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 SORCS3 22986 broad.mit.edu 37 10 106924113 106924113 + Silent SNP C C T TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr10:106924113C>T ENST00000369701.3 + 12 2012 c.1785C>T c.(1783-1785)tcC>tcT p.S595S NM_014978.1 NP_055793.1 Q9UPU3 SORC3_HUMAN sortilin-related VPS10 domain containing receptor 3 131 Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191) TCATCTCCTCCGATGGGGGCA 0.433000 NSCLC(116;1497 1690 7108 13108 14106) 0 SO:0001819 synonymous_variant ENST00000369701.3 1 1 hg19 CCDS7558.1 TCGA-HZ-7919-01A-11D-2154-08 SORCS3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050221.1 0 0 0 6 299 0 35 0 0 0 0 35 2 0 0 0 0 0 2 1 0.963558 6 294 0 35 2 -2.949334 1 1 121406 23 44 1 1 2 3 2.086066 0 0.400000 1.870000 0.405941 0.100000 0.030000 1.000000 0.100000 0.148218 0.100000 0 0.060000 0.160000 INPP5F 22876 broad.mit.edu 37 10 121510593 121510593 + Missense_Mutation SNP G G A TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr10:121510593G>A ENST00000361976.2 + 2 269 c.103G>A c.(103-105)Gat>Aat p.D35N INPP5F_ENST00000369083.3_Missense_Mutation_p.D35N NM_014937.3 NP_055752.1 Q01968 OCRL_HUMAN inositol polyphosphate-5-phosphatase F 42 Lung NSC(174;0.109)|all_lung(145;0.142) TTTAGCTACTGATCTACTTCT 0.328000 OREG0020583 type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip) 0 SO:0001583 missense ENST00000361976.2 1 1 hg19 CCDS7616.1 . . . . . . . . . . G 29.1 4.981610 0.93044 . . ENSG00000198825 ENST00000361976;ENST00000369083 T;T 0.58797 0.81;0.31 6.08 6.08 0.98989 . 0.000000 0.85682 D 0.000000 T 0.74520 0.3727 L 0.59436 1.845 0.80722 D 1 D;D 0.67145 0.988;0.996 P;D 0.79784 0.815;0.993 T 0.73395 -0.3996 10 0.59425 D 0.04 -30.4133 19.4436 0.94836 0.0:0.0:1.0:0.0 . 35;35 Q9Y2H2;Q9Y2H2-3 SAC2_HUMAN;. N 35 ENSP00000354519:D35N;ENSP00000358079:D35N ENSP00000354519:D35N D + 1 0 INPP5F 121500583 1.000000 0.71417 0.994000 0.49952 0.979000 0.70002 7.483000 0.81158 2.894000 0.99253 0.591000 0.81541 GAT TCGA-HZ-7919-01A-11D-2154-08 INPP5F-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000050679.1 1 0 1 80 253 0 52 1 8.804175e-01 2 12 0 52 2 0 0 0 0 0 2 1 1.000000 80 252 0 52 2 -20.000000 1 1 0 0 1 1 2 3 2.086066 0 0.400000 1.870000 0.405941 0.990000 0.980000 1.000000 1.000000 0.998857 0.990000 1 0.990000 1.000000 ZNF259 0 broad.mit.edu 37 11 116652933 116652933 + Missense_Mutation SNP C C T TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr11:116652933C>T ENST00000227322.3 - 12 1179 c.1120G>A c.(1120-1122)Gac>Aac p.D374N NM_003904.3 NP_003895.1 O75312 ZPR1_HUMAN 9 all_hematologic(175;0.0487) all_cancers(61;1.72e-06)|all_epithelial(67;0.000735)|Melanoma(852;0.022)|Acute lymphoblastic leukemia(157;0.0255)|Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(158;0.0588) TTGGAACTGTCGCCCAGTGTG 0.458000 0 SO:0001583 missense ENST00000227322.3 0 1 hg19 CCDS8375.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. C|C 36|36 5.735372|5.735372 0.96865|0.96865 .|. .|. ENSG00000109917|ENSG00000109917 ENST00000227322|ENST00000429220 T|. 0.44881|. 0.91|. 6.02|6.02 6.02|6.02 0.97574|0.97574 Zinc finger, ZPR1-type (3);|. 0.000000|. 0.85682|. D|. 0.000000|. D|D 0.88343|0.88343 0.6411|0.6411 H|H 0.95780|0.95780 3.72|3.72 0.80722|0.80722 D|D 1|1 D|. 0.89917|. 1.0|. D|. 0.97110|. 1.0|. D|D 0.90566|0.90566 0.4519|0.4519 10|5 0.72032|. D|. 0.01|. -35.8364|-35.8364 20.5407|20.5407 0.99260|0.99260 0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0 .|. 374|. O75312|. ZPR1_HUMAN|. N|Q 374|300 ENSP00000227322:D374N|. ENSP00000227322:D374N|. D|R -|- 1|2 0|0 ZNF259|ZNF259 116158143|116158143 1.000000|1.000000 0.71417|0.71417 0.994000|0.994000 0.49952|0.49952 0.861000|0.861000 0.49209|0.49209 6.708000|6.708000 0.74660|0.74660 2.865000|2.865000 0.98341|0.98341 0.655000|0.655000 0.94253|0.94253 GAC|CGA TCGA-HZ-7919-01A-11D-2154-08 ZNF259-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000106283.2 0 0 0 8 339 0 39 1 9.106167e-01 8 175 0 39 2 0 0 0 0 0 2 1 0.989196 8 336 0 39 2 -2.637301 1 1 0 0 1 1 2 3 2.075745 0 0.400000 1.870000 0.402390 0.120000 0.050000 0.240000 0.120000 0.137433 0.120000 0 0.080000 0.170000 SIDT2 51092 broad.mit.edu 37 11 117058103 117058103 + Missense_Mutation SNP G G C TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr11:117058103G>C ENST00000324225.4 + 11 1556 c.1025G>C c.(1024-1026)cGa>cCa p.R342P SIDT2_ENST00000431081.2_Missense_Mutation_p.R346P NM_001040455.1 NP_001035545.1 Q8NBJ9 SIDT2_HUMAN SID1 transmembrane family, member 2 36 all_hematologic(175;0.0487) Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234) GGTCACCCTCGAGTCCTGGCT 0.522000 0 SO:0001583 missense ENST00000324225.4 1 1 hg19 CCDS31682.1 . . . . . . . . . . G 13.48 2.250742 0.39797 . . ENSG00000149577 ENST00000324225;ENST00000278951;ENST00000431081 T;T;T 0.18810 2.19;2.22;2.21 4.93 4.93 0.64822 . 0.308789 0.32473 N 0.006059 T 0.14830 0.0358 N 0.03154 -0.405 0.34842 D 0.740825 B;P;B;P 0.40032 0.416;0.699;0.324;0.471 B;B;P;P 0.48488 0.443;0.224;0.482;0.579 T 0.28364 -1.0046 10 0.33940 T 0.23 -23.5708 12.0315 0.53399 0.0826:0.0:0.9174:0.0 . 342;346;342;342 Q8NBJ9-2;F5H8L4;Q8NBJ9;C9JBG5 .;.;SIDT2_HUMAN;. P 342;342;346 ENSP00000314023:R342P;ENSP00000278951:R342P;ENSP00000399635:R346P ENSP00000278951:R342P R + 2 0 SIDT2 116563313 0.924000 0.31332 1.000000 0.80357 0.972000 0.66771 4.485000 0.60279 2.576000 0.86940 0.561000 0.74099 CGA TCGA-HZ-7919-01A-11D-2154-08 SIDT2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000392836.1 1 0 1 117 531 0 92 1 9.975743e-01 6 37 0 92 2 0 0 0 0 0 2 1 1.000000 116 526 0 91 2 -2.972818 1 1 0 0 1 1 2 3 2.075745 0 0.400000 1.870000 0.402390 0.900000 0.760000 1.000000 1.000000 0.905483 0.900000 1 0.820000 0.990000 ESAM 90952 broad.mit.edu 37 11 124626110 124626110 + Silent SNP T T C TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr11:124626110T>C ENST00000278927.5 - 4 729 c.600A>G c.(598-600)ccA>ccG p.P200P RP11-677M14.3_ENST00000504932.2_RNA|ESAM_ENST00000442070.2_Intron NM_138961.2 NP_620411.2 Q96AP7 ESAM_HUMAN endothelial cell adhesion molecule 16 all_hematologic(175;0.215) Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112) CACCTAATGCTGGTGCAAAGA 0.562000 0 SO:0001819 synonymous_variant ENST00000278927.5 1 1 hg19 CCDS8453.1 TCGA-HZ-7919-01A-11D-2154-08 ESAM-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000324686.1 1 0 1 53 162 0 31 1 1 10 98 0 31 2 0 0 0 0 0 2 1 1.000000 53 162 0 31 2 -20.000000 1 1 0 0 1 1 2 3 2.075745 0 0.400000 1.870000 0.402390 0.990000 0.960000 1.000000 1.000000 0.997660 0.990000 1 0.990000 1.000000 TCP11L1 55346 broad.mit.edu 37 11 33094069 33094069 + Silent SNP G G A TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr11:33094069G>A ENST00000334274.4 + 10 1777 c.1377G>A c.(1375-1377)caG>caA p.Q459Q TCP11L1_ENST00000531632.2_Silent_p.Q459Q|TCP11L1_ENST00000432887.1_Silent_p.Q459Q|TCP11L1_ENST00000324357.9_Silent_p.Q238Q NM_018393.3 NP_060863.3 Q9NUJ3 T11L1_HUMAN t-complex 11, testis-specific-like 1 6 CGGGTCATCAGAAGCCATTGC 0.463000 0 SO:0001819 synonymous_variant ENST00000334274.4 1 1 hg19 CCDS7882.1 . . . . . . . . . . G 8.692 0.907562 0.17833 . . ENSG00000176148 ENST00000528962 . . . 5.41 5.41 0.78517 . . . . . T 0.70919 0.3279 . . . 0.80722 D 1 . . . . . . T 0.69383 -0.5160 4 . . . -34.9109 14.752 0.69533 0.0:0.1444:0.8556:0.0 . . . . K 75 . . E + 1 0 TCP11L1 33050645 1.000000 0.71417 1.000000 0.80357 0.968000 0.65278 2.822000 0.48073 2.530000 0.85305 0.313000 0.20887 GAA TCGA-HZ-7919-01A-11D-2154-08 TCP11L1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000383377.4 1 0 1 192 875 0 109 1 9.967641e-01 16 25 0 109 2 0 0 0 0 0 2 1 1.000000 191 870 0 107 2 -20.000000 1 1 0 0 1 1 2 3 2.075745 0 0.400000 1.870000 0.402390 0.890000 0.780000 1.000000 1.000000 0.904446 0.890000 1 0.840000 0.970000 OR5T3 390154 broad.mit.edu 37 11 56019769 56019769 + Missense_Mutation SNP C C T TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr11:56019769C>T ENST00000303059.3 + 1 94 c.94C>T c.(94-96)Cca>Tca p.P32S NM_001004747.1 NP_001004747.1 Q8NGG3 OR5T3_HUMAN olfactory receptor, family 5, subfamily T, member 3 39 Esophageal squamous(21;0.00448) ATACAGGAATCCACTGAAGAA 0.358000 0 SO:0001583 missense ENST00000303059.3 1 1 hg19 CCDS31524.1 . . . . . . . . . . C 0.416 -0.910669 0.02434 . . ENSG00000172489 ENST00000303059 T 0.02197 4.4 4.23 -0.0294 0.13918 . 4.020620 0.00871 U 0.002031 T 0.01222 0.0040 N 0.04705 -0.18 0.09310 N 1 B 0.13594 0.008 B 0.09377 0.004 T 0.41893 -0.9483 10 0.07990 T 0.79 . 2.0557 0.03581 0.156:0.4868:0.1525:0.2047 . 32 Q8NGG3 OR5T3_HUMAN S 32 ENSP00000305403:P32S ENSP00000305403:P32S P + 1 0 OR5T3 55776345 0.000000 0.05858 0.001000 0.08648 0.001000 0.01503 -0.396000 0.07278 0.131000 0.18576 -0.366000 0.07423 CCA TCGA-HZ-7919-01A-11D-2154-08 OR5T3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000391599.1 1 0 1 89 307 0 49 0 0 0 0 49 2 0 0 0 0 0 2 1 1.000000 89 305 0 48 2 -4.205829 1 1 0 0 1 1 2 3 2.075745 0 0.400000 1.870000 0.402390 0.990000 0.920000 1.000000 1.000000 0.995244 0.990000 1 0.990000 1.000000 KRAS 3845 broad.mit.edu 37 12 25398285 25398285 + Missense_Mutation SNP C C G rs121913530 TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 C G C C Valid Somatic Phase_I WXS targeted Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr12:25398285C>G ENST00000256078.4 - 2 97 c.34G>C c.(34-36)Ggt>Cgt p.G12R KRAS_ENST00000556131.1_Missense_Mutation_p.G12R|KRAS_ENST00000557334.1_Missense_Mutation_p.G12R|KRAS_ENST00000311936.3_Missense_Mutation_p.G12R NM_033360.2 NP_203524.1 P01116 RASK_HUMAN Kirsten rat sarcoma viral oncogene homolog p.G12C(3001)|p.G12S(1288)|p.G12R(789)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12W(3)|p.A11_G12insGA(2)|p.G12Y(2)|p.G12N(1) UBE2L3/KRAS(2) 25349 all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12) OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05) CCTACGCCACCAGCTCCAACT 0.348000 G12C(CALU1_LUNG)|G12C(HCC44_LUNG)|G12C(IALM_LUNG)|G12C(KHM1B_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12C(KYSE410_OESOPHAGUS)|G12C(LU65_LUNG)|G12C(LU99_LUNG)|G12C(MIAPACA2_PANCREAS)|G12C(NCIH1373_LUNG)|G12C(NCIH1792_LUNG)|G12C(NCIH2030_LUNG)|G12C(NCIH2122_LUNG)|G12C(NCIH23_LUNG)|G12C(NCIH358_LUNG)|G12C(OV56_OVARY)|G12C(SW1463_LARGE_INTESTINE)|G12C(SW1573_LUNG)|G12C(SW837_LARGE_INTESTINE)|G12C(UMUC3_URINARY_TRACT)|G12R(CAL62_THYROID)|G12R(HS274T_BREAST)|G12R(HUPT3_PANCREAS)|G12R(KP2_PANCREAS)|G12R(PSN1_PANCREAS)|G12R(TCCPAN2_PANCREAS)|G12S(A549_LUNG)|G12S(KMS20_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12S(LS123_LARGE_INTESTINE) 119 Mis pancreatic, colorectal, lung, thyroid, AML, others Noonan syndrome;Cardiofaciocutaneous syndrome TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6) Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869) Dom yes 12 12p12.1 3845 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog L, E, M, O 5144 Substitution - Missense(5142)|Insertion - In frame(2) GRCh37 CM076251 KRAS M rs121913530 SO:0001583 missense Familial Cancer Database Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS ENST00000256078.4 1 1 hg19 CCDS8703.1 . . . . . . . . . . C 28.6 4.930538 0.92389 . . ENSG00000133703 ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131 T;T;T;T 0.78246 -1.16;-1.16;-1.16;-1.16 5.68 5.68 0.88126 Small GTP-binding protein domain (1); 0.000000 0.85682 D 0.000000 D 0.84893 0.5573 M 0.84082 2.675 0.80722 D 1 P;P 0.43287 0.802;0.741 B;P 0.47941 0.36;0.562 D 0.86658 0.1902 10 0.66056 D 0.02 . 18.3719 0.90409 0.0:1.0:0.0:0.0 . 12;12 P01116-2;P01116 .;RASK_HUMAN R 12 ENSP00000308495:G12R;ENSP00000452512:G12R;ENSP00000256078:G12R;ENSP00000451856:G12R ENSP00000256078:G12R G - 1 0 KRAS 25289552 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.743000 0.85020 2.668000 0.90789 0.563000 0.77884 GGT TCGA-HZ-7919-01A-11D-2154-08 KRAS-004 KNOWN not_organism_supported|basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000412232.1 1 0 1 36 82 0 14 1 9.999963e-01 26 25 0 14 2 1 1 182 495 0 402 2 1 1.000000 36 81 0 14 2 -20.000000 1 1 0 0 1 1 2 3 2.514875 1 0.400000 1.870000 0.500000 0.990000 0.990000 1.000000 1.000000 0.999996 0.990000 1 0.990000 1.000000 KCNA5 3741 broad.mit.edu 37 12 5155075 5155075 + Missense_Mutation SNP G G A TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr12:5155075G>A ENST00000252321.3 + 1 1991 c.1762G>A c.(1762-1764)Gtc>Atc p.V588I NM_002234.3 NP_002225.2 P22460 KCNA5_HUMAN potassium voltage-gated channel, shaker-related subfamily, member 5 52 Dalfampridine(DB06637) GAAGTGTAACGTCAAGGCCAA 0.592000 0 SO:0001583 missense ENST00000252321.3 1 1 hg19 CCDS8536.1 . . . . . . . . . . G 7.036 0.561517 0.13498 . . ENSG00000130037 ENST00000252321 D 0.97279 -4.32 5.5 3.64 0.41730 . 0.104471 0.38492 U 0.001664 D 0.87665 0.6234 N 0.01352 -0.895 0.21445 N 0.999687 B 0.06786 0.001 B 0.04013 0.001 T 0.78513 -0.2175 10 0.24483 T 0.36 . 9.733 0.40372 0.2849:0.5814:0.1337:0.0 . 588 P22460 KCNA5_HUMAN I 588 ENSP00000252321:V588I ENSP00000252321:V588I V + 1 0 KCNA5 5025336 0.990000 0.36364 1.000000 0.80357 0.936000 0.57629 0.640000 0.24705 0.668000 0.31126 -0.311000 0.09066 GTC TCGA-HZ-7919-01A-11D-2154-08 KCNA5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000398925.2 1 0 1 48 163 0 33 0 8.830963e-01 0 15 0 33 2 0 0 0 0 0 2 1 1.000000 48 161 0 33 2 -20.000000 1 1 0 0 1 0 1 1 1.673073 1 0.400000 1.870000 0.257426 0.880000 0.690000 1.000000 1.000000 0.884370 0.880000 1 0.780000 0.980000 KRT4 3851 broad.mit.edu 37 12 53202606 53202606 + Missense_Mutation SNP C C G TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr12:53202606C>G ENST00000551956.1 - 5 1355 c.863G>C c.(862-864)aGc>aCc p.S288T KRT4_ENST00000293774.4_Missense_Mutation_p.S362T|KRT4_ENST00000458244.2_Missense_Mutation_p.S268T P19013 K2C4_HUMAN keratin 4 29 GGACGTGTCGCTGACATGGGT 0.577000 Pancreas(190;284 2995 41444 45903) 0 SO:0001583 missense ENST00000551956.1 1 1 hg19 CCDS41787.2 . . . . . . . . . . C 10.42 1.346494 0.24426 . . ENSG00000170477 ENST00000551956;ENST00000293774;ENST00000458244 D;T;D 0.88975 -2.45;-1.16;-2.45 5.75 1.28 0.21552 Filament (1); 0.601484 0.14726 N 0.302055 D 0.93109 0.7806 M 0.83012 2.62 0.09310 N 1 P 0.46277 0.875 P 0.49953 0.627 D 0.88388 0.3006 10 0.87932 D 0 . 22.2785 0.99969 0.0:0.2887:0.7113:0.0 . 302 P19013 K2C4_HUMAN T 288;362;268 ENSP00000448220:S288T;ENSP00000293774:S362T;ENSP00000387904:S268T ENSP00000293774:S362T S - 2 0 KRT4 51488873 0.954000 0.32549 0.007000 0.13788 0.290000 0.27261 1.644000 0.37228 0.329000 0.23460 0.655000 0.94253 AGC TCGA-HZ-7919-01A-11D-2154-08 KRT4-001 KNOWN upstream_ATG|basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000405931.1 1 0 1 87 363 0 75 1 8.156212e-01 12 3 0 75 2 0 0 0 0 0 2 1 1.000000 87 361 0 75 2 -20.000000 1 0 0 0 1 1 2 3 2.087795 0 0.400000 1.870000 0.405941 0.970000 0.790000 1.000000 1.000000 0.953336 0.970000 1 0.880000 1.000000 PRIM1 5557 broad.mit.edu 37 12 57144844 57144844 + Missense_Mutation SNP A A G TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr12:57144844A>G ENST00000338193.6 - 2 275 c.239T>C c.(238-240)aTa>aCa p.I80T HSD17B6_ENST00000554150.1_5'Flank|HSD17B6_ENST00000555805.1_5'Flank|HSD17B6_ENST00000554643.1_5'Flank|HSD17B6_ENST00000555159.1_5'Flank|PRIM1_ENST00000552408.1_5'UTR NM_000946.2 NP_000937.1 P49642 PRI1_HUMAN primase, DNA, polypeptide 1 (49kDa) 8 TACTGCGCCTATATCAATCTT 0.328000 0 SO:0001583 missense ENST00000338193.6 0 1 hg19 CCDS44926.1 . . . . . . . . . . A 22.9 4.350526 0.82132 . . ENSG00000198056 ENST00000537418;ENST00000338193;ENST00000550770 T;T 0.55052 0.54;0.6 5.16 5.16 0.70880 . 0.049442 0.85682 D 0.000000 T 0.77532 0.4144 M 0.92880 3.355 0.80722 D 1 D;D 0.65815 0.995;0.971 D;P 0.69142 0.962;0.821 T 0.82989 -0.0183 10 0.59425 D 0.04 -11.0372 14.3283 0.66534 1.0:0.0:0.0:0.0 . 80;80 F8VSB2;P49642 .;PRI1_HUMAN T 80;80;83 ENSP00000350491:I80T;ENSP00000450185:I83T ENSP00000350491:I80T I - 2 0 PRIM1 55431111 1.000000 0.71417 0.998000 0.56505 0.943000 0.58893 8.801000 0.91905 2.100000 0.63781 0.454000 0.30748 ATA TCGA-HZ-7919-01A-11D-2154-08 PRIM1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000406956.1 1 0 0 11 62 0 8 1 8.825210e-01 9 15 0 8 2 0 0 0 0 0 2 1 0.998774 11 62 0 8 2 -19.767750 1 1 0 0 1 1 2 3 2.087795 0 0.400000 1.870000 0.405941 0.780000 0.420000 1.000000 1.000000 0.780151 0.780000 0 0.580000 1.000000 CD163L1 283316 broad.mit.edu 37 12 7531847 7531847 + Missense_Mutation SNP C C A TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr12:7531847C>A ENST00000313599.3 - 9 2155 c.2098G>T c.(2098-2100)Gct>Tct p.A700S CD163L1_ENST00000396630.1_Missense_Mutation_p.A700S|CD163L1_ENST00000544331.1_5'UTR|CD163L1_ENST00000416109.2_Missense_Mutation_p.A710S Q9NR16 C163B_HUMAN CD163 molecule-like 1 96 ACTTTTCCAGCACACCTGCTG 0.463000 0 SO:0001583 missense ENST00000313599.3 0 1 hg19 CCDS8577.1 . . . . . . . . . . C 16.36 3.100219 0.56183 . . ENSG00000177675 ENST00000313599;ENST00000416109;ENST00000396630 T;T;T 0.34667 1.35;1.35;1.35 2.79 1.87 0.25490 Speract/scavenger receptor (2);Speract/scavenger receptor-related (2); 0.483859 0.14903 U 0.291704 T 0.29976 0.0750 N 0.17922 0.545 0.23331 N 0.997896 P;D 0.55605 0.926;0.972 P;P 0.57152 0.73;0.814 T 0.11891 -1.0569 10 0.10636 T 0.68 . 6.9468 0.24522 0.0:0.8482:0.0:0.1518 . 710;700 E7EVK4;Q9NR16 .;C163B_HUMAN S 700;710;700 ENSP00000315945:A700S;ENSP00000393474:A710S;ENSP00000379871:A700S ENSP00000315945:A700S A - 1 0 CD163L1 7423114 0.103000 0.21917 0.599000 0.28851 0.548000 0.35241 -0.006000 0.12833 1.492000 0.48499 0.455000 0.32223 GCT TCGA-HZ-7919-01A-11D-2154-08 CD163L1-001 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000399329.1 0 0 0 8 286 0 41 0 2.995674e-03 0 3 0 41 2 0 0 0 0 0 2 1 0.989336 8 284 0 41 2 -3.643158 1 1 0 0 1 0 1 1 1.673073 1 0.400000 1.870000 0.257426 0.110000 0.050000 0.200000 0.110000 0.121636 0.110000 0 0.070000 0.160000 GPR12 2835 broad.mit.edu 37 13 27333003 27333003 + Missense_Mutation SNP G G A TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr13:27333003G>A ENST00000381436.2 - 1 1424 c.962C>T c.(961-963)cCg>cTg p.P321L GPR12_ENST00000405846.3_Missense_Mutation_p.P321L P47775 GPR12_HUMAN G protein-coupled receptor 12 33 Colorectal(5;5.77e-05) Breast(139;0.198) GAGACTGGACGGGATGCAGCC 0.557000 0 SO:0001583 missense ENST00000381436.2 0 1 hg19 CCDS9319.1 . . . . . . . . . . G 19.81 3.896130 0.72639 . . ENSG00000132975 ENST00000405846;ENST00000381436 T;T 0.36157 1.27;1.27 5.49 5.49 0.81192 . 0.000000 0.85682 D 0.000000 T 0.41971 0.1182 L 0.58101 1.795 0.80722 D 1 D 0.53885 0.963 B 0.43082 0.407 T 0.44787 -0.9305 10 0.62326 D 0.03 . 19.3487 0.94376 0.0:0.0:1.0:0.0 . 321 P47775 GPR12_HUMAN L 321 ENSP00000384932:P321L;ENSP00000370844:P321L ENSP00000370844:P321L P - 2 0 GPR12 26231003 1.000000 0.71417 0.819000 0.32651 0.982000 0.71751 9.739000 0.98837 2.594000 0.87642 0.511000 0.50034 CCG TCGA-HZ-7919-01A-11D-2154-08 GPR12-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000044257.2 0 0 0 8 332 0 37 0 0 0 0 37 2 0 0 0 0 0 2 1 0.988792 8 326 0 35 2 -3.127367 1 1 121412 1 26 1 0 2 2 2.034786 1 0.400000 1.870000 0.400000 0.120000 0.050000 0.220000 0.120000 0.130983 0.120000 0 0.080000 0.170000 MDGA2 161357 broad.mit.edu 37 14 47504469 47504469 + Missense_Mutation SNP A A T TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr14:47504469A>T ENST00000399232.2 - 8 1721 c.1357T>A c.(1357-1359)Ttg>Atg p.L453M MDGA2_ENST00000357362.3_Missense_Mutation_p.L224M|MDGA2_ENST00000426342.1_Missense_Mutation_p.L224M|MDGA2_ENST00000439988.3_Missense_Mutation_p.L522M NM_001113498.2 NP_001106970.3 Q7Z553 MDGA2_HUMAN MAM domain containing glycosylphosphatidylinositol anchor 2 76 CTGGTGACCAATGGTGATTTT 0.378000 0 SO:0001583 missense ENST00000399232.2 0 1 hg19 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. A|A 10.99|10.99 1.506599|1.506599 0.26949|0.26949 .|. .|. ENSG00000139915|ENSG00000139915 ENST00000554762|ENST00000439988;ENST00000426342;ENST00000399232;ENST00000357362 .|T;T;T;T .|0.68624 .|-0.34;-0.34;-0.34;-0.34 5.52|5.52 1.83|1.83 0.25207|0.25207 .|Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1); .|0.154328 .|0.28470 .|U .|0.015227 T|T 0.50171|0.50171 0.1600|0.1600 L|L 0.33710|0.33710 1.025|1.025 0.80722|0.80722 D|D 1|1 .|B;B .|0.33528 .|0.234;0.416 .|B;B .|0.35114 .|0.087;0.196 T|T 0.37079|0.37079 -0.9721|-0.9721 5|10 .|0.52906 .|T .|0.07 .|. 4.4546|4.4546 0.11637|0.11637 0.5216:0.0:0.3346:0.1439|0.5216:0.0:0.3346:0.1439 .|. .|224;453 .|F6W3S7;Q7Z553 .|.;MDGA2_HUMAN N|M 227|453;224;522;224 .|ENSP00000400011:L453M;ENSP00000405456:L224M;ENSP00000382178:L522M;ENSP00000349925:L224M .|ENSP00000349925:L224M I|L -|- 2|1 0|2 MDGA2|MDGA2 46574219|46574219 0.995000|0.995000 0.38212|0.38212 0.999000|0.999000 0.59377|0.59377 0.971000|0.971000 0.66376|0.66376 1.154000|1.154000 0.31688|0.31688 0.068000|0.068000 0.16574|0.16574 -0.512000|-0.512000 0.04463|0.04463 ATT|TTG TCGA-HZ-7919-01A-11D-2154-08 MDGA2-001 KNOWN upstream_ATG|basic|appris_principal protein_coding protein_coding OTTHUMT00000073352.5 0 0 0 10 479 0 70 0 0 0 0 70 2 0 0 0 0 0 2 1 0.996776 10 474 0 70 2 -3.136223 1 1 0 0 1 0 0 0 2.009772 0 0.400000 1.870000 0.385246 0.100000 0.040000 0.180000 0.100000 0.108970 0.100000 0 0.070000 0.140000 TTLL5 23093 broad.mit.edu 37 14 76330128 76330128 + Nonsense_Mutation SNP C C T TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr14:76330128C>T ENST00000298832.9 + 29 3650 c.3445C>T c.(3445-3447)Caa>Taa p.Q1149* TTLL5_ENST00000557636.1_Nonsense_Mutation_p.Q1164*|TTLL5_ENST00000556893.1_Nonsense_Mutation_p.Q700*|TTLL5_ENST00000554510.1_Nonsense_Mutation_p.Q658* NM_015072.4 NP_055887.3 Q6EMB2 TTLL5_HUMAN tubulin tyrosine ligase-like family, member 5 50 CTATCAGCTTCAATTTGCCCT 0.522000 0 SO:0001587 stop_gained ENST00000298832.9 0 1 hg19 CCDS32124.1 . . . . . . . . . . C 43 10.490315 0.99415 . . ENSG00000119685 ENST00000286653;ENST00000557636;ENST00000298832;ENST00000393826;ENST00000556893;ENST00000554510 . . . 5.78 5.78 0.91487 . 0.432376 0.27424 N 0.019434 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.41790 T 0.15 . 14.9992 0.71459 0.1417:0.8583:0.0:0.0 . . . . X 223;1164;1149;700;700;658 . ENSP00000286653:Q223X Q + 1 0 TTLL5 75399881 0.991000 0.36638 0.999000 0.59377 0.945000 0.59286 2.927000 0.48900 2.894000 0.99253 0.655000 0.94253 CAA TCGA-HZ-7919-01A-11D-2154-08 TTLL5-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000414453.1 1 0 1 161 623 0 104 1 9.999535e-01 8 49 0 104 2 0 0 0 0 0 2 1 1.000000 159 608 0 104 2 -20.000000 1 1 0 0 1 0 0 0 2.009772 0 0.400000 1.870000 0.385246 0.990000 0.860000 1.000000 1.000000 0.973715 0.990000 1 0.920000 1.000000 DUOXA2 405753 broad.mit.edu 37 15 45406819 45406819 + Missense_Mutation SNP G G A TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr15:45406819G>A ENST00000323030.5 + 1 301 c.16G>A c.(16-18)Ggc>Agc p.G6S DUOX2_ENST00000603300.1_5'Flank|DUOX2_ENST00000389039.6_5'Flank NM_207581.3 NP_997464.2 Q1HG44 DOXA2_HUMAN dual oxidase maturation factor 2 all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027) CCTGTGGAACGGCGTACTGCC 0.632000 0 SO:0001583 missense ENST00000323030.5 1 1 hg19 CCDS10118.2 . . . . . . . . . . G 19.49 3.836709 0.71373 . . ENSG00000140274 ENST00000323030;ENST00000350243 T 0.57752 0.38 4.98 4.06 0.47325 . 0.262703 0.39475 N 0.001347 T 0.54159 0.1841 L 0.32530 0.975 0.46185 D 0.998911 D 0.76494 0.999 P 0.56088 0.791 T 0.56001 -0.8051 10 0.52906 T 0.07 -18.908 12.4824 0.55852 0.0813:0.0:0.9186:0.0 . 6 Q1HG44 DOXA2_HUMAN S 6 ENSP00000319705:G6S ENSP00000319705:G6S G + 1 0 DUOXA2 43194111 1.000000 0.71417 0.040000 0.18447 0.274000 0.26718 5.890000 0.69774 1.231000 0.43661 0.591000 0.81541 GGC TCGA-HZ-7919-01A-11D-2154-08 DUOXA2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254142.1 1 0 1 43 170 0 27 1 1 107 142 0 27 2 0 0 0 0 0 2 1 1.000000 42 165 0 27 2 -3.493627 1 1 121410 1 33 1 1 2 3 2.059272 0 0.400000 1.870000 0.401198 0.990000 0.750000 1.000000 1.000000 0.954320 0.990000 1 0.870000 1.000000 GLCE 26035 broad.mit.edu 37 15 69553486 69553486 + Missense_Mutation SNP A A C TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 A C A A Valid Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr15:69553486A>C ENST00000261858.2 + 4 875 c.647A>C c.(646-648)cAg>cCg p.Q216P GLCE_ENST00000559420.2_Missense_Mutation_p.Q152P|GLCE_ENST00000559500.1_3'UTR NM_015554.1 NP_056369.1 O94923 GLCE_HUMAN glucuronic acid epimerase 18 CAGATTGCACAGTATGGATTA 0.373000 0 SO:0001583 missense ENST00000261858.2 1 1 hg19 CCDS32277.1 . . . . . . . . . . A 22.4 4.278449 0.80692 . . ENSG00000138604 ENST00000261858 T 0.59502 0.26 5.94 5.94 0.96194 . 0.000000 0.85682 D 0.000000 T 0.76905 0.4053 M 0.81942 2.565 0.80722 D 1 D 0.61697 0.99 D 0.70487 0.969 T 0.80238 -0.1465 10 0.87932 D 0 -8.1086 15.2185 0.73288 1.0:0.0:0.0:0.0 . 216 O94923 GLCE_HUMAN P 216 ENSP00000261858:Q216P ENSP00000261858:Q216P Q + 2 0 GLCE 67340540 1.000000 0.71417 1.000000 0.80357 0.991000 0.79684 9.198000 0.94994 2.265000 0.75225 0.482000 0.46254 CAG TCGA-HZ-7919-01A-11D-2154-08 GLCE-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding 1 0 1 114 352 0 68 1 9.994562e-01 14 23 0 68 2 0 0 0 0 0 2 1 1.000000 114 348 0 68 2 -20.000000 1 1 0 0 1 1 2 3 2.059272 0 0.400000 1.870000 0.401198 0.990000 0.990000 1.000000 1.000000 0.999734 0.990000 1 0.990000 1.000000 THSD4 79875 broad.mit.edu 37 15 71704038 71704038 + Missense_Mutation SNP G G A TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr15:71704038G>A ENST00000355327.3 + 7 1162 c.1028G>A c.(1027-1029)cGc>cAc p.R343H THSD4_ENST00000261862.6_Missense_Mutation_p.R343H Q6ZMP0 THSD4_HUMAN thrombospondin, type I, domain containing 4 42 AAAGGCAATCGCAAATGTGAG 0.423000 0 SO:0001583 missense ENST00000355327.3 0 1 hg19 CCDS10238.2 1 4.578754578754579E-4 0 0.0 0 0.0 1 0.0017482517482517483 0 0.0 G 13.95 2.390891 0.42410 . . ENSG00000187720 ENST00000355327;ENST00000261862 T;T 0.71817 -0.6;-0.6 5.47 3.37 0.38596 . 0.225081 0.38605 N 0.001633 T 0.54532 0.1864 N 0.13168 0.305 0.27987 N 0.935816 D;B 0.59357 0.985;0.013 P;B 0.49683 0.619;0.003 T 0.51608 -0.8684 10 0.54805 T 0.06 . 2.8813 0.05648 0.2513:0.0:0.5304:0.2183 . 343;343 Q6ZMP0-2;Q6ZMP0 .;THSD4_HUMAN H 343 ENSP00000347484:R343H;ENSP00000261862:R343H ENSP00000261862:R343H R + 2 0 THSD4 69491092 1.000000 0.71417 1.000000 0.80357 0.677000 0.39632 1.507000 0.35758 1.324000 0.45282 -0.142000 0.14014 CGC TCGA-HZ-7919-01A-11D-2154-08 THSD4-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000257253.2 0 0 0 48 191 0 32 1 9.784606e-01 7 19 0 32 2 0 0 0 0 0 2 1 1.000000 48 185 0 32 2 -20.000000 1 1 120904 1 26 1 1 2 3 2.059272 0 0.400000 1.870000 0.401198 0.990000 0.760000 1.000000 1.000000 0.954636 0.990000 1 0.870000 1.000000 ARIH1 25820 broad.mit.edu 37 15 72858942 72858942 + Missense_Mutation SNP G G A TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr15:72858942G>A ENST00000379887.4 + 8 1264 c.950G>A c.(949-951)tGt>tAt p.C317Y NM_005744.3 NP_005735.2 Q9Y4X5 ARI1_HUMAN ariadne RBR E3 ubiquitin protein ligase 1 14 CCTGTTAAATGTAAGGTGAGT 0.318000 0 SO:0001583 missense ENST00000379887.4 0 1 hg19 CCDS10244.1 . . . . . . . . . . G 24.8 4.572572 0.86542 . . ENSG00000166233 ENST00000379887;ENST00000299305 D 0.94280 -3.39 5.27 5.27 0.74061 Zinc finger, C6HC-type (2);Zinc finger, RING-type (1); 0.000000 0.85682 D 0.000000 D 0.98257 0.9423 H 0.99026 4.405 0.80722 D 1 D 0.76494 0.999 D 0.68353 0.957 D 0.99809 1.1040 10 0.87932 D 0 . 18.9619 0.92680 0.0:0.0:1.0:0.0 . 317 Q9Y4X5 ARI1_HUMAN Y 317;287 ENSP00000369217:C317Y ENSP00000299305:C287Y C + 2 0 ARIH1 70645996 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 9.204000 0.95041 2.460000 0.83146 0.644000 0.83932 TGT TCGA-HZ-7919-01A-11D-2154-08 ARIH1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000257350.1 0 0 0 11 598 0 80 1 4.380575e-01 4 73 0 80 2 0 0 0 0 0 2 1 0.998291 11 594 0 79 2 -3.096007 1 1 0 0 1 1 2 3 2.059272 0 0.400000 1.870000 0.401198 0.090000 0.040000 0.160000 0.090000 0.098158 0.090000 0 0.060000 0.130000 BNC1 646 broad.mit.edu 37 15 83926674 83926674 + Silent SNP C C T TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr15:83926674C>T ENST00000345382.2 - 5 2590 c.2505G>A c.(2503-2505)acG>acA p.T835T BNC1_ENST00000569704.1_Silent_p.T828T|RP11-382A20.4_ENST00000565495.1_RNA NM_001717.3 NP_001708.3 Q01954 BNC1_HUMAN basonuclin 1 56 TGTGGACTTGCGTTATTGGGT 0.517000 0 SO:0001819 synonymous_variant ENST00000345382.2 1 1 hg19 CCDS10324.1 TCGA-HZ-7919-01A-11D-2154-08 BNC1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000304006.1 1 0 1 76 367 0 87 0 0 0 0 87 2 0 0 0 0 0 2 1 1.000000 76 362 0 87 2 -20.000000 1 1 0 0 1 1 2 3 2.060585 0 0.400000 1.870000 0.401198 0.850000 0.690000 1.000000 1.000000 0.860995 0.850000 1 0.760000 0.950000 AKAP13 11214 broad.mit.edu 37 15 86212982 86212982 + Silent SNP T T C TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr15:86212982T>C ENST00000394518.2 + 14 5117 c.5022T>C c.(5020-5022)ttT>ttC p.F1674F AKAP13_ENST00000361243.2_Silent_p.F1678F|AKAP13_ENST00000560579.1_3'UTR|RP11-815J21.4_ENST00000558980.1_RNA NM_001270546.1|NM_007200.4 NP_001257475.1|NP_009131.2 Q12802 AKP13_HUMAN A kinase (PRKA) anchor protein 13 98 AGCAGGGATTTAATTACTGTA 0.348000 Melanoma(94;603 1453 3280 32295 32951) 0 SO:0001819 synonymous_variant ENST00000394518.2 1 1 hg19 CCDS32319.1 TCGA-HZ-7919-01A-11D-2154-08 AKAP13-004 KNOWN basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000417318.1 1 0 1 83 392 0 56 1 9.999996e-01 42 59 0 56 2 0 0 0 0 0 2 1 1.000000 82 386 0 56 2 -20.000000 1 1 0 0 1 1 2 3 2.060585 0 0.400000 1.870000 0.401198 0.870000 0.700000 1.000000 1.000000 0.875690 0.870000 1 0.780000 0.970000 ITGAL 3683 broad.mit.edu 37 16 30505643 30505643 + Missense_Mutation SNP G G A TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr16:30505643G>A ENST00000356798.6 + 12 1504 c.1324G>A c.(1324-1326)Gga>Aga p.G442R ITGAL_ENST00000358164.5_Missense_Mutation_p.G359R|ITGAL_ENST00000433423.2_Intron|ITGAL_ENST00000568012.1_3'UTR NM_002209.2 NP_002200.2 P20701 ITAL_HUMAN integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide) 76 Antithymocyte globulin(DB00098)|Efalizumab(DB00095)|Lovastatin(DB00227) GCCACAGGGCGGAGGACACTG 0.647000 NSCLC(110;1462 1641 3311 33990 49495) 0 SO:0001583 missense ENST00000356798.6 1 1 hg19 CCDS32433.1 . . . . . . . . . . G 11.55 1.671567 0.29693 . . ENSG00000005844 ENST00000356798;ENST00000358164 T;T 0.10860 2.83;2.83 5.67 -11.3 0.00108 . 2.121790 0.01509 N 0.017858 T 0.07007 0.0178 L 0.31157 0.91 0.09310 N 1 B;B 0.16802 0.015;0.019 B;B 0.11329 0.004;0.006 T 0.09079 -1.0691 10 0.25751 T 0.34 . 9.7973 0.40742 0.0953:0.1684:0.6527:0.0836 . 359;442 Q96HB1;P20701 .;ITAL_HUMAN R 442;359 ENSP00000349252:G442R;ENSP00000350886:G359R ENSP00000349252:G442R G + 1 0 ITGAL 30413144 0.000000 0.05858 0.000000 0.03702 0.000000 0.00434 -0.357000 0.07651 -2.335000 0.00629 -1.012000 0.02466 GGA TCGA-HZ-7919-01A-11D-2154-08 ITGAL-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000434508.2 1 0 1 147 189 0 56 0 9.705919e-01 0 10 0 56 2 0 0 0 0 0 2 1 1.000000 147 184 0 55 2 -20.000000 1 1 121402 4 34 1 0 2 2 2.076500 1 0.400000 1.870000 0.400000 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 ZNF174 7727 broad.mit.edu 37 16 3452365 3452365 + Missense_Mutation SNP G G A TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr16:3452365G>A ENST00000268655.4 + 1 946 c.361G>A c.(361-363)Gtg>Atg p.V121M ZSCAN32_ENST00000439568.2_5'Flank|ZSCAN32_ENST00000304926.3_5'Flank|ZSCAN32_ENST00000396852.4_5'Flank|ZNF174_ENST00000571936.1_Missense_Mutation_p.V121M|ZSCAN32_ENST00000422427.2_5'Flank|ZNF174_ENST00000344823.5_Missense_Mutation_p.V121M|ZSCAN32_ENST00000573830.1_5'Flank|ZNF174_ENST00000572544.1_Missense_Mutation_p.V121M|ZNF174_ENST00000575752.1_Missense_Mutation_p.V121M NM_003450.2 NP_003441.1 Q15697 ZN174_HUMAN zinc finger protein 174 12 TGTGACCCTCGTGGAAGATTT 0.498000 0 SO:0001583 missense ENST00000268655.4 1 1 hg19 CCDS10504.1 . . . . . . . . . . G 13.92 2.380339 0.42207 . . ENSG00000103343 ENST00000344823;ENST00000268655 T;T 0.07021 3.23;3.23 4.5 4.5 0.54988 Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3); 0.000000 0.43747 D 0.000531 T 0.25232 0.0613 M 0.71206 2.165 0.36337 D 0.859256 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.79108 0.986;0.992;0.973 T 0.03761 -1.1006 10 0.87932 D 0 . 10.9404 0.47270 0.0:0.1892:0.8108:0.0 . 121;121;121 Q15697;Q15697-2;Q8IZN5 ZN174_HUMAN;.;. M 121 ENSP00000339781:V121M;ENSP00000268655:V121M ENSP00000268655:V121M V + 1 0 ZNF174 3392366 1.000000 0.71417 1.000000 0.80357 0.772000 0.43724 3.912000 0.56386 2.790000 0.95986 0.655000 0.94253 GTG TCGA-HZ-7919-01A-11D-2154-08 ZNF174-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000251510.1 1 0 0 32 575 0 66 0 2.754438e-01 0 19 0 66 2 0 0 0 0 0 2 1 1.000000 30 571 0 65 2 -6.228818 1 1 0 0 1 0 2 2 2.090281 1 0.400000 1.870000 0.400000 0.260000 0.180000 0.360000 0.260000 0.270253 0.260000 0 0.210000 0.310000 CDH11 1009 broad.mit.edu 37 16 64981819 64981819 + Missense_Mutation SNP C C T TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 C T C C Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr16:64981819C>T ENST00000268603.4 - 13 2693 c.2078G>A c.(2077-2079)cGc>cAc p.R693H CDH11_ENST00000394156.3_3'UTR|CDH11_ENST00000566827.1_Missense_Mutation_p.R567H NM_001797.2 NP_001788.2 P55287 CAD11_HUMAN cadherin 11, type 2, OB-cadherin (osteoblast) 88 Ovarian(137;0.0973) GATGTCTTTGCGGGGGATAAA 0.488000 T USP6 aneurysmal bone cysts TSP Lung(24;0.17) Dom yes 16 16q22.1 1009 cadherin 11, type 2, OB-cadherin (osteoblast) M 0 SO:0001583 missense ENST00000268603.4 1 1 hg19 CCDS10803.1 . . . . . . . . . . C 25.0 4.591103 0.86851 . . ENSG00000140937 ENST00000268603;ENST00000538390 T 0.78924 -1.22 6.17 6.17 0.99709 Cadherin, cytoplasmic domain (1); 0.000000 0.85682 D 0.000000 D 0.90549 0.7038 M 0.88241 2.94 0.80722 D 1 D 0.89917 1.0 D 0.79784 0.993 D 0.91017 0.4854 10 0.87932 D 0 . 19.8676 0.96824 0.0:1.0:0.0:0.0 . 693 P55287 CAD11_HUMAN H 693;676 ENSP00000268603:R693H ENSP00000268603:R693H R - 2 0 CDH11 63539320 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 7.818000 0.86416 2.941000 0.99782 0.655000 0.94253 CGC TCGA-HZ-7919-01A-11D-2154-08 CDH11-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268755.1 1 0 1 290 475 0 116 0 1 0 260 0 116 2 0 0 0 0 0 2 1 1.000000 288 471 0 114 2 -20.000000 1 1 121412 1 32 1 0 2 2 2.051423 1 0.400000 1.870000 0.400000 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 ST3GAL2 6483 broad.mit.edu 37 16 70415640 70415640 + Missense_Mutation SNP G G C TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr16:70415640G>C ENST00000393640.4 - 6 3112 c.1005C>G c.(1003-1005)atC>atG p.I335M RP11-529K1.4_ENST00000566960.1_RNA|ST3GAL2_ENST00000342907.2_Missense_Mutation_p.I335M Q16842 SIA4B_HUMAN ST3 beta-galactoside alpha-2,3-sialyltransferase 2 11 Ovarian(137;0.0694) CCAGCATGTCGATGATGTGGG 0.667000 0 SO:0001583 missense ENST00000393640.4 1 1 hg19 CCDS10890.1 . . . . . . . . . . g 22.1 4.248254 0.80024 . . ENSG00000157350 ENST00000342907;ENST00000393640 T;T 0.32515 1.45;1.45 6.07 -2.78 0.05859 . 0.042535 0.85682 D 0.000000 T 0.42131 0.1189 M 0.76727 2.345 0.49798 D 0.999827 D 0.63880 0.993 P 0.59487 0.858 T 0.41716 -0.9493 10 0.66056 D 0.02 -32.3009 7.3993 0.26954 0.4899:0.0:0.4023:0.1078 . 335 Q16842 SIA4B_HUMAN M 335 ENSP00000345477:I335M;ENSP00000377257:I335M ENSP00000345477:I335M I - 3 3 ST3GAL2 68973141 0.170000 0.23016 0.988000 0.46212 0.670000 0.39368 -0.349000 0.07731 -0.283000 0.09115 -0.224000 0.12420 ATC TCGA-HZ-7919-01A-11D-2154-08 ST3GAL2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000268968.1 1 0 1 137 262 0 47 1 9.312713e-01 4 7 0 47 2 0 0 0 0 0 2 1 1.000000 136 260 0 46 2 -20.000000 1 1 0 0 1 0 2 2 2.051423 1 0.400000 1.870000 0.400000 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 MBTPS1 8720 broad.mit.edu 37 16 84120998 84120998 + Missense_Mutation SNP T T C TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 T C T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr16:84120998T>C ENST00000343411.3 - 9 1594 c.1099A>G c.(1099-1101)Atc>Gtc p.I367V MBTPS1_ENST00000569770.1_5'UTR NM_003791.2 NP_003782.1 Q14703 MBTP1_HUMAN membrane-bound transcription factor peptidase, site 1 41 AAGCGGGCGATGTTATCTTCA 0.408000 0 SO:0001583 missense ENST00000343411.3 1 1 hg19 CCDS10941.1 . . . . . . . . . . T 16.00 2.997441 0.54147 . . ENSG00000140943 ENST00000343411 T 0.38887 1.11 5.26 5.26 0.73747 Peptidase S8/S53, subtilisin/kexin/sedolisin (3); 0.000000 0.85682 D 0.000000 T 0.36441 0.0967 N 0.12569 0.235 0.80722 D 1 B 0.34103 0.437 P 0.44422 0.449 T 0.36456 -0.9747 10 0.44086 T 0.13 -27.4813 15.4764 0.75485 0.0:0.0:0.0:1.0 . 367 Q14703 MBTP1_HUMAN V 367 ENSP00000344223:I367V ENSP00000344223:I367V I - 1 0 MBTPS1 82678499 1.000000 0.71417 1.000000 0.80357 0.975000 0.68041 7.972000 0.88022 2.113000 0.64589 0.460000 0.39030 ATC TCGA-HZ-7919-01A-11D-2154-08 MBTPS1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000269080.2 1 0 1 94 362 0 55 1 1 45 159 0 55 2 0 0 0 0 0 2 1 1.000000 93 356 0 55 2 -20.000000 1 1 121412 2 32 1 0 2 2 2.078655 1 0.400000 1.870000 0.400000 0.990000 0.840000 1.000000 1.000000 0.977037 0.990000 1 0.930000 1.000000 FANCA 2175 broad.mit.edu 37 16 89838200 89838200 + Silent SNP C C T TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr16:89838200C>T ENST00000389301.3 - 23 2067 c.2037G>A c.(2035-2037)gtG>gtA p.V679V FANCA_ENST00000568369.1_Silent_p.V679V|FANCA_ENST00000567284.2_5'UTR NM_000135.2 NP_000126.2 O15360 FANCA_HUMAN Fanconi anemia, complementation group A 47 Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194) TTTCAGAAATCACTGCCACCT 0.527000 D, Mis, N, F, S AML, leukemia Involved in tolerance or repair of DNA crosslinks Fanconi Anemia yes Rec Fanconi anaemia A 16 16q24.3 2175 Fanconi anemia, complementation group A L 0 SO:0001819 synonymous_variant Familial Cancer Database Pancytopenia Dysmelia, FA (several complementation groups) ENST00000389301.3 1 1 hg19 CCDS32515.1 TCGA-HZ-7919-01A-11D-2154-08 FANCA-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000421927.1 1 0 1 150 201 0 51 1 9.662978e-01 5 5 0 51 2 0 0 0 0 0 2 1 1.000000 147 201 0 50 2 -20.000000 1 1 0 0 1 0 2 2 2.078655 1 0.400000 1.870000 0.400000 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 ALDH3A2 224 broad.mit.edu 37 17 19575061 19575061 + Missense_Mutation SNP G G T TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 G T G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr17:19575061G>T ENST00000176643.6 + 9 1681 c.1235G>T c.(1234-1236)gGa>gTa p.G412V ALDH3A2_ENST00000571163.1_Intron|ALDH3A2_ENST00000581518.1_Missense_Mutation_p.G412V|ALDH3A2_ENST00000339618.4_Missense_Mutation_p.G412V|ALDH3A2_ENST00000395575.2_Missense_Mutation_p.G412V|ALDH3A2_ENST00000579855.1_Missense_Mutation_p.G412V P51648 AL3A2_HUMAN aldehyde dehydrogenase 3 family, member A2 13 all_cancers(12;1.39e-05)|all_epithelial(12;0.00158)|Breast(13;0.245) GCTTATCACGGAAAACATAGT 0.413000 0 SO:0001583 missense ENST00000176643.6 1 1 hg19 CCDS11210.1 . . . . . . . . . . G 41 8.756577 0.98941 . . ENSG00000072210 ENST00000176643;ENST00000395575;ENST00000339618 D;D;D 0.89123 -2.47;-2.47;-2.47 6.06 6.06 0.98353 Aldehyde dehydrogenase domain (1);Aldehyde/histidinol dehydrogenase (1); 0.000000 0.85682 D 0.000000 D 0.96543 0.8872 H 0.95402 3.665 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.91635 0.999;0.999 D 0.96956 0.9698 10 0.87932 D 0 -23.5621 19.6125 0.95613 0.0:0.0:1.0:0.0 . 412;412 P51648;P51648-2 AL3A2_HUMAN;. V 412 ENSP00000176643:G412V;ENSP00000378942:G412V;ENSP00000345774:G412V ENSP00000176643:G412V G + 2 0 ALDH3A2 19515653 1.000000 0.71417 0.993000 0.49108 0.773000 0.43773 8.292000 0.89930 2.879000 0.98667 0.650000 0.86243 GGA TCGA-HZ-7919-01A-11D-2154-08 ALDH3A2-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000132268.1 1 0 1 96 493 0 71 1 1 37 106 0 71 2 0 0 0 0 0 2 1 1.000000 94 488 0 71 2 -20.000000 1 1 0 0 1 1 2 3 2.083920 0 0.400000 1.870000 0.404762 0.820000 0.670000 1.000000 0.820000 0.829754 0.820000 0 0.740000 0.910000 MXRA7 439921 broad.mit.edu 37 17 74681156 74681156 + Missense_Mutation SNP C C G TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr17:74681156C>G ENST00000355797.3 - 3 506 c.498G>C c.(496-498)caG>caC p.Q166H MXRA7_ENST00000592148.1_Missense_Mutation_p.Q209H|MXRA7_ENST00000585519.1_Missense_Mutation_p.Q11H|MXRA7_ENST00000589082.1_Missense_Mutation_p.Q11H|MXRA7_ENST00000375036.2_Missense_Mutation_p.Q166H|MXRA7_ENST00000588114.1_Missense_Mutation_p.Q11H|MXRA7_ENST00000449428.2_Missense_Mutation_p.Q166H NM_001008528.1 NP_001008528.1 P84157 MXRA7_HUMAN matrix-remodelling associated 7 6 CAGCCTACCTCTGCTCCTCCT 0.622000 0 SO:0001583 missense ENST00000355797.3 1 1 hg19 CCDS32745.1 . . . . . . . . . . C 11.22 1.573895 0.28092 . . ENSG00000182534 ENST00000355797;ENST00000449428;ENST00000375036;ENST00000392488 T;T;T 0.35236 1.32;1.32;1.32 5.27 1.74 0.24563 . 0.144210 0.46758 N 0.000267 T 0.21427 0.0516 N 0.25647 0.755 0.22629 N 0.998912 B;B;B 0.25390 0.125;0.063;0.063 B;B;B 0.26202 0.067;0.037;0.037 T 0.13150 -1.0520 10 0.49607 T 0.09 -18.8343 4.6255 0.12476 0.0:0.5361:0.1835:0.2804 . 166;166;166 P84157-2;P84157-3;P84157 .;.;MXRA7_HUMAN H 166 ENSP00000348050:Q166H;ENSP00000391466:Q166H;ENSP00000364176:Q166H ENSP00000348050:Q166H Q - 3 2 MXRA7 72192751 1.000000 0.71417 1.000000 0.80357 0.971000 0.66376 0.740000 0.26188 0.590000 0.29694 0.462000 0.41574 CAG TCGA-HZ-7919-01A-11D-2154-08 MXRA7-007 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000450983.1 1 0 1 224 721 0 128 1 1 16 333 0 128 2 0 0 0 0 0 2 1 1.000000 222 709 0 127 2 -5.631252 1 1 0 0 1 0 1 1 1.659738 1 0.400000 1.870000 0.250000 0.930000 0.830000 1.000000 0.950000 0.931515 0.930000 1 0.880000 0.980000 RBBP8 5932 broad.mit.edu 37 18 20516852 20516852 + Missense_Mutation SNP C C G TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr18:20516852C>G ENST00000399722.2 + 2 389 c.38C>G c.(37-39)tCt>tGt p.S13C RBBP8_ENST00000360790.5_Missense_Mutation_p.S13C|RBBP8_ENST00000399725.2_Missense_Mutation_p.S13C|RBBP8_ENST00000327155.5_Missense_Mutation_p.S13C NM_203291.1 NP_976036.1 Q99708 COM1_HUMAN retinoblastoma binding protein 8 24 all_cancers(21;4.34e-05)|all_epithelial(16;8.3e-07)|Lung NSC(20;0.0107)|Colorectal(14;0.0202)|all_lung(20;0.0291)|Ovarian(20;0.19) OV - Ovarian serous cystadenocarcinoma(1;0.00196) AGCCCTAACTCTGCAGATACA 0.358000 Homologous recombination 0 SO:0001583 missense ENST00000399722.2 1 1 hg19 CCDS11875.1 . . . . . . . . . . C 22.7 4.322656 0.81580 . . ENSG00000101773 ENST00000327155;ENST00000399725;ENST00000399722;ENST00000399721;ENST00000360790 T;T;T;T;T 0.45276 1.16;0.9;1.16;0.93;1.16 5.42 5.42 0.78866 . 0.144596 0.48286 D 0.000188 T 0.64450 0.2599 M 0.66939 2.045 0.80722 D 1 D;D;D 0.89917 1.0;1.0;1.0 D;D;D 0.87578 0.998;0.998;0.998 T 0.67150 -0.5743 10 0.87932 D 0 -13.2429 17.4189 0.87508 0.0:1.0:0.0:0.0 . 13;13;13 E7ETY1;A6NKN2;Q99708 .;.;COM1_HUMAN C 13 ENSP00000323050:S13C;ENSP00000382630:S13C;ENSP00000382628:S13C;ENSP00000382627:S13C;ENSP00000354024:S13C ENSP00000323050:S13C S + 2 0 RBBP8 18770850 1.000000 0.71417 1.000000 0.80357 0.989000 0.77384 3.710000 0.54860 2.525000 0.85131 0.655000 0.94253 TCT TCGA-HZ-7919-01A-11D-2154-08 RBBP8-004 KNOWN alternative_5_UTR|basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000446387.1 1 0 1 289 582 0 98 1 1 33 42 0 98 2 0 0 0 0 0 2 1 1.000000 285 579 0 98 2 -19.997520 1 1 0 0 1 1 2 3 2.499969 1 0.400000 1.870000 0.500000 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 FHOD3 80206 broad.mit.edu 37 18 34289290 34289290 + Silent SNP G G A TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr18:34289290G>A ENST00000359247.4 + 14 1893 c.1893G>A c.(1891-1893)tcG>tcA p.S631S FHOD3_ENST00000587493.1_3'UTR|FHOD3_ENST00000591635.1_Intron|FHOD3_ENST00000590592.1_Silent_p.S823S|FHOD3_ENST00000445677.1_Silent_p.S610S|FHOD3_ENST00000257209.4_Silent_p.S648S NM_001281739.1 NP_001268668.1 Q2V2M9 FHOD3_HUMAN formin homology 2 domain containing 3 90 all_epithelial(2;0.0181)|Colorectal(2;0.0195) CCAGCGTCTCGTCCTCCAGCA 0.567000 0 SO:0001819 synonymous_variant ENST00000359247.4 1 1 hg19 TCGA-HZ-7919-01A-11D-2154-08 FHOD3-001 PUTATIVE basic protein_coding protein_coding OTTHUMT00000460884.1 0 0 0 9 253 0 28 1 1.643716e-01 3 16 0 28 2 0 0 0 0 0 2 1 0.994246 9 251 0 27 2 -10.260900 1 1 121412 1 34 1 0 1 1 1.689471 1 0.400000 1.870000 0.253731 0.140000 0.060000 0.250000 0.140000 0.150569 0.140000 0 0.090000 0.190000 SMAD4 4089 broad.mit.edu 37 18 48604787 48604787 + Missense_Mutation SNP G G C TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 G C G G Valid Somatic Phase_I WXS targeted Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr18:48604787G>C ENST00000342988.3 + 12 2147 c.1609G>C c.(1609-1611)Gac>Cac p.D537H SMAD4_ENST00000588745.1_Missense_Mutation_p.D441H|SMAD4_ENST00000586253.1_3'UTR|SMAD4_ENST00000398417.2_Missense_Mutation_p.D537H NM_005359.5 NP_005350.1 Q13485 SMAD4_HUMAN SMAD family member 4 p.0?(36)|p.D537Y(3)|p.?(2)|p.L536fs*11(1)|p.L536fs*14(1) 454 all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336) CCAGCTCCTAGACGAAGTACT 0.488000 43 Whole gene deletion(36)|Substitution - Missense(3)|Deletion - Frameshift(2)|Unknown(2) SO:0001583 missense ENST00000342988.3 1 1 hg19 CCDS11950.1 . . . . . . . . . . G 19.95 3.921809 0.73213 . . ENSG00000141646 ENST00000342988;ENST00000398417 D;D 0.98075 -4.7;-4.7 6.07 6.07 0.98685 SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (1); 0.000000 0.85682 D 0.000000 D 0.99133 0.9701 M 0.93420 3.415 0.80722 D 1 D 0.89917 1.0 D 0.91635 0.999 D 0.99323 1.0907 10 0.87932 D 0 . 19.4308 0.94765 0.0:0.0:1.0:0.0 . 537 Q13485 SMAD4_HUMAN H 537 ENSP00000341551:D537H;ENSP00000381452:D537H ENSP00000341551:D537H D + 1 0 SMAD4 46858785 1.000000 0.71417 0.972000 0.41901 0.957000 0.61999 9.633000 0.98432 2.885000 0.99019 0.655000 0.94253 GAC TCGA-HZ-7919-01A-11D-2154-08 SMAD4-201 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000255993.3 1 0 1 98 308 0 78 1 1 29 71 0 78 2 1 1 84 317 0 341 2 1 1.000000 97 307 0 77 2 -4.948732 1 1 0 0 1 0 1 1 1.689471 1 0.400000 1.870000 0.253731 0.930000 0.790000 1.000000 1.000000 0.930178 0.930000 1 0.860000 0.990000 SH3GL1 6455 broad.mit.edu 37 19 4364084 4364084 + Splice_Site SNP C C T TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr19:4364084C>T ENST00000269886.3 - 5 644 c.e5+1 AC007292.6_ENST00000594444.1_RNA|SH3GL1_ENST00000598564.1_Splice_Site|SH3GL1_ENST00000417295.2_Splice_Site NM_003025.3 NP_003016.1 Q99961 SH3G1_HUMAN SH3-domain GRB2-like 1 26 AGGAGCAGCACCTGGATCTCC 0.647000 T MLL AL NSCLC(94;1152 2133 30346 33362) Dom yes 19 19p13.3 6455 SH3-domain GRB2-like 1 (EEN) L 0 SO:0001630 splice_region_variant ENST00000269886.3 1 1 hg19 CCDS32874.1 . . . . . . . . . . . 21.9 4.212855 0.79352 . . ENSG00000141985 ENST00000269886;ENST00000417295 . . . 4.98 4.98 0.66077 . . . . . . . . . . . 0.80722 D 1 . . . . . . . . . . . . . . 17.2215 0.86958 0.0:1.0:0.0:0.0 . . . . . -1 . . . - . . SH3GL1 4315084 1.000000 0.71417 0.994000 0.49952 0.761000 0.43186 7.773000 0.85462 2.315000 0.78130 0.561000 0.74099 . TCGA-HZ-7919-01A-11D-2154-08 SH3GL1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000458302.1 1 0 1 45 177 0 36 1 4.365776e-01 6 1 0 36 2 0 0 0 0 0 2 1 1.000000 45 176 0 36 2 -20.000000 1 1 0 0 1 1 2 3 2.071686 0 0.400000 1.870000 0.402390 0.990000 0.760000 1.000000 1.000000 0.958266 0.990000 1 0.880000 1.000000 LMTK3 114783 broad.mit.edu 37 19 49000674 49000674 + Nonsense_Mutation SNP G G A TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr19:49000674G>A ENST00000600059.1 - 11 3879 c.3652C>T c.(3652-3654)Cag>Tag p.Q1218* LMTK3_ENST00000270238.3_Nonsense_Mutation_p.Q1247* Q96Q04 LMTK3_HUMAN lemur tyrosine kinase 3 16 all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113) CTGTTCCCCTGAGGGGGTCCC 0.662000 0 SO:0001587 stop_gained ENST00000600059.1 0 1 hg19 . . . . . . . . . . G 42 9.180309 0.99091 . . ENSG00000142235 ENST00000270238 . . . 3.8 3.8 0.43715 . 0.399027 0.19919 N 0.103125 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.31617 T 0.26 . 11.3704 0.49696 0.0:0.0:1.0:0.0 . . . . X 1247 . ENSP00000270238:Q1247X Q - 1 0 LMTK3 53692486 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 2.540000 0.45727 2.134000 0.65973 0.563000 0.77884 CAG TCGA-HZ-7919-01A-11D-2154-08 LMTK3-002 KNOWN not_organism_supported|basic|appris_principal protein_coding protein_coding OTTHUMT00000466137.1 1 0 1 83 386 0 65 1 2.918281e-01 2 4 0 65 2 0 0 0 0 0 2 1 1.000000 83 382 0 64 2 -3.370307 1 1 0 0 1 1 2 3 2.099785 0 0.400000 1.870000 0.407115 0.890000 0.720000 1.000000 1.000000 0.898291 0.890000 1 0.800000 1.000000 SPHK2 56848 broad.mit.edu 37 19 49129495 49129495 + Silent SNP C C T TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr19:49129495C>T ENST00000245222.4 + 3 753 c.387C>T c.(385-387)cgC>cgT p.R129R SPHK2_ENST00000600537.1_Silent_p.R70R|AC022154.7_ENST00000600303.1_RNA|SPHK2_ENST00000599748.1_Silent_p.R93R|AC022154.7_ENST00000594850.1_RNA|AC022154.7_ENST00000598735.1_RNA|SPHK2_ENST00000599033.1_3'UTR|SPHK2_ENST00000443164.1_Silent_p.R191R|SPHK2_ENST00000599029.1_Silent_p.R93R|SPHK2_ENST00000601712.1_Silent_p.R93R|SPHK2_ENST00000598088.1_Silent_p.R129R|SPHK2_ENST00000340932.3_Silent_p.R93R NM_001204158.2|NM_001243876.1|NM_020126.4 NP_001191087.1|NP_001230805.1|NP_064511.2 Q9NRA0 SPHK2_HUMAN sphingosine kinase 2 19 all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113) gggcccggcgcAGAGCCACTC 0.701000 0 SO:0001819 synonymous_variant ENST00000245222.4 1 1 hg19 CCDS12727.1 TCGA-HZ-7919-01A-11D-2154-08 SPHK2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000466153.1 1 0 1 37 98 0 10 0 0 1 0 0 10 2 0 0 0 0 0 2 1 1.000000 35 97 0 10 2 -20.000000 1 1 0 0 1 1 2 3 2.099785 0 0.400000 1.870000 0.407115 0.990000 0.990000 1.000000 1.000000 0.999139 0.990000 1 0.990000 1.000000 PALMD 54873 broad.mit.edu 37 1 100111897 100111897 + Missense_Mutation SNP G G C TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr1:100111897G>C ENST00000263174.4 + 1 399 c.24G>C c.(22-24)aaG>aaC p.K8N PALMD_ENST00000605497.1_Missense_Mutation_p.K8N NM_017734.4 NP_060204.1 Q9NP74 PALMD_HUMAN palmdelphin 31 all_epithelial(167;0.000813)|all_lung(203;0.0214)|Lung NSC(277;0.0216) AGCTGGTGAAGGGAAGACTCC 0.517000 0 SO:0001583 missense ENST00000263174.4 1 1 hg19 CCDS758.1 . . . . . . . . . . G 14.76 2.631881 0.46944 . . ENSG00000099260 ENST00000263174 T 0.22945 1.93 5.52 3.66 0.41972 . 0.171232 0.49916 D 0.000127 T 0.23133 0.0559 L 0.59436 1.845 0.53005 D 0.999967 D 0.54047 0.964 P 0.52672 0.706 T 0.02603 -1.1135 10 0.87932 D 0 -11.1216 9.9661 0.41725 0.2732:0.0:0.7268:0.0 . 8 Q9NP74 PALMD_HUMAN N 8 ENSP00000263174:K8N ENSP00000263174:K8N K + 3 2 PALMD 99884485 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 2.717000 0.47227 0.702000 0.31825 0.561000 0.74099 AAG TCGA-HZ-7919-01A-11D-2154-08 PALMD-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000029672.1 1 0 1 94 551 0 76 0 8.820106e-01 0 24 0 76 2 0 0 0 0 0 2 1 1.000000 92 545 0 75 2 -2.402428 0 1 0 0 1 1 2 3 2.095766 0 0.400000 1.870000 0.407115 0.730000 0.600000 1.000000 0.740000 0.753436 0.730000 0 0.660000 0.830000 KIF1B 23095 broad.mit.edu 37 1 10425167 10425167 + Missense_Mutation SNP G G C TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr1:10425167G>C ENST00000377086.1 + 42 4578 c.4376G>C c.(4375-4377)aGa>aCa p.R1459T KIF1B_ENST00000377081.1_Missense_Mutation_p.R1459T|KIF1B_ENST00000263934.6_Missense_Mutation_p.R1413T O60333 KIF1B_HUMAN kinesin family member 1B 71 Ovarian(185;0.203) all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255) GGTATGCAGAGAAGGAGAAGA 0.393000 0 SO:0001583 missense ENST00000377086.1 1 1 hg19 . . . . . . . . . . G 28.4 4.919984 0.92249 . . ENSG00000054523 ENST00000355249;ENST00000263934;ENST00000377086;ENST00000377081 T;T;T 0.77620 -1.01;-1.11;-1.11 5.29 5.29 0.74685 . 0.000000 0.85682 D 0.000000 D 0.87196 0.6117 M 0.62723 1.935 0.80722 D 1 D;D;D;D;D;D 0.89917 0.999;0.999;1.0;0.991;1.0;0.981 D;D;D;D;D;D 0.85130 0.997;0.996;0.996;0.992;0.997;0.943 D 0.88273 0.2931 10 0.87932 D 0 . 18.9755 0.92735 0.0:0.0:1.0:0.0 . 1445;1419;1459;1433;1459;1413 Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2 .;.;.;.;KIF1B_HUMAN;. T 1459;1413;1459;1459 ENSP00000263934:R1413T;ENSP00000366290:R1459T;ENSP00000366284:R1459T ENSP00000263934:R1413T R + 2 0 KIF1B 10347754 1.000000 0.71417 1.000000 0.80357 0.985000 0.73830 9.869000 0.99810 2.458000 0.83093 0.650000 0.86243 AGA TCGA-HZ-7919-01A-11D-2154-08 KIF1B-001 NOVEL basic protein_coding protein_coding OTTHUMT00000005102.1 1 0 1 44 274 0 35 1 8.446035e-01 5 18 0 35 2 0 0 0 0 0 2 1 1.000000 41 269 0 35 2 -20.000000 1 0 0 0 1 1 2 3 2.106042 0 0.400000 1.870000 0.408284 0.700000 0.520000 1.000000 0.700000 0.725801 0.700000 0 0.610000 0.830000 KIF1B 23095 broad.mit.edu 37 1 10425187 10425187 + Missense_Mutation SNP G G C TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr1:10425187G>C ENST00000377086.1 + 42 4598 c.4396G>C c.(4396-4398)Gat>Cat p.D1466H KIF1B_ENST00000377081.1_Missense_Mutation_p.D1466H|KIF1B_ENST00000263934.6_Missense_Mutation_p.D1420H O60333 KIF1B_HUMAN kinesin family member 1B 71 Ovarian(185;0.203) all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255) AAAAATCTTAGATACGTCAGT 0.448000 0 SO:0001583 missense ENST00000377086.1 1 1 hg19 . . . . . . . . . . G 27.4 4.828534 0.90955 . . ENSG00000054523 ENST00000355249;ENST00000263934;ENST00000377086;ENST00000377081 T;T;T 0.80393 -1.27;-1.36;-1.37 5.29 5.29 0.74685 . 0.000000 0.85682 D 0.000000 D 0.89846 0.6833 M 0.73962 2.25 0.80722 D 1 D;D;D;D;D;D 0.89917 1.0;1.0;1.0;1.0;1.0;1.0 D;D;D;D;D;D 0.91635 0.999;0.999;0.999;0.999;0.999;0.996 D 0.90856 0.4735 10 0.87932 D 0 . 18.9755 0.92735 0.0:0.0:1.0:0.0 . 1452;1426;1466;1440;1466;1420 Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2 .;.;.;.;KIF1B_HUMAN;. H 1466;1420;1466;1466 ENSP00000263934:D1420H;ENSP00000366290:D1466H;ENSP00000366284:D1466H ENSP00000263934:D1420H D + 1 0 KIF1B 10347774 1.000000 0.71417 0.999000 0.59377 0.957000 0.61999 9.869000 0.99810 2.458000 0.83093 0.650000 0.86243 GAT TCGA-HZ-7919-01A-11D-2154-08 KIF1B-001 NOVEL basic protein_coding protein_coding OTTHUMT00000005102.1 1 0 1 54 313 0 36 0 7.375224e-01 1 16 0 36 2 0 0 0 0 0 2 1 1.000000 51 308 0 36 2 -20.000000 1 0 0 0 1 1 2 3 2.106042 0 0.400000 1.870000 0.408284 0.750000 0.570000 1.000000 0.740000 0.766273 0.750000 0 0.650000 0.870000 KIF1B 23095 broad.mit.edu 37 1 10425500 10425500 + Missense_Mutation SNP G G A TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr1:10425500G>A ENST00000377086.1 + 43 4748 c.4546G>A c.(4546-4548)Gag>Aag p.E1516K KIF1B_ENST00000377081.1_Missense_Mutation_p.E1516K|KIF1B_ENST00000263934.6_Missense_Mutation_p.E1470K O60333 KIF1B_HUMAN kinesin family member 1B 71 Ovarian(185;0.203) all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255) GCTGCTGCGTGAGAGACTTGG 0.507000 0 SO:0001583 missense ENST00000377086.1 1 1 hg19 . . . . . . . . . . G 25.9 4.685715 0.88639 . . ENSG00000054523 ENST00000355249;ENST00000263934;ENST00000377086;ENST00000377081 T;T;T 0.74106 -0.74;-0.81;-0.81 5.48 5.48 0.80851 . 0.109676 0.64402 D 0.000010 D 0.84880 0.5570 M 0.67397 2.05 0.80722 D 1 P;P;P;D;P;B 0.65815 0.627;0.954;0.485;0.995;0.856;0.241 B;P;B;D;B;B 0.67548 0.242;0.541;0.146;0.952;0.193;0.051 D 0.83946 0.0314 10 0.42905 T 0.14 . 19.3772 0.94517 0.0:0.0:1.0:0.0 . 1502;1476;1516;1490;1516;1470 Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2 .;.;.;.;KIF1B_HUMAN;. K 1516;1470;1516;1516 ENSP00000263934:E1470K;ENSP00000366290:E1516K;ENSP00000366284:E1516K ENSP00000263934:E1470K E + 1 0 KIF1B 10348087 1.000000 0.71417 1.000000 0.80357 0.997000 0.91878 9.861000 0.99562 2.560000 0.86352 0.650000 0.86243 GAG TCGA-HZ-7919-01A-11D-2154-08 KIF1B-001 NOVEL basic protein_coding protein_coding OTTHUMT00000005102.1 1 0 1 69 290 0 51 1 9.943889e-01 5 31 0 51 2 0 0 0 0 0 2 1 1.000000 60 254 0 49 2 -3.347118 1 1 0 0 1 1 2 3 2.106042 0 0.400000 1.870000 0.408284 0.970000 0.770000 1.000000 1.000000 0.949555 0.970000 1 0.870000 1.000000 ANGPTL7 10218 broad.mit.edu 37 1 11252354 11252354 + Missense_Mutation SNP A A G TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr1:11252354A>G ENST00000376819.3 + 2 643 c.404A>G c.(403-405)tAc>tGc p.Y135C MTOR_ENST00000361445.4_Intron NM_021146.2 NP_066969.1 O43827 ANGL7_HUMAN angiopoietin-like 7 10 Ovarian(185;0.249) Renal(390;0.000469)|Lung NSC(185;0.000818)|all_lung(284;0.00105)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731) TCTTCCCTCTACCAGAAGAAC 0.502000 0 SO:0001583 missense ENST00000376819.3 1 1 hg19 CCDS128.1 . . . . . . . . . . A 22.5 4.304749 0.81247 . . ENSG00000171819 ENST00000376819 T 0.77358 -1.09 6.17 6.17 0.99709 Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1); 0.162445 0.56097 D 0.000024 D 0.87075 0.6087 M 0.80508 2.5 0.54753 D 0.999986 D 0.69078 0.997 D 0.68353 0.957 D 0.87855 0.2660 10 0.54805 T 0.06 . 11.8437 0.52371 0.8695:0.0:0.0:0.1305 . 135 O43827 ANGL7_HUMAN C 135 ENSP00000366015:Y135C ENSP00000366015:Y135C Y + 2 0 ANGPTL7 11174941 1.000000 0.71417 0.999000 0.59377 0.991000 0.79684 5.667000 0.68067 2.371000 0.80710 0.533000 0.62120 TAC TCGA-HZ-7919-01A-11D-2154-08 ANGPTL7-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000005564.1 1 0 1 124 461 0 106 0 1.172165e-01 0 3 0 106 2 0 0 0 0 0 2 1 1.000000 123 458 0 105 2 -20.000000 1 1 0 0 1 1 2 3 2.106042 0 0.400000 1.870000 0.408284 0.990000 0.910000 1.000000 1.000000 0.992217 0.990000 1 0.980000 1.000000 RSBN1 54665 broad.mit.edu 37 1 114340098 114340098 + Missense_Mutation SNP G G C TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr1:114340098G>C ENST00000261441.5 - 2 1327 c.1264C>G c.(1264-1266)Ctc>Gtc p.L422V NM_018364.3 NP_060834.2 Q5VWQ0 RSBN1_HUMAN round spermatid basic protein 1 29 Lung SC(450;0.184) all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05) AAGTCTGGGAGATAAGCAGCC 0.393000 0 SO:0001583 missense ENST00000261441.5 1 1 hg19 CCDS862.1 . . . . . . . . . . G 14.61 2.586901 0.46110 . . ENSG00000081019 ENST00000261441 . . . 5.95 5.95 0.96441 . 0.000000 0.85682 D 0.000000 T 0.73636 0.3612 M 0.81802 2.56 0.58432 D 0.999999 D 0.67145 0.996 D 0.75484 0.986 T 0.77490 -0.2568 9 0.87932 D 0 -8.013 10.3789 0.44099 0.1484:0.0:0.8516:0.0 . 422 Q5VWQ0 RSBN1_HUMAN V 422 . ENSP00000261441:L422V L - 1 0 RSBN1 114141621 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 4.716000 0.61916 2.824000 0.97209 0.655000 0.94253 CTC TCGA-HZ-7919-01A-11D-2154-08 RSBN1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000033022.2 1 0 1 46 260 0 54 1 9.247564e-01 6 21 0 54 2 0 0 0 0 0 2 1 1.000000 46 255 0 54 2 -20.000000 1 1 0 0 1 1 2 3 2.081241 0 0.400000 1.870000 0.404762 0.760000 0.570000 1.000000 0.750000 0.771509 0.760000 0 0.650000 0.880000 MUC1 4582 broad.mit.edu 37 1 155161799 155161799 + Missense_Mutation SNP T T G TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr1:155161799T>G ENST00000368395.1 - 2 405 c.334A>C c.(334-336)Acc>Ccc p.T112P RP11-201K10.3_ENST00000473363.2_5'Flank|MUC1_ENST00000368389.2_Intron|MUC1_ENST00000338684.5_Intron|MUC1_ENST00000368392.3_Intron|MUC1_ENST00000368393.3_Intron|MUC1_ENST00000462215.1_Intron|MUC1_ENST00000368396.4_Intron|MUC1_ENST00000343256.5_Intron|MUC1_ENST00000457295.2_Intron|MUC1_ENST00000368390.3_Intron|MUC1_ENST00000438413.1_Intron|MUC1_ENST00000342482.4_Intron|MUC1_ENST00000337604.5_Intron|MUC1_ENST00000368398.3_Intron NM_001204285.1|NM_001204286.1 NP_001191214.1|NP_001191215.1 P15941 MUC1_HUMAN mucin 1, cell surface associated 10 all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877) Epithelial(20;5.31e-10)|all cancers(21;2.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193) GCTGGCGGGGTGGTGGAGCCC 0.711000 T IGH@ B-NHL Dom yes 1 1q21 4582 mucin 1, transmembrane L 0 SO:0001583 missense ENST00000368395.1 0 1 hg19 CCDS55640.1 . . . . . . . . . . T 8.249 0.808546 0.16467 . . ENSG00000185499 ENST00000368395;ENST00000425082 T 0.20200 2.09 2.73 0.35 0.16037 . 2.188600 0.02617 N 0.102742 T 0.11024 0.0269 N 0.14661 0.345 0.09310 N 0.999999 D 0.65815 0.995 D 0.68483 0.958 T 0.17684 -1.0361 10 0.39692 T 0.17 . 3.1844 0.06596 0.0:0.2782:0.2183:0.5034 . 112 P15941 MUC1_HUMAN P 112 ENSP00000357380:T112P ENSP00000357380:T112P T - 1 0 MUC1 153428423 0.000000 0.05858 0.001000 0.08648 0.003000 0.03518 -0.417000 0.07088 0.027000 0.15297 -1.038000 0.02383 ACC TCGA-HZ-7919-01A-11D-2154-08 MUC1-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000086735.1 0 0 0 26 84 2 21 0 9.822628e-01 12 377 2 21 60 0 0 0 0 0 2 1 0.829618 25 80 2 21 20 -2.661886 1 1 120668 181 36 1 1 2 3 2.106713 0 0.400000 1.870000 0.408284 0.990000 0.830000 1.000000 1.000000 0.986776 0.990000 1 0.990000 1.000000 RNPEP 6051 broad.mit.edu 37 1 201966564 201966564 + Silent SNP C C T TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr1:201966564C>T ENST00000295640.4 + 5 1015 c.972C>T c.(970-972)atC>atT p.I324I RP11-465N4.5_ENST00000608886.1_RNA|RNPEP_ENST00000471105.1_3'UTR|RP11-465N4.4_ENST00000415582.1_RNA|RP11-465N4.4_ENST00000419190.1_RNA|RNPEP_ENST00000367286.3_Silent_p.I285I NM_020216.3 NP_064601.3 Q9H4A4 AMPB_HUMAN arginyl aminopeptidase (aminopeptidase B) 21 ATGTCATCATCCATGAGATCT 0.547000 GBM(19;39 479 7473 13131 19462) 0 SO:0001819 synonymous_variant ENST00000295640.4 1 1 hg19 CCDS1418.1 TCGA-HZ-7919-01A-11D-2154-08 RNPEP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000087345.1 1 0 0 109 503 0 102 1 1 58 162 0 102 2 0 0 0 0 0 2 1 1.000000 109 499 0 101 2 -20.000000 1 0 0 0 1 1 2 3 2.106713 0 0.400000 1.870000 0.408284 0.900000 0.750000 1.000000 1.000000 0.906802 0.900000 1 0.820000 1.000000 RNPEP 6051 broad.mit.edu 37 1 201966573 201966573 + Silent SNP C C T TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr1:201966573C>T ENST00000295640.4 + 5 1024 c.981C>T c.(979-981)atC>atT p.I327I RP11-465N4.5_ENST00000608886.1_RNA|RNPEP_ENST00000471105.1_3'UTR|RP11-465N4.4_ENST00000415582.1_RNA|RP11-465N4.4_ENST00000419190.1_RNA|RNPEP_ENST00000367286.3_Silent_p.I288I NM_020216.3 NP_064601.3 Q9H4A4 AMPB_HUMAN arginyl aminopeptidase (aminopeptidase B) 21 TCCATGAGATCTCCCACAGTT 0.542000 GBM(19;39 479 7473 13131 19462) 0 SO:0001819 synonymous_variant ENST00000295640.4 1 1 hg19 CCDS1418.1 TCGA-HZ-7919-01A-11D-2154-08 RNPEP-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000087345.1 1 0 1 100 508 0 99 1 1 53 160 0 99 2 0 0 0 0 0 2 1 1.000000 100 505 0 98 2 -20.000000 1 0 0 0 1 1 2 3 2.106713 0 0.400000 1.870000 0.408284 0.830000 0.680000 1.000000 0.830000 0.845933 0.830000 0 0.750000 0.930000 BTG2 7832 broad.mit.edu 37 1 203276480 203276480 + Missense_Mutation SNP T T G TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 T G T T Valid Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr1:203276480T>G ENST00000290551.4 + 2 462 c.391T>G c.(391-393)Tcc>Gcc p.S131A RP11-134P9.1_ENST00000457348.1_lincRNA NM_006763.2 NP_006754.1 P78543 BTG2_HUMAN BTG family, member 2 9 BRCA - Breast invasive adenocarcinoma(75;0.203) ACTGGCCGCCTCCTGTGGGCT 0.652000 0 SO:0001583 missense ENST00000290551.4 1 1 hg19 CCDS1437.1 . . . . . . . . . . T 8.763 0.924122 0.18056 . . ENSG00000159388 ENST00000290551 T 0.24151 1.87 5.06 3.91 0.45181 . 0.094228 0.45361 D 0.000365 T 0.19248 0.0462 L 0.44542 1.39 0.32156 N 0.58352 B 0.14805 0.011 B 0.16289 0.015 T 0.09164 -1.0687 10 0.38643 T 0.18 -12.5884 6.3092 0.21154 0.0:0.0854:0.1574:0.7572 . 131 P78543 BTG2_HUMAN A 131 ENSP00000290551:S131A ENSP00000290551:S131A S + 1 0 BTG2 201543103 1.000000 0.71417 0.995000 0.50966 0.423000 0.31445 1.427000 0.34881 1.911000 0.55334 0.260000 0.18958 TCC TCGA-HZ-7919-01A-11D-2154-08 BTG2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000087168.1 1 0 1 144 479 0 69 1 9.998827e-01 3 43 0 69 2 0 0 0 0 0 2 1 1.000000 142 475 0 68 2 -20.000000 1 1 0 0 1 1 2 3 2.106713 0 0.400000 1.870000 0.408284 0.990000 0.990000 1.000000 1.000000 0.999498 0.990000 1 0.990000 1.000000 MARK1 4139 broad.mit.edu 37 1 220752846 220752846 + Missense_Mutation SNP A A C TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr1:220752846A>C ENST00000366917.4 + 2 468 c.202A>C c.(202-204)Aag>Cag p.K68Q MARK1_ENST00000402574.1_5'UTR|MARK1_ENST00000485104.1_3'UTR|MARK1_ENST00000366918.4_Missense_Mutation_p.K68Q MAP/microtubule affinity-regulating kinase 1 63 AACAATAGGGAAGGGAAATTT 0.433000 0 SO:0001583 missense ENST00000366917.4 1 1 hg19 CCDS31029.2 . . . . . . . . . . A 29.7 5.032418 0.93575 . . ENSG00000116141 ENST00000366918;ENST00000366917 T;T 0.65364 1.78;-0.15 5.76 5.76 0.90799 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 0.64516 0.2605 N 0.16567 0.415 0.80722 D 1 P;D;D 0.69078 0.895;0.985;0.997 B;P;P 0.61592 0.313;0.681;0.891 T 0.70622 -0.4821 10 0.87932 D 0 . 16.0789 0.80985 1.0:0.0:0.0:0.0 . 68;68;68 B4DIB3;Q9P0L2;Q9P0L2-3 .;MARK1_HUMAN;. Q 68 ENSP00000355885:K68Q;ENSP00000355884:K68Q ENSP00000355884:K68Q K + 1 0 MARK1 218819469 1.000000 0.71417 1.000000 0.80357 0.998000 0.95712 9.339000 0.96797 2.192000 0.70111 0.460000 0.39030 AAG TCGA-HZ-7919-01A-11D-2154-08 MARK1-002 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000090899.1 1 0 1 122 356 0 51 0 1.639172e-01 0 3 0 51 2 0 0 0 0 0 2 1 1.000000 121 353 0 50 2 -20.000000 1 1 0 0 1 1 2 3 2.103513 0 0.400000 1.870000 0.408284 0.990000 0.990000 1.000000 1.000000 0.999976 0.990000 1 0.990000 1.000000 CCDC27 148870 broad.mit.edu 37 1 3673402 3673402 + Missense_Mutation SNP A A T TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr1:3673402A>T ENST00000294600.2 + 4 743 c.659A>T c.(658-660)cAg>cTg p.Q220L NM_152492.2 NP_689705.2 Q2M243 CCD27_HUMAN coiled-coil domain containing 27 36 all_cancers(77;0.0385)|Ovarian(185;0.0634)|Lung NSC(156;0.21)|all_lung(157;0.218) all_epithelial(116;5.52e-17)|all_lung(118;1.04e-06)|Lung NSC(185;0.000214)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Lung SC(97;0.0367)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127) GTCGCATCTCAGAGCTGCCTG 0.572000 0 SO:0001583 missense ENST00000294600.2 0 1 hg19 CCDS50.1 . . . . . . . . . . A 12.01 1.809654 0.31961 . . ENSG00000162592 ENST00000294600 T 0.21031 2.03 3.84 1.11 0.20524 . 0.944655 0.08686 N 0.908701 T 0.14570 0.0352 L 0.29908 0.895 0.09310 N 1 P 0.42584 0.784 B 0.40101 0.319 T 0.21484 -1.0244 10 0.66056 D 0.02 -10.1696 3.8496 0.08949 0.5575:0.2248:0.0:0.2177 . 220 Q2M243 CCD27_HUMAN L 220 ENSP00000294600:Q220L ENSP00000294600:Q220L Q + 2 0 CCDC27 3663262 0.065000 0.20965 0.006000 0.13384 0.246000 0.25737 1.393000 0.34497 0.584000 0.29591 0.260000 0.18958 CAG TCGA-HZ-7919-01A-11D-2154-08 CCDC27-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000009740.1 0 0 0 5 223 0 25 0 0 0 0 25 2 0 0 0 0 0 2 1 0.937506 5 222 0 25 2 -7.021168 1 0 0 0 1 1 2 3 2.106042 0 0.400000 1.870000 0.408284 0.120000 0.040000 1.000000 0.110000 0.179848 0.120000 0 0.070000 0.200000 RIN2 54453 broad.mit.edu 37 20 19981313 19981313 + Silent SNP C C G TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr20:19981313C>G ENST00000255006.6 + 12 2717 c.2568C>G c.(2566-2568)ctC>ctG p.L856L RIN2_ENST00000484638.1_3'UTR|RIN2_ENST00000440354.2_Silent_p.L374L NM_001242581.1|NM_018993.3 NP_001229510.1|NP_061866.1 Q8WYP3 RIN2_HUMAN Ras and Rab interactor 2 27 GAAAGACCCTCCTTGTGAGAC 0.498000 0 SO:0001819 synonymous_variant ENST00000255006.6 1 1 hg19 CCDS56182.1 TCGA-HZ-7919-01A-11D-2154-08 RIN2-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000078212.1 1 0 1 135 674 0 111 1 1 30 114 0 111 2 0 0 0 0 0 2 1 1.000000 133 669 0 111 2 -3.225761 1 1 0 0 1 1 2 3 2.055373 0 0.400000 1.870000 0.401198 0.830000 0.700000 0.970000 0.840000 0.838373 0.830000 0 0.760000 0.900000 TOX2 84969 broad.mit.edu 37 20 42694633 42694633 + Silent SNP C C T TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr20:42694633C>T ENST00000358131.5 + 6 1396 c.1188C>T c.(1186-1188)ggC>ggT p.G396G TOX2_ENST00000372999.1_Silent_p.G372G|TOX2_ENST00000435864.2_3'UTR|TOX2_ENST00000341197.4_Silent_p.G414G|TOX2_ENST00000423191.2_Silent_p.G372G NM_001098798.1 NP_001092268.1 Q96NM4 TOX2_HUMAN TOX high mobility group box family member 2 26 Myeloproliferative disorder(115;0.00452) COAD - Colon adenocarcinoma(18;0.00189) ACGCCCAGGGCGCCCTCCTCA 0.711000 0 SO:0001819 synonymous_variant ENST00000358131.5 1 1 hg19 CCDS42875.1 TCGA-HZ-7919-01A-11D-2154-08 TOX2-001 KNOWN basic|CCDS protein_coding protein_coding OTTHUMT00000079329.2 1 0 0 45 231 0 31 0 0 0 0 31 2 0 0 0 0 0 2 1 1.000000 43 225 0 31 2 -20.000000 1 1 0 0 1 1 2 3 2.055373 0 0.400000 1.870000 0.401198 0.810000 0.610000 1.000000 1.000000 0.821121 0.810000 0 0.700000 0.930000 COL6A2 1292 broad.mit.edu 37 21 47545202 47545202 + Missense_Mutation SNP T T A TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 T A T T Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr21:47545202T>A ENST00000300527.4 + 24 1897 c.1793T>A c.(1792-1794)gTg>gAg p.V598E COL6A2_ENST00000357838.4_Missense_Mutation_p.V598E|COL6A2_ENST00000397763.1_Missense_Mutation_p.V598E|COL6A2_ENST00000310645.5_Missense_Mutation_p.V598E|COL6A2_ENST00000409416.1_Missense_Mutation_p.V598E NM_001849.3 NP_001840.3 P12110 CO6A2_HUMAN collagen, type VI, alpha 2 43 Breast(49;0.245) ATGACCTACGTGAGGGAGACC 0.687000 0 SO:0001583 missense ENST00000300527.4 1 1 hg19 CCDS13728.1 . . . . . . . . . . T 26.8 4.773717 0.90108 . . ENSG00000142173 ENST00000300527;ENST00000357838;ENST00000310645;ENST00000409416;ENST00000397763;ENST00000413758 D;D;D;D;D;T 0.94000 -3.33;-3.33;-3.33;-3.33;-3.33;-1.12 4.51 4.51 0.55191 . 0.286383 0.35739 N 0.003001 D 0.95551 0.8554 M 0.65498 2.005 0.54753 D 0.999989 D;D;D 0.69078 0.995;0.997;0.994 P;D;P 0.66497 0.841;0.944;0.9 D 0.95952 0.8955 10 0.87932 D 0 -19.3525 13.8316 0.63384 0.0:0.0:0.0:1.0 . 598;598;598 P12110;P12110-2;P12110-3 CO6A2_HUMAN;.;. E 598;598;598;598;598;139 ENSP00000300527:V598E;ENSP00000350497:V598E;ENSP00000312529:V598E;ENSP00000387115:V598E;ENSP00000380870:V598E;ENSP00000395751:V139E ENSP00000300527:V598E V + 2 0 COL6A2 46369630 1.000000 0.71417 1.000000 0.80357 0.963000 0.63663 7.636000 0.83301 1.683000 0.51011 0.472000 0.43445 GTG TCGA-HZ-7919-01A-11D-2154-08 COL6A2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000206971.1 0 0 0 30 959 0 147 0 9.999976e-01 0 634 0 147 2 0 0 0 0 0 2 1 1.000000 30 943 0 144 2 -19.999730 1 1 0 0 1 0 1 1 1.747637 1 0.400000 1.870000 0.287411 0.120000 0.080000 0.180000 0.130000 0.131362 0.120000 0 0.100000 0.150000 SLC5A1 6523 broad.mit.edu 37 22 32464533 32464533 + Silent SNP C C A TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 C A C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr22:32464533C>A ENST00000266088.4 + 5 673 c.423C>A c.(421-423)atC>atA p.I141I SLC5A1_ENST00000543737.1_Silent_p.I14I NM_000343.3 NP_000334.1 P13866 SC5A1_HUMAN solute carrier family 5 (sodium/glucose cotransporter), member 1 37 Canagliflozin(DB08907) GCCAGCGGATCCAGGTCTACC 0.602000 0 SO:0001819 synonymous_variant ENST00000266088.4 1 1 hg19 CCDS13902.1 TCGA-HZ-7919-01A-11D-2154-08 SLC5A1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000075656.3 1 0 1 88 374 0 60 1 1 30 93 0 60 2 0 0 0 0 0 2 1 1.000000 88 370 0 60 2 -20.000000 1 1 0 0 1 1 2 3 2.095467 0 0.400000 1.870000 0.407115 0.960000 0.780000 1.000000 1.000000 0.946964 0.960000 1 0.870000 1.000000 ENTHD1 150350 broad.mit.edu 37 22 40257992 40257992 + Missense_Mutation SNP A A C TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr22:40257992A>C ENST00000325157.6 - 3 620 c.370T>G c.(370-372)Tct>Gct p.S124A NM_152512.3 NP_689725.2 Q8IYW4 ENTD1_HUMAN ENTH domain containing 1 32 Melanoma(58;0.0749) ACTTGCTTAGATTTTTCCCGG 0.353000 0 SO:0001583 missense ENST00000325157.6 1 1 hg19 CCDS13998.1 . . . . . . . . . . A 12.61 1.990702 0.35131 . . ENSG00000176177 ENST00000325157 T 0.37058 1.22 6.17 5.12 0.69794 Epsin domain, N-terminal (1);ENTH/VHS (2);Epsin-like, N-terminal (2); 0.175744 0.40385 N 0.001101 T 0.17152 0.0412 N 0.01410 -0.885 0.28314 N 0.92253 B 0.30870 0.298 B 0.43728 0.429 T 0.43261 -0.9402 10 0.06099 T 0.92 -9.4664 9.6484 0.39881 0.845:0.0:0.0:0.155 . 124 Q8IYW4 ENTD1_HUMAN A 124 ENSP00000317431:S124A ENSP00000317431:S124A S - 1 0 ENTHD1 38587938 1.000000 0.71417 1.000000 0.80357 0.249000 0.25844 3.170000 0.50816 1.105000 0.41606 0.533000 0.62120 TCT TCGA-HZ-7919-01A-11D-2154-08 ENTHD1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000321302.1 1 0 0 7 154 0 31 0 0 0 1 0 31 2 0 0 0 0 0 2 1 0.980479 7 152 0 31 2 -10.173050 1 1 0 0 1 0 1 1 1.658663 1 0.400000 1.870000 0.250000 0.170000 0.070000 0.330000 0.170000 0.192677 0.170000 0 0.120000 0.250000 GREB1 9687 broad.mit.edu 37 2 11742547 11742547 + Missense_Mutation SNP C C T TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr2:11742547C>T ENST00000381486.2 + 17 2845 c.2545C>T c.(2545-2547)Cat>Tat p.H849Y GREB1_ENST00000234142.5_Missense_Mutation_p.H849Y NM_014668.3 NP_055483.2 Q4ZG55 GREB1_HUMAN growth regulation by estrogen in breast cancer 1 30 all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155) GGACTTATATCATGAAAATAA 0.507000 Ovarian(39;850 945 2785 23371 33093) 0 SO:0001583 missense ENST00000381486.2 1 1 hg19 CCDS42655.1 . . . . . . . . . . C 15.95 2.984251 0.53827 . . ENSG00000196208 ENST00000381486;ENST00000234142;ENST00000432985 T;T;T 0.47869 0.83;0.83;0.83 5.64 5.64 0.86602 . 0.252735 0.39020 N 0.001498 T 0.45155 0.1328 L 0.50333 1.59 0.80722 D 1 B;P 0.40875 0.429;0.731 B;B 0.37091 0.241;0.241 T 0.33777 -0.9855 10 0.29301 T 0.29 -41.315 19.6906 0.95999 0.0:1.0:0.0:0.0 . 483;849 C9JIG0;Q4ZG55 .;GREB1_HUMAN Y 849;849;483 ENSP00000370896:H849Y;ENSP00000234142:H849Y;ENSP00000403886:H483Y ENSP00000234142:H849Y H + 1 0 GREB1 11659998 1.000000 0.71417 0.113000 0.21522 0.687000 0.40016 5.669000 0.68081 2.649000 0.89929 0.655000 0.94253 CAT TCGA-HZ-7919-01A-11D-2154-08 GREB1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000280490.1 1 0 1 343 585 0 118 0 0 0 1 0 118 2 0 0 0 0 0 2 1 1.000000 341 581 0 117 2 -20.000000 1 1 0 0 1 0 2 2 2.071645 1 0.400000 1.870000 0.400000 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 ARHGAP15 55843 broad.mit.edu 37 2 143913143 143913143 + Silent SNP C C A TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr2:143913143C>A ENST00000295095.6 + 2 251 c.84C>A c.(82-84)atC>atA p.I28I ARHGAP15_ENST00000409869.1_Silent_p.I28I NM_018460.3 NP_060930.3 Q53QZ3 RHG15_HUMAN Rho GTPase activating protein 15 34 AAATGAGAATCAAAAATGCCA 0.448000 0 SO:0001819 synonymous_variant ENST00000295095.6 1 1 hg19 CCDS2184.1 TCGA-HZ-7919-01A-11D-2154-08 ARHGAP15-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000254793.2 0 0 0 10 336 0 39 0 9.291647e-02 0 16 0 39 2 0 0 0 0 0 2 1 0.996288 10 322 0 39 2 -3.103658 1 1 0 0 1 0 2 2 2.071645 1 0.400000 1.870000 0.400000 0.140000 0.070000 0.260000 0.140000 0.157346 0.140000 0 0.100000 0.200000 PLEKHH2 130271 broad.mit.edu 37 2 43965587 43965587 + Missense_Mutation SNP G G C TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr2:43965587G>C ENST00000282406.4 + 20 3161 c.3051G>C c.(3049-3051)caG>caC p.Q1017H NM_172069.3 NP_742066.2 Q8IVE3 PKHH2_HUMAN pleckstrin homology domain containing, family H (with MyTH4 domain) member 2 56 all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17) CTGAGCTGCAGAATGAAATTT 0.393000 0 SO:0001583 missense ENST00000282406.4 1 1 hg19 CCDS1812.1 . . . . . . . . . . G 17.96 3.516918 0.64634 . . ENSG00000152527 ENST00000282406 D 0.91792 -2.91 5.53 3.74 0.42951 MyTH4 domain (3); 0.000000 0.85682 D 0.000000 D 0.95503 0.8539 M 0.82517 2.595 0.58432 D 0.999993 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;0.998 D 0.94785 0.7957 10 0.87932 D 0 -15.4565 9.9364 0.41554 0.2346:0.0:0.7654:0.0 . 1017;454 Q8IVE3;Q8IVE3-2 PKHH2_HUMAN;. H 1017 ENSP00000282406:Q1017H ENSP00000282406:Q1017H Q + 3 2 PLEKHH2 43819091 1.000000 0.71417 1.000000 0.80357 0.993000 0.82548 3.416000 0.52707 0.707000 0.31934 0.561000 0.74099 CAG TCGA-HZ-7919-01A-11D-2154-08 PLEKHH2-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000250537.1 1 0 1 270 418 0 96 1 8.831917e-01 4 4 0 96 2 0 0 0 0 0 2 1 1.000000 267 413 0 96 2 -20.000000 1 1 0 0 1 0 2 2 2.071645 1 0.400000 1.870000 0.400000 0.990000 0.990000 1.000000 1.000000 1.000000 0.990000 1 0.990000 1.000000 FBXO40 51725 broad.mit.edu 37 3 121345596 121345596 + Missense_Mutation SNP G G A TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr3:121345596G>A ENST00000338040.4 + 4 2383 c.1969G>A c.(1969-1971)Gtc>Atc p.V657I NM_016298.3 NP_057382.2 Q9UH90 FBX40_HUMAN F-box protein 40 46 GTTTAATGAAGTCACCTCCAT 0.458000 0 SO:0001583 missense ENST00000338040.4 1 1 hg19 CCDS33835.1 . . . . . . . . . . G 14.16 2.451162 0.43531 . . ENSG00000163833 ENST00000338040 T 0.30714 1.52 6.17 5.3 0.74995 F-box domain, Skp2-like (1); 0.244440 0.40144 N 0.001170 T 0.20333 0.0489 L 0.28608 0.87 0.37080 D 0.898954 B 0.31318 0.319 B 0.30105 0.111 T 0.07046 -1.0793 10 0.06494 T 0.89 -14.5867 13.5664 0.61822 0.0747:0.0:0.9253:0.0 . 657 Q9UH90 FBX40_HUMAN I 657 ENSP00000337510:V657I ENSP00000337510:V657I V + 1 0 FBXO40 122828286 0.692000 0.27719 0.985000 0.45067 0.990000 0.78478 1.954000 0.40362 1.626000 0.50381 0.655000 0.94253 GTC TCGA-HZ-7919-01A-11D-2154-08 FBXO40-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000355158.1 0 0 0 25 1119 0 139 0 0 0 0 139 2 0 0 0 0 0 2 1 1.000000 25 1109 0 138 2 -16.720990 1 1 0 0 1 1 2 3 2.069617 0 0.400000 1.870000 0.402390 0.100000 0.060000 0.170000 0.110000 0.122420 0.100000 0 0.080000 0.140000 ANKRD28 23243 broad.mit.edu 37 3 15718557 15718557 + Missense_Mutation SNP C C T TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr3:15718557C>T ENST00000399451.2 - 26 3074 c.2707G>A c.(2707-2709)Gaa>Aaa p.E903K ANKRD28_ENST00000497037.1_5'UTR|ANKRD28_ENST00000383777.1_Missense_Mutation_p.E936K NM_001195098.1|NM_001195099.1|NM_015199.3 NP_001182027.1|NP_001182028.1|NP_056014.2 O15084 ANR28_HUMAN ankyrin repeat domain 28 6 GCACTAGTTTCATGACCCTAT 0.358000 0 SO:0001583 missense ENST00000399451.2 1 1 hg19 CCDS46769.1 . . . . . . . . . . C 35 5.496535 0.96355 . . ENSG00000206560 ENST00000399451;ENST00000383777;ENST00000412318 T;T;T 0.64991 -0.13;-0.13;-0.13 5.38 5.38 0.77491 Ankyrin repeat-containing domain (4); 0.000000 0.85682 D 0.000000 T 0.63674 0.2531 L 0.35341 1.055 0.80722 D 1 P 0.51791 0.948 P 0.56343 0.796 T 0.55347 -0.8155 10 0.06365 T 0.9 . 19.4958 0.95072 0.0:1.0:0.0:0.0 . 903 O15084 ANR28_HUMAN K 903;936;903 ENSP00000382379:E903K;ENSP00000373287:E936K;ENSP00000397341:E903K ENSP00000373287:E936K E - 1 0 ANKRD28 15693561 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 7.647000 0.83462 2.681000 0.91329 0.650000 0.86243 GAA TCGA-HZ-7919-01A-11D-2154-08 ANKRD28-003 PUTATIVE basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000339758.1 1 0 1 78 327 0 49 1 9.999794e-01 25 43 0 49 2 0 0 0 0 0 2 1 1.000000 74 321 0 49 2 -20.000000 1 1 0 0 1 1 2 3 2.060951 0 0.400000 1.870000 0.401198 0.960000 0.770000 1.000000 1.000000 0.943102 0.960000 1 0.860000 1.000000 FBXO45 200933 broad.mit.edu 37 3 196311085 196311085 + Missense_Mutation SNP G G A TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr3:196311085G>A ENST00000311630.6 + 3 1054 c.757G>A c.(757-759)Gct>Act p.A253T FBXO45_ENST00000440469.1_Missense_Mutation_p.A74T NM_001105573.1 NP_001099043.1 P0C2W1 FBSP1_HUMAN F-box protein 45 7 all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135) Epithelial(36;2.75e-23)|all cancers(36;2.47e-21)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06) CCTGGGGGTTGCTTTTAGAGG 0.418000 0 SO:0001583 missense ENST00000311630.6 1 1 hg19 CCDS46985.1 . . . . . . . . . . G 25.4 4.629998 0.87660 . . ENSG00000174013 ENST00000440469;ENST00000311630 T;T 0.60548 0.18;0.18 4.97 4.97 0.65823 Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1); 0.000000 0.85682 D 0.000000 T 0.79592 0.4472 M 0.84948 2.725 0.80722 D 1 D 0.89917 1.0 D 0.97110 1.0 T 0.82756 -0.0300 10 0.87932 D 0 -10.3492 18.7709 0.91892 0.0:0.0:1.0:0.0 . 253 P0C2W1 FBSP1_HUMAN T 74;253 ENSP00000389868:A74T;ENSP00000310332:A253T ENSP00000310332:A253T A + 1 0 FBXO45 197795482 1.000000 0.71417 1.000000 0.80357 0.980000 0.70556 8.985000 0.93487 2.740000 0.93945 0.563000 0.77884 GCT TCGA-HZ-7919-01A-11D-2154-08 FBXO45-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000340687.2 1 0 1 73 278 0 55 1 9.703978e-01 8 16 0 55 2 0 0 0 0 0 2 1 1.000000 73 274 0 55 2 -3.792750 1 1 0 0 1 1 2 3 2.069617 0 0.400000 1.870000 0.402390 0.990000 0.830000 1.000000 1.000000 0.977236 0.990000 1 0.930000 1.000000 TRIML1 339976 broad.mit.edu 37 4 189060986 189060986 + Missense_Mutation SNP C C A TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr4:189060986C>A ENST00000332517.3 + 1 414 c.274C>A c.(274-276)Cag>Aag p.Q92K RP11-366H4.3_ENST00000501322.2_RNA NM_178556.3 NP_848651.2 Q8N9V2 TRIML_HUMAN tripartite motif family-like 1 60 all_cancers(14;1.33e-43)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)|all_hematologic(60;0.062) CGAGGATGAGCAGGGCAGCTA 0.647000 Melanoma(31;213 1036 16579 23968 32372) 0 SO:0001583 missense ENST00000332517.3 0 1 hg19 CCDS3851.1 . . . . . . . . . . C 3.439 -0.114406 0.06881 . . ENSG00000184108 ENST00000332517 T 0.61274 0.12 5.19 3.32 0.38043 . 0.645692 0.13834 N 0.359532 T 0.41465 0.1160 L 0.47716 1.5 0.09310 N 1 B 0.14438 0.01 B 0.09377 0.004 T 0.35822 -0.9773 10 0.05959 T 0.93 -6.5751 5.7084 0.17921 0.1928:0.7101:0.0:0.0971 . 92 Q8N9V2 TRIML_HUMAN K 92 ENSP00000327738:Q92K ENSP00000327738:Q92K Q + 1 0 TRIML1 189297980 0.000000 0.05858 0.002000 0.10522 0.019000 0.09904 -0.461000 0.06712 1.512000 0.48834 0.655000 0.94253 CAG TCGA-HZ-7919-01A-11D-2154-08 TRIML1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000359813.1 0 0 0 12 386 0 47 0 0 0 0 47 2 0 0 0 0 0 2 1 0.999106 11 384 0 46 2 -11.973240 1 1 0 0 1 1 2 3 2.075646 0 0.400000 1.870000 0.402390 0.150000 0.080000 0.270000 0.150000 0.170745 0.150000 0 0.110000 0.210000 YIPF7 285525 broad.mit.edu 37 4 44638040 44638040 + Missense_Mutation SNP G G A TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr4:44638040G>A ENST00000332990.5 - 3 267 c.251C>T c.(250-252)tCg>tTg p.S84L YIPF7_ENST00000415895.4_Missense_Mutation_p.S60L NM_182592.2 NP_872398.2 Q8N8F6 YIPF7_HUMAN Yip1 domain family, member 7 12 TGCGTAACCCGATGACATGAG 0.408000 0 SO:0001583 missense ENST00000332990.5 0 1 hg19 CCDS54766.1 . . . . . . . . . . G 13.34 2.207679 0.39003 . . ENSG00000177752 ENST00000332990 T 0.32023 1.47 5.02 5.02 0.67125 . 0.477948 0.20853 N 0.084492 T 0.33381 0.0861 L 0.60455 1.87 0.09310 N 1 P;B 0.43750 0.816;0.326 B;B 0.40134 0.32;0.069 T 0.26677 -1.0096 10 0.30078 T 0.28 -9.5458 17.5826 0.87972 0.0:0.0:1.0:0.0 . 84;84 Q8N8F6-4;Q8N8F6 .;YIPF7_HUMAN L 84 ENSP00000332772:S84L ENSP00000332772:S84L S - 2 0 YIPF7 44332797 0.978000 0.34361 0.165000 0.22776 0.058000 0.15608 2.196000 0.42686 2.636000 0.89361 0.650000 0.86243 TCG TCGA-HZ-7919-01A-11D-2154-08 YIPF7-201 KNOWN basic|CCDS protein_coding protein_coding 0 0 0 7 313 0 29 0 0 0 1 0 29 2 0 0 0 0 0 2 1 0.980248 7 310 0 29 2 -3.180670 1 1 120846 1 33 1 1 2 3 2.075646 0 0.400000 1.870000 0.402390 0.110000 0.040000 0.240000 0.110000 0.132720 0.110000 0 0.070000 0.170000 DMP1 1758 broad.mit.edu 37 4 88583249 88583249 + Missense_Mutation SNP G G T TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr4:88583249G>T ENST00000339673.6 + 6 418 c.319G>T c.(319-321)Gat>Tat p.D107Y RP11-742B18.1_ENST00000507894.1_RNA|DMP1_ENST00000282479.7_Missense_Mutation_p.D91Y|RP11-742B18.1_ENST00000506814.1_RNA|RP11-742B18.1_ENST00000506480.1_RNA NM_004407.3 NP_004398.1 Q13316 DMP1_HUMAN dentin matrix acidic phosphoprotein 1 32 Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.227) TGACGATGAAGATGACAGTGG 0.507000 0 SO:0001583 missense ENST00000339673.6 0 1 hg19 CCDS3623.1 . . . . . . . . . . G 14.91 2.677163 0.47886 . . ENSG00000152592 ENST00000339673;ENST00000282479 T;T 0.60171 0.21;0.21 5.24 5.24 0.73138 . 0.000000 0.56097 D 0.000023 T 0.72479 0.3465 L 0.54323 1.7 0.47862 D 0.99953 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;1.0 T 0.75071 -0.3447 10 0.87932 D 0 -12.8053 16.6154 0.84909 0.0:0.0:1.0:0.0 . 91;107 Q13316-2;Q13316 .;DMP1_HUMAN Y 107;91 ENSP00000340935:D107Y;ENSP00000282479:D91Y ENSP00000282479:D91Y D + 1 0 DMP1 88802273 1.000000 0.71417 1.000000 0.80357 0.205000 0.24178 6.210000 0.72176 2.457000 0.83068 0.455000 0.32223 GAT TCGA-HZ-7919-01A-11D-2154-08 DMP1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000253047.1 0 0 0 10 392 0 40 0 0 0 0 40 2 0 0 0 0 0 2 1 0.996847 9 390 0 40 2 -9.761817 1 1 0 0 1 1 2 3 2.075646 0 0.400000 1.870000 0.402390 0.120000 0.060000 0.240000 0.120000 0.144638 0.120000 0 0.090000 0.180000 SLC2A9 56606 broad.mit.edu 37 4 9998478 9998478 + Missense_Mutation SNP T T C TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr4:9998478T>C ENST00000264784.3 - 3 390 c.337A>G c.(337-339)Act>Gct p.T113A SLC2A9_ENST00000309065.3_Missense_Mutation_p.T84A|SLC2A9_ENST00000506583.1_Missense_Mutation_p.T84A NM_020041.2 NP_064425.2 Q9NRM0 GTR9_HUMAN solute carrier family 2 (facilitated glucose transporter), member 9 35 Losartan(DB00678)|Probenecid(DB01032) ATGGACACAGTCACAGACCAG 0.468000 0 SO:0001583 missense ENST00000264784.3 1 1 hg19 CCDS3407.1 . . . . . . . . . . T 19.24 3.790410 0.70337 . . ENSG00000109667 ENST00000506583;ENST00000264784;ENST00000309065;ENST00000513129 T;T;T;T 0.79845 0.4;-0.84;0.4;-1.31 5.21 5.21 0.72293 Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1); 0.107675 0.64402 D 0.000007 T 0.81517 0.4839 L 0.33485 1.01 0.40360 D 0.979237 P;P 0.47191 0.891;0.846 P;P 0.59546 0.72;0.859 T 0.80339 -0.1424 9 . . . . 11.9036 0.52697 0.0:0.0:0.0:1.0 . 84;113 Q9NRM0-2;Q9NRM0 .;GTR9_HUMAN A 84;113;84;84 ENSP00000422209:T84A;ENSP00000264784:T113A;ENSP00000311383:T84A;ENSP00000426800:T84A . T - 1 0 SLC2A9 9607576 1.000000 0.71417 0.990000 0.47175 0.946000 0.59487 4.346000 0.59367 2.136000 0.66102 0.524000 0.50904 ACT TCGA-HZ-7919-01A-11D-2154-08 SLC2A9-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000207055.1 1 0 1 108 395 0 82 0 6.081524e-01 1 8 0 82 2 0 0 0 0 0 2 1 1.000000 107 390 0 82 2 -20.000000 1 1 0 0 1 1 2 3 2.075646 0 0.400000 1.870000 0.402390 0.990000 0.900000 1.000000 1.000000 0.990887 0.990000 1 0.980000 1.000000 PCDHGA6 56109 broad.mit.edu 37 5 140754472 140754472 + Silent SNP C C T TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr5:140754472C>T ENST00000517434.1 + 1 822 c.822C>T c.(820-822)caC>caT p.H274H PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron NM_018919.2|NM_032086.1 NP_061742.1|NP_114475.1 Q9Y5G7 PCDG6_HUMAN protocadherin gamma subfamily A, 6 2 KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191) AAGGAGTCCACGGGGAAGTAA 0.433000 0 SO:0001819 synonymous_variant ENST00000517434.1 1 1 hg19 CCDS54926.1 TCGA-HZ-7919-01A-11D-2154-08 PCDHGA6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000374743.1 1 0 1 45 186 0 40 0 0 0 1 0 40 2 0 0 0 0 0 2 1 1.000000 44 186 0 40 2 -3.576604 1 1 120808 1 25 1 0 0 0 2.010940 0 0.400000 1.870000 0.385246 0.940000 0.710000 1.000000 1.000000 0.924625 0.940000 1 0.820000 1.000000 MAST4 375449 broad.mit.edu 37 5 66461307 66461307 + Missense_Mutation SNP G G C TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr5:66461307G>C ENST00000403625.2 + 29 6595 c.6300G>C c.(6298-6300)gaG>gaC p.E2100D MAST4_ENST00000403666.1_Missense_Mutation_p.E1911D|MAST4_ENST00000405643.1_Missense_Mutation_p.E1921D|MAST4_ENST00000404260.3_Missense_Mutation_p.E2103D|MAST4_ENST00000261569.7_Missense_Mutation_p.E1906D NM_001164664.1 NP_001158136.1 O15021 MAST4_HUMAN microtubule associated serine/threonine kinase family member 4 13 Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245) TTGAGAGTGAGAAGAGTGAAA 0.562000 0 SO:0001583 missense ENST00000403625.2 1 1 hg19 CCDS54861.1 .|. .|. .|. .|. .|. .|. .|. .|. .|. .|. G|G 10.68|10.68 1.417754|1.417754 0.25552|0.25552 .|. .|. ENSG00000069020|ENSG00000069020 ENST00000404260;ENST00000403625;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569|ENST00000443808 T;T;T;T;T|T 0.65732|0.04360 -0.15;-0.15;-0.17;-0.17;-0.15|3.64 4.58|4.58 0.327|0.327 0.15913|0.15913 .|. 1.030320|1.030320 0.07702|0.07702 N|N 0.940481|0.940481 T|T 0.03477|0.03477 0.0100|0.0100 N|N 0.19112|0.19112 0.55|0.55 0.09310|0.09310 N|N 1|1 B;B|. 0.02656|. 0.0;0.0|. B;B|. 0.01281|. 0.0;0.0|. T|T 0.47911|0.47911 -0.9080|-0.9080 10|8 0.06099|0.30078 T|T 0.92|0.28 -0.9085|-0.9085 3.6607|3.6607 0.08237|0.08237 0.0968:0.4337:0.2813:0.1881|0.0968:0.4337:0.2813:0.1881 .|. 2103;1911|. O15021;O15021-3|. MAST4_HUMAN;.|. D|Q 2103;2100;1911;1921;1921;1906|1157 ENSP00000385048:E2103D;ENSP00000385727:E2100D;ENSP00000384313:E1911D;ENSP00000384099:E1921D;ENSP00000261569:E1906D|ENSP00000400551:E1157Q ENSP00000261569:E1906D|ENSP00000400551:E1157Q E|E +|+ 3|1 2|0 MAST4|MAST4 66497063|66497063 0.000000|0.000000 0.05858|0.05858 0.017000|0.017000 0.16124|0.16124 0.605000|0.605000 0.37080|0.37080 -0.771000|-0.771000 0.04699|0.04699 0.151000|0.151000 0.19162|0.19162 -0.145000|-0.145000 0.13849|0.13849 GAG|GAA TCGA-HZ-7919-01A-11D-2154-08 MAST4-001 NOVEL not_organism_supported|basic|appris_candidate|CCDS protein_coding protein_coding OTTHUMT00000326324.2 1 0 1 79 319 0 43 1 9.561666e-01 2 21 0 43 2 0 0 0 0 0 2 1 1.000000 78 314 0 43 2 -20.000000 1 1 0 0 1 0 0 0 1.978057 0 0.400000 1.870000 0.375000 0.940000 0.760000 1.000000 1.000000 0.935484 0.940000 1 0.850000 1.000000 TAAR9 134860 broad.mit.edu 37 6 132859638 132859638 + RNA SNP G G C TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr6:132859638G>C ENST00000434551.1 + 0 210 NM_175057.3 NP_778227.3 Q96RI9 TAAR9_HUMAN trace amine associated receptor 9 (gene/pseudogene) Breast(56;0.112) CAAACTTTCTGATTGCGTCGC 0.512000 Colon(10;433 445 15992 45047 47213) 0 ENST00000434551.1 1 1 hg19 TCGA-HZ-7919-01A-11D-2154-08 TAAR9-001 KNOWN mRNA_end_NF|cds_end_NF|basic polymorphic_pseudogene polymorphic_pseudogene OTTHUMT00000042254.2 0 0 0 76 240 0 51 0 0 0 0 51 2 0 0 0 0 0 2 1 1.000000 75 238 0 51 2 -4.772349 1 1 0 0 1 0 1 1 1.627988 1 0.400000 1.870000 0.250000 0.910000 0.760000 1.000000 0.950000 0.909626 0.910000 1 0.830000 0.980000 DEK 7913 broad.mit.edu 37 6 18258216 18258216 + Missense_Mutation SNP G G C TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr6:18258216G>C ENST00000397239.3 - 4 772 c.325C>G c.(325-327)Cta>Gta p.L109V DEK_ENST00000244776.7_Missense_Mutation_p.L75V NM_003472.3 NP_003463.1 P35659 DEK_HUMAN DEK proto-oncogene 7 Ovarian(93;0.00769)|Breast(50;0.0495) all_hematologic(90;0.053) OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332) AGTTTGTGTAGATTTCTAAGT 0.333000 T NUP214 AML Dom yes 6 6p23 7913 DEK oncogene (DNA binding) L 0 SO:0001583 missense ENST00000397239.3 1 1 hg19 CCDS34344.1 . . . . . . . . . . G 18.95 3.732566 0.69189 . . ENSG00000124795 ENST00000397239;ENST00000244776;ENST00000503715;ENST00000515742 T;T;T;T 0.75938 -0.98;-0.85;-0.19;-0.5 6.17 5.31 0.75309 . 0.000000 0.85682 D 0.000000 T 0.77498 0.4139 L 0.59436 1.845 0.44000 D 0.996703 D;D 0.54772 0.968;0.968 D;D 0.70716 0.97;0.97 T 0.79976 -0.1576 10 0.52906 T 0.07 -12.7977 11.3849 0.49778 0.1365:0.0:0.8635:0.0 . 75;109 B4DN37;P35659 .;DEK_HUMAN V 109;75;42;114 ENSP00000380414:L109V;ENSP00000244776:L75V;ENSP00000425399:L42V;ENSP00000423553:L114V ENSP00000244776:L75V L - 1 2 DEK 18366195 1.000000 0.71417 1.000000 0.80357 0.996000 0.88848 3.999000 0.57031 1.631000 0.50456 0.655000 0.94253 CTA TCGA-HZ-7919-01A-11D-2154-08 DEK-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000039962.4 1 0 1 37 150 0 41 1 1 83 78 0 41 2 0 0 0 0 0 2 1 1.000000 37 150 0 41 2 -20.000000 1 1 0 0 1 0 1 1 1.579168 1 0.400000 1.870000 0.250000 0.770000 0.570000 0.960000 0.780000 0.780847 0.770000 0 0.660000 0.890000 C6orf195 154386 broad.mit.edu 37 6 2624100 2624100 + Translation_Start_Site SNP G G C TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr6:2624100G>C ENST00000296847.3 - 0 480 NM_152554.2 NP_689767.2 Q96MT4 CF195_HUMAN chromosome 6 open reading frame 195 5 Ovarian(93;0.0412) all_hematologic(90;0.0895) TTCTTATGTTGATTCTTCTAT 0.418000 0 ENST00000296847.3 0 1 hg19 CCDS43416.1 TCGA-HZ-7919-01A-11D-2154-08 C6orf195-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000039633.1 0 0 0 36 107 0 27 0 0 0 1 0 27 2 0 0 0 0 0 2 1 1.000000 36 107 0 27 2 -20.000000 1 1 0 0 1 0 1 1 1.579168 1 0.400000 1.870000 0.250000 0.900000 0.700000 1.000000 0.990000 0.892432 0.900000 1 0.800000 0.970000 UBR2 23304 broad.mit.edu 37 6 42541728 42541728 + Missense_Mutation SNP G G C TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr6:42541728G>C ENST00000372899.1 + 2 593 c.335G>C c.(334-336)tGc>tCc p.C112S UBR2_ENST00000372903.2_Missense_Mutation_p.C112S|UBR2_ENST00000372901.1_Missense_Mutation_p.C112S NM_015255.2 NP_056070.1 Q8IWV8 UBR2_HUMAN ubiquitin protein ligase E3 component n-recognin 2 64 Colorectal(47;0.196) Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196) ACATATTCTTGCAGGTAAAAT 0.328000 0 SO:0001583 missense ENST00000372899.1 1 1 hg19 CCDS4870.1 . . . . . . . . . . G 27.6 4.843827 0.91197 . . ENSG00000024048 ENST00000372903;ENST00000372899;ENST00000372901 D;D;D 0.97553 -4.43;-4.43;-4.43 5.68 5.68 0.88126 Zinc finger, N-recognin, metazoa (1);Zinc finger, N-recognin (2); 0.045834 0.85682 D 0.000000 D 0.99233 0.9733 H 0.97962 4.115 0.80722 D 1 D;D 0.76494 0.998;0.999 D;D 0.83275 0.996;0.995 D 0.98951 1.0794 10 0.87932 D 0 -3.8635 19.7873 0.96444 0.0:0.0:1.0:0.0 . 112;112 Q8IWV8;Q8IWV8-2 UBR2_HUMAN;. S 112 ENSP00000361994:C112S;ENSP00000361990:C112S;ENSP00000361992:C112S ENSP00000361990:C112S C + 2 0 UBR2 42649706 1.000000 0.71417 1.000000 0.80357 0.990000 0.78478 9.476000 0.97823 2.673000 0.90976 0.655000 0.94253 TGC TCGA-HZ-7919-01A-11D-2154-08 UBR2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000040558.2 1 0 0 13 284 0 55 0 3.080939e-01 1 23 0 55 2 0 0 0 0 0 2 1 0.999544 12 283 0 55 2 -14.531040 1 1 0 0 1 0 1 1 1.627988 1 0.400000 1.870000 0.250000 0.170000 0.090000 0.280000 0.170000 0.185399 0.170000 0 0.130000 0.230000 EPHB4 2050 broad.mit.edu 37 7 100414848 100414848 + Silent SNP G G A rs148818692 TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr7:100414848G>A ENST00000358173.3 - 8 2022 c.1554C>T c.(1552-1554)ttC>ttT p.F518F EPHB4_ENST00000360620.3_Silent_p.F518F|EPHB4_ENST00000477446.1_Intron NM_004444.4 NP_004435.3 P54760 EPHB4_HUMAN EPH receptor B4 47 Lung NSC(181;0.041)|all_lung(186;0.0581) GTTCCTGGCCGAAGGGCCCGT 0.652000 GBM(200;2113 3072 25865 52728) 0 SO:0001819 synonymous_variant ENST00000358173.3 1 0 hg19 CCDS5706.1 TCGA-HZ-7919-01A-11D-2154-08 EPHB4-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000347222.1 1 0 0 33 103 0 15 1 9.996739e-01 16 27 0 15 2 0 0 0 0 0 2 1 1.000000 33 103 0 14 2 -20.000000 1 0 121354 7 35 1 1 2 3 2.064848 0 0.400000 1.870000 0.401198 0.990000 0.870000 1.000000 1.000000 0.991735 0.990000 1 0.990000 1.000000 PKD1L1 168507 broad.mit.edu 37 7 47869028 47869028 + Missense_Mutation SNP C C G TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr7:47869028C>G ENST00000289672.2 - 44 6780 c.6730G>C c.(6730-6732)Gaa>Caa p.E2244Q NM_138295.3 NP_612152.1 Q8TDX9 PK1L1_HUMAN polycystic kidney disease 1 like 1 BBS9/PKD1L1(2) 142 TTTACTTTTTCAACCTCGCCT 0.408000 0 SO:0001583 missense ENST00000289672.2 1 1 hg19 CCDS34633.1 . . . . . . . . . . C 13.47 2.247339 0.39697 . . ENSG00000158683 ENST00000289672 T 0.20200 2.09 4.11 3.2 0.36748 . 1.614660 0.03691 N 0.247120 T 0.27933 0.0688 L 0.59436 1.845 0.09310 N 1 P 0.51933 0.949 B 0.43331 0.416 T 0.24584 -1.0156 10 0.44086 T 0.13 -3.216 9.4856 0.38928 0.0:0.7832:0.2168:0.0 . 2244 Q8TDX9 PK1L1_HUMAN Q 2244 ENSP00000289672:E2244Q ENSP00000289672:E2244Q E - 1 0 PKD1L1 47835553 0.006000 0.16342 0.026000 0.17262 0.179000 0.23085 1.491000 0.35583 0.905000 0.36596 0.563000 0.77884 GAA TCGA-HZ-7919-01A-11D-2154-08 PKD1L1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000340974.1 1 0 0 108 386 0 68 0 0 0 1 0 68 2 0 0 0 0 0 2 1 1.000000 107 383 0 68 2 -20.000000 1 1 0 0 1 0 0 0 2.052918 0 0.400000 1.870000 0.400000 0.990000 0.910000 1.000000 1.000000 0.993129 0.990000 1 0.990000 1.000000 ZNF789 285989 broad.mit.edu 37 7 99084963 99084963 + Missense_Mutation SNP C C T TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr7:99084963C>T ENST00000331410.5 + 5 1400 c.1130C>T c.(1129-1131)aCg>aTg p.T377M ZNF789_ENST00000493485.1_Intron|ZNF789_ENST00000494186.1_Intron NM_213603.2 NP_998768.2 Q5FWF6 ZN789_HUMAN zinc finger protein 789 11 all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166) TGTGGGAAAACGTTTAGTTTT 0.403000 0 SO:0001583 missense ENST00000331410.5 0 1 hg19 CCDS34693.1 . . . . . . . . . . C 2.833 -0.242182 0.05906 . . ENSG00000198556 ENST00000331410 T 0.21031 2.03 2.89 1.98 0.26296 Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1); . . . . T 0.29684 0.0741 L 0.60455 1.87 0.19300 N 0.99998 D 0.76494 0.999 P 0.54815 0.761 T 0.09250 -1.0683 9 0.66056 D 0.02 . 5.4818 0.16727 0.2327:0.5406:0.2266:0.0 . 377 Q5FWF6 ZN789_HUMAN M 377 ENSP00000331927:T377M ENSP00000331927:T377M T + 2 0 ZNF789 98922899 0.000000 0.05858 0.232000 0.24009 0.029000 0.11900 0.055000 0.14229 0.774000 0.33427 -0.188000 0.12872 ACG TCGA-HZ-7919-01A-11D-2154-08 ZNF789-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000336266.1 0 0 0 17 935 1 125 0 2.499246e-02 1 12 1 125 2 0 0 0 0 0 2 1 0.999962 17 930 0 122 2 -2.926437 1 1 121412 2 35 1 1 2 3 2.064848 0 0.400000 1.870000 0.401198 0.080000 0.040000 0.140000 0.090000 0.094383 0.080000 0 0.060000 0.120000 FAM135B 51059 broad.mit.edu 37 8 139180258 139180258 + Missense_Mutation SNP G G A TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr8:139180258G>A ENST00000395297.1 - 12 1308 c.1138C>T c.(1138-1140)Cgg>Tgg p.R380W NM_015912.3 NP_056996.2 Q49AJ0 F135B_HUMAN family with sequence similarity 135, member B 238 all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155) BRCA - Breast invasive adenocarcinoma(115;0.0805) TCCGAGTTCCGGATATCCAGG 0.597000 HNSCC(54;0.14) 0 SO:0001583 missense ENST00000395297.1 1 1 hg19 CCDS6375.2 . . . . . . . . . . G 18.53 3.644994 0.67358 . . ENSG00000147724 ENST00000395297 D 0.90676 -2.71 5.66 4.77 0.60923 . 0.000000 0.85682 D 0.000000 D 0.95169 0.8434 M 0.80982 2.52 0.58432 D 0.999996 D 0.89917 1.0 D 0.91635 0.999 D 0.95690 0.8739 10 0.87932 D 0 -19.8469 14.775 0.69724 0.0:0.0:0.8544:0.1456 . 380 Q49AJ0 F135B_HUMAN W 380 ENSP00000378710:R380W ENSP00000276737:R380W R - 1 2 FAM135B 139249440 1.000000 0.71417 0.858000 0.33744 0.238000 0.25445 3.644000 0.54381 1.460000 0.47911 0.655000 0.94253 CGG TCGA-HZ-7919-01A-11D-2154-08 FAM135B-003 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000313590.3 0 0 0 21 721 0 93 0 0 0 0 93 2 0 0 0 0 0 2 1 0.999997 21 710 0 93 2 -2.527257 1 1 121082 2 35 1 1 2 3 2.062111 0 0.400000 1.870000 0.401198 0.140000 0.080000 0.220000 0.140000 0.147846 0.140000 0 0.110000 0.180000 SPTAN1 6709 broad.mit.edu 37 9 131386635 131386635 + Nonsense_Mutation SNP C C G TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 C G C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr9:131386635C>G ENST00000372731.4 + 45 5956 c.5846C>G c.(5845-5847)tCa>tGa p.S1949* SPTAN1_ENST00000358161.5_Nonsense_Mutation_p.S1954*|SPTAN1_ENST00000372739.3_Nonsense_Mutation_p.S1954* NM_001195532.1|NM_003127.3 NP_001182461.1|NP_003118.2 Q13813 SPTN1_HUMAN spectrin, alpha, non-erythrocytic 1 87 AACATCTCTTCAAAGATGAAG 0.527000 NSCLC(120;833 1744 2558 35612 37579) 0 SO:0001587 stop_gained ENST00000372731.4 0 1 hg19 CCDS6905.1 . . . . . . . . . . C 46 12.783765 0.99696 . . ENSG00000197694 ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719;ENST00000372721 . . . 5.23 4.32 0.51571 . 0.166830 0.52532 D 0.000064 . . . . . . 0.80722 A 1 . . . . . . . . . . 0.37606 T 0.19 . 14.3956 0.67007 0.0:0.9275:0.0:0.0725 . . . . X 1954;1949;1954;1929;198 . ENSP00000350882:S1954X S + 2 0 SPTAN1 130426456 1.000000 0.71417 0.563000 0.28383 0.993000 0.82548 5.710000 0.68392 1.317000 0.45149 0.655000 0.94253 TCA TCGA-HZ-7919-01A-11D-2154-08 SPTAN1-004 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054472.1 1 0 1 55 202 0 43 1 1 14 367 0 43 2 0 0 0 0 0 2 1 1.000000 55 201 0 43 2 -20.000000 1 1 0 0 1 0 1 1 2.052461 0 0.400000 1.870000 0.398798 0.990000 0.820000 1.000000 1.000000 0.978371 0.990000 1 0.940000 1.000000 ZER1 10444 broad.mit.edu 37 9 131513437 131513437 + Silent SNP G G A TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 G A G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr9:131513437G>A ENST00000291900.2 - 7 1555 c.1149C>T c.(1147-1149)cgC>cgT p.R383R snoU13_ENST00000459043.1_RNA|ZER1_ENST00000494461.1_5'Flank NM_006336.2 NP_006327.2 Q7Z7L7 ZER1_HUMAN zyg-11 related, cell cycle regulator 15 AACGCTCGATGCGGGCGATGT 0.627000 0 SO:0001819 synonymous_variant ENST00000291900.2 0 1 hg19 CCDS6910.1 TCGA-HZ-7919-01A-11D-2154-08 ZER1-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000054491.1 1 0 1 30 109 0 11 1 9.999989e-01 23 64 0 11 2 0 0 0 0 0 2 1 1.000000 30 109 0 11 2 -20.000000 1 1 0 0 1 0 1 1 2.052461 0 0.400000 1.870000 0.398798 0.990000 0.760000 1.000000 1.000000 0.967116 0.990000 1 0.900000 1.000000 MRPS2 51116 broad.mit.edu 37 9 138393703 138393703 + Missense_Mutation SNP G G C TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 G C G G Valid Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chr9:138393703G>C ENST00000371785.1 + 4 392 c.183G>C c.(181-183)aaG>aaC p.K61N MRPS2_ENST00000241600.5_Missense_Mutation_p.K61N|C9orf116_ENST00000371789.3_5'Flank|RP11-426A6.5_ENST00000415062.1_RNA|MRPS2_ENST00000488610.1_3'UTR|C9orf116_ENST00000429260.2_5'Flank|C9orf116_ENST00000371791.1_5'Flank Q9Y399 RT02_HUMAN mitochondrial ribosomal protein S2 6 TCAACGACAAGATTTTGAATG 0.572000 0 SO:0001583 missense ENST00000371785.1 1 1 hg19 CCDS6990.1 . . . . . . . . . . G 13.54 2.266862 0.40095 . . ENSG00000122140 ENST00000371785;ENST00000241600;ENST00000453385 T;T;T 0.35236 1.81;1.81;1.32 4.7 0.553 0.17235 . 0.218719 0.45361 D 0.000376 T 0.26011 0.0634 L 0.57536 1.79 0.09310 N 1 P 0.44429 0.835 B 0.38378 0.272 T 0.18429 -1.0337 10 0.49607 T 0.09 -5.9199 2.9054 0.05719 0.2189:0.1206:0.5366:0.1239 . 61 Q9Y399 RT02_HUMAN N 61;61;75 ENSP00000360850:K61N;ENSP00000241600:K61N;ENSP00000400082:K75N ENSP00000241600:K61N K + 3 2 MRPS2 137533524 0.901000 0.30685 0.000000 0.03702 0.160000 0.22226 1.674000 0.37544 -0.203000 0.10251 0.655000 0.94253 AAG TCGA-HZ-7919-01A-11D-2154-08 MRPS2-001 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000054998.1 1 0 1 114 494 0 89 1 9.999944e-01 17 57 0 89 2 0 0 0 0 0 2 1 1.000000 112 486 0 89 2 -20.000000 1 1 0 0 1 0 1 1 2.052461 0 0.400000 1.870000 0.398798 0.930000 0.780000 1.000000 1.000000 0.928163 0.930000 1 0.850000 1.000000 SLC25A6 293 broad.mit.edu 37 X 1508186 1508186 + Silent SNP C C T TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 C T C C Valid Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chrX:1508186C>T ENST00000381401.5 - 2 1260 c.546G>A c.(544-546)caG>caA p.Q182Q SLC25A6_ENST00000475167.1_5'UTR NM_001636.3 NP_001627.2 P12236 ADT3_HUMAN solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 6 11 all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122) Clodronate(DB00720) TGATGATGCCCTGCACGGAGA 0.627000 0 SO:0001819 synonymous_variant ENST00000381401.5 1 1 hg19 CCDS14114.1 TCGA-HZ-7919-01A-11D-2154-08 SLC25A6-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000055596.1 1 0 0 143 664 0 95 1 1 232 1049 0 95 2 0 0 0 0 0 2 1 1.000000 143 655 0 93 2 -3.246038 1 1 0 0 1 0 1 1 0.400000 1.870000 0.400000 0.880000 0.750000 1.000000 1.000000 0.886738 0.880000 1 0.810000 0.950000 FLNA 2316 broad.mit.edu 37 X 153583275 153583275 + Missense_Mutation SNP T T C TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 T C T T Inconclusive Somatic Phase_I WXS RNA Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chrX:153583275T>C ENST00000369850.3 - 31 5371 c.5135A>G c.(5134-5136)tAc>tGc p.Y1712C FLNA_ENST00000369856.3_5'UTR|FLNA_ENST00000422373.1_Missense_Mutation_p.Y1704C|FLNA_ENST00000344736.4_Missense_Mutation_p.Y1704C|FLNA_ENST00000360319.4_Missense_Mutation_p.Y1704C NM_001110556.1 NP_001104026.1 P21333 FLNA_HUMAN filamin A, alpha 6 all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176) GGGGGCCGTGTAGAAGATGTC 0.617000 OREG0003595 type=REGULATORY REGION|Gene=FLNA|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay 0 SO:0001583 missense ENST00000369850.3 1 1 hg19 CCDS48194.1 . . . . . . . . . . T 16.21 3.057671 0.55325 . . ENSG00000196924 ENST00000360319;ENST00000369852;ENST00000422373;ENST00000369850;ENST00000344736 D;D;D;D 0.95412 -3.7;-3.7;-3.7;-3.7 5.12 5.12 0.69794 Immunoglobulin E-set (1);Immunoglobulin-like fold (1); 0.000000 0.64402 D 0.000002 D 0.98485 0.9495 H 0.96748 3.875 0.80722 D 1 D;D 0.89917 1.0;1.0 D;D 0.97110 1.0;0.999 D 0.99605 1.0979 10 0.87932 D 0 . 14.2282 0.65873 0.0:0.0:0.0:1.0 . 1704;1712 P21333-2;P21333 .;FLNA_HUMAN C 1704;1685;1704;1712;1704 ENSP00000353467:Y1704C;ENSP00000416926:Y1704C;ENSP00000358866:Y1712C;ENSP00000358863:Y1704C ENSP00000358863:Y1704C Y - 2 0 FLNA 153236469 1.000000 0.71417 1.000000 0.80357 0.828000 0.46876 6.061000 0.71148 1.806000 0.52798 0.486000 0.48141 TAC TCGA-HZ-7919-01A-11D-2154-08 FLNA-002 KNOWN basic|appris_candidate_longest|CCDS protein_coding protein_coding OTTHUMT00000058942.3 1 0 1 109 332 0 65 0 1 0 603 0 65 2 0 0 0 0 0 2 1 1.000000 107 330 0 65 2 -20.000000 1 1 0 0 1 0 1 1 0.400000 1.870000 0.400000 0.990000 0.990000 1.000000 1.000000 0.999759 0.990000 1 0.990000 1.000000 BRWD3 254065 broad.mit.edu 37 X 79985487 79985487 + Missense_Mutation SNP G G A TCGA-HZ-7919-01A-11D-2154-08 TCGA-HZ-7919-10A-01D-2154-08 Untested Somatic Phase_I WXS none Illumina GAIIx 079bd60d-6112-4dc3-a9f8-d81ae2525b56 38e63aa2-a48f-464b-b927-ab6524cb5cc1 g.chrX:79985487G>A ENST00000373275.4 - 13 1376 c.1160C>T c.(1159-1161)aCg>aTg p.T387M NM_153252.4 NP_694984 Q6RI45 BRWD3_HUMAN bromodomain and WD repeat domain containing 3 87 AATTCTTGCCGTTCCATCTCG 0.299000 0 SO:0001583 missense ENST00000373275.4 1 1 hg19 CCDS14447.1 . . . . . . . . . . G 22.0 4.237206 0.79800 . . ENSG00000165288 ENST00000373275 T 0.69561 -0.41 4.37 4.37 0.52481 WD40/YVTN repeat-like-containing domain (1);Quinoprotein amine dehydrogenase, beta chain-like (1);WD40-repeat-containing domain (1); 0.000000 0.85682 D 0.000000 D 0.82655 0.5084 M 0.83953 2.67 0.58432 D 0.999999 D 0.89917 1.0 D 0.87578 0.998 D 0.85220 0.1026 9 . . . -2.364 16.3826 0.83473 0.0:0.0:1.0:0.0 . 387 Q6RI45 BRWD3_HUMAN M 387 ENSP00000362372:T387M . T - 2 0 BRWD3 79872143 1.000000 0.71417 1.000000 0.80357 0.913000 0.54294 7.207000 0.77899 2.035000 0.60131 0.513000 0.50165 ACG TCGA-HZ-7919-01A-11D-2154-08 BRWD3-001 KNOWN basic|appris_principal|CCDS protein_coding protein_coding OTTHUMT00000057344.1 0 0 1 70 306 1 43 0 4.591915e-01 0 8 1 43 2 0 0 0 0 0 2 1 1.000000 69 303 1 43 25 -3.356559 1 1 0 0 1 0 1 1 0.400000 1.870000 0.400000 0.920000 0.740000 1.000000 1.000000 0.919170 0.920000 1 0.830000 1.000000