#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_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_Mutation_Status	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	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_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_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
DLGAP2	9228	broad.mit.edu	37	8	1649537	1649537	+	Missense_Mutation	SNP	G	G	A			TCGA-FY-A2QD-01A-11D-A19J-08	TCGA-FY-A2QD-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e7335a24-e5fc-4558-9eba-511c5a802320	7aeb39cd-79b5-4b8b-b801-9ea170d402c5	g.chr8:1649537G>A	ENST00000421627.2	+	12	3027	c.2893G>A	c.(2893-2895)Gag>Aag	p.E965K		NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	1044					neuron-neuron synaptic transmission (GO:0007270)	cell junction (GO:0030054)|neurofilament (GO:0005883)|postsynaptic membrane (GO:0045211)		p.E973K(1)		breast(1)|endometrium(6)|lung(31)|prostate(3)	41		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		GGACAGCATCGAGATCTACAT	0.716																																						uc003wpl.3																			1	Substitution - Missense(1)	p.E973K(1)	NS(1)	breast(1)|endometrium(6)|lung(31)|prostate(3)	41						c.(2893-2895)Gag>Aag		Homo sapiens discs, large (Drosophila) homolog-associated protein 2 (DLGAP2), mRNA.							12.0	16.0	14.0					8																	1649537		2191	4295	6486	SO:0001583	missense	9228				neuron-neuron synaptic transmission	cell junction|neurofilament|postsynaptic density|postsynaptic membrane	protein binding	g.chr8:1649537G>A	AB000275	CCDS47760.1, CCDS75689.1	8p23	2007-12-06	2001-11-28		ENSG00000198010	ENSG00000198010			2906	protein-coding gene	gene with protein product		605438	"""discs, large (Drosophila) homolog-associated protein 2"""			9286858, 10854099	Standard	NM_004745		Approved	DAP-2	uc003wpl.4	Q9P1A6	OTTHUMG00000163599	ENST00000421627.2:c.2893G>A	8.37:g.1649537G>A	ENSP00000400258:p.Glu965Lys		Somatic				DLGAP2_uc003wpm.3_Missense_Mutation_p.E951K	p.E965K	NM_004745	NP_004736	WXS	Illumina GAIIx	Phase_I	Q9P1A6	DLGP2_HUMAN		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)	11	2990	+		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)	1044					A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	Missense_Mutation	SNP	ENST00000421627.2	37	c.2893G>A	CCDS47760.1	.	.	.	.	.	.	.	.	.	.	G	37	6.346695	0.97494	.	.	ENSG00000198010	ENST00000356067;ENST00000421627	T	0.21734	1.99	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.55097	0.1899	M	0.86864	2.845	0.58432	D	0.999994	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	T	0.62300	-0.6883	10	0.87932	D	0	-19.4228	19.3914	0.94584	0.0:0.0:1.0:0.0	.	1030;1044	Q9P1A6-2;Q9P1A6	.;DLGP2_HUMAN	K	996;965	ENSP00000400258:E965K	ENSP00000348366:E996K	E	+	1	0	DLGAP2	1636944	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.302000	0.96175	2.587000	0.87381	0.491000	0.48974	GAG		0.716	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374478.1	NM_004745		4	4	0	0	0	1	0	4	4				
STK38	11329	broad.mit.edu	37	6	36475299	36475299	+	Silent	SNP	G	G	A			TCGA-FY-A2QD-01A-11D-A19J-08	TCGA-FY-A2QD-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e7335a24-e5fc-4558-9eba-511c5a802320	7aeb39cd-79b5-4b8b-b801-9ea170d402c5	g.chr6:36475299G>A	ENST00000229812.7	-	8	1035	c.750C>T	c.(748-750)aaC>aaT	p.N250N	Z85986.1_ENST00000583113.1_RNA	NM_007271.2	NP_009202.1			serine/threonine kinase 38											NS(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GGAGGCTGTGGTTCAGATTCC	0.418																																					Colon(180;997 3561 16158)	uc003omg.3																			0				NS(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						c.(748-750)aaC>aaT		Homo sapiens serine/threonine kinase 38 (STK38), mRNA.							288.0	303.0	298.0					6																	36475299		2203	4300	6503	SO:0001819	synonymous_variant	11329				intracellular protein kinase cascade|negative regulation of MAP kinase activity	MLL5-L complex|cytoplasm	ATP binding|magnesium ion binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine kinase activity	g.chr6:36475299G>A		CCDS4822.1	6p21	2006-10-06			ENSG00000112079	ENSG00000112079			17847	protein-coding gene	gene with protein product		606964				7761441	Standard	NM_007271		Approved	NDR	uc003omh.3	Q15208	OTTHUMG00000014598	ENST00000229812.7:c.750C>T	6.37:g.36475299G>A			Somatic				STK38_uc003omh.3_Silent_p.N250N|STK38_uc003omi.3_Silent_p.N250N	p.N250N	NM_007271	NP_009202	WXS	Illumina GAIIx	Phase_I	Q15208	STK38_HUMAN			6	1338	-			250			Protein kinase.			Silent	SNP	ENST00000229812.7	37	c.750C>T	CCDS4822.1																																																																																				0.418	STK38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040346.1	NM_007271		114	171	0	0	0	1	0	114	171				
MECP2	4204	broad.mit.edu	37	X	153296900	153296900	+	Splice_Site	SNP	G	G	A	rs267608466		TCGA-FY-A2QD-01A-11D-A19J-08	TCGA-FY-A2QD-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e7335a24-e5fc-4558-9eba-511c5a802320	7aeb39cd-79b5-4b8b-b801-9ea170d402c5	g.chrX:153296900G>A	ENST00000303391.6	-	4	628	c.379C>T	c.(379-381)Ccc>Tcc	p.P127S	MECP2_ENST00000407218.1_Splice_Site_p.P127S|MECP2_ENST00000453960.2_Splice_Site_p.P139S|MECP2_ENST00000460227.1_5'Flank	NM_004992.3	NP_004983.1	P51608	MECP2_HUMAN	methyl CpG binding protein 2	127	MBD. {ECO:0000255|PROSITE- ProRule:PRU00338}.				adult locomotory behavior (GO:0008344)|behavioral fear response (GO:0001662)|cardiolipin metabolic process (GO:0032048)|catecholamine secretion (GO:0050432)|cerebellum development (GO:0021549)|chromatin silencing (GO:0006342)|dendrite development (GO:0016358)|glucocorticoid metabolic process (GO:0008211)|glutamine metabolic process (GO:0006541)|histone acetylation (GO:0016573)|histone methylation (GO:0016571)|inositol metabolic process (GO:0006020)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|negative regulation of histone acetylation (GO:0035067)|negative regulation of histone methylation (GO:0031061)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|neuron maturation (GO:0042551)|pathogenesis (GO:0009405)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of cell proliferation (GO:0008284)|positive regulation of synapse assembly (GO:0051965)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|proprioception (GO:0019230)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|sensory perception of pain (GO:0019233)|social behavior (GO:0035176)|startle response (GO:0001964)|synapse assembly (GO:0007416)|transcription, DNA-templated (GO:0006351)|ventricular system development (GO:0021591)|visual learning (GO:0008542)	cytosol (GO:0005829)|extracellular space (GO:0005615)|heterochromatin (GO:0000792)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded methylated DNA binding (GO:0010385)|methyl-CpG binding (GO:0008327)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|siRNA binding (GO:0035197)|transcription corepressor activity (GO:0003714)			breast(2)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(8)|prostate(2)|urinary_tract(1)	23	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TTTCCCTGGGGACTGTGGGGA	0.488																																						uc004fjw.2																			0				breast(2)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(8)|prostate(2)|urinary_tract(1)	23						c.e3-1		Homo sapiens methyl CpG binding protein 2 (Rett syndrome) (MECP2), transcript variant 2, mRNA.							70.0	69.0	70.0					X																	153296900		2203	4300	6503	SO:0001630	splice_region_variant	4204				negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	heterochromatin|nucleus	double-stranded methylated DNA binding|protein N-terminus binding|protein domain specific binding|transcription corepressor activity	g.chrX:153296900G>A	AF158180	CCDS14741.1, CCDS48193.1	Xq28	2014-09-17	2014-06-18		ENSG00000169057	ENSG00000169057			6990	protein-coding gene	gene with protein product		300005	"""mental retardation, X-linked 16"", ""mental retardation, X-linked 79"", ""Rett syndrome"", ""methyl CpG binding protein 2 (Rett syndrome)"""	RTT, MRX16, MRX79		1606614, 10508514	Standard	NM_004992		Approved		uc004fjw.2	P51608	OTTHUMG00000024229	ENST00000303391.6:c.378-1C>T	X.37:g.153296900G>A			Somatic				MECP2_uc004fjv.2_Splice_Site_p.N126_splice	p.N138_splice	NM_001110792	NP_001104262	WXS	Illumina GAIIx	Phase_I	P51608	MECP2_HUMAN			3	480	-	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)		126			MBD.		O15233|Q6QHH9|Q7Z384	Splice_Site	SNP	ENST00000303391.6	37	c.414_splice	CCDS14741.1	.	.	.	.	.	.	.	.	.	.	G	15.35	2.807971	0.50421	.	.	ENSG00000169057	ENST00000303391;ENST00000545451;ENST00000453960;ENST00000369964;ENST00000407218	D;D;D	0.99980	-10.21;-10.21;-10.21	5.24	5.24	0.73138	Methyl-CpG DNA binding (4);DNA-binding, integrase-type (1);	0.055461	0.64402	D	0.000001	D	0.99966	0.9987	M	0.84948	2.725	0.80722	D	1	B;B	0.33694	0.368;0.421	B;P	0.44897	0.333;0.463	D	0.89826	0.3992	10	0.48119	T	0.1	-15.7176	16.5773	0.84705	0.0:0.0:1.0:0.0	.	139;127	P51608-2;P51608	.;MECP2_HUMAN	S	127;127;139;127;127	ENSP00000301948:P127S;ENSP00000395535:P139S;ENSP00000384865:P127S	ENSP00000301948:P127S	P	-	1	0	MECP2	152950094	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	7.103000	0.77014	2.172000	0.68678	0.600000	0.82982	CCC		0.488	MECP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061144.1	NM_004992	Missense_Mutation	8	73	0	0	0	1	0	8	73				
SLC23A2	9962	broad.mit.edu	37	20	4839991	4839991	+	Missense_Mutation	SNP	G	G	T			TCGA-FY-A2QD-01A-11D-A19J-08	TCGA-FY-A2QD-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e7335a24-e5fc-4558-9eba-511c5a802320	7aeb39cd-79b5-4b8b-b801-9ea170d402c5	g.chr20:4839991G>T	ENST00000379333.1	-	16	2056	c.1664C>A	c.(1663-1665)aCa>aAa	p.T555K	SLC23A2_ENST00000424750.2_Missense_Mutation_p.T441K|SLC23A2_ENST00000338244.1_Missense_Mutation_p.T555K	NM_203327.1	NP_976072.1	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 2	555					L-ascorbic acid metabolic process (GO:0019852)|L-ascorbic acid transport (GO:0015882)|molecular hydrogen transport (GO:0015993)|nucleobase transport (GO:0015851)|nucleobase-containing compound metabolic process (GO:0006139)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|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)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-ascorbate:sodium symporter activity (GO:0008520)|L-ascorbic acid transporter activity (GO:0015229)|nucleobase transmembrane transporter activity (GO:0015205)|sodium-dependent L-ascorbate transmembrane transporter activity (GO:0070890)|sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)			endometrium(1)|kidney(3)|large_intestine(9)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						CATAGCAGTTGTGAGAAGGAC	0.433																																						uc002wlg.1																			0				endometrium(1)|kidney(3)|large_intestine(9)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						c.(1663-1665)aCa>aAa		Homo sapiens solute carrier family 23 (nucleobase transporters), member 2 (SLC23A2), transcript variant 1, mRNA.							175.0	156.0	162.0					20																	4839991		2203	4300	6503	SO:0001583	missense	9962				L-ascorbic acid metabolic process|molecular hydrogen transport|nucleobase, nucleoside, nucleotide and nucleic acid metabolic process|transepithelial L-ascorbic acid transport	apical plasma membrane|integral to plasma membrane|membrane fraction	nucleobase transmembrane transporter activity|sodium-dependent L-ascorbate transmembrane transporter activity|sodium-dependent multivitamin transmembrane transporter activity	g.chr20:4839991G>T	AF058319	CCDS13085.1	20p13	2013-07-18	2013-07-18	2003-03-21	ENSG00000089057	ENSG00000089057		"""Solute carriers"""	10973	protein-coding gene	gene with protein product		603791	"""solute carrier family 23 (nucleobase transporters), member 1"""	SLC23A1		9804989, 10331392	Standard	NM_005116		Approved	SVCT2, KIAA0238, YSPL2	uc002wlh.1	Q9UGH3	OTTHUMG00000031793	ENST00000379333.1:c.1664C>A	20.37:g.4839991G>T	ENSP00000368637:p.Thr555Lys		Somatic				SLC23A2_uc010zqr.1_Missense_Mutation_p.T440K|SLC23A2_uc002wlh.1_Missense_Mutation_p.T555K	p.T555K	NM_005116	NP_976072	WXS	Illumina GAIIx	Phase_I	Q9UGH3	S23A2_HUMAN			15	2039	-			555					B4DJZ1|Q8WWR4|Q92512|Q96D54|Q9UNU1|Q9UP85	Missense_Mutation	SNP	ENST00000379333.1	37	c.1664C>A	CCDS13085.1	.	.	.	.	.	.	.	.	.	.	G	18.32	3.598389	0.66332	.	.	ENSG00000089057	ENST00000379333;ENST00000338244;ENST00000424750	T;T;T	0.18174	2.23;2.23;2.27	5.08	5.08	0.68730	.	0.092067	0.85682	D	0.000000	T	0.32645	0.0836	L	0.39633	1.23	0.80722	D	1	D;D	0.69078	0.981;0.997	D;P	0.69824	0.966;0.907	T	0.00514	-1.1695	10	0.33141	T	0.24	-20.3644	17.5691	0.87930	0.0:0.0:1.0:0.0	.	441;555	B4DJZ1;Q9UGH3	.;S23A2_HUMAN	K	555;555;441	ENSP00000368637:T555K;ENSP00000344322:T555K;ENSP00000406601:T441K	ENSP00000344322:T555K	T	-	2	0	SLC23A2	4787991	1.000000	0.71417	0.997000	0.53966	0.889000	0.51656	9.100000	0.94213	2.813000	0.96785	0.655000	0.94253	ACA		0.433	SLC23A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077832.1			36	85	0	0	0	1	0	36	85				
HPS1	3257	broad.mit.edu	37	10	100189586	100189586	+	Missense_Mutation	SNP	G	G	A			TCGA-FY-A2QD-01A-11D-A19J-08	TCGA-FY-A2QD-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e7335a24-e5fc-4558-9eba-511c5a802320	7aeb39cd-79b5-4b8b-b801-9ea170d402c5	g.chr10:100189586G>A	ENST00000325103.6	-	9	1062	c.829C>T	c.(829-831)Cac>Tac	p.H277Y	HPS1_ENST00000338546.5_Missense_Mutation_p.H277Y|HPS1_ENST00000467246.1_Intron|MIR4685_ENST00000578185.1_RNA|HPS1_ENST00000361490.4_Missense_Mutation_p.H277Y	NM_000195.3	NP_000186.2	Q92902	HPS1_HUMAN	Hermansky-Pudlak syndrome 1	277					blood coagulation (GO:0007596)|eye pigmentation (GO:0048069)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of natural killer cell activation (GO:0032816)|retina development in camera-type eye (GO:0060041)|secretion of lysosomal enzymes (GO:0033299)|visual perception (GO:0007601)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	protein dimerization activity (GO:0046983)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.234)		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)		CCCGTGGAGTGAGGGCTCCAG	0.677									Hermansky-Pudlak syndrome																													uc021pwv.1																			0				breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23						c.(829-831)Cac>Tac		Homo sapiens Hermansky-Pudlak syndrome 1 (HPS1), transcript variant 1, mRNA.							78.0	82.0	81.0					10																	100189586		2203	4300	6503	SO:0001583	missense	3257	Hermansky-Pudlak syndrome	Familial Cancer Database	HPS, HPS1-8	lysosome organization|response to stimulus|visual perception	cytoplasmic membrane-bounded vesicle|integral to plasma membrane|lysosome|membrane fraction|soluble fraction	protein dimerization activity	g.chr10:100189586G>A	U79136	CCDS7475.1, CCDS7476.1	10q23.1-q23.3	2014-06-18		2002-05-01	ENSG00000107521	ENSG00000107521			5163	protein-coding gene	gene with protein product		604982	"""Hermansky-Pudlak syndrome"""	HPS		8541858, 7573033	Standard	NM_182639		Approved		uc021pwv.1	Q92902	OTTHUMG00000018876	ENST00000325103.6:c.829C>T	10.37:g.100189586G>A	ENSP00000326649:p.His277Tyr		Somatic				HPS1_uc009xwb.3_Intron|HPS1_uc010qph.1_Missense_Mutation_p.H277Y|HPS1_uc001kpl.3_Missense_Mutation_p.H277Y	p.H277Y	NM_000195	NP_000186	WXS	Illumina GAIIx	Phase_I	Q92902	HPS1_HUMAN		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)	8	1075	-		Colorectal(252;0.234)	277					A8MRT2|O15402|O15502|Q5TAA3|Q8WXE5	Missense_Mutation	SNP	ENST00000325103.6	37	c.829C>T	CCDS7475.1	.	.	.	.	.	.	.	.	.	.	G	12.40	1.927202	0.34002	.	.	ENSG00000107521	ENST00000325103;ENST00000361490;ENST00000338546	T;T;T	0.42513	1.57;1.57;0.97	5.0	-10.0	0.00425	.	3.210380	0.00714	N	0.000853	T	0.28632	0.0709	L	0.36672	1.1	0.09310	N	1	P;P;P	0.39376	0.482;0.666;0.67	B;B;B	0.37833	0.259;0.162;0.245	T	0.43245	-0.9403	10	0.54805	T	0.06	.	6.0983	0.20033	0.2265:0.5309:0.0924:0.1502	.	277;277;277	Q92902;Q92902-3;D3DR62	HPS1_HUMAN;.;.	Y	277	ENSP00000326649:H277Y;ENSP00000355310:H277Y;ENSP00000343638:H277Y	ENSP00000326649:H277Y	H	-	1	0	HPS1	100179576	0.000000	0.05858	0.000000	0.03702	0.130000	0.20726	-1.766000	0.01797	-3.014000	0.00272	0.561000	0.74099	CAC		0.677	HPS1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049776.1	NM_000195, NM_182637, NM_182638, NM_182639		7	90	0	0	0	1	0	7	90				
ESX1	80712	broad.mit.edu	37	X	103498972	103498972	+	Silent	SNP	C	C	T			TCGA-FY-A2QD-01A-11D-A19J-08	TCGA-FY-A2QD-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e7335a24-e5fc-4558-9eba-511c5a802320	7aeb39cd-79b5-4b8b-b801-9ea170d402c5	g.chrX:103498972C>T	ENST00000372588.4	-	2	452	c.369G>A	c.(367-369)ccG>ccA	p.P123P		NM_153448.3	NP_703149.1	Q8N693	ESX1_HUMAN	ESX homeobox 1	123					labyrinthine layer blood vessel development (GO:0060716)|labyrinthine layer morphogenesis (GO:0060713)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(10)|lung(12)|ovary(1)|skin(2)	27						GCCCCTCCGCCGGCTGTGGCC	0.682																																					Pancreas(200;1705 2227 25194 28471 45274)	uc004ely.3																			0				endometrium(2)|large_intestine(10)|lung(12)|ovary(1)|skin(2)	27						c.(367-369)ccG>ccA		Homo sapiens ESX homeobox 1 (ESX1), mRNA.							25.0	27.0	26.0					X																	103498972		2196	4290	6486	SO:0001819	synonymous_variant	80712				negative regulation of transcription, DNA-dependent|regulation of cell cycle	cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chrX:103498972C>T	AL049631	CCDS14516.1	Xq22.2	2011-06-20	2007-07-11	2006-02-08	ENSG00000123576	ENSG00000123576		"""Homeoboxes / PRD class"""	14865	protein-coding gene	gene with protein product		300154	"""extraembryonic, spermatogenesis, homeobox 1 homolog (mouse)"""	ESX1L		11374906, 17242862	Standard	NM_153448		Approved	ESXR1	uc004ely.3	Q8N693	OTTHUMG00000022125	ENST00000372588.4:c.369G>A	X.37:g.103498972C>T			Somatic					p.P123P	NM_153448	NP_703149	WXS	Illumina GAIIx	Phase_I	Q8N693	ESX1_HUMAN			1	438	-			123					B0QYU3|Q7Z6K7	Silent	SNP	ENST00000372588.4	37	c.369G>A	CCDS14516.1																																																																																				0.682	ESX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057763.2	NM_153448		8	50	0	0	0	1	0	8	50				
