08 0.68730 von Willebrand factor, type A (3); 0.000000 0.52532 D 0.000069 D 0.90335 0.6976 M 0.71581 2.175 0.80722 D 1 D;D;D;D 0.89917 1.0;1.0;1.0;1.0 D;D;D;D 0.91635 0.999;0.999;0.998;0.999 D 0.88468 0.3060 10 0.30854 T 0.27 . 18.8647 0.92287 0.0:1.0:0.0:0.0 . 1947;1947;2348;2554 E9PFQ6;B7ZMJ7;P12111-2;P12111 .;.;.;CO6A3_HUMAN T 2554;2353;2348;1947;2348;2354 ENSP00000295550:A2554T;ENSP00000315609:A2353T;ENSP00000315873:A2348T;ENSP00000418285:A1947T;ENSP00000386844:A2348T;ENSP00000295546:A2354T ENSP00000295550:A2554T A - 1 0 COL6A3 237917740 1.000000 0.71417 0.210000 0.23637 0.878000 0.50629 7.308000 0.78929 2.507000 0.84556 0.655000 0.94253 GCT TCGA-RB-A7B8-01A-12D-A33T-08 COL6A3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000315790.2 0 0 0 9 1249 0 213 0 9.874261e-01 0 1052 0 213 2 0 0 0 0 0 2 1 9.940544e-01 9 1242 0 210 2 0 0 0 0 213 2 -2.597499 1 1 0 0 1 0 0 0 1.939708 0 0.270000 2.180000 0.266037 0.050000 2.000000e-02 0.100000 0.060000 0.058377 0.050000 0 0.030000 0.080000 D2HGDH 728294 broad.mit.edu 37 2 242695366 242695366 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr2:242695366G>A ENST00000321264.4 + 9 1452 c.1243G>A c.(1243-1245)Gtg>Atg p.V415M D2HGDH_ENST00000486953.1_3'UTR|AC114730.7_ENST00000417267.1_RNA|D2HGDH_ENST00000403782.1_Missense_Mutation_p.V281M NM_152783.3 NP_689996.4 Q8N465 D2HDH_HUMAN D-2-hydroxyglutarate dehydrogenase 16 all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244) CTACGACATCGTGACTGACCT 0.687000 0 SO:0001583 missense ENST00000321264.4 1 1 hg19 CCDS33426.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 17.80|17.80 3.477180|3.477180 0.63849|0.63849 2.27E-4|2.27E-4 0.0|0.0 ENSG00000180902|ENSG00000180902 ENST00000432449|ENST00000321264;ENST00000403782;ENST00000542211 .|D;D .|0.85773 .|-2.03;-2.03 5.31|5.31 5.31|5.31 0.75309|0.75309 .|FAD-linked oxidase-like, C-terminal (1);FAD-linked oxidase, C-terminal (1); .|0.071537 .|0.56097 .|D .|0.000031 D|D 0.93585|0.93585 0.7952|0.7952 M|M 0.87381|0.87381 2.88|2.88 0.80722|0.80722 D|D 1|1 .|D .|0.89917 .|1.0 .|D .|0.85130 .|0.997 D|D 0.94453|0.94453 0.7669|0.7669 6|10 0.49607|0.87932 T|D 0.09|0 -3.3567|-3.3567 18.9757|18.9757 0.92735|0.92735 0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0 .|. .|415 .|Q8N465 .|D2HDH_HUMAN H|M 168|415;281;35 .|ENSP00000315351:V415M;ENSP00000384723:V281M ENSP00000383580:R319H|ENSP00000315351:V415M R|V +|+ 2|1 0|0 D2HGDH|D2HGDH 242344039|242344039 1.000000|1.000000 0.71417|0.71417 0.088000|0.088000 0.20740|0.20740 0.088000|0.088000 0.18126|0.18126 8.597000|8.597000 0.90847|0.90847 2.485000|2.485000 0.83878|0.83878 0.467000|0.467000 0.42956|0.42956 CGT|GTG TCGA-RB-A7B8-01A-12D-A33T-08 D2HGDH-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000322794.2 1 0 1 82 409 0 106 1 9.992473e-01 17 38 0 106 2 0 0 0 0 0 2 1 1 81 404 0 105 2 0 0 0 0 106 2 -20.000000 1 0 121390 3 41 1 0 0 0 1.939708 0 0.270000 2.180000 0.266037 0.990000 9.900000e-01 1.000000 1.000000 0.999007 0.990000 1 0.990000 1.000000 CNNM4 26504 broad.mit.edu 37 2 97463316 97463316 + Missense_Mutation SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr2:97463316C>T ENST00000377075.2 + 3 1711 c.1613C>T c.(1612-1614)gCg>gTg p.A538V CNNM4_ENST00000496186.1_3'UTR|CNNM4_ENST00000540067.1_Missense_Mutation_p.A25V|MIR3127_ENST00000583925.1_RNA NM_020184.3 NP_064569.3 Q6P4Q7 CNNM4_HUMAN cyclin and CBS domain divalent metal cation transport mediator 4 20 TTCAAGGATGCGGACAATGAG 0.562000 0 SO:0001583 missense ENST00000377075.2 0 1 hg19 CCDS2024.2 . . . . . . . . . . C 12.31 1.899383 0.33535 . . ENSG00000158158 ENST00000377075;ENST00000540067 T 0.72505 -0.66 5.25 5.25 0.73442 . 0.737333 0.12913 N 0.428840 T 0.61350 0.2340 L 0.40543 1.245 0.18873 N 0.999981 P;B 0.47841 0.901;0.065 B;B 0.37601 0.254;0.01 T 0.59408 -0.7460 10 0.51188 T 0.08 -2.8163 13.5984 0.62004 0.156:0.844:0.0:0.0 . 25;538 B7Z1U0;Q6P4Q7 .;CNNM4_HUMAN V 538;25 ENSP00000366275:A538V ENSP00000366275:A538V A + 2 0 CNNM4 96827043 0.002000 0.14202 0.448000 0.26945 0.001000 0.01503 1.755000 0.38379 2.608000 0.88229 0.655000 0.94253 GCG TCGA-RB-A7B8-01A-12D-A33T-08 CNNM4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000252954.1 0 0 0 5 441 0 58 0 6.920286e-03 0 9 0 58 2 0 0 0 0 0 2 1 9.352416e-01 5 434 0 58 2 0 0 0 0 58 2 -2.499394 0 1 121412 2 39 1 0 0 0 1.939708 0 0.270000 2.180000 0.266037 0.080000 2.000000e-02 0.180000 0.080000 0.098064 0.080000 0 0.050000 0.140000 VWA3B 200403 broad.mit.edu 37 2 98736133 98736133 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr2:98736133G>A ENST00000477737.1 + 4 653 c.449G>A c.(448-450)gGc>gAc p.G150D VWA3B_ENST00000451075.2_Intron|VWA3B_ENST00000435344.1_Missense_Mutation_p.G150D NM_144992.4 NP_659429.4 Q502W6 VWA3B_HUMAN von Willebrand factor A domain containing 3B 70 GATTTTGGCGGCATTCTGGAG 0.522000 0 SO:0001583 missense ENST00000477737.1 0 1 hg19 CCDS42718.1 . . . . . . . . . . G 1.464 -0.561569 0.03939 . . ENSG00000168658 ENST00000435344;ENST00000477737 T;T 0.35973 1.28;1.28 6.02 -3.25 0.05079 . 1.332560 0.04551 N 0.389819 T 0.19967 0.0480 N 0.17474 0.49 0.09310 N 1 B;B 0.13145 0.007;0.001 B;B 0.13407 0.009;0.002 T 0.17501 -1.0367 10 0.32370 T 0.25 . 4.4567 0.11647 0.553:0.1139:0.2439:0.0893 . 150;150 Q502W6;Q502W6-8 VWA3B_HUMAN;. D 150 ENSP00000401959:G150D;ENSP00000417955:G150D ENSP00000411168:G150D G + 2 0 VWA3B 98102565 0.000000 0.05858 0.000000 0.03702 0.107000 0.19398 0.140000 0.16056 -0.462000 0.06984 -0.150000 0.13652 GGC TCGA-RB-A7B8-01A-12D-A33T-08 VWA3B-020 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000353469.2 0 0 0 7 1058 0 175 0 0 0 1 0 175 2 0 0 0 0 0 2 1 9.799996e-01 7 1049 0 175 2 0 0 0 0 175 2 -1.905977 0 1 0 0 1 0 0 0 1.939708 0 0.270000 2.180000 0.266037 0.040000 1.000000e-02 0.100000 0.050000 0.055162 0.040000 0 0.020000 0.070000 GTPBP8 29083 broad.mit.edu 37 3 112710121 112710121 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr3:112710121G>A ENST00000383678.2 + 1 357 c.275G>A c.(274-276)cGc>cAc p.R92H GTPBP8_ENST00000467752.1_5'Flank|RP11-484K9.4_ENST00000609673.1_RNA|GTPBP8_ENST00000383677.3_Missense_Mutation_p.R92H|GTPBP8_ENST00000473129.1_5'Flank NM_014170.2 NP_054889.2 Q8N3Z3 GTPB8_HUMAN GTP-binding protein 8 (putative) 6 GAACGGAACCGCATCGACTAC 0.647000 0 SO:0001583 missense ENST00000383678.2 0 1 hg19 CCDS33820.1 . . . . . . . . . . G 17.87 3.494060 0.64186 0.0 1.16E-4 ENSG00000163607 ENST00000383678;ENST00000383677;ENST00000305485 T;T 0.48836 2.35;0.8 6.08 5.19 0.71726 . 0.293519 0.38897 N 0.001533 T 0.61022 0.2314 M 0.72118 2.19 0.80722 D 1 D;D 0.89917 1.0;0.993 D;P 0.67382 0.951;0.821 T 0.64093 -0.6488 10 0.56958 D 0.05 -1.0752 5.3975 0.16276 0.0749:0.1445:0.6305:0.1501 . 92;92 Q8N3Z3-2;Q8N3Z3 .;GTPB8_HUMAN H 92 ENSP00000373176:R92H;ENSP00000373175:R92H ENSP00000295864:R92H R + 2 0 GTPBP8 114192811 1.000000 0.71417 1.000000 0.80357 0.306000 0.27790 2.285000 0.43487 1.564000 0.49628 0.655000 0.94253 CGC TCGA-RB-A7B8-01A-12D-A33T-08 GTPBP8-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000354260.2 0 0 0 5 388 0 37 0 6.815765e-02 0 27 0 37 2 0 0 0 0 0 2 1 9.358000e-01 5 383 0 37 2 0 0 0 0 37 2 -3.128482 1 1 121376 1 34 1 1 4 5 2.528806 1 0.270000 2.180000 0.440077 0.150000 4.000000e-02 1.000000 0.130000 0.299346 0.150000 0 0.080000 1.000000 GSK3B 2932 broad.mit.edu 37 3 119595270 119595270 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr3:119595270G>A ENST00000264235.8 - 8 1881 c.899C>T c.(898-900)cCt>cTt p.P300L GSK3B_ENST00000473886.1_5'UTR|GSK3B_ENST00000316626.5_Missense_Mutation_p.P300L NM_001146156.1|NM_002093.3 NP_001139628.1|NP_002084.2 P49841 GSK3B_HUMAN glycogen synthase kinase 3 beta 18 Lithium(DB01356) CTTAGTCCAAGGATGTGCCTT 0.333000 0 SO:0001583 missense ENST00000264235.8 0 1 hg19 CCDS54628.1 . . . . . . . . . . G 17.54 3.414006 0.62511 . . ENSG00000082701 ENST00000264235;ENST00000316626;ENST00000539838 T;T 0.41400 1.0;1.0 4.62 4.62 0.57501 Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1); 0.000000 0.85682 D 0.000000 T 0.39118 0.1066 L 0.43152 1.355 0.80722 D 1 B;P 0.38129 0.416;0.619 B;B 0.36335 0.222;0.142 T 0.45789 -0.9237 10 0.72032 D 0.01 -6.4785 18.0111 0.89224 0.0:0.0:1.0:0.0 . 300;300 P49841;P49841-2 GSK3B_HUMAN;. L 300;300;17 ENSP00000264235:P300L;ENSP00000324806:P300L ENSP00000264235:P300L P - 2 0 GSK3B 121077960 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 9.142000 0.94618 2.561000 0.86390 0.650000 0.86243 CCT TCGA-RB-A7B8-01A-12D-A33T-08 GSK3B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000258240.2 0 0 0 6 424 0 52 0 4.247183e-01 0 92 0 52 2 0 0 0 0 0 2 1 9.642000e-01 6 420 0 52 2 0 0 0 0 52 2 -2.838193 1 1 0 0 1 1 4 5 2.528806 1 0.270000 2.180000 0.440077 0.160000 5.000000e-02 1.000000 0.130000 0.307444 0.160000 0 0.090000 1.000000 MYLK 4638 broad.mit.edu 37 3 123428605 123428605 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr3:123428605G>A ENST00000475616.1 - 11 1939 c.1940C>T c.(1939-1941)tCa>tTa p.S647L MYLK_ENST00000360772.3_Missense_Mutation_p.S647L|MYLK_ENST00000359169.1_Missense_Mutation_p.S647L|MYLK_ENST00000346322.5_Missense_Mutation_p.S578L|MYLK_ENST00000360304.3_Missense_Mutation_p.S647L Q15746 MYLK_HUMAN myosin light chain kinase 113 Lung NSC(201;0.0496) AGACAGACCTGACACTTGGAC 0.537000 0 SO:0001583 missense ENST00000475616.1 0 1 hg19 CCDS46896.1 . . . . . . . . . . G 28.1 4.887908 0.91814 . . ENSG00000065534 ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000475616 T;T;T;T;T 0.68765 -0.35;-0.35;-0.35;-0.35;-0.35 5.05 5.05 0.67936 Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); . . . . T 0.70675 0.3251 L 0.28649 0.875 0.80722 D 1 P;B;D;P;P 0.55172 0.944;0.355;0.97;0.858;0.955 P;B;P;P;P 0.60541 0.804;0.171;0.804;0.491;0.876 T 0.66806 -0.5830 9 0.27082 T 0.32 . 18.5896 0.91204 0.0:0.0:1.0:0.0 . 647;578;647;578;647 Q15746-6;Q15746-4;Q15746-3;Q15746-2;Q15746 .;.;.;.;MYLK_HUMAN L 647;647;647;578;647 ENSP00000354004:S647L;ENSP00000353452:S647L;ENSP00000352088:S647L;ENSP00000320622:S578L;ENSP00000418335:S647L ENSP00000320622:S578L S - 2 0 MYLK 124911295 1.000000 0.71417 1.000000 0.80357 0.965000 0.64279 5.742000 0.68646 2.622000 0.88805 0.650000 0.86243 TCA TCGA-RB-A7B8-01A-12D-A33T-08 MYLK-004 KNOWN not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000356464.1 0 0 0 19 2015 0 235 0 1.011705e-04 0 2 0 235 2 0 0 0 0 0 2 1 9.999892e-01 19 2000 0 234 2 0 0 0 0 235 2 -2.559127 1 1 0 0 1 1 4 5 2.528806 1 0.270000 2.180000 0.440077 0.090000 4.000000e-02 1.000000 0.090000 0.256705 0.090000 0 0.060000 1.000000 ZBTB38 253461 broad.mit.edu 37 3 141163339 141163339 + Silent SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr3:141163339C>T ENST00000514251.1 + 4 2388 c.2109C>T c.(2107-2109)gcC>gcT p.A703A ZBTB38_ENST00000441582.2_Silent_p.A703A|ZBTB38_ENST00000321464.5_Silent_p.A704A zinc finger and BTB domain containing 38 41 GTGAGAATGCCGCCTCTGTGA 0.498000 0 SO:0001819 synonymous_variant ENST00000514251.1 1 1 hg19 CCDS43157.1 TCGA-RB-A7B8-01A-12D-A33T-08 ZBTB38-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000359329.2 1 0 1 54 691 0 79 1 8.613664e-01 6 41 0 79 2 0 0 0 0 0 2 1 1 54 688 0 77 2 0 0 0 0 79 2 -2.665581 1 1 120978 2 37 1 1 4 5 2.528806 1 0.270000 2.180000 0.440077 0.720000 5.300000e-01 1.000000 0.690000 0.761825 0.720000 0 0.620000 1.000000 SLC7A14 57709 broad.mit.edu 37 3 170198095 170198095 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr3:170198095G>A ENST00000231706.5 - 7 2291 c.1976C>T c.(1975-1977)gCg>gTg p.A659V CLDN11_ENST00000486975.1_Intron|CLDN11_ENST00000451576.1_Intron NM_020949.2 NP_066000.2 Q8TBB6 S7A14_HUMAN solute carrier family 7, member 14 p.A659V(1) 53 all_cancers(22;2.41e-22)|all_epithelial(15;4.2e-27)|all_lung(20;1.17e-16)|Lung NSC(18;4.91e-16)|Ovarian(172;0.000902)|Breast(254;0.137) Lung(28;6.23e-13)|LUSC - Lung squamous cell carcinoma(14;1.48e-12) GCACCAGACCGCAAACCGGAT 0.498000 1 Substitution - Missense(1) SO:0001583 missense ENST00000231706.5 0 1 hg19 CCDS33892.1 . . . . . . . . . . G 14.40 2.525393 0.44969 0.0 2.33E-4 ENSG00000013293 ENST00000231706 D 0.87103 -2.21 5.81 4.94 0.65067 . 0.154542 0.56097 D 0.000025 T 0.72867 0.3514 N 0.04203 -0.255 0.47065 D 0.999306 B 0.24576 0.106 B 0.15484 0.013 T 0.68349 -0.5432 10 0.25751 T 0.34 . 14.9962 0.71433 0.0683:0.0:0.9317:0.0 . 659 Q8TBB6 S7A14_HUMAN V 659 ENSP00000231706:A659V ENSP00000231706:A659V A - 2 0 SLC7A14 171680789 1.000000 0.71417 0.906000 0.35671 0.997000 0.91878 7.611000 0.82962 1.455000 0.47813 0.655000 0.94253 GCG TCGA-RB-A7B8-01A-12D-A33T-08 SLC7A14-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000352598.2 0 0 0 9 793 0 103 0 0 0 1 0 103 2 0 0 0 0 0 2 1 9.940047e-01 8 787 0 102 2 0 0 0 0 103 2 -1.895576 0 1 120976 23 48 1 1 4 5 2.528806 1 0.270000 2.180000 0.440077 0.120000 4.000000e-02 1.000000 0.120000 0.277899 0.120000 0 0.070000 1.000000 PIK3CA 5290 broad.mit.edu 37 3 178952072 178952072 + Missense_Mutation SNP A A T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 A T A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr3:178952072A>T ENST00000263967.3 + 21 3284 c.3127A>T c.(3127-3129)Atg>Ttg p.M1043L RP11-245C23.3_ENST00000609807.1_RNA NM_006218.2 NP_006209.2 P42336 PK3CA_HUMAN phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha p.M1043V(22) 5269 all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155) OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282) Caffeine(DB00201) CATGAAACAAATGAATGATGC 0.368000 57 Mis colorectal, gastric, gliobastoma, breast HNSCC(19;0.045)|TSP Lung(28;0.18) Colon(199;1504 1750 3362 26421 31210 32040) Dom yes 3 3q26.3 5290 phosphoinositide-3-kinase, catalytic, alpha polypeptide E, O 22 Substitution - Missense(22) SO:0001583 missense ENST00000263967.3 1 1 hg19 CCDS43171.1 . . . . . . . . . . A 13.69 2.313034 0.40895 . . ENSG00000121879 ENST00000263967 T 0.79845 -1.31 6.08 6.08 0.98989 Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3); 0.000000 0.85682 D 0.000000 T 0.61464 0.2349 N 0.01761 -0.735 0.80722 D 1 B 0.06786 0.001 B 0.04013 0.001 T 0.59674 -0.7410 10 0.46703 T 0.11 -20.5202 16.6512 0.85203 1.0:0.0:0.0:0.0 . 1043 P42336 PK3CA_HUMAN L 1043 ENSP00000263967:M1043L ENSP00000263967:M1043L M + 1 0 PIK3CA 180434766 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 8.859000 0.92264 2.333000 0.79357 0.482000 0.46254 ATG TCGA-RB-A7B8-01A-12D-A33T-08 PIK3CA-001 KNOWN basic|appris_principal|exp_conf|CCDS protein_coding protein_coding OTTHUMT00000348409.2 1 0 1 160 318 0 51 1 1 22 35 0 51 2 0 0 0 0 0 2 1 1 158 315 0 51 2 0 0 0 0 51 2 -20.000000 1 1 0 0 1 1 4 5 2.528806 1 0.270000 2.180000 0.440077 0.990000 9.900000e-01 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 OPA1 4976 broad.mit.edu 37 3 193366601 193366601 + Missense_Mutation SNP A A C TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr3:193366601A>C ENST00000392438.3 + 19 2022 c.1788A>C c.(1786-1788)aaA>aaC p.K596N OPA1_ENST00000361908.3_Missense_Mutation_p.K633N|OPA1_ENST00000361715.2_Missense_Mutation_p.K615N|OPA1_ENST00000361828.2_Missense_Mutation_p.K614N|OPA1_ENST00000361510.2_Missense_Mutation_p.K651N|OPA1_ENST00000361150.2_Missense_Mutation_p.K597N NM_015560.2 NP_056375.2 O60313 OPA1_HUMAN optic atrophy 1 (autosomal dominant) 31 all_cancers(143;9.56e-09)|Ovarian(172;0.0386) OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06) TATTTGAAAAAGCTAAAAATG 0.308000 0 SO:0001583 missense ENST00000392438.3 1 1 hg19 CCDS43186.1 . . . . . . . . . . A 20.4 3.985177 0.74474 . . ENSG00000198836 ENST00000361908;ENST00000392438;ENST00000361510;ENST00000361715;ENST00000361828;ENST00000361150 D;D;D;D;D;D 0.96041 -3.48;-3.47;-3.44;-3.46;-3.49;-3.89 6.08 -4.14 0.03892 . 0.000000 0.85682 D 0.000000 D 0.96207 0.8763 M 0.71036 2.16 0.80722 D 1 D;D;D;D;D;D;D;D 0.76494 0.993;0.999;0.996;0.996;0.999;0.996;0.999;0.998 D;D;D;D;D;D;D;D 0.70487 0.933;0.922;0.969;0.969;0.942;0.969;0.941;0.969 D 0.94142 0.7398 10 0.56958 D 0.05 -27.0205 12.8665 0.57941 0.541:0.0:0.459:0.0 . 560;596;578;597;614;633;615;651 E5KLK2;O60313;E5KLK0;E5KLK1;E5KLJ6;E5KLJ7;E5KLJ9;E5KLJ5 .;OPA1_HUMAN;.;.;.;.;.;. N 633;596;651;615;614;597 ENSP00000354681:K633N;ENSP00000376233:K596N;ENSP00000355324:K651N;ENSP00000355311:K615N;ENSP00000354429:K614N;ENSP00000354781:K597N ENSP00000354781:K597N K + 3 2 OPA1 194849295 0.998000 0.40836 0.922000 0.36590 0.981000 0.71138 0.731000 0.26058 -1.012000 0.03387 -0.408000 0.06270 AAA TCGA-RB-A7B8-01A-12D-A33T-08 OPA1-002 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000313812.2 1 0 0 32 505 0 63 1 9.131675e-01 3 65 0 63 2 0 0 0 0 0 2 1 1 32 498 0 63 2 0 0 0 0 63 2 -7.010273 1 1 0 0 1 1 4 5 2.528806 1 0.270000 2.180000 0.440077 0.600000 4.000000e-01 1.000000 0.590000 0.663433 0.600000 0 0.490000 1.000000 CACNA1D 776 broad.mit.edu 37 3 53769492 53769492 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr3:53769492G>A ENST00000350061.5 + 20 3224 c.2713G>A c.(2713-2715)Gca>Aca p.A905T CACNA1D_ENST00000288139.4_Missense_Mutation_p.A925T|CACNA1D_ENST00000422281.2_Missense_Mutation_p.A905T NM_001128840.1 NP_001122312.1 Q01668 CAC1D_HUMAN calcium channel, voltage-dependent, L type, alpha 1D subunit 90 Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661) TGCCCTGGCCGCAGAGGACCC 0.627000 0 SO:0001583 missense ENST00000350061.5 0 1 hg19 CCDS46848.1 . . . . . . . . . . G 18.31 3.595482 0.66219 . . ENSG00000157388 ENST00000350061;ENST00000288139;ENST00000422281;ENST00000481478 D;D;D;D 0.97505 -4.41;-4.41;-4.41;-4.41 5.46 4.58 0.56647 . 0.066144 0.64402 N 0.000015 D 0.98601 0.9532 M 0.89414 3.03 0.80722 D 1 D;D;D;D 0.89917 1.0;0.986;1.0;0.972 D;P;D;P 0.79108 0.988;0.659;0.992;0.816 D 0.99655 1.0992 10 0.87932 D 0 . 16.7269 0.85424 0.0:0.1292:0.8708:0.0 . 905;598;905;925 B0FYA3;Q59GD8;Q01668;Q01668-2 .;.;CAC1D_HUMAN;. T 905;925;905;598 ENSP00000288133:A905T;ENSP00000288139:A925T;ENSP00000409174:A905T;ENSP00000418014:A598T ENSP00000288139:A925T A + 1 0 CACNA1D 53744532 1.000000 0.71417 0.106000 0.21319 0.197000 0.23852 7.906000 0.87423 1.407000 0.46875 0.555000 0.69702 GCA TCGA-RB-A7B8-01A-12D-A33T-08 CACNA1D-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000350557.1 0 0 0 6 457 1 70 0 7.653401e-04 0 3 1 70 2 0 0 0 0 0 2 0 2.489373e-03 8 453 1 69 21 0 0 0 1 70 2 -2.691434 1 1 121412 2 39 1 0 1 1 1.948477 0 0.270000 2.180000 0.268024 0.100000 3.000000e-02 0.200000 0.100000 0.110555 0.100000 0 0.060000 0.150000 SRGAP3 9901 broad.mit.edu 37 3 9100157 9100157 + Splice_Site SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr3:9100157C>T ENST00000383836.3 - 7 1229 c.e7-1 SRGAP3_ENST00000433332.3_Splice_Site|SRGAP3_ENST00000360413.3_Splice_Site NM_014850.3 NP_055665.1 O43295 SRGP3_HUMAN SLIT-ROBO Rho GTPase activating protein 3 SRGAP3/RAF1(6) 54 AATCACAGCACTTGGGGAGAG 0.577000 T RAF1 pilocytic astrocytoma Dom yes 3 3p25.3 9901 SLIT-ROBO Rho GTPase activating protein 3 M 0 SO:0001630 splice_region_variant ENST00000383836.3 0 1 hg19 CCDS2572.1 . . . . . . . . . . C 23.5 4.424679 0.83667 . . ENSG00000196220 ENST00000383836;ENST00000360413;ENST00000544908 . . . 5.55 5.55 0.83447 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 19.1098 0.93312 0.0:1.0:0.0:0.0 . . . . . -1 . . . - . . SRGAP3 9075157 1.000000 0.71417 0.998000 0.56505 0.868000 0.49771 7.663000 0.83820 2.596000 0.87737 0.650000 0.86243 . TCGA-RB-A7B8-01A-12D-A33T-08 SRGAP3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000207137.3 0 0 0 8 376 0 68 0 0 0 0 68 2 0 0 0 0 0 2 1 9.889666e-01 8 371 0 68 2 0 0 0 0 68 2 -8.141846 1 1 0 0 1 0 0 0 1.920345 0 0.270000 2.180000 0.255937 0.150000 7.000000e-02 0.280000 0.150000 0.168169 0.150000 0 0.100000 0.220000 DCAF4L1 285429 broad.mit.edu 37 4 41984154 41984154 + Silent SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr4:41984154C>T ENST00000333141.5 + 1 442 c.345C>T c.(343-345)taC>taT p.Y115Y NM_001029955.3 NP_001025126.2 Q3SXM0 DC4L1_HUMAN DDB1 and CUL4 associated factor 4-like 1 37 TCCACGTGTACGTGCTCAGAA 0.562000 0 SO:0001819 synonymous_variant ENST00000333141.5 1 1 hg19 CCDS33978.1 TCGA-RB-A7B8-01A-12D-A33T-08 DCAF4L1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000360958.1 1 0 1 67 402 0 73 0 0 0 0 73 2 0 0 0 0 0 2 1 1 66 397 0 73 2 0 0 0 0 73 2 -20.000000 1 1 121412 1 33 1 0 0 0 1.930260 0 0.270000 2.180000 0.260010 0.990000 8.200000e-01 1.000000 1.000000 0.974019 0.990000 1 0.920000 1.000000 GPR78 27201 broad.mit.edu 37 4 8582937 8582937 + Silent SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr4:8582937C>T ENST00000382487.4 + 1 645 c.228C>T c.(226-228)ccC>ccT p.P76P GPR78_ENST00000509216.1_Intron NM_080819.4 NP_543009.2 Q96P69 GPR78_HUMAN G protein-coupled receptor 78 26 CGTCGGCGCCCGGCGCATGCC 0.687000 0 SO:0001819 synonymous_variant ENST00000382487.4 0 1 hg19 CCDS3403.1 TCGA-RB-A7B8-01A-12D-A33T-08 GPR78-005 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000359201.1 1 0 1 15 86 0 16 0 0 0 0 16 2 0 0 0 0 0 2 1 9.999088e-01 15 85 0 15 2 0 0 0 0 16 2 -19.999990 1 1 0 0 1 0 0 0 1.930260 0 0.270000 2.180000 0.260010 0.990000 6.500000e-01 1.000000 1.000000 0.945651 0.990000 1 0.840000 1.000000 PCDHA12 56137 broad.mit.edu 37 5 140257259 140257259 + Silent SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr5:140257259G>A ENST00000398631.2 + 1 2202 c.2202G>A c.(2200-2202)ccG>ccA p.P734P PCDHA6_ENST00000529310.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA8_ENST00000531613.1_Intron NM_018903.2|NM_031864.2 NP_061726.1|NP_114070.1 Q9UN75 PCDAC_HUMAN protocadherin alpha 12 78 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) GGTGCGCGCCGGGCAAGCCCA 0.682000 Pancreas(113;759 1672 13322 24104 50104) 0 SO:0001819 synonymous_variant ENST00000398631.2 1 1 hg19 CCDS47285.1 TCGA-RB-A7B8-01A-12D-A33T-08 PCDHA12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000372882.2 1 0 1 55 177 0 36 0 0 0 1 0 36 2 0 0 0 0 0 2 1 1 55 177 0 35 2 0 0 0 0 36 2 -3.933300 1 1 0 0 1 0 1 1 1.948940 0 0.270000 2.180000 0.268024 0.990000 9.900000e-01 1.000000 1.000000 0.999999 0.990000 1 0.990000 1.000000 PCDHB11 56125 broad.mit.edu 37 5 140581503 140581503 + Missense_Mutation SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr5:140581503C>T ENST00000354757.3 + 1 2156 c.2156C>T c.(2155-2157)gCg>gTg p.A719V PCDHB11_ENST00000536699.1_Missense_Mutation_p.A354V NM_018931.2 NP_061754.1 Q9Y5F2 PCDBB_HUMAN protocadherin beta 11 63 KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339) AGGAGCAGGGCGGCCTCGGTG 0.652000 0 SO:0001583 missense ENST00000354757.3 1 1 hg19 CCDS4253.1 . . . . . . . . . . c 12.20 1.867239 0.32977 0.0 2.33E-4 ENSG00000197479 ENST00000536699;ENST00000354757 T;T 0.17528 2.27;2.27 2.77 0.731 0.18277 . . . . . T 0.19846 0.0477 M 0.88031 2.925 0.09310 N 1 P 0.36599 0.56 B 0.22880 0.042 T 0.14952 -1.0454 9 0.72032 D 0.01 . 6.2507 0.20843 0.2201:0.5842:0.1957:0.0 . 719 Q9Y5F2 PCDBB_HUMAN V 354;719 ENSP00000440344:A354V;ENSP00000346802:A719V ENSP00000346802:A719V A + 2 0 PCDHB11 140561687 0.000000 0.05858 0.004000 0.12327 0.229000 0.25112 -0.444000 0.06854 0.020000 0.15106 0.549000 0.68633 GCG TCGA-RB-A7B8-01A-12D-A33T-08 PCDHB11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251813.1 1 0 1 165 969 0 181 0 2.146277e-02 1 1 0 181 2 0 0 0 0 0 2 1 1 162 943 0 183 2 0 0 0 0 181 2 -20.000000 1 1 121412 3 39 1 0 1 1 1.948940 0 0.270000 2.180000 0.268024 0.990000 9.200000e-01 1.000000 1.000000 0.993813 0.990000 1 0.990000 1.000000 ASCC3 10973 broad.mit.edu 37 6 101073182 101073182 + Silent SNP A A G TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr6:101073182A>G ENST00000369162.2 - 30 5015 c.4671T>C c.(4669-4671)ccT>ccC p.P1557P NM_006828.2 NP_006819.2 Q8N3C0 ASCC3_HUMAN activating signal cointegrator 1 complex subunit 3 92 all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13) ATATCAAAACAGGTTTGGCTG 0.378000 0 SO:0001819 synonymous_variant ENST00000369162.2 1 1 hg19 CCDS5046.1 TCGA-RB-A7B8-01A-12D-A33T-08 ASCC3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041632.2 0 0 0 14 355 0 51 0 7.293107e-02 1 10 0 51 2 0 0 0 0 0 2 1 9.997531e-01 14 352 0 50 2 0 0 0 0 51 2 -14.517800 1 1 0 0 1 0 0 0 1.929623 0 0.270000 2.180000 0.260010 0.280000 1.500000e-01 0.440000 0.280000 0.293176 0.280000 0 0.210000 0.360000 PHACTR1 221692 broad.mit.edu 37 6 13206143 13206143 + Missense_Mutation SNP C C A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr6:13206143C>A ENST00000379350.1 + 7 890 c.761C>A c.(760-762)cCa>cAa p.P254Q PHACTR1_ENST00000379345.2_Intron|PHACTR1_ENST00000332995.7_Missense_Mutation_p.P254Q|PHACTR1_ENST00000457702.2_Missense_Mutation_p.P109Q Q9C0D0 PHAR1_HUMAN phosphatase and actin regulator 1 26 Breast(50;0.0427)|Ovarian(93;0.12) all_hematologic(90;0.122)|Lung SC(78;0.195) Epithelial(50;0.146)|BRCA - Breast invasive adenocarcinoma(129;0.239) GTGGGGGGGCCAGACCTCTCA 0.602000 0 SO:0001583 missense ENST00000379350.1 1 1 hg19 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 20.4|20.4 3.984897|3.984897 0.74474|0.74474 .|. .|. ENSG00000112137|ENSG00000112137 ENST00000379350;ENST00000332995;ENST00000432934;ENST00000457702|ENST00000415087 T;T;T|. 0.31510|. 1.49;1.53;1.52|. 5.12|5.12 5.12|5.12 0.69794|0.69794 .|. 0.598284|. 0.18257|. N|. 0.146764|. T|T 0.37489|0.37489 0.1005|0.1005 N|N 0.14661|0.14661 0.345|0.345 0.80722|0.80722 D|D 1|1 D;P;P|. 0.61697|. 0.99;0.838;0.899|. P;B;B|. 0.58780|. 0.845;0.276;0.367|. T|T 0.29119|0.29119 -1.0022|-1.0022 10|5 0.15499|. T|. 0.54|. -7.9901|-7.9901 17.722|17.722 0.88355|0.88355 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. 323;254;254|. E7ESR5;Q9C0D0;Q9C0D0-2|. .;PHAR1_HUMAN;.|. Q|K 254;254;323;109|89 ENSP00000368655:P254Q;ENSP00000329880:P254Q;ENSP00000397669:P109Q|. ENSP00000329880:P254Q|. P|Q +|+ 2|1 0|0 PHACTR1|PHACTR1 13314122|13314122 1.000000|1.000000 0.71417|0.71417 0.995000|0.995000 0.50966|0.50966 0.973000|0.973000 0.67179|0.67179 3.146000|3.146000 0.50631|0.50631 2.653000|2.653000 0.90120|0.90120 0.561000|0.561000 0.74099|0.74099 CCA|CAG TCGA-RB-A7B8-01A-12D-A33T-08 PHACTR1-001 KNOWN basic|appris_candidate_longest protein_coding protein_coding OTTHUMT00000039876.1 1 0 1 83 358 0 72 0 3.597521e-02 0 2 0 72 2 0 0 0 0 0 2 1 1 82 354 0 72 2 0 0 0 0 72 2 -20.000000 1 1 0 0 1 0 0 0 1.929623 0 0.270000 2.180000 0.260010 0.990000 9.900000e-01 1.000000 1.000000 0.999957 0.990000 1 0.990000 1.000000 STXBP5 134957 broad.mit.edu 37 6 147680320 147680320 + Silent SNP G G A rs142207202 TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr6:147680320G>A ENST00000321680.6 + 23 2406 c.2406G>A c.(2404-2406)acG>acA p.T802T STXBP5_ENST00000367481.3_Silent_p.T766T|STXBP5_ENST00000179882.6_Silent_p.T457T|STXBP5_ENST00000367480.3_Silent_p.T749T NM_001127715.2 NP_001121187.1 Q5T5C0 STXB5_HUMAN syntaxin binding protein 5 (tomosyn) 42 Ovarian(120;0.0164) TCTGTGAAACGTTTACTCGAA 0.488000 0 SO:0001819 synonymous_variant ENST00000321680.6 1 1 hg19 CCDS47499.1 . . . . . . . . . . A 0.141 -1.102263 0.01828 2.27E-4 3.49E-4 ENSG00000164506 ENST00000367475 . . . 5.46 -8.64 0.00874 . . . . . T 0.17959 0.0431 . . . 0.80722 D 1 . . . . . . T 0.38457 -0.9660 4 . . . . 3.0411 0.06139 0.2097:0.1742:0.4436:0.1725 . . . . I 128 . . V + 1 0 STXBP5 147722013 0.026000 0.19158 0.003000 0.11579 0.052000 0.14988 -0.885000 0.04161 -2.023000 0.00937 -2.952000 0.00084 GTT TCGA-RB-A7B8-01A-12D-A33T-08 STXBP5-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000042606.1 1 0 1 38 327 0 47 0 4.446599e-01 1 13 0 47 2 0 0 0 0 0 2 1 1 38 323 0 46 2 0 0 0 0 47 2 -9.575886 1 1 121406 17 46 1 0 0 0 1.929623 0 0.270000 2.180000 0.260010 0.750000 5.500000e-01 0.990000 0.760000 0.768818 0.750000 0 0.640000 0.880000 GMPR 2766 broad.mit.edu 37 6 16279069 16279069 + Missense_Mutation SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr6:16279069C>T ENST00000259727.4 + 6 716 c.602C>T c.(601-603)gCc>gTc p.A201V NM_006877.3 NP_006868.3 P36959 GMPR1_HUMAN guanosine monophosphate reductase 20 Breast(50;0.0427)|Ovarian(93;0.103) all_hematologic(90;0.0895) CAGCTGAGTGCCGTCATTGAG 0.592000 0 SO:0001583 missense ENST00000259727.4 0 1 hg19 CCDS4537.1 . . . . . . . . . . C 19.74 3.883826 0.72410 . . ENSG00000137198 ENST00000259727 D 0.90385 -2.66 4.85 4.85 0.62838 Aldolase-type TIM barrel (1);IMP dehydrogenase/GMP reductase (1); 0.000000 0.85682 D 0.000000 D 0.97554 0.9199 H 0.99815 4.805 0.80722 D 1 D 0.69078 0.997 D 0.64877 0.93 D 0.99605 1.0979 10 0.87932 D 0 -8.3541 16.7414 0.85460 0.0:1.0:0.0:0.0 . 201 P36959 GMPR1_HUMAN V 201 ENSP00000259727:A201V ENSP00000259727:A201V A + 2 0 GMPR 16387048 1.000000 0.71417 0.792000 0.32020 0.153000 0.21895 7.327000 0.79147 2.237000 0.73441 0.462000 0.41574 GCC TCGA-RB-A7B8-01A-12D-A33T-08 GMPR-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000039942.2 0 0 0 5 420 0 70 0 5.223545e-02 0 25 0 70 2 0 0 0 0 0 2 1 9.343130e-01 5 411 0 70 2 0 0 0 0 70 2 -2.872093 1 1 0 0 1 0 0 0 1.929623 0 0.270000 2.180000 0.260010 0.090000 3.000000e-02 0.190000 0.090000 0.101995 0.090000 0 0.050000 0.140000 GNL1 2794 broad.mit.edu 37 6 30514571 30514571 + Missense_Mutation SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr6:30514571C>T ENST00000376621.3 - 11 2454 c.1484G>A c.(1483-1485)cGg>cAg p.R495Q NM_005275.3 NP_005266.2 P36915 GNL1_HUMAN guanine nucleotide binding protein-like 1 25 CACATCATTCCGAGCCGCCTT 0.522000 0 SO:0001583 missense ENST00000376621.3 0 1 hg19 CCDS4680.1 . . . . . . . . . . C 35 5.554718 0.96514 . . ENSG00000204590 ENST00000376621;ENST00000426875;ENST00000429126 T 0.49720 0.77 5.44 5.44 0.79542 . 0.119786 0.56097 D 0.000022 T 0.45458 0.1343 L 0.37630 1.12 0.58432 D 0.999999 P;D;B 0.89917 0.889;1.0;0.052 P;D;B 0.74674 0.617;0.984;0.007 T 0.24512 -1.0158 10 0.09338 T 0.73 -40.1993 18.0176 0.89246 0.0:1.0:0.0:0.0 . 493;292;495 B4DYK6;B4DWZ0;P36915 .;.;GNL1_HUMAN Q 495;317;292 ENSP00000365806:R495Q ENSP00000365806:R495Q R - 2 0 GNL1 30622550 1.000000 0.71417 0.233000 0.24025 0.996000 0.88848 6.691000 0.74573 2.560000 0.86352 0.561000 0.74099 CGG TCGA-RB-A7B8-01A-12D-A33T-08 GNL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000076241.2 0 0 0 7 479 0 63 1 8.073134e-01 3 207 0 63 2 0 0 0 0 0 2 1 9.792697e-01 7 469 0 59 2 0 0 0 0 63 2 -2.712494 1 1 0 0 1 0 0 0 1.929623 0 0.270000 2.180000 0.260010 0.100000 4.000000e-02 0.210000 0.110000 0.119090 0.100000 0 0.070000 0.160000 ANKS1A 23294 broad.mit.edu 37 6 34985688 34985688 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr6:34985688G>A ENST00000360359.3 + 11 2000 c.1862G>A c.(1861-1863)cGc>cAc p.R621H ANKS1A_ENST00000535627.1_Intron NM_015245.2 NP_056060.2 Q92625 ANS1A_HUMAN ankyrin repeat and sterile alpha motif domain containing 1A 31 AAACTCAGCCGCAGCTTGTCC 0.597000 0 SO:0001583 missense ENST00000360359.3 0 1 hg19 CCDS4798.1 . . . . . . . . . . G 23.2 4.388694 0.82902 . . ENSG00000064999 ENST00000360359 T 0.46819 0.86 5.41 5.41 0.78517 . 0.000000 0.50627 D 0.000117 T 0.61640 0.2363 L 0.59436 1.845 0.80722 D 1 D 0.89917 1.0 D 0.78314 0.991 T 0.63314 -0.6665 10 0.72032 D 0.01 -18.3484 19.5669 0.95397 0.0:0.0:1.0:0.0 . 621 Q92625 ANS1A_HUMAN H 621 ENSP00000353518:R621H ENSP00000353518:R621H R + 2 0 ANKS1A 35093666 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 9.374000 0.97172 2.694000 0.91930 0.655000 0.94253 CGC TCGA-RB-A7B8-01A-12D-A33T-08 ANKS1A-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000040262.1 0 0 0 9 1025 0 160 0 7.340053e-03 0 13 0 160 2 0 0 0 0 0 2 0 1.935047e-02 8 1017 1 159 21 0 0 0 0 160 2 -1.899855 0 1 0 0 1 0 0 0 1.929623 0 0.270000 2.180000 0.260010 0.060000 2.000000e-02 0.120000 0.060000 0.070343 0.060000 0 0.040000 0.090000 F13A1 2162 broad.mit.edu 37 6 6318801 6318801 + Nonsense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr6:6318801G>A ENST00000264870.3 - 2 362 c.97C>T c.(97-99)Cag>Tag p.Q33* NM_000129.3 NP_000120.2 P00488 F13A_HUMAN coagulation factor XIII, A1 polypeptide 62 Ovarian(93;0.0816) all_hematologic(90;0.152) L-Glutamine(DB00130) ACCACGCCCTGAAGCTCCACT 0.602000 0 SO:0001587 stop_gained ENST00000264870.3 0 1 hg19 CCDS4496.1 . . . . . . . . . . G 11.67 1.708509 0.30322 . . ENSG00000124491 ENST00000264870;ENST00000441301;ENST00000414279;ENST00000431222 . . . 4.64 2.72 0.32119 . 0.685255 0.14021 N 0.346817 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.25751 T 0.34 . 6.3836 0.21548 0.1029:0.3924:0.5047:0.0 . . . . X 33;33;33;71 . ENSP00000264870:Q33X Q - 1 0 F13A1 6263800 0.009000 0.17119 0.141000 0.22245 0.004000 0.04260 1.095000 0.30964 1.130000 0.42092 0.643000 0.83706 CAG TCGA-RB-A7B8-01A-12D-A33T-08 F13A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000039756.3 0 0 0 7 673 0 84 0 8.793137e-02 0 41 0 84 2 0 0 0 0 0 2 1 9.797276e-01 7 664 0 84 2 0 0 0 0 84 2 -2.773046 1 1 0 0 1 0 0 0 1.929623 0 0.270000 2.180000 0.260010 0.070000 2.000000e-02 0.150000 0.080000 0.085365 0.070000 0 0.040000 0.110000 DSP 1832 broad.mit.edu 37 6 7580347 7580347 + Silent SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr6:7580347G>A ENST00000379802.3 + 23 4265 c.3924G>A c.(3922-3924)cgG>cgA p.R1308R DSP_ENST00000418664.2_Intron NM_004415.2 NP_004406.2 P15924 DESP_HUMAN desmoplakin 101 Ovarian(93;0.0584) all_hematologic(90;0.236) ACAATGCCCGGCACAAGCAGT 0.532000 0 SO:0001819 synonymous_variant ENST00000379802.3 0 1 hg19 CCDS4501.1 TCGA-RB-A7B8-01A-12D-A33T-08 DSP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000039786.2 0 0 0 5 563 0 106 0 5.703726e-02 0 35 0 106 2 0 0 0 0 0 2 1 9.357355e-01 5 556 0 106 2 0 0 0 0 106 2 -2.239055 0 1 0 0 1 0 0 0 1.929623 0 0.270000 2.180000 0.260010 0.060000 2.000000e-02 0.140000 0.060000 0.076538 0.060000 0 0.040000 0.110000 RRAGD 58528 broad.mit.edu 37 6 90087442 90087442 + Missense_Mutation SNP C C G TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr6:90087442C>G ENST00000369415.4 - 5 1126 c.850G>C c.(850-852)Gag>Cag p.E284Q RRAGD_ENST00000492783.1_5'UTR|RRAGD_ENST00000359203.3_Missense_Mutation_p.E133Q NM_021244.4 NP_067067.1 Ras-related GTP binding D 15 all_cancers(76;7.01e-07)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00139) CAGCAGAGCTCATAGGTTTGC 0.353000 0 SO:0001583 missense ENST00000369415.4 1 1 hg19 CCDS5022.1 . . . . . . . . . . C 31 5.070456 0.93950 . . ENSG00000025039 ENST00000369415;ENST00000359203 . . . 5.43 5.43 0.79202 . 0.000000 0.85682 D 0.000000 D 0.83885 0.5351 M 0.90019 3.08 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 D 0.86571 0.1847 9 0.66056 D 0.02 -13.7325 19.2342 0.93851 0.0:1.0:0.0:0.0 . 284 Q9NQL2 RRAGD_HUMAN Q 284;133 . ENSP00000352131:E133Q E - 1 0 RRAGD 90144161 1.000000 0.71417 0.997000 0.53966 0.988000 0.76386 7.771000 0.85420 2.553000 0.86117 0.462000 0.41574 GAG TCGA-RB-A7B8-01A-12D-A33T-08 RRAGD-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000041484.1 1 0 1 62 348 0 70 0 9.564632e-01 1 29 0 70 2 0 0 0 0 0 2 1 1 61 346 0 70 2 0 0 0 0 70 2 -3.224601 1 1 0 0 1 0 0 0 1.929623 0 0.270000 2.180000 0.260010 0.990000 8.600000e-01 1.000000 1.000000 0.986938 0.990000 1 0.970000 1.000000 EPHB4 2050 broad.mit.edu 37 7 100402884 100402884 + Missense_Mutation SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr7:100402884C>T ENST00000358173.3 - 16 3206 c.2738G>A c.(2737-2739)gGc>gAc p.G913D EPHB4_ENST00000360620.3_Intron NM_004444.4 NP_004435.3 P54760 EPHB4_HUMAN EPH receptor B4 47 Lung NSC(181;0.041)|all_lung(186;0.0581) AAGCCACTCGCCCACAGAGCC 0.587000 GBM(200;2113 3072 25865 52728) 0 SO:0001583 missense ENST00000358173.3 1 1 hg19 CCDS5706.1 . . . . . . . . . . C 18.10 3.549037 0.65311 . . ENSG00000196411 ENST00000358173 T 0.51325 0.71 5.07 5.07 0.68467 Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1); 0.000000 0.51477 D 0.000085 T 0.53334 0.1790 L 0.33624 1.015 0.47374 D 0.999405 D 0.61080 0.989 P 0.59357 0.856 T 0.48328 -0.9045 10 0.32370 T 0.25 . 15.9362 0.79712 0.0:1.0:0.0:0.0 . 913 P54760 EPHB4_HUMAN D 913 ENSP00000350896:G913D ENSP00000350896:G913D G - 2 0 EPHB4 100240820 0.999000 0.42202 0.987000 0.45799 0.985000 0.73830 4.063000 0.57499 2.372000 0.80975 0.561000 0.74099 GGC TCGA-RB-A7B8-01A-12D-A33T-08 EPHB4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347222.1 1 0 1 26 128 0 24 1 9.999995e-01 30 95 0 24 2 0 0 0 0 0 2 1 1 26 128 0 21 2 0 0 0 0 24 2 -20.000000 1 1 0 0 1 1 2 3 2.250672 1 0.270000 2.180000 0.356828 0.990000 9.700000e-01 1.000000 1.000000 0.997630 0.990000 1 0.990000 1.000000 SERPINE1 5054 broad.mit.edu 37 7 100780300 100780300 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr7:100780300G>A ENST00000223095.4 + 8 1263 c.1106G>A c.(1105-1107)cGc>cAc p.R369H SERPINE1_ENST00000445463.2_Missense_Mutation_p.R354H NM_000602.4 NP_000593.1 P05121 PAI1_HUMAN serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 20 Lung NSC(181;0.136)|all_lung(186;0.182) Alteplase(DB00009)|Anistreplase(DB00029)|Drotrecogin alfa(DB00055)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013) GTCTCAGCCCGCATGGCCCCC 0.582000 0 SO:0001583 missense ENST00000223095.4 0 1 hg19 CCDS5711.1 . . . . . . . . . . G 17.61 3.432084 0.62844 . . ENSG00000106366 ENST00000223095;ENST00000445463;ENST00000536888 T;T 0.24350 1.86;1.86 5.67 5.67 0.87782 Serpin domain (3); 0.000000 0.85682 D 0.000000 T 0.55114 0.1900 M 0.85945 2.785 0.54753 D 0.999988 D;D 0.89917 1.0;1.0 D;D 0.70016 0.945;0.967 T 0.60505 -0.7250 10 0.72032 D 0.01 . 15.2607 0.73621 0.0:0.0:1.0:0.0 . 354;369 F8WD53;P05121 .;PAI1_HUMAN H 369;354;146 ENSP00000223095:R369H;ENSP00000396766:R354H ENSP00000223095:R369H R + 2 0 SERPINE1 100567020 1.000000 0.71417 0.998000 0.56505 0.024000 0.10985 7.941000 0.87700 2.664000 0.90586 0.555000 0.69702 CGC TCGA-RB-A7B8-01A-12D-A33T-08 SERPINE1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347458.1 0 0 0 5 621 0 76 0 8.855814e-01 0 486 0 76 2 0 0 0 0 0 2 1 9.375008e-01 5 620 0 74 2 0 0 0 0 76 2 -1.789342 0 1 121412 2 36 1 1 2 3 2.250672 1 0.270000 2.180000 0.356828 0.070000 1.000000e-02 0.150000 0.060000 0.079932 0.070000 0 0.040000 0.110000 RNF133 168433 broad.mit.edu 37 7 122338189 122338189 + Missense_Mutation SNP G G A rs137950690 TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr7:122338189G>A ENST00000340112.2 - 1 1021 c.784C>T c.(784-786)Cgc>Tgc p.R262C CADPS2_ENST00000449022.2_Intron|CADPS2_ENST00000313070.7_Intron|CADPS2_ENST00000334010.7_Intron|CADPS2_ENST00000412584.2_Intron NM_139175.1 NP_631914.1 Q8WVZ7 RN133_HUMAN ring finger protein 133 21 GGCTTATAGCGTTCAAAGCAA 0.403000 Colon(198;1778 2057 7449 19869 45985) 0 SO:0001583 missense ENST00000340112.2 0 1 hg19 CCDS5784.1 . . . . . . . . . . G 0.871 -0.731875 0.03135 0.0 2.33E-4 ENSG00000188050 ENST00000340112 T 0.43294 0.95 5.53 2.62 0.31277 Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, RING-H2-type (1); 0.713262 0.12945 U 0.426283 T 0.26011 0.0634 N 0.21282 0.65 0.09310 N 0.999999 B 0.23891 0.093 B 0.20767 0.031 T 0.20306 -1.0279 10 0.62326 D 0.03 . 4.5179 0.11945 0.091:0.4253:0.36:0.1236 . 262 Q8WVZ7 RN133_HUMAN C 262 ENSP00000344489:R262C ENSP00000344489:R262C R - 1 0 RNF133 122125425 0.051000 0.20477 0.293000 0.24932 0.004000 0.04260 0.822000 0.27352 0.672000 0.31204 -0.424000 0.05967 CGC TCGA-RB-A7B8-01A-12D-A33T-08 RNF133-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347413.1 0 0 0 8 722 0 98 0 0 0 0 98 2 0 0 0 0 0 2 1 9.891059e-01 7 718 0 98 2 0 0 0 0 98 2 -2.598465 1 1 121412 4 41 1 1 2 3 2.250672 1 0.270000 2.180000 0.356828 0.090000 3.000000e-02 0.180000 0.090000 0.103130 0.090000 0 0.060000 0.140000 TAS2R38 5726 broad.mit.edu 37 7 141673468 141673468 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr7:141673468G>A ENST00000547270.1 - 1 105 c.22C>T c.(22-24)Cgc>Tgc p.R8C NM_176817.4 NP_789787 P59533 T2R38_HUMAN taste receptor, type 2, member 38 21 Melanoma(164;0.0171) GACACAGTGCGGATGCGAGTT 0.443000 0 SO:0001583 missense ENST00000547270.1 0 1 hg19 CCDS34765.1 . . . . . . . . . . G 3.866 -0.028883 0.07589 0.0 1.16E-4 ENSG00000257138 ENST00000547270 T 0.00816 5.66 5.1 -9.6 0.00553 . 4.375660 0.01228 N 0.008298 T 0.00412 0.0013 N 0.03608 -0.345 0.09310 N 1 B 0.22276 0.067 B 0.04013 0.001 T 0.51220 -0.8733 10 0.15066 T 0.55 . 1.5776 0.02627 0.1848:0.4484:0.1652:0.2016 . 8 P59533 T2R38_HUMAN C 8 ENSP00000448219:R8C ENSP00000331291:R8C R - 1 0 TAS2R38 141319937 0.000000 0.05858 0.000000 0.03702 0.001000 0.01503 -0.787000 0.04618 -1.782000 0.01275 -0.294000 0.09567 CGC TCGA-RB-A7B8-01A-12D-A33T-08 TAS2R38-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000350810.2 1 0 1 59 518 1 74 0 0 0 1 74 2 0 0 0 0 0 2 1 9.999819e-01 59 515 1 73 24 0 0 0 1 74 2 -2.376785 0 1 121400 1 34 1 1 2 3 2.250672 1 0.270000 2.180000 0.356828 0.850000 6.600000e-01 1.000000 1.000000 0.862080 0.850000 1 0.750000 0.970000 PSMA2 5683 broad.mit.edu 37 7 42957275 42957275 + Silent SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr7:42957275C>T ENST00000223321.4 - 8 667 c.603G>A c.(601-603)ggG>ggA p.G201G PSMA2_ENST00000442788.1_Silent_p.G201G|PSMA2_ENST00000445517.1_Silent_p.G131G NM_002787.4 NP_002778.1 P25787 PSA2_HUMAN proteasome (prosome, macropain) subunit, alpha type, 2 10 CTGTCATTTGCCCTTCAAAGC 0.378000 0 SO:0001819 synonymous_variant ENST00000223321.4 0 1 hg19 CCDS5467.1 TCGA-RB-A7B8-01A-12D-A33T-08 PSMA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250816.1 0 0 0 5 336 1 35 0 3.382081e-05 2 530 1 35 39 0 0 0 0 0 2 0 3.549933e-05 5 334 1 35 27 0 0 0 1 35 2 -2.957537 1 1 0 0 1 1 2 3 2.250672 1 0.270000 2.180000 0.356828 0.130000 4.000000e-02 0.270000 0.120000 0.146290 0.130000 0 0.080000 0.200000 TYW1 55253 broad.mit.edu 37 7 66479413 66479413 + Silent SNP T T C rs145686658 by1000genomes TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr7:66479413T>C ENST00000359626.5 + 5 599 c.435T>C c.(433-435)acT>acC p.T145T NM_018264.2 NP_060734.2 Q9NV66 TYW1_HUMAN tRNA-yW synthesizing protein 1 homolog (S. cerevisiae) p.T145T(1) 46 Lung NSC(55;0.0846)|all_lung(88;0.183) GCCTACCAACTGAAAGTGCAG 0.428000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000359626.5 0 1 hg19 CCDS5538.1 TCGA-RB-A7B8-01A-12D-A33T-08 TYW1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251932.2 0 0 0 6 721 0 107 0 9.939520e-03 0 15 0 107 2 0 0 0 0 0 2 1 9.633777e-01 6 710 0 106 2 0 0 0 0 107 2 -1.817161 0 1 121412 80 43 1 1 2 3 2.250672 1 0.270000 2.180000 0.356828 0.070000 1.000000e-02 0.150000 0.060000 0.080527 0.070000 0 0.040000 0.110000 VPS37D 155382 broad.mit.edu 37 7 73085559 73085559 + Silent SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr7:73085559C>T ENST00000324941.4 + 4 743 c.609C>T c.(607-609)gcC>gcT p.A203A VPS37D_ENST00000451519.1_Silent_p.A118A NM_001077621.1 NP_001071089.1 vacuolar protein sorting 37 homolog D (S. cerevisiae) 2 Lung NSC(55;0.0908)|all_lung(88;0.198) CCACTGGGGCCGCCCGGGGGC 0.766000 0 SO:0001819 synonymous_variant ENST00000324941.4 0 1 hg19 CCDS43596.1 TCGA-RB-A7B8-01A-12D-A33T-08 VPS37D-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000348064.1 1 0 0 4 66 0 12 0 1.604344e-02 0 3 0 12 2 0 0 0 0 0 2 1 8.923721e-01 4 66 0 12 2 0 0 0 0 12 2 -8.478669 1 1 0 0 1 1 2 3 2.250672 1 0.270000 2.180000 0.356828 0.520000 1.800000e-01 1.000000 1.000000 0.560420 0.520000 0 0.320000 0.800000 TRHR 7201 broad.mit.edu 37 8 110099973 110099973 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr8:110099973G>A ENST00000518632.1 + 2 583 c.232G>A c.(232-234)Gca>Aca p.A78T TRHR_ENST00000311762.2_Missense_Mutation_p.A78T P34981 TRFR_HUMAN thyrotropin-releasing hormone receptor 37 OV - Ovarian serous cystadenocarcinoma(57;2.3e-11) CTTGGTGGCCGCAGGCCTCCC 0.512000 0 SO:0001583 missense ENST00000518632.1 0 1 hg19 CCDS6311.1 . . . . . . . . . . G 24.8 4.571768 0.86542 . . ENSG00000174417 ENST00000518632;ENST00000311762 T;T 0.71698 -0.59;-0.59 5.85 5.85 0.93711 GPCR, rhodopsin-like superfamily (1); 0.000000 0.85682 D 0.000000 D 0.83275 0.5219 M 0.74467 2.265 0.80722 D 1 D 0.89917 1.0 D 0.71184 0.972 T 0.78974 -0.1992 10 0.23302 T 0.38 -37.8444 19.1516 0.93491 0.0:0.0:1.0:0.0 . 78 P34981 TRFR_HUMAN T 78 ENSP00000430711:A78T;ENSP00000309818:A78T ENSP00000309818:A78T A + 1 0 TRHR 110169149 1.000000 0.71417 0.809000 0.32408 0.898000 0.52572 9.860000 0.99555 2.773000 0.95371 0.655000 0.94253 GCA TCGA-RB-A7B8-01A-12D-A33T-08 TRHR-002 KNOWN alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000380892.1 0 0 0 5 481 0 78 0 0 0 0 78 2 0 0 0 0 0 2 1 9.364760e-01 5 477 0 76 2 0 0 0 0 78 2 -2.216887 0 1 121412 1 32 1 0 0 0 1.943555 0 0.270000 2.180000 0.266037 0.070000 2.000000e-02 0.170000 0.080000 0.090072 0.070000 0 0.040000 0.120000 HAS2 3037 broad.mit.edu 37 8 122626809 122626809 + Missense_Mutation SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr8:122626809C>T ENST00000303924.4 - 4 1736 c.1199G>A c.(1198-1200)cGg>cAg p.R400Q 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) AATTTTACCCCGGTAGAAGAG 0.413000 0 SO:0001583 missense ENST00000303924.4 1 1 hg19 CCDS6335.1 . . . . . . . . . . C 12.10 1.837061 0.32421 . . ENSG00000170961 ENST00000303924 T 0.59083 0.29 6.04 6.04 0.98038 . 0.096875 0.64402 N 0.000001 T 0.48114 0.1482 L 0.37630 1.12 0.50171 D 0.999857 B 0.19583 0.037 B 0.19666 0.026 T 0.48186 -0.9057 10 0.02654 T 1 -10.3761 20.5792 0.99380 0.0:1.0:0.0:0.0 . 400 Q92819 HAS2_HUMAN Q 400 ENSP00000306991:R400Q ENSP00000306991:R400Q R - 2 0 HAS2 122695990 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 3.848000 0.55903 2.873000 0.98535 0.561000 0.74099 CGG TCGA-RB-A7B8-01A-12D-A33T-08 HAS2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000381150.2 1 0 1 130 688 0 147 0 5.416174e-01 0 11 0 147 2 0 0 0 0 0 2 1 1 129 682 0 146 2 0 0 0 0 147 2 -2.416326 0 1 0 0 1 0 0 0 1.943555 0 0.270000 2.180000 0.266037 0.990000 9.800000e-01 1.000000 1.000000 0.999050 0.990000 1 0.990000 1.000000 EPHX2 2053 broad.mit.edu 37 8 27373915 27373915 + Splice_Site SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr8:27373915G>A ENST00000521400.1 + 8 1340 c.910G>A c.(910-912)Gaa>Aaa p.E304K EPHX2_ENST00000521780.1_Splice_Site_p.E238K|EPHX2_ENST00000517536.1_Splice_Site_p.E121K|EPHX2_ENST00000518379.1_Splice_Site_p.E272K|EPHX2_ENST00000380476.3_Splice_Site_p.E251K NM_001979.5 NP_001970.2 P34913 HYES_HUMAN epoxide hydrolase 2, cytoplasmic 27 Ovarian(32;2.61e-05)|all_epithelial(46;0.207) TGCTCCTCCCGGTGGGTGTGC 0.567000 OREG0018668 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001630 splice_region_variant ENST00000521400.1 0 1 hg19 CCDS6060.1 . . . . . . . . . . G 13.65 2.299688 0.40694 . . ENSG00000120915 ENST00000521400;ENST00000517536;ENST00000521780;ENST00000380476;ENST00000415449;ENST00000518379 T;T;T;T;T 0.63255 -0.03;-0.03;-0.03;-0.03;-0.03 5.67 5.67 0.87782 Alpha/beta hydrolase fold-1 (1); 0.288097 0.42821 D 0.000645 T 0.65749 0.2721 M 0.80183 2.485 0.80722 D 1 B;B;B 0.25521 0.026;0.109;0.128 B;B;B 0.20955 0.031;0.028;0.032 T 0.63761 -0.6564 10 0.39692 T 0.17 -5.1595 17.2762 0.87116 0.0:0.0:1.0:0.0 . 272;304;304 E5RFU2;E7ETW9;P34913 .;.;HYES_HUMAN K 304;121;238;251;308;272 ENSP00000430269:E304K;ENSP00000428875:E121K;ENSP00000430302:E238K;ENSP00000369843:E251K;ENSP00000427956:E272K ENSP00000369843:E251K E + 1 0 EPHX2 27429832 1.000000 0.71417 0.736000 0.30914 0.054000 0.15201 5.558000 0.67319 2.677000 0.91161 0.561000 0.74099 GAA TCGA-RB-A7B8-01A-12D-A33T-08 EPHX2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000219954.4 0 0 0 6 791 1 121 0 9.474816e-03 0 16 1 121 2 0 0 0 0 0 2 0 2.772110e-05 9 786 2 120 30 0 0 0 1 121 2 -1.726731 0 1 121412 9 45 1 0 0 0 1.939885 0 0.270000 2.180000 0.266037 0.050000 1.000000e-02 0.120000 0.060000 0.064345 0.050000 0 0.030000 0.090000 RGS20 8601 broad.mit.edu 37 8 54791937 54791937 + Silent SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr8:54791937C>T ENST00000297313.3 + 2 377 c.285C>T c.(283-285)ccC>ccT p.P95P RGS20_ENST00000522225.1_5'Flank|RGS20_ENST00000344277.6_Intron|RGS20_ENST00000276500.4_5'Flank|RP11-1070A24.2_ENST00000606037.1_RNA NM_170587.2 NP_733466.1 O76081 RGS20_HUMAN regulator of G-protein signaling 20 21 OV - Ovarian serous cystadenocarcinoma(7;1.37e-06)|Epithelial(17;0.000126)|all cancers(17;0.0009) GACCCCCTCCCGAGGCTCCCC 0.726000 0 SO:0001819 synonymous_variant ENST00000297313.3 0 1 hg19 CCDS6155.1 TCGA-RB-A7B8-01A-12D-A33T-08 RGS20-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000380058.1 0 0 0 8 609 0 93 0 0 0 0 93 2 0 0 0 0 0 2 1 9.887066e-01 8 599 0 92 2 0 0 0 0 93 2 -2.805586 1 1 0 0 1 0 0 0 1.939885 0 0.270000 2.180000 0.266037 0.090000 4.000000e-02 0.180000 0.100000 0.106641 0.090000 0 0.060000 0.140000 DNAJC5B 85479 broad.mit.edu 37 8 66988979 66988979 + Silent SNP C C T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr8:66988979C>T ENST00000276570.5 + 4 491 c.204C>T c.(202-204)caC>caT p.H68H DNAJC5B_ENST00000519330.1_3'UTR NM_033105.4 NP_149096.2 Q9UF47 DNJ5B_HUMAN DnaJ (Hsp40) homolog, subfamily C, member 5 beta p.H68H(1) 20 Lung NSC(129;0.114)|all_lung(136;0.188) Epithelial(68;0.0213)|all cancers(69;0.0839)|BRCA - Breast invasive adenocarcinoma(89;0.0886)|OV - Ovarian serous cystadenocarcinoma(28;0.112) ACAACGCCCACGCAATACTTA 0.428000 1 Substitution - coding silent(1) SO:0001819 synonymous_variant ENST00000276570.5 0 1 hg19 CCDS6183.1 TCGA-RB-A7B8-01A-12D-A33T-08 DNAJC5B-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000378915.1 0 0 0 7 711 0 93 0 1.386963e-04 0 2 0 93 2 0 0 0 0 0 2 1 9.803707e-01 7 708 0 93 2 0 0 0 0 93 2 -2.917093 1 1 0 0 1 0 0 0 1.939885 0 0.270000 2.180000 0.266037 0.070000 2.000000e-02 0.140000 0.080000 0.081553 0.070000 0 0.040000 0.110000 WWP1 11059 broad.mit.edu 37 8 87423766 87423766 + Splice_Site SNP G G T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr8:87423766G>T ENST00000517970.1 + 9 1031 c.e9-1 WWP1_ENST00000265428.4_Splice_Site|WWP1_ENST00000349423.2_Splice_Site|WWP1_ENST00000341922.2_Splice_Site NM_007013.3 NP_008944.1 Q9H0M0 WWP1_HUMAN WW domain containing E3 ubiquitin protein ligase 1 31 TCCCTTCTCAGTTAATGGAGA 0.368000 0 SO:0001630 splice_region_variant ENST00000517970.1 0 1 hg19 CCDS6242.1 . . . . . . . . . . G 15.77 2.930378 0.52866 . . ENSG00000123124 ENST00000517970;ENST00000265428;ENST00000341922;ENST00000349423 . . . 5.31 5.31 0.75309 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 17.1564 0.86792 0.0:0.0:1.0:0.0 . . . . . -1 . . . + . . WWP1 87492882 1.000000 0.71417 0.992000 0.48379 0.603000 0.37013 4.394000 0.59671 2.492000 0.84095 0.650000 0.86243 . TCGA-RB-A7B8-01A-12D-A33T-08 WWP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000374755.1 0 0 0 8 362 0 51 0 0 0 0 51 2 0 0 0 0 0 2 1 9.888312e-01 7 357 0 51 2 0 0 0 0 51 2 -8.050176 1 1 0 0 1 0 0 0 1.939885 0 0.270000 2.180000 0.266037 0.160000 7.000000e-02 0.300000 0.160000 0.176919 0.160000 0 0.110000 0.230000 ABCA1 19 broad.mit.edu 37 9 107620844 107620844 + Nonsense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr9:107620844G>A ENST00000374736.3 - 7 1073 c.679C>T c.(679-681)Cga>Tga p.R227* ABCA1_ENST00000423487.2_Nonsense_Mutation_p.R227* NM_005502.3 NP_005493.2 O95477 ABCA1_HUMAN ATP-binding cassette, sub-family A (ABC1), member 1 115 Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599) CGAAGTACTCGCTCTGCTGCA 0.468000 0 SO:0001587 stop_gained ENST00000374736.3 0 1 hg19 CCDS6762.1 . . . . . . . . . . G 28.4 4.915688 0.92178 . . ENSG00000165029 ENST00000374736;ENST00000423487 . . . 6.17 3.26 0.37387 . 1.116260 0.06418 N 0.721847 . . . . . . 0.09310 N 0.999999 . . . . . . . . . . 0.09843 T 0.71 . 8.0132 0.30365 0.0726:0.0:0.5413:0.3861 . . . . X 227 . ENSP00000363868:R227X R - 1 2 ABCA1 106660665 0.015000 0.18098 0.018000 0.16275 0.002000 0.02628 0.895000 0.28363 0.924000 0.37069 0.655000 0.94253 CGA TCGA-RB-A7B8-01A-12D-A33T-08 ABCA1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000053491.1 0 0 1 90 439 1 103 0 2.059487e-01 0 5 1 103 2 0 0 0 0 0 2 1 1 89 436 1 103 18 0 0 0 1 103 2 -20.000000 1 1 0 0 1 0 1 1 1.636751 1 0.270000 2.180000 0.156069 0.950000 8.300000e-01 1.000000 0.990000 0.949173 0.950000 1 0.890000 0.990000 MELK 9833 broad.mit.edu 37 9 36665452 36665452 + Missense_Mutation SNP A A G TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr9:36665452A>G ENST00000298048.2 + 14 1466 c.1282A>G c.(1282-1284)Act>Gct p.T428A MELK_ENST00000541717.1_Missense_Mutation_p.T387A|MELK_ENST00000543751.1_Missense_Mutation_p.T396A|MELK_ENST00000536329.1_Missense_Mutation_p.T357A|MELK_ENST00000545008.1_Missense_Mutation_p.T357A|MELK_ENST00000538311.1_Missense_Mutation_p.T234A|MELK_ENST00000536987.1_Missense_Mutation_p.T297A|MELK_ENST00000536860.1_Missense_Mutation_p.T380A NM_014791.3 NP_055606.1 Q14680 MELK_HUMAN maternal embryonic leucine zipper kinase 29 Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06) STAD - Stomach adenocarcinoma(86;0.228) AAATGTATATACTCCTAAGTC 0.368000 Ovarian(82;980 1317 7225 14391 18624) 0 SO:0001583 missense ENST00000298048.2 1 1 hg19 CCDS6606.1 . . . . . . . . . . A 11.72 1.722290 0.30503 . . ENSG00000165304 ENST00000298048;ENST00000538311;ENST00000536987;ENST00000545008;ENST00000536860;ENST00000536329;ENST00000541717;ENST00000543751 T;T;T;T;T;T;T;T 0.71222 -0.37;0.61;0.41;0.94;0.32;-0.55;-0.37;-0.37 5.65 5.65 0.86999 . 0.373797 0.33110 N 0.005277 T 0.64305 0.2586 L 0.54323 1.7 0.30079 N 0.809352 B;B;B;B;B;B;B 0.22276 0.001;0.015;0.002;0.001;0.014;0.067;0.001 B;B;B;B;B;B;B 0.20767 0.002;0.007;0.011;0.006;0.021;0.031;0.002 T 0.58470 -0.7631 10 0.15499 T 0.54 -1.347 13.825 0.63346 1.0:0.0:0.0:0.0 . 348;357;380;387;357;396;428 B7Z1G6;F5H2R4;F5H0Y0;F5H689;A6P3A8;A6P3A7;Q14680 .;.;.;.;.;.;MELK_HUMAN A 428;234;297;357;380;357;387;396 ENSP00000298048:T428A;ENSP00000438226:T234A;ENSP00000439184:T297A;ENSP00000445452:T357A;ENSP00000439792:T380A;ENSP00000443550:T357A;ENSP00000437804:T387A;ENSP00000441596:T396A ENSP00000298048:T428A T + 1 0 MELK 36655452 0.976000 0.34144 0.997000 0.53966 0.749000 0.42624 3.706000 0.54830 2.146000 0.66826 0.528000 0.53228 ACT TCGA-RB-A7B8-01A-12D-A33T-08 MELK-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052428.3 1 0 1 68 332 0 65 1 6.323303e-01 5 7 0 65 2 0 0 0 0 0 2 1 1 67 332 0 65 2 0 0 0 0 65 2 -20.000000 1 1 0 0 1 0 0 0 1.933291 0 0.270000 2.180000 0.260010 0.990000 9.800000e-01 1.000000 1.000000 0.998608 0.990000 1 0.990000 1.000000 ANXA1 301 broad.mit.edu 37 9 75775738 75775738 + Missense_Mutation SNP A A T rs111698970 TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 A T A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chr9:75775738A>T ENST00000376911.1 + 5 1286 c.404A>T c.(403-405)gAt>gTt p.D135V ANXA1_ENST00000257497.6_Missense_Mutation_p.D135V P04083 ANXA1_HUMAN annexin A1 8 all_epithelial(88;2.54e-11) Amcinonide(DB00288)|Dexamethasone(DB01234)|Hydrocortisone(DB00741) ACTGATGAAGATACTCTAATT 0.358000 0 SO:0001583 missense ENST00000376911.1 1 1 hg19 CCDS6645.1 . . . . . . . . . . A 24.6 4.544955 0.86022 . . ENSG00000135046 ENST00000257497;ENST00000456643;ENST00000376911 T;T;T 0.03689 3.84;3.84;3.84 5.86 5.86 0.93980 Annexin repeat, conserved site (1); 0.087076 0.85682 D 0.000000 T 0.17323 0.0416 M 0.72353 2.195 0.80722 D 1 D 0.53885 0.963 D 0.69824 0.966 T 0.00150 -1.1986 10 0.44086 T 0.13 . 16.2565 0.82519 1.0:0.0:0.0:0.0 . 135 P04083 ANXA1_HUMAN V 135;146;135 ENSP00000257497:D135V;ENSP00000412489:D146V;ENSP00000366109:D135V ENSP00000257497:D135V D + 2 0 ANXA1 74965558 1.000000 0.71417 0.997000 0.53966 0.962000 0.63368 8.466000 0.90387 2.235000 0.73313 0.533000 0.62120 GAT TCGA-RB-A7B8-01A-12D-A33T-08 ANXA1-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000052665.1 1 0 1 135 624 0 113 1 1 151 457 0 113 2 0 0 0 0 0 2 1 1 135 618 0 113 2 0 0 0 0 113 2 -20.000000 1 1 0 0 1 0 0 0 1.929503 0 0.270000 2.180000 0.260010 0.990000 9.900000e-01 1.000000 1.000000 0.999981 0.990000 1 0.990000 1.000000 ARMCX3 51566 broad.mit.edu 37 X 100880318 100880318 + Missense_Mutation SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chrX:100880318G>A ENST00000341189.4 + 5 1215 c.349G>A c.(349-351)Gtt>Att p.V117I ARMCX3_ENST00000471229.2_Missense_Mutation_p.V117I|ARMCX3-AS1_ENST00000454228.1_RNA|RP4-545K15.5_ENST00000564612.1_RNA|ARMCX3_ENST00000537169.1_Missense_Mutation_p.V117I NM_016607.3 NP_057691.1 Q9UH62 ARMX3_HUMAN armadillo repeat containing, X-linked 3 11 AGATGATACCGTTTTGTCCCC 0.517000 0 SO:0001583 missense ENST00000341189.4 1 1 hg19 CCDS14489.1 . . . . . . . . . . G 0.008 -1.915094 0.00503 . . ENSG00000102401 ENST00000341189;ENST00000537169 T;T 0.28895 1.59;1.59 4.08 -5.45 0.02616 Armadillo-like helical (1); 0.708561 0.13313 N 0.397312 T 0.09113 0.0225 N 0.01640 -0.785 0.09310 N 1 B 0.12630 0.006 B 0.09377 0.004 T 0.35748 -0.9776 9 . . . -2.6702 12.8785 0.58003 0.2698:0.0:0.7302:0.0 . 117 Q9UH62 ARMX3_HUMAN I 117 ENSP00000340672:V117I;ENSP00000439032:V117I . V + 1 0 ARMCX3 100766974 0.031000 0.19500 0.318000 0.25279 0.907000 0.53573 -0.504000 0.06375 -1.484000 0.01856 -2.493000 0.00193 GTT TCGA-RB-A7B8-01A-12D-A33T-08 ARMCX3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057568.2 1 0 0 40 464 0 95 0 8.708759e-01 0 44 0 95 2 0 0 0 0 0 2 1 1 39 459 0 94 2 0 0 0 0 95 2 -10.778100 1 1 0 0 1 0 1 1 0.270000 2.180000 0.270000 0.580000 4.200000e-01 0.770000 0.580000 0.596982 0.580000 0 0.500000 0.680000 CXorf56 63932 broad.mit.edu 37 X 118699217 118699217 + Silent SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chrX:118699217G>A ENST00000371594.4 - 1 180 c.102C>T c.(100-102)tgC>tgT p.C34C CXorf56_ENST00000320339.4_5'UTR|CXorf56_ENST00000536133.1_Silent_p.C34C NM_022101.3 NP_071384.1 Q9H5V9 CX056_HUMAN chromosome X open reading frame 56 10 CCATCTGGCCGCACAAACAGT 0.577000 0 SO:0001819 synonymous_variant ENST00000371594.4 0 1 hg19 CCDS14579.1 TCGA-RB-A7B8-01A-12D-A33T-08 CXorf56-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding 0 0 0 6 649 0 68 0 5.199959e-02 0 33 0 68 2 0 0 0 0 0 2 1 9.644229e-01 7 644 0 67 2 0 0 0 0 68 2 -1.981537 0 1 0 0 1 0 1 1 0.270000 2.180000 0.270000 0.060000 2.000000e-02 0.140000 0.070000 0.078592 0.060000 0 0.040000 0.110000 GPC3 2719 broad.mit.edu 37 X 132730547 132730547 + Silent SNP G G A TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chrX:132730547G>A ENST00000370818.3 - 7 1939 c.1494C>T c.(1492-1494)tgC>tgT p.C498C GPC3_ENST00000394299.2_Silent_p.C521C|GPC3_ENST00000543339.1_Silent_p.C444C NM_001164618.1|NM_004484.3 NP_001158090.1|NP_004475.1 P51654 GPC3_HUMAN glypican 3 36 Acute lymphoblastic leukemia(192;0.000127) CATCATCACCGCAGTCTCCAC 0.463000 T, D, Mis, N, F, S Wilms tumour Simpson-Golabi-Behmel syndrome yes Rec/X Simpson-Golabi-Behmel syndrome X Xq26.1 2719 glypican 3 O 0 SO:0001819 synonymous_variant Familial Cancer Database SGBS ENST00000370818.3 0 1 hg19 CCDS14638.1 . . . . . . . . . . G 2.995 -0.207259 0.06180 . . ENSG00000147257 ENST00000406757 . . . 4.73 -9.46 0.00597 . . . . . T 0.72803 0.3506 . . . 0.48040 D 0.999576 . . . . . . T 0.82566 -0.0393 4 . . . . 22.4363 0.99971 0.2327:0.0:0.7673:0.0 . . . . V 228 . . A - 2 0 GPC3 132558213 0.000000 0.05858 0.008000 0.14137 0.665000 0.39181 -3.320000 0.00513 -3.839000 0.00100 -1.679000 0.00737 GCG TCGA-RB-A7B8-01A-12D-A33T-08 GPC3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000058356.1 0 0 0 6 854 0 109 0 1.058172e-01 0 66 0 109 2 0 0 0 0 0 2 1 9.649078e-01 6 853 0 109 2 0 0 0 0 109 2 -2.115266 0 1 121410 6 41 1 0 1 1 0.270000 2.180000 0.270000 0.050000 1.000000e-02 0.110000 0.060000 0.059967 0.050000 0 0.030000 0.080000 MAGEC2 51438 broad.mit.edu 37 X 141291654 141291654 + Silent SNP G G T TCGA-RB-A7B8-01A-12D-A33T-08 TCGA-RB-A7B8-10A-01D-A33W-08 Untested Somatic Phase_I WXS none Illumina GAIIx 6e601f5b-bebf-4205-9a88-48e18d07178c 8244dc39-8b03-44b8-bdee-7bf0c4d51f66 g.chrX:141291654G>T ENST00000247452.3 - 3 467 c.120C>A c.(118-120)tcC>tcA p.S40S NM_016249.3 NP_057333.1 Q9UBF1 MAGC2_HUMAN melanoma antigen family C, 2 47 Acute lymphoblastic leukemia(192;6.56e-05) AAGAGGCGGAGGAGGCTTCCT 0.522000 HNSCC(46;0.14) 0 SO:0001819 synonymous_variant ENST00000247452.3 1 1 hg19 CCDS14678.1 TCGA-RB-A7B8-01A-12D-A33T-08 MAGEC2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000058611.1 1 0 0 54 799 0 140 0 0 0 0 140 2 0 0 0 0 0 2 1 1 51 791 0 139 2 0 0 0 0 140 2 -9.367000 1 1 0 0 1 0 1 1 0.270000 2.180000 0.270000 0.460000 3.500000e-01 0.590000 0.470000 0.474981 0.460000 0 0.400000 0.530000