#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
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	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_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	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_EVS_AA	i_EVS_All	i_EVS_EA	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_name_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
ADAMTS7	11173	genome.wustl.edu	37	15	79067099	79067099	+	Silent	SNP	G	G	C	rs142017909	byFrequency	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	g.chr15:79067099G>C	ENST00000388820.4	-	12	1953	c.1743C>G	c.(1741-1743)cgC>cgG	p.R581R	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	581	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R581R(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						GGAAGCGCTTGCGCTCACCCA	0.647																																						dbGAP											1	Substitution - coding silent(1)	large_intestine(1)											69.0	79.0	76.0					15																	79067099		2196	4292	6488	-	-	-	SO:0001819	synonymous_variant	0			AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	223	protein-coding gene	gene with protein product	"""COMPase"", ""a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"""	605009	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"""			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.1743C>G	15.37:g.79067099G>C		Somatic		WXS	Illumina GAIIx	Phase_IV	Q14F51|Q6P7J9	Silent	SNP	pfam_ADAM_spacer1,pfam_Peptidase_M12B_N,pfam_Thrombospondin_1_rpt,pfam_Peptidase_M12B,superfamily_Thrombospondin_1_rpt,smart_Thrombospondin_1_rpt,pfscan_PLAC,pfscan_Thrombospondin_1_rpt,pfscan_Peptidase_M12B,prints_Peptidase_M12B_ADAM-TS	p.R581	ENST00000388820.4	37	c.1743	CCDS32303.1	15																																																																																			ADAMTS7	-	pfam_Thrombospondin_1_rpt,superfamily_Thrombospondin_1_rpt,smart_Thrombospondin_1_rpt,pfscan_Thrombospondin_1_rpt	ENSG00000136378		0.647	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ADAMTS7	HGNC	protein_coding	OTTHUMT00000421331.1	30	0.00	0	G	NM_014272		79067099	79067099	-1	no_errors	ENST00000388820	ensembl	human	known	69_37n	silent	49	15.52	9	SNP	0.974	C
AK9	221264	genome.wustl.edu	37	6	109906330	109906332	+	In_Frame_Del	DEL	CTT	CTT	-	rs71770197|rs73519211|rs568921203|rs141134529	byFrequency	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	CTT	CTT					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	g.chr6:109906330_109906332delCTT	ENST00000424296.2	-	19	2184_2186	c.2108_2110delAAG	c.(2107-2112)gaagca>gca	p.E703del	AK9_ENST00000341338.6_5'UTR|AK9_ENST00000368948.2_In_Frame_Del_p.E703del	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	703					ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)										TTTTACCTTGCTTCTTCTTCTTC	0.227														1863	0.372005	0.2542	0.4092	5008	,	,		14640	0.377		0.4095	False		,,,				2504	0.4611					dbGAP											0										396,1116		113,170,473						-0.1	0.2		dbSNP_130	6	1116,1910		355,406,752	no	coding	AKD1	NM_001145128.2		468,576,1225	A1A1,A1R,RR		36.8804,26.1905,33.3186				1512,3026				-	-	-	SO:0001651	inframe_deletion	0			AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"""chromosome 6 open reading frame 224"", ""adenylate kinase domain containing 2"", ""chromosome 6 open reading frame 199"", ""adenylate kinase domain containing 1"""	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.2108_2110delAAG	6.37:g.109906339_109906341delCTT	ENSP00000410186:p.Glu703del	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	In_Frame_Del	DEL	pfam_Adenylate_kin,pfam_YHS,smart_AAA+_ATPase	p.E703in_frame_del	ENST00000424296.2	37	c.2110_2108	CCDS55048.1	6																																																																																			AKD1	-	NULL	ENSG00000155085		0.227	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	AKD1	HGNC	protein_coding		9	0	0	CTT	NM_001145128		109906330	109906332	-1	no_errors	ENST00000424296	ensembl	human	known	69_37n	in_frame_del	2	60	3	DEL	0.004:0.003:0.004	0
ATM	472	genome.wustl.edu	37	11	108098605	108098605	+	Missense_Mutation	SNP	G	G	T			TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	g.chr11:108098605G>T	ENST00000452508.2	+	4	364	c.175G>T	c.(175-177)Gct>Tct	p.A59S	Y_RNA_ENST00000384240.1_RNA|ATM_ENST00000278616.4_Missense_Mutation_p.A59S			Q13315	ATM_HUMAN	ATM serine/threonine kinase	59					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	GAATTGGGATGCTGTTTTTAG	0.294			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																												dbGAP	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	0													75.0	84.0	81.0					11																	108098605		2201	4295	6496	-	-	-	SO:0001583	missense	0	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.175G>T	11.37:g.108098605G>T	ENSP00000388058:p.Ala59Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	pfam_PIK-rel_kinase_FAT,pfam_PI3/4_kinase_cat_dom,pfam_TAN,pfam_FATC,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,smart_PI3/4_kinase_cat_dom,pfscan_PIK_FAT,pfscan_FATC,pfscan_PI3/4_kinase_cat_dom	p.A59S	ENST00000452508.2	37	c.175	CCDS31669.1	11	.	.	.	.	.	.	.	.	.	.	G	19.10	3.762123	0.69763	.	.	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000527891;ENST00000532931;ENST00000452508	T;T;T;T;T	0.58940	0.3;0.3;0.3;0.3;0.3	5.14	5.14	0.70334	Telomere-length maintenance and DNA damage repair (1);	0.192439	0.45361	D	0.000374	T	0.61223	0.2330	M	0.67953	2.075	0.33799	D	0.62639	P;D	0.54207	0.749;0.965	B;P	0.53006	0.388;0.715	T	0.65475	-0.6159	10	0.14252	T	0.57	.	9.7036	0.40203	0.1557:0.0:0.8443:0.0	.	59;59	Q6P7P1;Q13315	.;ATM_HUMAN	S	59	ENSP00000435747:A59S;ENSP00000278616:A59S;ENSP00000433955:A59S;ENSP00000432318:A59S;ENSP00000388058:A59S	ENSP00000278616:A59S	A	+	1	0	ATM	107603815	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.240000	0.51368	2.543000	0.85770	0.557000	0.71058	GCT	ATM	-	pfam_TAN	ENSG00000149311		0.294	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	ATM	HGNC	protein_coding	OTTHUMT00000389938.1	44	0.00	0	G	NM_000051		108098605	108098605	+1	no_errors	ENST00000278616	ensembl	human	known	69_37n	missense	33	10.81	4	SNP	1.000	T
C6orf57	135154	genome.wustl.edu	37	6	71298411	71298411	+	Missense_Mutation	SNP	G	G	T	rs200376688		TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	g.chr6:71298411G>T	ENST00000370474.3	+	3	335	c.311G>T	c.(310-312)cGc>cTc	p.R104L		NM_145267.2	NP_660310.2	Q5VUM1	SDHF4_HUMAN	chromosome 6 open reading frame 57	104					innate immune response (GO:0045087)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)				kidney(1)|lung(1)|skin(1)	3						CGAAAAGGACGCTGTATTGAT	0.348																																						dbGAP											0													73.0	83.0	79.0					6																	71298411		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC018085	CCDS4972.1	6q12	2011-12-13			ENSG00000154079	ENSG00000154079			20957	protein-coding gene	gene with protein product							Standard	NM_145267		Approved		uc003pfq.1	Q5VUM1	OTTHUMG00000014992	ENST00000370474.3:c.311G>T	6.37:g.71298411G>T	ENSP00000359505:p.Arg104Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	E1P532	Missense_Mutation	SNP	pfam_DUF1674	p.R104L	ENST00000370474.3	37	c.311	CCDS4972.1	6	.	.	.	.	.	.	.	.	.	.	G	34	5.381921	0.95967	.	.	ENSG00000154079	ENST00000370474	T	0.51071	0.72	6.03	6.03	0.97812	.	0.047118	0.85682	D	0.000000	T	0.54334	0.1852	M	0.68317	2.08	0.80722	D	1	D	0.56035	0.974	P	0.53035	0.716	T	0.54111	-0.8342	10	0.54805	T	0.06	-0.0647	19.3381	0.94329	0.0:0.0:1.0:0.0	.	104	Q5VUM1	CF057_HUMAN	L	104	ENSP00000359505:R104L	ENSP00000359505:R104L	R	+	2	0	C6orf57	71355132	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	8.894000	0.92506	2.854000	0.98071	0.655000	0.94253	CGC	C6orf57	-	pfam_DUF1674	ENSG00000154079		0.348	C6orf57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C6orf57	HGNC	protein_coding	OTTHUMT00000041140.1	28	0.00	0	G	NM_145267		71298411	71298411	+1	no_errors	ENST00000370474	ensembl	human	known	69_37n	missense	27	12.90	4	SNP	1.000	T
CDH1	999	genome.wustl.edu	37	16	68857397	68857398	+	Frame_Shift_Ins	INS	-	-	T			TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	g.chr16:68857397_68857398insT	ENST00000261769.5	+	13	2223_2224	c.2032_2033insT	c.(2032-2034)gtgfs	p.V678fs	CDH1_ENST00000422392.2_Frame_Shift_Ins_p.V617fs|CDH1_ENST00000562836.1_3'UTR|RP11-354M1.2_ENST00000563916.1_RNA	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	678	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)			NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		TAAAGACCAAGTGACCACCTTA	0.49			"""Mis, N, F, S"""		"""lobular breast, gastric"""	gastric			Hereditary Diffuse Gastric Cancer																													dbGAP	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"""cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"""		E	0																																										-	-	-	SO:0001589	frameshift_variant	0	Familial Cancer Database	HDGC	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"""CD molecules"", ""Cadherins / Major cadherins"""	1748	protein-coding gene	gene with protein product	"""E-Cadherin"""	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.2033dupT	16.37:g.68857398_68857398dupT	ENSP00000261769:p.Val678fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Frame_Shift_Ins	INS	pfam_Cadherin,pfam_Cadherin_cytoplasmic-dom,pfam_Cadherin_pro_dom,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.T679fs	ENST00000261769.5	37	c.2032_2033	CCDS10869.1	16																																																																																			CDH1	-	pfam_Cadherin,superfamily_Cadherin-like,pfscan_Cadherin	ENSG00000039068		0.490	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CDH1	HGNC	protein_coding	OTTHUMT00000268897.2	38	0.00	0	-	NM_004360		68857397	68857398	+1	no_errors	ENST00000261769	ensembl	human	known	69_37n	frame_shift_ins	20	25.93	7	INS	1.000:1.000	T
FAM153A	285596	genome.wustl.edu	37	5	177171957	177171957	+	Missense_Mutation	SNP	G	G	A			TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	g.chr5:177171957G>A	ENST00000440605.3	-	4	323	c.40C>T	c.(40-42)Cgg>Tgg	p.R14W	FAM153A_ENST00000393518.3_Missense_Mutation_p.R14W|FAM153A_ENST00000513554.1_Missense_Mutation_p.R14W|FAM153A_ENST00000510276.1_Missense_Mutation_p.R14W	NM_173663.3	NP_775934.3	Q9UHL3	F153A_HUMAN	family with sequence similarity 153, member A	14										kidney(6)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|stomach(1)	11	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CGTAGTTGCCGTTTCATCTCA	0.522																																						dbGAP											0													14.0	17.0	16.0					5																	177171957		1369	3101	4470	-	-	-	SO:0001583	missense	0			AB018295	CCDS34305.1	5q35.3	2010-05-12			ENSG00000170074	ENSG00000170074			29940	protein-coding gene	gene with protein product	"""NY REN 7 antigen"""					10508479, 9872452	Standard	NM_173663		Approved	NY-REN-7	uc003mic.3	Q9UHL3	OTTHUMG00000163394	ENST00000440605.3:c.40C>T	5.37:g.177171957G>A	ENSP00000411506:p.Arg14Trp	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K0F3|O94852	Missense_Mutation	SNP	prints_FAM153	p.R14W	ENST00000440605.3	37	c.40	CCDS34305.1	5	.	.	.	.	.	.	.	.	.	.	.	5.098	0.203698	0.09704	.	.	ENSG00000170074	ENST00000440977;ENST00000393518;ENST00000510276;ENST00000440605;ENST00000513554;ENST00000505531;ENST00000504518	.	.	.	.	.	.	.	.	.	.	.	T	0.16557	0.0398	N	0.08118	0	0.09310	N	1	.;B	0.02656	.;0.0	.;B	0.01281	.;0.0	T	0.19321	-1.0309	6	0.45353	T	0.12	.	.	.	.	.	14;14	A8MWQ6;Q9UHL3	.;F153A_HUMAN	W	91;14;14;14;14;14;43	.	ENSP00000353887:R14W	R	-	1	2	FAM153A	177104563	0.840000	0.29493	0.011000	0.14972	0.012000	0.07955	0.720000	0.25896	0.000000	0.14550	0.000000	0.15137	CGG	FAM153A	-	prints_FAM153	ENSG00000170074		0.522	FAM153A-022	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	FAM153A	HGNC	protein_coding	OTTHUMT00000417242.1	47	0.00	0	G	NM_173663		177171957	177171957	-1	no_errors	ENST00000360669	ensembl	human	known	69_37n	missense	30	14.29	5	SNP	0.012	A
GPNMB	10457	genome.wustl.edu	37	7	23309653	23309653	+	Missense_Mutation	SNP	A	A	C			TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	g.chr7:23309653A>C	ENST00000381990.2	+	9	1485	c.1324A>C	c.(1324-1326)Agc>Cgc	p.S442R	GPNMB_ENST00000539136.1_Missense_Mutation_p.S331R|GPNMB_ENST00000453162.2_Missense_Mutation_p.S384R|GPNMB_ENST00000258733.4_Missense_Mutation_p.S430R	NM_001005340.1|NM_002510.2	NP_001005340.1|NP_002501.1	Q14956	GPNMB_HUMAN	glycoprotein (transmembrane) nmb	442					bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|negative regulation of cell proliferation (GO:0008285)|osteoblast differentiation (GO:0001649)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)			breast(5)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(3)|stomach(2)	41			GBM - Glioblastoma multiforme(13;0.154)			CACAGTCTGCAGCCCTGTGGA	0.582																																						dbGAP											0													184.0	149.0	161.0					7																	23309653		2203	4300	6503	-	-	-	SO:0001583	missense	0			X76534	CCDS5380.1, CCDS34610.1	7p	2008-07-18			ENSG00000136235	ENSG00000136235			4462	protein-coding gene	gene with protein product	"""transmembrane glycoprotein"", ""glycoprotein NMB"", ""glycoprotein nmb-like protein"", ""osteoactivin"""	604368				7814155	Standard	NM_002510		Approved	NMB, HGFIN	uc003swc.3	Q14956	OTTHUMG00000022811	ENST00000381990.2:c.1324A>C	7.37:g.23309653A>C	ENSP00000371420:p.Ser442Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	A4D155|Q6UVX1|Q8N1A1	Missense_Mutation	SNP	pfam_PKD_dom,superfamily_PKD_dom,smart_PKD/Chitinase_dom,pfscan_PKD_dom	p.S442R	ENST00000381990.2	37	c.1324	CCDS34610.1	7	.	.	.	.	.	.	.	.	.	.	A	13.66	2.302733	0.40795	.	.	ENSG00000136235	ENST00000258733;ENST00000435486;ENST00000381990;ENST00000425903;ENST00000539136;ENST00000453162	T;T;T;T	0.14516	2.52;2.51;2.51;2.5	6.03	2.82	0.32997	.	0.550372	0.19234	N	0.119324	T	0.11665	0.0284	L	0.40543	1.245	0.09310	N	1	B;B;B;B	0.33413	0.355;0.404;0.411;0.302	B;B;B;B	0.32980	0.156;0.148;0.07;0.075	T	0.15578	-1.0432	10	0.66056	D	0.02	-4.1049	8.4462	0.32843	0.2949:0.0:0.7051:0.0	.	331;384;442;430	F6SKP1;F5GY20;Q14956;Q14956-2	.;.;GPNMB_HUMAN;.	R	430;477;442;325;331;384	ENSP00000258733:S430R;ENSP00000371420:S442R;ENSP00000445266:S331R;ENSP00000405586:S384R	ENSP00000258733:S430R	S	+	1	0	GPNMB	23276178	0.002000	0.14202	0.002000	0.10522	0.013000	0.08279	1.112000	0.31172	0.269000	0.21961	-0.321000	0.08615	AGC	GPNMB	-	NULL	ENSG00000136235		0.582	GPNMB-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	GPNMB	HGNC	protein_coding	OTTHUMT00000327152.1	33	0.00	0	A	NM_001005340		23309653	23309653	+1	no_errors	ENST00000381990	ensembl	human	known	69_37n	missense	36	36.84	21	SNP	0.036	C
GSR	2936	genome.wustl.edu	37	8	30557645	30557645	+	Silent	SNP	G	G	A			TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	g.chr8:30557645G>A	ENST00000221130.5	-	6	738	c.648C>T	c.(646-648)agC>agT	p.S216S	GSR_ENST00000414019.1_Silent_p.S173S|GSR_ENST00000537535.1_Silent_p.S216S|GSR_ENST00000541648.1_Silent_p.S216S|GSR_ENST00000546342.1_Silent_p.S216S	NM_000637.3|NM_001195102.1|NM_001195103.1	NP_000628.2|NP_001182031.1|NP_001182032.1	P00390	GSHR_HUMAN	glutathione reductase	216					cell redox homeostasis (GO:0045454)|glutathione metabolic process (GO:0006749)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|glutathione-disulfide reductase activity (GO:0004362)|NADP binding (GO:0050661)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(2)	23				KIRC - Kidney renal clear cell carcinoma(542;0.105)|Kidney(114;0.125)	Carmustine(DB00262)|Flavin adenine dinucleotide(DB03147)|Glutathione(DB00143)	TTATTCCTAAGCTGGCACCTA	0.433																																						dbGAP											0													120.0	111.0	114.0					8																	30557645		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0				CCDS34877.1, CCDS56530.1, CCDS56531.1, CCDS56532.1	8p21.1	2012-10-02			ENSG00000104687	ENSG00000104687	1.8.1.7		4623	protein-coding gene	gene with protein product		138300					Standard	NM_000637		Approved		uc003xih.2	P00390	OTTHUMG00000163946	ENST00000221130.5:c.648C>T	8.37:g.30557645G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	C8KIL8|C8KIL9|C8KIM0|D3DSV3|Q7Z5C9|Q9NP63	Missense_Mutation	SNP	pfam_Pyr_nucl-diS_OxRdtase_FAD/NAD,pfam_Pyr_OxRdtase_NAD-bd_dom,prints_FAD_pyr_nucl-diS_OxRdtase,prints_Hg_reductase	p.L172F	ENST00000221130.5	37	c.514	CCDS34877.1	8	.	.	.	.	.	.	.	.	.	.	g	1.641	-0.516356	0.04200	.	.	ENSG00000104687	ENST00000520888	.	.	.	5.96	0.0469	0.14278	.	.	.	.	.	T	0.50633	0.1627	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37798	-0.9690	4	.	.	.	0.0088	5.291	0.15727	0.3748:0.139:0.4862:0.0	.	.	.	.	F	172	.	.	L	-	1	0	GSR	30677187	1.000000	0.71417	0.904000	0.35570	0.156000	0.22039	0.631000	0.24568	0.142000	0.18901	-0.737000	0.03537	CTT	GSR	-	pfam_Pyr_nucl-diS_OxRdtase_FAD/NAD	ENSG00000104687		0.433	GSR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GSR	HGNC	protein_coding	OTTHUMT00000376519.1	45	0.00	0	G			30557645	30557645	-1	pseudogene:no_stop_codon	ENST00000520888	ensembl	human	novel	69_37n	missense	35	12.50	5	SNP	0.754	A
HDAC2	3066	genome.wustl.edu	37	6	114292109	114292110	+	5'UTR	INS	-	-	CTG	rs545748113|rs528988883	byFrequency	TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	g.chr6:114292109_114292110insCTG	ENST00000519065.1	-	0	339_340				RP3-399L15.3_ENST00000519104.1_RNA|RP3-399L15.3_ENST00000449620.2_RNA|RP3-399L15.3_ENST00000521888.1_RNA|RP3-399L15.3_ENST00000436876.2_RNA|RP3-399L15.3_ENST00000520891.1_RNA|RP3-399L15.3_ENST00000520554.1_RNA|RP3-399L15.3_ENST00000522844.1_RNA|HDAC2_ENST00000519108.1_5'Flank|HDAC2_ENST00000398283.2_In_Frame_Ins_p.81_82insS|HDAC2_ENST00000368632.2_5'UTR			Q92769	HDAC2_HUMAN	histone deacetylase 2						ATP-dependent chromatin remodeling (GO:0043044)|blood coagulation (GO:0007596)|cardiac muscle cell development (GO:0055013)|chromatin remodeling (GO:0006338)|circadian regulation of gene expression (GO:0032922)|dendrite development (GO:0016358)|embryonic digit morphogenesis (GO:0042733)|epidermal cell differentiation (GO:0009913)|eyelid development in camera-type eye (GO:0061029)|fungiform papilla formation (GO:0061198)|hair follicle placode formation (GO:0060789)|hippocampus development (GO:0021766)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|maintenance of chromatin silencing (GO:0006344)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell cycle (GO:0045786)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of neuron projection development (GO:0010977)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of proteolysis (GO:0045862)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of protein deacetylation (GO:0090311)|regulation of protein kinase B signaling (GO:0051896)|regulation of sarcomere organization (GO:0060297)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)|replication fork (GO:0005657)|Sin3 complex (GO:0016580)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|poly(A) RNA binding (GO:0044822)|protein deacetylase activity (GO:0033558)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			biliary_tract(1)|central_nervous_system(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(87;0.000629)|all_epithelial(87;0.00274)|Colorectal(196;0.0317)|all_lung(197;0.24)		all cancers(137;0.00318)|OV - Ovarian serous cystadenocarcinoma(136;0.00569)|Epithelial(106;0.0112)|GBM - Glioblastoma multiforme(226;0.0832)	Aminophylline(DB01223)|Lovastatin(DB00227)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Valproic Acid(DB00313)|Vorinostat(DB02546)	GGCTCCTCCTCctgctgctgct	0.688														365	0.0728834	0.0227	0.1297	5008	,	,		15962	0.0258		0.1034	False		,,,				2504	0.1176					dbGAP											0																																										-	-	-	SO:0001623	5_prime_UTR_variant	0			U31814	CCDS43493.1, CCDS43493.2	6q21	2008-08-29			ENSG00000196591	ENSG00000196591			4853	protein-coding gene	gene with protein product		605164				9782097	Standard	NM_001527		Approved	RPD3, YAF1	uc003pwd.2	Q92769	OTTHUMG00000015411	ENST00000519065.1:c.-38->CAG	6.37:g.114292116_114292118dupCTG		Somatic		WXS	Illumina GAIIx	Phase_IV	B3KRS5|B4DL58|E1P561|Q5SRI8|Q5SZ86|Q8NEH4	In_Frame_Ins	INS	pfam_His_deacetylse_dom,prints_His_deacetylse_1,prints_His_deacetylse	p.82in_frame_insS	ENST00000519065.1	37	c.246_245	CCDS43493.2	6																																																																																			HDAC2	-	NULL	ENSG00000196591		0.688	HDAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HDAC2	HGNC	protein_coding	OTTHUMT00000041909.2	11	0.00	0	-			114292109	114292110	-1	no_errors	ENST00000398283	ensembl	human	known	69_37n	in_frame_ins	13	13.33	2	INS	0.014:0.004	CTG
HSP90AB1	3326	genome.wustl.edu	37	6	44219526	44219527	+	Missense_Mutation	DNP	GC	GC	TT			TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	G|C	G|C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	g.chr6:44219526_44219527GC>TT	ENST00000371554.1	+	9	1581_1582	c.1367_1368GC>TT	c.(1366-1368)cGC>cTT	p.R456L	HSP90AB1_ENST00000371646.5_Missense_Mutation_p.R456L|SLC35B2_ENST00000495706.1_5'Flank|MIR4647_ENST00000583964.1_RNA|HSP90AB1_ENST00000353801.3_Missense_Mutation_p.R456L			P08238	HS90B_HUMAN	heat shock protein 90kDa alpha (cytosolic), class B member 1	456					axon guidance (GO:0007411)|cellular response to interleukin-4 (GO:0071353)|cellular response to organic cyclic compound (GO:0071407)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|placenta development (GO:0001890)|positive regulation of cell size (GO:0045793)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein folding (GO:0006457)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to salt stress (GO:0009651)|response to unfolded protein (GO:0006986)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|CTP binding (GO:0002135)|dATP binding (GO:0032564)|double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|poly(A) RNA binding (GO:0044822)|TPR domain binding (GO:0030911)|UTP binding (GO:0002134)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(12)|prostate(2)|skin(2)|urinary_tract(2)	33	all_cancers(18;1.7e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GAGCTGCTGCGCTATCATACCT	0.485																																						dbGAP											0																																										-	-	-	SO:0001583	missense	0			AF275719	CCDS4909.1	6p12	2011-09-02	2006-02-24	2006-02-24	ENSG00000096384	ENSG00000096384		"""Heat shock proteins / HSPC"""	5258	protein-coding gene	gene with protein product		140572	"""heat shock 90kD protein 1, beta"", ""heat shock 90kDa protein 1, beta"""	HSPC2, HSPCB		2768249, 16269234	Standard	NM_001271969		Approved		uc031sor.1	P08238	OTTHUMG00000014761	Exception_encountered	6.37:g.44219526_44219527delinsTT	ENSP00000360609:p.Arg456Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	B2R5P0|Q5T9W7|Q9NQW0|Q9NTK6	Missense_Mutation	SNP	pfam_Hsp90,pfam_ATPase-like_ATP-bd,superfamily_Ribosomal_S5_D2-typ_fold,superfamily_ATPase-like_ATP-bd,smart_ATPase-like_ATP-bd,pirsf_Hsp90,prints_Hsp90_N|pfam_Hsp90,superfamily_Ribosomal_S5_D2-typ_fold	p.R456L|p.A82V	ENST00000371554.1	37	c.1367|c.245	CCDS4909.1	6																																																																																			HSP90AB1	-	pfam_Hsp90,superfamily_Ribosomal_S5_D2-typ_fold,pirsf_Hsp90|pfam_Hsp90,superfamily_Ribosomal_S5_D2-typ_fold	ENSG00000096384		0.485	HSP90AB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	HSP90AB1	HGNC	protein_coding	OTTHUMT00000040730.1	52|53	0.00	0	G|C	NM_007355		44219526|44219527	44219526|44219527	+1	no_errors|no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000353801|ENST00000435812	ensembl	human	known	69_37n	missense	52	17.46|16.13	11|10	SNP	1.000|0.997	T
NUP214	8021	genome.wustl.edu	37	9	134027158	134027158	+	Silent	SNP	T	T	G			TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	g.chr9:134027158T>G	ENST00000359428.5	+	17	2457	c.2313T>G	c.(2311-2313)acT>acG	p.T771T	RP11-544A12.4_ENST00000588378.1_RNA|RP11-544A12.4_ENST00000589667.1_RNA|RP11-544A12.4_ENST00000415391.2_RNA|NUP214_ENST00000451030.1_Silent_p.T772T|RP11-544A12.4_ENST00000590461.1_RNA|RP11-544A12.4_ENST00000587264.1_RNA|RP11-544A12.4_ENST00000589540.1_RNA|RP11-544A12.4_ENST00000586290.1_RNA|RP11-544A12.4_ENST00000587408.1_RNA|NUP214_ENST00000411637.2_Silent_p.T761T			P35658	NU214_HUMAN	nucleoporin 214kDa	771	11 X 5 AA approximate repeats.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		TGAAAACAACTTTACTTGAGG	0.378			T	"""DEK, SET, ABL1"""	"""AML, T-ALL"""																																Pancreas(4;24 48 25510 30394 32571)	dbGAP		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	0													132.0	133.0	133.0					9																	134027158		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"""nuclear pore complex protein Nup214"", ""CAN protein, putative oncogene"""	114350	"""nucleoporin 214kD (CAIN)"""			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.2313T>G	9.37:g.134027158T>G		Somatic		WXS	Illumina GAIIx	Phase_IV	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Silent	SNP	smart_WD40_repeat	p.T772	ENST00000359428.5	37	c.2316	CCDS6940.1	9																																																																																			NUP214	-	NULL	ENSG00000126883		0.378	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NUP214	HGNC	protein_coding	OTTHUMT00000054694.2	75	0.00	0	T	NM_005085		134027158	134027158	+1	no_errors	ENST00000451030	ensembl	human	known	69_37n	silent	58	19.44	14	SNP	0.000	G
OPN4	94233	genome.wustl.edu	37	10	88421081	88421081	+	Missense_Mutation	SNP	G	G	A			TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	g.chr10:88421081G>A	ENST00000241891.5	+	7	1176	c.1009G>A	c.(1009-1011)Gtc>Atc	p.V337I	OPN4_ENST00000372071.2_Missense_Mutation_p.V348I	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 4	337					phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|rhodopsin mediated signaling pathway (GO:0016056)|rhythmic process (GO:0048511)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	11-cis retinal binding (GO:0005502)|G-protein coupled photoreceptor activity (GO:0008020)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(5)|ovary(3)	18						GGTGCCAGCCGTCATCGCCAA	0.582																																						dbGAP											0													248.0	173.0	198.0					10																	88421081		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF147788	CCDS7376.1, CCDS31237.1	10q22	2012-08-08	2008-04-16		ENSG00000122375	ENSG00000122375		"""GPCR / Class A : Opsin receptors"""	14449	protein-coding gene	gene with protein product	"""melanopsin"""	606665	"""opsin 4 (melanopsin)"""			10632589	Standard	NM_001030015		Approved	MOP, melanopsin	uc001kdp.3	Q9UHM6	OTTHUMG00000018654	ENST00000241891.5:c.1009G>A	10.37:g.88421081G>A	ENSP00000241891:p.Val337Ile	Somatic		WXS	Illumina GAIIx	Phase_IV	B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Missense_Mutation	SNP	pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam,prints_7TM_GPCR_Rhodpsn,prints_Opsin	p.V348I	ENST00000241891.5	37	c.1042	CCDS7376.1	10	.	.	.	.	.	.	.	.	.	.	G	15.63	2.889294	0.52014	.	.	ENSG00000122375	ENST00000372071;ENST00000241891;ENST00000443292	T;T;T	0.72282	-0.64;-0.64;-0.64	5.03	2.8	0.32819	GPCR, rhodopsin-like superfamily (1);	0.396730	0.24156	N	0.041024	T	0.60612	0.2282	L	0.48260	1.515	0.41849	D	0.990162	P;B;B	0.38827	0.649;0.195;0.252	B;B;B	0.34418	0.182;0.079;0.089	T	0.64313	-0.6437	10	0.51188	T	0.08	.	12.2616	0.54652	0.1644:0.0:0.8356:0.0	.	348;337;348	C9JWU6;Q9UHM6;Q9UHM6-2	.;OPN4_HUMAN;.	I	348;337;348	ENSP00000361141:V348I;ENSP00000241891:V337I;ENSP00000393132:V348I	ENSP00000241891:V337I	V	+	1	0	OPN4	88411061	1.000000	0.71417	0.987000	0.45799	0.961000	0.63080	4.720000	0.61944	1.120000	0.41904	0.561000	0.74099	GTC	OPN4	-	pfam_7TM_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_supfam,prints_7TM_GPCR_Rhodpsn,prints_Opsin	ENSG00000122375		0.582	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OPN4	HGNC	protein_coding	OTTHUMT00000049158.2	44	0.00	0	G	NM_033282		88421081	88421081	+1	no_errors	ENST00000372071	ensembl	human	known	69_37n	missense	26	16.13	5	SNP	0.995	A
PAXIP1	22976	genome.wustl.edu	37	7	154767672	154767672	+	Frame_Shift_Del	DEL	C	C	-			TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	g.chr7:154767672delC	ENST00000404141.1	-	6	962	c.808delG	c.(808-810)gaafs	p.E270fs	PAXIP1_ENST00000397192.1_Frame_Shift_Del_p.E270fs|PAXIP1_ENST00000473219.1_5'UTR			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	270					adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		TGTGGGACTTCGGCCGGGGTC	0.463																																						dbGAP											0													49.0	47.0	47.0					7																	154767672		1838	4080	5918	-	-	-	SO:0001589	frameshift_variant	0			U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"""PAX transcription activation domain interacting protein 1 like"""	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.808delG	7.37:g.154767672delC	ENSP00000384048:p.Glu270fs	Somatic		WXS	Illumina GAIIx	Phase_IV	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Frame_Shift_Del	DEL	pfam_BRCT_dom,superfamily_BRCT_dom,smart_BRCT_dom,pfscan_BRCT_dom	p.E270fs	ENST00000404141.1	37	c.808	CCDS47753.1	7																																																																																			PAXIP1	-	NULL	ENSG00000157212		0.463	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	PAXIP1	HGNC	protein_coding	OTTHUMT00000322223.1	56	0.00	0	C	NM_007349		154767672	154767672	-1	no_errors	ENST00000397192	ensembl	human	known	69_37n	frame_shift_del	49	16.39	10	DEL	1.000	-
SLX4	84464	genome.wustl.edu	37	16	3656563	3656563	+	Missense_Mutation	SNP	C	C	A			TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	g.chr16:3656563C>A	ENST00000294008.3	-	3	1312	c.672G>T	c.(670-672)ttG>ttT	p.L224F		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	224	Interaction with SLX4IP, ERCC4 and MSH2.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						AAGCGTGTCTCAAACGCTCGG	0.547								Direct reversal of damage																														dbGAP											0													216.0	215.0	215.0					16																	3656563		2197	4300	6497	-	-	-	SO:0001583	missense	0			AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.672G>T	16.37:g.3656563C>A	ENSP00000294008:p.Leu224Phe	Somatic		WXS	Illumina GAIIx	Phase_IV	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	pfam_BTB_POZ,superfamily_BTB/POZ_fold,smart_BTB/POZ-like,pfscan_BTB/POZ-like	p.L224F	ENST00000294008.3	37	c.672	CCDS10506.2	16	.	.	.	.	.	.	.	.	.	.	C	20.7	4.029310	0.75504	.	.	ENSG00000188827	ENST00000294008	T	0.03094	4.05	5.16	2.11	0.27256	.	0.088392	0.44902	D	0.000420	T	0.10594	0.0259	L	0.55990	1.75	0.25433	N	0.988167	D	0.89917	1.0	D	0.79108	0.992	T	0.05257	-1.0896	10	0.72032	D	0.01	.	6.2509	0.20845	0.0:0.6321:0.136:0.2319	.	224	Q8IY92	SLX4_HUMAN	F	224	ENSP00000294008:L224F	ENSP00000294008:L224F	L	-	3	2	SLX4	3596564	0.999000	0.42202	0.003000	0.11579	0.562000	0.35680	1.830000	0.39131	0.286000	0.22352	-0.136000	0.14681	TTG	SLX4	-	NULL	ENSG00000188827		0.547	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLX4	HGNC	protein_coding	OTTHUMT00000157301.3	92	0.00	0	C	NM_032444		3656563	3656563	-1	no_errors	ENST00000294008	ensembl	human	known	69_37n	missense	90	26.83	33	SNP	0.588	A
SOGA1	140710	genome.wustl.edu	37	20	35443694	35443694	+	Silent	SNP	C	C	A			TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	g.chr20:35443694C>A	ENST00000357779.3	-	5	1763	c.1437G>T	c.(1435-1437)ctG>ctT	p.L479L	SOGA1_ENST00000456801.2_Silent_p.L320L|SOGA1_ENST00000237536.4_Silent_p.L717L|SOGA1_ENST00000279034.6_Silent_p.L479L			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	479					insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						GCAGCACGCTCAGGCGCACCA	0.622																																						dbGAP											0													48.0	54.0	52.0					20																	35443694		2201	4300	6501	-	-	-	SO:0001819	synonymous_variant	0			AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639			16111	protein-coding gene	gene with protein product	"""suppressor of glucose by autophagy"", ""suppressor of glucose from autophagy"""		"""chromosome 20 open reading frame 117"", ""KIAA0889"""	C20orf117, KIAA0889		20813965	Standard	NM_080627		Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000357779.3:c.1437G>T	20.37:g.35443694C>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Nonsense_Mutation	SNP	pfam_DUF3166	p.E331*	ENST00000357779.3	37	c.991		20																																																																																			SOGA1	-	NULL	ENSG00000149639		0.622	SOGA1-201	KNOWN	basic	protein_coding	SOGA1	HGNC	protein_coding		22	0.00	0	C	NM_199181		35443694	35443694	-1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000465671	ensembl	human	known	69_37n	nonsense	18	18.18	4	SNP	0.938	A
TAS2R38	5726	genome.wustl.edu	37	7	141672880	141672880	+	Missense_Mutation	SNP	G	G	T			TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	g.chr7:141672880G>T	ENST00000547270.1	-	1	693	c.610C>A	c.(610-612)Cct>Act	p.P204T		NM_176817.4	NP_789787	P59533	T2R38_HUMAN	taste receptor, type 2, member 38	204					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			NS(2)|breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|skin(1)|stomach(1)	21	Melanoma(164;0.0171)					AGGAAAGGAGGCACAGACCAC	0.428																																						dbGAP											0													112.0	119.0	117.0					7																	141672880		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF494231	CCDS34765.1	7q34	2012-10-03	2003-05-29	2003-05-30	ENSG00000257138	ENSG00000257138		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	9584	protein-coding gene	gene with protein product		607751	"""phenylthiocarbamide tasting"""	PTC		12624758, 12584440	Standard	NM_176817		Approved	T2R61	uc003vwx.1	P59533	OTTHUMG00000158374	ENST00000547270.1:c.610C>A	7.37:g.141672880G>T	ENSP00000448219:p.Pro204Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	A4D1U6|P59552|Q2M3E8|Q645W3|Q86UK3	Missense_Mutation	SNP	pfam_TAS2_rcpt	p.P204T	ENST00000547270.1	37	c.610	CCDS34765.1	7	.	.	.	.	.	.	.	.	.	.	G	5.147	0.212796	0.09757	.	.	ENSG00000257138	ENST00000547270	T	0.36520	1.25	5.0	1.07	0.20283	.	0.448828	0.19970	N	0.102019	T	0.31327	0.0793	L	0.59436	1.845	0.09310	N	1	B	0.17852	0.024	B	0.28385	0.089	T	0.30880	-0.9963	10	0.54805	T	0.06	.	4.5901	0.12302	0.2737:0.1618:0.5645:0.0	.	204	P59533	T2R38_HUMAN	T	204	ENSP00000448219:P204T	ENSP00000331291:P204T	P	-	1	0	TAS2R38	141319349	0.002000	0.14202	0.001000	0.08648	0.079000	0.17450	1.066000	0.30604	0.288000	0.22398	0.655000	0.94253	CCT	TAS2R38	-	pfam_TAS2_rcpt	ENSG00000257138		0.428	TAS2R38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TAS2R38	HGNC	protein_coding	OTTHUMT00000350810.2	43	0.00	0	G	NM_176817		141672880	141672880	-1	no_errors	ENST00000547270	ensembl	human	known	69_37n	missense	24	14.29	4	SNP	0.000	T
TBX3	6926	genome.wustl.edu	37	12	115115446	115115446	+	Frame_Shift_Del	DEL	T	T	-			TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	g.chr12:115115446delT	ENST00000257566.3	-	5	1269	c.880delA	c.(880-882)atafs	p.I294fs	TBX3_ENST00000349155.2_Frame_Shift_Del_p.I274fs	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	294					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		TTGTTGTCTATTTTTAACTGG	0.358																																						dbGAP											0													91.0	87.0	89.0					12																	115115446		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0			BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"""T-boxes"""	11602	protein-coding gene	gene with protein product		601621	"""ulnar mammary syndrome"""	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.880delA	12.37:g.115115446delT	ENSP00000257566:p.Ile294fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q8TB20|Q9UKF8	Frame_Shift_Del	DEL	pfam_TF_T-box,pfam_TBX,superfamily_p53-like_TF_DNA-bd,smart_TF_T-box,pfscan_TF_T-box,prints_TF_T-box	p.I294fs	ENST00000257566.3	37	c.880	CCDS9176.1	12																																																																																			TBX3	-	pfam_TF_T-box,superfamily_p53-like_TF_DNA-bd,smart_TF_T-box,pfscan_TF_T-box	ENSG00000135111		0.358	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TBX3	HGNC	protein_coding	OTTHUMT00000404947.2	66	0.00	0	T	NM_016569, NM_005996		115115446	115115446	-1	no_errors	ENST00000257566	ensembl	human	known	69_37n	frame_shift_del	37	19.57	9	DEL	1.000	-
TBX5	6910	genome.wustl.edu	37	12	114793417	114793417	+	Missense_Mutation	SNP	C	C	T	rs556197042		TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	g.chr12:114793417C>T	ENST00000310346.4	-	9	2143	c.1477G>A	c.(1477-1479)Gtg>Atg	p.V493M	TBX5_ENST00000405440.2_Missense_Mutation_p.V493M|TBX5_ENST00000349716.5_Missense_Mutation_p.V443M	NM_000192.3	NP_000183.2	Q99593	TBX5_HUMAN	T-box 5	493					apoptotic nuclear changes (GO:0030262)|atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His development (GO:0003166)|cardiac left ventricle formation (GO:0003218)|cardiac muscle cell differentiation (GO:0055007)|cell migration involved in coronary vasculogenesis (GO:0060980)|cell-cell signaling (GO:0007267)|embryonic forelimb morphogenesis (GO:0035115)|embryonic limb morphogenesis (GO:0030326)|endocardial cushion development (GO:0003197)|forelimb morphogenesis (GO:0035136)|gene expression (GO:0010467)|heart development (GO:0007507)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|pattern specification process (GO:0007389)|pericardium development (GO:0060039)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of execution phase of apoptosis (GO:1900117)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(29)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0893)		GTCCTTGGCACGCCATGAGAG	0.602													C|||	1	0.000199681	0.0	0.0014	5008	,	,		19229	0.0		0.0	False		,,,				2504	0.0				NSCLC(152;1358 1980 4050 23898 40356)	dbGAP											0													57.0	55.0	56.0					12																	114793417		2203	4300	6503	-	-	-	SO:0001583	missense	0			U89353	CCDS9173.1, CCDS9174.1	12q24.1	2014-09-17			ENSG00000089225	ENSG00000089225		"""T-boxes"""	11604	protein-coding gene	gene with protein product		601620		HOS		8988165, 8054982	Standard	NM_000192		Approved		uc001tvo.4	Q99593	OTTHUMG00000166191	ENST00000310346.4:c.1477G>A	12.37:g.114793417C>T	ENSP00000309913:p.Val493Met	Somatic		WXS	Illumina GAIIx	Phase_IV	A6ND77|O15301|Q96TB0|Q9Y4I2	Missense_Mutation	SNP	pfam_TF_T-box,superfamily_p53-like_TF_DNA-bd,smart_TF_T-box,prints_TF_T-box,pfscan_TF_T-box	p.V493M	ENST00000310346.4	37	c.1477	CCDS9173.1	12	.	.	.	.	.	.	.	.	.	.	C	12.78	2.040309	0.35989	.	.	ENSG00000089225	ENST00000349716;ENST00000310346;ENST00000405440	D;D;D	0.88277	-2.32;-2.36;-2.36	5.42	3.61	0.41365	.	0.326142	0.33180	N	0.005181	T	0.81851	0.4910	L	0.40543	1.245	0.80722	D	1	P	0.39071	0.658	B	0.31245	0.126	T	0.79332	-0.1847	10	0.51188	T	0.08	.	11.91	0.52733	0.0:0.8596:0.0:0.1404	.	493	Q99593	TBX5_HUMAN	M	443;493;493	ENSP00000337723:V443M;ENSP00000309913:V493M;ENSP00000384152:V493M	ENSP00000309913:V493M	V	-	1	0	TBX5	113277800	1.000000	0.71417	0.904000	0.35570	0.689000	0.40095	2.771000	0.47670	0.680000	0.31366	-0.122000	0.15005	GTG	TBX5	-	NULL	ENSG00000089225		0.602	TBX5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	TBX5	HGNC	protein_coding	OTTHUMT00000388297.1	19	0.00	0	C	NM_080717		114793417	114793417	-1	no_errors	ENST00000310346	ensembl	human	known	69_37n	missense	15	34.78	8	SNP	0.986	T
TNRC6C	57690	genome.wustl.edu	37	17	76089144	76089144	+	Nonsense_Mutation	SNP	G	G	A			TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	g.chr17:76089144G>A	ENST00000588061.1	+	17	4828	c.4101G>A	c.(4099-4101)tgG>tgA	p.W1367*	TNRC6C_ENST00000588847.1_Nonsense_Mutation_p.W1364*|TNRC6C_ENST00000301624.4_Nonsense_Mutation_p.W1367*|TNRC6C_ENST00000544502.1_Nonsense_Mutation_p.W1364*|TNRC6C_ENST00000335749.4_Nonsense_Mutation_p.W1364*|TNRC6C_ENST00000541771.1_Nonsense_Mutation_p.W1367*			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	1367	Silencing domain; interaction with CNOT1 and PAN3.				embryonic hemopoiesis (GO:0035162)|endoderm formation (GO:0001706)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of gene silencing by miRNA (GO:0060964)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			CCCATAGCTGGTCACGTGCCA	0.512																																						dbGAP											0													68.0	66.0	66.0					17																	76089144		2005	4189	6194	-	-	-	SO:0001587	stop_gained	0			AL834429	CCDS45798.1, CCDS45799.1	17q25.3	2012-10-04			ENSG00000078687	ENSG00000078687		"""Trinucleotide (CAG) repeat containing"""	29318	protein-coding gene	gene with protein product		610741					Standard	NM_018996		Approved	KIAA1582, FLJ20015	uc002juf.2	Q9HCJ0	OTTHUMG00000132642	ENST00000588061.1:c.4101G>A	17.37:g.76089144G>A	ENSP00000468647:p.Trp1367*	Somatic		WXS	Illumina GAIIx	Phase_IV	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Nonsense_Mutation	SNP	pfam_Argonaute_hook_dom,pfam_UBA/transl_elong_EF1B_N,superfamily_UBA-like,smart_UBA/transl_elong_EF1B_N_euk,pfscan_UBA/transl_elong_EF1B_N_euk	p.W1364*	ENST00000588061.1	37	c.4092	CCDS45798.1	17	.	.	.	.	.	.	.	.	.	.	G	48	14.842509	0.99812	.	.	ENSG00000078687	ENST00000455761;ENST00000395801;ENST00000335749;ENST00000301624;ENST00000541771;ENST00000544502	.	.	.	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.3542	20.4062	0.99009	0.0:0.0:1.0:0.0	.	.	.	.	X	1367;1364;1364;1367;1367;1364	.	ENSP00000301624:W1367X	W	+	3	0	TNRC6C	73600739	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.338000	0.96553	2.831000	0.97527	0.655000	0.94253	TGG	TNRC6C	-	NULL	ENSG00000078687		0.512	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	TNRC6C	HGNC	protein_coding	OTTHUMT00000395947.1	59	0.00	0	G	NM_018996		76089144	76089144	+1	no_errors	ENST00000335749	ensembl	human	known	69_37n	nonsense	35	23.91	11	SNP	1.000	A
TSC22D1	8848	genome.wustl.edu	37	13	45010182	45010182	+	Missense_Mutation	SNP	T	T	C			TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	g.chr13:45010182T>C	ENST00000458659.2	-	2	3452	c.2962A>G	c.(2962-2964)Atg>Gtg	p.M988V	RP11-71C5.2_ENST00000426579.2_RNA|TSC22D1_ENST00000261489.2_Missense_Mutation_p.M59V|TSC22D1_ENST00000501704.2_Intron	NM_183422.3	NP_904358.2	Q15714	T22D1_HUMAN	TSC22 domain family, member 1	988					negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(4;8.74e-08)|Acute lymphoblastic leukemia(4;1.78e-07)|Lung NSC(96;2.21e-05)|Breast(139;0.000625)|Prostate(109;0.000947)|Hepatocellular(98;0.0202)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000522)|BRCA - Breast invasive adenocarcinoma(63;0.118)		GTACATACCATAGCTTGCTCG	0.383																																						dbGAP											0													115.0	97.0	103.0					13																	45010182		2203	4300	6503	-	-	-	SO:0001583	missense	0			AJ222700	CCDS9392.1, CCDS31966.1, CCDS58291.1, CCDS73565.1	13q14	2008-02-05	2005-03-01	2005-03-03	ENSG00000102804	ENSG00000102804			16826	protein-coding gene	gene with protein product		607715	"""transforming growth factor beta 1 induced transcript 4"""	TGFB1I4		8651929, 9022669	Standard	NM_183422		Approved	TSC22, MGC17597	uc001uzn.4	Q15714	OTTHUMG00000016838	ENST00000458659.2:c.2962A>G	13.37:g.45010182T>C	ENSP00000397435:p.Met988Val	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KRL7|B9EGI0|O00666|Q6AHX5|Q6IBU1|Q8NCN1|Q96JS5	Missense_Mutation	SNP	pfam_TSC-22_Dip_Bun	p.M988V	ENST00000458659.2	37	c.2962	CCDS31966.1	13	.	.	.	.	.	.	.	.	.	.	T	22.8	4.340785	0.81911	.	.	ENSG00000102804	ENST00000458659;ENST00000261489	T	0.55760	0.5	5.53	5.53	0.82687	.	0.000000	0.53938	D	0.000041	T	0.72953	0.3525	M	0.79258	2.445	0.80722	D	1	D;P	0.63046	0.992;0.917	D;D	0.76071	0.987;0.915	T	0.76997	-0.2751	10	0.87932	D	0	.	14.8695	0.70444	0.0:0.0:0.0:1.0	.	988;59	Q15714;Q15714-2	T22D1_HUMAN;.	V	988;59	ENSP00000397435:M988V	ENSP00000261489:M59V	M	-	1	0	TSC22D1	43908182	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.698000	0.84413	2.100000	0.63781	0.533000	0.62120	ATG	TSC22D1	-	pfam_TSC-22_Dip_Bun	ENSG00000102804		0.383	TSC22D1-001	KNOWN	basic|CCDS	protein_coding	TSC22D1	HGNC	protein_coding	OTTHUMT00000044743.2	87	0.00	0	T	NM_006022		45010182	45010182	-1	no_errors	ENST00000458659	ensembl	human	known	69_37n	missense	39	20.41	10	SNP	1.000	C
ZNF761	388561	genome.wustl.edu	37	19	53959457	53959457	+	RNA	DEL	A	A	-			TCGA-E2-A1IJ-01A-11D-A142-09	TCGA-E2-A1IJ-10A-01D-A142-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	3aff2da1-1647-4b95-abdb-c9db923cfc22	62243d12-b286-4315-b6da-71ef06c668c8	g.chr19:53959457delA	ENST00000454407.1	+	0	2149							Q86XN6	ZN761_HUMAN	zinc finger protein 761						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		GTTAACCCTTAAACGCCATCG	0.403																																						dbGAP											0													94.0	95.0	95.0					19																	53959457		2203	4300	6503	-	-	-			0			AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336		"""Zinc fingers, C2H2-type"""	23179	protein-coding gene	gene with protein product							Standard	NM_001008401		Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999		19.37:g.53959457delA		Somatic		WXS	Illumina GAIIx	Phase_IV	Q6ZNB9	RNA	DEL	-	NULL	ENST00000454407.1	37	NULL		19																																																																																			ZNF761	-	-	ENSG00000160336		0.403	ZNF761-203	KNOWN	basic	processed_transcript	ZNF761	HGNC	processed_transcript		54	0.00	0	A	NM_001008401		53959457	53959457	+1	no_errors	ENST00000334095	ensembl	human	known	69_37n	rna	17	10.53	2	DEL	0.000	-
