#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_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	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_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Confidence	i_Drug_Target	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_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	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_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	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_dbSNPPopFreq	i_dbSNP_AF	i_dbSNP_PopFreq	i_dbSNP_Strength	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
TGFBRAP1	9392	hgsc.bcm.edu	37	2	105886051	105886051	+	Missense_Mutation	SNP	G	G	A			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr2:105886051G>A	ENST00000393359.2	-	11	2510	c.2084C>T	c.(2083-2085)gCg>gTg	p.A695V	TGFBRAP1_ENST00000258449.1_Missense_Mutation_p.A695V			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	695					intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|membrane (GO:0016020)	SMAD binding (GO:0046332)|small GTPase regulator activity (GO:0005083)|transforming growth factor beta receptor binding (GO:0005160)			central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	31						GTCCTCGGCCGCTGCAAAGTC	0.657																																					p.A695V	Esophageal Squamous(183;794 2019 9730 21801 48859)	Atlas-SNP	.											.	TGFBRAP1	70	.	0			c.C2084T						PASS	.						26.0	27.0	27.0					2																	105886051		2203	4300	6503	SO:0001583	missense	9392	exon11			TCGGCCGCTGCAA	AF022795	CCDS2067.1	2q12.1	2008-02-05			ENSG00000135966	ENSG00000135966			16836	protein-coding gene	gene with protein product		606237				9545258, 11278302	Standard	NM_001142621		Approved	TRAP-1, TRAP1	uc002tcr.4	Q8WUH2	OTTHUMG00000130809	ENST00000393359.2:c.2084C>T	chr2.hg19:g.105886051G>A	ENSP00000377027:p.Ala695Val	45.0	0.0	.		35.0	6.0	.	NM_004257	A8K5R7|D3DVJ8|O60466	Missense_Mutation	SNP	ENST00000393359.2	hg19	CCDS2067.1	.	.	.	.	.	.	.	.	.	.	G	18.44	3.625045	0.66901	.	.	ENSG00000135966	ENST00000393359;ENST00000258449;ENST00000543724	T;T	0.19806	2.12;2.12	5.54	4.64	0.57946	.	0.053015	0.85682	D	0.000000	T	0.49406	0.1555	M	0.86178	2.8	0.54753	D	0.999985	D;D	0.89917	1.0;0.992	D;D	0.68039	0.955;0.909	T	0.56098	-0.8035	10	0.46703	T	0.11	-29.6428	15.5761	0.76387	0.0:0.0:0.8611:0.1389	.	150;695	B3KMM9;Q8WUH2	.;TGFA1_HUMAN	V	695;695;150	ENSP00000377027:A695V;ENSP00000258449:A695V	ENSP00000258449:A695V	A	-	2	0	TGFBRAP1	105252483	1.000000	0.71417	0.404000	0.26397	0.158000	0.22134	9.470000	0.97683	1.293000	0.44690	0.462000	0.41574	GCG	.	.	.	none		0.657	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257	
DEFB114	245928	hgsc.bcm.edu	37	6	49931770	49931770	+	Silent	SNP	G	G	A			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr6:49931770G>A	ENST00000322066.3	-	1	48	c.49C>T	c.(49-51)Cta>Tta	p.L17L		NM_001037499.1	NP_001032588.1	Q30KQ6	DB114_HUMAN	defensin, beta 114	17					defense response to bacterium (GO:0042742)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)	extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)			kidney(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	8	Lung NSC(77;0.042)					TTACCTGGTAGAATGAAGGTC	0.284																																					p.L17L		Atlas-SNP	.											.	DEFB114	12	.	0			c.C49T						PASS	.						69.0	68.0	68.0					6																	49931770		2202	4293	6495	SO:0001819	synonymous_variant	245928	exon1			CTGGTAGAATGAA	DQ012018	CCDS34474.1	6p12.3	2010-03-30			ENSG00000177684	ENSG00000177684		"""Defensins, beta"""	18095	protein-coding gene	gene with protein product		615243				11854508, 16033865	Standard	NM_001037499		Approved	DEFB-14	uc011dwp.2	Q30KQ6	OTTHUMG00000160209	ENST00000322066.3:c.49C>T	chr6.hg19:g.49931770G>A		71.0	0.0	.		60.0	11.0	.	NM_001037499	Q8NES9	Silent	SNP	ENST00000322066.3	hg19	CCDS34474.1																																																																																			.	.	.	none		0.284	DEFB114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359665.1	NM_001037499	
SEPT7	989	hgsc.bcm.edu	37	7	35930362	35930362	+	Silent	SNP	T	T	C	rs530929455	byFrequency	TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr7:35930362T>C	ENST00000435235.1	+	10	1230	c.798T>C	c.(796-798)taT>taC	p.Y266Y	SEPT7_ENST00000399035.3_Silent_p.Y318Y|SEPT7_ENST00000399034.2_Silent_p.Y320Y|SEPT7_ENST00000432293.2_Intron|SEPT7_ENST00000350320.6_Silent_p.Y318Y|SEPT7_ENST00000494488.2_Silent_p.Y305Y			Q16181	SEPT7_HUMAN	septin 7	319	Septin-type G.				cilium morphogenesis (GO:0060271)|cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein heterooligomerization (GO:0051291)|regulation of embryonic cell shape (GO:0016476)	actin cytoskeleton (GO:0015629)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|septin complex (GO:0031105)|stress fiber (GO:0001725)	GTP binding (GO:0005525)|identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)	p.Y320Y(3)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)	14						CTGTGACTTATAATGGAGTTG	0.323													T|||	6	0.00119808	0.0	0.0	5008	,	,		16353	0.005		0.0	False		,,,				2504	0.001				p.Y318Y		Atlas-SNP	.											SEPT7,NS,carcinoma,0,3	SEPT7	24	.	3	Substitution - coding silent(3)	kidney(2)|prostate(1)	c.T954C						PASS	.						47.0	41.0	43.0					7																	35930362		1836	4080	5916	SO:0001819	synonymous_variant	989	exon10			GACTTATAATGGA	S72008	CCDS75582.1	7p14.2	2013-01-21	2005-01-11	2005-01-12	ENSG00000122545	ENSG00000122545		"""Septins"""	1717	protein-coding gene	gene with protein product		603151	"""CDC10 cell division cycle 10 homolog (S. cerevisiae)"""	CDC10		8037772	Standard	NM_001788		Approved	CDC3, SEPT7A	uc011kau.2	Q16181	OTTHUMG00000155063	ENST00000435235.1:c.798T>C	chr7.hg19:g.35930362T>C		29.0	1.0	.		48.0	3.0	.	NM_001011553	Q52M76|Q6NX50	Silent	SNP	ENST00000435235.1	hg19																																																																																				.	.	.	none		0.323	SEPT7-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000338285.1	NM_001788	
CRY1	1407	hgsc.bcm.edu	37	12	107399011	107399011	+	Missense_Mutation	SNP	T	T	C			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr12:107399011T>C	ENST00000008527.5	-	3	1150	c.283A>G	c.(283-285)Aaa>Gaa	p.K95E		NM_004075.4	NP_004066.1	Q16526	CRY1_HUMAN	cryptochrome circadian clock 1	95	Photolyase/cryptochrome alpha/beta.				blue light signaling pathway (GO:0009785)|circadian regulation of gene expression (GO:0032922)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|entrainment of circadian clock by photoperiod (GO:0043153)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|lipid storage (GO:0019915)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of glucocorticoid secretion (GO:2000850)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|regulation of DNA damage checkpoint (GO:2000001)|response to glucagon (GO:0033762)|response to insulin (GO:0032868)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	blue light photoreceptor activity (GO:0009882)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|DNA photolyase activity (GO:0003913)|double-stranded DNA binding (GO:0003690)|nuclear hormone receptor binding (GO:0035257)|nucleotide binding (GO:0000166)|phosphatase binding (GO:0019902)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin binding (GO:0043130)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|skin(1)	29						ATTGAAAGTTTAGTAATGTTC	0.343																																					p.K95E		Atlas-SNP	.											.	CRY1	74	.	0			c.A283G						PASS	.						137.0	132.0	134.0					12																	107399011		2203	4300	6503	SO:0001583	missense	1407	exon3			AAAGTTTAGTAAT	BC030519	CCDS9112.1	12q23-q24.1	2014-01-17	2014-01-17		ENSG00000008405	ENSG00000008405			2384	protein-coding gene	gene with protein product		601933	"""cryptochrome 1 (photolyase-like)"""	PHLL1		8921389	Standard	NM_004075		Approved		uc001tmi.4	Q16526	OTTHUMG00000170005	ENST00000008527.5:c.283A>G	chr12.hg19:g.107399011T>C	ENSP00000008527:p.Lys95Glu	149.0	0.0	.		167.0	64.0	.	NM_004075		Missense_Mutation	SNP	ENST00000008527.5	hg19	CCDS9112.1	.	.	.	.	.	.	.	.	.	.	T	15.48	2.847284	0.51164	.	.	ENSG00000008405	ENST00000008527	.	.	.	5.61	5.61	0.85477	Rossmann-like alpha/beta/alpha sandwich fold (1);DNA photolyase, N-terminal (2);	0.160218	0.53938	D	0.000048	T	0.54319	0.1851	L	0.49640	1.575	0.41632	D	0.989029	B	0.19073	0.033	B	0.19666	0.026	T	0.52472	-0.8571	9	0.06757	T	0.87	-12.0027	15.8086	0.78538	0.0:0.0:0.0:1.0	.	95	Q16526	CRY1_HUMAN	E	95	.	ENSP00000008527:K95E	K	-	1	0	CRY1	105923141	1.000000	0.71417	0.996000	0.52242	0.955000	0.61496	5.296000	0.65698	2.147000	0.66899	0.477000	0.44152	AAA	.	.	.	none		0.343	CRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406827.1	NM_004075	
PTPN11	5781	hgsc.bcm.edu	37	12	112892407	112892407	+	Missense_Mutation	SNP	T	T	G	rs79068130		TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr12:112892407T>G	ENST00000351677.2	+	5	763	c.565T>G	c.(565-567)Tct>Gct	p.S189A	PTPN11_ENST00000392597.1_Missense_Mutation_p.S189A	NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	189	SH2 2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				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.S189A(1)		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						ACGGTTTGATTCTTTGACAGA	0.368			Mis		"""JMML, AML, MDS"""		Noonan Syndrome		Noonan syndrome																												p.S189A		Atlas-SNP	.		Dom	yes		12	12q24.1	5781	"""protein tyrosine phosphatase, non-receptor type 11"""	yes	L	PTPN11,NS,carcinoma,0,1	PTPN11	623	.	1	Substitution - Missense(1)	stomach(1)	c.T565G						PASS	.						112.0	105.0	108.0					12																	112892407		2203	4300	6503	SO:0001583	missense	5781	exon5	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	TTTGATTCTTTGA	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.565T>G	chr12.hg19:g.112892407T>G	ENSP00000340944:p.Ser189Ala	56.0	1.0	.		48.0	3.0	.	NM_080601	A8K1D9|Q96HD7	Missense_Mutation	SNP	ENST00000351677.2	hg19	CCDS9163.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.87|17.87	3.494925|3.494925	0.64186|0.64186	.|.	.|.	ENSG00000179295|ENSG00000179295	ENST00000530818|ENST00000392597;ENST00000351677;ENST00000392596	.|T;T	.|0.80824	.|-1.42;-1.42	5.65|5.65	5.65|5.65	0.86999|0.86999	.|.	.|0.051687	.|0.85682	.|D	.|0.000000	D|D	0.86151|0.86151	0.5864|0.5864	M|M	0.90977|0.90977	3.165|3.165	0.53005|0.53005	D|D	0.99996|0.99996	.|B;B	.|0.22480	.|0.07;0.07	.|B;B	.|0.36845	.|0.234;0.234	D|D	0.84453|0.84453	0.0589|0.0589	5|10	.|0.44086	.|T	.|0.13	.|.	11.0193|11.0193	0.47709|0.47709	0.1389:0.0:0.0:0.8611|0.1389:0.0:0.0:0.8611	.|.	.|189;189	.|Q06124-2;Q06124-3	.|.;.	M|A	33|189	.|ENSP00000376376:S189A;ENSP00000340944:S189A	.|ENSP00000340944:S189A	I|S	+|+	3|1	3|0	PTPN11|PTPN11	111376790|111376790	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.954000|0.954000	0.61252|0.61252	4.663000|4.663000	0.61532|0.61532	2.144000|2.144000	0.66660|0.66660	0.397000|0.397000	0.26171|0.26171	ATT|TCT	.	T|0.500;G|0.500	0.500	weak		0.368	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2		
SYT3	84258	hgsc.bcm.edu	37	19	51135675	51135675	+	Missense_Mutation	SNP	G	G	A			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr19:51135675G>A	ENST00000338916.4	-	2	1175	c.542C>T	c.(541-543)cCg>cTg	p.P181L	SYT3_ENST00000544769.1_Missense_Mutation_p.P181L|SYT3_ENST00000600079.1_Missense_Mutation_p.P181L|SYT3_ENST00000593901.1_Missense_Mutation_p.P181L	NM_032298.2	NP_115674.1	Q9BQG1	SYT3_HUMAN	synaptotagmin III	181					calcium ion-dependent exocytosis (GO:0017156)|positive regulation of vesicle fusion (GO:0031340)|response to calcium ion (GO:0051592)	cell junction (GO:0030054)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(2)|skin(3)|urinary_tract(2)	35		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00462)|GBM - Glioblastoma multiforme(134;0.0188)		TGTTTGGCTCGGTTTGACCCC	0.657																																					p.P181L		Atlas-SNP	.											.	SYT3	85	.	0			c.C542T						PASS	.						33.0	34.0	34.0					19																	51135675		2203	4300	6503	SO:0001583	missense	84258	exon2			TGGCTCGGTTTGA	AL136594	CCDS12798.1	19q13.33	2014-07-02			ENSG00000213023	ENSG00000213023		"""Synaptotagmins"""	11511	protein-coding gene	gene with protein product		600327				7749232	Standard	NM_032298		Approved		uc002psv.3	Q9BQG1	OTTHUMG00000183064	ENST00000338916.4:c.542C>T	chr19.hg19:g.51135675G>A	ENSP00000340914:p.Pro181Leu	71.0	0.0	.		74.0	23.0	.	NM_032298	Q8N5Z1|Q8N640	Missense_Mutation	SNP	ENST00000338916.4	hg19	CCDS12798.1	.	.	.	.	.	.	.	.	.	.	G	12.34	1.907284	0.33628	.	.	ENSG00000213023	ENST00000338916;ENST00000544769	T;T	0.54479	0.57;0.57	5.24	5.24	0.73138	.	0.715640	0.12228	U	0.487701	T	0.29355	0.0731	N	0.03608	-0.345	0.09310	N	0.999994	B	0.09022	0.002	B	0.04013	0.001	T	0.06110	-1.0845	10	0.49607	T	0.09	.	8.4467	0.32847	0.169:0.0:0.831:0.0	.	181	Q9BQG1	SYT3_HUMAN	L	181	ENSP00000340914:P181L;ENSP00000438883:P181L	ENSP00000340914:P181L	P	-	2	0	SYT3	55827487	0.978000	0.34361	0.974000	0.42286	0.996000	0.88848	3.207000	0.51106	2.605000	0.88082	0.655000	0.94253	CCG	.	.	.	none		0.657	SYT3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464910.1	NM_032298	
ZNF304	57343	hgsc.bcm.edu	37	19	57869057	57869057	+	Missense_Mutation	SNP	G	G	A			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr19:57869057G>A	ENST00000282286.5	+	3	1993	c.1820G>A	c.(1819-1821)aGg>aAg	p.R607K	ZNF304_ENST00000443917.2_Missense_Mutation_p.R654K|ZNF304_ENST00000598744.1_Missense_Mutation_p.R565K|ZNF304_ENST00000391705.3_Missense_Mutation_p.R607K			Q9HCX3	ZN304_HUMAN	zinc finger protein 304	607					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)	26		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		CTGCACCAGAGGGTTCACACT	0.478																																					p.R607K		Atlas-SNP	.											.	ZNF304	74	.	0			c.G1820A						PASS	.						84.0	81.0	82.0					19																	57869057		2203	4300	6503	SO:0001583	missense	57343	exon3			ACCAGAGGGTTCA	AJ276316	CCDS12950.1, CCDS74462.1	19q13.4	2013-01-08				ENSG00000131845		"""Zinc fingers, C2H2-type"", ""-"""	13505	protein-coding gene	gene with protein product		613840					Standard	XM_005259090		Approved		uc010ygw.2	Q9HCX3		ENST00000282286.5:c.1820G>A	chr19.hg19:g.57869057G>A	ENSP00000282286:p.Arg607Lys	90.0	0.0	.		106.0	23.0	.	NM_020657		Missense_Mutation	SNP	ENST00000282286.5	hg19	CCDS12950.1	.	.	.	.	.	.	.	.	.	.	G	19.37	3.814001	0.70912	.	.	ENSG00000131845	ENST00000282286;ENST00000391705;ENST00000443917	T;T;T	0.18338	2.22;2.22;2.22	3.89	1.75	0.24633	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.29126	0.0724	L	0.42744	1.35	0.23056	N	0.998366	P;D	0.58970	0.898;0.984	P;D	0.69142	0.483;0.962	T	0.07462	-1.0771	9	0.45353	T	0.12	.	9.2462	0.37527	0.1894:0.0:0.8106:0.0	.	607;654	Q9HCX3;E7EQD3	ZN304_HUMAN;.	K	607;607;654	ENSP00000282286:R607K;ENSP00000375586:R607K;ENSP00000401642:R654K	ENSP00000282286:R607K	R	+	2	0	ZNF304	62560869	0.892000	0.30473	0.763000	0.31416	0.981000	0.71138	5.266000	0.65525	0.600000	0.29862	0.650000	0.86243	AGG	.	.	.	none		0.478	ZNF304-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465785.1		
CCDC71	64925	hgsc.bcm.edu	37	3	49200861	49200862	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-BQ-7055-01A-11D-1961-08	TCGA-BQ-7055-11A-01D-1961-08	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	69910e4a-5f3a-49c8-9c58-5f5fc0b4625a	1a7e89d4-822a-4ca2-b6e3-e3114990152b	g.chr3:49200861_49200862delCT	ENST00000321895.6	-	2	886_887	c.780_781delAG	c.(778-783)agagccfs	p.RA260fs		NM_022903.3	NP_075054.3	Q8IV32	CCD71_HUMAN	coiled-coil domain containing 71	260										endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)	10				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GACCCAGTGGCTCTGTTGGTTT	0.624																																					p.261_261del		Atlas-INDEL	.											.	CCDC71	33	.	0			c.781_782del						PASS	.																																			SO:0001589	frameshift_variant	64925	exon2			.	AK022862	CCDS2790.1	3p21.31	2014-02-12			ENSG00000177352	ENSG00000177352			25760	protein-coding gene	gene with protein product						12477932	Standard	NM_022903		Approved	FLJ12800	uc003cwg.4	Q8IV32	OTTHUMG00000156815	ENST00000321895.6:c.780_781delAG	chr3.hg19:g.49200863_49200864delCT	ENSP00000319006:p.Arg260fs	194.0	0.0	0		152.0	43.0	0.282895	NM_022903	Q6IPE2|Q9H8H4|Q9H9F1	Frame_Shift_Del	DEL	ENST00000321895.6	hg19	CCDS2790.1																																																																																			.	.	.	none		0.624	CCDC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345980.1	NM_022903	
