#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
TMEM47	83604	genome.wustl.edu	37	X	34657408	34657408	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2846-03B-01W-0728-08	TCGA-AB-2846-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	67e8fb6c-72b9-4cb8-ad4e-cb9da7c77c88	a377205f-d22d-4637-b728-0d9decbdf206	g.chrX:34657408C>T	ENST00000275954.3	-	2	581	c.323G>A	c.(322-324)cGa>cAa	p.R108Q		NM_031442.3	NP_113630.1	Q9BQJ4	TMM47_HUMAN	transmembrane protein 47	108						cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(1)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						GAAACGCCTTCGAGATCCCAC	0.448																																						dbGAP											0			X											71.0	59.0	64.0					X																	34657408		2202	4300	6502	34567329	SO:0001583	missense	0			AK090917	CCDS14235.1	Xp11.4	2008-02-05	2005-03-21	2005-03-21	ENSG00000147027	ENSG00000147027			18515	protein-coding gene	gene with protein product		300698	"""transmembrane 4 superfamily member 10"""	TM4SF10		11472633	Standard	NM_031442		Approved	BCMP1, DKFZP761J17121, DKFZp564E153	uc004ddh.3	Q9BQJ4	OTTHUMG00000021343	ENST00000275954.3:c.323G>A	X.37:g.34657408C>T	ENSP00000275954:p.Arg108Gln	104	3.70	4		1	0.00	0	34567329	18	35.71	10	Q5JR44	Missense_Mutation	SNP	NULL	p.R108Q	ENST00000275954.3	37	c.323	CCDS14235.1	X	.	.	.	.	.	.	.	.	.	.	C	20.2	3.951728	0.73787	.	.	ENSG00000147027	ENST00000275954	T	0.68903	-0.36	5.71	4.84	0.62591	.	0.111342	0.64402	D	0.000012	T	0.46308	0.1386	N	0.22421	0.69	0.58432	D	0.999999	P	0.35348	0.496	B	0.22753	0.041	T	0.47275	-0.9130	10	0.28530	T	0.3	-0.3699	12.17	0.54152	0.0:0.9167:0.0:0.0833	.	108	Q9BQJ4	TMM47_HUMAN	Q	108	ENSP00000275954:R108Q	ENSP00000275954:R108Q	R	-	2	0	TMEM47	34567329	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.624000	0.61254	2.391000	0.81399	0.538000	0.68166	CGA	-	NULL		0.448	TMEM47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TMEM47	protein_coding	OTTHUMT00000056209.1	C	NM_031442		34567329	-1	no_errors	NM_031442.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
CENPF	1063	genome.wustl.edu	37	1	214819808	214819808	+	Missense_Mutation	SNP	C	C	G			TCGA-AB-2846-03B-01W-0728-08	TCGA-AB-2846-11B-01W-0729-08	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	67e8fb6c-72b9-4cb8-ad4e-cb9da7c77c88	a377205f-d22d-4637-b728-0d9decbdf206	g.chr1:214819808C>G	ENST00000366955.3	+	13	7063	c.6895C>G	c.(6895-6897)Ctg>Gtg	p.L2299V		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2395	2 X 177 AA tandem repeats.|Interaction with NDE1 and NDEL1.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		AGAGCATCAGCTGAGAAATAG	0.458																																					Colon(80;575 1284 11000 14801 43496)	dbGAP											0			1											62.0	68.0	66.0					1																	214819808		2203	4300	6503	212886431	SO:0001583	missense	0			U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"""mitosin"""	600236	"""centromere protein F, 350/400kDa (mitosin)"""			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.6895C>G	1.37:g.214819808C>G	ENSP00000355922:p.Leu2299Val	46	0.00	0		16	57.89	22	212886431	16	36.00	9	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	superfamily_Prefoldin,HMMPfam_Rb-bdg_C_Cenp-F,HMMPfam_Cenp-F_N,HMMPfam_Cenp-F_leu_zip,superfamily_Spectrin repeat	p.L2299V	ENST00000366955.3	37	c.6895	CCDS31023.1	1	.	.	.	.	.	.	.	.	.	.	C	15.49	2.849988	0.51270	.	.	ENSG00000117724	ENST00000366955	T	0.03607	3.87	4.59	1.57	0.23409	.	0.703587	0.10984	N	0.612370	T	0.02304	0.0071	N	0.19112	0.55	0.09310	N	1	P	0.50819	0.939	B	0.40165	0.321	T	0.44636	-0.9315	10	0.32370	T	0.25	.	2.855	0.05570	0.3374:0.3705:0.0:0.2922	.	2395	P49454	CENPF_HUMAN	V	2299	ENSP00000355922:L2299V	ENSP00000355922:L2299V	L	+	1	2	CENPF	212886431	0.001000	0.12720	0.010000	0.14722	0.384000	0.30261	0.299000	0.19138	0.224000	0.20940	0.407000	0.27541	CTG	-	NULL		0.458	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CENPF	protein_coding	OTTHUMT00000089749.1	C	NM_016343		212886431	+1	no_errors	NM_016343.3	genbank	human	reviewed	54_36p	missense	SNP	0.000	G
CLDN11	5010	genome.wustl.edu	37	3	170140969	170140969	+	Missense_Mutation	SNP	G	G	A	rs559887015		TCGA-AB-2846-03B-01W-0728-08	TCGA-AB-2846-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	67e8fb6c-72b9-4cb8-ad4e-cb9da7c77c88	a377205f-d22d-4637-b728-0d9decbdf206	g.chr3:170140969G>A	ENST00000064724.3	+	2	447	c.245G>A	c.(244-246)cGc>cAc	p.R82H	CLDN11_ENST00000486975.1_Missense_Mutation_p.R82H|CLDN11_ENST00000451576.1_Missense_Mutation_p.R82H|CLDN11_ENST00000489485.1_3'UTR	NM_005602.5	NP_005593.2	O75508	CLD11_HUMAN	claudin 11	82					axon ensheathment (GO:0008366)|calcium-independent cell-cell adhesion (GO:0016338)|spermatogenesis (GO:0007283)	basal part of cell (GO:0045178)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			central_nervous_system(2)|endometrium(2)|large_intestine(1)|liver(2)|lung(3)|ovary(2)	12	all_cancers(22;5.62e-23)|all_epithelial(15;7.54e-28)|all_lung(20;2.51e-17)|Lung NSC(18;1.02e-16)|Ovarian(172;0.000567)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			CAGGCCTGCCGCGCCCTGATG	0.602													G|||	1	0.000199681	0.0	0.0014	5008	,	,		18359	0.0		0.0	False		,,,				2504	0.0					dbGAP											0			3											143.0	140.0	141.0					3																	170140969		2203	4300	6503	171623663	SO:0001583	missense	0			AF068863	CCDS3213.1	3q26.2-q26.3	2008-08-01	2008-08-01		ENSG00000013297	ENSG00000013297		"""Claudins"""	8514	protein-coding gene	gene with protein product		601326	"""oligodendrocyte transmembrane protein"""	OTM		8661061, 8797478	Standard	NM_005602		Approved	OSP	uc003fgx.3	O75508	OTTHUMG00000158940	ENST00000064724.3:c.245G>A	3.37:g.170140969G>A	ENSP00000064724:p.Arg82His	106	0.00	0		NA	NA	NA	171623663	15	48.28	14	B2R7C1|D3DNQ5|Q5U0P3	Missense_Mutation	SNP	HMMPfam_PMP22_Claudin,PatternScan_CLAUDIN	p.R82H	ENST00000064724.3	37	c.245	CCDS3213.1	3	.	.	.	.	.	.	.	.	.	.	G	23.1	4.379020	0.82682	.	.	ENSG00000013297	ENST00000064724;ENST00000486975;ENST00000451576	D;D;D	0.89875	-2.58;-2.58;-2.58	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	D	0.96525	0.8866	H	0.95224	3.64	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.97261	0.9904	10	0.87932	D	0	.	19.7503	0.96265	0.0:0.0:1.0:0.0	.	82;82	B4DFI2;O75508	.;CLD11_HUMAN	H	82	ENSP00000064724:R82H;ENSP00000417434:R82H;ENSP00000410185:R82H	ENSP00000064724:R82H	R	+	2	0	CLDN11	171623663	1.000000	0.71417	0.984000	0.44739	0.293000	0.27360	9.441000	0.97557	2.675000	0.91044	0.557000	0.71058	CGC	-	HMMPfam_PMP22_Claudin		0.602	CLDN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CLDN11	protein_coding	OTTHUMT00000352403.1	G	NM_005602		171623663	+1	no_errors	NM_005602.5	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
ARAP2	116984	genome.wustl.edu	37	4	36152619	36152619	+	Missense_Mutation	SNP	A	A	G			TCGA-AB-2846-03B-01W-0728-08	TCGA-AB-2846-11B-01W-0729-08	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	67e8fb6c-72b9-4cb8-ad4e-cb9da7c77c88	a377205f-d22d-4637-b728-0d9decbdf206	g.chr4:36152619A>G	ENST00000303965.4	-	16	3289	c.2800T>C	c.(2800-2802)Tat>Cat	p.Y934H		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	934	PH 3. {ECO:0000255|PROSITE- ProRule:PRU00145}.				regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						TCATTTTCATAGTAACTCAAG	0.328																																						dbGAP											0			4											139.0	140.0	140.0					4																	36152619		2203	4299	6502	35829014	SO:0001583	missense	0			AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16924	protein-coding gene	gene with protein product		606645	"""centaurin, delta 1"""	CENTD1			Standard	NM_015230		Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:c.2800T>C	4.37:g.36152619A>G	ENSP00000302895:p.Tyr934His	132	3.65	5		7	53.33	8	35829014	14	30.00	6	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Missense_Mutation	SNP	HMMPfam_RA,HMMPfam_RhoGAP,HMMSmart_SM00324,HMMPfam_ArfGap,HMMSmart_SM00105,superfamily_Pyk2-associated protein beta ARF-GAP domain,HMMPfam_SAM_1,HMMSmart_SM00454,HMMPfam_PH,HMMSmart_SM00233,superfamily_GTPase activation domain GAP,superfamily_SAM/Pointed domain,superfamily_PH domain-like	p.Y934H	ENST00000303965.4	37	c.2800	CCDS3441.1	4	.	.	.	.	.	.	.	.	.	.	A	23.3	4.397534	0.83120	.	.	ENSG00000047365	ENST00000303965	T	0.79141	-1.24	5.69	5.69	0.88448	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	D	0.88890	0.6560	M	0.82517	2.595	0.47245	D	0.999362	D	0.89917	1.0	D	0.91635	0.999	D	0.90495	0.4470	10	0.87932	D	0	.	15.9451	0.79787	1.0:0.0:0.0:0.0	.	934	Q8WZ64	ARAP2_HUMAN	H	934	ENSP00000302895:Y934H	ENSP00000302895:Y934H	Y	-	1	0	ARAP2	35829014	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.022000	0.88759	2.177000	0.69029	0.533000	0.62120	TAT	-	HMMPfam_PH,HMMSmart_SM00233,superfamily_PH domain-like		0.328	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ARAP2	protein_coding	OTTHUMT00000215074.2	A	NM_015230		35829014	-1	no_errors	NM_015230.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	G
ZFP42	132625	genome.wustl.edu	37	4	188924151	188924151	+	Missense_Mutation	SNP	G	G	A	rs201496236		TCGA-AB-2846-03B-01W-0728-08	TCGA-AB-2846-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	67e8fb6c-72b9-4cb8-ad4e-cb9da7c77c88	a377205f-d22d-4637-b728-0d9decbdf206	g.chr4:188924151G>A	ENST00000326866.4	+	4	598	c.190G>A	c.(190-192)Gga>Aga	p.G64R	ZFP42_ENST00000509524.1_Missense_Mutation_p.G64R	NM_174900.3	NP_777560.2	Q96MM3	ZFP42_HUMAN	ZFP42 zinc finger protein	64					female gonad development (GO:0008585)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|meiotic nuclear division (GO:0007126)|regulation of genetic imprinting (GO:2000653)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(14;6.2e-52)|all_epithelial(14;7.36e-37)|all_lung(41;2.29e-15)|Lung NSC(41;6.7e-15)|Breast(6;1.53e-05)|Melanoma(20;3.01e-05)|Hepatocellular(41;0.00335)|all_hematologic(60;0.014)|Renal(120;0.0183)|Prostate(90;0.0421)|Colorectal(36;0.227)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;4.21e-06)|GBM - Glioblastoma multiforme(59;8.93e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.157)		TCAGGCTCTCGGAGGGGATGA	0.507													G|||	0	0.0	0.0	0.0	5008	,	,		18506	0.0		0.0	False		,,,				2504	0.0					dbGAP											0			4											100.0	92.0	95.0					4																	188924151		2203	4300	6503	189161145	SO:0001583	missense	0			AK056719	CCDS3849.1	4q35.2	2014-09-04	2012-11-27		ENSG00000179059	ENSG00000179059		"""Zinc fingers, C2H2-type"""	30949	protein-coding gene	gene with protein product		614572	"""zinc finger protein 42 homolog (mouse)"", ""zinc finger protein 42"""			12110702	Standard	NM_174900		Approved	REX1, ZNF754	uc003izh.1	Q96MM3	OTTHUMG00000160235	ENST00000326866.4:c.190G>A	4.37:g.188924151G>A	ENSP00000317686:p.Gly64Arg	71	1.39	1		NA	NA	NA	189161145	19	40.62	13	D3DP65|Q8WXE2	Missense_Mutation	SNP	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers	p.G64R	ENST00000326866.4	37	c.190	CCDS3849.1	4	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	14.85	2.658482	0.47467	.	.	ENSG00000179059	ENST00000326866;ENST00000509524	T;T	0.65364	-0.15;-0.15	4.52	2.81	0.32909	.	0.238817	0.33382	U	0.004978	T	0.43523	0.1251	L	0.46157	1.445	0.09310	N	1	P	0.50819	0.939	B	0.37144	0.242	T	0.33879	-0.9851	10	0.13108	T	0.6	.	6.5888	0.22636	0.2869:0.0:0.7131:0.0	.	64	Q96MM3	ZFP42_HUMAN	R	64	ENSP00000317686:G64R;ENSP00000424662:G64R	ENSP00000317686:G64R	G	+	1	0	ZFP42	189161145	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.202000	0.17295	0.851000	0.35264	0.655000	0.94253	GGA	-	NULL		0.507	ZFP42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZFP42	protein_coding	OTTHUMT00000359794.1	G	NM_174900		189161145	+1	no_errors	NM_174900.3	genbank	human	validated	54_36p	missense	SNP	0.001	A
PDE6A	5145	genome.wustl.edu	37	5	149324044	149324044	+	Silent	SNP	G	G	A			TCGA-AB-2846-03B-01W-0728-08	TCGA-AB-2846-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	67e8fb6c-72b9-4cb8-ad4e-cb9da7c77c88	a377205f-d22d-4637-b728-0d9decbdf206	g.chr5:149324044G>A	ENST00000255266.5	-	1	312	c.193C>T	c.(193-195)Ctg>Ttg	p.L65L		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	65					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	AAGTCCCGCAGGAGATCAAAG	0.532																																						dbGAP											0			5											72.0	71.0	72.0					5																	149324044		2203	4300	6503	149304237	SO:0001819	synonymous_variant	0				CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"""Phosphodiesterases"""	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.193C>T	5.37:g.149324044G>A		204	1.45	3		NA	NA	NA	149304237	38	39.68	25	Q0P638	Silent	SNP	HMMPfam_PDEase_I,PatternScan_PDEASE_I,HMMPfam_GAF,HMMSmart_GAF,HMMSmart_HDc,superfamily_SSF109604,superfamily_SSF55781	p.L65	ENST00000255266.5	37	c.193	CCDS4299.1	5																																																																																			-	superfamily_SSF55781		0.532	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PDE6A	protein_coding	OTTHUMT00000252326.2	G			149304237	-1	no_errors	NM_000440.2	genbank	human	reviewed	54_36p	silent	SNP	0.999	A
RPL7P20	728843	genome.wustl.edu	37	5	165455921	165455921	+	IGR	SNP	C	C	A			TCGA-AB-2846-03B-01W-0728-08	TCGA-AB-2846-11B-01W-0729-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	67e8fb6c-72b9-4cb8-ad4e-cb9da7c77c88	a377205f-d22d-4637-b728-0d9decbdf206	g.chr5:165455921C>A								CTC-535M15.2 (250227 upstream) : RP11-67M9.1 (99581 downstream)																							CTACAATCCTCAGCATGTTAA	0.413																																						dbGAP											0			5																																								165388499	SO:0001628	intergenic_variant	0																															5.37:g.165455921C>A		93	2.08	2		1	0.00	0	165388499	25	39.02	16		RNA	SNP	-	NULL		37	NULL		5																																																																																			-	-	0	0.413					LOC728843			C			165388499	-1	pseudogene	XR_015391.1	genbank	human	model	54_36p	rna	SNP	1.000	A
DST	667	genome.wustl.edu	37	6	56401599	56401599	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2846-03B-01W-0728-08	TCGA-AB-2846-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	67e8fb6c-72b9-4cb8-ad4e-cb9da7c77c88	a377205f-d22d-4637-b728-0d9decbdf206	g.chr6:56401599C>T	ENST00000361203.3	-	58	16122	c.16115G>A	c.(16114-16116)cGg>cAg	p.R5372Q	DST_ENST00000370754.5_Missense_Mutation_p.R5552Q|DST_ENST00000340834.4_5'UTR|DST_ENST00000312431.6_3'UTR|DST_ENST00000421834.2_Missense_Mutation_p.R3286Q|DST_ENST00000244364.6_Missense_Mutation_p.R2960Q|DST_ENST00000446842.2_Missense_Mutation_p.R5048Q|DST_ENST00000370769.4_Missense_Mutation_p.R5374Q|DST_ENST00000370788.2_Missense_Mutation_p.R3286Q			Q03001	DYST_HUMAN	dystonin	5372					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			AGTCTTCCACCGTGCATTGAC	0.428																																						dbGAP											0			6											154.0	153.0	153.0					6																	56401599		2035	4203	6238	56509558	SO:0001583	missense	0			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.16115G>A	6.37:g.56401599C>T	ENSP00000354508:p.Arg5372Gln	70	5.41	4		2	0.00	0	56509558	13	43.48	10	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	PatternScan_ACTININ_1,PatternScan_ACTININ_2,HMMPfam_CH,HMMSmart_SM00033,HMMPfam_Spectrin,HMMSmart_SM00054,HMMPfam_GAS2,HMMSmart_SM00243,superfamily_Calponin-homology domain CH-domain,HMMSmart_SM00150,PatternScan_EF_HAND_1,HMMPfam_efhand,superfamily_Spectrin repeat,superfamily_EF-hand	p.R3286Q	ENST00000361203.3	37	c.9857		6	.	.	.	.	.	.	.	.	.	.	C	17.89	3.499641	0.64298	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68;0.68;0.68	5.7	5.7	0.88788	.	0.000000	0.47455	D	0.000237	T	0.56366	0.1980	M	0.74647	2.275	0.27013	N	0.964632	D;D;D;P;P	0.89917	0.987;1.0;0.999;0.91;0.719	P;D;D;B;B	0.74348	0.71;0.983;0.936;0.267;0.206	T	0.54016	-0.8356	9	0.18276	T	0.48	.	14.0397	0.64667	0.0:0.928:0.0:0.072	.	3286;5374;5552;5372;2960	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	Q	2960;5552;5374;3286;5048;3286;5372	ENSP00000244364:R2960Q;ENSP00000359790:R5552Q;ENSP00000359805:R5374Q;ENSP00000400883:R3286Q;ENSP00000393645:R5048Q;ENSP00000359824:R3286Q;ENSP00000354508:R5372Q	ENSP00000244364:R2960Q	R	-	2	0	DST	56509558	0.998000	0.40836	0.637000	0.29366	0.945000	0.59286	4.693000	0.61753	2.697000	0.92050	0.585000	0.79938	CGG	-	HMMPfam_Spectrin,HMMSmart_SM00150,superfamily_Spectrin repeat		0.428	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	DST	protein_coding	OTTHUMT00000041021.3	C	NM_001723		56509558	-1	no_errors	NM_183380.1	genbank	human	reviewed	54_36p	missense	SNP	0.169	T
MGAM	8972	genome.wustl.edu	37	7	141767223	141767223	+	Intron	SNP	C	C	T			TCGA-AB-2846-03B-01W-0728-08	TCGA-AB-2846-11B-01W-0729-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	67e8fb6c-72b9-4cb8-ad4e-cb9da7c77c88	a377205f-d22d-4637-b728-0d9decbdf206	g.chr7:141767223C>T	ENST00000549489.2	+	38	4713				MGAM_ENST00000475668.2_Missense_Mutation_p.R1668C	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)						carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TGTCCTGGAGCGCGTGAGTAT	0.592																																						dbGAP											0			7											68.0	54.0	59.0					7																	141767223		874	1947	2821	141413692	SO:0001627	intron_variant	0			AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.4618+1955C>T	7.37:g.141767223C>T		77	8.33	7		NA	NA	NA	141413692	18	33.33	9	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	HMMPfam_Glyco_hydro_31,PatternScan_GLYCOSYL_HYDROL_F31_1,PatternScan_GLYCOSYL_HYDROL_F31_2,HMMPfam_Trefoil,HMMSmart_SM00018,superfamily_Trefoil,superfamily_(Trans)glycosidases,PatternScan_P_TREFOIL	p.R1668C	ENST00000549489.2	37	c.5002	CCDS47727.1	7	.	.	.	.	.	.	.	.	.	.	C	6.892	0.534010	0.13188	.	.	ENSG00000257335	ENST00000475668;ENST00000548812	.	.	.	3.98	1.92	0.25849	.	.	.	.	.	T	0.51839	0.1698	.	.	.	0.21782	N	0.999546	.	.	.	.	.	.	T	0.48305	-0.9047	5	0.62326	D	0.03	.	12.2054	0.54348	0.0:0.5086:0.4914:0.0	.	.	.	.	C	1668;1545	.	ENSP00000316431:R1545C	R	+	1	0	MGAM	141413692	0.000000	0.05858	0.975000	0.42487	0.113000	0.19764	0.013000	0.13310	0.619000	0.30197	0.306000	0.20318	CGC	-	HMMPfam_Glyco_hydro_31		0.592	MGAM-001	KNOWN	basic|CCDS	protein_coding	MGAM	protein_coding	OTTHUMT00000351244.3	C			141413692	+1	no_stop_codon	ENST00000312952	ensembl	human	known	54_36p	missense	SNP	0.019	T
RP11-383M4.6	0	genome.wustl.edu	37	9	84547723	84547723	+	lincRNA	SNP	G	G	A			TCGA-AB-2846-03B-01W-0728-08	TCGA-AB-2846-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	67e8fb6c-72b9-4cb8-ad4e-cb9da7c77c88	a377205f-d22d-4637-b728-0d9decbdf206	g.chr9:84547723G>A	ENST00000585776.1	-	0	1039				RP11-383M4.2_ENST00000427387.1_lincRNA|SPATA31D4_ENST00000341875.4_RNA																							GGACCACGGCGTTGATACCTC	0.418																																						dbGAP											0			9											112.0	94.0	99.0					9																	84547723		664	1532	2196	83737543			0																															9.37:g.84547723G>A		82	0.00	0		NA	NA	NA	83737543	21	46.15	18		Missense_Mutation	SNP	NULL	p.V883I	ENST00000585776.1	37	c.2647		9																																																																																			-	NULL		0.418	RP11-383M4.6-001	KNOWN	basic	lincRNA	uc004amh.1	lincRNA	OTTHUMT00000453562.1	G			83737543	+1	no_errors	ENST00000341875	ensembl	human	known	54_36p	missense	SNP	0.000	A
WSCD2	9671	genome.wustl.edu	37	12	108600074	108600074	+	Missense_Mutation	SNP	A	A	G			TCGA-AB-2846-03B-01W-0728-08	TCGA-AB-2846-11B-01W-0729-08	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	67e8fb6c-72b9-4cb8-ad4e-cb9da7c77c88	a377205f-d22d-4637-b728-0d9decbdf206	g.chr12:108600074A>G	ENST00000332082.4	+	4	1209	c.391A>G	c.(391-393)Atc>Gtc	p.I131V	WSCD2_ENST00000547525.1_Missense_Mutation_p.I131V|WSCD2_ENST00000261400.3_Missense_Mutation_p.I131V|WSCD2_ENST00000549903.1_Missense_Mutation_p.I131V			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	131	WSC 1. {ECO:0000255|PROSITE- ProRule:PRU00558}.					integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(1)|large_intestine(16)|liver(2)|lung(23)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	57						AGCCAAGTACATCGGCTGCTA	0.517																																						dbGAP											0			12											80.0	79.0	80.0					12																	108600074		1940	4144	6084	107124204	SO:0001583	missense	0				CCDS41828.1	12q23.3	2008-02-05				ENSG00000075035			29117	protein-coding gene	gene with protein product							Standard	NM_014653		Approved	KIAA0789	uc001tms.3	Q2TBF2		ENST00000332082.4:c.391A>G	12.37:g.108600074A>G	ENSP00000331933:p.Ile131Val	176	6.38	12		NA	NA	NA	107124204	34	41.38	24	B2RN48|B4DES1|Q8IY35|Q9Y4B7	Missense_Mutation	SNP	HMMPfam_WSC,HMMSmart_SM00321,superfamily_P-loop containing nucleoside triphosphate hydrolases	p.I131V	ENST00000332082.4	37	c.391	CCDS41828.1	12	.	.	.	.	.	.	.	.	.	.	A	7.226	0.598434	0.13939	.	.	ENSG00000075035	ENST00000547525;ENST00000261400;ENST00000332082;ENST00000549903	T;T;T;T	0.53206	0.63;0.63;0.63;0.63	5.29	2.58	0.30949	Carbohydrate-binding WSC (2);Carbohydrate-binding WSC, subgroup (1);	0.162631	0.52532	N	0.000063	T	0.22282	0.0537	N	0.04994	-0.135	0.53005	D	0.999966	B	0.06786	0.001	B	0.08055	0.003	T	0.04737	-1.0930	10	0.13853	T	0.58	-27.3841	9.612	0.39668	0.8282:0.0:0.1718:0.0	.	131	Q2TBF2	WSCD2_HUMAN	V	131	ENSP00000448047:I131V;ENSP00000261400:I131V;ENSP00000331933:I131V;ENSP00000447272:I131V	ENSP00000261400:I131V	I	+	1	0	WSCD2	107124204	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.737000	0.47393	0.856000	0.35383	0.528000	0.53228	ATC	-	HMMPfam_WSC,HMMSmart_SM00321		0.517	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	WSCD2	protein_coding	OTTHUMT00000405554.1	A	NM_014653		107124204	+1	no_errors	NM_014653.2	genbank	human	validated	54_36p	missense	SNP	1.000	G
OR4Q3	441669	genome.wustl.edu	37	14	20215692	20215692	+	Missense_Mutation	SNP	A	A	G			TCGA-AB-2846-03B-01W-0728-08	TCGA-AB-2846-11B-01W-0729-08	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	67e8fb6c-72b9-4cb8-ad4e-cb9da7c77c88	a377205f-d22d-4637-b728-0d9decbdf206	g.chr14:20215692A>G	ENST00000331723.1	+	1	106	c.106A>G	c.(106-108)Att>Gtt	p.I36V		NM_172194.1	NP_751944.1	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q, member 3	36						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(4)|endometrium(3)|kidney(2)|large_intestine(1)|lung(28)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		GTTTTTTTACATTGCTATTGT	0.378																																						dbGAP											0			14											175.0	179.0	177.0					14																	20215692		2203	4300	6503	19285532	SO:0001583	missense	0			AF179768	CCDS32020.1	14p13	2012-08-09				ENSG00000182652		"""GPCR / Class A : Olfactory receptors"""	15426	protein-coding gene	gene with protein product				OR4Q4			Standard	NM_172194		Approved	C14orf13	uc010tkt.2	Q8NH05		ENST00000331723.1:c.106A>G	14.37:g.20215692A>G	ENSP00000330049:p.Ile36Val	464	2.52	12		NA	NA	NA	19285532	61	42.59	46	Q6IEX4	Missense_Mutation	SNP	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321	p.I36V	ENST00000331723.1	37	c.106	CCDS32020.1	14	.	.	.	.	.	.	.	.	.	.	.	0.019	-1.457137	0.01071	.	.	ENSG00000182652	ENST00000331723	T	0.03035	4.07	4.32	-4.07	0.03975	.	1.116690	0.07031	U	0.828475	T	0.01254	0.0041	N	0.02202	-0.64	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.47086	-0.9144	10	0.02654	T	1	.	6.3055	0.21137	0.2397:0.4155:0.3448:0.0	.	36	Q8NH05	OR4Q3_HUMAN	V	36	ENSP00000330049:I36V	ENSP00000330049:I36V	I	+	1	0	OR4Q3	19285532	0.000000	0.05858	0.002000	0.10522	0.876000	0.50452	-4.802000	0.00184	-0.517000	0.06461	0.416000	0.27883	ATT	-	superfamily_SSF81321		0.378	OR4Q3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR4Q3	protein_coding	OTTHUMT00000409818.2	A			19285532	+1	no_errors	NM_172194.1	genbank	human	provisional	54_36p	missense	SNP	0.004	G
GEMIN4	50628	genome.wustl.edu	37	17	649463	649463	+	Missense_Mutation	SNP	A	A	T			TCGA-AB-2846-03B-01W-0728-08	TCGA-AB-2846-11B-01W-0729-08	A	A	A	T	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	67e8fb6c-72b9-4cb8-ad4e-cb9da7c77c88	a377205f-d22d-4637-b728-0d9decbdf206	g.chr17:649463A>T	ENST00000319004.5	-	2	1938	c.1820T>A	c.(1819-1821)cTc>cAc	p.L607H	GEMIN4_ENST00000576778.1_Missense_Mutation_p.L596H	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	607					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		GGTTTCTTTGAGGCATGACAC	0.498																																						dbGAP											0			17											129.0	130.0	130.0					17																	649463		1923	4148	6071	596213	SO:0001583	missense	0			AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"""HCC-associated protein 1"", ""component of gems 4"""	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.1820T>A	17.37:g.649463A>T	ENSP00000321706:p.Leu607His	55	1.79	1		18	53.85	21	596213	3	62.50	5	Q9NZS7|Q9UG32|Q9Y4Q2	Missense_Mutation	SNP	NULL	p.L607H	ENST00000319004.5	37	c.1820	CCDS45559.1	17	.	.	.	.	.	.	.	.	.	.	A	16.69	3.193098	0.58017	.	.	ENSG00000179409	ENST00000319004	T	0.18657	2.2	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.45518	0.1346	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.44360	-0.9333	10	0.87932	D	0	-12.3314	14.7489	0.69511	1.0:0.0:0.0:0.0	.	607	P57678	GEMI4_HUMAN	H	607	ENSP00000321706:L607H	ENSP00000321706:L607H	L	-	2	0	GEMIN4	596213	1.000000	0.71417	1.000000	0.80357	0.683000	0.39861	8.741000	0.91583	2.081000	0.62600	0.482000	0.46254	CTC	-	NULL		0.498	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GEMIN4	protein_coding	OTTHUMT00000437181.1	A	NM_015721		596213	-1	no_errors	NM_015721.2	genbank	human	reviewed	54_36p	missense	SNP	0.999	T
SLC17A7	57030	genome.wustl.edu	37	19	49933846	49933846	+	Missense_Mutation	SNP	G	G	A	rs148110556	byFrequency	TCGA-AB-2846-03B-01W-0728-08	TCGA-AB-2846-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	67e8fb6c-72b9-4cb8-ad4e-cb9da7c77c88	a377205f-d22d-4637-b728-0d9decbdf206	g.chr19:49933846G>A	ENST00000221485.3	-	12	1784	c.1613C>T	c.(1612-1614)cCg>cTg	p.P538L	SLC17A7_ENST00000543531.1_Missense_Mutation_p.P526L|SLC17A7_ENST00000600601.1_Missense_Mutation_p.P471L	NM_020309.3	NP_064705.1	Q9P2U7	VGLU1_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 7	538	Pro-rich.				glutamate secretion (GO:0014047)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|long-term memory (GO:0007616)|neurotransmitter secretion (GO:0007269)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|sequestering of neurotransmitter (GO:0042137)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|clathrin-sculpted glutamate transport vesicle membrane (GO:0060203)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|synaptic vesicle membrane (GO:0030672)	inorganic phosphate transmembrane transporter activity (GO:0005315)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:inorganic phosphate symporter activity (GO:0015319)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(7)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	26		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(486;0.0245)		ATAGGAGGGCGGGGGTGCAGG	0.652													G|||	4	0.000798722	0.003	0.0	5008	,	,		12349	0.0		0.0	False		,,,				2504	0.0					dbGAP											0			19						G	LEU/PRO	10,4376		0,10,2183	19.0	20.0	20.0		1613	4.7	0.9	19	dbSNP_134	20	0,8576		0,0,4288	yes	missense	SLC17A7	NM_020309.3	98	0,10,6471	AA,AG,GG		0.0,0.228,0.0771	benign	538/561	49933846	10,12952	2193	4288	6481	54625658	SO:0001583	missense	0			AB032436	CCDS12764.1	19q13.33	2013-07-18	2013-07-18		ENSG00000104888	ENSG00000104888		"""Solute carriers"""	16704	protein-coding gene	gene with protein product	"""vesicular glutamate transporter 1"""	605208	"""solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 7"""			8632143, 10820226	Standard	NM_020309		Approved	BNPI, VGLUT1	uc002pnp.3	Q9P2U7		ENST00000221485.3:c.1613C>T	19.37:g.49933846G>A	ENSP00000221485:p.Pro538Leu	18	0.00	0		NA	NA	NA	54625658	7	36.36	4	B4DFR9|B4DG46|Q6PCD0	Missense_Mutation	SNP	HMMPfam_MFS_1,superfamily_MFS_gen_substrate_transporter	p.P538L	ENST00000221485.3	37	c.1613	CCDS12764.1	19	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	9.524	1.108947	0.20714	0.00228	0.0	ENSG00000104888	ENST00000221485;ENST00000543531	T;T	0.63580	-0.04;-0.05	4.68	4.68	0.58851	.	0.428985	0.21729	N	0.069992	T	0.36936	0.0985	N	0.22421	0.69	0.44241	D	0.997087	B;B	0.27117	0.106;0.168	B;B	0.15484	0.008;0.013	T	0.29458	-1.0011	10	0.26408	T	0.33	.	13.2923	0.60278	0.0:0.0:1.0:0.0	.	538;380	Q9P2U7;A8K0Q7	VGLU1_HUMAN;.	L	538;526	ENSP00000221485:P538L;ENSP00000441767:P526L	ENSP00000221485:P538L	P	-	2	0	SLC17A7	54625658	0.925000	0.31364	0.935000	0.37517	0.458000	0.32498	2.662000	0.46766	2.614000	0.88457	0.585000	0.79938	CCG	-	NULL		0.652	SLC17A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC17A7	protein_coding	OTTHUMT00000465367.2	G			54625658	-1	no_errors	NM_020309.3	genbank	human	reviewed	54_36p	missense	SNP	0.264	A
TM9SF4	9777	genome.wustl.edu	37	20	30747885	30747885	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2846-03B-01W-0728-08	TCGA-AB-2846-11B-01W-0729-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	67e8fb6c-72b9-4cb8-ad4e-cb9da7c77c88	a377205f-d22d-4637-b728-0d9decbdf206	g.chr20:30747885G>A	ENST00000398022.2	+	16	1895	c.1660G>A	c.(1660-1662)Gtc>Atc	p.V554I	TM9SF4_ENST00000217315.5_Missense_Mutation_p.V537I	NM_014742.3	NP_055557.2	Q92544	TM9S4_HUMAN	transmembrane 9 superfamily protein member 4	554						integral component of membrane (GO:0016021)				central_nervous_system(2)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			AATCAGCATCGTCATGGTGTA	0.522																																						dbGAP											0			20											261.0	190.0	214.0					20																	30747885		2203	4300	6503	30211546	SO:0001583	missense	0			BC021107	CCDS13196.2	20q11.21	2004-04-19			ENSG00000101337	ENSG00000101337			30797	protein-coding gene	gene with protein product						9039502	Standard	NM_014742		Approved	KIAA0255, dJ836N17.2	uc002wxj.2	Q92544	OTTHUMG00000032206	ENST00000398022.2:c.1660G>A	20.37:g.30747885G>A	ENSP00000381104:p.Val554Ile	245	5.04	13		56	40.43	38	30211546	14	61.11	22	B0QYT7|Q9NUA3	Missense_Mutation	SNP	HMMPfam_EMP70	p.V537I	ENST00000398022.2	37	c.1609	CCDS13196.2	20	.	.	.	.	.	.	.	.	.	.	G	33	5.290265	0.95546	.	.	ENSG00000101337	ENST00000398022;ENST00000217315	T;T	0.44881	0.91;0.91	4.8	4.8	0.61643	.	0.134155	0.50627	D	0.000120	T	0.62672	0.2447	M	0.66506	2.035	0.80722	D	1	P;D	0.69078	0.951;0.997	B;D	0.66497	0.446;0.944	T	0.67039	-0.5771	10	0.87932	D	0	-26.3911	18.045	0.89329	0.0:0.0:1.0:0.0	.	461;554	B4DH88;Q92544	.;TM9S4_HUMAN	I	554;537	ENSP00000381104:V554I;ENSP00000217315:V537I	ENSP00000217315:V537I	V	+	1	0	TM9SF4	30211546	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	9.431000	0.97494	2.500000	0.84329	0.650000	0.86243	GTC	-	HMMPfam_EMP70		0.522	TM9SF4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	TM9SF4	protein_coding	OTTHUMT00000323568.1	G	NM_014742		30211546	+1	no_errors	NM_014742.3	genbank	human	validated	54_36p	missense	SNP	1.000	A
KIT	3815	genome.wustl.edu	37	4	55589766	55589766	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AB-2846-03B-01W-0728-08	TCGA-AB-2846-11B-01W-0729-08	G	G	G	-	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	67e8fb6c-72b9-4cb8-ad4e-cb9da7c77c88	a377205f-d22d-4637-b728-0d9decbdf206	g.chr4:55589766delG	ENST00000288135.5	+	8	1345	c.1248delG	c.(1246-1248)ctgfs	p.L416fs		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	416	Ig-like C2-type 5.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CAGAAATCCTGACTTACGACA	0.468		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													dbGAP	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	0			4											97.0	82.0	87.0					4																	55589766		2203	4300	6503	55284523	SO:0001589	frameshift_variant	0	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.1248delG	4.37:g.55589766delG	ENSP00000288135:p.Leu416fs	41	2.38	1		71	0.00	0	55284523	17	24.00	6	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Frame_Shift_Del	DEL	HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_IGc2,HMMSmart_IG,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726	p.T417fs	ENST00000288135.5	37	c.1248	CCDS3496.1	4																																																																																			-	NULL		0.468	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	KIT	protein_coding	OTTHUMT00000250618.1	G			55284523	+1	no_errors	NM_000222.2	genbank	human	reviewed	54_36p	frame_shift_del	DEL	0.990	-
KIT	3815	genome.wustl.edu	37	4	55589770	55589771	+	Frame_Shift_Ins	INS	-	-	AGGTGGG			TCGA-AB-2846-03B-01W-0728-08	TCGA-AB-2846-11B-01W-0729-08	-	-	-	AGGTGGG	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	67e8fb6c-72b9-4cb8-ad4e-cb9da7c77c88	a377205f-d22d-4637-b728-0d9decbdf206	g.chr4:55589770_55589771insAGGTGGG	ENST00000288135.5	+	8	1349_1350	c.1252_1253insAGGTGGG	c.(1252-1254)tacfs	p.Y418fs		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	418	Ig-like C2-type 5.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.Y418_D419>G(4)|p.T417_D419>I(2)|p.T417_D419>RG(2)|p.T417_D419>Y(2)|p.T417_R420>R(1)|p.T417_V422>SRIL(1)|p.T417_D419>F(1)|p.T417_D419>G(1)|p.T417_D419>KT(1)|p.T417_D419>L(1)|p.T417_D419>N(1)|p.T417_D419>KS(1)|p.Y418_R420>V(1)|p.T417_D419>RA(1)|p.T417_D419>S(1)|p.T417_D419>V(1)|p.T417_R420>SVIVG(1)|p.Y418_D419del(1)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AATCCTGACTTACGACAGGCTC	0.47		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													dbGAP	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	24	Complex - deletion inframe(22)|Deletion - In frame(1)|Complex - insertion inframe(1)	haematopoietic_and_lymphoid_tissue(24)	4																																								55284528	SO:0001589	frameshift_variant	0	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	Exception_encountered	4.37:g.55589770_55589771insAGGTGGG	ENSP00000288135:p.Tyr418fs	NA	NA	NA		NA	NA	NA	55284527	NA	NA	NA	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Frame_Shift_Ins	INS	HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_IGc2,HMMSmart_IG,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726	p.Y418fs	ENST00000288135.5	37	c.1252_1253	CCDS3496.1	4																																																																																			-	NULL		0.470	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	KIT	protein_coding	OTTHUMT00000250618.1	-			55284528	+1	no_errors	NM_000222.2	genbank	human	reviewed	54_36p	frame_shift_ins	INS	0.005:0.002	AGGTGGG
WT1	7490	genome.wustl.edu	37	11	32417909	32417910	+	Frame_Shift_Ins	INS	-	-	A	rs377446096|rs142937387		TCGA-AB-2846-03B-01W-0728-08	TCGA-AB-2846-11B-01W-0729-08	-	-	-	A	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	67e8fb6c-72b9-4cb8-ad4e-cb9da7c77c88	a377205f-d22d-4637-b728-0d9decbdf206	g.chr11:32417909_32417910insA	ENST00000379079.2	-	7	779_780	c.506_507insT	c.(505-507)tcgfs	p.S169fs	WT1_ENST00000448076.3_Frame_Shift_Ins_p.S381fs|WT1_ENST00000530998.1_Frame_Shift_Ins_p.S152fs|WT1_ENST00000332351.3_Frame_Shift_Ins_p.S381fs	NM_001198551.1	NP_001185480.1	P19544	WT1_HUMAN	Wilms tumor 1	313					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*69(11)|p.S313*(9)|p.S313fs*70(5)|p.A314fs*3(3)|p.A314fs*7(2)|p.V311fs*3(2)|p.A314fs*6(2)|p.S313fs*71(2)|p.L310fs*63(1)|p.P308fs*67(1)|p.S313del(1)|p.A314fs*68(1)|p.S313fs*4(1)|p.T309fs*4(1)|p.S313fs*6(1)|p.?fs(1)|p.A314fs*4(1)|p.A314fs*15(1)|p.S313fs*12(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)			TCTCAGATGCCGACCGTACAAG	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	47	Insertion - Frameshift(31)|Substitution - Nonsense(9)|Deletion - Frameshift(3)|Complex - frameshift(3)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(44)|kidney(3)	11	GRCh37	CM971595	WT1	M	rs142937387																																			32374486	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.506_507insT	11.37:g.32417909_32417910insA	ENSP00000368370:p.Ser169fs	53	0.00	0		13	0.00	0	32374485	6	14.29	1	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.A382fs	ENST00000379079.2	37	c.1143_1142	CCDS55751.1	11																																																																																			-	HMMPfam_WT1		0.520	WT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	WT1	protein_coding	OTTHUMT00000095434.1	-	NM_000378		32374486	-1	no_errors	NM_024426.3	genbank	human	reviewed	54_36p	frame_shift_ins	INS	0.771:0.996	A
