#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_ORegAnno_bin	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
ARHGEF7	8874	genome.wustl.edu	37	13	111953173	111953173	+	Missense_Mutation	SNP	G	G	T			TCGA-E2-A14U-01A-11D-A228-09	TCGA-E2-A14U-10A-01D-A22A-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	21ab25e4-107c-4257-8d60-cb912587fbf6	e5a4fdab-9e5e-4c17-b01f-8a3e55b08c53	g.chr13:111953173G>T	ENST00000218789.5	+	19	2416	c.1919G>T	c.(1918-1920)gGt>gTt	p.G640V	ARHGEF7_ENST00000426073.2_Missense_Mutation_p.G581V|ARHGEF7_ENST00000375736.4_Missense_Mutation_p.G581V|ARHGEF7_ENST00000375737.5_Missense_Mutation_p.G656V|ARHGEF7_ENST00000370623.3_Missense_Mutation_p.G666V			Q14155	ARHG7_HUMAN	Rho guanine nucleotide exchange factor (GEF) 7	0					apoptotic signaling pathway (GO:0097190)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|hematopoietic progenitor cell differentiation (GO:0002244)|lamellipodium assembly (GO:0030032)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of GTPase activity (GO:0043547)|positive regulation of lamellipodium morphogenesis (GO:2000394)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase binding (GO:0019901)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	41	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			AAAAGTAATGGTCAGACAGTG	0.403																																						dbGAP											0													81.0	97.0	91.0					13																	111953173		2203	4300	6503	-	-	-	SO:0001583	missense	0			D63476	CCDS9521.1, CCDS32009.1, CCDS45068.1, CCDS45069.1	13q33.3	2013-01-10			ENSG00000102606	ENSG00000102606		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	15607	protein-coding gene	gene with protein product	"""SH3 domain-containing proline-rich protein"", ""PAK-interacting exchange factor beta"", ""rho"", ""guanine nucleotide exchange factor 7"""	605477				9207241, 9726964	Standard	NM_003899		Approved	KIAA0142, PIXB, DKFZp761K1021, Nbla10314, DKFZp686C12170, BETA-PIX, COOL1, P85SPR, P85, P85COOL1, P50BP, PAK3, P50	uc001vrs.2	Q14155	OTTHUMG00000017357	ENST00000218789.5:c.1919G>T	13.37:g.111953173G>T	ENSP00000218789:p.Gly640Val		B1ALK6|B1ALK8|Q3LIA4|Q5W9H0|Q6P9G3|Q6PII2|Q86W63|Q8N3M1	Missense_Mutation	SNP	pfam_DH-domain,pfam_SH3_2,pfam_SH3_domain,pfam_Pleckstrin_homology,pfam_CH-domain,superfamily_DH-domain,superfamily_SH3_domain,superfamily_CH-domain,smart_CH-domain,smart_SH3_domain,smart_DH-domain,smart_Pleckstrin_homology,pfscan_CH-domain,pfscan_Pleckstrin_homology,pfscan_SH3_domain,pfscan_DH-domain,prints_SH3_domain	p.G666V	ENST00000218789.5	37	c.1997		13	.	.	.	.	.	.	.	.	.	.	G	24.9	4.582470	0.86748	.	.	ENSG00000102606	ENST00000370623;ENST00000218789;ENST00000375736;ENST00000426073;ENST00000375737	T;T;T;T;T	0.60548	0.5;0.18;0.51;0.51;0.53	5.25	5.25	0.73442	.	.	.	.	.	T	0.74718	0.3753	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.72323	-0.4328	9	0.33141	T	0.24	.	18.8414	0.92186	0.0:0.0:1.0:0.0	.	656	B7Z6G2	.	V	666;640;581;581;656	ENSP00000359657:G666V;ENSP00000218789:G640V;ENSP00000364888:G581V;ENSP00000397068:G581V;ENSP00000364889:G656V	ENSP00000218789:G640V	G	+	2	0	ARHGEF7	110751174	1.000000	0.71417	0.188000	0.23233	0.981000	0.71138	8.627000	0.90974	2.420000	0.82092	0.561000	0.74099	GGT	ARHGEF7	-	NULL	ENSG00000102606		0.403	ARHGEF7-001	NOVEL	basic	protein_coding	ARHGEF7	HGNC	protein_coding	OTTHUMT00000045805.3	19	0.00	0	G	NM_001113511		111953173	111953173	+1	no_errors	ENST00000370623	ensembl	human	known	69_37n	missense	17	19.05	4	SNP	1.000	T
ATP10B	23120	genome.wustl.edu	37	5	160097653	160097653	+	Silent	SNP	C	C	T			TCGA-E2-A14U-01A-11D-A228-09	TCGA-E2-A14U-10A-01D-A22A-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	21ab25e4-107c-4257-8d60-cb912587fbf6	e5a4fdab-9e5e-4c17-b01f-8a3e55b08c53	g.chr5:160097653C>T	ENST00000327245.5	-	7	1338	c.492G>A	c.(490-492)caG>caA	p.Q164Q		NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	164					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCCAGCACTTCTGCACATAGG	0.463																																						dbGAP											0													120.0	123.0	122.0					5																	160097653		2030	4197	6227	-	-	-	SO:0001819	synonymous_variant	0			AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"""ATPases / P-type"""	13543	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10B"""			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.492G>A	5.37:g.160097653C>T			Q9H725	Silent	SNP	pfam_ATPase_P-typ_ATPase-assoc-dom,pfam_Dehalogen-like_hydro,superfamily_HAD-like_dom,superfamily_ATPase_cation_domN,prints_ATPase_P-typ_ion-transptr,tigrfam_ATPase_P-typ_Plipid-transl,tigrfam_ATPase_P-typ_ion-transptr	p.Q164	ENST00000327245.5	37	c.492	CCDS43394.1	5																																																																																			ATP10B	-	pfam_ATPase_P-typ_ATPase-assoc-dom,tigrfam_ATPase_P-typ_Plipid-transl	ENSG00000118322		0.463	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ATP10B	HGNC	protein_coding	OTTHUMT00000374127.1	33	0.00	0	C	NM_025153		160097653	160097653	-1	no_errors	ENST00000327245	ensembl	human	known	69_37n	silent	32	11.11	4	SNP	0.995	T
C21orf58	54058	genome.wustl.edu	37	21	47722406	47722406	+	Missense_Mutation	SNP	G	G	T			TCGA-E2-A14U-01A-11D-A228-09	TCGA-E2-A14U-10A-01D-A22A-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	21ab25e4-107c-4257-8d60-cb912587fbf6	e5a4fdab-9e5e-4c17-b01f-8a3e55b08c53	g.chr21:47722406G>T	ENST00000291691.7	-	7	1942	c.806C>A	c.(805-807)gCc>gAc	p.A269D	C21orf58_ENST00000397680.1_Missense_Mutation_p.A163D|C21orf58_ENST00000397683.1_Missense_Mutation_p.A163D|C21orf58_ENST00000397682.3_Missense_Mutation_p.A163D|C21orf58_ENST00000397679.1_Missense_Mutation_p.A163D|C21orf58_ENST00000472607.1_5'UTR	NM_058180.3	NP_478060.2	P58505	CU058_HUMAN	chromosome 21 open reading frame 58	269										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(1)|pancreas(1)	9	Breast(49;0.112)			Colorectal(79;0.239)		TACCTGCAGGGCTGGGGGCAG	0.572																																						dbGAP											0													27.0	24.0	25.0					21																	47722406		2203	4298	6501	-	-	-	SO:0001583	missense	0				CCDS13735.1, CCDS68229.1	21q22.3	2008-07-07			ENSG00000160298	ENSG00000160298			1300	protein-coding gene	gene with protein product							Standard	XM_005261149		Approved		uc002zjf.3	P58505	OTTHUMG00000090634	ENST00000291691.7:c.806C>A	21.37:g.47722406G>T	ENSP00000291691:p.Ala269Asp		B3KPI1	Missense_Mutation	SNP	NULL	p.A269D	ENST00000291691.7	37	c.806	CCDS13735.1	21	.	.	.	.	.	.	.	.	.	.	G	15.53	2.861937	0.51482	.	.	ENSG00000160298	ENST00000397683;ENST00000417060;ENST00000397682;ENST00000291691;ENST00000397679;ENST00000397680	T;T;T;T;T;T	0.48201	0.83;0.83;0.83;0.82;0.83;0.83	3.95	1.08	0.20341	.	0.921434	0.09024	N	0.859816	T	0.47857	0.1468	L	0.50333	1.59	0.09310	N	1	D;D;P	0.53745	0.962;0.962;0.899	P;P;B	0.52481	0.7;0.7;0.39	T	0.31861	-0.9928	10	0.40728	T	0.16	-2.8963	3.7141	0.08431	0.3123:0.1867:0.5011:0.0	.	269;163;269	P58505;Q8N7N9;P58505-2	CU058_HUMAN;.;.	D	163;231;163;269;163;163	ENSP00000380799:A163D;ENSP00000402356:A231D;ENSP00000380798:A163D;ENSP00000291691:A269D;ENSP00000380796:A163D;ENSP00000380797:A163D	ENSP00000291691:A269D	A	-	2	0	C21orf58	46546834	0.003000	0.15002	0.004000	0.12327	0.243000	0.25628	1.010000	0.29898	0.229000	0.21039	0.462000	0.41574	GCC	C21orf58	-	NULL	ENSG00000160298		0.572	C21orf58-002	KNOWN	basic|appris_principal|CCDS	protein_coding	C21orf58	HGNC	protein_coding	OTTHUMT00000207283.1	35	0.00	0	G	NM_058180		47722406	47722406	-1	no_errors	ENST00000291691	ensembl	human	known	69_37n	missense	32	11.11	4	SNP	0.003	T
WASH4P	374677	genome.wustl.edu	37	16	61730	61730	+	IGR	SNP	C	C	G	rs201731689	byFrequency	TCGA-E2-A14U-01A-11D-A228-09	TCGA-E2-A14U-10A-01D-A22A-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	21ab25e4-107c-4257-8d60-cb912587fbf6	e5a4fdab-9e5e-4c17-b01f-8a3e55b08c53	g.chr16:61730C>G	ENST00000326592.9	-	0	2431				DDX11L10_ENST00000513886.1_RNA			A8MWX3	WASH4_HUMAN	WAS protein family homolog 4 pseudogene						Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)										TGCCAGGGTGCAAGCTGAGCA	0.557													.|||	2846	0.568291	0.7179	0.4669	5008	,	,		16113	0.5903		0.4682	False		,,,				2504	0.5184					dbGAP											0																																										-	-	-	SO:0001628	intergenic_variant	0					16p13.3	2014-08-28	2008-01-16	2008-01-16	ENSG00000234769	ENSG00000234769		"""WAS protein homologs"""	14126	other	unknown			"""family with sequence similarity 39, member C pseudogene"""	FAM39CP		9054936, 11701968, 18159949	Standard	NG_003159		Approved	FLJ31670		A8MWX3	OTTHUMG00000059914		16.37:g.61730C>G				RNA	SNP	-	NULL	ENST00000326592.9	37	NULL		16																																																																																			DDX11L10	-	-	ENSG00000233614		0.557	WASH4P-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal	protein_coding	DDX11L10	HGNC	protein_coding	OTTHUMT00000133175.2	11	0.00	0	C	NG_003159		61730	61730	+1	no_errors	ENST00000513886	ensembl	human	known	69_37n	rna	4	63.64	7	SNP	0.342	G
DLGAP3	58512	genome.wustl.edu	37	1	35370591	35370591	+	Frame_Shift_Del	DEL	G	G	-			TCGA-E2-A14U-01A-11D-A228-09	TCGA-E2-A14U-10A-01D-A22A-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	21ab25e4-107c-4257-8d60-cb912587fbf6	e5a4fdab-9e5e-4c17-b01f-8a3e55b08c53	g.chr1:35370591delG	ENST00000373347.1	-	3	662	c.394delC	c.(394-396)caafs	p.Q133fs	DLGAP3_ENST00000235180.4_Frame_Shift_Del_p.Q133fs|DLGAP3_ENST00000495979.1_5'Flank			O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated protein 3	133					cell-cell signaling (GO:0007267)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(23)|ovary(4)|prostate(3)|skin(3)|urinary_tract(1)	46		Myeloproliferative disorder(586;0.0393)				CCATCTTGTTGAACTGGCAAC	0.642																																						dbGAP											0													31.0	27.0	29.0					1																	35370591		2202	4300	6502	-	-	-	SO:0001589	frameshift_variant	0			AF131778	CCDS30670.1	1p35.3-p34.1	2008-02-05			ENSG00000116544	ENSG00000116544			30368	protein-coding gene	gene with protein product		611413				8619474, 9110174	Standard	NM_001080418		Approved	SAPAP3, DAP3	uc001byc.3	O95886	OTTHUMG00000004049	ENST00000373347.1:c.394delC	1.37:g.35370591delG	ENSP00000362444:p.Gln133fs		Q5TDD5|Q9H3X7	Frame_Shift_Del	DEL	pfam_GKAP	p.Q132fs	ENST00000373347.1	37	c.394	CCDS30670.1	1																																																																																			DLGAP3	-	NULL	ENSG00000116544		0.642	DLGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DLGAP3	HGNC	protein_coding	OTTHUMT00000011554.1	10	0.00	0	G	NM_021234		35370591	35370591	-1	no_errors	ENST00000235180	ensembl	human	known	69_37n	frame_shift_del	4	33.33	2	DEL	1.000	-
EIF4G1	1981	genome.wustl.edu	37	3	184040637	184040638	+	Frame_Shift_Ins	INS	-	-	A			TCGA-E2-A14U-01A-11D-A228-09	TCGA-E2-A14U-10A-01D-A22A-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	21ab25e4-107c-4257-8d60-cb912587fbf6	e5a4fdab-9e5e-4c17-b01f-8a3e55b08c53	g.chr3:184040637_184040638insA	ENST00000346169.2	+	13	2095_2096	c.1824_1825insA	c.(1825-1827)aaafs	p.K609fs	EIF4G1_ENST00000352767.3_Frame_Shift_Ins_p.K616fs|EIF4G1_ENST00000435046.2_Frame_Shift_Ins_p.K413fs|EIF4G1_ENST00000382330.3_Frame_Shift_Ins_p.K616fs|EIF4G1_ENST00000427845.1_Frame_Shift_Ins_p.K522fs|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000319274.6_Frame_Shift_Ins_p.K609fs|EIF4G1_ENST00000434061.2_Frame_Shift_Ins_p.K413fs|EIF4G1_ENST00000441154.1_Frame_Shift_Ins_p.K445fs|EIF4G1_ENST00000414031.1_Frame_Shift_Ins_p.K569fs|SNORD66_ENST00000390856.1_RNA|EIF4G1_ENST00000350481.5_Frame_Shift_Ins_p.K445fs|EIF4G1_ENST00000342981.4_Frame_Shift_Ins_p.K609fs|EIF4G1_ENST00000392537.2_Frame_Shift_Ins_p.K522fs|EIF4G1_ENST00000411531.1_Frame_Shift_Ins_p.K569fs|EIF4G1_ENST00000424196.1_Frame_Shift_Ins_p.K616fs	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	609	EIF4E-binding.|MIF4G. {ECO:0000255|PROSITE- ProRule:PRU00698}.				cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			ACCTAGAGGAGAAAAAACGTTA	0.46																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"""Parkinson disease"""	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.1830dupA	3.37:g.184040643_184040643dupA	ENSP00000316879:p.Lys609fs		D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Frame_Shift_Ins	INS	pfam_MIF4G-like_typ-3,pfam_Initiation_fac_eIF4g_MI,pfam_W2_domain,superfamily_ARM-type_fold,smart_MIF4G-like_typ-3,smart_Initiation_fac_eIF4g_MI,smart_W2_domain	p.R617fs	ENST00000346169.2	37	c.1845_1846	CCDS3259.1	3																																																																																			EIF4G1	-	NULL	ENSG00000114867		0.460	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	EIF4G1	HGNC	protein_coding	OTTHUMT00000345733.1	64	0.00	0	-	NM_182917		184040637	184040638	+1	no_errors	ENST00000352767	ensembl	human	known	69_37n	frame_shift_ins	44	16.98	9	INS	1.000:1.000	A
FOLH1	2346	genome.wustl.edu	37	11	49204779	49204779	+	Missense_Mutation	SNP	C	C	T	rs116795343	byFrequency	TCGA-E2-A14U-01A-11D-A228-09	TCGA-E2-A14U-10A-01D-A22A-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	21ab25e4-107c-4257-8d60-cb912587fbf6	e5a4fdab-9e5e-4c17-b01f-8a3e55b08c53	g.chr11:49204779C>T	ENST00000256999.2	-	7	1102	c.842G>A	c.(841-843)cGt>cAt	p.R281H	FOLH1_ENST00000340334.7_Missense_Mutation_p.R266H|FOLH1_ENST00000356696.3_Missense_Mutation_p.R281H|FOLH1_ENST00000533034.1_Missense_Mutation_p.R266H|FOLH1_ENST00000343844.4_De_novo_Start_OutOfFrame	NM_004476.1	NP_004467.1	Q04609	FOLH1_HUMAN	folate hydrolase (prostate-specific membrane antigen) 1	281	NAALADase.				folic acid-containing compound metabolic process (GO:0006760)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)	p.R281L(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(34)|ovary(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	60					Capromab(DB00089)	TGCAATTCCACGCCTATAAGC	0.348																																						dbGAP											1	Substitution - Missense(1)	lung(1)											72.0	73.0	73.0					11																	49204779		2201	4298	6499	-	-	-	SO:0001583	missense	0			M99487	CCDS7946.1, CCDS31493.1, CCDS53626.1, CCDS53627.1, CCDS53628.1	11p11.2	2011-07-22			ENSG00000086205	ENSG00000086205	3.4.17.21		3788	protein-coding gene	gene with protein product	"""glutamate carboxylase II"", ""glutamate carboxypeptidase II"""	600934		FOLH		9838072	Standard	NM_001193472		Approved	PSM, PSMA, NAALAD1, NAALAdase, GCP2, GCPII	uc001ngy.3	Q04609	OTTHUMG00000166625	ENST00000256999.2:c.842G>A	11.37:g.49204779C>T	ENSP00000256999:p.Arg281His		A4UU12|A9CB79|B7Z312|B7Z343|D3DQS5|E9PDX8|O43748|Q16305|Q541A4|Q8TAY3|Q9NP15|Q9NYE2|Q9P1P8	Missense_Mutation	SNP	pfam_TFR-like_dimer_dom,pfam_Protease-assoc_domain,pfam_Peptidase_M28,superfamily_TFR-like_dimer_dom	p.R281H	ENST00000256999.2	37	c.842	CCDS7946.1	11	.	.	.	.	.	.	.	.	.	.	C	2.929	-0.221410	0.06061	.	.	ENSG00000086205	ENST00000256999;ENST00000356696;ENST00000340334;ENST00000533034;ENST00000389724	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	2.76	-1.12	0.09808	.	0.978445	0.08346	N	0.960084	T	0.21427	0.0516	N	0.14661	0.345	0.80722	D	1	B;B;B;B	0.06786	0.001;0.001;0.0;0.0	B;B;B;B	0.06405	0.001;0.0;0.002;0.0	T	0.23655	-1.0182	10	0.14656	T	0.56	.	6.6038	0.22714	0.0:0.3193:0.0:0.6807	.	266;266;281;281	Q04609-9;Q04609-7;Q04609-8;Q04609	.;.;.;FOLH1_HUMAN	H	281;281;266;266;281	ENSP00000256999:R281H;ENSP00000349129:R281H;ENSP00000344131:R266H;ENSP00000431463:R266H	ENSP00000256999:R281H	R	-	2	0	FOLH1	49161355	0.002000	0.14202	0.792000	0.32020	0.272000	0.26649	-0.922000	0.04004	-0.085000	0.12573	0.194000	0.17425	CGT	FOLH1	-	NULL	ENSG00000086205		0.348	FOLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FOLH1	HGNC	protein_coding	OTTHUMT00000390896.1	36	0.00	0	C	NM_004476		49204779	49204779	-1	no_errors	ENST00000256999	ensembl	human	known	69_37n	missense	29	14.71	5	SNP	0.843	T
FOLH1	2346	genome.wustl.edu	37	11	49204790	49204790	+	Silent	SNP	A	A	G	rs76509850	byFrequency	TCGA-E2-A14U-01A-11D-A228-09	TCGA-E2-A14U-10A-01D-A22A-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	21ab25e4-107c-4257-8d60-cb912587fbf6	e5a4fdab-9e5e-4c17-b01f-8a3e55b08c53	g.chr11:49204790A>G	ENST00000256999.2	-	7	1091	c.831T>C	c.(829-831)taT>taC	p.Y277Y	FOLH1_ENST00000340334.7_Silent_p.Y262Y|FOLH1_ENST00000356696.3_Silent_p.Y277Y|FOLH1_ENST00000533034.1_Silent_p.Y262Y|FOLH1_ENST00000343844.4_5'UTR	NM_004476.1	NP_004467.1	Q04609	FOLH1_HUMAN	folate hydrolase (prostate-specific membrane antigen) 1	277	NAALADase.				folic acid-containing compound metabolic process (GO:0006760)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(34)|ovary(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	60					Capromab(DB00089)	GCCTATAAGCATATTCTGAAA	0.343																																						dbGAP											0													61.0	61.0	61.0					11																	49204790		2201	4298	6499	-	-	-	SO:0001819	synonymous_variant	0			M99487	CCDS7946.1, CCDS31493.1, CCDS53626.1, CCDS53627.1, CCDS53628.1	11p11.2	2011-07-22			ENSG00000086205	ENSG00000086205	3.4.17.21		3788	protein-coding gene	gene with protein product	"""glutamate carboxylase II"", ""glutamate carboxypeptidase II"""	600934		FOLH		9838072	Standard	NM_001193472		Approved	PSM, PSMA, NAALAD1, NAALAdase, GCP2, GCPII	uc001ngy.3	Q04609	OTTHUMG00000166625	ENST00000256999.2:c.831T>C	11.37:g.49204790A>G			A4UU12|A9CB79|B7Z312|B7Z343|D3DQS5|E9PDX8|O43748|Q16305|Q541A4|Q8TAY3|Q9NP15|Q9NYE2|Q9P1P8	Silent	SNP	pfam_TFR-like_dimer_dom,pfam_Protease-assoc_domain,pfam_Peptidase_M28,superfamily_TFR-like_dimer_dom	p.Y277	ENST00000256999.2	37	c.831	CCDS7946.1	11																																																																																			FOLH1	-	NULL	ENSG00000086205		0.343	FOLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FOLH1	HGNC	protein_coding	OTTHUMT00000390896.1	38	0.00	0	A	NM_004476		49204790	49204790	-1	no_errors	ENST00000256999	ensembl	human	known	69_37n	silent	18	21.74	5	SNP	1.000	G
GRAMD1B	57476	genome.wustl.edu	37	11	123484325	123484325	+	Missense_Mutation	SNP	C	C	T			TCGA-E2-A14U-01A-11D-A228-09	TCGA-E2-A14U-10A-01D-A22A-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	21ab25e4-107c-4257-8d60-cb912587fbf6	e5a4fdab-9e5e-4c17-b01f-8a3e55b08c53	g.chr11:123484325C>T	ENST00000529750.1	+	15	2084	c.1757C>T	c.(1756-1758)cCc>cTc	p.P586L	GRAMD1B_ENST00000322282.7_Missense_Mutation_p.P586L|GRAMD1B_ENST00000456860.2_Missense_Mutation_p.P593L|GRAMD1B_ENST00000450171.2_Missense_Mutation_p.P277L	NM_020716.1	NP_065767.1	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	586						integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)		GTCACCACGCCCACAGATGAG	0.622																																						dbGAP											0													51.0	56.0	54.0					11																	123484325		2196	4288	6484	-	-	-	SO:0001583	missense	0			AB033027	CCDS53720.1, CCDS66253.1, CCDS66254.1	11q24.1	2005-11-02				ENSG00000023171			29214	protein-coding gene	gene with protein product						10574462	Standard	NM_001286564		Approved	KIAA1201	uc001pyx.2	Q3KR37		ENST00000529750.1:c.1757C>T	11.37:g.123484325C>T	ENSP00000436500:p.Pro586Leu		Q6UW85|Q9ULL9	Missense_Mutation	SNP	pfam_GRAM,smart_GRAM	p.P586L	ENST00000529750.1	37	c.1757	CCDS53720.1	11	.	.	.	.	.	.	.	.	.	.	C	32	5.128222	0.94473	.	.	ENSG00000023171	ENST00000539133;ENST00000456860;ENST00000322282;ENST00000529750;ENST00000529432;ENST00000450171	T;T;T;T;T	0.21734	1.99;1.99;1.99;1.99;1.99	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.40272	0.1110	L	0.40543	1.245	0.80722	D	1	P;D;P;B	0.89917	0.63;1.0;0.651;0.128	B;D;B;B	0.91635	0.354;0.999;0.273;0.101	T	0.04203	-1.0969	10	0.40728	T	0.16	.	19.4327	0.94778	0.0:1.0:0.0:0.0	.	546;277;586;593	B7Z4N9;Q3KR37-3;Q3KR37;E7EPH8	.;.;GRM1B_HUMAN;.	L	593;593;586;586;546;277	ENSP00000402457:P593L;ENSP00000325628:P586L;ENSP00000436500:P586L;ENSP00000432987:P546L;ENSP00000388458:P277L	ENSP00000325628:P586L	P	+	2	0	GRAMD1B	122989535	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	7.085000	0.76875	2.594000	0.87642	0.561000	0.74099	CCC	GRAMD1B	-	NULL	ENSG00000023171		0.622	GRAMD1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	GRAMD1B	HGNC	protein_coding	OTTHUMT00000387404.2	27	0.00	0	C	XM_370660		123484325	123484325	+1	no_errors	ENST00000322282	ensembl	human	known	69_37n	missense	28	15.15	5	SNP	1.000	T
IL27RA	9466	genome.wustl.edu	37	19	14161654	14161654	+	Missense_Mutation	SNP	G	G	T			TCGA-E2-A14U-01A-11D-A228-09	TCGA-E2-A14U-10A-01D-A22A-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	21ab25e4-107c-4257-8d60-cb912587fbf6	e5a4fdab-9e5e-4c17-b01f-8a3e55b08c53	g.chr19:14161654G>T	ENST00000263379.2	+	11	1612	c.1487G>T	c.(1486-1488)gGa>gTa	p.G496V		NM_004843.3	NP_004834.1	Q6UWB1	I27RA_HUMAN	interleukin 27 receptor, alpha	496	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T-helper 1 type immune response (GO:0002827)|regulation of isotype switching to IgG isotypes (GO:0048302)	integral component of plasma membrane (GO:0005887)	interleukin-27 receptor activity (GO:0045509)|transmembrane signaling receptor activity (GO:0004888)			breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	26						ACCATCGCTGGACAGGGCCCT	0.602																																					Colon(164;1849 1896 4443 37792 47834)	dbGAP											0													96.0	72.0	80.0					19																	14161654		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF053004	CCDS12303.1	19p13.11	2013-02-11				ENSG00000104998		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	17290	protein-coding gene	gene with protein product	"""T-cell cytokine receptor type 1"""	605350				9600072, 11057672	Standard	NM_004843		Approved	WSX-1, TCCR, CRL1, WSX1, zcytor1, IL-27R	uc002mxx.4	Q6UWB1		ENST00000263379.2:c.1487G>T	19.37:g.14161654G>T	ENSP00000263379:p.Gly496Val		A0N0L1|O60624	Missense_Mutation	SNP	pfam_Fibronectin_type3,superfamily_Fibronectin_type3,smart_Fibronectin_type3,pfscan_Fibronectin_type3	p.G496V	ENST00000263379.2	37	c.1487	CCDS12303.1	19	.	.	.	.	.	.	.	.	.	.	G	13.92	2.380718	0.42207	.	.	ENSG00000104998	ENST00000263379	T	0.68903	-0.36	4.69	4.69	0.59074	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.38778	N	0.001577	T	0.72811	0.3507	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.76019	-0.3112	10	0.87932	D	0	-21.1807	13.1198	0.59318	0.0:0.0:1.0:0.0	.	496	Q6UWB1	I27RA_HUMAN	V	496	ENSP00000263379:G496V	ENSP00000263379:G496V	G	+	2	0	IL27RA	14022654	1.000000	0.71417	0.992000	0.48379	0.033000	0.12548	4.485000	0.60279	2.151000	0.67156	0.461000	0.40582	GGA	IL27RA	-	superfamily_Fibronectin_type3,smart_Fibronectin_type3,pfscan_Fibronectin_type3	ENSG00000104998		0.602	IL27RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	IL27RA	HGNC	protein_coding	OTTHUMT00000458539.1	28	0.00	0	G	NM_004843		14161654	14161654	+1	no_errors	ENST00000263379	ensembl	human	known	69_37n	missense	26	13.33	4	SNP	0.987	T
INTS1	26173	genome.wustl.edu	37	7	1538684	1538684	+	Missense_Mutation	SNP	G	G	T			TCGA-E2-A14U-01A-11D-A228-09	TCGA-E2-A14U-10A-01D-A22A-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	21ab25e4-107c-4257-8d60-cb912587fbf6	e5a4fdab-9e5e-4c17-b01f-8a3e55b08c53	g.chr7:1538684G>T	ENST00000404767.3	-	8	1149	c.1064C>A	c.(1063-1065)aCc>aAc	p.T355N	INTS1_ENST00000389470.4_Missense_Mutation_p.T483N|INTS1_ENST00000493531.1_5'Flank	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	355					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		GCAGGTGGAGGTGAGGAGCCG	0.682																																						dbGAP											0													14.0	17.0	16.0					7																	1538684		1997	4172	6169	-	-	-	SO:0001583	missense	0			AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.1064C>A	7.37:g.1538684G>T	ENSP00000385722:p.Thr355Asn		A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Missense_Mutation	SNP	pfam_DUF3677,superfamily_ARM-type_fold	p.T483N	ENST00000404767.3	37	c.1448	CCDS47526.1	7	.	.	.	.	.	.	.	.	.	.	G	29.7	5.030285	0.93575	.	.	ENSG00000164880	ENST00000404767;ENST00000389470	T;T	0.48836	2.7;0.8	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.63628	0.2527	L	0.47716	1.5	0.80722	D	1	D;D	0.71674	0.992;0.998	D;D	0.73708	0.965;0.981	T	0.65500	-0.6153	10	0.59425	D	0.04	.	18.5042	0.90892	0.0:0.0:1.0:0.0	.	483;355	A4D212;Q8N201	.;INT1_HUMAN	N	355;483	ENSP00000385722:T355N;ENSP00000374121:T483N	ENSP00000374121:T483N	T	-	2	0	INTS1	1505210	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.389000	0.97243	2.363000	0.80096	0.650000	0.86243	ACC	INTS1	-	pfam_DUF3677	ENSG00000164880		0.682	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	INTS1	HGNC	protein_coding	OTTHUMT00000323683.1	32	0.00	0	G			1538684	1538684	-1	no_errors	ENST00000389470	ensembl	human	known	69_37n	missense	36	10.00	4	SNP	1.000	T
KCNS2	3788	genome.wustl.edu	37	8	99440759	99440759	+	Silent	SNP	G	G	A			TCGA-E2-A14U-01A-11D-A228-09	TCGA-E2-A14U-10A-01D-A22A-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	21ab25e4-107c-4257-8d60-cb912587fbf6	e5a4fdab-9e5e-4c17-b01f-8a3e55b08c53	g.chr8:99440759G>A	ENST00000287042.4	+	2	902	c.552G>A	c.(550-552)gtG>gtA	p.V184V	KCNS2_ENST00000521839.1_Silent_p.V184V	NM_020697.2	NP_065748.1	Q9ULS6	KCNS2_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 2	184					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			autonomic_ganglia(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	31	Breast(36;2.4e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.0448)			GCTACTCAGTGCTGAGCAGGG	0.597																																					Pancreas(138;844 2489 9202 24627)	dbGAP											0													51.0	52.0	52.0					8																	99440759		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AB032970	CCDS6279.1	8q22	2011-07-05			ENSG00000156486	ENSG00000156486		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6301	protein-coding gene	gene with protein product		602906				9305895, 16382104	Standard	NM_020697		Approved	Kv9.2	uc003yin.3	Q9ULS6	OTTHUMG00000044337	ENST00000287042.4:c.552G>A	8.37:g.99440759G>A			A8KAN1	Silent	SNP	pfam_T1-type_BTB,pfam_Ion_trans_dom,pfam_Ion_trans_2,superfamily_BTB/POZ_fold,smart_BTB/POZ-like,prints_K_chnl,prints_K_chnl_volt-dep_Kv9,prints_K_chnl_volt-dep_Kv,prints_K_chnl_volt-dep_Kv3,prints_K_chnl_volt-dep_Kv6,prints_K_chnl_volt-dep_Kv2	p.V184	ENST00000287042.4	37	c.552	CCDS6279.1	8																																																																																			KCNS2	-	prints_K_chnl	ENSG00000156486		0.597	KCNS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KCNS2	HGNC	protein_coding	OTTHUMT00000103134.1	31	0.00	0	G	NM_020697		99440759	99440759	+1	no_errors	ENST00000287042	ensembl	human	known	69_37n	silent	30	11.76	4	SNP	0.918	A
TUNAR	100507043	genome.wustl.edu	37	14	96389173	96389173	+	lincRNA	SNP	A	A	G	rs7160831	byFrequency	TCGA-E2-A14U-01A-11D-A228-09	TCGA-E2-A14U-10A-01D-A22A-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	21ab25e4-107c-4257-8d60-cb912587fbf6	e5a4fdab-9e5e-4c17-b01f-8a3e55b08c53	g.chr14:96389173A>G	ENST00000503525.2	+	0	462					NR_038861.1																						ATCACTAGTGAAAATGATGAA	0.408													G|||	1700	0.339457	0.6785	0.2161	5008	,	,		24107	0.1905		0.1312	False		,,,				2504	0.3364					dbGAP											0																																										-	-	-			0																															14.37:g.96389173A>G				RNA	SNP	-	NULL	ENST00000503525.2	37	NULL		14																																																																																			LINC00617	-	-	ENSG00000250366		0.408	LINC00617-002	KNOWN	basic	lincRNA	LINC00617	HGNC	lincRNA	OTTHUMT00000413257.1	34	0.00	0	A			96389173	96389173	+1	no_errors	ENST00000503525	ensembl	human	known	69_37n	rna	26	16.13	5	SNP	1.000	G
MAPT	4137	genome.wustl.edu	37	17	44061292	44061292	+	Silent	SNP	C	C	A			TCGA-E2-A14U-01A-11D-A228-09	TCGA-E2-A14U-10A-01D-A22A-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	21ab25e4-107c-4257-8d60-cb912587fbf6	e5a4fdab-9e5e-4c17-b01f-8a3e55b08c53	g.chr17:44061292C>A	ENST00000571987.1	+	5	1122	c.1122C>A	c.(1120-1122)ctC>ctA	p.L374L	MAPT_ENST00000535772.1_Intron|MAPT_ENST00000347967.5_Intron|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000415613.2_Silent_p.L374L|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000262410.5_Silent_p.L374L|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000344290.5_Silent_p.L374L|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000446361.3_Intron			P10636	TAU_HUMAN	microtubule-associated protein tau	374					adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	TCCCTCAACTCAAAGGTCTGT	0.632																																						dbGAP											0													65.0	79.0	74.0					17																	44061292		2060	4029	6089	-	-	-	SO:0001819	synonymous_variant	0			J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"""G protein beta1/gamma2 subunit-interacting factor 1"", ""microtubule-associated protein tau, isoform 4"", ""protein phosphatase 1, regulatory subunit 103"""	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.1122C>A	17.37:g.44061292C>A			P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Silent	SNP	pfam_Tau/MAP_tubulin-bd_rpt,prints_Tau_protein	p.L374	ENST00000571987.1	37	c.1122	CCDS11501.1	17																																																																																			MAPT	-	NULL	ENSG00000186868		0.632	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	MAPT	HGNC	protein_coding	OTTHUMT00000440133.1	42	0.00	0	C	NM_016835		44061292	44061292	+1	no_errors	ENST00000344290	ensembl	human	known	69_37n	silent	62	10.14	7	SNP	1.000	A
MUC20P1	651714	genome.wustl.edu	37	3	195345599	195345599	+	IGR	SNP	G	G	A	rs565796471	byFrequency	TCGA-E2-A14U-01A-11D-A228-09	TCGA-E2-A14U-10A-01D-A22A-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	21ab25e4-107c-4257-8d60-cb912587fbf6	e5a4fdab-9e5e-4c17-b01f-8a3e55b08c53	g.chr3:195345599G>A								APOD (34523 upstream) : RP11-141C7.4 (21261 downstream)																							AAACTCAAACGCTGAGCGCTG	0.612													.|||	222	0.0443291	0.09	0.0288	5008	,	,		29536	0.006		0.0457	False		,,,				2504	0.0317					dbGAP											0																																										-	-	-	SO:0001628	intergenic_variant	0																															3.37:g.195345599G>A				Silent	SNP	NULL	p.T24		37	c.72		3																																																																																			MUC20	-	NULL	ENSG00000176945	0	0.612					MUC20	HGNC			13	0.00	0	G			195345599	195345599	+1	no_errors	ENST00000381954	ensembl	human	known	69_37n	silent	3	50.00	3	SNP	0.014	A
NCOA6	23054	genome.wustl.edu	37	20	33328866	33328866	+	Missense_Mutation	SNP	A	A	T			TCGA-E2-A14U-01A-11D-A228-09	TCGA-E2-A14U-10A-01D-A22A-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	21ab25e4-107c-4257-8d60-cb912587fbf6	e5a4fdab-9e5e-4c17-b01f-8a3e55b08c53	g.chr20:33328866A>T	ENST00000374796.2	-	12	7764	c.5194T>A	c.(5194-5196)Ttg>Atg	p.L1732M	NCOA6_ENST00000359003.2_Missense_Mutation_p.L1732M			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1732	EP300/CRSP3-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						CTAAGGACCAAAGGTCGACCT	0.512																																						dbGAP											0													103.0	112.0	109.0					20																	33328866		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"""nuclear receptor coactivator RAP250"", ""activating signal cointegrator-2"", ""peroxisome proliferator-activated receptor interacting protein"""	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.5194T>A	20.37:g.33328866A>T	ENSP00000363929:p.Leu1732Met		A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	NULL	p.L1732M	ENST00000374796.2	37	c.5194	CCDS13241.1	20	.	.	.	.	.	.	.	.	.	.	A	15.39	2.819657	0.50633	.	.	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.25414	1.8;1.8	5.54	0.497	0.16902	.	0.257437	0.24851	N	0.035093	T	0.13243	0.0321	N	0.24115	0.695	0.27548	N	0.950594	B	0.33857	0.429	B	0.31614	0.133	T	0.11767	-1.0574	10	0.59425	D	0.04	-0.732	4.8892	0.13719	0.5332:0.0:0.3321:0.1347	.	1732	Q14686	NCOA6_HUMAN	M	1732	ENSP00000363929:L1732M;ENSP00000351894:L1732M	ENSP00000351894:L1732M	L	-	1	2	NCOA6	32792527	0.746000	0.28272	0.895000	0.35142	0.901000	0.52897	0.679000	0.25291	-0.096000	0.12329	0.533000	0.62120	TTG	NCOA6	-	NULL	ENSG00000198646		0.512	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NCOA6	HGNC	protein_coding	OTTHUMT00000078811.2	63	0.00	0	A	NM_014071		33328866	33328866	-1	no_errors	ENST00000359003	ensembl	human	known	69_37n	missense	57	18.57	13	SNP	0.439	T
NOTCH4	4855	genome.wustl.edu	37	6	32169121	32169121	+	Missense_Mutation	SNP	G	G	T			TCGA-E2-A14U-01A-11D-A228-09	TCGA-E2-A14U-10A-01D-A22A-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	21ab25e4-107c-4257-8d60-cb912587fbf6	e5a4fdab-9e5e-4c17-b01f-8a3e55b08c53	g.chr6:32169121G>T	ENST00000375023.3	-	22	4050	c.3912C>A	c.(3910-3912)agC>agA	p.S1304R		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1304					cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						GGGCTGGGGGGCTCAGTACCA	0.642																																						dbGAP											0													36.0	39.0	38.0					6																	32169121		1508	2709	4217	-	-	-	SO:0001583	missense	0				CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"""Ankyrin repeat domain containing"""	7884	protein-coding gene	gene with protein product		164951	"""Notch (Drosophila) homolog 4"", ""Notch homolog 4 (Drosophila)"""	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.3912C>A	6.37:g.32169121G>T	ENSP00000364163:p.Ser1304Arg		B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Missense_Mutation	SNP	pfam_EGF-like_dom,pfam_Ankyrin_rpt,pfam_EGF-like_Ca-bd,pfam_Notch_dom,pfam_Notch_NODP_dom,superfamily_Ankyrin_rpt-contain_dom,superfamily_Notch_dom,smart_EGF-like,smart_EGF-like_Ca-bd,smart_Notch_dom,smart_Ankyrin_rpt,pirsf_Notch,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,pfscan_EG-like_dom,pfscan_Notch_dom,prints_Notch_4,prints_Notch_dom	p.S1304R	ENST00000375023.3	37	c.3912	CCDS34420.1	6	.	.	.	.	.	.	.	.	.	.	G	10.66	1.414041	0.25465	.	.	ENSG00000204301	ENST00000375023	T	0.81078	-1.45	4.72	0.811	0.18739	.	0.767557	0.11108	N	0.598889	T	0.41373	0.1156	N	0.12182	0.205	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.20571	-1.0271	10	0.33141	T	0.24	.	4.5655	0.12184	0.082:0.2825:0.4897:0.1458	.	1304	Q99466	NOTC4_HUMAN	R	1304	ENSP00000364163:S1304R	ENSP00000364163:S1304R	S	-	3	2	NOTCH4	32277099	0.024000	0.19004	0.774000	0.31636	0.771000	0.43674	-0.649000	0.05384	-0.025000	0.13918	-0.232000	0.12228	AGC	NOTCH4	-	pirsf_Notch,prints_Notch_4	ENSG00000204301		0.642	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NOTCH4	HGNC	protein_coding	OTTHUMT00000076045.2	33	0.00	0	G			32169121	32169121	-1	no_errors	ENST00000375023	ensembl	human	known	69_37n	missense	22	15.38	4	SNP	0.999	T
PIK3CA	5290	genome.wustl.edu	37	3	178936082	178936082	+	Missense_Mutation	SNP	G	G	A	rs121913273		TCGA-E2-A14U-01A-11D-A228-09	TCGA-E2-A14U-10A-01D-A22A-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	21ab25e4-107c-4257-8d60-cb912587fbf6	e5a4fdab-9e5e-4c17-b01f-8a3e55b08c53	g.chr3:178936082G>A	ENST00000263967.3	+	10	1781	c.1624G>A	c.(1624-1626)Gaa>Aaa	p.E542K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	542	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> K (in CLOVE, KERSEB, CRC and BC; also found in glioblastoma multiforme and endometrial carcinoma; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N- terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|E -> Q (found in an endometrial carcinoma sample; unknown pathological significance). {ECO:0000269|PubMed:16322209}.|E -> V (in BC; unknown pathological significance). {ECO:0000269|PubMed:16353168}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E542K(545)|p.E542Q(10)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TCCTCTCTCTGAAATCACTGA	0.333	E542K(BT483_BREAST)|E542K(CAL51_BREAST)|E542K(HGC27_STOMACH)|E542K(IM95_STOMACH)|E542K(JHUEM1_ENDOMETRIUM)|E542K(NCIH1341_LUNG)|E542K(SW948_LARGE_INTESTINE)|E542K(T84_LARGE_INTESTINE)|E542K(VMCUB1_URINARY_TRACT)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)	dbGAP		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	555	Substitution - Missense(555)	breast(176)|large_intestine(166)|urinary_tract(45)|endometrium(37)|skin(19)|lung(18)|stomach(16)|ovary(16)|thyroid(14)|upper_aerodigestive_tract(9)|central_nervous_system(7)|cervix(6)|liver(6)|oesophagus(5)|penis(4)|kidney(3)|soft_tissue(2)|haematopoietic_and_lymphoid_tissue(2)|prostate(2)|biliary_tract(1)|pituitary(1)											56.0	56.0	56.0					3																	178936082		1809	4069	5878	-	-	-	SO:0001583	missense	0				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1624G>A	3.37:g.178936082G>A	ENSP00000263967:p.Glu542Lys		Q14CW1|Q99762	Missense_Mutation	SNP	pfam_PInositide-3_kin_accessory_dom,pfam_PI3/4_kinase_cat_dom,pfam_PI3K_Ras-bd_dom,pfam_PI3K_C2_dom,pfam_PI3K_adapt-bd_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_PI3K_adapt-bd_dom,smart_PI3K_Ras-bd_dom,smart_PI3K_C2_dom,smart_PInositide-3_kin_accessory_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	p.E542K	ENST00000263967.3	37	c.1624	CCDS43171.1	3	.	.	.	.	.	.	.	.	.	.	G	34	5.360420	0.95877	.	.	ENSG00000121879	ENST00000263967	T	0.62105	0.05	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.69287	0.3094	L	0.41356	1.27	0.80722	D	1	D	0.65815	0.995	D	0.63192	0.912	T	0.60296	-0.7291	10	0.09843	T	0.71	-23.9623	20.0024	0.97423	0.0:0.0:1.0:0.0	.	542	P42336	PK3CA_HUMAN	K	542	ENSP00000263967:E542K	ENSP00000263967:E542K	E	+	1	0	PIK3CA	180418776	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAA	PIK3CA	-	pfam_PInositide-3_kin_accessory_dom,superfamily_ARM-type_fold,smart_PInositide-3_kin_accessory_dom	ENSG00000121879		0.333	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	PIK3CA	HGNC	protein_coding	OTTHUMT00000348409.2	58	0.00	0	G			178936082	178936082	+1	no_errors	ENST00000263967	ensembl	human	known	69_37n	missense	51	10.53	6	SNP	1.000	A
TPM3P9	147804	genome.wustl.edu	37	19	53945215	53945215	+	RNA	SNP	G	G	A	rs4803125	byFrequency	TCGA-E2-A14U-01A-11D-A228-09	TCGA-E2-A14U-10A-01D-A22A-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	21ab25e4-107c-4257-8d60-cb912587fbf6	e5a4fdab-9e5e-4c17-b01f-8a3e55b08c53	g.chr19:53945215G>A	ENST00000424846.3	+	0	212				ZNF761_ENST00000454407.1_RNA	NR_003148.3				tropomyosin 3 pseudogene 9																		CCTCCAGTGAGAAGCTGAGGG	0.582													g|||	3185	0.635982	0.6248	0.6614	5008	,	,		17633	0.3998		0.7068	False		,,,				2504	0.8037					dbGAP											0																																										-	-	-			0					19q13.42	2012-07-04			ENSG00000241015	ENSG00000241015			44142	pseudogene	pseudogene							Standard	NR_003148		Approved				OTTHUMG00000157312		19.37:g.53945215G>A				RNA	SNP	-	NULL	ENST00000424846.3	37	NULL		19																																																																																			TPM3P9	-	-	ENSG00000241015		0.582	TPM3P9-002	KNOWN	basic	processed_transcript	TPM3P9	HGNC	pseudogene	OTTHUMT00000347070.1	20	0.00	0	G	NR_003148		53945215	53945215	+1	no_errors	ENST00000424846	ensembl	human	known	69_37n	rna	21	16.00	4	SNP	0.017	A
TUBBP5	643224	genome.wustl.edu	37	9	141070897	141070897	+	RNA	SNP	G	G	A	rs28414745	byFrequency	TCGA-E2-A14U-01A-11D-A228-09	TCGA-E2-A14U-10A-01D-A22A-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	21ab25e4-107c-4257-8d60-cb912587fbf6	e5a4fdab-9e5e-4c17-b01f-8a3e55b08c53	g.chr9:141070897G>A	ENST00000503395.1	+	0	1672									tubulin, beta pseudogene 5																		TCCTGCCCTCGCCCAAGGTGT	0.557													.|||	241	0.048123	0.1634	0.0187	5008	,	,		15511	0.0		0.006	False		,,,				2504	0.0061					dbGAP											0																																										-	-	-			0			AF355123		9q34.3	2012-03-06	2005-11-15		ENSG00000159247	ENSG00000159247			23674	pseudogene	pseudogene			"""tubulin, beta polypeptide pseudogene 5"""			11731935	Standard	NR_027156		Approved		uc010ncq.3		OTTHUMG00000021001		9.37:g.141070897G>A				RNA	SNP	-	NULL	ENST00000503395.1	37	NULL		9																																																																																			TUBBP5	-	-	ENSG00000159247		0.557	TUBBP5-003	KNOWN	basic	processed_transcript	TUBBP5	HGNC	pseudogene	OTTHUMT00000373087.1	29	0.00	0	G	NR_027156		141070897	141070897	+1	no_errors	ENST00000290377	ensembl	human	known	69_37n	rna	27	18.18	6	SNP	1.000	A
