#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_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_default_gene_name	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_name_source	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	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_type	i_ucsc_cons	i_variant
ABCA2	20	genome.wustl.edu	37	9	139907932	139907932	+	Missense_Mutation	SNP	C	C	T			TCGA-MY-A5BF-01A-11D-A26G-09	TCGA-MY-A5BF-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	aa95dabb-5ce6-4379-a7be-300ceaedbd5c	e1dd766d-8d09-4066-b1fa-535efff9dd32	g.chr9:139907932C>T	ENST00000371605.3	-	28	4675	c.4528G>A	c.(4528-4530)Gag>Aag	p.E1510K	ABCA2_ENST00000341511.6_Missense_Mutation_p.E1511K|ABCA2_ENST00000265662.5_Missense_Mutation_p.E1511K			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	1510					ATP catabolic process (GO:0006200)|cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|regulation of intracellular cholesterol transport (GO:0032383)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|nucleotide binding (GO:0000166)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|liver(1)|lung(25)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	41	all_cancers(76;0.16)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		CGGCGCTCCTCGTTGGCGTAG	0.692																																																	0													39.0	46.0	44.0					9																	139907932		1967	4116	6083	SO:0001583	missense	20			U18235	CCDS43909.1	9q34	2012-03-14			ENSG00000107331	ENSG00000107331		"""ATP binding cassette transporters / subfamily A"""	32	protein-coding gene	gene with protein product		600047		ABC2		8088782	Standard	NM_212533		Approved		uc022bpy.1	Q9BZC7	OTTHUMG00000020958	ENST00000371605.3:c.4528G>A	9.37:g.139907932C>T	ENSP00000360666:p.Glu1510Lys		A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Missense_Mutation	SNP	pfam_ABC_transporter-like,smart_AAA+_ATPase,pfscan_ABC_transporter-like	p.E1511K	ENST00000371605.3	37	c.4531		9	.	.	.	.	.	.	.	.	.	.	C	36	5.743216	0.96873	.	.	ENSG00000107331	ENST00000265662;ENST00000371605;ENST00000355090;ENST00000341511	D;D;D	0.89415	-2.51;-2.51;-2.51	4.86	4.86	0.63082	.	0.495392	0.17562	U	0.169776	D	0.93288	0.7861	L	0.60455	1.87	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.73708	0.981;0.981	D	0.93357	0.6723	10	0.54805	T	0.06	.	17.9576	0.89074	0.0:1.0:0.0:0.0	.	1510;1541	Q9BZC7;E7ETC3	ABCA2_HUMAN;.	K	1511;1510;1541;1511	ENSP00000265662:E1511K;ENSP00000360666:E1510K;ENSP00000344155:E1511K	ENSP00000265662:E1511K	E	-	1	0	ABCA2	139027753	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.980000	0.76160	2.235000	0.73313	0.484000	0.47621	GAG	ABCA2	-	NULL		0.692	ABCA2-202	KNOWN	basic	protein_coding	ABCA2	HGNC	protein_coding		C	NM_001606		139907932	-1	no_errors	ENST00000265662	ensembl	human	known	70_37	missense	SNP	1.000	T
LEFTY2	7044	genome.wustl.edu	37	1	226127176	226127176	+	Silent	SNP	G	G	A			TCGA-MY-A5BF-01A-11D-A26G-09	TCGA-MY-A5BF-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	aa95dabb-5ce6-4379-a7be-300ceaedbd5c	e1dd766d-8d09-4066-b1fa-535efff9dd32	g.chr1:226127176G>A	ENST00000366820.5	-	3	970	c.622C>T	c.(622-624)Ctg>Ttg	p.L208L	LEFTY2_ENST00000474493.1_5'UTR|RP4-559A3.6_ENST00000513672.1_RNA|LEFTY2_ENST00000420304.2_Silent_p.L174L	NM_003240.3	NP_003231.2	O00292	LFTY2_HUMAN	left-right determination factor 2	208					blood coagulation (GO:0007596)|cell growth (GO:0016049)|multicellular organismal development (GO:0007275)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|platelet alpha granule lumen (GO:0031093)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16	Breast(184;0.197)					AGCGGGCCCAGATGCTCCCTC	0.711																																					Colon(172;116 2643 9098 43333)												0													9.0	13.0	12.0					1																	226127176		2160	4198	6358	SO:0001819	synonymous_variant	7044			U81523	CCDS1549.1, CCDS53479.1	1q42.1	2008-07-18	2004-11-17	2004-11-17	ENSG00000143768	ENSG00000143768			3122	protein-coding gene	gene with protein product	"""transforming growth factor, beta-4 (endometrial bleeding-associated factor; LEFTY A)"""	601877	"""endometrial bleeding associated factor (left-right determination, factor A; transforming growth factor beta superfamily)"""	TGFB4, EBAF		9153275	Standard	NM_001172425		Approved	LEFTA, LEFTYA	uc001hpt.2	O00292	OTTHUMG00000037441	ENST00000366820.5:c.622C>T	1.37:g.226127176G>A			B3KNH4|B4E332|E9PDM4|O75611|Q5TE89|Q8NBQ9	Silent	SNP	pfam_TGF-b_N,pfam_TGF-b_C,smart_TGF-b_C,pirsf_LRDF,prints_LRDF	p.L208	ENST00000366820.5	37	c.622	CCDS1549.1	1																																																																																			LEFTY2	-	pfam_TGF-b_N,pirsf_LRDF,prints_LRDF		0.711	LEFTY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LEFTY2	HGNC	protein_coding	OTTHUMT00000091152.1	G	NM_003240		226127176	-1	no_errors	ENST00000366820	ensembl	human	known	70_37	silent	SNP	0.972	A
NR1H2	7376	genome.wustl.edu	37	19	50881965	50881965	+	Missense_Mutation	SNP	C	C	T			TCGA-MY-A5BF-01A-11D-A26G-09	TCGA-MY-A5BF-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	aa95dabb-5ce6-4379-a7be-300ceaedbd5c	e1dd766d-8d09-4066-b1fa-535efff9dd32	g.chr19:50881965C>T	ENST00000253727.5	+	6	894	c.659C>T	c.(658-660)aCa>aTa	p.T220I	NR1H2_ENST00000411902.2_Missense_Mutation_p.T123I|NR1H2_ENST00000599105.1_Missense_Mutation_p.T220I|NR1H2_ENST00000542413.1_5'UTR|NR1H2_ENST00000593926.1_Missense_Mutation_p.T220I|NR1H2_ENST00000598168.1_Missense_Mutation_p.T220I	NM_007121.5	NP_009052	P55055	NR1H2_HUMAN	nuclear receptor subfamily 1, group H, member 2	220					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of lipid transport (GO:0032369)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of pinocytosis (GO:0048550)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cholesterol homeostasis (GO:2000188)|retinoic acid receptor signaling pathway (GO:0048384)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	apolipoprotein A-I receptor binding (GO:0034191)|ATPase binding (GO:0051117)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity (GO:0001133)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(2)	8		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)		GTCCAGCTAACAGCGGCTCAA	0.642																																																	0													48.0	56.0	53.0					19																	50881965		2124	4246	6370	SO:0001583	missense	7376			U14534	CCDS42593.1, CCDS58673.1	19q13.3	2013-01-16				ENSG00000131408		"""Nuclear hormone receptors"""	7965	protein-coding gene	gene with protein product	"""liver X receptor-beta"""	600380	"""ubiquitously-expressed nuclear receptor"""	UNR		7782080, 7971966	Standard	NM_007121		Approved	NER, NER-I, RIP15, LXR-b	uc010enw.4	P55055		ENST00000253727.5:c.659C>T	19.37:g.50881965C>T	ENSP00000253727:p.Thr220Ile		A8K490|B4DNM6|E7EWA6|Q12970|Q5I0Y1	Missense_Mutation	SNP	pfam_Nucl_hrmn_rcpt_lig-bd_core,pfam_Znf_hrmn_rcpt,superfamily_Nucl_hormone_rcpt_ligand-bd,smart_Znf_hrmn_rcpt,smart_Nucl_hrmn_rcpt_lig-bd_core,pfscan_Znf_hrmn_rcpt,prints_Liver_X_rcpt,prints_Str_hrmn_rcpt,prints_Znf_hrmn_rcpt,prints_Ecdystd_rcpt,prints_ThyrH_rcpt	p.T220I	ENST00000253727.5	37	c.659	CCDS42593.1	19	.	.	.	.	.	.	.	.	.	.	C	15.67	2.901025	0.52227	.	.	ENSG00000131408	ENST00000253727;ENST00000411902;ENST00000376942	D;D	0.92249	-3.0;-2.98	4.74	3.69	0.42338	Nuclear hormone receptor, ligand-binding (1);	0.000000	0.64402	D	0.000007	D	0.91202	0.7228	L	0.38175	1.15	0.80722	D	1	P;D;P	0.69078	0.908;0.997;0.909	B;P;P	0.54889	0.36;0.763;0.499	D	0.91658	0.5340	10	0.87932	D	0	.	12.2036	0.54340	0.1722:0.8278:0.0:0.0	.	220;123;221	P55055;E7EWA6;F1D8P7	NR1H2_HUMAN;.;.	I	220;123;220	ENSP00000253727:T220I;ENSP00000396151:T123I	ENSP00000253727:T220I	T	+	2	0	NR1H2	55573777	.	.	0.067000	0.19924	0.461000	0.32589	.	.	1.331000	0.45412	0.511000	0.50034	ACA	NR1H2	-	superfamily_Nucl_hormone_rcpt_ligand-bd		0.642	NR1H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NR1H2	HGNC	protein_coding	OTTHUMT00000464724.2	C			50881965	+1	no_errors	ENST00000253727	ensembl	human	known	70_37	missense	SNP	0.504	T
NYX	60506	genome.wustl.edu	37	X	41333611	41333611	+	Missense_Mutation	SNP	C	C	T			TCGA-MY-A5BF-01A-11D-A26G-09	TCGA-MY-A5BF-10A-01D-A26G-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	aa95dabb-5ce6-4379-a7be-300ceaedbd5c	e1dd766d-8d09-4066-b1fa-535efff9dd32	g.chrX:41333611C>T	ENST00000342595.2	+	2	1361	c.905C>T	c.(904-906)tCg>tTg	p.S302L	NYX_ENST00000378220.1_Missense_Mutation_p.S302L	NM_022567.2	NP_072089.1	Q9GZU5	NYX_HUMAN	nyctalopin	302					response to stimulus (GO:0050896)|visual perception (GO:0007601)	intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(11)|upper_aerodigestive_tract(1)	17						CAGAACCTCTCGGGTCTCCTC	0.687																																																	0													43.0	40.0	41.0					X																	41333611		2202	4300	6502	SO:0001583	missense	60506			AF254868	CCDS14256.1	Xp11.4	2014-01-28			ENSG00000188937	ENSG00000188937			8082	protein-coding gene	gene with protein product		300278		CSNB1, CSNB4		11062471, 11062472	Standard	NM_022567		Approved	CLRP, CSNB1A	uc004dfh.2	Q9GZU5	OTTHUMG00000021370	ENST00000342595.2:c.905C>T	X.37:g.41333611C>T	ENSP00000340328:p.Ser302Leu		D3DWC0|Q2M1S4|Q5H983|Q9H4J0	Missense_Mutation	SNP	pfam_Leu-rich_rpt,pfam_LRR-contain_N,smart_Leu-rich_rpt_typical-subtyp,smart_Cys-rich_flank_reg_C	p.S302L	ENST00000342595.2	37	c.905	CCDS14256.1	X	.	.	.	.	.	.	.	.	.	.	C	18.31	3.595772	0.66219	.	.	ENSG00000188937	ENST00000342595;ENST00000378220	T;T	0.59772	0.24;0.24	5.19	5.19	0.71726	.	0.057306	0.64402	D	0.000002	T	0.50837	0.1639	L	0.60067	1.865	0.43662	D	0.996082	P	0.48998	0.918	B	0.33454	0.164	T	0.58702	-0.7590	10	0.41790	T	0.15	.	17.8738	0.88818	0.0:1.0:0.0:0.0	.	302	Q9GZU5	NYX_HUMAN	L	302	ENSP00000340328:S302L;ENSP00000367465:S302L	ENSP00000340328:S302L	S	+	2	0	NYX	41218555	1.000000	0.71417	0.997000	0.53966	0.940000	0.58332	4.703000	0.61824	2.154000	0.67381	0.600000	0.82982	TCG	NYX	-	smart_Leu-rich_rpt_typical-subtyp		0.687	NYX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NYX	HGNC	protein_coding	OTTHUMT00000056256.1	C	NM_022567		41333611	+1	no_errors	ENST00000342595	ensembl	human	known	70_37	missense	SNP	1.000	T
RNASEL	6041	genome.wustl.edu	37	1	182555093	182555093	+	Silent	SNP	G	G	C			TCGA-MY-A5BF-01A-11D-A26G-09	TCGA-MY-A5BF-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	aa95dabb-5ce6-4379-a7be-300ceaedbd5c	e1dd766d-8d09-4066-b1fa-535efff9dd32	g.chr1:182555093G>C	ENST00000367559.3	-	2	1102	c.849C>G	c.(847-849)ctC>ctG	p.L283L	RNASEL_ENST00000444138.1_Silent_p.L283L|RNASEL_ENST00000539397.1_Silent_p.L283L	NM_021133.3	NP_066956.1	Q05823	RN5A_HUMAN	ribonuclease L (2',5'-oligoisoadenylate synthetase-dependent)	283					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|mRNA processing (GO:0006397)|negative regulation of viral genome replication (GO:0045071)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA processing (GO:0006364)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)|endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(4)|prostate(1)|stomach(1)|urinary_tract(1)	27						TCTTCAGTTTGAGTTCAACAG	0.483																																																	0													107.0	107.0	107.0					1																	182555093		2203	4300	6503	SO:0001819	synonymous_variant	6041			L10381	CCDS1347.1	1q25	2013-01-10			ENSG00000135828	ENSG00000135828	3.1.26.-	"""Ankyrin repeat domain containing"""	10050	protein-coding gene	gene with protein product		180435	"""prostate cancer 1"""	RNS4, PRCA1		7514564	Standard	NM_021133		Approved		uc009wxz.2	Q05823	OTTHUMG00000035213	ENST00000367559.3:c.849C>G	1.37:g.182555093G>C			Q5W0L2|Q6AI46	Silent	SNP	pfam_Ankyrin_rpt,pfam_KEN_RNase_activator,pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_LipoPS_kinase,superfamily_Ankyrin_rpt-contain_dom,superfamily_Kinase-like_dom,smart_Ankyrin_rpt,smart_Ser/Thr_dual-sp_kinase_dom,smart_PUG-dom,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,pfscan_Prot_kinase_cat_dom,prints_Ankyrin_rpt	p.L283	ENST00000367559.3	37	c.849	CCDS1347.1	1																																																																																			RNASEL	-	superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom		0.483	RNASEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RNASEL	HGNC	protein_coding	OTTHUMT00000085189.1	G	NM_021133		182555093	-1	no_errors	ENST00000367559	ensembl	human	known	70_37	silent	SNP	0.000	C
SH2B1	25970	genome.wustl.edu	37	16	28877740	28877740	+	Missense_Mutation	SNP	G	G	C			TCGA-MY-A5BF-01A-11D-A26G-09	TCGA-MY-A5BF-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	aa95dabb-5ce6-4379-a7be-300ceaedbd5c	e1dd766d-8d09-4066-b1fa-535efff9dd32	g.chr16:28877740G>C	ENST00000322610.8	+	4	764	c.325G>C	c.(325-327)Gag>Cag	p.E109Q	SH2B1_ENST00000563674.1_Intron|SH2B1_ENST00000545570.1_Intron|SH2B1_ENST00000337120.5_Missense_Mutation_p.E109Q|SH2B1_ENST00000395532.4_Missense_Mutation_p.E109Q|SH2B1_ENST00000359285.5_Missense_Mutation_p.E109Q|SH2B1_ENST00000538342.1_Intron			Q9NRF2	SH2B1_HUMAN	SH2B adaptor protein 1	109	Interaction with JAK2 (low-affinity binding; independent of JAK2 phosphorylation). {ECO:0000250}.|Interaction with RAC1. {ECO:0000250}.|Required for NGF signaling. {ECO:0000250}.				blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|intracellular signal transduction (GO:0035556)|lamellipodium assembly (GO:0030032)|positive regulation of mitosis (GO:0045840)|regulation of DNA biosynthetic process (GO:2000278)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25						CCTGTCCCTTGAGAGCTGCAG	0.662																																																	0													33.0	32.0	32.0					16																	28877740		2197	4300	6497	SO:0001583	missense	25970			AK055104	CCDS32424.1, CCDS53996.1, CCDS53997.1	16p11.2	2013-02-14						"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	30417	protein-coding gene	gene with protein product	"""SH2-B homolog"""	608937				11827956, 10594240	Standard	NM_001145812		Approved	FLJ30542, SH2B	uc002drl.3	Q9NRF2		ENST00000322610.8:c.325G>C	16.37:g.28877740G>C	ENSP00000321221:p.Glu109Gln		A8K2R7|Q96FK3|Q96SX3|Q9NRF1|Q9NRF3|Q9P2P7|Q9Y3Y3	Missense_Mutation	SNP	pfam_Phe_ZIP,pfam_Pleckstrin_homology,pfam_SH2,superfamily_Phe_ZIP,smart_Pleckstrin_homology,smart_SH2,pfscan_SH2,prints_SH2	p.E109Q	ENST00000322610.8	37	c.325	CCDS53996.1	16	.	.	.	.	.	.	.	.	.	.	G	19.19	3.778996	0.70107	.	.	ENSG00000178188	ENST00000322610;ENST00000359285;ENST00000395532;ENST00000337120	T;T;T;T	0.48201	0.82;0.83;0.83;0.83	4.77	4.77	0.60923	.	0.421578	0.21745	N	0.069763	T	0.34164	0.0888	N	0.14661	0.345	0.30487	N	0.771794	B;B;B	0.24823	0.112;0.112;0.068	B;B;B	0.27076	0.076;0.076;0.051	T	0.27571	-1.0070	10	0.32370	T	0.25	-10.7577	16.6033	0.84821	0.0:0.0:1.0:0.0	.	109;109;109	Q9NRF2-2;Q9NRF2-3;Q9NRF2	.;.;SH2B1_HUMAN	Q	109	ENSP00000321221:E109Q;ENSP00000352232:E109Q;ENSP00000378903:E109Q;ENSP00000337163:E109Q	ENSP00000321221:E109Q	E	+	1	0	SH2B1	28785241	0.972000	0.33761	1.000000	0.80357	0.963000	0.63663	2.113000	0.41902	2.208000	0.71279	0.436000	0.28706	GAG	SH2B1	-	NULL		0.662	SH2B1-001	KNOWN	basic|CCDS	protein_coding	SH2B1	HGNC	protein_coding	OTTHUMT00000432666.1	G	NM_015503		28877740	+1	no_errors	ENST00000322610	ensembl	human	known	70_37	missense	SNP	1.000	C
TMEM237	65062	genome.wustl.edu	37	2	202501582	202501582	+	Missense_Mutation	SNP	G	G	C			TCGA-MY-A5BF-01A-11D-A26G-09	TCGA-MY-A5BF-10A-01D-A26G-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	aa95dabb-5ce6-4379-a7be-300ceaedbd5c	e1dd766d-8d09-4066-b1fa-535efff9dd32	g.chr2:202501582G>C	ENST00000409883.2	-	5	279	c.163C>G	c.(163-165)Cag>Gag	p.Q55E	TMEM237_ENST00000409444.2_Missense_Mutation_p.Q47E	NM_001044385.2	NP_001037850.1	Q96Q45	TM237_HUMAN	transmembrane protein 237	55					cilium assembly (GO:0042384)|regulation of Wnt signaling pathway (GO:0030111)	ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(2)|kidney(1)|large_intestine(1)|lung(3)	7						CCAGCAGTCTGAGCAAGGCCT	0.423																																																	0													45.0	41.0	42.0					2																	202501582		1829	4077	5906	SO:0001583	missense	65062			AB053301	CCDS46489.1, CCDS46490.1	2q33	2012-05-08	2011-05-20	2011-05-20	ENSG00000155755	ENSG00000155755			14432	protein-coding gene	gene with protein product		614423	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 4"""	ALS2CR4		11586298, 20375344	Standard	NM_001044385		Approved	JBTS14	uc021vvg.2	Q96Q45	OTTHUMG00000154526	ENST00000409883.2:c.163C>G	2.37:g.202501582G>C	ENSP00000386264:p.Gln55Glu		B4E1R8|B4E2R8|E9PAR8|E9PBF8|E9PG24|E9PGX0|Q53TS9|Q53TT2|Q7Z3B6|Q8IZ18|Q8NBF8|Q96CY1	Missense_Mutation	SNP	NULL	p.Q55E	ENST00000409883.2	37	c.163	CCDS46489.1	2	.	.	.	.	.	.	.	.	.	.	G	10.12	1.262927	0.23051	.	.	ENSG00000155755	ENST00000409444;ENST00000409883;ENST00000435876;ENST00000426684	T;T	0.39406	1.08;1.08	5.27	3.45	0.39498	.	0.565014	0.19130	N	0.121952	T	0.34513	0.0900	L	0.41824	1.3	0.25422	N	0.988261	B;B	0.12013	0.005;0.001	B;B	0.13407	0.009;0.003	T	0.16129	-1.0413	10	0.25751	T	0.34	-1.4796	14.3317	0.66561	0.0:0.3447:0.6553:0.0	.	55;79	E9PAR8;Q96Q45	.;TM237_HUMAN	E	47;55;55;77	ENSP00000387203:Q47E;ENSP00000386264:Q55E	ENSP00000387203:Q47E	Q	-	1	0	TMEM237	202209827	0.989000	0.36119	0.133000	0.22050	0.986000	0.74619	2.862000	0.48388	0.768000	0.33290	0.650000	0.86243	CAG	TMEM237	-	NULL		0.423	TMEM237-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TMEM237	HGNC	protein_coding	OTTHUMT00000335753.1	G	NM_152388		202501582	-1	no_errors	ENST00000409883	ensembl	human	known	70_37	missense	SNP	0.627	C
