#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
Unknown	0	genome.wustl.edu	37	Unknown	0	0	+	IGR	SNP	G	G	A			TCGA-AB-2885-03A-01W-0732-08	TCGA-AB-2885-11A-01W-0732-08	G	G	G	A	G	G	Verified	Invalid:failed_liftOver	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	d5c78933-a17c-449c-a24d-730ea0f7a9cd	f62da227-622a-4139-9229-acd0939a17c3	g.chrUnknown:0G>A								None (None upstream) : None (None downstream)																								0.0																																						dbGAP											0			MT																																								8156	SO:0001628	intergenic_variant	0																															Unknown.37:g.0G>A		Somatic	2103	0.09	2		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	8156	940	26.71	343		Silent	SNP	PatternScan_COX2,HMMPfam_COX2,superfamily_Cupredoxins,HMMPfam_COX2_TM,superfamily_Cytochrome^^_^^c^^_^^oxidase^^_^^subunit^^_^^II-like^^_^^transmembrane^^_^^region	p.G190		37	c.570		MT																																																																																			-	PatternScan_COX2,HMMPfam_COX2,superfamily_Cupredoxins	0	0					MT-CO2			G			8156	+1	no_errors	ENST00000361739	ensembl	human	known	54_36p	silent	SNP	NULL	A
MTMR8	55613	genome.wustl.edu	37	X	63574712	63574712	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2885-03A-01W-0732-08	TCGA-AB-2885-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	d5c78933-a17c-449c-a24d-730ea0f7a9cd	f62da227-622a-4139-9229-acd0939a17c3	g.chrX:63574712C>T	ENST00000374852.3	-	4	480	c.413G>A	c.(412-414)cGt>cAt	p.R138H	MTMR8_ENST00000453546.1_Missense_Mutation_p.R138H	NM_017677.3	NP_060147.2	Q96EF0	MTMR8_HUMAN	myotubularin related protein 8	138	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.					nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.0?(1)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|skin(3)	37						TATTCCCATACGCCCAAAGTC	0.378																																						dbGAP											1	Whole gene deletion(1)	ovary(1)	X											157.0	123.0	135.0					X																	63574712		2203	4300	6503	63491437	SO:0001583	missense	0			AK000133	CCDS14379.1	Xq11.2-q12	2013-01-11			ENSG00000102043	ENSG00000102043		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	16825	protein-coding gene	gene with protein product						11275328	Standard	NM_017677		Approved	FLJ20126	uc004dvs.3	Q96EF0	OTTHUMG00000021707	ENST00000374852.3:c.413G>A	X.37:g.63574712C>T	ENSP00000363985:p.Arg138His	Somatic	199	1.97	4		0	100.00	3	WXS	Illumina HiSeq	Phase_IV	63491437	14	77.94	53	Q5JT99|Q9NXP6	Missense_Mutation	SNP	HMMSmart_SM00404,HMMPfam_Myotub-related,PatternScan_TYR_PHOSPHATASE_1,superfamily_PH domain-like,superfamily_(Phosphotyrosine protein) phosphatases II	p.R138H	ENST00000374852.3	37	c.413	CCDS14379.1	X	.	.	.	.	.	.	.	.	.	.	C	15.27	2.784315	0.49997	.	.	ENSG00000102043	ENST00000453546;ENST00000374852;ENST00000247400	D;D	0.95949	-3.86;-3.86	2.67	0.83	0.18854	Myotubularin phosphatase domain (1);	0.000000	0.42682	U	0.000668	D	0.94905	0.8353	H	0.95950	3.745	0.23459	N	0.997637	B;P	0.52842	0.018;0.956	B;B	0.41691	0.001;0.364	D	0.87198	0.2239	10	0.17369	T	0.5	.	5.6204	0.17453	0.1941:0.6863:0.0:0.1196	.	138;138	B4DQL0;Q96EF0	.;MTMR8_HUMAN	H	138;138;137	ENSP00000394003:R138H;ENSP00000363985:R138H	ENSP00000247400:R137H	R	-	2	0	MTMR8	63491437	0.982000	0.34865	0.051000	0.19133	0.763000	0.43281	2.226000	0.42963	0.096000	0.17463	0.506000	0.49869	CGT	-	superfamily_(Phosphotyrosine protein) phosphatases II		0.378	MTMR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MTMR8	protein_coding	OTTHUMT00000056949.2	C	NM_017677		63491437	-1	no_errors	NM_017677.2	genbank	human	provisional	54_36p	missense	SNP	0.799	T
ITGA10	8515	genome.wustl.edu	37	1	145541826	145541826	+	Missense_Mutation	SNP	C	C	T	rs140404631		TCGA-AB-2885-03A-01W-0732-08	TCGA-AB-2885-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	d5c78933-a17c-449c-a24d-730ea0f7a9cd	f62da227-622a-4139-9229-acd0939a17c3	g.chr1:145541826C>T	ENST00000369304.3	+	29	3524	c.3349C>T	c.(3349-3351)Cgg>Tgg	p.R1117W	RP11-315I20.3_ENST00000415065.2_RNA|ITGA10_ENST00000539363.1_Missense_Mutation_p.R974W|ITGA10_ENST00000538811.1_Missense_Mutation_p.R986W	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	1117					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	integrin alpha10-beta1 complex (GO:0034680)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GGTTCAGACCCGGCCTATCCT	0.532													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18710	0.0		0.0	False		,,,				2504	0.0					dbGAP											0			1						C	TRP/ARG	3,4403	6.2+/-15.9	0,3,2200	136.0	116.0	123.0		3349	6.2	0.4	1	dbSNP_134	123	1,8599	1.2+/-3.3	0,1,4299	no	missense	ITGA10	NM_003637.3	101	0,4,6499	TT,TC,CC		0.0116,0.0681,0.0308	probably-damaging	1117/1168	145541826	4,13002	2203	4300	6503	144253183	SO:0001583	missense	0			AF074015	CCDS72869.1	1q21.1	2010-03-23			ENSG00000143127	ENSG00000143127		"""Integrins"""	6135	protein-coding gene	gene with protein product		604042				9685391, 10702680	Standard	NM_003637		Approved		uc001eoa.3	O75578	OTTHUMG00000013751	ENST00000369304.3:c.3349C>T	1.37:g.145541826C>T	ENSP00000358310:p.Arg1117Trp	Somatic	282	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	144253183	78	48.39	75	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Missense_Mutation	SNP	HMMPfam_VWA,HMMSmart_SM00327,HMMPfam_FG-GAP,HMMSmart_SM00191,HMMPfam_Integrin_alpha2,superfamily_vWA-like,superfamily_Integrin domains,superfamily_Integrin alpha N-terminal domain	p.R1117W	ENST00000369304.3	37	c.3349	CCDS918.1	1	.	.	.	.	.	.	.	.	.	.	C	14.71	2.615663	0.46631	6.81E-4	1.16E-4	ENSG00000143127	ENST00000369304;ENST00000543043;ENST00000539363;ENST00000538811	T;T;T	0.58940	0.3;0.31;0.31	6.16	6.16	0.99307	.	0.354215	0.28659	N	0.014564	T	0.54287	0.1849	L	0.50333	1.59	0.30741	N	0.746132	D;D;D;D	0.71674	0.998;0.998;0.996;0.99	P;P;P;P	0.56916	0.809;0.809;0.53;0.53	T	0.55237	-0.8172	10	0.39692	T	0.17	.	13.1939	0.59728	0.1591:0.8409:0.0:0.0	.	1045;986;974;1117	F5H3T9;F5GY13;B2RTV5;O75578	.;.;.;ITA10_HUMAN	W	1117;1045;974;986	ENSP00000358310:R1117W;ENSP00000439894:R974W;ENSP00000440011:R986W	ENSP00000358310:R1117W	R	+	1	2	ITGA10	144253183	0.028000	0.19301	0.372000	0.25991	0.149000	0.21700	2.975000	0.49281	2.937000	0.99478	0.650000	0.86243	CGG	-	superfamily_Integrin domains		0.532	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ITGA10	protein_coding	OTTHUMT00000038537.2	C	NM_003637		144253183	+1	no_errors	NM_003637.3	genbank	human	reviewed	54_36p	missense	SNP	0.811	T
LRP1B	53353	genome.wustl.edu	37	2	141526782	141526782	+	Splice_Site	SNP	C	C	T			TCGA-AB-2885-03A-01W-0732-08	TCGA-AB-2885-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	d5c78933-a17c-449c-a24d-730ea0f7a9cd	f62da227-622a-4139-9229-acd0939a17c3	g.chr2:141526782C>T	ENST00000389484.3	-	35	6729	c.5758G>A	c.(5758-5760)Gaa>Aaa	p.E1920K		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1920					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		AGCTATTTACCTGCATGGAAA	0.343										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)	dbGAP											0			2											66.0	67.0	67.0					2																	141526782		2203	4300	6503	141243252	SO:0001630	splice_region_variant	0			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.5758+1G>A	2.37:g.141526782C>T		Somatic	104	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	141243252	39	41.79	28	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	HMMPfam_Ldl_recept_b,HMMSmart_LY,PatternScan_ASX_HYDROXYL,HMMPfam_NHL,HMMSmart_EGF_CA,HMMPfam_Ldl_recept_a,HMMSmart_LDLa,PatternScan_LDLRA_1,superfamily_LDL_rcpt_classA_cys-rich,HMMPfam_EGF,HMMSmart_EGF,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_CA,HMMPfam_EGF_2,PatternScan_EGF_CA,superfamily_SSF57196,superfamily_SSF63825	p.E1920K	ENST00000389484.3	37	c.5758	CCDS2182.1	2	.	.	.	.	.	.	.	.	.	.	C	18.09	3.546754	0.65198	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.91068	-2.78	5.28	5.28	0.74379	Six-bladed beta-propeller, TolB-like (1);	0.071658	0.56097	U	0.000037	D	0.83640	0.5298	N	0.13235	0.315	0.52501	D	0.999954	B	0.19817	0.039	B	0.24006	0.05	T	0.77683	-0.2496	9	.	.	.	.	19.0962	0.93253	0.0:1.0:0.0:0.0	.	1920	Q9NZR2	LRP1B_HUMAN	K	1920;1858	ENSP00000374135:E1920K	.	E	-	1	0	LRP1B	141243252	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.640000	0.83355	2.748000	0.94277	0.650000	0.86243	GAA	-	HMMSmart_LY,superfamily_SSF63825		0.343	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LRP1B	protein_coding	OTTHUMT00000254736.2	C	NM_018557	Missense_Mutation	141243252	-1	no_errors	NM_018557.2	genbank	human	validated	54_36p	missense	SNP	1.000	T
XIRP2	129446	genome.wustl.edu	37	2	168107404	168107404	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2885-03A-01W-0732-08	TCGA-AB-2885-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	d5c78933-a17c-449c-a24d-730ea0f7a9cd	f62da227-622a-4139-9229-acd0939a17c3	g.chr2:168107404G>A	ENST00000409195.1	+	9	9591	c.9502G>A	c.(9502-9504)Gca>Aca	p.A3168T	XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.A3168T|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.A2946T|XIRP2_ENST00000420519.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2993					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AATTCACAGAGCAAACACTTC	0.483																																						dbGAP											0			2											84.0	83.0	83.0					2																	168107404		1903	4119	6022	167815650	SO:0001583	missense	0			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.9502G>A	2.37:g.168107404G>A	ENSP00000386840:p.Ala3168Thr	Somatic	179	0.00	0		1	0.00	0	WXS	Illumina HiSeq	Phase_IV	167815650	50	46.24	43	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	HMMPfam_Xin	p.A3168T	ENST00000409195.1	37	c.9502	CCDS42769.1	2	.	.	.	.	.	.	.	.	.	.	G	1.241	-0.621347	0.03636	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.02890	4.12;4.12;4.12	5.88	-0.0743	0.13731	.	0.598876	0.17100	N	0.187030	T	0.01523	0.0049	N	0.12961	0.28	0.09310	N	1	B;B;B	0.10296	0.001;0.003;0.001	B;B;B	0.10450	0.002;0.005;0.004	T	0.46034	-0.9220	10	0.29301	T	0.29	-0.4656	1.7872	0.03044	0.3615:0.1238:0.3875:0.1272	.	2993;2993;2946	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	T	3168;3168;2946;582	ENSP00000386840:A3168T;ENSP00000295237:A3168T;ENSP00000387255:A2946T	ENSP00000295237:A3168T	A	+	1	0	XIRP2	167815650	0.000000	0.05858	0.000000	0.03702	0.174000	0.22865	-0.466000	0.06672	-0.310000	0.08766	-0.252000	0.11476	GCA	-	NULL		0.483	XIRP2-001	KNOWN	basic|CCDS	protein_coding	XIRP2	protein_coding	OTTHUMT00000333547.1	G	NM_152381		167815650	+1	no_errors	NM_152381.2	genbank	human	validated	54_36p	missense	SNP	0.001	A
BSN	8927	genome.wustl.edu	37	3	49689598	49689598	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2885-03A-01W-0732-08	TCGA-AB-2885-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	d5c78933-a17c-449c-a24d-730ea0f7a9cd	f62da227-622a-4139-9229-acd0939a17c3	g.chr3:49689598C>T	ENST00000296452.4	+	5	2723	c.2609C>T	c.(2608-2610)gCc>gTc	p.A870V		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	870					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		CGTGGCCTGGCCAAACATGGC	0.622																																						dbGAP											0			3											32.0	35.0	34.0					3																	49689598		2202	4299	6501	49664602	SO:0001583	missense	0			AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"""zinc finger protein 231"", ""neuronal double zinc finger protein"""	604020	"""bassoon (presynaptic cytomatrix protein)"""	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.2609C>T	3.37:g.49689598C>T	ENSP00000296452:p.Ala870Val	Somatic	65	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	49664602	1	88.89	8	O43161|Q7LGH3	Missense_Mutation	SNP	HMMPfam_zf-piccolo,superfamily_FYVE_PHD_ZnF	p.A870V	ENST00000296452.4	37	c.2609	CCDS2800.1	3	.	.	.	.	.	.	.	.	.	.	C	10.07	1.250540	0.22880	.	.	ENSG00000164061	ENST00000296452	T	0.18016	2.24	5.02	4.15	0.48705	.	0.205916	0.40385	N	0.001117	T	0.13798	0.0334	L	0.44542	1.39	0.22880	N	0.998611	B	0.06786	0.001	B	0.04013	0.001	T	0.17077	-1.0381	10	0.40728	T	0.16	.	7.1355	0.25525	0.2881:0.6304:0.0:0.0815	.	870	Q9UPA5	BSN_HUMAN	V	870	ENSP00000296452:A870V	ENSP00000296452:A870V	A	+	2	0	BSN	49664602	0.005000	0.15991	0.990000	0.47175	0.884000	0.51177	0.303000	0.19210	1.108000	0.41662	0.561000	0.74099	GCC	-	NULL		0.622	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	BSN	protein_coding	OTTHUMT00000258164.1	C	NM_003458		49664602	+1	no_errors	NM_003458.3	genbank	human	validated	54_36p	missense	SNP	1.000	T
STRIP2	57464	genome.wustl.edu	37	7	129093996	129093996	+	Missense_Mutation	SNP	T	T	C			TCGA-AB-2885-03A-01W-0732-08	TCGA-AB-2885-11A-01W-0732-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	d5c78933-a17c-449c-a24d-730ea0f7a9cd	f62da227-622a-4139-9229-acd0939a17c3	g.chr7:129093996T>C	ENST00000249344.2	+	6	584	c.544T>C	c.(544-546)Tgt>Cgt	p.C182R	STRIP2_ENST00000435494.2_Missense_Mutation_p.C182R	NM_020704.2	NP_065755.1	Q9ULQ0	STRP2_HUMAN	striatin interacting protein 2	182					cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)											CAGCCAGGCCTGTAGCAGTGC	0.498																																						dbGAP											0			7											69.0	66.0	67.0					7																	129093996		2203	4300	6503	128881232	SO:0001583	missense	0			AB032996	CCDS34752.1, CCDS47709.1	7q32.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000128578	ENSG00000128578			22209	protein-coding gene	gene with protein product	"""FAR11 factor arrest 11 homolog B (yeast)"""		"""family with sequence similarity 40, member B"""	FAM40B		22782902, 22298706, 18782753	Standard	NM_020704		Approved	KIAA1170, FAR11B	uc011koy.2	Q9ULQ0	OTTHUMG00000157695	ENST00000249344.2:c.544T>C	7.37:g.129093996T>C	ENSP00000249344:p.Cys182Arg	Somatic	215	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	128881232	10	67.74	21	Q8WUZ4	Missense_Mutation	SNP	HMMPfam_N1221	p.C182R	ENST00000249344.2	37	c.544	CCDS34752.1	7	.	.	.	.	.	.	.	.	.	.	T	18.29	3.591090	0.66219	.	.	ENSG00000128578	ENST00000249344;ENST00000435494	T;T	0.47177	0.86;0.85	5.51	4.33	0.51752	.	0.049518	0.85682	D	0.000000	T	0.52980	0.1768	M	0.80616	2.505	0.80722	D	1	P;P	0.44946	0.846;0.565	P;B	0.46629	0.522;0.444	T	0.51934	-0.8642	10	0.17832	T	0.49	-3.6316	10.7793	0.46369	0.0:0.0:0.1594:0.8406	.	182;182	Q9ULQ0;Q9ULQ0-2	FA40B_HUMAN;.	R	182	ENSP00000249344:C182R;ENSP00000392393:C182R	ENSP00000249344:C182R	C	+	1	0	FAM40B	128881232	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.917000	0.69989	0.897000	0.36392	0.459000	0.35465	TGT	-	HMMPfam_N1221		0.498	STRIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM40B	protein_coding	OTTHUMT00000349418.1	T	NM_001134336		128881232	+1	no_errors	NM_020704.1	genbank	human	validated	54_36p	missense	SNP	1.000	C
RFX3	5991	genome.wustl.edu	37	9	3271010	3271010	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2885-03A-01W-0732-08	TCGA-AB-2885-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	d5c78933-a17c-449c-a24d-730ea0f7a9cd	f62da227-622a-4139-9229-acd0939a17c3	g.chr9:3271010C>T	ENST00000382004.3	-	11	1506	c.1195G>A	c.(1195-1197)Gaa>Aaa	p.E399K	RFX3_ENST00000358730.2_Missense_Mutation_p.E399K|RFX3_ENST00000302303.1_Missense_Mutation_p.E399K	NM_001282116.1|NM_134428.1	NP_001269045.1|NP_602304.1	P48380	RFX3_HUMAN	regulatory factor X, 3 (influences HLA class II expression)	399					cell maturation (GO:0048469)|cilium assembly (GO:0042384)|cilium-dependent cell motility (GO:0060285)|endocrine pancreas development (GO:0031018)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of insulin secretion (GO:0050796)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|type B pancreatic cell maturation (GO:0072560)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(11)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(50;0.00124)|Lung(2;0.0337)		GACCTCGATTCGGTAATGGTA	0.388																																						dbGAP											0			9											166.0	151.0	156.0					9																	3271010		2203	4300	6503	3261010	SO:0001583	missense	0			AI811824	CCDS6449.1, CCDS6450.1, CCDS75809.1	9p24.2	2008-02-05			ENSG00000080298	ENSG00000080298			9984	protein-coding gene	gene with protein product		601337				8289803	Standard	XM_005251534		Approved		uc003zhr.3	P48380	OTTHUMG00000019456	ENST00000382004.3:c.1195G>A	9.37:g.3271010C>T	ENSP00000371434:p.Glu399Lys	Somatic	386	0.00	0		11	38.89	7	WXS	Illumina HiSeq	Phase_IV	3261010	93	42.24	68	A8K0H5|D3DRH8|D3DRH9|Q5JTL7|Q5JTL8|Q6NW13|Q8WTU4|Q95HL5|Q95HL6	Missense_Mutation	SNP	"HMMPfam_RFX_DNA_binding,HMMPfam_RFX1_trans_act,superfamily_""Winged helix"" DNA-binding domain"	p.E399K	ENST00000382004.3	37	c.1195	CCDS6449.1	9	.	.	.	.	.	.	.	.	.	.	C	14.99	2.701281	0.48307	.	.	ENSG00000080298	ENST00000382004;ENST00000358730;ENST00000302303	T;T;T	0.07216	3.21;3.21;3.21	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.18045	0.0433	L	0.36672	1.1	0.80722	D	1	D;P;P	0.65815	0.995;0.457;0.702	D;B;B	0.68192	0.956;0.024;0.174	T	0.03566	-1.1024	10	0.06891	T	0.86	-15.3284	19.7151	0.96113	0.0:1.0:0.0:0.0	.	399;399;399	P48380-3;P48380-2;P48380	.;.;RFX3_HUMAN	K	399	ENSP00000371434:E399K;ENSP00000351574:E399K;ENSP00000303847:E399K	ENSP00000303847:E399K	E	-	1	0	RFX3	3261010	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	4.544000	0.60691	2.742000	0.94016	0.650000	0.86243	GAA	-	NULL		0.388	RFX3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	RFX3	protein_coding	OTTHUMT00000051545.1	C	NM_002919		3261010	-1	no_errors	NM_134428.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
MRE11A	4361	genome.wustl.edu	37	11	94192645	94192645	+	Missense_Mutation	SNP	G	G	C			TCGA-AB-2885-03A-01W-0732-08	TCGA-AB-2885-11A-01W-0732-08	G	G	G	C	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	d5c78933-a17c-449c-a24d-730ea0f7a9cd	f62da227-622a-4139-9229-acd0939a17c3	g.chr11:94192645G>C	ENST00000323929.3	-	13	1651	c.1429C>G	c.(1429-1431)Cag>Gag	p.Q477E	MRE11A_ENST00000407439.3_Missense_Mutation_p.Q480E|MRE11A_ENST00000393241.4_Missense_Mutation_p.Q477E|MRE11A_ENST00000323977.3_Missense_Mutation_p.Q477E	NM_005591.3	NP_005582.1	P49959	MRE11_HUMAN	MRE11 meiotic recombination 11 homolog A (S. cerevisiae)	477					base-excision repair (GO:0006284)|cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|innate immune response (GO:0045087)|intra-S DNA damage checkpoint (GO:0031573)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of DNA endoreduplication (GO:0032876)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair (GO:0006289)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of type I interferon production (GO:0032481)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|sister chromatid cohesion (GO:0007062)|synapsis (GO:0007129)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromatin (GO:0000785)|cytosol (GO:0005829)|Mre11 complex (GO:0030870)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|manganese ion binding (GO:0030145)|nuclease activity (GO:0004518)|protein C-terminus binding (GO:0008022)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			breast(5)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	29		Acute lymphoblastic leukemia(157;2.37e-05)|all_hematologic(158;0.00824)				TTTTCCAACTGGTATTTCACT	0.413								Homologous recombination	Ataxia-Telangiectasia-Like Disorder																													dbGAP											0			11											202.0	185.0	190.0					11																	94192645		2201	4298	6499	93832293	SO:0001583	missense	0	Familial Cancer Database	ATLD	BC063458	CCDS8298.1, CCDS8299.1	11q21	2014-09-17	2001-11-28		ENSG00000020922	ENSG00000020922			7230	protein-coding gene	gene with protein product	"""AT-like disease"""	600814	"""meiotic recombination (S. cerevisiae) 11 homolog A"""	MRE11		8530104	Standard	XM_005274007		Approved	ATLD	uc001peu.2	P49959	OTTHUMG00000167780	ENST00000323929.3:c.1429C>G	11.37:g.94192645G>C	ENSP00000325863:p.Gln477Glu	Somatic	331	0.30	1		53	39.77	35	WXS	Illumina HiSeq	Phase_IV	93832293	165	31.40	76	O43475	Missense_Mutation	SNP	HMMPfam_Metallophos,HMMPfam_Mre11_DNA_bind,superfamily_Metallo-dependent phosphatases	p.Q477E	ENST00000323929.3	37	c.1429	CCDS8299.1	11	.	.	.	.	.	.	.	.	.	.	G	26.9	4.785108	0.90282	.	.	ENSG00000020922	ENST00000323929;ENST00000407439;ENST00000323977;ENST00000393241	T;T;T;T	0.73681	-0.77;-0.77;-0.75;-0.77	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.79857	0.4518	M	0.64997	1.995	0.80722	D	1	D;B;P	0.56521	0.976;0.216;0.714	P;B;B	0.55785	0.784;0.284;0.406	T	0.73827	-0.3860	10	0.06365	T	0.9	-14.8465	20.0493	0.97618	0.0:0.0:1.0:0.0	.	480;477;477	B3KTC7;P49959-2;P49959	.;.;MRE11_HUMAN	E	477;480;477;477	ENSP00000325863:Q477E;ENSP00000385614:Q480E;ENSP00000326094:Q477E;ENSP00000376933:Q477E	ENSP00000325863:Q477E	Q	-	1	0	MRE11A	93832293	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	9.787000	0.99055	2.745000	0.94114	0.491000	0.48974	CAG	-	NULL		0.413	MRE11A-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	MRE11A	protein_coding	OTTHUMT00000396237.3	G	NM_005591		93832293	-1	no_errors	NM_005591.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	C
PTPN11	5781	genome.wustl.edu	37	12	112888163	112888163	+	Missense_Mutation	SNP	G	G	T	rs121918471|rs397507508|rs80338836|rs397507509		TCGA-AB-2885-03A-01W-0732-08	TCGA-AB-2885-11A-01W-0732-08	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	d5c78933-a17c-449c-a24d-730ea0f7a9cd	f62da227-622a-4139-9229-acd0939a17c3	g.chr12:112888163G>T	ENST00000351677.2	+	3	377	c.179G>T	c.(178-180)gGt>gTt	p.G60V	PTPN11_ENST00000392597.1_Missense_Mutation_p.G60V	NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	60	SH2 1. {ECO:0000255|PROSITE- ProRule:PRU00191}.		G -> A (in NS1). {ECO:0000269|PubMed:11992261}.|G -> V (in myelodysplastic syndrome). {ECO:0000269|PubMed:12717436}.		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.G60V(20)|p.G60A(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						CAGAACACTGGTGATTACTAT	0.418			Mis		"""JMML, AML, MDS"""		Noonan Syndrome		Noonan syndrome																													dbGAP		Dom	yes		12	12q24.1	5781	"""protein tyrosine phosphatase, non-receptor type 11"""	yes	L	21	Substitution - Missense(21)	haematopoietic_and_lymphoid_tissue(21)	12	GRCh37	CD041931|CM021126|CX060726	PTPN11	D|M|X	rs80338836						140.0	132.0	135.0					12																	112888163		2203	4300	6503	111372546	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.179G>T	12.37:g.112888163G>T	ENSP00000340944:p.Gly60Val	Somatic	62	0.00	0		75	38.52	47	WXS	Illumina HiSeq	Phase_IV	111372546	52	23.19	16	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.G60V	ENST00000351677.2	37	c.179	CCDS9163.1	12	.	.	.	.	.	.	.	.	.	.	G	32	5.185189	0.94885	.	.	ENSG00000179295	ENST00000392597;ENST00000351677;ENST00000392596	D;D	0.96856	-4.15;-4.15	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	D	0.98845	0.9610	H	0.95574	3.69	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.99170	1.0864	10	0.87932	D	0	.	20.2787	0.98501	0.0:0.0:1.0:0.0	.	60;60	Q06124-2;Q06124-3	.;.	V	60	ENSP00000376376:G60V;ENSP00000340944:G60V	ENSP00000340944:G60V	G	+	2	0	PTPN11	111372546	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.860000	0.99555	2.798000	0.96311	0.650000	0.86243	GGT	-	HMMPfam_SH2,HMMSmart_SM00252,superfamily_SH2 domain		0.418	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PTPN11	protein_coding	OTTHUMT00000259496.2	G			111372546	+1	no_errors	NM_002834.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
TP53	7157	genome.wustl.edu	37	17	7578272	7578272	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2885-03A-01W-0732-08	TCGA-AB-2885-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	d5c78933-a17c-449c-a24d-730ea0f7a9cd	f62da227-622a-4139-9229-acd0939a17c3	g.chr17:7578272G>A	ENST00000269305.4	-	6	766	c.577C>T	c.(577-579)Cat>Tat	p.H193Y	TP53_ENST00000420246.2_Missense_Mutation_p.H193Y|TP53_ENST00000455263.2_Missense_Mutation_p.H193Y|TP53_ENST00000574684.1_Intron|TP53_ENST00000445888.2_Missense_Mutation_p.H193Y|TP53_ENST00000413465.2_Missense_Mutation_p.H193Y|TP53_ENST00000359597.4_Missense_Mutation_p.H193Y	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	193	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		H -> D (in sporadic cancers; somatic mutation).|H -> L (in sporadic cancers; somatic mutation).|H -> N (in sporadic cancers; somatic mutation).|H -> P (in sporadic cancers; somatic mutation).|H -> Q (in sporadic cancers; somatic mutation).|H -> R (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7887414}.|H -> Y (in sporadic cancers; somatic mutation).|QH -> HN (in a sporadic cancer; somatic mutation).|QH -> HY (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.H193Y(29)|p.H193D(13)|p.0?(8)|p.?(6)|p.H193N(4)|p.A189_V197delAPPQHLIRV(4)|p.H193fs*16(3)|p.P191_E198>Q(3)|p.P191fs*53(2)|p.H61D(2)|p.H100D(2)|p.P191fs*15(1)|p.H61Y(1)|p.P191fs*6(1)|p.H100Y(1)|p.P98_E105>Q(1)|p.H193_I195delHLI(1)|p.P59_E66>Q(1)|p.H193_I195>AP(1)|p.A189fs*53(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CGGATAAGATGCTGAGGAGGG	0.557		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	dbGAP	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	85	Substitution - Missense(52)|Whole gene deletion(8)|Complex - deletion inframe(6)|Unknown(6)|Deletion - In frame(5)|Deletion - Frameshift(4)|Insertion - Frameshift(3)|Complex - frameshift(1)	breast(14)|lung(12)|haematopoietic_and_lymphoid_tissue(8)|biliary_tract(7)|ovary(6)|upper_aerodigestive_tract(5)|liver(5)|oesophagus(5)|central_nervous_system(4)|skin(4)|bone(4)|large_intestine(3)|stomach(2)|urinary_tract(2)|pancreas(2)|adrenal_gland(1)|soft_tissue(1)	17											95.0	85.0	88.0					17																	7578272		2203	4300	6503	7518997	SO:0001583	missense	0	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.577C>T	17.37:g.7578272G>A	ENSP00000269305:p.His193Tyr	Somatic	161	0.00	0		1	99.33	149	WXS	Illumina HiSeq	Phase_IV	7518997	17	79.07	68	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain,HMMPfam_P53,HMMPfam_P53_TAD	p.H193Y	ENST00000269305.4	37	c.577	CCDS11118.1	17	.	.	.	.	.	.	.	.	.	.	G	17.43	3.387715	0.61956	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99851	-7.17;-7.17;-7.17;-7.17;-7.17;-7.17;-7.17;-7.17	5.41	5.41	0.78517	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99873	0.9940	M	0.88906	2.99	0.58432	D	0.999999	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.96559	0.9414	10	0.87932	D	0	-29.0766	17.0767	0.86588	0.0:0.0:1.0:0.0	.	154;193;193;100;193;193;193	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	Y	193;193;193;193;193;193;182;100;61;100;61	ENSP00000410739:H193Y;ENSP00000352610:H193Y;ENSP00000269305:H193Y;ENSP00000398846:H193Y;ENSP00000391127:H193Y;ENSP00000391478:H193Y;ENSP00000425104:H61Y;ENSP00000423862:H100Y	ENSP00000269305:H193Y	H	-	1	0	TP53	7518997	1.000000	0.71417	0.971000	0.41717	0.032000	0.12392	9.813000	0.99286	2.702000	0.92279	0.655000	0.94253	CAT	-	superfamily_p53-like transcription factors,HMMPfam_P53		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TP53	protein_coding	OTTHUMT00000367397.1	G	NM_000546		7518997	-1	no_errors	NM_000546.4	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
ASXL3	80816	genome.wustl.edu	37	18	31314300	31314300	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2885-03A-01W-0732-08	TCGA-AB-2885-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	d5c78933-a17c-449c-a24d-730ea0f7a9cd	f62da227-622a-4139-9229-acd0939a17c3	g.chr18:31314300C>T	ENST00000269197.5	+	10	1003	c.1003C>T	c.(1003-1005)Cgg>Tgg	p.R335W		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	335					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(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						AATGCAGTTGCGGATAAGGCA	0.303																																						dbGAP											0			18											55.0	54.0	55.0					18																	31314300		1796	4059	5855	29568298	SO:0001583	missense	0			AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"""KIAA1713"", ""additional sex combs like 3 (Drosophila)"""	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.1003C>T	18.37:g.31314300C>T	ENSP00000269197:p.Arg335Trp	Somatic	131	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	29568298	15	72.22	39	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	NULL	p.R335W	ENST00000269197.5	37	c.1003	CCDS45847.1	18	.	.	.	.	.	.	.	.	.	.	C	27.6	4.843961	0.91197	.	.	ENSG00000141431	ENST00000269197	T	0.36157	1.27	5.71	5.71	0.89125	.	0.262703	0.32608	N	0.005861	T	0.62780	0.2456	M	0.71036	2.16	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	T	0.64245	-0.6453	10	0.87932	D	0	.	19.8549	0.96755	0.0:1.0:0.0:0.0	.	335	Q9C0F0	ASXL3_HUMAN	W	335	ENSP00000269197:R335W	ENSP00000269197:R335W	R	+	1	2	ASXL3	29568298	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.621000	0.67743	2.699000	0.92147	0.460000	0.39030	CGG	-	NULL		0.303	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	ASXL3	protein_coding	OTTHUMT00000441865.2	C			29568298	+1	no_errors	NM_030632.1	genbank	human	validated	54_36p	missense	SNP	1.000	T
PTPRT	11122	genome.wustl.edu	37	20	40747084	40747084	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2885-03A-01W-0732-08	TCGA-AB-2885-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	d5c78933-a17c-449c-a24d-730ea0f7a9cd	f62da227-622a-4139-9229-acd0939a17c3	g.chr20:40747084C>T	ENST00000373187.1	-	21	2940	c.2941G>A	c.(2941-2943)Gcc>Acc	p.A981T	PTPRT_ENST00000373201.1_Missense_Mutation_p.A971T|PTPRT_ENST00000373198.4_Missense_Mutation_p.A1000T|PTPRT_ENST00000373193.3_Missense_Mutation_p.A984T|PTPRT_ENST00000373184.1_Missense_Mutation_p.A971T|PTPRT_ENST00000356100.2_Missense_Mutation_p.A990T|PTPRT_ENST00000373190.1_Missense_Mutation_p.A980T			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	981	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				ACGATGCTGGCGGAGTTCTCC	0.532																																						dbGAP											0			20											95.0	94.0	95.0					20																	40747084		2019	4185	6204	40180498	SO:0001583	missense	0			AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.2941G>A	20.37:g.40747084C>T	ENSP00000362283:p.Ala981Thr	Somatic	234	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	40180498	58	40.21	39	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Missense_Mutation	SNP	HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMPfam_MAM,HMMSmart_SM00137,PatternScan_MAM_1,HMMSmart_SM00404,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,PatternScan_TYR_PHOSPHATASE_1,superfamily_Immunoglobulin,superfamily_(Phosphotyrosine protein) phosphatases II	p.A1000T	ENST00000373187.1	37	c.2998	CCDS42874.1	20	.	.	.	.	.	.	.	.	.	.	C	19.32	3.804244	0.70682	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	T;T;T;T;T;T;T	0.26810	1.71;1.71;1.71;1.71;1.71;1.71;1.71	5.43	5.43	0.79202	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.111536	0.64402	D	0.000012	T	0.29061	0.0722	N	0.16656	0.425	0.58432	D	0.999994	D;D	0.63880	0.991;0.993	P;P	0.52627	0.67;0.704	T	0.05321	-1.0892	10	0.51188	T	0.08	.	19.2449	0.93898	0.0:1.0:0.0:0.0	.	1003;981	O14522-1;O14522	.;PTPRT_HUMAN	T	980;981;984;990;1003;971;971	ENSP00000362286:A980T;ENSP00000362283:A981T;ENSP00000362289:A984T;ENSP00000348408:A990T;ENSP00000362294:A1003T;ENSP00000362280:A971T;ENSP00000362297:A971T	ENSP00000348408:A990T	A	-	1	0	PTPRT	40180498	0.993000	0.37304	0.956000	0.39512	0.959000	0.62525	3.099000	0.50267	2.560000	0.86352	0.561000	0.74099	GCC	-	HMMPfam_Y_phosphatase,HMMSmart_SM00194,superfamily_(Phosphotyrosine protein) phosphatases II		0.532	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	PTPRT	protein_coding	OTTHUMT00000080315.1	C			40180498	-1	no_errors	NM_133170.5	genbank	human	reviewed	54_36p	missense	SNP	0.987	T
FOXP4	116113	genome.wustl.edu	37	6	41555574	41555575	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AB-2885-03A-01W-0732-08	TCGA-AB-2885-11A-01W-0732-08	-	-	-	A	-	-	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	d5c78933-a17c-449c-a24d-730ea0f7a9cd	f62da227-622a-4139-9229-acd0939a17c3	g.chr6:41555574_41555575insA	ENST00000307972.4	+	7	928_929	c.916_917insA	c.(916-918)cacfs	p.H306fs	FOXP4_ENST00000373057.3_Frame_Shift_Ins_p.H304fs|FOXP4_ENST00000409208.1_Frame_Shift_Ins_p.H306fs|FOXP4_ENST00000373060.1_Frame_Shift_Ins_p.H306fs|FOXP4_ENST00000373063.3_Frame_Shift_Ins_p.H305fs			Q8IVH2	FOXP4_HUMAN	forkhead box P4	306					embryonic foregut morphogenesis (GO:0048617)|heart development (GO:0007507)|lung secretory cell differentiation (GO:0061140)|negative regulation of lung goblet cell differentiation (GO:1901250)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					CCTGTACGGACACGGAGAGTGC	0.658																																						dbGAP											0			6																																								41663553	SO:0001589	frameshift_variant	0			AB080747	CCDS4856.1, CCDS34447.1, CCDS34448.1	6p21.1	2008-02-05			ENSG00000137166	ENSG00000137166		"""Forkhead boxes"""	20842	protein-coding gene	gene with protein product		608924					Standard	XM_006714991		Approved	FLJ40908	uc003oql.3	Q8IVH2	OTTHUMG00000014679	ENST00000307972.4:c.917dupA	6.37:g.41555575_41555575dupA	ENSP00000309823:p.His306fs	Somatic	48	0.00	0		1	0.00	0	WXS	Illumina HiSeq	Phase_IV	41663552	11	31.25	5	Q5W098|Q7Z7F8|Q8IW55|Q96E19	Frame_Shift_Ins	INS	"HMMPfam_Fork_head,HMMSmart_SM00339,PatternScan_ZINC_FINGER_C2H2_1,PatternScan_FORK_HEAD_2,superfamily_""Winged helix"" DNA-binding domain"	p.H306fs	ENST00000307972.4	37	c.916_917	CCDS34447.1	6																																																																																			-	NULL		0.658	FOXP4-002	KNOWN	basic|CCDS	protein_coding	FOXP4	protein_coding	OTTHUMT00000106767.1	-	NM_138457		41663553	+1	no_errors	NM_001012426.1	genbank	human	reviewed	54_36p	frame_shift_ins	INS	1.000:1.000	A
