#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_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	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
NRAS	4893	genome.wustl.edu	37	1	115258744	115258744	+	Missense_Mutation	SNP	C	C	T	rs121434596		TCGA-AB-2839-03B-01W-0728-08	TCGA-AB-2839-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	e46ca5db-40a6-4119-8f57-d5739cce62fe	2702acd2-a374-44e7-b9d5-c5caecdcbea0	g.chr1:115258744C>T	ENST00000369535.4	-	2	291	c.38G>A	c.(37-39)gGt>gAt	p.G13D	CSDE1_ENST00000483407.1_5'Flank	NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	13			G -> D (in ALPS4). {ECO:0000269|PubMed:17517660}.|G -> R (in CMNS and colorectal cancer; somatic mutation). {ECO:0000269|PubMed:18633438, ECO:0000269|PubMed:3102434}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G13D(188)|p.G13V(56)|p.G13A(16)|p.G13N(1)|p.G13Y(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTTCCCAACACCACCTGCTCC	0.498	G13D(HDMYZ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(MINO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13D(NCIH929_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G13V(AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	50	Mis		"""melanoma, MM, AML, thyroid"""				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																												dbGAP		Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"""L, E"""	262	Substitution - Missense(262)	haematopoietic_and_lymphoid_tissue(217)|skin(36)|thyroid(2)|large_intestine(2)|soft_tissue(2)|central_nervous_system(1)|endometrium(1)|NS(1)	1	GRCh37	CM071907	NRAS	M	rs121434596						208.0	185.0	193.0					1																	115258744		2203	4300	6503	115060267	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	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.38G>A	1.37:g.115258744C>T	ENSP00000358548:p.Gly13Asp	92	2.13	2		37	26.00	13	115060267	58	37.63	35	Q14971|Q15104|Q15282	Missense_Mutation	SNP	HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases	p.G13D	ENST00000369535.4	37	c.38	CCDS877.1	1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.048221	0.93740	.	.	ENSG00000213281	ENST00000369535	T	0.72942	-0.7	5.58	5.58	0.84498	Small GTP-binding protein domain (1);	0.000000	0.56097	U	0.000022	T	0.79644	0.4481	M	0.92604	3.325	0.80722	D	1	B	0.33964	0.434	B	0.42319	0.383	T	0.81673	-0.0826	10	0.62326	D	0.03	.	19.3769	0.94514	0.0:1.0:0.0:0.0	.	13	P01111	RASN_HUMAN	D	13	ENSP00000358548:G13D	ENSP00000358548:G13D	G	-	2	0	NRAS	115060267	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.651000	0.83577	2.906000	0.99361	0.655000	0.94253	GGT	-	HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases		0.498	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NRAS	protein_coding	OTTHUMT00000033395.2	C	NM_002524		115060267	-1	no_errors	NM_002524.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
DNMT3A	1788	genome.wustl.edu	37	2	25468133	25468133	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AB-2839-03B-01W-0728-08	TCGA-AB-2839-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	e46ca5db-40a6-4119-8f57-d5739cce62fe	2702acd2-a374-44e7-b9d5-c5caecdcbea0	g.chr2:25468133G>A	ENST00000264709.3	-	13	1880	c.1543C>T	c.(1543-1545)Caa>Taa	p.Q515*	DNMT3A_ENST00000402667.1_Nonsense_Mutation_p.Q292*|DNMT3A_ENST00000380746.4_Nonsense_Mutation_p.Q326*|DNMT3A_ENST00000474887.1_5'Flank|DNMT3A_ENST00000321117.5_Nonsense_Mutation_p.Q515*	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	515	ADD. {ECO:0000255|PROSITE- ProRule:PRU00865}.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTGCAGTTTTGGCACATTCCT	0.587			"""Mis, F, N, S"""		AML																																	dbGAP		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	0			2											102.0	97.0	99.0					2																	25468133		2203	4300	6503	25321637	SO:0001587	stop_gained	0				CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.1543C>T	2.37:g.25468133G>A	ENSP00000264709:p.Gln515*	18	0.00	0		27	37.21	16	25321637	12	55.56	15	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Nonsense_Mutation	SNP	HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT	p.Q515*	ENST00000264709.3	37	c.1543	CCDS33157.1	2	.	.	.	.	.	.	.	.	.	.	G	39	7.378791	0.98248	.	.	ENSG00000119772	ENST00000380746;ENST00000321117;ENST00000264709;ENST00000402667	.	.	.	5.27	5.27	0.74061	.	0.059362	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	-5.893	16.4462	0.83935	0.0:0.0:1.0:0.0	.	.	.	.	X	326;515;515;292	.	ENSP00000264709:Q515X	Q	-	1	0	DNMT3A	25321637	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.624000	0.83124	2.735000	0.93741	0.655000	0.94253	CAA	-	NULL		0.587	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	DNMT3A	protein_coding	OTTHUMT00000211587.1	G	NM_022552		25321637	-1	no_errors	NM_022552.3	genbank	human	reviewed	54_36p	nonsense	SNP	1.000	A
CNTN6	27255	genome.wustl.edu	37	3	1415299	1415299	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2839-03B-01W-0728-08	TCGA-AB-2839-11B-01W-0729-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	e46ca5db-40a6-4119-8f57-d5739cce62fe	2702acd2-a374-44e7-b9d5-c5caecdcbea0	g.chr3:1415299C>A	ENST00000446702.2	+	15	2425	c.1798C>A	c.(1798-1800)Cct>Act	p.P600T	CNTN6_ENST00000350110.2_Missense_Mutation_p.P600T|CNTN6_ENST00000539053.1_Missense_Mutation_p.P528T			Q9UQ52	CNTN6_HUMAN	contactin 6	600	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		TCCACCAGGTCCTCCTGAGGA	0.378																																						dbGAP											0			3											67.0	69.0	68.0					3																	1415299		2203	4300	6503	1390299	SO:0001583	missense	0			AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	2176	protein-coding gene	gene with protein product	"""neural adhesion molecule"""	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.1798C>A	3.37:g.1415299C>A	ENSP00000407822:p.Pro600Thr	81	0.00	0		NA	NA	NA	1390299	60	33.33	30	Q2KHM2	Missense_Mutation	SNP	HMMSmart_IGc2,HMMSmart_IG,HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like,HMMPfam_I-set,superfamily_SSF48726	p.P600T	ENST00000446702.2	37	c.1798	CCDS2557.1	3	.	.	.	.	.	.	.	.	.	.	C	17.69	3.450971	0.63290	.	.	ENSG00000134115	ENST00000446702;ENST00000539053;ENST00000350110	T;T;T	0.59502	0.26;0.26;0.26	4.96	4.96	0.65561	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.53938	D	0.000046	D	0.84651	0.5519	H	0.96889	3.9	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90232	0.4280	10	0.87932	D	0	.	18.5527	0.91071	0.0:1.0:0.0:0.0	.	600	Q9UQ52	CNTN6_HUMAN	T	600;528;600	ENSP00000407822:P600T;ENSP00000442791:P528T;ENSP00000341882:P600T	ENSP00000341882:P600T	P	+	1	0	CNTN6	1390299	1.000000	0.71417	0.951000	0.38953	0.379000	0.30106	7.217000	0.77982	2.443000	0.82685	0.591000	0.81541	CCT	-	HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like		0.378	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CNTN6	protein_coding	OTTHUMT00000239235.2	C	NM_014461		1390299	+1	no_errors	NM_014461.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
VPRBP	9730	genome.wustl.edu	37	3	51466813	51466813	+	Intron	SNP	T	T	C			TCGA-AB-2839-03B-01W-0728-08	TCGA-AB-2839-11B-01W-0729-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	e46ca5db-40a6-4119-8f57-d5739cce62fe	2702acd2-a374-44e7-b9d5-c5caecdcbea0	g.chr3:51466813T>C	ENST00000335891.5	-	7	682							Q9Y4B6	VPRBP_HUMAN	Vpr (HIV-1) binding protein						B cell differentiation (GO:0030183)|cell competition in a multicellular organism (GO:0035212)|histone H2A-T120 phosphorylation (GO:1990245)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H2A-T120 specific) (GO:1990244)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)		CTCAAAGTATTTGCGCAAGGC	0.473																																						dbGAP											0			3											100.0	99.0	99.0					3																	51466813		1934	4141	6075	51441853	SO:0001627	intron_variant	0			AB018343	CCDS74943.1, CCDS74944.1	3p21.2	2011-06-17			ENSG00000145041	ENSG00000145041		"""DDB1 and CUL4 associated factors"""	30911	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 1"""					8195203, 11223251	Standard	NM_014703		Approved	KIAA0800, MGC102804, DCAF1	uc003dbe.2	Q9Y4B6	OTTHUMG00000156895	ENST00000335891.5:c.673-8409A>G	3.37:g.51466813T>C		67	8.22	6		16	30.43	7	51441853	55	43.88	43	Q2YD74|Q8TBD9|Q9HCA1|Q9UG37	Missense_Mutation	SNP	HMMSmart_SM00667,superfamily_WD40 repeat-like,HMMPfam_LisH,superfamily_ARM repeat	p.K530R	ENST00000335891.5	37	c.1589		3	.	.	.	.	.	.	.	.	.	.	T	9.261	1.043263	0.19748	.	.	ENSG00000145041	ENST00000423656	T	0.19669	2.13	6.07	4.94	0.65067	Armadillo-type fold (1);	0.042517	0.85682	D	0.000000	T	0.05410	0.0143	N	0.01771	-0.73	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34650	-0.9820	10	0.02654	T	1	-23.8416	3.4818	0.07605	0.0:0.305:0.0:0.695	.	526	Q9Y4B6	VPRBP_HUMAN	R	97	ENSP00000393183:K97R	ENSP00000393183:K97R	K	-	2	0	VPRBP	51441853	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.627000	0.67784	2.330000	0.79161	0.528000	0.53228	AAA	-	superfamily_ARM repeat		0.473	VPRBP-201	KNOWN	basic|appris_principal	protein_coding	VPRBP	protein_coding		T	NM_014703		51441853	-1	no_errors	ENST00000273612	ensembl	human	known	54_36p	missense	SNP	1.000	C
KDR	3791	genome.wustl.edu	37	4	55980300	55980300	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2839-03B-01W-0728-08	TCGA-AB-2839-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	e46ca5db-40a6-4119-8f57-d5739cce62fe	2702acd2-a374-44e7-b9d5-c5caecdcbea0	g.chr4:55980300G>A	ENST00000263923.4	-	6	1086	c.791C>T	c.(790-792)tCt>tTt	p.S264F		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	264	Ig-like C2-type 3.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TACCTTCGAAGAAGGGTATTC	0.413			Mis		"""NSCLC, angiosarcoma"""					TSP Lung(20;0.16)																												dbGAP		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	0			4											181.0	176.0	177.0					4																	55980300		2203	4300	6503	55675057	SO:0001583	missense	0			AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.791C>T	4.37:g.55980300G>A	ENSP00000263923:p.Ser264Phe	108	6.09	7		NA	NA	NA	55675057	55	53.72	65	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_IGc2,HMMSmart_IG,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_I-set,HMMPfam_V-set,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726	p.S264F	ENST00000263923.4	37	c.791	CCDS3497.1	4	.	.	.	.	.	.	.	.	.	.	G	14.35	2.508624	0.44660	.	.	ENSG00000128052	ENST00000263923	T	0.29655	1.56	5.45	4.59	0.56863	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.474802	0.24532	N	0.037709	T	0.52208	0.1720	M	0.65975	2.015	0.33164	D	0.547345	D;D	0.76494	0.999;0.97	D;P	0.69307	0.963;0.879	T	0.64968	-0.6282	10	0.40728	T	0.16	.	15.3228	0.74135	0.0:0.0:0.8589:0.1411	.	264;264	P35968-2;P35968	.;VGFR2_HUMAN	F	264	ENSP00000263923:S264F	ENSP00000263923:S264F	S	-	2	0	KDR	55675057	1.000000	0.71417	0.966000	0.40874	0.148000	0.21650	3.377000	0.52425	1.245000	0.43885	0.563000	0.77884	TCT	-	HMMSmart_IG,HMMPfam_V-set,superfamily_SSF48726		0.413	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KDR	protein_coding	OTTHUMT00000250645.1	G			55675057	-1	no_errors	NM_002253.2	genbank	human	validated	54_36p	missense	SNP	0.630	A
TGFBI	7045	genome.wustl.edu	37	5	135396553	135396553	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2839-03B-01W-0728-08	TCGA-AB-2839-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	e46ca5db-40a6-4119-8f57-d5739cce62fe	2702acd2-a374-44e7-b9d5-c5caecdcbea0	g.chr5:135396553C>T	ENST00000442011.2	+	14	1995	c.1834C>T	c.(1834-1836)Cct>Tct	p.P612S	TGFBI_ENST00000508076.1_5'UTR|TGFBI_ENST00000305126.8_Missense_Mutation_p.P612S	NM_000358.2	NP_000349.1	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	612	FAS1 4. {ECO:0000255|PROSITE- ProRule:PRU00082}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)			breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CAACAAGGAGCCTGTTGCCGA	0.418																																						dbGAP											0			5											50.0	51.0	51.0					5																	135396553		2033	4186	6219	135424452	SO:0001583	missense	0			M77349	CCDS47266.1	5q31	2008-02-05	2002-08-29		ENSG00000120708	ENSG00000120708			11771	protein-coding gene	gene with protein product		601692	"""transforming growth factor, beta-induced, 68kD"""	CSD3, LCD1, CSD1, CSD2		9463327	Standard	NM_000358		Approved	BIGH3, CDB1, CDGG1	uc003lbf.4	Q15582	OTTHUMG00000163213	ENST00000442011.2:c.1834C>T	5.37:g.135396553C>T	ENSP00000416330:p.Pro612Ser	213	1.39	3		0	100.00	1	135424452	49	35.53	27	D3DQB1|O14471|O14472|O14476|O43216|O43217|O43218|O43219|Q53XM1	Missense_Mutation	SNP	HMMPfam_Fasciclin,HMMSmart_SM00554,superfamily_FAS1 domain,HMMPfam_EMI	p.P612S	ENST00000442011.2	37	c.1834	CCDS47266.1	5	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.46|13.46	2.244953|2.244953	0.39697|0.39697	.|.	.|.	ENSG00000120708|ENSG00000120708	ENST00000514554|ENST00000442011;ENST00000398813;ENST00000305126	.|D;D	.|0.89552	.|-2.53;-2.53	5.83|5.83	4.96|4.96	0.65561|0.65561	.|FAS1 domain (5);	.|0.147684	.|0.64402	.|D	.|0.000006	D|D	0.91270|0.91270	0.7248|0.7248	L|L	0.33710|0.33710	1.025|1.025	0.46044|0.46044	D|D	0.998833|0.998833	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.999;0.999	D|D	0.90977|0.90977	0.4824|0.4824	5|10	.|0.39692	.|T	.|0.17	-18.5252|-18.5252	16.9755|16.9755	0.86312|0.86312	0.0:0.8723:0.1277:0.0|0.0:0.8723:0.1277:0.0	.|.	.|345;612	.|B9ZVW9;Q15582	.|.;BGH3_HUMAN	V|S	329|612;345;612	.|ENSP00000416330:P612S;ENSP00000306306:P612S	.|ENSP00000306306:P612S	A|P	+|+	2|1	0|0	TGFBI|TGFBI	135424452|135424452	0.903000|0.903000	0.30736|0.30736	0.260000|0.260000	0.24451|0.24451	0.014000|0.014000	0.08584|0.08584	3.200000|3.200000	0.51051|0.51051	1.456000|1.456000	0.47831|0.47831	-0.315000|-0.315000	0.08773|0.08773	GCC|CCT	-	HMMPfam_Fasciclin,HMMSmart_SM00554,superfamily_FAS1 domain		0.418	TGFBI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TGFBI	protein_coding	OTTHUMT00000372108.1	C			135424452	+1	no_errors	NM_000358.2	genbank	human	reviewed	54_36p	missense	SNP	0.998	T
SLC1A1	6505	genome.wustl.edu	37	9	4576050	4576050	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2839-03B-01W-0728-08	TCGA-AB-2839-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	e46ca5db-40a6-4119-8f57-d5739cce62fe	2702acd2-a374-44e7-b9d5-c5caecdcbea0	g.chr9:4576050G>A	ENST00000262352.3	+	9	1161	c.925G>A	c.(925-927)Gta>Ata	p.V309I		NM_004170.5	NP_004161.4	P43005	EAA3_HUMAN	solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	309					D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|pancreas(1)|skin(1)	15		Acute lymphoblastic leukemia(2;0.0359)|Breast(48;0.0457)		GBM - Glioblastoma multiforme(50;0.0124)|Lung(218;0.183)	L-Aspartic Acid(DB00128)|Pregabalin(DB00230)	TTTCATAGTCGTACGAAAGAA	0.438																																						dbGAP											0			9											99.0	94.0	96.0					9																	4576050		2203	4300	6503	4566050	SO:0001583	missense	0				CCDS6452.1	9p24	2013-05-22			ENSG00000106688	ENSG00000106688		"""Solute carriers"""	10939	protein-coding gene	gene with protein product		133550				8020993	Standard	NM_004170		Approved	EAAC1, EAAT3	uc003zij.2	P43005	OTTHUMG00000019468	ENST00000262352.3:c.925G>A	9.37:g.4576050G>A	ENSP00000262352:p.Val309Ile	141	5.37	8		NA	NA	NA	4566050	71	51.37	75	O75587|Q5VZ24|Q8N199|Q9UEW2	Missense_Mutation	SNP	HMMPfam_SDF,PatternScan_NA_DICARBOXYL_SYMP_1,PatternScan_NA_DICARBOXYL_SYMP_2	p.V309I	ENST00000262352.3	37	c.925	CCDS6452.1	9	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.63|19.63	3.863960|3.863960	0.71949|0.71949	.|.	.|.	ENSG00000106688|ENSG00000106688	ENST00000422398|ENST00000262352	.|T	.|0.58797	.|0.31	5.39|5.39	5.39|5.39	0.77823|0.77823	.|.	.|0.057496	.|0.64402	.|D	.|0.000001	T|T	0.55721|0.55721	0.1938|0.1938	L|L	0.53561|0.53561	1.675|1.675	0.80722|0.80722	D|D	1|1	.|P	.|0.38335	.|0.627	.|B	.|0.34301	.|0.179	T|T	0.62604|0.62604	-0.6819|-0.6819	5|10	.|0.87932	.|D	.|0	.|.	19.5203|19.5203	0.95182|0.95182	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|309	.|P43005	.|EAA3_HUMAN	H|I	71|309	.|ENSP00000262352:V309I	.|ENSP00000262352:V309I	R|V	+|+	2|1	0|0	SLC1A1|SLC1A1	4566050|4566050	1.000000|1.000000	0.71417|0.71417	0.251000|0.251000	0.24312|0.24312	0.867000|0.867000	0.49689|0.49689	4.869000|4.869000	0.63028|0.63028	2.678000|2.678000	0.91216|0.91216	0.655000|0.655000	0.94253|0.94253	CGT|GTA	-	HMMPfam_SDF		0.438	SLC1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC1A1	protein_coding	OTTHUMT00000051571.1	G			4566050	+1	no_errors	NM_004170.4	genbank	human	validated	54_36p	missense	SNP	0.986	A
PRSS3	5646	genome.wustl.edu	37	9	33795590	33795590	+	Intron	SNP	C	C	T			TCGA-AB-2839-03B-01W-0728-08	TCGA-AB-2839-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	e46ca5db-40a6-4119-8f57-d5739cce62fe	2702acd2-a374-44e7-b9d5-c5caecdcbea0	g.chr9:33795590C>T	ENST00000361005.5	+	2	211				PRSS3_ENST00000429677.3_Intron|PRSS3_ENST00000342836.4_Intron|PRSS3_ENST00000379405.3_Missense_Mutation_p.L7F|RP11-133O22.6_ENST00000454429.2_RNA	NM_007343.3	NP_031369	P35030	TRY3_HUMAN	protease, serine, 3						cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|endothelial cell migration (GO:0043542)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	13			LUSC - Lung squamous cell carcinoma(29;0.0176)			ATTCCTGATCCTTGCCTTTGT	0.567																																						dbGAP											0			9											175.0	126.0	143.0					9																	33795590		2203	4300	6503	33785590	SO:0001627	intron_variant	0				CCDS6545.1, CCDS47958.1, CCDS56570.1, CCDS56571.1	9p13	2010-05-07	2008-03-11		ENSG00000010438	ENSG00000010438	3.4.21.4	"""Serine peptidases / Serine peptidases"""	9486	protein-coding gene	gene with protein product	"""mesotrypsin"""	613578	"""protease, serine, 4 (trypsin 4, brain)"", ""protease, serine, 3 (mesotrypsin)"""	PRSS4		2326201, 8294000	Standard	NM_002771		Approved	TRY3, TRY4	uc003ztj.4	P35030	OTTHUMG00000019798	ENST00000361005.5:c.212-1051C>T	9.37:g.33795590C>T		105	7.08	8		NA	NA	NA	33785590	48	43.53	37	A8CED1|A8CED3|A9Z1Y4|E7ES07|F8W7P3|P15951|Q15665|Q5VXV0|Q6ISJ4|Q9UQV3	Missense_Mutation	SNP	HMMPfam_Trypsin,HMMSmart_SM00020,superfamily_Trypsin-like serine proteases,PatternScan_TRYPSIN_HIS	p.L7F	ENST00000361005.5	37	c.19	CCDS47958.1	9	.	.	.	.	.	.	.	.	.	.	C	6.043	0.376267	0.11466	.	.	ENSG00000010438	ENST00000379405	D	0.90069	-2.61	3.85	2.62	0.31277	.	.	.	.	.	T	0.81408	0.4816	L	0.42744	1.35	0.80722	D	1	B	0.09022	0.002	B	0.12156	0.007	T	0.76342	-0.2994	9	0.38643	T	0.18	.	4.0875	0.09953	0.0:0.6632:0.0:0.3368	.	7	P35030-3	.	F	7	ENSP00000368715:L7F	ENSP00000368715:L7F	L	+	1	0	PRSS3	33785590	0.980000	0.34600	0.991000	0.47740	0.046000	0.14306	0.392000	0.20801	1.892000	0.54788	0.306000	0.20318	CTT	-	NULL		0.567	PRSS3-003	KNOWN	basic|CCDS	protein_coding	PRSS3	protein_coding	OTTHUMT00000052121.1	C	NM_002771		33785590	+1	no_errors	NM_002771.3	genbank	human	reviewed	54_36p	missense	SNP	0.941	T
SMC3	9126	genome.wustl.edu	37	10	112362987	112362987	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2839-03B-01W-0728-08	TCGA-AB-2839-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	e46ca5db-40a6-4119-8f57-d5739cce62fe	2702acd2-a374-44e7-b9d5-c5caecdcbea0	g.chr10:112362987C>T	ENST00000361804.4	+	28	3647	c.3521C>T	c.(3520-3522)aCt>aTt	p.T1174I		NM_005445.3	NP_005436.1	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3	1174					DNA repair (GO:0006281)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid cohesion (GO:0007064)|mitotic spindle organization (GO:0007052)|negative regulation of DNA endoreduplication (GO:0032876)|regulation of DNA replication (GO:0006275)|signal transduction (GO:0007165)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	basement membrane (GO:0005604)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cohesin core heterodimer (GO:0008280)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear matrix (GO:0016363)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|dynein binding (GO:0045502)|microtubule motor activity (GO:0003777)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(5)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)		ATTACAACTACTTTTAGGCCT	0.289																																						dbGAP											0			10											66.0	69.0	68.0					10																	112362987		2203	4291	6494	112352977	SO:0001583	missense	0			AF020043	CCDS31285.1	10q25	2014-09-17	2006-07-06	2006-07-06	ENSG00000108055	ENSG00000108055		"""Structural maintenance of chromosomes proteins"", ""Proteoglycans / Extracellular Matrix : Other"""	2468	protein-coding gene	gene with protein product	"""bamacan proteoglycan"""	606062	"""chondroitin sulfate proteoglycan 6 (bamacan)"""	CSPG6		9506951, 10358101	Standard	NM_005445		Approved	HCAP, BAM, SMC3L1, bamacan	uc001kze.3	Q9UQE7	OTTHUMG00000019042	ENST00000361804.4:c.3521C>T	10.37:g.112362987C>T	ENSP00000354720:p.Thr1174Ile	23	14.81	4		25	41.86	18	112352977	50	44.57	41	A8K156|O60464|Q5T482	Missense_Mutation	SNP	HMMPfam_SMC_N,HMMPfam_SMC_hinge,superfamily_Smc hinge domain,PatternScan_ABC_TRANSPORTER_1,superfamily_P-loop containing nucleoside triphosphate hydrolases,superfamily_BAG domain	p.T1174I	ENST00000361804.4	37	c.3521	CCDS31285.1	10	.	.	.	.	.	.	.	.	.	.	C	20.2	3.957801	0.73902	.	.	ENSG00000108055	ENST00000361804	D	0.93953	-3.32	5.41	5.41	0.78517	RecF/RecN/SMC (1);	0.042624	0.85682	D	0.000000	D	0.97739	0.9258	M	0.93594	3.435	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98391	1.0563	10	0.87932	D	0	.	19.5802	0.95464	0.0:1.0:0.0:0.0	.	1174	Q9UQE7	SMC3_HUMAN	I	1174	ENSP00000354720:T1174I	ENSP00000354720:T1174I	T	+	2	0	SMC3	112352977	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.414000	0.80117	2.712000	0.92718	0.650000	0.86243	ACT	-	HMMPfam_SMC_N,superfamily_P-loop containing nucleoside triphosphate hydrolases		0.289	SMC3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	SMC3	protein_coding	OTTHUMT00000050337.1	C	NM_005445		112352977	+1	no_errors	NM_005445.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
OR5AS1	219447	genome.wustl.edu	37	11	55798094	55798094	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2839-03B-01W-0728-08	TCGA-AB-2839-11B-01W-0729-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	e46ca5db-40a6-4119-8f57-d5739cce62fe	2702acd2-a374-44e7-b9d5-c5caecdcbea0	g.chr11:55798094C>A	ENST00000313555.1	+	1	200	c.200C>A	c.(199-201)tCt>tAt	p.S67Y		NM_001001921.1	NP_001001921.1	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS, member 1	67						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(7)|large_intestine(7)|liver(1)|lung(22)|ovary(3)|prostate(4)|skin(3)|stomach(1)	48	Esophageal squamous(21;0.00693)					AGCAACTTATCTTTCTTAGAC	0.343																																						dbGAP											0			11											58.0	58.0	58.0					11																	55798094		2201	4296	6497	55554670	SO:0001583	missense	0			AB065543	CCDS31516.1	11q11	2012-08-09			ENSG00000181785	ENSG00000181785		"""GPCR / Class A : Olfactory receptors"""	15261	protein-coding gene	gene with protein product							Standard	NM_001001921		Approved		uc010riw.2	Q8N127	OTTHUMG00000166830	ENST00000313555.1:c.200C>A	11.37:g.55798094C>A	ENSP00000324111:p.Ser67Tyr	67	9.46	7		NA	NA	NA	55554670	83	40.29	56	Q6IFB8	Missense_Mutation	SNP	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321	p.S67Y	ENST00000313555.1	37	c.200	CCDS31516.1	11	.	.	.	.	.	.	.	.	.	.	C	16.44	3.124884	0.56613	.	.	ENSG00000181785	ENST00000313555	T	0.12361	2.69	5.65	5.65	0.86999	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34580	U	0.003849	T	0.52629	0.1746	H	0.97783	4.075	0.28729	N	0.902588	D	0.64830	0.994	P	0.60173	0.87	T	0.67063	-0.5765	10	0.87932	D	0	.	18.3047	0.90176	0.0:1.0:0.0:0.0	.	67	Q8N127	O5AS1_HUMAN	Y	67	ENSP00000324111:S67Y	ENSP00000324111:S67Y	S	+	2	0	OR5AS1	55554670	0.017000	0.18338	1.000000	0.80357	0.507000	0.33981	2.774000	0.47694	2.663000	0.90544	0.643000	0.83706	TCT	-	HMMPfam_7tm_1,superfamily_SSF81321		0.343	OR5AS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR5AS1	protein_coding	OTTHUMT00000391538.1	C	NM_001001921		55554670	+1	no_errors	NM_001001921.1	genbank	human	provisional	54_36p	missense	SNP	0.965	A
CACNA2D4	93589	genome.wustl.edu	37	12	1963133	1963133	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2839-03B-01W-0728-08	TCGA-AB-2839-11B-01W-0729-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	e46ca5db-40a6-4119-8f57-d5739cce62fe	2702acd2-a374-44e7-b9d5-c5caecdcbea0	g.chr12:1963133C>A	ENST00000382722.5	-	23	2592	c.2230G>T	c.(2230-2232)Gcc>Tcc	p.A744S	CACNA2D4_ENST00000588077.1_Missense_Mutation_p.A680S|CACNA2D4_ENST00000586184.1_Missense_Mutation_p.A744S|CACNA2D4_ENST00000587995.1_Missense_Mutation_p.A719S|CACNA2D4_ENST00000585708.1_Missense_Mutation_p.A680S|CACNA2D4_ENST00000539048.2_Intron|CACNA2D4_ENST00000585732.1_Missense_Mutation_p.A605S	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	744					calcium ion transmembrane transport (GO:0070588)|detection of light stimulus involved in visual perception (GO:0050908)	voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			endometrium(3)|kidney(2)|large_intestine(1)|liver(1)|lung(27)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	39	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		ATGTTGAGGGCCAGCGCTGTC	0.617																																					Colon(2;101 179 21030 23310 28141)	dbGAP											0			12											46.0	55.0	52.0					12																	1963133		2032	4188	6220	1833394	SO:0001583	missense	0			AF516695	CCDS44785.1	12p13.33	2003-03-05			ENSG00000151062	ENSG00000151062		"""Calcium channel subunits"""	20202	protein-coding gene	gene with protein product		608171				12181424	Standard	NM_172364		Approved		uc021qsx.1	Q7Z3S7	OTTHUMG00000168111	ENST00000382722.5:c.2230G>T	12.37:g.1963133C>A	ENSP00000372169:p.Ala744Ser	89	6.32	6		6	64.71	11	1833394	25	58.33	35	Q7Z3S8|Q86XZ5|Q8IZS9	Missense_Mutation	SNP	HMMPfam_VWA,HMMSmart_SM00327,HMMPfam_Cache_1,HMMPfam_VWA_N,superfamily_vWA-like	p.A744S	ENST00000382722.5	37	c.2230	CCDS44785.1	12	.	.	.	.	.	.	.	.	.	.	C	4.402	0.074267	0.08485	.	.	ENSG00000151062	ENST00000456077;ENST00000280663;ENST00000382722	T	0.30714	1.52	5.4	3.58	0.41010	.	0.224864	0.47093	D	0.000248	T	0.23054	0.0557	L	0.48935	1.535	0.31821	N	0.625925	B;B	0.32350	0.2;0.366	B;B	0.32022	0.139;0.08	T	0.20874	-1.0262	10	0.10636	T	0.68	.	9.8913	0.41292	0.1382:0.7881:0.0:0.0737	.	744;744	Q7Z3S7-2;Q7Z3S7	.;CA2D4_HUMAN	S	680;744;744	ENSP00000372169:A744S	ENSP00000280663:A744S	A	-	1	0	CACNA2D4	1833394	1.000000	0.71417	0.400000	0.26346	0.044000	0.14063	1.835000	0.39181	0.669000	0.31146	-0.123000	0.14984	GCC	-	NULL		0.617	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	CACNA2D4	protein_coding	OTTHUMT00000398230.2	C			1833394	-1	no_errors	NM_172364.4	genbank	human	reviewed	54_36p	missense	SNP	0.824	A
SLC39A5	283375	genome.wustl.edu	37	12	56631037	56631037	+	Silent	SNP	G	G	T			TCGA-AB-2839-03B-01W-0728-08	TCGA-AB-2839-11B-01W-0729-08	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	e46ca5db-40a6-4119-8f57-d5739cce62fe	2702acd2-a374-44e7-b9d5-c5caecdcbea0	g.chr12:56631037G>T	ENST00000266980.4	+	10	1685	c.1392G>T	c.(1390-1392)gtG>gtT	p.V464V	SLC39A5_ENST00000419232.1_3'UTR|ANKRD52_ENST00000548241.1_5'Flank|SLC39A5_ENST00000454355.2_Silent_p.V464V	NM_001135195.1	NP_001128667.1	Q6ZMH5	S39A5_HUMAN	solute carrier family 39 (zinc transporter), member 5	464					cellular response to zinc ion starvation (GO:0034224)|G1 to G0 transition involved in cell differentiation (GO:0070315)|neural precursor cell proliferation (GO:0061351)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			NS(1)|cervix(6)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						TCCTGGGGGTGGGGCTCAGCC	0.642																																						dbGAP											0			12											58.0	61.0	60.0					12																	56631037		2203	4300	6503	54917304	SO:0001819	synonymous_variant	0				CCDS8912.2	12q13.3	2013-07-17	2013-07-17		ENSG00000139540	ENSG00000139540		"""Solute carriers"""	20502	protein-coding gene	gene with protein product		608730	"""solute carrier family 39 (metal ion transporter), member 5"""				Standard	NM_173596		Approved		uc010sqj.2	Q6ZMH5	OTTHUMG00000156962	ENST00000266980.4:c.1392G>T	12.37:g.56631037G>T		37	2.63	1		2	0.00	0	54917304	14	46.15	12	B2R808|Q8N6Y3	Silent	SNP	HMMPfam_Zip	p.V463	ENST00000266980.4	37	c.1389	CCDS8912.2	12																																																																																			-	HMMPfam_Zip		0.642	SLC39A5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	SLC39A5	protein_coding	OTTHUMT00000346834.1	G	NM_173596		54917304	+1	no_errors	NM_173596.1	genbank	human	validated	54_36p	silent	SNP	0.997	T
PTPN11	5781	genome.wustl.edu	37	12	112939981	112939981	+	Missense_Mutation	SNP	A	A	C			TCGA-AB-2839-03B-01W-0728-08	TCGA-AB-2839-11B-01W-0729-08	A	A	A	C	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	e46ca5db-40a6-4119-8f57-d5739cce62fe	2702acd2-a374-44e7-b9d5-c5caecdcbea0	g.chr12:112939981A>C	ENST00000351677.2	+	14	1831	c.1633A>C	c.(1633-1635)Att>Ctt	p.I545L		NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	549					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						ATATACAAATATTAAGTATTC	0.443			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											74.0	77.0	76.0					12																	112939981		2203	4300	6503	111424364	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.1633A>C	12.37:g.112939981A>C	ENSP00000340944:p.Ile545Leu	65	4.41	3		23	48.89	22	111424364	35	50.70	36	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.I545L	ENST00000351677.2	37	c.1633	CCDS9163.1	12	.	.	.	.	.	.	.	.	.	.	A	20.5	3.993191	0.74703	.	.	ENSG00000179295	ENST00000351677	T	0.10288	2.89	5.38	5.38	0.77491	.	0.106709	0.64402	D	0.000006	T	0.12390	0.0301	L	0.36672	1.1	0.80722	D	1	B	0.29936	0.262	B	0.34536	0.185	T	0.07868	-1.0750	10	0.41790	T	0.15	.	15.4198	0.75003	1.0:0.0:0.0:0.0	.	545	Q06124-2	.	L	545	ENSP00000340944:I545L	ENSP00000340944:I545L	I	+	1	0	PTPN11	111424364	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.463000	0.90377	2.030000	0.59900	0.533000	0.62120	ATT	-	NULL		0.443	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PTPN11	protein_coding	OTTHUMT00000259496.2	A			111424364	+1	no_errors	NM_002834.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	C
C15orf57	90416	genome.wustl.edu	37	15	40855085	40855085	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2839-03B-01W-0728-08	TCGA-AB-2839-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	e46ca5db-40a6-4119-8f57-d5739cce62fe	2702acd2-a374-44e7-b9d5-c5caecdcbea0	g.chr15:40855085C>T	ENST00000358005.3	-	2	403	c.130G>A	c.(130-132)Gtg>Atg	p.V44M	C15orf57_ENST00000558750.1_Missense_Mutation_p.V53M|C15orf57_ENST00000560305.1_Missense_Mutation_p.V44M|C15orf57_ENST00000559911.1_Missense_Mutation_p.V44M|C15orf57_ENST00000561011.1_Missense_Mutation_p.V44M|C15orf57_ENST00000416810.2_Missense_Mutation_p.V44M|C15orf57_ENST00000558113.1_Missense_Mutation_p.V44M|C15orf57_ENST00000558871.1_Missense_Mutation_p.V44M|C15orf57_ENST00000560109.1_5'UTR	NM_001080791.1|NM_052849.2	NP_001074260.1|NP_443081.1	Q9BV29	CO057_HUMAN	chromosome 15 open reading frame 57	44										endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	9						CAAGAATCCACAAAGGAGTCT	0.512																																						dbGAP											0			15											184.0	177.0	179.0					15																	40855085		2203	4300	6503	38642377	SO:0001583	missense	0			BC012189	CCDS10060.1, CCDS42022.1, CCDS73706.1	15q15.1	2008-05-30	2008-05-30	2008-05-30	ENSG00000128891	ENSG00000128891			28295	protein-coding gene	gene with protein product			"""coiled-coil domain containing 32"""	CCDC32		12477932	Standard	NM_001080791		Approved	MGC20481	uc001zma.1	Q9BV29	OTTHUMG00000129993	ENST00000358005.3:c.130G>A	15.37:g.40855085C>T	ENSP00000350695:p.Val44Met	119	2.46	3		26	43.48	20	38642377	33	45.00	27	A8KAL4|Q86TC4|Q8N788|Q8NAR7	Missense_Mutation	SNP	NULL	p.V53M	ENST00000358005.3	37	c.157	CCDS10060.1	15	.	.	.	.	.	.	.	.	.	.	C	4.287	0.052482	0.08291	.	.	ENSG00000128891	ENST00000358005;ENST00000416810	T	0.43688	0.94	4.92	-0.845	0.10737	.	0.729179	0.13713	N	0.367942	T	0.11580	0.0282	N	0.00926	-1.1	0.19945	N	0.999946	B;B;B	0.12630	0.006;0.006;0.002	B;B;B	0.10450	0.005;0.005;0.005	T	0.21690	-1.0238	10	0.27785	T	0.31	-22.3122	2.6985	0.05141	0.1082:0.4377:0.211:0.2431	.	44;53;44	Q9BV29;Q9BV29-2;Q9BV29-3	CO057_HUMAN;.;.	M	44;53	ENSP00000350695:V44M	ENSP00000350695:V44M	V	-	1	0	C15orf57	38642377	0.121000	0.22262	0.869000	0.34112	0.279000	0.26890	-0.687000	0.05156	-0.109000	0.12044	-0.324000	0.08512	GTG	-	NULL		0.512	C15orf57-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	C15orf57	protein_coding	OTTHUMT00000252259.2	C	NM_052849		38642377	-1	no_errors	NM_001080791.1	genbank	human	validated	54_36p	missense	SNP	0.251	T
DUOXA2	405753	genome.wustl.edu	37	15	45408364	45408364	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2839-03B-01W-0728-08	TCGA-AB-2839-11B-01W-0729-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	e46ca5db-40a6-4119-8f57-d5739cce62fe	2702acd2-a374-44e7-b9d5-c5caecdcbea0	g.chr15:45408364C>A	ENST00000323030.5	+	3	533	c.248C>A	c.(247-249)aCc>aAc	p.T83N	DUOX2_ENST00000603300.1_5'Flank|DUOX2_ENST00000389039.6_5'Flank	NM_207581.3	NP_997464.2	Q1HG44	DOXA2_HUMAN	dual oxidase maturation factor 2	83					hydrogen peroxide metabolic process (GO:0042743)|protein transport (GO:0015031)|regulation of inflammatory response (GO:0050727)|regulation of thyroid hormone generation (GO:2000609)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)							all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;2.88e-18)|GBM - Glioblastoma multiforme(94;3.95e-07)|COAD - Colon adenocarcinoma(120;0.0652)|Colorectal(133;0.0659)		ACAGTGAACACCAACACATCC	0.557																																						dbGAP											0			15											141.0	136.0	138.0					15																	45408364		2002	4166	6168	43195656	SO:0001583	missense	0			BX537581	CCDS10118.2	15q21.1	2008-10-30		2006-07-25	ENSG00000140274	ENSG00000140274			32698	protein-coding gene	gene with protein product		612772				16651268	Standard	NM_207581		Approved		uc001zuo.3	Q1HG44	OTTHUMG00000131354	ENST00000323030.5:c.248C>A	15.37:g.45408364C>A	ENSP00000319705:p.Thr83Asn	29	3.33	1		NA	NA	NA	43195656	15	44.44	12	B2RPI9|H0YNQ6	Missense_Mutation	SNP	HMMPfam_DuoxA	p.T83N	ENST00000323030.5	37	c.248	CCDS10118.2	15	.	.	.	.	.	.	.	.	.	.	C	17.94	3.512593	0.64522	.	.	ENSG00000140274	ENST00000323030	T	0.57107	0.42	5.41	4.5	0.54988	.	0.151564	0.64402	D	0.000015	T	0.67859	0.2938	M	0.76574	2.34	0.32053	N	0.596716	D	0.58970	0.984	P	0.59424	0.857	T	0.76974	-0.2760	10	0.72032	D	0.01	-20.0443	13.3282	0.60471	0.0:0.9236:0.0:0.0764	.	83	Q1HG44	DOXA2_HUMAN	N	83	ENSP00000319705:T83N	ENSP00000319705:T83N	T	+	2	0	DUOXA2	43195656	0.998000	0.40836	0.405000	0.26409	0.768000	0.43524	5.546000	0.67243	1.284000	0.44531	0.561000	0.74099	ACC	-	HMMPfam_DuoxA		0.557	DUOXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DUOXA2	protein_coding	OTTHUMT00000254142.1	C	NM_207581		43195656	+1	no_errors	NM_207581.2	genbank	human	validated	54_36p	missense	SNP	0.999	A
TM6SF1	53346	genome.wustl.edu	37	15	83784622	83784622	+	Silent	SNP	C	C	T	rs552226250		TCGA-AB-2839-03B-01W-0728-08	TCGA-AB-2839-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	e46ca5db-40a6-4119-8f57-d5739cce62fe	2702acd2-a374-44e7-b9d5-c5caecdcbea0	g.chr15:83784622C>T	ENST00000322019.9	+	3	496	c.222C>T	c.(220-222)agC>agT	p.S74S	TM6SF1_ENST00000565774.1_Silent_p.S74S|TM6SF1_ENST00000564988.1_3'UTR|RP11-382A20.2_ENST00000565513.1_RNA|TM6SF1_ENST00000379386.4_Silent_p.S74S|TM6SF1_ENST00000379390.6_Silent_p.S74S			Q9BZW5	TM6S1_HUMAN	transmembrane 6 superfamily member 1	74						integral component of membrane (GO:0016021)				endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	15						GATTTACCAGCGTGGTGAACC	0.418													C|||	1	0.000199681	0.0008	0.0	5008	,	,		22127	0.0		0.0	False		,,,				2504	0.0					dbGAP											0			15											169.0	143.0	152.0					15																	83784622		2203	4300	6503	81575626	SO:0001819	synonymous_variant	0			AF255922	CCDS10323.1, CCDS45338.1	15q24-q26	2003-04-04			ENSG00000136404	ENSG00000136404			11860	protein-coding gene	gene with protein product		606562				11124529	Standard	NM_001144903		Approved		uc002bjp.3	Q9BZW5	OTTHUMG00000147365	ENST00000322019.9:c.222C>T	15.37:g.83784622C>T		222	4.72	11		NA	NA	NA	81575626	56	39.78	37	A8K7T5|H3BU56|Q4U0U5	Silent	SNP	NULL	p.S74	ENST00000322019.9	37	c.222	CCDS10323.1	15																																																																																			-	NULL		0.418	TM6SF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	TM6SF1	protein_coding	OTTHUMT00000304009.1	C	NM_023003		81575626	+1	no_errors	NM_023003.1	genbank	human	validated	54_36p	silent	SNP	0.954	T
RALGAPA2	57186	genome.wustl.edu	37	20	20610211	20610211	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2839-03B-01W-0728-08	TCGA-AB-2839-11B-01W-0729-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	e46ca5db-40a6-4119-8f57-d5739cce62fe	2702acd2-a374-44e7-b9d5-c5caecdcbea0	g.chr20:20610211C>A	ENST00000202677.7	-	10	1036	c.1029G>T	c.(1027-1029)caG>caT	p.Q343H		NM_020343.3	NP_065076.2	Q2PPJ7	RGPA2_HUMAN	Ral GTPase activating protein, alpha subunit 2 (catalytic)	343					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	54						GCGCTCTCTCCTGCACAGCAC	0.552																																						dbGAP											0			20											88.0	91.0	90.0					20																	20610211		2159	4256	6415	20558211	SO:0001583	missense	0			AL078634, DQ310704	CCDS46584.1	20p11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000188559	ENSG00000188559			16207	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 74"""	C20orf74		16490346, 19520869	Standard	NM_020343		Approved	dJ1049G11.4, AS250, KIAA1272, RapGAPalpha2	uc002wrz.3	Q2PPJ7	OTTHUMG00000032010	ENST00000202677.7:c.1029G>T	20.37:g.20610211C>A	ENSP00000202677:p.Gln343His	78	6.02	5		9	60.87	14	20558211	74	43.08	56	Q4VXU6|Q5JUA3|Q5JUA4|Q5T9K3|Q96CX9|Q9BQT7|Q9H9D9|Q9ULE8	Missense_Mutation	SNP	HMMPfam_Rap_GAP,superfamily_Rap/Ran-GAP (Pfam 02145)	p.Q343H	ENST00000202677.7	37	c.1029	CCDS46584.1	20	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	18.42|18.42|18.42	3.620824|3.620824|3.620824	0.66787|0.66787|0.66787	.|.|.	.|.|.	ENSG00000188559|ENSG00000188559|ENSG00000188559	ENST00000432524|ENST00000202677|ENST00000430436	.|T|.	.|0.79352|.	.|-1.26|.	5.1|5.1|5.1	-1.47|-1.47|-1.47	0.08772|0.08772|0.08772	.|.|.	.|1.692890|.	.|0.03207|.	.|N|.	.|0.175641|.	.|T|T	.|0.48484|0.48484	.|0.1502|0.1502	M|M|M	0.62723|0.62723|0.62723	1.935|1.935|1.935	0.36628|0.36628|0.36628	D|D|D	0.876138|0.876138|0.876138	.|P|.	.|0.45348|.	.|0.856|.	.|P|.	.|0.46758|.	.|0.526|.	.|T|T	.|0.48647|0.48647	.|-0.9017|-0.9017	.|10|5	.|0.54805|.	.|T|.	.|0.06|.	.|.|.	2.1868|2.1868|2.1868	0.03889|0.03889|0.03889	0.1147:0.2785:0.1187:0.4882|0.1147:0.2785:0.1187:0.4882|0.1147:0.2785:0.1187:0.4882	.|.|.	.|343|.	.|Q2PPJ7|.	.|RGPA2_HUMAN|.	X|H|M	195|343|160	.|ENSP00000202677:Q343H|.	.|ENSP00000202677:Q343H|.	G|Q|R	-|-|-	1|3|2	0|2|0	RALGAPA2|RALGAPA2|RALGAPA2	20558211|20558211|20558211	0.915000|0.915000|0.915000	0.31059|0.31059|0.31059	0.005000|0.005000|0.005000	0.12908|0.12908|0.12908	0.342000|0.342000|0.342000	0.28953|0.28953|0.28953	-0.013000|-0.013000|-0.013000	0.12678|0.12678|0.12678	-0.621000|-0.621000|-0.621000	0.05633|0.05633|0.05633	-0.378000|-0.378000|-0.378000	0.06908|0.06908|0.06908	GGA|CAG|AGG	-	NULL		0.552	RALGAPA2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	C20orf74	protein_coding	OTTHUMT00000471941.1	C	NM_020343		20558211	-1	no_errors	NM_020343.2	genbank	human	validated	54_36p	missense	SNP	0.972	A
IGSF5	150084	genome.wustl.edu	37	21	41143070	41143070	+	Missense_Mutation	SNP	G	G	A	rs117910095		TCGA-AB-2839-03B-01W-0728-08	TCGA-AB-2839-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	e46ca5db-40a6-4119-8f57-d5739cce62fe	2702acd2-a374-44e7-b9d5-c5caecdcbea0	g.chr21:41143070G>A	ENST00000380588.4	+	4	749	c.646G>A	c.(646-648)Gtg>Atg	p.V216M	IGSF5_ENST00000479378.1_3'UTR	NM_001080444.1	NP_001073913.1	Q9NSI5	IGSF5_HUMAN	immunoglobulin superfamily, member 5	216	Ig-like V-type 2.				single organismal cell-cell adhesion (GO:0016337)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(7)|skin(2)|stomach(1)	23		Prostate(19;5.35e-06)				TTTGACTTGCGTGGCTACCTG	0.502													G|||	1	0.000199681	0.0	0.0	5008	,	,		16569	0.0		0.001	False		,,,				2504	0.0					dbGAP											0			21						G	MET/VAL	0,4406	2.1+/-5.4	0,0,2203	74.0	71.0	72.0		646	2.3	0.8	21	dbSNP_132	72	5,8595	4.3+/-15.6	0,5,4295	yes	missense	IGSF5	NM_001080444.1	21	0,5,6498	AA,AG,GG		0.0581,0.0,0.0384	probably-damaging	216/408	41143070	5,13001	2203	4300	6503	40064940	SO:0001583	missense	0				CCDS33562.1	21q22.2	2013-01-29			ENSG00000183067	ENSG00000183067		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5952	protein-coding gene	gene with protein product	"""junctional adhesion molecule 4"""	610638					Standard	NM_001080444		Approved	JAM4	uc002yyo.3	Q9NSI5	OTTHUMG00000086724	ENST00000380588.4:c.646G>A	21.37:g.41143070G>A	ENSP00000369962:p.Val216Met	36	5.26	2		NA	NA	NA	40064940	42	44.00	33		Missense_Mutation	SNP	HMMSmart_IG,HMMPfam_I-set,superfamily_SSF48726	p.V216M	ENST00000380588.4	37	c.646	CCDS33562.1	21	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	10.77	1.444394	0.25987	0.0	5.81E-4	ENSG00000183067	ENST00000380588	T	0.10477	2.87	5.12	2.33	0.28932	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.465144	0.22581	N	0.058209	T	0.14743	0.0356	L	0.50333	1.59	0.31962	N	0.608248	D	0.61697	0.99	P	0.55011	0.766	T	0.14643	-1.0465	10	0.42905	T	0.14	-14.4481	2.8032	0.05420	0.1623:0.1343:0.5477:0.1558	.	216	Q9NSI5	IGSF5_HUMAN	M	216	ENSP00000369962:V216M	ENSP00000369962:V216M	V	+	1	0	IGSF5	40064940	0.991000	0.36638	0.836000	0.33094	0.080000	0.17528	1.286000	0.33273	0.399000	0.25367	-0.119000	0.15052	GTG	-	HMMSmart_IG,superfamily_SSF48726		0.502	IGSF5-001	NOVEL	basic|appris_principal|CCDS	protein_coding	IGSF5	protein_coding	OTTHUMT00000195005.1	G			40064940	+1	no_errors	NM_001080444.1	genbank	human	provisional	54_36p	missense	SNP	0.992	A
NPM1	4869	genome.wustl.edu	37	5	170837543	170837544	+	Frame_Shift_Ins	INS	-	-	TATG	rs17850940		TCGA-AB-2839-03B-01W-0728-08	TCGA-AB-2839-11B-01W-0729-08	-	-	-	TATG	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	e46ca5db-40a6-4119-8f57-d5739cce62fe	2702acd2-a374-44e7-b9d5-c5caecdcbea0	g.chr5:170837543_170837544insTATG	ENST00000296930.5	+	11	1160_1161	c.859_860insTATG	c.(859-861)ctcfs	p.-287fs	NPM1_ENST00000351986.6_Frame_Shift_Ins_p.-258fs|NPM1_ENST00000517671.1_Frame_Shift_Ins_p.-287fs	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	Exception_encountered	5.37:g.170837543_170837544insTATG	ENSP00000296930:p.Leu287fs	NA	NA	NA		NA	NA	NA	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	TATG
WT1	7490	genome.wustl.edu	37	11	32417908	32417909	+	Frame_Shift_Ins	INS	-	-	CCGA	rs377446096		TCGA-AB-2839-03B-01W-0728-08	TCGA-AB-2839-11B-01W-0729-08	-	-	-	CCGA	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	e46ca5db-40a6-4119-8f57-d5739cce62fe	2702acd2-a374-44e7-b9d5-c5caecdcbea0	g.chr11:32417908_32417909insCCGA	ENST00000379079.2	-	7	780_781	c.507_508insTCGG	c.(505-510)tcggcafs	p.A170fs	WT1_ENST00000448076.3_Frame_Shift_Ins_p.A382fs|WT1_ENST00000530998.1_Frame_Shift_Ins_p.A153fs|WT1_ENST00000332351.3_Frame_Shift_Ins_p.A382fs	NM_001198551.1	NP_001185480.1	P19544	WT1_HUMAN	Wilms tumor 1	314					adrenal cortex formation (GO:0035802)|adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|diaphragm development (GO:0060539)|epithelial cell differentiation (GO:0030855)|germ cell development (GO:0007281)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|gonad development (GO:0008406)|heart development (GO:0007507)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|mesenchymal to epithelial transition (GO:0060231)|metanephric epithelium development (GO:0072207)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of female gonad development (GO:2000195)|negative regulation of metanephric glomerular mesangial cell proliferation (GO:0072302)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of heart growth (GO:0060421)|positive regulation of male gonad development (GO:2000020)|positive regulation of metanephric ureteric bud development (GO:2001076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior mesonephric tubule development (GO:0072166)|regulation of organ formation (GO:0003156)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|sex determination (GO:0007530)|thorax and anterior abdomen determination (GO:0007356)|tissue development (GO:0009888)|ureteric bud development (GO:0001657)|vasculogenesis (GO:0001570)|visceral serous pericardium development (GO:0061032)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.A314fs*4(19)|p.A314fs*69(11)|p.A314fs*3(3)|p.A314fs*7(2)|p.V311fs*3(2)|p.A314fs*6(2)|p.L310fs*63(1)|p.P308fs*67(1)|p.S313del(1)|p.A314fs*68(1)|p.A314fs*65(1)|p.T309fs*4(1)|p.A314fs*71(1)|p.?fs(1)|p.S313fs*70(1)|p.A314fs*15(1)	EWSR1/WT1(234)	NS(1)|haematopoietic_and_lymphoid_tissue(348)|kidney(149)|large_intestine(9)|lung(20)|peritoneum(1)|pleura(2)|skin(2)|upper_aerodigestive_tract(1)	533	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)			GTCTCAGATGCCGACCGTACAA	0.52			"""D, Mis, N, F, S"""	EWSR1	"""Wilms, desmoplastic small round cell tumor"""	Wilms			Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation;Frasier syndrome;Familial Wilms' tumor;Denys-Drash syndrome																													dbGAP	yes	Rec	yes	"""Denys-Drash syndrome, Frasier syndrome, Familial Wilms tumor"""	11	11p13	7490	Wilms tumour 1 gene		O	49	Insertion - Frameshift(41)|Deletion - Frameshift(4)|Complex - frameshift(3)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(47)|kidney(2)	11																																								32374485	SO:0001589	frameshift_variant	0	Familial Cancer Database	WAGR syndrome; ; ;incl.: Early Onset Nephrotic Syndrome-WT1 associated		CCDS7878.2, CCDS44561.1, CCDS44562.1, CCDS55750.1, CCDS55751.1	11p13	2014-09-17			ENSG00000184937	ENSG00000184937		"""Zinc fingers, C2H2-type"""	12796	protein-coding gene	gene with protein product		607102		GUD		14681303	Standard	NM_024424		Approved	WAGR, WIT-2, AWT1	uc001mtn.2	P19544	OTTHUMG00000039556	ENST00000379079.2:c.507_508insTCGG	11.37:g.32417908_32417909insCCGA	ENSP00000368370:p.Ala170fs	NA	NA	NA		NA	NA	NA	32374484	NA	NA	NA	A8K6S1|B3KSA5|Q15881|Q16256|Q16575|Q4VXV4|Q4VXV5|Q4VXV6|Q8IYZ5	Frame_Shift_Ins	INS	HMMPfam_WT1,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers	p.A381fs	ENST00000379079.2	37	c.1144_1143	CCDS55751.1	11																																																																																			-	HMMPfam_WT1		0.520	WT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	WT1	protein_coding	OTTHUMT00000095434.1	-	NM_000378		32374485	-1	no_errors	NM_024426.3	genbank	human	reviewed	54_36p	frame_shift_ins	INS	0.833:0.771	CCGA
CEBPA	1050	genome.wustl.edu	37	19	33792294	33792294	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AB-2839-03B-01W-0728-08	TCGA-AB-2839-11B-01W-0729-08	G	G	G	-	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	e46ca5db-40a6-4119-8f57-d5739cce62fe	2702acd2-a374-44e7-b9d5-c5caecdcbea0	g.chr19:33792294delG	ENST00000498907.2	-	1	1176	c.1027delC	c.(1027-1029)cgcfs	p.R343fs	CEBPA-AS1_ENST00000592982.2_RNA|CTD-2540B15.7_ENST00000587312.1_RNA|CTD-2540B15.11_ENST00000589932.1_RNA	NM_004364.3	NP_004355.2	P49715	CEBPA_HUMAN	CCAAT/enhancer binding protein (C/EBP), alpha	343	Leucine-zipper. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				acute-phase response (GO:0006953)|brown fat cell differentiation (GO:0050873)|cell maturation (GO:0048469)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|cholesterol metabolic process (GO:0008203)|cytokine-mediated signaling pathway (GO:0019221)|embryonic placenta development (GO:0001892)|generation of precursor metabolites and energy (GO:0006091)|inner ear development (GO:0048839)|liver development (GO:0001889)|lung development (GO:0030324)|macrophage differentiation (GO:0030225)|mitochondrion organization (GO:0007005)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ regeneration (GO:0031100)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|response to glucocorticoid (GO:0051384)|response to vitamin B2 (GO:0033274)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|urea cycle (GO:0000050)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|Rb-E2F complex (GO:0035189)	DNA binding (GO:0003677)|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 positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.R343fs*17(2)|p.H200_K352>Q(1)|p.?(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(912)|lung(5)|prostate(1)|stomach(1)	920	Esophageal squamous(110;0.137)					GGCAGCTGGCGGAAGATGCCC	0.692			"""Mis, N, F"""		"""AML, MDS"""				Acute Myeloid Leukemia, Familial, associated with CEBPA germline mutation																													dbGAP		Dom	yes		19	19q13.1	1050	"""CCAAT/enhancer binding protein (C/EBP), alpha"""		L	4	Deletion - Frameshift(2)|Unknown(1)|Complex - deletion inframe(1)	haematopoietic_and_lymphoid_tissue(4)	19											20.0	23.0	22.0					19																	33792294		2188	4276	6464	38484134	SO:0001589	frameshift_variant	0	Familial Cancer Database	Familial AML	M37197	CCDS54243.1	19q13.1	2014-09-17				ENSG00000245848		"""basic leucine zipper proteins"""	1833	protein-coding gene	gene with protein product		116897		CEBP		1535333, 1840554	Standard	NM_004364		Approved	C/EBP-alpha	uc002nun.3	P49715		ENST00000498907.2:c.1027delC	19.37:g.33792294delG	ENSP00000427514:p.Arg343fs	1	0.00	0		66	41.59	47	38484134	9	30.77	4	A7LNP2|P78319|Q05CA4	Frame_Shift_Del	DEL	HMMSmart_BRLZ,PatternScan_BZIP_BASIC,HMMPfam_bZIP_2	p.R343fs	ENST00000498907.2	37	c.1027	CCDS54243.1	19																																																																																			-	HMMSmart_BRLZ		0.692	CEBPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CEBPA	protein_coding	OTTHUMT00000365012.1	G	NM_004364		38484134	-1	no_errors	NM_004364.3	genbank	human	reviewed	54_36p	frame_shift_del	DEL	1.000	-
