#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_Chromosome_hg18	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_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	i_TumorRefReads_WU	i_TumorVAF_WU	i_TumorVarReads_WU	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_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
SAGE1	55511	genome.wustl.edu	37	X	134989144	134989144	+	Missense_Mutation	SNP	G	G	A	rs531224334		TCGA-AB-2855-03B-01W-0728-08	TCGA-AB-2855-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8bdab9f4-ca3d-4f77-b83e-6ec7df6c2a27	56552b20-8a32-4584-a3dc-91cc0e4196f4	g.chrX:134989144G>A	ENST00000370709.3	+	7	796	c.796G>A	c.(796-798)Gat>Aat	p.D266N	SAGE1_ENST00000324447.3_Missense_Mutation_p.D266N|SAGE1_ENST00000537770.1_Intron|SAGE1_ENST00000535938.1_Missense_Mutation_p.D266N			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	266						nucleus (GO:0005634)				breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					ACCCCAACCTGATAACATCTT	0.458																																						dbGAP											0			X											144.0	117.0	126.0					X																	134989144		2203	4300	6503	134816810	SO:0001583	missense	0			AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"""cancer/testis antigen 14"""	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.796G>A	X.37:g.134989144G>A	ENSP00000359743:p.Asp266Asn	Somatic	105	17.32	22		0	0.00	0	WXS	Illumina HiSeq	Phase_IV	134816810	7	90.36	75	Q5JNW0	Missense_Mutation	SNP	NULL	p.D266N	ENST00000370709.3	37	c.796	CCDS14652.1	X	.	.	.	.	.	.	.	.	.	.	-	10.83	1.461312	0.26248	.	.	ENSG00000181433	ENST00000324447;ENST00000535938;ENST00000370709	T;T;T	0.34667	1.35;1.35;1.35	1.76	1.76	0.24704	.	0.221066	0.36740	U	0.002424	T	0.14570	0.0352	N	0.17082	0.46	0.09310	N	0.999994	B	0.28350	0.208	B	0.22152	0.038	T	0.27872	-1.0061	10	0.05351	T	0.99	.	6.3503	0.21373	0.0:0.0:1.0:0.0	.	266	Q9NXZ1	SAGE1_HUMAN	N	266	ENSP00000323191:D266N;ENSP00000445959:D266N;ENSP00000359743:D266N	ENSP00000323191:D266N	D	+	1	0	SAGE1	134816810	0.909000	0.30893	0.006000	0.13384	0.011000	0.07611	1.725000	0.38074	1.158000	0.42547	0.171000	0.16805	GAT	-	NULL		0.458	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SAGE1	protein_coding	OTTHUMT00000058448.1	G	NM_018666		134816810	+1	no_errors	NM_018666.2	genbank	human	reviewed	54_36p	missense	SNP	0.516	A
WASH7P	653635	genome.wustl.edu	37	1	17829	17829	+	IGR	SNP	G	G	A			TCGA-AB-2855-03B-01W-0728-08	TCGA-AB-2855-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8bdab9f4-ca3d-4f77-b83e-6ec7df6c2a27	56552b20-8a32-4584-a3dc-91cc0e4196f4	g.chr1:17829G>A								DDX11L1 (3420 upstream) : MIR1302-11 (12536 downstream)																							GCCTCCTCTGGGGGACAGAAC	0.617																																						dbGAP											0			1																																								7692	SO:0001628	intergenic_variant	0																															1.37:g.17829G>A		Somatic	0	0.00	0		1	0.00	0	WXS	Illumina HiSeq	Phase_IV	7692	0	0.00	0		RNA	SNP	-	NULL		37	NULL		1																																																																																			-	-	0	0.617					LOC727882			G			7692	+1	pseudogene	XR_015152.2	genbank	human	model	54_36p	rna	SNP	0.043	A
ANKRD18A	253650	genome.wustl.edu	37	9	38615714	38615714	+	Silent	SNP	G	G	A	rs375586322		TCGA-AB-2855-03B-01W-0728-08	TCGA-AB-2855-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8bdab9f4-ca3d-4f77-b83e-6ec7df6c2a27	56552b20-8a32-4584-a3dc-91cc0e4196f4	g.chr9:38615714G>A	ENST00000399703.5	-	3	746	c.372C>T	c.(370-372)ggC>ggT	p.G124G		NM_147195.2	NP_671728.2	Q8IVF6	AN18A_HUMAN	ankyrin repeat domain 18A	124										NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)|skin(2)|stomach(1)	16						TTGGATTGGCGCCACATTCCA	0.428																																						dbGAP											0			9						G		2,1382		0,2,690	89.0	70.0	76.0		372	0.2	0.1	9		76	0,3182		0,0,1591	no	coding-synonymous	ANKRD18A	NM_147195.2		0,2,2281	AA,AG,GG		0.0,0.1445,0.0438		124/993	38615714	2,4564	692	1591	2283	38605714	SO:0001819	synonymous_variant	0			AB095935	CCDS55311.1	9p13.1	2013-01-10			ENSG00000180071	ENSG00000180071		"""Ankyrin repeat domain containing"""	23643	protein-coding gene	gene with protein product							Standard	NM_147195		Approved	KIAA2015, FLJ35740	uc004abg.4	Q8IVF6	OTTHUMG00000019950	ENST00000399703.5:c.372C>T	9.37:g.38615714G>A		Somatic	25	7.41	2		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	38605714	60	46.90	53	A7MD11|A8MVU5|Q5SY86|Q7Z468|Q8NA88	Silent	SNP	HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat	p.G124	ENST00000399703.5	37	c.372	CCDS55311.1	9																																																																																			-	HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat		0.428	ANKRD18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ANKRD18A	protein_coding	OTTHUMT00000052506.3	G			38605714	-1	no_errors	XM_001726105.1	genbank	human	model	54_36p	silent	SNP	0.950	A
TET1	80312	genome.wustl.edu	37	10	70450649	70450649	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2855-03B-01W-0728-08	TCGA-AB-2855-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8bdab9f4-ca3d-4f77-b83e-6ec7df6c2a27	56552b20-8a32-4584-a3dc-91cc0e4196f4	g.chr10:70450649C>T	ENST00000373644.4	+	12	5698	c.5489C>T	c.(5488-5490)aCt>aTt	p.T1830I		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1830					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						AACACTAAAACTTATTCGCTG	0.483																																						dbGAP											0			10											95.0	97.0	96.0					10																	70450649		2203	4300	6503	70120655	SO:0001583	missense	0			AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"""leukemia-associated protein with a CXXC domain"", ""ten-eleven translocation-1"""	607790	"""CXXC zinc finger 6"", ""tet oncogene 1"""	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.5489C>T	10.37:g.70450649C>T	ENSP00000362748:p.Thr1830Ile	Somatic	79	16.67	16		6	45.45	5	WXS	Illumina HiSeq	Phase_IV	70120655	87	42.21	65	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	HMMPfam_zf-CXXC	p.T1830I	ENST00000373644.4	37	c.5489	CCDS7281.1	10	.	.	.	.	.	.	.	.	.	.	C	14.93	2.683663	0.47991	.	.	ENSG00000138336	ENST00000373644	T	0.06687	3.27	4.8	-6.81	0.01704	Methylcytosine dioxygenase TET, double-stranded beta helix fold domain (1);	13.615900	0.00682	N	0.000688	T	0.06234	0.0161	L	0.33485	1.01	0.19945	N	0.999944	B	0.09022	0.002	B	0.08055	0.003	T	0.40346	-0.9568	10	0.72032	D	0.01	.	3.491	0.07637	0.1089:0.2488:0.411:0.2313	.	1830	Q8NFU7	TET1_HUMAN	I	1830	ENSP00000362748:T1830I	ENSP00000362748:T1830I	T	+	2	0	TET1	70120655	0.132000	0.22450	0.129000	0.21949	0.870000	0.49936	-0.909000	0.04058	-0.923000	0.03785	-0.165000	0.13383	ACT	-	NULL		0.483	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TET1	protein_coding	OTTHUMT00000048354.1	C	NM_030625		70120655	+1	no_errors	NM_030625.2	genbank	human	validated	54_36p	missense	SNP	0.944	T
PTPN11	5781	genome.wustl.edu	37	12	112926852	112926852	+	Missense_Mutation	SNP	C	C	T	rs397507540		TCGA-AB-2855-03B-01W-0728-08	TCGA-AB-2855-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8bdab9f4-ca3d-4f77-b83e-6ec7df6c2a27	56552b20-8a32-4584-a3dc-91cc0e4196f4	g.chr12:112926852C>T	ENST00000351677.2	+	13	1670	c.1472C>T	c.(1471-1473)cCc>cTc	p.P491L		NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	495	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)	p.P491L(2)		NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						ATTGACGTTCCCAAAACCATC	0.433			Mis		"""JMML, AML, MDS"""		Noonan Syndrome		Noonan syndrome																													dbGAP		Dom	yes		12	12q24.1	5781	"""protein tyrosine phosphatase, non-receptor type 11"""	yes	L	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	12	GRCh37	CM053389|CM067454	PTPN11	M							160.0	146.0	151.0					12																	112926852		2203	4300	6503	111411235	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	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"", ""SH2 domain containing"""	9644	protein-coding gene	gene with protein product		176876	"""Noonan syndrome 1"""	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.1472C>T	12.37:g.112926852C>T	ENSP00000340944:p.Pro491Leu	Somatic	261	11.49	34		13	56.67	17	WXS	Illumina HiSeq	Phase_IV	111411235	333	50.00	341	A8K1D9|Q96HD7	Missense_Mutation	SNP	HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMPfam_SH2,HMMSmart_SM00252,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II,superfamily_SH2 domain	p.P491L	ENST00000351677.2	37	c.1472	CCDS9163.1	12	.	.	.	.	.	.	.	.	.	.	C	29.2	4.984335	0.93044	.	.	ENSG00000179295	ENST00000351677	D	0.81821	-1.54	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.73799	0.3633	L	0.38733	1.17	0.80722	D	1	P	0.36010	0.532	B	0.35182	0.197	T	0.70941	-0.4735	10	0.21014	T	0.42	.	18.9358	0.92584	0.0:1.0:0.0:0.0	.	491	Q06124-2	.	L	491	ENSP00000340944:P491L	ENSP00000340944:P491L	P	+	2	0	PTPN11	111411235	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.445000	0.80570	2.553000	0.86117	0.650000	0.86243	CCC	-	HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMSmart_SM00404,superfamily_(Phosphotyrosine protein) phosphatases II		0.433	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PTPN11	protein_coding	OTTHUMT00000259496.2	C			111411235	+1	no_errors	NM_002834.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
PHF6	84295	genome.wustl.edu	37	X	133547903	133547904	+	Frame_Shift_Ins	INS	-	-	GGATA			TCGA-AB-2855-03B-01W-0728-08	TCGA-AB-2855-11B-01W-0729-08	-	-	-	GGATA	-	-	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	8bdab9f4-ca3d-4f77-b83e-6ec7df6c2a27	56552b20-8a32-4584-a3dc-91cc0e4196f4	g.chrX:133547903_133547904insGGATA	ENST00000332070.3	+	7	838_839	c.636_637insGGATA	c.(637-639)ggafs	p.-213fs	PHF6_ENST00000416404.2_Frame_Shift_Ins_p.-179fs|PHF6_ENST00000394292.1_Frame_Shift_Ins_p.-214fs|PHF6_ENST00000370800.4_Frame_Shift_Ins_p.-214fs|PHF6_ENST00000370799.1_Frame_Shift_Ins_p.-214fs|PHF6_ENST00000370803.3_Frame_Shift_Ins_p.-213fs	NM_032458.2	NP_115834.1	Q8IWS0	PHF6_HUMAN	PHD finger protein 6						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|histone deacetylase binding (GO:0042826)|phosphoprotein binding (GO:0051219)|poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)|scaffold protein binding (GO:0097110)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(88)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|ovary(1)|skin(1)|urinary_tract(1)	103	Acute lymphoblastic leukemia(192;0.000127)					GGCCTAAATGTGGATTTTGCCA	0.401			"""F, N, Splice, Mis"""		ETP ALL																																Colon(100;666 1493 6344 21231 35807)	dbGAP		Rec	yes		X	Xq26.3	84295	PHD finger protein 6		L	0			X																																								133375570	SO:0001589	frameshift_variant	0			AB058726	CCDS14639.1, CCDS14640.1	Xq26	2014-09-17			ENSG00000156531	ENSG00000156531		"""Zinc fingers, PHD-type"""	18145	protein-coding gene	gene with protein product	"""centromere protein 31"""	300414	"""Borjeson-Forssman-Lehmann syndrome"""	BFLS, BORJ		12415272, 15466013	Standard	NM_032335		Approved	KIAA1823, MGC14797, CENP-31	uc004exk.3	Q8IWS0	OTTHUMG00000022453	Exception_encountered	X.37:g.133547903_133547904insGGATA	ENSP00000329097:p.Gly213fs	Somatic	NA	NA	NA		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	133375569	NA	NA	NA	A8K230|B4E0G4|D3DTG3|E9PC97|Q5JRC7|Q5JRC8|Q96JK3|Q9BRU0	Frame_Shift_Ins	INS	HMMSmart_SM00249,superfamily_FYVE/PHD zinc finger	p.F213fs	ENST00000332070.3	37	c.636_637	CCDS14639.1	X																																																																																			-	NULL		0.401	PHF6-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	PHF6	protein_coding	OTTHUMT00000058367.1	-	NM_032458		133375570	+1	no_errors	NM_001015877.1	genbank	human	reviewed	54_36p	frame_shift_ins	INS	1.000:1.000	GGATA
