#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_CAF	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_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	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	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_deletion_substructures	i_domain	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	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_ref_reads_val	i_normal_vaf	i_normal_vaf_val	i_normal_var_reads	i_normal_var_reads_val	i_reference	i_refseq_mrna_id	i_rsID	i_rsID_ref_var_alleles	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_tumor_ref_reads	i_tumor_ref_reads_val	i_tumor_vaf	i_tumor_vaf_val	i_tumor_var_reads	i_tumor_var_reads_val	i_type	i_ucsc_cons	i_variant
DNAJC8	22826	genome.wustl.edu	37	1	28536509	28536509	+	Missense_Mutation	SNP	C	C	A			TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr1:28536509C>A	ENST00000263697.4	-	5	399	c.373G>T	c.(373-375)Gca>Tca	p.A125S	DNAJC8_ENST00000489277.1_5'UTR	NM_014280.2	NP_055095.2	O75937	DNJC8_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 8	125					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)				kidney(1)|large_intestine(3)|lung(2)	6		Colorectal(325;3.46e-05)|Lung NSC(340;4.08e-05)|all_lung(284;4.29e-05)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.0105)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		OV - Ovarian serous cystadenocarcinoma(117;2.81e-22)|Colorectal(126;2.99e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00275)|BRCA - Breast invasive adenocarcinoma(304;0.0059)|STAD - Stomach adenocarcinoma(196;0.00671)|READ - Rectum adenocarcinoma(331;0.0649)		TCTTTTCCTGCCTGAATTACA	0.418																																							0											0													128.0	111.0	117.0					1																	28536509		1890	4113	6003	SO:0001583	missense	0			AF083190	CCDS41292.1	1p35	2011-09-02			ENSG00000126698	ENSG00000126698		"""Heat shock proteins / DNAJ (HSP40)"""	15470	protein-coding gene	gene with protein product						11147971	Standard	NM_014280		Approved	SPF31	uc001bpn.3	O75937	OTTHUMG00000003538	ENST00000263697.4:c.373G>T	1.37:g.28536509C>A	ENSP00000263697:p.Ala125Ser		B4DUU4|D3DPM0|Q6IBA4|Q8N4Z5|Q9P051|Q9P067	Missense_Mutation	SNP	pfam_DnaJ_domain,superfamily_DnaJ_domain,smart_DnaJ_domain,pfscan_DnaJ_domain,prints_DnaJ_domain	p.A125S	ENST00000263697.4	37	c.373	CCDS41292.1	1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.403492	0.83230	.	.	ENSG00000126698	ENST00000263697	T	0.65364	-0.15	6.05	6.05	0.98169	Heat shock protein DnaJ, N-terminal (1);	0.096800	0.64402	D	0.000001	T	0.65207	0.2669	L	0.57536	1.79	0.80722	D	1	B	0.33777	0.425	B	0.37387	0.248	T	0.60556	-0.7240	10	0.35671	T	0.21	-20.2445	20.5934	0.99428	0.0:1.0:0.0:0.0	.	125	O75937	DNJC8_HUMAN	S	125	ENSP00000263697:A125S	ENSP00000263697:A125S	A	-	1	0	DNAJC8	28409096	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.396000	0.79891	2.872000	0.98467	0.650000	0.86243	GCA	0	superfamily_DnaJ_domain		0.418	DNAJC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DNAJC8	protein_coding	OTTHUMT00000009860.1	42	76	0	0.00	0	0	C	NM_014280	0	0		28536509	-1	no_errors	ENST00000263697	ensembl	human	known	74_37	missense	46	82	24.59	27.43	15	31	SNP	1	A
NRAS	4893	genome.wustl.edu	37	1	115256529	115256529	+	Missense_Mutation	SNP	T	T	C	rs11554290	byFrequency	TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr1:115256529T>C	ENST00000369535.4	-	3	435	c.182A>G	c.(181-183)cAa>cGa	p.Q61R		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	61			Q -> K (in CMNS and NCMS; somatic mutation). {ECO:0000269|PubMed:23392294}.|Q -> R (in CMNS, NCMS and KNEN; also found in lung carcinoma cell and melanoma; dbSNP:rs11554290). {ECO:0000269|PubMed:18633438, ECO:0000269|PubMed:22499344, ECO:0000269|PubMed:23392294, ECO:0000269|PubMed:3276402}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.Q61R(817)|p.Q61L(175)|p.Q61P(23)|p.Q61K(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTACTCTTCTTGTCCAGCTGT	0.458	Q61L(C3A_LIVER)|Q61L(HEPG2_LIVER)|Q61L(HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(IPC298_SKIN)|Q61L(KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(MELJUSO_SKIN)|Q61L(MHHES1_BONE)|Q61L(MOLP8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61L(OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61P(TF1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(HT1197_URINARY_TRACT)|Q61R(KMS27_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61R(KU1919_URINARY_TRACT)|Q61R(NCIH2347_LUNG)|Q61R(ONS76_CENTRAL_NERVOUS_SYSTEM)|Q61R(SKMEL2_SKIN)|Q61R(SW1271_LUNG)|Q61R(TT2609C02_THYROID)	50	Mis		"""melanoma, MM, AML, thyroid"""				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																													0		Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"""L, E"""	1016	Substitution - Missense(1016)	skin(466)|thyroid(279)|haematopoietic_and_lymphoid_tissue(124)|NS(50)|large_intestine(27)|lung(17)|urinary_tract(11)|adrenal_gland(7)|liver(7)|breast(7)|soft_tissue(4)|testis(3)|endometrium(3)|ovary(3)|central_nervous_system(2)|pancreas(2)|eye(1)|prostate(1)|meninges(1)|autonomic_ganglia(1)											180.0	156.0	164.0					1																	115256529		2203	4300	6503	SO:0001583	missense	0	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.182A>G	1.37:g.115256529T>C	ENSP00000358548:p.Gln61Arg		Q14971|Q15104|Q15282	Missense_Mutation	SNP	pfam_Small_GTPase,pfam_MIRO-like,pfam_Small_GTPase_ARF/SAR,pfam_EF_GTP-bd_dom,superfamily_P-loop_NTPase,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho,prints_Small_GTPase,tigrfam_Small_GTP-bd_dom	p.Q61R	ENST00000369535.4	37	c.182	CCDS877.1	1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.004139	0.74932	.	.	ENSG00000213281	ENST00000369535	D	0.83673	-1.75	5.08	5.08	0.68730	Small GTP-binding protein domain (1);	0.000000	0.53938	U	0.000043	D	0.86489	0.5945	M	0.92604	3.325	0.80722	D	1	B	0.28512	0.214	B	0.39590	0.304	D	0.88255	0.2919	10	0.66056	D	0.02	.	15.0132	0.71565	0.0:0.0:0.0:1.0	rs11554290;rs11554290	61	P01111	RASN_HUMAN	R	61	ENSP00000358548:Q61R	ENSP00000358548:Q61R	Q	-	2	0	NRAS	115058052	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.761000	0.85260	2.120000	0.65058	0.533000	0.62120	CAA	0	pfam_Small_GTPase,pfam_MIRO-like,pfam_Small_GTPase_ARF/SAR,pfam_EF_GTP-bd_dom,superfamily_P-loop_NTPase,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho,prints_Small_GTPase,tigrfam_Small_GTP-bd_dom		0.458	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NRAS	protein_coding	OTTHUMT00000033395.2	60	223	0	0.00	0	0	T	NM_002524	rs11554290	T->A,C,G		115256529	-1	no_errors	ENST00000369535	ensembl	human	known	74_37	missense	58	140	26.58	39.74	21	93	SNP	1	C
ATP1A2	477	genome.wustl.edu	37	1	160098515	160098515	+	Missense_Mutation	SNP	C	C	T			TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr1:160098515C>T	ENST00000361216.3	+	9	1180	c.1091C>T	c.(1090-1092)aCg>aTg	p.T364M	ATP1A2_ENST00000392233.3_Missense_Mutation_p.T364M	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	364					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			GCGGTGGAGACGCTGGGCTCC	0.577																																							0											0													119.0	102.0	107.0					1																	160098515		2203	4300	6503	SO:0001583	missense	0			AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"""ATPases / P-type"""	800	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-2"", ""sodium pump subunit alpha-2"", ""sodium-potassium ATPase catalytic subunit alpha-2"""	182340	"""migraine, hemiplegic 2"", ""ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"""	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.1091C>T	1.37:g.160098515C>T	ENSP00000354490:p.Thr364Met		D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Missense_Mutation	SNP	pfam_ATPase_P-typ_transduc_dom_A,pfam_ATPase_P-typ_cation-transptr_C,pfam_HAD-like_dom,pfam_ATPase_P-typ_cation-transptr_N,superfamily_ATPase_P-typ_cyto_domN,superfamily_HAD-like_dom,smart_ATPase_P-typ_cation-transptr_N,prints_Cation_transp_P_typ_ATPase,tigrfam_ATPase_P-typ_Na/K_IIC,tigrfam_Cation_transp_P_typ_ATPase	p.T364M	ENST00000361216.3	37	c.1091	CCDS1196.1	1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.8|27.8	4.862909|4.862909	0.91511|0.91511	.|.	.|.	ENSG00000018625|ENSG00000018625	ENST00000447527|ENST00000538123;ENST00000361216;ENST00000392233;ENST00000435866	.|D;D	.|0.92397	.|-3.03;-3.03	4.77|4.77	4.77|4.77	0.60923|0.60923	.|ATPase, P-type, cytoplasmic domain N (1);ATPase, P-type, ATPase-associated domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.97514|0.97514	0.9186|0.9186	H|H	0.97516|0.97516	4.02|4.02	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.97110	.|1.0;1.0;0.999;1.0	D|D	0.99010|0.99010	1.0814|1.0814	5|10	.|0.87932	.|D	.|0	.|.	16.9484|16.9484	0.86236|0.86236	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|209;364;264;364	.|B4DHD7;B1AKY9;F5GXJ7;P50993	.|.;.;.;AT1A2_HUMAN	C|M	75|209;364;364;67	.|ENSP00000354490:T364M;ENSP00000376066:T364M	.|ENSP00000354490:T364M	R|T	+|+	1|2	0|0	ATP1A2|ATP1A2	158365139|158365139	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.998000|0.998000	0.95712|0.95712	7.757000|7.757000	0.85209|0.85209	2.359000|2.359000	0.80004|0.80004	0.561000|0.561000	0.74099|0.74099	CGC|ACG	0	pfam_ATPase_P-typ_transduc_dom_A,tigrfam_ATPase_P-typ_Na/K_IIC,tigrfam_Cation_transp_P_typ_ATPase		0.577	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ATP1A2	protein_coding	OTTHUMT00000060642.2	28	60	0	0.00	0	0	C	NM_000702	0	0		160098515	1	no_errors	ENST00000361216	ensembl	human	known	74_37	missense	16	37	58.97	46.38	23	32	SNP	1	T
RFWD2	64326	genome.wustl.edu	37	1	176105648	176105648	+	Missense_Mutation	SNP	C	C	G			TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr1:176105648C>G	ENST00000367669.3	-	7	1381	c.867G>C	c.(865-867)ttG>ttC	p.L289F	RFWD2_ENST00000308769.8_Intron	NM_022457.5	NP_071902.2	Q8NHY2	RFWD2_HUMAN	ring finger and WD repeat domain 2, E3 ubiquitin protein ligase	289					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin protein ligase activity (GO:0061630)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						TATCCTCTTCCAAAACACTTA	0.353																																					Ovarian(134;1413 1765 5706 35534 51541)		0											0													109.0	103.0	105.0					1																	176105648		2203	4300	6503	SO:0001583	missense	0			AK001278	CCDS30944.1, CCDS44279.1	1q25.1-q25.2	2013-01-09	2012-02-23		ENSG00000143207	ENSG00000143207		"""WD repeat domain containing"", ""RING-type (C3HC4) zinc fingers"""	17440	protein-coding gene	gene with protein product		608067	"""ring finger and WD repeat domain 2"""			10395541	Standard	XM_005245447		Approved	FLJ10416, COP1, RNF200	uc001gku.1	Q8NHY2	OTTHUMG00000034986	ENST00000367669.3:c.867G>C	1.37:g.176105648C>G	ENSP00000356641:p.Leu289Phe		E9PKI0|Q504W6|Q6H103|Q9H6L7|X5D9B4	Missense_Mutation	SNP	pfam_WD40_repeat,pfam_Znf_C3HC4_RING-type,superfamily_WD40_repeat_dom,smart_Znf_RING,smart_WD40_repeat,pfscan_Znf_RING,pfscan_WD40_repeat,pfscan_WD40_repeat_dom	p.L289F	ENST00000367669.3	37	c.867	CCDS30944.1	1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.105287	0.77096	.	.	ENSG00000143207	ENST00000367665;ENST00000367669	T	0.12569	2.67	5.4	4.49	0.54785	.	0.000000	0.64402	D	0.000001	T	0.30324	0.0761	L	0.50333	1.59	0.80722	D	1	P;P;D	0.65815	0.817;0.824;0.995	P;P;D	0.70487	0.561;0.879;0.969	T	0.02238	-1.1190	10	0.87932	D	0	-6.9909	13.3225	0.60440	0.0:0.9237:0.0:0.0763	.	25;49;289	Q8NHY2-3;B1AMD2;Q8NHY2	.;.;RFWD2_HUMAN	F	25;289	ENSP00000356641:L289F	ENSP00000356637:L25F	L	-	3	2	RFWD2	174372271	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.301000	0.51842	1.291000	0.44653	0.650000	0.86243	TTG	0	NULL		0.353	RFWD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RFWD2	protein_coding	OTTHUMT00000084672.2	26	151	0	0.00	0	0	C	NM_022457	0	0		176105648	-1	no_errors	ENST00000367669	ensembl	human	known	74_37	missense	21	177	8.7	5.85	2	11	SNP	1	G
ADCY3	109	genome.wustl.edu	37	2	25043661	25043661	+	Missense_Mutation	SNP	C	C	T			TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr2:25043661C>T	ENST00000260600.5	-	20	4035	c.3184G>A	c.(3184-3186)Gac>Aac	p.D1062N	ADCY3_ENST00000405392.1_Missense_Mutation_p.D649N|CENPO_ENST00000380834.2_3'UTR|CENPO_ENST00000473706.1_3'UTR	NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	1062					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			NS(1)|breast(5)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(4)|skin(2)	44	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					CCCCAGATGTCGTAGTGTGGT	0.572																																							0											0													175.0	144.0	154.0					2																	25043661		2203	4300	6503	SO:0001583	missense	0			AF033861	CCDS1715.1	2p23.3	2013-02-04			ENSG00000138031	ENSG00000138031	4.6.1.1	"""Adenylate cyclases"""	234	protein-coding gene	gene with protein product		600291				9920776	Standard	NM_004036		Approved	AC3	uc002rfs.4	O60266	OTTHUMG00000094765	ENST00000260600.5:c.3184G>A	2.37:g.25043661C>T	ENSP00000260600:p.Asp1062Asn		B3KT86|Q53T54|Q9UDB1	Missense_Mutation	SNP	pfam_A/G_cyclase,superfamily_A/G_cyclase,smart_A/G_cyclase,pfscan_A/G_cyclase	p.D1062N	ENST00000260600.5	37	c.3184	CCDS1715.1	2	.	.	.	.	.	.	.	.	.	.	C	37	5.989646	0.97179	.	.	ENSG00000138031	ENST00000260600;ENST00000405392;ENST00000415879	D;D	0.85411	-1.98;-1.98	5.93	5.93	0.95920	Adenylyl cyclase class-3/4/guanylyl cyclase, conserved site (1);Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.85682	D	0.000000	D	0.96015	0.8702	H	0.98525	4.255	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.97109	0.9803	10	0.87932	D	0	.	19.936	0.97142	0.0:1.0:0.0:0.0	.	1063;1062;649	B7ZLX9;O60266;B3KT86	.;ADCY3_HUMAN;.	N	1062;649;1037	ENSP00000260600:D1062N;ENSP00000384484:D649N	ENSP00000260600:D1062N	D	-	1	0	ADCY3	24897165	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.818000	0.86416	2.814000	0.96858	0.655000	0.94253	GAC	0	pfam_A/G_cyclase,superfamily_A/G_cyclase,smart_A/G_cyclase,pfscan_A/G_cyclase		0.572	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ADCY3	protein_coding	OTTHUMT00000211574.2	80	159	0	0.00	0	0	C		0	0		25043661	-1	no_errors	ENST00000260600	ensembl	human	known	74_37	missense	57	136	29.63	33.00	24	67	SNP	1	T
ANXA4	307	genome.wustl.edu	37	2	70008648	70008648	+	Intron	SNP	A	A	T			TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr2:70008648A>T	ENST00000418066.2	+	4	864				ANXA4_ENST00000409920.1_Intron|ANXA4_ENST00000536030.1_Intron|ANXA4_ENST00000394295.4_Intron			P09525	ANXA4_HUMAN	annexin A4						epithelial cell differentiation (GO:0030855)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of interleukin-8 secretion (GO:2000483)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phospholipase inhibitor activity (GO:0004859)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)	11						TGCTTTTATCACAGAAGAACT	0.433																																							0											0													115.0	98.0	104.0					2																	70008648		2203	4300	6503	SO:0001627	intron_variant	0			M82809	CCDS1894.1	2p13.3	2008-02-05			ENSG00000196975	ENSG00000196975		"""Annexins"""	542	protein-coding gene	gene with protein product		106491		ANX4		1346776	Standard	NM_001153		Approved		uc002sfr.4	P09525	OTTHUMG00000129649	ENST00000418066.2:c.865-4A>T	2.37:g.70008648A>T			B4DDF9|Q96F33|Q9BWK1	RNA	SNP	0	NULL	ENST00000418066.2	37	NULL		2																																																																																			0	0		0.433	ANXA4-013	KNOWN	basic|exp_conf	processed_transcript	ANXA4	protein_coding	OTTHUMT00000470748.1	53	197	0	0.00	0	0	A	NM_001153	0	0		70008648	1	no_errors	ENST00000460439	ensembl	human	known	74_37	rna	34	113	27.66	40.31	13	77	SNP	0.807	T
PLXND1	23129	genome.wustl.edu	37	3	129278491	129278491	+	Missense_Mutation	SNP	C	C	T			TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr3:129278491C>T	ENST00000324093.4	-	32	5447	c.5269G>A	c.(5269-5271)Gac>Aac	p.D1757N	PLXND1_ENST00000393239.1_Missense_Mutation_p.D1757N|PLXND1_ENST00000504689.1_5'Flank	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	1757					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						TGTAGGGTGTCGGGGTCGGAG	0.602																																					Ovarian(97;366 1484 3738 22084 39045)		0											0													98.0	104.0	102.0					3																	129278491		2203	4300	6503	SO:0001583	missense	0			AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"""Plexins"""	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.5269G>A	3.37:g.129278491C>T	ENSP00000317128:p.Asp1757Asn		A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	pfam_Plexin_cytoplasmic_RasGAP_dom,pfam_IPT,pfam_Semap_dom,pfam_Plexin_repeat,superfamily_Semap_dom,superfamily_Rho_GTPase_activation_prot,superfamily_Ig_E-set,superfamily_Plexin-like_fold,smart_Semap_dom,smart_Plexin-like_fold,smart_IPT,pfscan_Semap_dom	p.D1757N	ENST00000324093.4	37	c.5269	CCDS33854.1	3	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.539044|5.539044	0.96474|0.96474	.|.	.|.	ENSG00000004399|ENSG00000004399	ENST00000324093;ENST00000393239|ENST00000506979	T;T|.	0.14022|.	2.54;2.54|.	4.95|4.95	4.95|4.95	0.65309|0.65309	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);|.	0.112812|.	0.56097|.	D|.	0.000022|.	T|T	0.73063|0.73063	0.3539|0.3539	M|M	0.63843|0.63843	1.955|1.955	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	0.999;1.0|.	D;D|.	0.91635|.	0.994;0.999|.	T|T	0.72304|0.72304	-0.4333|-0.4333	10|5	0.87932|.	D|.	0|.	.|.	18.2048|18.2048	0.89851|0.89851	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	352;1757|.	B4DRU3;Q9Y4D7|.	.;PLXD1_HUMAN|.	N|Q	1757|100	ENSP00000317128:D1757N;ENSP00000376931:D1757N|.	ENSP00000317128:D1757N|.	D|R	-|-	1|2	0|0	PLXND1|PLXND1	130761181|130761181	1.000000|1.000000	0.71417|0.71417	0.976000|0.976000	0.42696|0.42696	0.917000|0.917000	0.54804|0.54804	7.813000|7.813000	0.86123|0.86123	2.292000|2.292000	0.77174|0.77174	0.563000|0.563000	0.77884|0.77884	GAC|CGA	0	pfam_Plexin_cytoplasmic_RasGAP_dom,superfamily_Rho_GTPase_activation_prot		0.602	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PLXND1	protein_coding	OTTHUMT00000356132.4	83	120	0	0.00	0	0	C	NM_015103	0	0		129278491	-1	no_errors	ENST00000324093	ensembl	human	known	74_37	missense	92	158	7.07	6.51	7	11	SNP	1	T
SLC23A1	9963	genome.wustl.edu	37	5	138716555	138716555	+	Missense_Mutation	SNP	C	C	T			TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr5:138716555C>T	ENST00000348729.3	-	4	375	c.329G>A	c.(328-330)aGt>aAt	p.S110N	SLC23A1_ENST00000503919.1_5'UTR|SLC23A1_ENST00000353963.3_Missense_Mutation_p.S110N	NM_005847.4	NP_005838	Q9UHI7	S23A1_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 1	110					brain development (GO:0007420)|dehydroascorbic acid transport (GO:0070837)|L-ascorbic acid metabolic process (GO:0019852)|L-ascorbic acid transport (GO:0015882)|lung development (GO:0030324)|nucleobase transport (GO:0015851)|nucleobase-containing compound metabolic process (GO:0006139)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transepithelial L-ascorbic acid transport (GO:0070904)|vitamin metabolic process (GO:0006766)|vitamin transmembrane transport (GO:0035461)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|brush border (GO:0005903)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular organelle (GO:0043229)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dehydroascorbic acid transporter activity (GO:0033300)|L-ascorbate:sodium symporter activity (GO:0008520)|L-ascorbic acid transporter activity (GO:0015229)|nucleobase transmembrane transporter activity (GO:0015205)|sodium ion transmembrane transporter activity (GO:0015081)|sodium-dependent L-ascorbate transmembrane transporter activity (GO:0070890)			biliary_tract(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(5)|ovary(1)	19			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)		Vitamin C(DB00126)	TGCAAAGGCACTGGCCTGGAA	0.602																																							0											0													14.0	14.0	14.0					5																	138716555		2195	4297	6492	SO:0001583	missense	0			AF058317	CCDS4212.1, CCDS4213.1	5q31.2	2013-07-18	2013-07-18	2003-03-21	ENSG00000170482	ENSG00000170482		"""Solute carriers"""	10974	protein-coding gene	gene with protein product		603790	"""solute carrier family 23 (nucleobase transporters), member 2"""	SLC23A2		9804989, 10331392	Standard	NM_005847		Approved	YSPL3, SVCT1	uc003leg.3	Q9UHI7	OTTHUMG00000129228	ENST00000348729.3:c.329G>A	5.37:g.138716555C>T	ENSP00000302701:p.Ser110Asn		O95191|Q8WWB6|Q9UGH4|Q9UI39	Missense_Mutation	SNP	pfam_Xant/urac/vitC	p.S110N	ENST00000348729.3	37	c.329	CCDS4212.1	5	.	.	.	.	.	.	.	.	.	.	C	31	5.100701	0.94245	.	.	ENSG00000170482	ENST00000353963;ENST00000348729;ENST00000453898	T;T	0.19669	2.13;2.13	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.47266	0.1436	M	0.73598	2.24	0.80722	D	1	D;P	0.56035	0.974;0.746	D;B	0.73380	0.98;0.43	T	0.40289	-0.9571	10	0.54805	T	0.06	-23.14	16.1656	0.81754	0.0:1.0:0.0:0.0	.	110;110	Q9UHI7;Q9UHI7-2	S23A1_HUMAN;.	N	110	ENSP00000302851:S110N;ENSP00000302701:S110N	ENSP00000302701:S110N	S	-	2	0	SLC23A1	138744454	1.000000	0.71417	0.997000	0.53966	0.950000	0.60333	7.541000	0.82084	2.677000	0.91161	0.561000	0.74099	AGT	0	pfam_Xant/urac/vitC		0.602	SLC23A1-001	KNOWN	basic|CCDS	protein_coding	SLC23A1	protein_coding	OTTHUMT00000374185.1	23	33	0	0.00	0	0	C	NM_152685	0	0		138716555	-1	no_errors	ENST00000353963	ensembl	human	known	74_37	missense	15	44	28.57	30.77	6	20	SNP	1	T
PCDHB18	54660	genome.wustl.edu	37	5	140615380	140615380	+	RNA	SNP	C	C	T			TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr5:140615380C>T	ENST00000526308.1	+	0	1443					NR_001281.1		Q96TA0	PCDBI_HUMAN	protocadherin beta 18 pseudogene						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(9)|lung(7)|ovary(1)|urinary_tract(1)	18						ATGAATATAACATCACCATCA	0.502																																							0											0																																												0			AF152528		5q31.3	2014-03-20			ENSG00000146001	ENSG00000146001		"""Cadherins / Protocadherins : Clustered"""	14548	pseudogene	pseudogene						10380929	Standard	NR_001281		Approved	PCDH-psi2	uc003ljc.1	Q96TA0	OTTHUMG00000167484		5.37:g.140615380C>T			B3KTF8	RNA	SNP	0	NULL	ENST00000526308.1	37	NULL		5																																																																																			0	0		0.502	PCDHB18-002	KNOWN	basic	processed_transcript	PCDHB18	pseudogene	OTTHUMT00000394776.1	86	72	0	0.00	0	0	C		0	0		140615380	1	no_errors	ENST00000526308	ensembl	human	known	74_37	rna	52	62	33.75	40.19	27	43	SNP	0.871	T
EEF1D	1936	genome.wustl.edu	37	8	144661891	144661891	+	3'UTR	SNP	C	C	A			TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr8:144661891C>A	ENST00000419152.2	-	0	1427				NAPRT1_ENST00000426292.3_5'Flank|NAPRT1_ENST00000276844.7_5'Flank|EEF1D_ENST00000532400.1_Intron|NAPRT1_ENST00000435154.3_5'Flank|RP11-661A12.9_ENST00000531730.1_RNA|NAPRT1_ENST00000449291.2_5'Flank|RP11-661A12.7_ENST00000529247.1_RNA	NM_001130055.2	NP_001123527.1	P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|translation elongation factor activity (GO:0003746)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|cervix(1)|endometrium(1)|kidney(4)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			CAGGACGGAGCCAGAGGGCCG	0.597																																							0											0													35.0	33.0	34.0					8																	144661891		692	1591	2283	SO:0001624	3_prime_UTR_variant	0			AK024550	CCDS6404.1, CCDS6405.1, CCDS47930.1, CCDS56559.1	8q24	2011-09-15			ENSG00000104529	ENSG00000104529			3211	protein-coding gene	gene with protein product		130592				8334168	Standard	NM_001960		Approved	EF-1D, FLJ20897	uc003yyt.3	P29692	OTTHUMG00000165191	ENST00000419152.2:c.*71G>T	8.37:g.144661891C>A			B4DDU4|D3DWK3|E9PBQ9|Q4VBZ6|Q969J1|Q96I38	RNA	SNP	0	NULL	ENST00000419152.2	37	NULL	CCDS6405.1	8																																																																																			0	0		0.597	EEF1D-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ENSG00000254741	protein_coding		20	128	0	0.00	0	0	C	NM_032378	0	0		144661891	1	no_errors	ENST00000529247	ensembl	human	known	74_37	rna	17	87	32	33.08	8	43	SNP	0.01	A
GBA2	57704	genome.wustl.edu	37	9	35748561	35748561	+	Missense_Mutation	SNP	A	A	T			TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr9:35748561A>T	ENST00000378103.3	-	1	664	c.141T>A	c.(139-141)agT>agA	p.S47R	RGP1_ENST00000378078.4_5'Flank|RGP1_ENST00000456972.2_5'Flank|GBA2_ENST00000545786.1_Missense_Mutation_p.S47R|GBA2_ENST00000378094.4_Missense_Mutation_p.S47R	NM_020944.2	NP_065995.1	Q9HCG7	GBA2_HUMAN	glucosidase, beta (bile acid) 2	47					bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|central nervous system neuron development (GO:0021954)|glucosylceramide catabolic process (GO:0006680)|glycoside catabolic process (GO:0016139)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)	beta-glucosidase activity (GO:0008422)|glucosylceramidase activity (GO:0004348)			NS(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(4)|skin(3)	21	all_epithelial(49;0.167)		Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TGTCTTCGGGACTCTTACAGT	0.547																																							0											0													133.0	138.0	136.0					9																	35748561		2203	4300	6503	SO:0001583	missense	0			AJ309567	CCDS6589.1	9p13.2	2013-09-11			ENSG00000070610	ENSG00000070610			18986	protein-coding gene	gene with protein product	"""bile acid beta-glucosidase"", ""non-lysosomal glucosylceramidase"""	609471	"""spastic paraplegia 46 (autosomal recessive)"""	SPG46		11489889, 23332916, 23332917	Standard	NM_020944		Approved	KIAA1605, AD035, DKFZp762K054	uc003zxw.3	Q9HCG7	OTTHUMG00000021024	ENST00000378103.3:c.141T>A	9.37:g.35748561A>T	ENSP00000367343:p.Ser47Arg		D3DRP2|Q5TCV6|Q96A51|Q96LY1|Q96SJ2|Q9H2L8	Missense_Mutation	SNP	pfam_Glucosylceramidase,pfam_GBA2_N,superfamily_6-hairpin_glycosidase-like,pirsf_Beta_glucosidase_GBA2-type	p.S47R	ENST00000378103.3	37	c.141	CCDS6589.1	9	.	.	.	.	.	.	.	.	.	.	A	14.05	2.418823	0.42918	.	.	ENSG00000070610	ENST00000378103;ENST00000378094;ENST00000545786	.	.	.	5.04	0.937	0.19494	.	0.503467	0.18600	N	0.136461	T	0.24509	0.0594	N	0.22421	0.69	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.15578	-1.0432	9	0.59425	D	0.04	-0.2773	5.2805	0.15673	0.2534:0.1473:0.5993:0.0	.	47;47;47	F5H7P6;Q9HCG7-2;Q9HCG7	.;.;GBA2_HUMAN	R	47	.	ENSP00000367334:S47R	S	-	3	2	GBA2	35738561	0.217000	0.23597	0.004000	0.12327	0.048000	0.14542	1.615000	0.36922	0.074000	0.16767	-0.427000	0.05922	AGT	0	NULL		0.547	GBA2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	GBA2	protein_coding	OTTHUMT00000055456.1	36	164	0	1.20	0	2	A	NM_020944	0	0		35748561	-1	no_errors	ENST00000545786	ensembl	human	known	74_37	missense	21	144	38.24	26.90	13	53	SNP	0.001	T
GFI1B	8328	genome.wustl.edu	37	9	135862743	135862743	+	Missense_Mutation	SNP	A	A	C			TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr9:135862743A>C	ENST00000339463.3	+	7	994	c.175A>C	c.(175-177)Aac>Cac	p.N59H	GFI1B_ENST00000534944.1_Missense_Mutation_p.N59H|GFI1B_ENST00000372123.1_Missense_Mutation_p.N59H|GFI1B_ENST00000372124.1_Missense_Mutation_p.N59H|GFI1B_ENST00000372122.1_Missense_Mutation_p.N59H|GFI1B_ENST00000450530.1_Missense_Mutation_p.N59H			Q5VTD9	GFI1B_HUMAN	growth factor independent 1B transcription repressor	59					cell proliferation (GO:0008283)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of histone H3-K9 methylation (GO:0051574)|regulation of erythrocyte differentiation (GO:0045646)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II transcription factor binding (GO:0001085)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)	21				OV - Ovarian serous cystadenocarcinoma(145;9.04e-07)|Epithelial(140;1.17e-05)		GGACTGGACCAACCTCAAACG	0.602																																							0											0													89.0	76.0	80.0					9																	135862743		2203	4300	6503	SO:0001583	missense	0			AF081946	CCDS6957.1, CCDS48049.1	9q34.13	2014-09-17	2007-10-04		ENSG00000165702	ENSG00000165702		"""Zinc fingers, C2H2-type"""	4238	protein-coding gene	gene with protein product		604383	"""growth factor independent 1B (potential regulator of CDKN1A, translocated in CML)"""			9878267	Standard	NM_001135031		Approved		uc004ccg.3	Q5VTD9	OTTHUMG00000020848	ENST00000339463.3:c.175A>C	9.37:g.135862743A>C	ENSP00000344782:p.Asn59His		O95270|Q5VTD8|Q6FHZ2|Q6T888	Missense_Mutation	SNP	pfam_Znf_C2H2,smart_Znf_C2H2-like,pfscan_Znf_C2H2	p.N59H	ENST00000339463.3	37	c.175	CCDS6957.1	9	.	.	.	.	.	.	.	.	.	.	A	3.110	-0.182872	0.06340	.	.	ENSG00000165702	ENST00000372124;ENST00000339463;ENST00000450530;ENST00000534944;ENST00000372123;ENST00000372122	T;T;T;T;T;T	0.08984	3.19;3.03;3.03;3.19;3.19;3.03	4.33	-1.13	0.09775	.	2.229410	0.02184	N	0.060775	T	0.04724	0.0128	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.37220	-0.9715	10	0.45353	T	0.12	-0.0194	3.9865	0.09517	0.3837:0.367:0.2492:0.0	.	59;59	Q5VTD9-2;Q5VTD9	.;GFI1B_HUMAN	H	59	ENSP00000361197:N59H;ENSP00000344782:N59H;ENSP00000409546:N59H;ENSP00000446134:N59H;ENSP00000361196:N59H;ENSP00000361195:N59H	ENSP00000344782:N59H	N	+	1	0	GFI1B	134852564	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.085000	0.14912	-0.273000	0.09246	-0.313000	0.08912	AAC	0	NULL		0.602	GFI1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	GFI1B	protein_coding	OTTHUMT00000393840.1	56	121	0	0.00	0	0	A	NM_004188	0	0		135862743	1	no_errors	ENST00000339463	ensembl	human	known	74_37	missense	27	106	20.59	29.80	7	45	SNP	0	C
NRG3	10718	genome.wustl.edu	37	10	83992498	83992498	+	Intron	SNP	G	G	T			TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr10:83992498G>T	ENST00000404547.1	+	2	823				NRG3_ENST00000404576.2_Intron|NRG3-AS1_ENST00000502725.1_RNA|NRG3_ENST00000372142.2_Intron|NRG3-AS1_ENST00000448936.2_RNA|NRG3_ENST00000556918.1_Splice_Site_p.C79F|NRG3_ENST00000372141.2_Intron			P56975	NRG3_HUMAN	neuregulin 3						activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		ctactcacaggtcctagagac	0.453																																							0											0																																										SO:0001627	intron_variant	0			AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737			7999	protein-coding gene	gene with protein product		605533				9275162	Standard	NM_001010848		Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000404547.1:c.824-125997G>T	10.37:g.83992498G>T			A4D7U1|Q0PEH2|Q5VYH3	Missense_Mutation	SNP	pfam_Neuregulin_1_C,pfscan_EG-like_dom	p.C79F	ENST00000404547.1	37	c.236	CCDS31233.1	10	.	.	.	.	.	.	.	.	.	.	G	5.324	0.245186	0.10077	.	.	ENSG00000185737	ENST00000556918	T	0.35236	1.32	1.81	-1.49	0.08718	.	.	.	.	.	T	0.21387	0.0515	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.26538	-1.0100	5	.	.	.	.	3.5697	0.07913	0.0:0.3479:0.3239:0.3281	.	.	.	.	F	79	ENSP00000451376:C79F	.	C	+	2	0	NRG3	83982478	0.000000	0.05858	0.001000	0.08648	0.311000	0.27955	-0.399000	0.07250	-0.403000	0.07622	0.467000	0.42956	TGT	0	NULL		0.453	NRG3-005	KNOWN	basic|CCDS	protein_coding	NRG3	protein_coding	OTTHUMT00000412262.1	51	120	0	0.00	0	0	G	XM_166086	0	0		83992498	1	no_errors	ENST00000556918	ensembl	human	novel	74_37	missense	22	124	32.35	20.00	11	31	SNP	0.001	T
GALNT9	50614	genome.wustl.edu	37	12	132683757	132683757	+	Missense_Mutation	SNP	G	G	A			TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr12:132683757G>A	ENST00000328957.8	-	9	1458	c.1459C>T	c.(1459-1461)Cgg>Tgg	p.R487W	GALNT9_ENST00000535228.1_Missense_Mutation_p.R238W|GALNT9_ENST00000397325.2_Missense_Mutation_p.R121W|GALNT9_ENST00000541995.1_Missense_Mutation_p.R121W	NM_001122636.1	NP_001116108.1	Q9HCQ5	GALT9_HUMAN	polypeptide N-acetylgalactosaminyltransferase 9	487	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(1)|large_intestine(2)|lung(5)	9	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.49e-08)|Epithelial(86;3.55e-07)|all cancers(50;2.09e-05)		AGGATCGCCCGGTCGCCGTCC	0.657																																					Colon(186;2147 2752 13553 41466)		0											0													45.0	54.0	51.0					12																	132683757		2028	4156	6184	SO:0001583	missense	0			AB040672	CCDS41866.1	12q24.33	2014-03-13	2014-03-13		ENSG00000182870	ENSG00000182870	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4131	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 9"""	606251	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9 (GalNAc-T9)"""			10978536, 12407114	Standard	NM_021808		Approved	GALNAC-T9	uc001ukc.4	Q9HCQ5	OTTHUMG00000168256	ENST00000328957.8:c.1459C>T	12.37:g.132683757G>A	ENSP00000329846:p.Arg487Trp		Q52LR8|Q6NT54|Q8NFR1	Missense_Mutation	SNP	pfam_Glyco_trans_2,pfam_Ricin_B_lectin,superfamily_Ricin_B_lectin,smart_Ricin_B_lectin,pfscan_Ricin_B_lectin	p.R487W	ENST00000328957.8	37	c.1459		12	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	16.43|16.43	3.121336|3.121336	0.56613|0.56613	.|.	.|.	ENSG00000182870|ENSG00000182870	ENST00000411988|ENST00000397325;ENST00000328957;ENST00000535228;ENST00000541995	.|T;T;T;T	.|0.27720	.|1.65;1.65;1.65;1.65	4.49|4.49	2.37|2.37	0.29283|0.29283	.|Ricin B-related lectin (1);Ricin B lectin (3);	.|0.478359	.|0.22616	.|N	.|0.057778	T|T	0.46698|0.46698	0.1406|0.1406	L|L	0.60455|0.60455	1.87|1.87	0.38625|0.38625	D|D	0.951248|0.951248	.|D;D;D	.|0.89917	.|1.0;0.992;0.98	.|D;P;P	.|0.68765	.|0.96;0.773;0.606	T|T	0.54022|0.54022	-0.8355|-0.8355	5|10	.|0.72032	.|D	.|0.01	.|.	11.036|11.036	0.47802|0.47802	0.0:0.0:0.5637:0.4363|0.0:0.0:0.5637:0.4363	.|.	.|238;487;344	.|B3KNR7;Q9HCQ5;B3KP58	.|.;GALT9_HUMAN;.	L|W	259|121;487;238;121	.|ENSP00000380488:R121W;ENSP00000329846:R487W;ENSP00000439745:R238W;ENSP00000440544:R121W	.|ENSP00000329846:R487W	P|R	-|-	2|1	0|2	GALNT9|GALNT9	131249710|131249710	0.999000|0.999000	0.42202|0.42202	0.825000|0.825000	0.32803|0.32803	0.165000|0.165000	0.22458|0.22458	2.961000|2.961000	0.49168|0.49168	2.025000|2.025000	0.59659|0.59659	0.563000|0.563000	0.77884|0.77884	CCG|CGG	0	pfam_Ricin_B_lectin,superfamily_Ricin_B_lectin,smart_Ricin_B_lectin,pfscan_Ricin_B_lectin		0.657	GALNT9-009	KNOWN	basic|appris_principal	protein_coding	GALNT9	protein_coding	OTTHUMT00000402967.1	90	29	0	0.00	0	0	G	NM_001122636	0	0		132683757	-1	no_errors	ENST00000328957	ensembl	human	known	74_37	missense	62	35	42.06	32.69	45	17	SNP	0.983	A
TBC1D3P5	440419	genome.wustl.edu	37	17	25756876	25756876	+	RNA	SNP	G	G	A	rs564957228		TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr17:25756876G>A	ENST00000586223.1	+	0	1710					NR_033892.1				TBC1 domain family, member 3 pseudogene 5																		CGGTTCCAGCGGCCCATTTGG	0.667													G|||	1	0.000199681	0.0	0.0	5008	,	,		13911	0.0		0.001	False		,,,				2504	0.0						0.9998,0.0001997											0																																												0					17q11.1	2014-03-20			ENSG00000266433	ENSG00000266433			43567	pseudogene	pseudogene							Standard	NR_033892		Approved		uc002gzg.3		OTTHUMG00000179156		17.37:g.25756876G>A				RNA	SNP	0	NULL	ENST00000586223.1	37	NULL		17																																																																																			0	0		0.667	TBC1D3P5-003	KNOWN	non_canonical_TEC|basic	processed_transcript	TBC1D3P5	pseudogene	OTTHUMT00000451073.1	51	69	0	0.00	0	0	G	NR_033892	rs564957228	G->A		25756876	1	no_errors	ENST00000581469	ensembl	human	known	74_37	rna	27	64	27.03	35.35	10	35	SNP	0.229	A
EVI5L	115704	genome.wustl.edu	37	19	7913876	7913876	+	Missense_Mutation	SNP	G	G	A			TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr19:7913876G>A	ENST00000270530.4	+	4	593	c.397G>A	c.(397-399)Gac>Aac	p.D133N	EVI5L_ENST00000538904.2_Missense_Mutation_p.D133N	NM_145245.3	NP_660288.1	Q96CN4	EVI5L_HUMAN	ecotropic viral integration site 5-like	133	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				negative regulation of cilium assembly (GO:1902018)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	12						CAGCGCCACGGACATGCCCGT	0.652																																							0											0													42.0	37.0	39.0					19																	7913876		2203	4300	6503	SO:0001583	missense	0			BC014111	CCDS12188.1, CCDS54209.1	19p13	2013-07-09				ENSG00000142459			30464	protein-coding gene	gene with protein product						23669355	Standard	NM_001159944		Approved		uc010xjz.2	Q96CN4		ENST00000270530.4:c.397G>A	19.37:g.7913876G>A	ENSP00000270530:p.Asp133Asn		B9A6I9	Missense_Mutation	SNP	pfam_Rab-GTPase-TBC_dom,superfamily_Rab-GTPase-TBC_dom,smart_Rab-GTPase-TBC_dom,pfscan_Rab-GTPase-TBC_dom	p.D133N	ENST00000270530.4	37	c.397	CCDS12188.1	19	.	.	.	.	.	.	.	.	.	.	G	11.16	1.557159	0.27827	.	.	ENSG00000142459	ENST00000270530;ENST00000538904	T;T	0.11495	2.77;2.77	4.48	2.35	0.29111	Rab-GAP/TBC domain (4);	0.169791	0.51477	N	0.000096	T	0.06690	0.0171	N	0.21240	0.645	0.48696	D	0.999699	B;B	0.06786	0.0;0.001	B;B	0.11329	0.006;0.005	T	0.34129	-0.9841	10	0.23891	T	0.37	-36.1866	8.1748	0.31275	0.1977:0.0:0.8023:0.0	.	133;133	B9A6I9;Q96CN4	.;EVI5L_HUMAN	N	133	ENSP00000270530:D133N;ENSP00000445905:D133N	ENSP00000270530:D133N	D	+	1	0	EVI5L	7819876	1.000000	0.71417	0.490000	0.27465	0.428000	0.31595	3.807000	0.55591	0.514000	0.28300	0.462000	0.41574	GAC	0	pfam_Rab-GTPase-TBC_dom,superfamily_Rab-GTPase-TBC_dom,smart_Rab-GTPase-TBC_dom,pfscan_Rab-GTPase-TBC_dom		0.652	EVI5L-001	KNOWN	basic|CCDS	protein_coding	EVI5L	protein_coding	OTTHUMT00000461347.1	55	55	0	0.00	0	0	G	NM_145245	0	0		7913876	1	no_errors	ENST00000538904	ensembl	human	known	74_37	missense	36	40	33.33	24.53	18	13	SNP	0.977	A
MUC16	94025	genome.wustl.edu	37	19	9088508	9088508	+	Missense_Mutation	SNP	C	C	T	rs533537740		TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr19:9088508C>T	ENST00000397910.4	-	1	3510	c.3307G>A	c.(3307-3309)Gtt>Att	p.V1103I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1103	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AATGTGTCAACGAATTGGCTT	0.433													C|||	1	0.000199681	0.0008	0.0	5008	,	,		25015	0.0		0.0	False		,,,				2504	0.0						0.9998,0.0001997											0													96.0	92.0	93.0					19																	9088508		2013	4189	6202	SO:0001583	missense	0			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.3307G>A	19.37:g.9088508C>T	ENSP00000381008:p.Val1103Ile		Q6ZQW5|Q96RK2	Missense_Mutation	SNP	pfam_SEA_dom,smart_SEA_dom,pfscan_SEA_dom	p.V1103I	ENST00000397910.4	37	c.3307	CCDS54212.1	19	.	.	.	.	.	.	.	.	.	.	c	2.432	-0.330665	0.05314	.	.	ENSG00000181143	ENST00000397910	T	0.02421	4.3	1.51	-3.02	0.05446	.	.	.	.	.	T	0.01489	0.0048	N	0.08118	0	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.45731	-0.9241	8	0.87932	D	0	.	3.0439	0.06147	0.5063:0.3152:0.0:0.1785	.	1103	B5ME49	.	I	1103	ENSP00000381008:V1103I	ENSP00000381008:V1103I	V	-	1	0	MUC16	8949508	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-2.928000	0.00690	-1.104000	0.03015	-0.704000	0.03662	GTT	0	NULL		0.433	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MUC16	protein_coding	OTTHUMT00000402806.1	57	121	0	0.00	0	0	C	NM_024690	rs533537740	C->T		9088508	-1	no_errors	ENST00000397910	ensembl	human	known	74_37	missense	54	95	21.74	26.72	15	35	SNP	0	T
ANGPTL6	83854	genome.wustl.edu	37	19	10205575	10205575	+	Missense_Mutation	SNP	G	G	C	rs140248826		TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr19:10205575G>C	ENST00000253109.4	-	3	860	c.622C>G	c.(622-624)Cgt>Ggt	p.R208G	ANGPTL6_ENST00000589181.1_Missense_Mutation_p.R208G|ANGPTL6_ENST00000592641.1_Missense_Mutation_p.R208G	NM_031917.2	NP_114123.2	Q8NI99	ANGL6_HUMAN	angiopoietin-like 6	208					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)				endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)	12			OV - Ovarian serous cystadenocarcinoma(20;3.58e-08)|Epithelial(33;2.5e-05)|all cancers(31;5.96e-05)			CCCACAAGACGGACCGGAACC	0.627																																							0											0													50.0	42.0	44.0					19																	10205575		2203	4300	6503	SO:0001583	missense	0			AB054064	CCDS12224.1	19p13.2	2013-02-06				ENSG00000130812		"""Fibrinogen C domain containing"""	23140	protein-coding gene	gene with protein product	"""angiopoietin-related protein 5"""	609336				12871997	Standard	NM_031917		Approved	ARP5, AGF	uc002mmy.1	Q8NI99		ENST00000253109.4:c.622C>G	19.37:g.10205575G>C	ENSP00000253109:p.Arg208Gly		A5PKV7|Q9BZZ0	Missense_Mutation	SNP	pfam_Fibrinogen_a/b/g_C_dom,superfamily_Fibrinogen_a/b/g_C_dom,smart_Fibrinogen_a/b/g_C_dom	p.R208G	ENST00000253109.4	37	c.622	CCDS12224.1	19	.	.	.	.	.	.	.	.	.	.	G	0.048	-1.260466	0.01445	.	.	ENSG00000130812	ENST00000253109	T	0.52983	0.64	4.23	2.1	0.27182	.	1.753130	0.03221	N	0.177639	T	0.27900	0.0687	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16808	-1.0390	10	0.23891	T	0.37	.	5.3672	0.16121	0.0:0.1004:0.1847:0.7149	.	208	Q8NI99	ANGL6_HUMAN	G	208	ENSP00000253109:R208G	ENSP00000253109:R208G	R	-	1	0	ANGPTL6	10066575	0.393000	0.25237	0.435000	0.26784	0.121000	0.20230	1.378000	0.34328	0.765000	0.33221	-0.749000	0.03505	CGT	0	NULL		0.627	ANGPTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ANGPTL6	protein_coding	OTTHUMT00000451142.1	30	122	0	0.00	0	0	G	NM_031917	0	0		10205575	-1	no_errors	ENST00000253109	ensembl	human	known	74_37	missense	18	92	40.62	32.85	13	45	SNP	0.006	C
SMARCA4	6597	genome.wustl.edu	37	19	11141406	11141406	+	Splice_Site	SNP	G	G	T			TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr19:11141406G>T	ENST00000429416.3	+	26	3664	c.3383G>T	c.(3382-3384)gGa>gTa	p.G1128V	SMARCA4_ENST00000444061.3_Splice_Site_p.G1128V|SMARCA4_ENST00000413806.3_Splice_Site_p.G1128V|SMARCA4_ENST00000450717.3_Splice_Site_p.G1128V|SMARCA4_ENST00000358026.2_Splice_Site_p.G1128V|SMARCA4_ENST00000589677.1_Splice_Site_p.G1128V|SMARCA4_ENST00000541122.2_Splice_Site_p.G1128V|SMARCA4_ENST00000344626.4_Splice_Site_p.G1128V|SMARCA4_ENST00000590574.1_Splice_Site_p.G1128V	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1128	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|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 transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				TGCCCGTCAGGAACCACGAAG	0.622			"""F, N, Mis"""		NSCLC																																		0		Rec	yes		19	19p13.2	6597	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""		E	1	Unknown(1)	lung(1)											25.0	28.0	27.0					19																	11141406		2203	4299	6502	SO:0001630	splice_region_variant	0			D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"""SNF2-like 4"", ""global transcription activator homologous sequence"", ""sucrose nonfermenting-like 4"", ""mitotic growth and transcription activator"", ""BRM/SWI2-related gene 1"", ""homeotic gene regulator"", ""nuclear protein GRB1"", ""brahma protein-like 1"", ""ATP-dependent helicase SMARCA4"""	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.3383-1G>T	19.37:g.11141406G>T			B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	pfam_SNF2_N,pfam_Bromodomain,pfam_BRK_domain,pfam_Helicase/SANT-assoc_DNA-bd,pfam_Helicase_C,pfam_Gln-Leu-Gln_QLQ,superfamily_P-loop_NTPase,superfamily_Bromodomain,smart_Gln-Leu-Gln_QLQ,smart_HAS_subgr,smart_BRK_domain,smart_Helicase_ATP-bd,smart_Helicase_C,smart_Bromodomain,prints_Bromodomain,pfscan_Helicase/SANT-assoc_DNA-bd,pfscan_Helicase_ATP-bd,pfscan_Helicase_C,pfscan_Bromodomain	p.G1128V	ENST00000429416.3	37	c.3383	CCDS12253.1	19	.	.	.	.	.	.	.	.	.	.	G	23.4	4.412666	0.83340	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.85339	-1.97;-1.97;-1.97;-1.97;-1.97;-1.97;-1.97	4.59	4.59	0.56863	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.96682	0.8917	H	0.99983	5.215	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.98701	1.0700	9	.	.	.	.	16.3247	0.82975	0.0:0.0:1.0:0.0	.	1128;1128;1128;1128;1128;348;1128;1128	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;A7E2E1;P51532	.;.;.;.;.;.;.;SMCA4_HUMAN	V	1128;1128;1192;1128;1128;1128;1128;1128	ENSP00000395654:G1128V;ENSP00000350720:G1128V;ENSP00000343896:G1128V;ENSP00000445036:G1128V;ENSP00000392837:G1128V;ENSP00000397783:G1128V;ENSP00000414727:G1128V	.	G	+	2	0	SMARCA4	11002406	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	9.411000	0.97342	2.389000	0.81357	0.563000	0.77884	GGA	0	pfam_Helicase_C,superfamily_P-loop_NTPase,smart_Helicase_C,pfscan_Helicase_C		0.622	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	SMARCA4	protein_coding	OTTHUMT00000452638.2	61	158	0	1.25	0	2	G	NM_003072	0	0	Missense_Mutation	11141406	1	no_errors	ENST00000358026	ensembl	human	known	74_37	missense	48	149	26.15	35.78	17	83	SNP	1	T
NF2	4771	genome.wustl.edu	37	22	30050679	30050679	+	Nonsense_Mutation	SNP	G	G	T			TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr22:30050679G>T	ENST00000338641.4	+	5	922	c.481G>T	c.(481-483)Gga>Tga	p.G161*	NF2_ENST00000403435.1_Nonsense_Mutation_p.G161*|NF2_ENST00000403999.3_Nonsense_Mutation_p.G161*|NF2_ENST00000413209.2_Intron|NF2_ENST00000361676.4_Nonsense_Mutation_p.G119*|NF2_ENST00000334961.7_Nonsense_Mutation_p.G78*|NF2_ENST00000397789.3_Nonsense_Mutation_p.G161*|NF2_ENST00000347330.5_Intron|NF2_ENST00000361452.4_Nonsense_Mutation_p.G120*|NF2_ENST00000353887.4_Nonsense_Mutation_p.G78*|NF2_ENST00000361166.4_Nonsense_Mutation_p.G161*	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	161	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(3)|p.G161*(1)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						TCACAAGCGGGGATTTTTGGC	0.428			"""D, Mis, N, F, S, O"""		"""meningioma, acoustic neuroma, renal """	"""meningioma, acoustic neuroma"""			Neurofibromatosis, type 2																														0	yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	4	Unknown(3)|Substitution - Nonsense(1)	meninges(1)|large_intestine(1)|stomach(1)|central_nervous_system(1)											144.0	147.0	146.0					22																	30050679		2203	4300	6503	SO:0001587	stop_gained	0	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"""A-kinase anchor proteins"""	7773	protein-coding gene	gene with protein product	"""moesin-ezrin-radixin like"", ""schwannomin"""	607379	"""neurofibromin 2 (bilateral acoustic neuroma)"""			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.481G>T	22.37:g.30050679G>T	ENSP00000344666:p.Gly161*		O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Nonsense_Mutation	SNP	pirsf_ERM,pfam_ERM_C_dom,pfam_FERM_PH-like_C,pfam_FERM_central,pfam_FERM_N,superfamily_FERM_central,superfamily_Moesin_tail,smart_Band_41_domain,pfscan_FERM_domain,prints_Ez/rad/moesin_like,prints_Band_41_fam,prints_Tropomyosin	p.G161*	ENST00000338641.4	37	c.481	CCDS13861.1	22	.	.	.	.	.	.	.	.	.	.	G	41	8.739335	0.98935	.	.	ENSG00000186575	ENST00000338641;ENST00000403435;ENST00000361452;ENST00000397822;ENST00000403999;ENST00000334961;ENST00000353887;ENST00000397789;ENST00000361676;ENST00000361166	.	.	.	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.4777	0.99188	0.0:0.0:1.0:0.0	.	.	.	.	X	161;161;120;161;161;78;78;161;119;161	.	.	G	+	1	0	NF2	28380679	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.705000	0.98719	2.840000	0.97914	0.655000	0.94253	GGA	0	pirsf_ERM,pfam_FERM_central,superfamily_FERM_central,smart_Band_41_domain,pfscan_FERM_domain		0.428	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NF2	protein_coding	OTTHUMT00000075615.3	60	255	0	0.00	0	0	G	NM_000268	0	0		30050679	1	no_errors	ENST00000338641	ensembl	human	known	74_37	nonsense	23	98	42.86	52.20	18	107	SNP	1	T
C22orf24	25775	genome.wustl.edu	37	22	32330345	32330345	+	Missense_Mutation	SNP	G	G	T			TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr22:32330345G>T	ENST00000248984.3	-	3	408	c.242C>A	c.(241-243)cCc>cAc	p.P81H	C22orf24_ENST00000543051.1_Missense_Mutation_p.P148H|C22orf24_ENST00000486651.1_5'UTR	NM_015372.1	NP_056187.1	Q9Y442	CV024_HUMAN	chromosome 22 open reading frame 24	81						integral component of membrane (GO:0016021)				central_nervous_system(1)|urinary_tract(1)	2						ttgaagaaagggagaaatcca	0.532																																							0											0													89.0	92.0	91.0					22																	32330345		2020	4191	6211	SO:0001583	missense	0				CCDS46693.1	22q12.1-q12.3	2004-05-05			ENSG00000128254	ENSG00000128254			23051	protein-coding gene	gene with protein product							Standard	XM_005261497		Approved	HSN44A4A	uc003aly.3	Q9Y442	OTTHUMG00000030834	ENST00000248984.3:c.242C>A	22.37:g.32330345G>T	ENSP00000248984:p.Pro81His		B2RCT4|Q5K3R1	Missense_Mutation	SNP	NULL	p.P148H	ENST00000248984.3	37	c.443	CCDS46693.1	22	.	.	.	.	.	.	.	.	.	.	G	6.193	0.403805	0.11754	.	.	ENSG00000128254	ENST00000248984;ENST00000543051	T;T	0.47528	0.84;0.84	3.68	-2.58	0.06228	.	.	.	.	.	T	0.22513	0.0543	N	0.08118	0	0.09310	N	1	B	0.21452	0.056	B	0.20577	0.03	T	0.18650	-1.0330	9	0.87932	D	0	.	3.5958	0.08005	0.476:0.0:0.3291:0.1949	.	81	Q9Y442	CV024_HUMAN	H	81;148	ENSP00000248984:P81H;ENSP00000437643:P148H	ENSP00000248984:P81H	P	-	2	0	C22orf24	30660345	0.004000	0.15560	0.007000	0.13788	0.085000	0.17905	-0.320000	0.08028	-0.433000	0.07286	-0.397000	0.06425	CCC	0	NULL		0.532	C22orf24-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	C22orf24	protein_coding	OTTHUMT00000075722.2	48	158	0	0.00	0	0	G	NM_015372	0	0		32330345	-1	no_errors	ENST00000543051	ensembl	human	known	74_37	missense	34	95	24.44	23.39	11	29	SNP	0.009	T
CUL4B	8450	genome.wustl.edu	37	X	119694117	119694119	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	GAG	GAG	GAG	-	GAG	GAG	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chrX:119694117_119694119delGAG	ENST00000404115.3	-	3	830_832	c.429_431delCTC	c.(427-432)tcctca>tca	p.143_144SS>S	CUL4B_ENST00000336592.6_In_Frame_Del_p.130_131SS>S|CUL4B_ENST00000371322.5_In_Frame_Del_p.125_126SS>S	NM_003588.3	NP_003579.3	Q13620	CUL4B_HUMAN	cullin 4B	143	Ser-rich.				cell cycle (GO:0007049)|histone H2A monoubiquitination (GO:0035518)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of protein catabolic process (GO:0045732)|ubiquitin-dependent protein catabolic process (GO:0006511)|UV-damage excision repair (GO:0070914)	Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						TGGTGAAGATgaggaggaggagg	0.488																																							0											0									,	18,3703		0,6,12,1586,525					,	-9.6	0.5			58	72,6412		1,19,51,2337,1719	no	coding,coding	CUL4B	NM_003588.3,NM_001079872.1	,	1,25,63,3923,2244	A1A1,A1R,A1,RR,R		1.1104,0.4837,0.8819	,	,		90,10115				SO:0001651	inframe_deletion	0			U58091	CCDS35379.1, CCDS43987.1	Xq23	2011-05-24			ENSG00000158290	ENSG00000158290			2555	protein-coding gene	gene with protein product		300304				8681378	Standard	NM_003588		Approved		uc004esw.3	Q13620	OTTHUMG00000022302	ENST00000404115.3:c.429_431delCTC	X.37:g.119694126_119694128delGAG	ENSP00000384109:p.Ser146del		B1APK5|B3KVX4|B7Z5K8|Q6PIE4|Q6UP07|Q7Z673|Q9BY37|Q9UEB7|Q9UED7	In_Frame_Del	DEL	pfam_Cullin_N,pfam_Cullin_neddylation_domain,superfamily_Cullin_repeat-like_dom,superfamily_Cullin_homology,smart_Cullin_homology,smart_Cullin_neddylation_domain,pfscan_Cullin_homology	p.S146in_frame_del	ENST00000404115.3	37	c.431_429	CCDS35379.1	X																																																																																			0	NULL		0.488	CUL4B-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	CUL4B	protein_coding	OTTHUMT00000058103.1	36	76	2.7	1.30	1	1	GAG	NM_003588	0	0		119694119	-1	no_errors	ENST00000404115	ensembl	human	known	74_37	in_frame_del	31	110	11.43	5.17	4	6	DEL	0.999:1.000:1.000	0
MALAT1	378938	genome.wustl.edu	37	11	65269764	65269765	+	lincRNA	INS	-	-	T			TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr11:65269764_65269765insT	ENST00000534336.1	+	0	4532_4533					NR_002819.2		Q9UHZ2	MALAT_HUMAN	metastasis associated lung adenocarcinoma transcript 1 (non-protein coding)																		TTTTCAGGTGATTTAATAATAA	0.356																																							0											0																																												0			AF001540		11q13.1	2013-12-11	2007-11-20		ENSG00000251562	ENSG00000251562		"""Long non-coding RNAs"", ""-"""	29665	non-coding RNA	RNA, long non-coding	"""metastasis associated in lung adenocarcinoma transcript 1"", ""non-protein coding RNA 47"", ""hepcarcin"", ""nuclear enriched abundant transcript 2"", ""nuclear paraspeckle assembly transcript 2 (non-protein coding)"", ""long intergenic non-protein coding RNA 47"""	607924				12970751, 22560368	Standard	NR_002819		Approved	PRO1073, MALAT-1, NCRNA00047, HCN, NEAT2, LINC00047, mascRNA	uc010roh.3	Q9UHZ2	OTTHUMG00000166322		11.37:g.65269767_65269767dupT				RNA	INS	0	NULL	ENST00000534336.1	37	NULL		11																																																																																			0	0		0.356	MALAT1-001	KNOWN	basic	lincRNA	MALAT1	lincRNA	OTTHUMT00000389143.1	64	283	0	0.00	0	0	0	NR_002819	0	0		65269765	1	no_errors	ENST00000534336	ensembl	human	known	74_37	rna	63	232	37.62	30.12	38	100	INS	0.981:0.994	T
IRX3	79191	genome.wustl.edu	37	16	54318612	54318614	+	In_Frame_Del	DEL	GCG	GCG	-			TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	GCG	GCG	GCG	-	GCG	GCG	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr16:54318612_54318614delGCG	ENST00000329734.3	-	2	1891_1893	c.1179_1181delCGC	c.(1177-1182)gccgct>gct	p.393_394AA>A		NM_024336.2	NP_077312.2	P78415	IRX3_HUMAN	iroquois homeobox 3	393	Poly-Ala.|Pro-rich.				mesoderm development (GO:0007498)|metanephros development (GO:0001656)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of neuron differentiation (GO:0045666)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)|transcription, DNA-templated (GO:0006351)	axon (GO:0030424)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|soft_tissue(1)|urinary_tract(1)	14						CAGTCTGTGAgcggcggcggcgg	0.778																																					GBM(143;1830 1866 4487 4646 37383)		0											0										12,890		5,2,444						-2.0	0.9			2	24,2396		7,10,1193	no	coding	IRX3	NM_024336.2		12,12,1637	A1A1,A1R,RR		0.9917,1.3304,1.0837				36,3286				SO:0001651	inframe_deletion	0			U90308	CCDS10750.1	16q12.2	2011-06-20	2007-07-13		ENSG00000177508	ENSG00000177508		"""Homeoboxes / TALE class"""	14360	protein-coding gene	gene with protein product		612985					Standard	NM_024336		Approved	IRX-1	uc002eht.1	P78415	OTTHUMG00000133200	ENST00000329734.3:c.1179_1181delCGC	16.37:g.54318621_54318623delGCG	ENSP00000331608:p.Ala394del		Q7Z4A4|Q7Z4A5|Q8IVC6	In_Frame_Del	DEL	pfam_Homeobox_dom,superfamily_Homeodomain-like,smart_Homeobox_dom,smart_Iroquois_homeo,pfscan_Homeobox_dom	p.A394in_frame_del	ENST00000329734.3	37	c.1181_1179	CCDS10750.1	16																																																																																			0	NULL		0.778	IRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	IRX3	protein_coding	OTTHUMT00000256910.2	14	25	0	0.00	0	0	GCG		0	0		54318614	-1	no_errors	ENST00000329734	ensembl	human	known	74_37	in_frame_del	13	11	18.75	15.38	3	2	DEL	0.605:0.606:0.549	0
ZNF714	148206	genome.wustl.edu	37	19	21300350	21300350	+	Frame_Shift_Del	DEL	A	A	-			TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr19:21300350delA	ENST00000596143.1	+	5	1205	c.880delA	c.(880-882)aacfs	p.N294fs	ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_3'UTR|ZNF714_ENST00000601416.1_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	294					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(2)|kidney(3)|lung(11)|urinary_tract(2)	18						CAAAGCTTTTAACCGATTCTC	0.353																																							0											0													24.0	26.0	25.0					19																	21300350		2182	4290	6472	SO:0001589	frameshift_variant	0			AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"""Zinc fingers, C2H2-type"""	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.880delA	19.37:g.21300350delA	ENSP00000472368:p.Asn294fs		Q49AI1|Q86W65|Q8ND40	Frame_Shift_Del	DEL	pfam_Znf_C2H2,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	p.N294fs	ENST00000596143.1	37	c.880	CCDS54239.1	19																																																																																			0	pfam_Znf_C2H2,smart_Znf_C2H2-like,pfscan_Znf_C2H2		0.353	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF714	protein_coding	OTTHUMT00000463930.1	43	78	0	0.00	0	0	A	NM_182515	0	0		21300350	1	no_errors	ENST00000596143	ensembl	human	known	74_37	frame_shift_del	37	64	27.45	24.71	14	21	DEL	0.085	0
ERVW-1	30816	genome.wustl.edu	37	7	92098389	92098389	+	Missense_Mutation	SNP	C	C	T			TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr7:92098389C>T	ENST00000493463.2	-	1	2230	c.1307G>A	c.(1306-1308)gGa>gAa	p.G436E	ERVW-1_ENST00000603053.1_Missense_Mutation_p.G436E|AC007566.10_ENST00000427458.1_RNA|ERVW-1_ENST00000604270.1_Intron	NM_014590.3	NP_055405.3	Q9UQF0	SYCY1_HUMAN	endogenous retrovirus group W, member 1	436					anatomical structure morphogenesis (GO:0009653)|syncytium formation (GO:0006949)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|viral envelope (GO:0019031)				endometrium(1)|large_intestine(1)|lung(15)	17						gccccagggtccagtgtttcg	0.453																																							0											0													5.0	4.0	4.0					7																	92098389		1597	2887	4484	SO:0001583	missense	0			AF208161	CCDS5626.1	7q21.2	2011-06-16	2011-05-05	2011-05-05	ENSG00000242950	ENSG00000242950			13525	other	endogenous retrovirus	"""envelope protein"", ""HERV-W Env glycoprotein"", ""enverin"", ""syncytin-1"", ""HERV-tryptophan envelope protein"", ""HERV-W{7q21.1} provirus ancestral Env polyprotein"", ""HERV-7q envelope protein"", ""envelope glycoprotein"", ""syncytin"""	604659	"""endogenous retroviral family W, env(C7), member 1"""	ERVWE1		9835022, 9882319, 21542922	Standard	NM_001130925		Approved	HERV-W, HERV-W-ENV, HERVW, HERV-7q	uc022ahe.1	Q9UQF0	OTTHUMG00000131249	ENST00000493463.2:c.1307G>A	7.37:g.92098389C>T	ENSP00000419945:p.Gly436Glu		B2RPD4|O95244|O95245|Q8NHY7|Q9NRZ2|Q9NZG3	Missense_Mutation	SNP	pfam_TLV/ENV_coat_polyprotein	p.G436E	ENST00000493463.2	37	c.1307	CCDS5626.1	7	.	.	.	.	.	.	.	.	.	.	C	6.159	0.397519	0.11638	.	.	ENSG00000242950	ENST00000493463	T	0.16597	2.33	0.0465	0.0465	0.14256	.	3.494710	0.03412	U	0.204946	T	0.07234	0.0183	N	0.04636	-0.2	0.09310	N	1	.	.	.	.	.	.	T	0.26815	-1.0092	7	0.15952	T	0.53	.	.	.	.	.	.	.	.	E	436	ENSP00000419945:G436E	ENSP00000419945:G436E	G	-	2	0	ERVW-1	91936325	0.509000	0.26163	0.266000	0.24541	0.270000	0.26580	0.145000	0.16157	0.132000	0.18615	0.134000	0.15878	GGA	0	pfam_TLV/ENV_coat_polyprotein		0.453	ERVW-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ERVW-1	protein_coding	OTTHUMT00000254009.2	29	0	0	0.00	0	0	C	NM_014590	0	0		92098389	-1	no_errors	ENST00000493463	ensembl	human	known	74_37	missense	15	0	42.31	0.00	11	0	SNP	0.295	T
RP11-122L4.1	0	genome.wustl.edu	37	8	39418512	39418512	+	lincRNA	SNP	C	C	T	rs79987949	byFrequency	TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr8:39418512C>T	ENST00000518465.1	+	0	1360				AC123767.1_ENST00000516367.1_RNA																							tatatatacacatacacatac	0.289																																							0											0																																												0																															8.37:g.39418512C>T				RNA	SNP	0	NULL	ENST00000518465.1	37	NULL		8																																																																																			0	0		0.289	RP11-122L4.1-001	KNOWN	basic|exp_conf	lincRNA	ENSG00000252176	lincRNA	OTTHUMT00000376912.1	17	0	0	0.00	0	0	C		rs79987949	C->T		39418512	1	no_errors	ENST00000516367	ensembl	human	novel	74_37	rna	24	0	25	0.00	8	0	SNP	0	T
COL4A2	1284	genome.wustl.edu	37	13	111109415	111109415	+	Intron	SNP	C	C	G	rs9521779		TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr13:111109415C>G	ENST00000360467.5	+	21	1645				COL4A2-AS2_ENST00000458403.2_RNA	NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2						angiogenesis (GO:0001525)|axon guidance (GO:0007411)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of angiogenesis (GO:0016525)|transcription, DNA-templated (GO:0006351)	collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	extracellular matrix structural constituent (GO:0005201)			NS(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|liver(2)|lung(48)|ovary(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	80	all_cancers(4;2.21e-12)|all_epithelial(4;2.63e-07)|all_lung(23;5.81e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00323)|all_neural(89;0.0565)|Lung SC(71;0.0753)|Medulloblastoma(90;0.0922)	Breast(118;0.212)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.151)			GGCTGATGCCCTGCGTCTGCG	0.731																																							0											0																																										SO:0001627	intron_variant	0			AK025912	CCDS41907.1	13q34	2013-09-05			ENSG00000134871	ENSG00000134871		"""Collagens"""	2203	protein-coding gene	gene with protein product	"""canstatin"", ""collagen type IV alpha 2"""	120090				2439508, 3025878	Standard	NM_001846		Approved	FLJ22259, DKFZp686I14213	uc001vqx.3	P08572	OTTHUMG00000017344	ENST00000360467.5:c.1340-275C>G	13.37:g.111109415C>G			Q14052|Q548C3|Q5VZA9|Q66K23	RNA	SNP	0	NULL	ENST00000360467.5	37	NULL	CCDS41907.1	13	.	.	.	.	.	.	.	.	.	.	-	11.77	1.736380	0.30774	.	.	ENSG00000224821	ENST00000458403	.	.	.	1.2	-0.579	0.11720	.	.	.	.	.	T	0.23926	0.0579	.	.	.	0.29806	P	0.832006	.	.	.	.	.	.	T	0.37731	-0.9693	4	0.15066	T	0.55	.	6.2066	0.20606	0.0:0.6822:0.3178:0.0	rs9521779	.	.	.	H	256	.	ENSP00000390212:Q256H	Q	-	3	2	COL4A2-AS2	109907416	0.269000	0.24143	0.014000	0.15608	0.139000	0.21198	0.342000	0.19926	0.513000	0.28278	0.186000	0.17326	CAG	0	0		0.731	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL4A2-AS2	protein_coding	OTTHUMT00000045761.2	16	0	0	0.00	0	0	C	NM_001846	rs9521779	C->G		111109415	-1	no_errors	ENST00000458403	ensembl	human	known	74_37	rna	9	0	57.14	0.00	12	0	SNP	0.656	G
GOLGA6L17P	642402	genome.wustl.edu	37	15	85053254	85053254	+	RNA	SNP	T	T	C			TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr15:85053254T>C	ENST00000414190.2	-	0	198					NR_003246.2																						TACCAACAGCTTCTCCACTCA	0.577																																							0											0																																												0																															15.37:g.85053254T>C				RNA	SNP	0	NULL	ENST00000414190.2	37	NULL		15																																																																																			0	0		0.577	GOLGA6L5-003	KNOWN	mRNA_end_NF|basic	processed_transcript	GOLGA6L5	pseudogene	OTTHUMT00000418579.1	12	0	0	0.00	0	0	T		0	0		85053254	-1	no_errors	ENST00000414190	ensembl	human	known	74_37	rna	6	0	33.33	0.00	3	0	SNP	0.973	C
RP11-122L4.1	0	genome.wustl.edu	37	8	39418521	39418522	+	lincRNA	DEL	AC	AC	-	rs149857381|rs370187960		TCGA-XU-A92Z-01A-11D-A423-09	TCGA-XU-A92Z-10A-01D-A426-09	AC	AC					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	ec301622-3933-4ba4-8190-7bb2a99e3a8d	281773d4-370a-40bc-aa2e-eaa2777e70f3	g.chr8:39418521_39418522delAC	ENST00000518465.1	+	0	1360				AC123767.1_ENST00000516367.1_RNA																							acatacacatacacacacacac	0.297																																							0											0																																												0																															8.37:g.39418531_39418532delAC				RNA	DEL	0	NULL	ENST00000518465.1	37	NULL		8																																																																																			0	0		0.297	RP11-122L4.1-001	KNOWN	basic|exp_conf	lincRNA	ENSG00000252176	lincRNA	OTTHUMT00000376912.1	15	0	0	0.00	0	0	AC		rs370187960	TAC->T		39418522	1	no_errors	ENST00000516367	ensembl	human	novel	74_37	rna	21	0	16	0.00	4	0	DEL	0.000:0.000	0
