#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
STAG2	10735	genome.wustl.edu	37	X	123191828	123191828	+	Splice_Site	SNP	G	G	A			TCGA-AB-2871-03A-01W-0732-08	TCGA-AB-2871-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3e8efa46-6045-4be1-b41b-e7b98f165d24	6c7c2063-37fc-45fc-8401-6169345b8c05	g.chrX:123191828G>A	ENST00000371160.1	+	15	1706		c.e15+1		STAG2_ENST00000371145.3_Splice_Site|STAG2_ENST00000354548.5_Splice_Site|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Splice_Site|STAG2_ENST00000371144.3_Splice_Site|STAG2_ENST00000371157.3_Splice_Site	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2						meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						AGAAAGTGAGGTTAGTTGATA	0.328																																						dbGAP											0			X											113.0	102.0	106.0					X																	123191828		2203	4300	6503	123019509	SO:0001630	splice_region_variant	0			Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.1416+1G>A	X.37:g.123191828G>A		Somatic	33	0.00	0		1	0.00	0	WXS	Illumina HiSeq	Phase_IV	123019509	34	30.77	16	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Splice_Site	SNP	-	e13+1	ENST00000371160.1	37	c.1416+1	CCDS14607.1	X	.	.	.	.	.	.	.	.	.	.	G	27.5	4.838358	0.91117	.	.	ENSG00000101972	ENST00000218089;ENST00000455404;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	.	.	.	5.57	5.57	0.84162	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.565	0.91114	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	STAG2	123019509	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.753000	0.85153	2.327000	0.79052	0.600000	0.82982	.	-	-		0.328	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	STAG2	protein_coding	OTTHUMT00000156159.2	G	NM_006603	Intron	123019509	+1	no_errors	NM_001042749.1	genbank	human	validated	54_36p	splice_site	SNP	1.000	A
ELF4	2000	genome.wustl.edu	37	X	129205024	129205024	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2871-03A-01W-0732-08	TCGA-AB-2871-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3e8efa46-6045-4be1-b41b-e7b98f165d24	6c7c2063-37fc-45fc-8401-6169345b8c05	g.chrX:129205024C>T	ENST00000308167.5	-	7	1179	c.800G>A	c.(799-801)cGg>cAg	p.R267Q	ELF4_ENST00000335997.7_Missense_Mutation_p.R267Q	NM_001421.3	NP_001412.1			E74-like factor 4 (ets domain transcription factor)											breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	22						CCTTAGTGCCCGCCCCATTGT	0.527			T	ERG	AML																																	dbGAP		Dom	yes		X	Xq26	2000	E74-like factor 4 (ets domain transcription factor)		L	0			X											209.0	177.0	188.0					X																	129205024		2203	4300	6503	129032705	SO:0001583	missense	0			U32645	CCDS14617.1	Xq26	2014-09-17			ENSG00000102034	ENSG00000102034			3319	protein-coding gene	gene with protein product		300775				8895518	Standard	NM_001421		Approved	MEF, ELFR	uc004eve.4	Q99607	OTTHUMG00000022390	ENST00000308167.5:c.800G>A	X.37:g.129205024C>T	ENSP00000311280:p.Arg267Gln	Somatic	43	0.00	0		28	76.86	93	WXS	Illumina HiSeq	Phase_IV	129032705	113	35.23	62		Missense_Mutation	SNP	HMMPfam_Ets,HMMSmart_ETS,PatternScan_ETS_DOMAIN_1,PatternScan_ETS_DOMAIN_2,superfamily_SSF46785	p.R267Q	ENST00000308167.5	37	c.800	CCDS14617.1	X	.	.	.	.	.	.	.	.	.	.	C	29.2	4.989221	0.93106	.	.	ENSG00000102034	ENST00000335997;ENST00000308167	T;T	0.70399	-0.48;-0.48	5.27	5.27	0.74061	Winged helix-turn-helix transcription repressor DNA-binding (1);Ets (5);	0.000000	0.85682	D	0.000000	D	0.87289	0.6140	M	0.92970	3.365	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	D	0.90464	0.4448	10	0.87932	D	0	.	15.2366	0.73436	0.0:1.0:0.0:0.0	.	267	Q99607	ELF4_HUMAN	Q	267	ENSP00000338608:R267Q;ENSP00000311280:R267Q	ENSP00000311280:R267Q	R	-	2	0	ELF4	129032705	1.000000	0.71417	1.000000	0.80357	0.795000	0.44927	7.775000	0.85489	2.187000	0.69744	0.466000	0.42574	CGG	-	HMMPfam_Ets,HMMSmart_ETS,PatternScan_ETS_DOMAIN_2,superfamily_SSF46785		0.527	ELF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ELF4	protein_coding	OTTHUMT00000058243.1	C	NM_001421		129032705	-1	no_errors	NM_001421.1	genbank	human	validated	54_36p	missense	SNP	1.000	T
THRAP3	9967	genome.wustl.edu	37	1	36767160	36767160	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AB-2871-03A-01W-0732-08	TCGA-AB-2871-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3e8efa46-6045-4be1-b41b-e7b98f165d24	6c7c2063-37fc-45fc-8401-6169345b8c05	g.chr1:36767160C>T	ENST00000354618.5	+	11	2733	c.2509C>T	c.(2509-2511)Cga>Tga	p.R837*	THRAP3_ENST00000469141.2_Nonsense_Mutation_p.R837*	NM_005119.3	NP_005110.2	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	837	Required for mRNA decay activity.				androgen receptor signaling pathway (GO:0030521)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|phosphoprotein binding (GO:0051219)|poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(5)|stomach(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				ATAGCAGTTTCGAGCCAGAGG	0.453			T	USP6	aneurysmal bone cysts																																Pancreas(129;785 1795 20938 23278 32581)	dbGAP		Dom	yes		1	1p34.3	9967	thyroid hormone receptor associated protein 3 (TRAP150)		M	0			1											61.0	64.0	63.0					1																	36767160		2203	4300	6503	36539747	SO:0001587	stop_gained	0			AF117756	CCDS405.1	1p34.3	2008-02-05			ENSG00000054118	ENSG00000054118			22964	protein-coding gene	gene with protein product		603809					Standard	NM_005119		Approved	TRAP150	uc001cae.4	Q9Y2W1	OTTHUMG00000007866	ENST00000354618.5:c.2509C>T	1.37:g.36767160C>T	ENSP00000346634:p.Arg837*	Somatic	135	0.00	0		35	7.89	3	WXS	Illumina HiSeq	Phase_IV	36539747	128	16.46	26	D3DPS5|Q5VTK6	Nonsense_Mutation	SNP	NULL	p.R837*	ENST00000354618.5	37	c.2509	CCDS405.1	1	.	.	.	.	.	.	.	.	.	.	C	39	7.683530	0.98431	.	.	ENSG00000054118	ENST00000354618;ENST00000469141	.	.	.	5.74	5.74	0.90152	.	0.000000	0.64402	D	0.000019	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.745	14.4103	0.67111	0.1566:0.8434:0.0:0.0	.	.	.	.	X	837	.	ENSP00000346634:R837X	R	+	1	2	THRAP3	36539747	0.955000	0.32602	1.000000	0.80357	0.592000	0.36648	0.847000	0.27696	2.720000	0.93068	0.650000	0.86243	CGA	-	NULL		0.453	THRAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	THRAP3	protein_coding	OTTHUMT00000021688.2	C	NM_005119		36539747	+1	no_errors	NM_005119.3	genbank	human	validated	54_36p	nonsense	SNP	0.969	T
NEB	4703	genome.wustl.edu	37	2	152419193	152419193	+	Missense_Mutation	SNP	G	G	T	rs369143071		TCGA-AB-2871-03A-01W-0732-08	TCGA-AB-2871-11A-01W-0732-08	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3e8efa46-6045-4be1-b41b-e7b98f165d24	6c7c2063-37fc-45fc-8401-6169345b8c05	g.chr2:152419193G>T	ENST00000172853.10	-	92	13867	c.13720C>A	c.(13720-13722)Cag>Aag	p.Q4574K	NEB_ENST00000603639.1_Missense_Mutation_p.Q6275K|NEB_ENST00000409198.1_Missense_Mutation_p.Q4574K|NEB_ENST00000397345.3_Missense_Mutation_p.Q6275K|NEB_ENST00000604864.1_Missense_Mutation_p.Q6275K|NEB_ENST00000427231.2_Missense_Mutation_p.Q6275K			P20929	NEBU_HUMAN	nebulin	4574					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		GACGTCCACTGGTGGAAATAG	0.478																																						dbGAP											0			2											137.0	128.0	131.0					2																	152419193		2009	4160	6169	152127439	SO:0001583	missense	0			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.13720C>A	2.37:g.152419193G>T	ENSP00000172853:p.Gln4574Lys	Somatic	129	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	152127439	208	25.52	73	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	HMMPfam_Nebulin,HMMSmart_SM00227,HMMPfam_SH3_1,HMMSmart_SM00326,superfamily_SH3-domain	p.Q4574K	ENST00000172853.10	37	c.13720		2	.	.	.	.	.	.	.	.	.	.	G	20.6	4.024039	0.75390	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853	T;T;T;T;T	0.30448	1.53;1.53;1.53;1.53;1.53	5.74	4.87	0.63330	.	0.108055	0.64402	D	0.000004	T	0.44561	0.1299	L	0.50333	1.59	0.80722	D	1	P;P	0.44877	0.458;0.845	B;D	0.63033	0.23;0.91	T	0.21793	-1.0235	10	0.23891	T	0.37	.	10.7053	0.45952	0.069:0.1311:0.7999:0.0	.	4574;1005	P20929;Q14215	NEBU_HUMAN;.	K	4574;6275;6275;623;1005;4574	ENSP00000386259:Q4574K;ENSP00000380505:Q6275K;ENSP00000416578:Q6275K;ENSP00000410961:Q1005K;ENSP00000172853:Q4574K	ENSP00000172853:Q4574K	Q	-	1	0	NEB	152127439	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	6.573000	0.74009	1.571000	0.49722	0.563000	0.77884	CAG	-	HMMSmart_SM00227		0.478	NEB-201	KNOWN	basic	protein_coding	NEB	protein_coding		G	NM_004543		152127439	-1	no_errors	NM_004543.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
RAP1GDS1	5910	genome.wustl.edu	37	4	99264373	99264373	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2871-03A-01W-0732-08	TCGA-AB-2871-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3e8efa46-6045-4be1-b41b-e7b98f165d24	6c7c2063-37fc-45fc-8401-6169345b8c05	g.chr4:99264373G>A	ENST00000408927.3	+	3	309	c.196G>A	c.(196-198)Gcc>Acc	p.A66T	RAP1GDS1_ENST00000380158.4_Missense_Mutation_p.A67T|RAP1GDS1_ENST00000512857.1_3'UTR|RAP1GDS1_ENST00000339360.5_Missense_Mutation_p.A67T|RAP1GDS1_ENST00000264572.7_Missense_Mutation_p.A67T|RAP1GDS1_ENST00000453712.2_Missense_Mutation_p.A67T|RAP1GDS1_ENST00000408900.3_Missense_Mutation_p.A66T	NM_001100426.1|NM_001100427.1|NM_021159.4	NP_001093896.1|NP_001093897.1|NP_066982.3	P52306	GDS1_HUMAN	RAP1, GTP-GDP dissociation stimulator 1	66					myosin filament assembly (GO:0031034)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of Rho GTPase activity (GO:0032321)|vascular smooth muscle contraction (GO:0014829)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)	28				OV - Ovarian serous cystadenocarcinoma(123;2.9e-07)|LUSC - Lung squamous cell carcinoma(1;0.0253)|Lung(1;0.0576)		TTCCTGCAAAGCCAAAGTAGC	0.398			T	NUP98	T-ALL																																	dbGAP		Dom	yes		4	4q21-q25	5910	"""RAP1, GTP-GDP dissociation stimulator 1"""		L	0			4											88.0	85.0	86.0					4																	99264373		1863	4099	5962	99483396	SO:0001583	missense	0				CCDS43253.1, CCDS43254.1, CCDS47105.1, CCDS47106.1, CCDS47107.1, CCDS47108.1	4q23-q25	2013-02-14			ENSG00000138698	ENSG00000138698		"""Armadillo repeat containing"""	9859	protein-coding gene	gene with protein product		179502				8262526, 17951244	Standard	NM_001100426		Approved	SmgGDS	uc003htw.4	P52306	OTTHUMG00000160987	ENST00000408927.3:c.196G>A	4.37:g.99264373G>A	ENSP00000386153:p.Ala66Thr	Somatic	83	0.00	0		33	36.54	19	WXS	Illumina HiSeq	Phase_IV	99483396	134	20.59	35	E9PH06|G5E9P9|Q499L7|Q4KMV2|Q4QQI8|Q9BUW9|Q9BUX6|Q9NYM2|Q9NZA8	Missense_Mutation	SNP	HMMPfam_Arm,HMMSmart_SM00185,superfamily_ARM repeat	p.A67T	ENST00000408927.3	37	c.199	CCDS43253.1	4	.	.	.	.	.	.	.	.	.	.	G	15.63	2.890153	0.52014	.	.	ENSG00000138698	ENST00000380158;ENST00000264572;ENST00000408927;ENST00000514122;ENST00000453712;ENST00000511212;ENST00000408900;ENST00000339360	T;T;T;T;T;T;T;T	0.52057	0.78;1.55;0.75;1.32;0.75;0.68;0.78;0.75	5.78	5.78	0.91487	Armadillo-like helical (1);Armadillo-type fold (1);	0.256944	0.39544	N	0.001335	T	0.42585	0.1209	L	0.29908	0.895	0.38386	D	0.945263	B;B;B;D;B;B	0.57257	0.036;0.003;0.002;0.979;0.011;0.011	B;B;B;P;B;B	0.49999	0.03;0.004;0.003;0.628;0.035;0.038	T	0.21075	-1.0256	10	0.09843	T	0.71	-1.2868	14.8015	0.69919	0.0:0.0:0.8559:0.1441	.	67;66;67;66;67;67	E9PH06;P52306-2;Q499L7;P52306;Q4QQI8;G5E9P9	.;.;.;GDS1_HUMAN;.;.	T	67;67;66;66;67;67;66;67	ENSP00000369503:A67T;ENSP00000264572:A67T;ENSP00000386153:A66T;ENSP00000424324:A66T;ENSP00000407157:A67T;ENSP00000421599:A67T;ENSP00000386223:A66T;ENSP00000340454:A67T	ENSP00000264572:A67T	A	+	1	0	RAP1GDS1	99483396	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.711000	0.54868	2.714000	0.92807	0.650000	0.86243	GCC	-	superfamily_ARM repeat		0.398	RAP1GDS1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	RAP1GDS1	protein_coding	OTTHUMT00000363273.2	G	NM_001100426		99483396	+1	no_errors	NM_001100426.1	genbank	human	validated	54_36p	missense	SNP	1.000	A
PCDHB12	56124	genome.wustl.edu	37	5	140589778	140589778	+	Silent	SNP	C	C	T			TCGA-AB-2871-03A-01W-0732-08	TCGA-AB-2871-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3e8efa46-6045-4be1-b41b-e7b98f165d24	6c7c2063-37fc-45fc-8401-6169345b8c05	g.chr5:140589778C>T	ENST00000239450.2	+	1	1488	c.1299C>T	c.(1297-1299)acC>acT	p.T433T	PCDHB12_ENST00000541609.1_Silent_p.T96T	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	433	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGCTAAAAACCGAGCACAACA	0.572																																						dbGAP											0			5											101.0	96.0	98.0					5																	140589778		2203	4300	6503	140569962	SO:0001819	synonymous_variant	0			AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"""Cadherins / Protocadherins : Clustered"""	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.1299C>T	5.37:g.140589778C>T		Somatic	30	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	140569962	60	22.50	18	B4DDU1	Silent	SNP	HMMPfam_Cadherin,HMMSmart_CA,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin	p.T433	ENST00000239450.2	37	c.1299	CCDS4254.1	5																																																																																			-	HMMPfam_Cadherin,HMMSmart_CA,superfamily_Cadherin		0.572	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCDHB12	protein_coding	OTTHUMT00000251815.2	C	NM_018932		140569962	+1	no_errors	NM_018932.3	genbank	human	reviewed	54_36p	silent	SNP	0.000	T
COL12A1	1303	genome.wustl.edu	37	6	75860989	75860989	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2871-03A-01W-0732-08	TCGA-AB-2871-11A-01W-0732-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3e8efa46-6045-4be1-b41b-e7b98f165d24	6c7c2063-37fc-45fc-8401-6169345b8c05	g.chr6:75860989C>A	ENST00000322507.8	-	21	4324	c.4015G>T	c.(4015-4017)Gat>Tat	p.D1339Y	COL12A1_ENST00000483888.2_Missense_Mutation_p.D1339Y|COL12A1_ENST00000345356.6_Missense_Mutation_p.D175Y|COL12A1_ENST00000416123.2_Missense_Mutation_p.D1339Y	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1339	VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						TCGACTTCATCAGCATTTTTA	0.338																																						dbGAP											0			6											118.0	119.0	119.0					6																	75860989		1846	4088	5934	75917709	SO:0001583	missense	0			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"", ""Fibronectin type III domain containing"""	2188	protein-coding gene	gene with protein product	"""collagen type XII proteoglycan"""	120320	"""collagen, type XII, alpha 1-like"""	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.4015G>T	6.37:g.75860989C>A	ENSP00000325146:p.Asp1339Tyr	Somatic	129	0.77	1		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	75917709	109	17.29	23	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	HMMPfam_VWA,HMMSmart_SM00327,HMMSmart_SM00210,HMMPfam_fn3,HMMSmart_SM00060,HMMPfam_Collagen,superfamily_Fibronectin type III,superfamily_Concanavalin A-like lectins/glucanases,superfamily_vWA-like	p.D1339Y	ENST00000322507.8	37	c.4015	CCDS43482.1	6	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.5|23.5	4.424165|4.424165	0.83667|0.83667	.|.	.|.	ENSG00000111799|ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888|ENST00000419671	D;D;D;D|.	0.81659|.	-1.52;-1.52;-1.52;-1.52|.	5.59|5.59	5.59|5.59	0.84812|0.84812	von Willebrand factor, type A (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.81744|.	0.4887|.	M|M	0.87547|0.87547	2.89|2.89	0.80722|0.80722	D|D	1|1	P;D|.	0.76494|.	0.777;0.999|.	B;D|.	0.77004|.	0.404;0.989|.	T|.	0.83259|.	-0.0049|.	10|.	0.87932|.	D|.	0|.	.|.	19.5815|19.5815	0.95469|0.95469	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	175;1339|.	Q99715-2;Q99715|.	.;COCA1_HUMAN|.	Y|L	1339;1339;175;1339;1339|80	ENSP00000325146:D1339Y;ENSP00000305147:D175Y;ENSP00000412864:D1339Y;ENSP00000421216:D1339Y|.	ENSP00000325146:D1339Y|.	D|X	-|-	1|2	0|2	COL12A1|COL12A1	75917709|75917709	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.948000|0.948000	0.59901|0.59901	7.443000|7.443000	0.80521|0.80521	2.626000|2.626000	0.88956|0.88956	0.650000|0.650000	0.86243|0.86243	GAT|TGA	-	HMMPfam_VWA,HMMSmart_SM00327,superfamily_vWA-like		0.338	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL12A1	protein_coding	OTTHUMT00000041249.3	C	NM_004370		75917709	-1	no_errors	NM_004370.5	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
TMEM55A	55529	genome.wustl.edu	37	8	92007979	92007979	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2871-03A-01W-0732-08	TCGA-AB-2871-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3e8efa46-6045-4be1-b41b-e7b98f165d24	6c7c2063-37fc-45fc-8401-6169345b8c05	g.chr8:92007979C>T	ENST00000285419.3	-	7	1014	c.700G>A	c.(700-702)Gga>Aga	p.G234R		NM_018710.2	NP_061180.1	Q8N4L2	TM55A_HUMAN	transmembrane protein 55A	234						endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)			breast(1)|endometrium(2)|large_intestine(5)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	13			BRCA - Breast invasive adenocarcinoma(11;0.033)			CAGATCAATCCTAGGAGATAA	0.388																																						dbGAP											0			8											109.0	104.0	106.0					8																	92007979		2203	4300	6503	92077155	SO:0001583	missense	0			BC033892	CCDS6252.1	8q21.3	2005-08-09			ENSG00000155099	ENSG00000155099			25452	protein-coding gene	gene with protein product		609864				12477932	Standard	NM_018710		Approved	DKFZp762O076	uc003yes.3	Q8N4L2	OTTHUMG00000164019	ENST00000285419.3:c.700G>A	8.37:g.92007979C>T	ENSP00000285419:p.Gly234Arg	Somatic	49	2.00	1		4	63.64	7	WXS	Illumina HiSeq	Phase_IV	92077155	134	21.64	37	B2R9H4|Q68CU2	Missense_Mutation	SNP	HMMPfam_Tmemb_55A	p.G234R	ENST00000285419.3	37	c.700	CCDS6252.1	8	.	.	.	.	.	.	.	.	.	.	C	23.1	4.372304	0.82573	.	.	ENSG00000155099	ENST00000285419;ENST00000520014	.	.	.	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.66645	0.2810	N	0.24115	0.695	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.70941	-0.4735	9	0.87932	D	0	-30.0047	19.4348	0.94786	0.0:1.0:0.0:0.0	.	234	Q8N4L2	TM55A_HUMAN	R	234;240	.	ENSP00000285419:G234R	G	-	1	0	TMEM55A	92077155	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.442000	0.80503	2.663000	0.90544	0.650000	0.86243	GGA	-	HMMPfam_Tmemb_55A		0.388	TMEM55A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TMEM55A	protein_coding	OTTHUMT00000376778.1	C	NM_018710		92077155	-1	no_errors	NM_018710.2	genbank	human	validated	54_36p	missense	SNP	1.000	T
PTPN11	5781	genome.wustl.edu	37	12	112926909	112926909	+	Missense_Mutation	SNP	A	A	T	rs121918470		TCGA-AB-2871-03A-01W-0732-08	TCGA-AB-2871-11A-01W-0732-08	A	A	A	T	A	A	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3e8efa46-6045-4be1-b41b-e7b98f165d24	6c7c2063-37fc-45fc-8401-6169345b8c05	g.chr12:112926909A>T	ENST00000351677.2	+	13	1727	c.1529A>T	c.(1528-1530)cAg>cTg	p.Q510L		NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	514	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.		Q -> P (in LEOPARD1). {ECO:0000269|PubMed:14961557, ECO:0000269|PubMed:15121796, ECO:0000269|PubMed:15690106}.|Q -> R (in NS1). {ECO:0000269|PubMed:15948193}.		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)			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						ACAGAAGCACAGTACCGATTT	0.498			Mis		"""JMML, AML, MDS"""		Noonan Syndrome		Noonan syndrome																													dbGAP		Dom	yes		12	12q24.1	5781	"""protein tyrosine phosphatase, non-receptor type 11"""	yes	L	0			12	GRCh37	CM043070|CM052358	PTPN11	M	rs121918470						182.0	170.0	174.0					12																	112926909		2203	4300	6503	111411292	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.1529A>T	12.37:g.112926909A>T	ENSP00000340944:p.Gln510Leu	Somatic	116	0.00	0		35	30.00	15	WXS	Illumina HiSeq	Phase_IV	111411292	335	24.78	112	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.Q510L	ENST00000351677.2	37	c.1529	CCDS9163.1	12	.	.	.	.	.	.	.	.	.	.	A	32	5.128559	0.94473	.	.	ENSG00000179295	ENST00000351677	D	0.99663	-6.33	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	D	0.99764	0.9904	H	0.97051	3.93	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.96994	0.9724	10	0.87932	D	0	.	15.2256	0.73348	1.0:0.0:0.0:0.0	.	510	Q06124-2	.	L	510	ENSP00000340944:Q510L	ENSP00000340944:Q510L	Q	+	2	0	PTPN11	111411292	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.910000	0.92685	2.064000	0.61679	0.528000	0.53228	CAG	-	HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMSmart_SM00404,superfamily_(Phosphotyrosine protein) phosphatases II		0.498	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PTPN11	protein_coding	OTTHUMT00000259496.2	A			111411292	+1	no_errors	NM_002834.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
ATG14	22863	genome.wustl.edu	37	14	55852586	55852586	+	Missense_Mutation	SNP	G	G	A	rs140426113		TCGA-AB-2871-03A-01W-0732-08	TCGA-AB-2871-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3e8efa46-6045-4be1-b41b-e7b98f165d24	6c7c2063-37fc-45fc-8401-6169345b8c05	g.chr14:55852586G>A	ENST00000247178.5	-	5	673	c.638C>T	c.(637-639)aCg>aTg	p.T213M		NM_014924.4	NP_055739.2	Q6ZNE5	BAKOR_HUMAN	autophagy related 14	213					autophagic vacuole assembly (GO:0000045)|endosome to lysosome transport (GO:0008333)|positive regulation of autophagy (GO:0010508)	autophagic vacuole (GO:0005776)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|pre-autophagosomal structure membrane (GO:0034045)				central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(6)|prostate(2)	13						CCTCACACCCGTCTTTACTTC	0.373																																						dbGAP											0			14						G	MET/THR	2,4404	4.2+/-10.8	0,2,2201	100.0	92.0	95.0		638	4.7	0.9	14	dbSNP_134	95	0,8600		0,0,4300	no	missense	ATG14	NM_014924.4	81	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging	213/493	55852586	2,13004	2203	4300	6503	54922339	SO:0001583	missense	0			AB020638	CCDS32087.1	14q22.2	2014-02-12	2012-06-06	2010-06-29	ENSG00000126775	ENSG00000126775			19962	protein-coding gene	gene with protein product	"""Barkor"", ""beclin 1-associated autophagy-related key regulator"""	613515	"""KIAA0831"", ""ATG14 autophagy related 14 homolog (S. cerevisiae)"""	KIAA0831		18843052	Standard	NM_014924		Approved	ATG14L	uc001xbx.2	Q6ZNE5	OTTHUMG00000172129	ENST00000247178.5:c.638C>T	14.37:g.55852586G>A	ENSP00000247178:p.Thr213Met	Somatic	117	0.00	0		15	50.00	15	WXS	Illumina HiSeq	Phase_IV	54922339	199	22.39	58	A6NJE4|A8K9U5|B7ZWP5|O94920|Q32MK7|Q32MK8	Missense_Mutation	SNP	HMMPfam_DUF2355	p.T213M	ENST00000247178.5	37	c.638	CCDS32087.1	14	.	.	.	.	.	.	.	.	.	.	g	18.14	3.558603	0.65538	4.54E-4	0.0	ENSG00000126775	ENST00000247178	T	0.32272	1.46	5.66	4.74	0.60224	.	0.251316	0.40469	N	0.001099	T	0.25382	0.0617	N	0.22421	0.69	0.39359	D	0.965886	D	0.55800	0.973	P	0.50109	0.631	T	0.07654	-1.0761	10	0.48119	T	0.1	-12.9479	5.8015	0.18416	0.0725:0.1393:0.6438:0.1445	.	213	Q6ZNE5	BAKOR_HUMAN	M	213	ENSP00000247178:T213M	ENSP00000247178:T213M	T	-	2	0	ATG14	54922339	0.999000	0.42202	0.870000	0.34147	0.922000	0.55478	2.909000	0.48758	1.346000	0.45694	0.650000	0.86243	ACG	-	HMMPfam_DUF2355		0.373	ATG14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KIAA0831	protein_coding	OTTHUMT00000416992.1	G	NM_014924		54922339	-1	no_errors	NM_014924.3	genbank	human	predicted	54_36p	missense	SNP	0.819	A
HEATR4	399671	genome.wustl.edu	37	14	73989454	73989454	+	Missense_Mutation	SNP	C	C	T	rs376151634		TCGA-AB-2871-03A-01W-0732-08	TCGA-AB-2871-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3e8efa46-6045-4be1-b41b-e7b98f165d24	6c7c2063-37fc-45fc-8401-6169345b8c05	g.chr14:73989454C>T	ENST00000553558.1	-	3	724	c.403G>A	c.(403-405)Gct>Act	p.A135T	HEATR4_ENST00000334988.2_Missense_Mutation_p.A135T|RP3-414A15.2_ENST00000555972.2_RNA|HEATR4_ENST00000560393.1_Missense_Mutation_p.A88T|RP3-414A15.11_ENST00000553394.1_RNA	NM_001220484.1	NP_001207413.1	Q86WZ0	HEAT4_HUMAN	HEAT repeat containing 4	135										breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		GTCTTCACAGCCAGGGAGGTG	0.547																																						dbGAP											0			14						C	THR/ALA,THR/ALA	0,4406		0,0,2203	76.0	74.0	75.0		403,403	-3.8	0.0	14		75	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	HEATR4	NM_203309.2,NM_001220484.1	58,58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	135/1027,135/1027	73989454	1,13005	2203	4300	6503	73059207	SO:0001583	missense	0			BC047590	CCDS9815.1, CCDS9815.2	14q24.3	2013-09-20			ENSG00000187105	ENSG00000187105			16761	protein-coding gene	gene with protein product						15489334	Standard	NM_203309		Approved	MGC48595	uc021rwf.2	Q86WZ0	OTTHUMG00000171602	ENST00000553558.1:c.403G>A	14.37:g.73989454C>T	ENSP00000450444:p.Ala135Thr	Somatic	135	0.00	0		2	33.33	1	WXS	Illumina HiSeq	Phase_IV	73059207	239	20.20	61	B7Z7V9|E9KL41	Missense_Mutation	SNP	HMMPfam_HEAT,superfamily_ARM-type_fold	p.A88T	ENST00000553558.1	37	c.262	CCDS9815.2	14	.	.	.	.	.	.	.	.	.	.	C	14.68	2.609078	0.46527	0.0	1.16E-4	ENSG00000187105	ENST00000553558;ENST00000334988;ENST00000556455	T	0.22539	1.95	6.07	-3.77	0.04346	.	1.341570	0.04732	N	0.421274	T	0.14442	0.0349	N	0.24115	0.695	0.09310	N	1	B	0.30763	0.294	B	0.27887	0.084	T	0.37888	-0.9686	10	0.45353	T	0.12	0.6013	11.7017	0.51575	0.2565:0.2035:0.54:0.0	.	135	Q86WZ0	HEAT4_HUMAN	T	135;88;135	ENSP00000450444:A135T	ENSP00000335447:A88T	A	-	1	0	HEATR4	73059207	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	0.003000	0.13083	-0.220000	0.09988	-0.165000	0.13383	GCT	-	NULL		0.547	HEATR4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	HEATR4	protein_coding	OTTHUMT00000414422.2	C	NM_203309		73059207	-1	no_errors	NM_203309.1	genbank	human	provisional	54_36p	missense	SNP	0.001	T
VPS13C	54832	genome.wustl.edu	37	15	62182560	62182560	+	Missense_Mutation	SNP	T	T	C			TCGA-AB-2871-03A-01W-0732-08	TCGA-AB-2871-11A-01W-0732-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3e8efa46-6045-4be1-b41b-e7b98f165d24	6c7c2063-37fc-45fc-8401-6169345b8c05	g.chr15:62182560T>C	ENST00000261517.5	-	67	9218	c.9145A>G	c.(9145-9147)Ata>Gta	p.I3049V	VPS13C_ENST00000395896.4_Missense_Mutation_p.I3049V|VPS13C_ENST00000249837.3_Missense_Mutation_p.I3006V|VPS13C_ENST00000395898.3_Missense_Mutation_p.I3006V	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						ACCCAGTGTATCTGGATGTTT	0.408																																						dbGAP											0			15											58.0	52.0	54.0					15																	62182560		2203	4300	6503	59969852	SO:0001583	missense	0			AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.9145A>G	15.37:g.62182560T>C	ENSP00000261517:p.Ile3049Val	Somatic	114	0.00	0		58	26.58	21	WXS	Illumina HiSeq	Phase_IV	59969852	121	22.78	36		Missense_Mutation	SNP	HMMPfam_DUF1162	p.I3049V	ENST00000261517.5	37	c.9145	CCDS32257.1	15	.	.	.	.	.	.	.	.	.	.	T	11.70	1.717694	0.30413	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.42900	0.96;0.96;0.96	5.5	4.39	0.52855	.	0.115206	0.64402	D	0.000015	T	0.32285	0.0824	L	0.35854	1.095	0.47737	D	0.999503	B;B;B;B	0.27765	0.034;0.144;0.069;0.188	B;B;B;B	0.28553	0.029;0.091;0.043;0.074	T	0.06197	-1.0840	10	0.27785	T	0.31	.	10.9218	0.47169	0.0:0.073:0.0:0.927	.	3006;3049;3006;3049	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	V	3006;3049;3049;3049	ENSP00000249837:I3006V;ENSP00000261517:I3049V;ENSP00000379233:I3049V	ENSP00000249837:I3006V	I	-	1	0	VPS13C	59969852	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.011000	0.49567	0.934000	0.37316	0.533000	0.62120	ATA	-	NULL		0.408	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	VPS13C	protein_coding	OTTHUMT00000415997.1	T	NM_017684		59969852	-1	no_errors	NM_020821.1	genbank	human	validated	54_36p	missense	SNP	1.000	C
LRFN3	79414	genome.wustl.edu	37	19	36435683	36435683	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2871-03A-01W-0732-08	TCGA-AB-2871-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3e8efa46-6045-4be1-b41b-e7b98f165d24	6c7c2063-37fc-45fc-8401-6169345b8c05	g.chr19:36435683C>T	ENST00000588831.1	+	4	2703	c.1649C>T	c.(1648-1650)tCg>tTg	p.S550L	LRFN3_ENST00000246529.3_Missense_Mutation_p.S550L|AF038458.3_ENST00000592518.1_lincRNA			Q9BTN0	LRFN3_HUMAN	leucine rich repeat and fibronectin type III domain containing 3	550					cell adhesion (GO:0007155)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)		p.S550*(1)|p.S550L(1)		cervix(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	12	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			ATCGTAGCCTCGGTACTGGTC	0.667																																						dbGAP											2	Substitution - Missense(1)|Substitution - Nonsense(1)	upper_aerodigestive_tract(1)|kidney(1)	19											41.0	29.0	33.0					19																	36435683		2203	4300	6503	41127523	SO:0001583	missense	0			BC003578	CCDS12483.1	19q13.13	2013-02-11				ENSG00000126243		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	28370	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 1"""	612809				12975309, 16495444, 16828986	Standard	NM_024509		Approved	MGC2656, SALM4, FIGLER1	uc002oco.3	Q9BTN0		ENST00000588831.1:c.1649C>T	19.37:g.36435683C>T	ENSP00000466989:p.Ser550Leu	Somatic	27	0.00	0		5	0.00	0	WXS	Illumina HiSeq	Phase_IV	41127523	72	17.24	15	Q6UY10	Missense_Mutation	SNP	HMMSmart_LRRNT,HMMSmart_LRRCT,HMMPfam_LRR_1,HMMSmart_LRR_TYP,HMMSmart_IGc2,HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like,HMMPfam_I-set,superfamily_SSF48726,superfamily_SSF52058	p.S550L	ENST00000588831.1	37	c.1649	CCDS12483.1	19	.	.	.	.	.	.	.	.	.	.	C	25.2	4.610405	0.87258	.	.	ENSG00000126243	ENST00000246529	T	0.56941	0.43	5.08	5.08	0.68730	.	0.000000	0.32655	N	0.005801	T	0.60919	0.2306	M	0.64170	1.965	0.52099	D	0.999941	D	0.57571	0.98	P	0.51016	0.656	T	0.64214	-0.6460	10	0.51188	T	0.08	.	15.9413	0.79756	0.0:1.0:0.0:0.0	.	550	Q9BTN0	LRFN3_HUMAN	L	550	ENSP00000246529:S550L	ENSP00000246529:S550L	S	+	2	0	LRFN3	41127523	1.000000	0.71417	0.848000	0.33437	0.456000	0.32438	7.745000	0.85046	2.359000	0.80004	0.591000	0.81541	TCG	-	NULL		0.667	LRFN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LRFN3	protein_coding	OTTHUMT00000457403.2	C	NM_024509		41127523	+1	no_errors	NM_024509.1	genbank	human	provisional	54_36p	missense	SNP	0.979	T
KCNJ6	3763	genome.wustl.edu	37	21	39086792	39086792	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2871-03A-01W-0732-08	TCGA-AB-2871-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3e8efa46-6045-4be1-b41b-e7b98f165d24	6c7c2063-37fc-45fc-8401-6169345b8c05	g.chr21:39086792C>T	ENST00000609713.1	-	3	1257	c.668G>A	c.(667-669)cGg>cAg	p.R223Q	KCNJ6_ENST00000288309.6_Missense_Mutation_p.R223Q|KCNJ6-IT1_ENST00000435001.1_RNA	NM_002240.3	NP_002231.1	P48051	KCNJ6_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 6	223					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	G-protein activated inward rectifier potassium channel activity (GO:0015467)|inward rectifier potassium channel activity (GO:0005242)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	22					Halothane(DB01159)	GTCCCCTACCCGGAACATCAG	0.512																																					Pancreas(48;379 1118 2936 19024 28214)	dbGAP											0			21											71.0	70.0	70.0					21																	39086792		1926	4154	6080	38008662	SO:0001583	missense	0			U24660	CCDS42927.1	21q22.1	2011-07-05			ENSG00000157542	ENSG00000157542		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6267	protein-coding gene	gene with protein product		600877		KCNJ7		7796919, 16382105	Standard	NM_002240		Approved	Kir3.2, GIRK2, KATP2, BIR1, hiGIRK2	uc002ywo.3	P48051	OTTHUMG00000086667	ENST00000609713.1:c.668G>A	21.37:g.39086792C>T	ENSP00000477437:p.Arg223Gln	Somatic	42	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	38008662	72	27.00	27	Q3MJ74|Q53WW6	Missense_Mutation	SNP	HMMPfam_IRK,superfamily_Ig_E-set,superfamily_SSF81324	p.R223Q	ENST00000609713.1	37	c.668	CCDS42927.1	21	.	.	.	.	.	.	.	.	.	.	C	33	5.283424	0.95489	.	.	ENSG00000157542	ENST00000400482;ENST00000288309	D;D	0.97089	-4.24;-4.24	6.17	6.17	0.99709	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.000000	0.85682	D	0.000000	D	0.98745	0.9578	M	0.86573	2.825	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99004	1.0812	10	0.87932	D	0	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	223	P48051	IRK6_HUMAN	Q	223	ENSP00000383330:R223Q;ENSP00000288309:R223Q	ENSP00000288309:R223Q	R	-	2	0	KCNJ6	38008662	1.000000	0.71417	0.993000	0.49108	0.999000	0.98932	7.818000	0.86416	2.941000	0.99782	0.655000	0.94253	CGG	-	HMMPfam_IRK,superfamily_Ig_E-set		0.512	KCNJ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KCNJ6	protein_coding	OTTHUMT00000194828.2	C	NM_002240		38008662	-1	no_errors	NM_002240.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
NPM1	4869	genome.wustl.edu	37	5	170837543	170837544	+	Frame_Shift_Ins	INS	-	-	TCTG	rs17850940		TCGA-AB-2871-03A-01W-0732-08	TCGA-AB-2871-11A-01W-0732-08	-	-	-	TCTG	-	-	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3e8efa46-6045-4be1-b41b-e7b98f165d24	6c7c2063-37fc-45fc-8401-6169345b8c05	g.chr5:170837543_170837544insTCTG	ENST00000296930.5	+	11	1160_1161	c.859_860insTCTG	c.(859-861)ctcfs	p.-287fs	NPM1_ENST00000517671.1_Frame_Shift_Ins_p.-287fs|NPM1_ENST00000351986.6_Frame_Shift_Ins_p.-258fs	NM_002520.6	NP_002511.1	P06748	NPM_HUMAN	nucleophosmin (nucleolar phosphoprotein B23, numatrin)						cell aging (GO:0007569)|CENP-A containing nucleosome assembly (GO:0034080)|centrosome cycle (GO:0007098)|DNA repair (GO:0006281)|intracellular protein transport (GO:0006886)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of centrosome duplication (GO:0010826)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|nucleocytoplasmic transport (GO:0006913)|nucleosome assembly (GO:0006334)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of translation (GO:0045727)|protein localization (GO:0008104)|protein oligomerization (GO:0051259)|regulation of centriole replication (GO:0046599)|regulation of eIF2 alpha phosphorylation by dsRNA (GO:0060735)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of endoribonuclease activity (GO:0060699)|response to stress (GO:0006950)|ribosome assembly (GO:0042255)|signal transduction (GO:0007165)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle pole centrosome (GO:0031616)	histone binding (GO:0042393)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)|ribosomal large subunit binding (GO:0043023)|ribosomal small subunit binding (GO:0043024)|RNA binding (GO:0003723)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|unfolded protein binding (GO:0051082)	p.W288fs*12(7)|p.W288fs*>9(5)|p.L287fs*11(2)|p.L287F(1)	NPM1/ALK(632)	central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4261)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	4269	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TATTCAAGATCTCTGGCAGTGG	0.317			"""T, F """	"""ALK, RARA, MLF1"""	"""NHL, APL, AML"""																																	dbGAP		Dom	yes		5	5q35	4869	"""nucleophosmin (nucleolar phosphoprotein B23, numatrin)"""		L	15	Insertion - Frameshift(14)|Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(15)	5																																								170770149	SO:0001589	frameshift_variant	0			M26697	CCDS4376.1, CCDS4377.1, CCDS43399.1	5q35.1	2014-09-17			ENSG00000181163	ENSG00000181163			7910	protein-coding gene	gene with protein product	"""nucleolar phosphoprotein B23"", ""numatrin"", ""nucleophosmin/nucleoplasmin family, member 1"""	164040				8471164, 8122112	Standard	NM_002520		Approved	B23, NPM	uc003mbi.3	P06748	OTTHUMG00000130465	ENST00000296930.5:c.860_863dupTCTG	5.37:g.170837544_170837547dupTCTG	ENSP00000296930:p.Leu287fs	Somatic	NA	NA	NA		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	170770148	NA	NA	NA	A8K3N7|B5BU00|D3DQL6|P08693|Q12826|Q13440|Q13441|Q14115|Q5EU94|Q5EU95|Q5EU96|Q5EU97|Q5EU98|Q5EU99|Q6V962|Q8WTW5|Q96AT6|Q96DC4|Q96EA5|Q9BYG9|Q9UDJ7	Frame_Shift_Ins	INS	HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain	p.W288fs	ENST00000296930.5	37	c.859_860	CCDS4376.1	5																																																																																			-	NULL		0.317	NPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NPM1	protein_coding	OTTHUMT00000252858.2	-	NM_002520		170770149	+1	no_errors	NM_002520.1	genbank	human	validated	54_36p	frame_shift_ins	INS	1.000:1.000	TCTG
FLT3	2322	genome.wustl.edu	37	13	28608262	28608263	+	In_Frame_Ins	INS	-	-	TCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCTGTACCATC			TCGA-AB-2871-03A-01W-0732-08	TCGA-AB-2871-11A-01W-0732-08	-	-	-	TCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCTGTACCATC	-	-	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	3e8efa46-6045-4be1-b41b-e7b98f165d24	6c7c2063-37fc-45fc-8401-6169345b8c05	g.chr13:28608262_28608263insTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCTGTACCATC	ENST00000241453.7	-	14	1874_1875	c.1793_1794insGATGGTACAGGTGACCGGCTCCTCAGATAATGAGTACTTCTACGTTGATTTCAGAGAATATGA	c.(1792-1794)gaa>gaGATGGTACAGGTGACCGGCTCCTCAGATAATGAGTACTTCTACGTTGATTTCAGAGAATATGAa	p.598_598E>EMVQVTGSSDNEYFYVDFREYE	FLT3_ENST00000380982.4_In_Frame_Ins_p.598_598E>EMVQVTGSSDNEYFYVDFREYE|FLT3_ENST00000537084.1_In_Frame_Ins_p.598_598E>EMVQVTGSSDNEYFYVDFREYE	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	598					B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.597_598>DYVDFREY(1)|p.E598_Y599ins22(1)|p.E598_Y599ins25(1)|p.E598_Y599ins14(1)|p.E598>DMISPEDMK(1)|p.E598_Y599insFYVDFREYE(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	TGAGATCATATTCATATTCTCT	0.376			"""Mis, O"""		"""AML, ALL"""																																	dbGAP		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	6	Insertion - In frame(4)|Complex - insertion inframe(2)	haematopoietic_and_lymphoid_tissue(6)	13																																								27506263	SO:0001652	inframe_insertion	0			U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.1731_1793dupGATGGTACAGGTGACCGGCTCCTCAGATAATGAGTACTTCTACGTTGATTTCAGAGAATATGA	13.37:g.28608262_28608263insTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCTGTACCATC	ENSP00000241453:p.MetValGlnValThrGlySerSerAspAsnGluTyrPheTyrValAspPheArgGluTyrGlu598dup	Somatic	NA	NA	NA		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	27506262	NA	NA	NA	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	In_Frame_Ins	INS	HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726	p.599in_frame_insMVQVTGSSDNEYFYVDFREYE	ENST00000241453.7	37	c.1794_1793	CCDS31953.1	13																																																																																			-	superfamily_Kinase_like		0.376	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	FLT3	protein_coding	OTTHUMT00000044319.2	-			27506263	-1	no_errors	NM_004119.2	genbank	human	reviewed	54_36p	in_frame_ins	INS	0.789:0.821	TCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCTGTACCATC
