#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_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_EVS_AA	i_EVS_All	i_EVS_EA	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_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	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_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	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_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
ARHGEF1	9138	genome.wustl.edu	37	19	42396193	42396193	+	Splice_Site	SNP	C	C	T			TCGA-A2-A04Q-01A-21W-A050-09	TCGA-A2-A04Q-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	02eb17d4-9e9e-4e32-96b0-90ccdda3f167	41482042-a515-4e00-985b-f18952dfcbf3	g.chr19:42396193C>T	ENST00000354532.3	+	5	471	c.323C>T	c.(322-324)gCg>gTg	p.A108V	ARHGEF1_ENST00000599846.1_Splice_Site_p.A108V|ARHGEF1_ENST00000347545.4_Intron|ARHGEF1_ENST00000378152.4_Intron|ARHGEF1_ENST00000596957.1_3'UTR|ARHGEF1_ENST00000337665.4_Splice_Site_p.A123V	NM_004706.3	NP_004697.2	Q92888	ARHG1_HUMAN	Rho guanine nucleotide exchange factor (GEF) 1	108	RGSL.				cell proliferation (GO:0008283)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of axonogenesis (GO:0050770)|Rho protein signal transduction (GO:0007266)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|poly(A) RNA binding (GO:0044822)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		Renal(1328;0.000518)|Hepatocellular(1079;0.0046)|Medulloblastoma(540;0.0425)		Epithelial(262;5.89e-46)|GBM - Glioblastoma multiforme(1328;2.49e-12)|STAD - Stomach adenocarcinoma(1328;0.00644)		GAGAAGACAGCGGTGAGAGAC	0.617																																						dbGAP											0													50.0	47.0	48.0					19																	42396193		2203	4300	6503	-	-	-	SO:0001630	splice_region_variant	0			U64105	CCDS12590.1, CCDS12591.1, CCDS12592.1	19q13.13	2014-06-19			ENSG00000076928	ENSG00000076928		"""Rho guanine nucleotide exchange factors"""	681	protein-coding gene	gene with protein product		601855				8810315, 9135076	Standard	NM_004706		Approved	P115-RHOGEF, SUB1.5, LBCL2	uc002osa.3	Q92888	OTTHUMG00000182679	ENST00000354532.3:c.324+1C>T	19.37:g.42396193C>T			O00513|Q8N4J4|Q96BF4|Q96F17|Q9BSB1	Missense_Mutation	SNP	pfam_Regulat_G_prot_signal-like,pfam_DH-domain,superfamily_Regulat_G_prot_signal_superfam,superfamily_DH-domain,smart_DH-domain,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology,pfscan_DH-domain	p.A123V	ENST00000354532.3	37	c.368	CCDS12591.1	19	.	.	.	.	.	.	.	.	.	.	C	21.8	4.198506	0.79015	.	.	ENSG00000076928	ENST00000354532;ENST00000316079;ENST00000337665	D;D	0.88354	-2.37;-2.37	3.59	3.59	0.41128	Regulator of G protein signalling superfamily (1);Regulator of G protein signalling-like fold (1);	.	.	.	.	D	0.92496	0.7617	M	0.64997	1.995	0.80722	D	1	D;D;D	0.89917	0.996;0.999;1.0	P;P;D	0.71656	0.702;0.902;0.974	D	0.93118	0.6522	9	0.87932	D	0	.	13.1634	0.59557	0.0:1.0:0.0:0.0	.	123;108;168	Q92888-3;Q92888;Q8NF33	.;ARHG1_HUMAN;.	V	108;144;123	ENSP00000346532:A108V;ENSP00000337261:A123V	ENSP00000323044:A144V	A	+	2	0	ARHGEF1	47088033	1.000000	0.71417	0.980000	0.43619	0.870000	0.49936	1.700000	0.37815	2.039000	0.60335	0.306000	0.20318	GCG	ARHGEF1	-	pfam_Regulat_G_prot_signal-like,superfamily_Regulat_G_prot_signal_superfam	ENSG00000076928		0.617	ARHGEF1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	ARHGEF1	HGNC	protein_coding	OTTHUMT00000463360.1	72	0.00	0	C	NM_199002	Missense_Mutation	42396193	42396193	+1	no_errors	ENST00000337665	ensembl	human	known	69_37n	missense	70	13.41	11	SNP	1.000	T
ARHGEF10L	55160	genome.wustl.edu	37	1	17964411	17964411	+	Silent	SNP	C	C	A			TCGA-A2-A04Q-01A-21W-A050-09	TCGA-A2-A04Q-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	02eb17d4-9e9e-4e32-96b0-90ccdda3f167	41482042-a515-4e00-985b-f18952dfcbf3	g.chr1:17964411C>A	ENST00000361221.3	+	19	2115	c.1956C>A	c.(1954-1956)ctC>ctA	p.L652L	ARHGEF10L_ENST00000375420.3_Silent_p.L410L|ARHGEF10L_ENST00000375408.3_Silent_p.L425L|ARHGEF10L_ENST00000469726.1_3'UTR|ARHGEF10L_ENST00000167825.4_Silent_p.L355L|ARHGEF10L_ENST00000452522.1_Silent_p.L613L|ARHGEF10L_ENST00000375415.1_Silent_p.L613L|ARHGEF10L_ENST00000434513.1_Silent_p.L647L	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like	652						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		CCCCACGCCTCTTCCAGGAGC	0.597																																						dbGAP											0													51.0	37.0	41.0					1																	17964411		2200	4299	6499	-	-	-	SO:0001819	synonymous_variant	0			AB046846	CCDS182.1, CCDS30617.1	1p36.13	2011-11-16			ENSG00000074964	ENSG00000074964		"""Rho guanine nucleotide exchange factors"""	25540	protein-coding gene	gene with protein product	"""GrinchGEF"""	612494				10997877, 16112081	Standard	XM_005245923		Approved	FLJ10521, KIAA1626	uc001ban.3	Q9HCE6	OTTHUMG00000002514	ENST00000361221.3:c.1956C>A	1.37:g.17964411C>A			B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	Silent	SNP	pfam_DH-domain,superfamily_DH-domain,superfamily_WD40_repeat_dom,smart_DH-domain,pfscan_DH-domain	p.L652	ENST00000361221.3	37	c.1956	CCDS182.1	1																																																																																			ARHGEF10L	-	NULL	ENSG00000074964		0.597	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	ARHGEF10L	HGNC	protein_coding	OTTHUMT00000007147.1	31	0.00	0	C	NM_018125		17964411	17964411	+1	no_errors	ENST00000361221	ensembl	human	known	69_37n	silent	21	16.00	4	SNP	1.000	A
ARID2	196528	genome.wustl.edu	37	12	46230605	46230605	+	Missense_Mutation	SNP	G	G	A			TCGA-A2-A04Q-01A-21W-A050-09	TCGA-A2-A04Q-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	02eb17d4-9e9e-4e32-96b0-90ccdda3f167	41482042-a515-4e00-985b-f18952dfcbf3	g.chr12:46230605G>A	ENST00000334344.6	+	8	1026	c.854G>A	c.(853-855)cGg>cAg	p.R285Q	ARID2_ENST00000444670.1_5'Flank|ARID2_ENST00000422737.1_Missense_Mutation_p.R136Q|ARID2_ENST00000479608.1_3'UTR	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	285					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R285Q(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		GAAGGACAGCGGGTACTTCAG	0.403			"""N, S, F"""		hepatocellular carcinoma																																	dbGAP		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	1	Substitution - Missense(1)	large_intestine(1)											157.0	153.0	155.0					12																	46230605		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"""-"""	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.854G>A	12.37:g.46230605G>A	ENSP00000335044:p.Arg285Gln		Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Missense_Mutation	SNP	pfam_ARID/BRIGHT_DNA-bd,pfam_DNA-bd_RFX,superfamily_ARID/BRIGHT_DNA-bd,superfamily_ARM-type_fold,smart_ARID/BRIGHT_DNA-bd,pfscan_ARID/BRIGHT_DNA-bd	p.R285Q	ENST00000334344.6	37	c.854	CCDS31783.1	12	.	.	.	.	.	.	.	.	.	.	G	35	5.482817	0.96307	.	.	ENSG00000189079	ENST00000334344;ENST00000422737	T;T	0.48522	0.81;0.81	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.71195	0.3311	M	0.73598	2.24	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.72616	-0.4239	10	0.87932	D	0	-12.5418	20.2009	0.98259	0.0:0.0:1.0:0.0	.	285	Q68CP9	ARID2_HUMAN	Q	285;136	ENSP00000335044:R285Q;ENSP00000415650:R136Q	ENSP00000335044:R285Q	R	+	2	0	ARID2	44516872	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.822000	0.99363	2.767000	0.95098	0.591000	0.81541	CGG	ARID2	-	superfamily_ARM-type_fold	ENSG00000189079		0.403	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ARID2	HGNC	protein_coding	OTTHUMT00000318380.2	136	0.73	1	G	XM_350875		46230605	46230605	+1	no_errors	ENST00000334344	ensembl	human	known	69_37n	missense	269	12.66	39	SNP	1.000	A
CHADL	150356	genome.wustl.edu	37	22	41636845	41636846	+	Intron	INS	-	-	C			TCGA-A2-A04Q-01A-21W-A050-09	TCGA-A2-A04Q-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	02eb17d4-9e9e-4e32-96b0-90ccdda3f167	41482042-a515-4e00-985b-f18952dfcbf3	g.chr22:41636845_41636846insC	ENST00000216241.9	-	1	61					NM_138481.1	NP_612490.1	Q6NUI6	CHADL_HUMAN	chondroadherin-like							proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|kidney(1)|skin(1)	4						CTGCTCTGAATCCCCCCTTGCA	0.673																																						dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			BC012882	CCDS46715.1	22q13.2	2008-10-31			ENSG00000100399	ENSG00000100399			25165	protein-coding gene	gene with protein product						12477932	Standard	NM_138481		Approved	SLRR4B	uc003azq.4	Q6NUI6	OTTHUMG00000150936	ENST00000216241.9:c.8+31->G	22.37:g.41636851_41636851dupC			Q05CY2|Q4G0S0|Q5JY13|Q86XY1|Q96E60	Frame_Shift_Ins	INS	pfam_Leu-rich_rpt,smart_Leu-rich_rpt_typical-subtyp,smart_Cys-rich_flank_reg_C	p.F19fs	ENST00000216241.9	37	c.54_53	CCDS46715.1	22																																																																																			CHADL	-	NULL	ENSG00000100399		0.673	CHADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CHADL	HGNC	protein_coding	OTTHUMT00000320597.1	28	0.00	0	-	NM_138481		41636845	41636846	-1	no_start_codon:no_stop_codon:bad_bp_length_for_coding_region	ENST00000455425	ensembl	human	putative	69_37n	frame_shift_ins	26	10.34	3	INS	0.005:0.003	C
CHAF1A	10036	genome.wustl.edu	37	19	4432011	4432011	+	Missense_Mutation	SNP	G	G	T	rs11556317	byFrequency	TCGA-A2-A04Q-01A-21W-A050-09	TCGA-A2-A04Q-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	02eb17d4-9e9e-4e32-96b0-90ccdda3f167	41482042-a515-4e00-985b-f18952dfcbf3	g.chr19:4432011G>T	ENST00000301280.5	+	12	2111	c.2010G>T	c.(2008-2010)gaG>gaT	p.E670D	CHAF1A_ENST00000587368.1_3'UTR|CTB-50L17.5_ENST00000590159.1_RNA	NM_005483.2	NP_005474	Q13111	CAF1A_HUMAN	chromatin assembly factor 1, subunit A (p150)	670	Binds to p60.|Necessary for homodimerization and competence for chromatin assembly.				cell cycle (GO:0007049)|chromatin assembly (GO:0031497)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|protein complex assembly (GO:0006461)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|identical protein binding (GO:0042802)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	27		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		AGTGGGACGAGTTCCTGGCTA	0.557								Chromatin Structure																														dbGAP											0													102.0	93.0	96.0					19																	4432011		2203	4300	6503	-	-	-	SO:0001583	missense	0			U20979	CCDS32875.1	19p13.3	2008-07-16				ENSG00000167670			1910	protein-coding gene	gene with protein product	"""chromatin assembly factor I (150 kDa)"""	601246				7600578	Standard	NM_005483		Approved	CAF1P150, CAF1B, CAF-1, CAF1, P150, MGC71229	uc002mal.3	Q13111		ENST00000301280.5:c.2010G>T	19.37:g.4432011G>T	ENSP00000301280:p.Glu670Asp		Q6NXG5|Q7Z7K3|Q9UJY8	Missense_Mutation	SNP	pfam_CAF1A,pfam_CAF-1_p150	p.E670D	ENST00000301280.5	37	c.2010	CCDS32875.1	19	.	.	.	.	.	.	.	.	.	.	G	11.15	1.552865	0.27739	.	.	ENSG00000167670	ENST00000344143;ENST00000535117;ENST00000301280	T	0.30448	1.53	4.71	2.59	0.31030	.	.	.	.	.	T	0.26340	0.0643	L	0.53249	1.67	0.54753	D	0.99998	P	0.36144	0.539	B	0.31547	0.132	T	0.20140	-1.0284	9	0.87932	D	0	-48.5194	10.1137	0.42579	0.2295:0.0:0.7705:0.0	.	670	Q13111	CAF1A_HUMAN	D	670	ENSP00000301280:E670D	ENSP00000301280:E670D	E	+	3	2	CHAF1A	4383011	1.000000	0.71417	0.894000	0.35097	0.204000	0.24138	2.857000	0.48349	1.333000	0.45449	-0.258000	0.10820	GAG	CHAF1A	-	NULL	ENSG00000167670		0.557	CHAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CHAF1A	HGNC	protein_coding	OTTHUMT00000458310.2	105	0.00	0	G	NM_005483		4432011	4432011	+1	no_errors	ENST00000301280	ensembl	human	known	69_37n	missense	64	11.11	8	SNP	0.991	T
CLSTN2	64084	genome.wustl.edu	37	3	140251267	140251267	+	Silent	SNP	C	C	T			TCGA-A2-A04Q-01A-21W-A050-09	TCGA-A2-A04Q-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	02eb17d4-9e9e-4e32-96b0-90ccdda3f167	41482042-a515-4e00-985b-f18952dfcbf3	g.chr3:140251267C>T	ENST00000458420.3	+	9	1636	c.1446C>T	c.(1444-1446)aaC>aaT	p.N482N		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	482					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						TGGTGACCAACGACTGGCCCA	0.458										HNSCC(16;0.037)																											GBM(45;858 913 3709 36904 37282)	dbGAP											0													167.0	139.0	149.0					3																	140251267		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"""Cadherins / Cadherin-related"""	17448	protein-coding gene	gene with protein product	"""cadherin-related family member 13"""	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.1446C>T	3.37:g.140251267C>T			B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Silent	SNP	pfam_Cadherin,superfamily_ConA-like_lec_gl,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.N482	ENST00000458420.3	37	c.1446	CCDS3112.1	3																																																																																			CLSTN2	-	superfamily_ConA-like_lec_gl	ENSG00000158258		0.458	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CLSTN2	HGNC	protein_coding	OTTHUMT00000359393.3	112	0.00	0	C	NM_022131		140251267	140251267	+1	no_errors	ENST00000458420	ensembl	human	known	69_37n	silent	124	16.22	24	SNP	0.984	T
GPI	2821	genome.wustl.edu	37	19	34856187	34856188	+	Frame_Shift_Ins	INS	-	-	G			TCGA-A2-A04Q-01A-21W-A050-09	TCGA-A2-A04Q-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	02eb17d4-9e9e-4e32-96b0-90ccdda3f167	41482042-a515-4e00-985b-f18952dfcbf3	g.chr19:34856187_34856188insG	ENST00000356487.5	+	1	257_258	c.16_17insG	c.(16-18)cggfs	p.R6fs	GPI_ENST00000586425.1_Frame_Shift_Ins_p.R6fs|GPI_ENST00000415930.3_Frame_Shift_Ins_p.R45fs	NM_000175.3	NP_000166.2	P06744	G6PI_HUMAN	glucose-6-phosphate isomerase	6					aldehyde catabolic process (GO:0046185)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|hemostasis (GO:0007599)|humoral immune response (GO:0006959)|learning or memory (GO:0007611)|methylglyoxal biosynthetic process (GO:0019242)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glucose-6-phosphate isomerase activity (GO:0004347)|intramolecular transferase activity (GO:0016866)|monosaccharide binding (GO:0048029)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	25	Esophageal squamous(110;0.162)					CGCTCTCACCCGGGACCCCCAG	0.668																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			M61214	CCDS12437.1, CCDS54246.1	19q13.1	2012-10-02	2010-05-11			ENSG00000105220	5.3.1.9		4458	protein-coding gene	gene with protein product		172400	"""glucose phosphate isomerase"""			2387591, 8575767	Standard	NM_001184722		Approved	AMF, NLK	uc002nvg.2	P06744		ENST00000356487.5:c.19dupG	19.37:g.34856190_34856190dupG	ENSP00000348877:p.Arg6fs		B4DG39|Q9BRD3|Q9BSK5|Q9UHE6	Frame_Shift_Ins	INS	pfam_G6P_Isomerase,prints_G6P_Isomerase	p.D46fs	ENST00000356487.5	37	c.133_134	CCDS12437.1	19																																																																																			GPI	-	NULL	ENSG00000105220		0.668	GPI-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	GPI	HGNC	protein_coding	OTTHUMT00000451693.3	33	0.00	0	-			34856187	34856188	+1	no_errors	ENST00000415930	ensembl	human	known	69_37n	frame_shift_ins	9	18.18	2	INS	0.460:0.410	G
HECW1	23072	genome.wustl.edu	37	7	43590145	43590145	+	Silent	SNP	C	C	T			TCGA-A2-A04Q-01A-21W-A050-09	TCGA-A2-A04Q-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	02eb17d4-9e9e-4e32-96b0-90ccdda3f167	41482042-a515-4e00-985b-f18952dfcbf3	g.chr7:43590145C>T	ENST00000395891.2	+	27	4955	c.4350C>T	c.(4348-4350)cgC>cgT	p.R1450R	HECW1_ENST00000453890.1_Silent_p.R1416R	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1450	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						GGGTGGAGCGCGGCGTGGTAC	0.627																																						dbGAP											0													59.0	67.0	64.0					7																	43590145		2178	4280	6458	-	-	-	SO:0001819	synonymous_variant	0			AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.4350C>T	7.37:g.43590145C>T			A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	pfam_HECT,pfam_WW_Rsp5_WWP,pfam_C2_Ca-dep,superfamily_HECT,superfamily_WW_Rsp5_WWP,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_C2_Ca-dep,smart_WW_Rsp5_WWP,smart_HECT,pfscan_HECT,pfscan_C2_membr_targeting,pfscan_WW_Rsp5_WWP	p.R1450	ENST00000395891.2	37	c.4350	CCDS5469.2	7																																																																																			HECW1	-	pfam_HECT,superfamily_HECT,smart_HECT,pfscan_HECT	ENSG00000002746		0.627	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HECW1	HGNC	protein_coding	OTTHUMT00000250893.2	155	0.00	0	C	NM_015052		43590145	43590145	+1	no_errors	ENST00000395891	ensembl	human	known	69_37n	silent	138	12.03	19	SNP	0.091	T
KCNQ5	56479	genome.wustl.edu	37	6	73843189	73843189	+	Silent	SNP	G	G	A			TCGA-A2-A04Q-01A-21W-A050-09	TCGA-A2-A04Q-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	02eb17d4-9e9e-4e32-96b0-90ccdda3f167	41482042-a515-4e00-985b-f18952dfcbf3	g.chr6:73843189G>A	ENST00000370398.1	+	10	1402	c.1293G>A	c.(1291-1293)agG>agA	p.R431R	KCNQ5_ENST00000402622.2_Silent_p.R441R|KCNQ5_ENST00000355635.3_Silent_p.R432R|KCNQ5_ENST00000355194.4_Silent_p.R431R|KCNQ5-AS1_ENST00000429832.1_RNA|KCNQ5_ENST00000414165.2_Intron|KCNQ5_ENST00000342056.2_Silent_p.R450R|KCNQ5_ENST00000403813.2_Silent_p.R422R	NM_019842.3	NP_062816.2	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 5	431					protein complex assembly (GO:0006461)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242)			breast(1)|cervix(1)|endometrium(6)|kidney(7)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	57		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)	Ezogabine(DB04953)	CTAGCCCCAGGGGCCAGAGTA	0.522																																					GBM(142;1375 1859 14391 23261 44706)	dbGAP											0													75.0	77.0	76.0					6																	73843189		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF202977	CCDS4976.1, CCDS55034.1	6q14	2012-07-05			ENSG00000185760	ENSG00000185760		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6299	protein-coding gene	gene with protein product		607357				10787416, 10816588, 16382104	Standard	NM_019842		Approved	Kv7.5	uc011dyh.2	Q9NR82	OTTHUMG00000015020	ENST00000370398.1:c.1293G>A	6.37:g.73843189G>A			A6NKT6|A6PVT6|A8MSQ5|B4DS33|B5MC83|B7ZL37|F5GZV0|Q17RE1|Q5VVP3|Q86W40|Q9NRN0|Q9NYA6	Missense_Mutation	SNP	pfam_K_chnl_volt-dep_KCNQ_C	p.G23R	ENST00000370398.1	37	c.67	CCDS4976.1	6	.	.	.	.	.	.	.	.	.	.	G	9.527	1.109937	0.20714	.	.	ENSG00000185760	ENST00000427928	.	.	.	5.59	2.59	0.31030	.	.	.	.	.	T	0.41673	0.1169	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.30357	-0.9981	4	.	.	.	.	7.5212	0.27629	0.4063:0.0:0.5937:0.0	.	.	.	.	R	23	.	.	G	+	1	0	KCNQ5	73899910	0.868000	0.29978	0.989000	0.46669	0.978000	0.69477	0.006000	0.13152	0.710000	0.31997	0.563000	0.77884	GGG	KCNQ5	-	NULL	ENSG00000185760		0.522	KCNQ5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	KCNQ5	HGNC	protein_coding	OTTHUMT00000041198.3	254	0.00	0	G	NM_019842		73843189	73843189	+1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000427928	ensembl	human	putative	69_37n	missense	124	10.14	14	SNP	1.000	A
NF1	4763	genome.wustl.edu	37	17	29548939	29548939	+	Nonsense_Mutation	SNP	G	G	A			TCGA-A2-A04Q-01A-21W-A050-09	TCGA-A2-A04Q-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	02eb17d4-9e9e-4e32-96b0-90ccdda3f167	41482042-a515-4e00-985b-f18952dfcbf3	g.chr17:29548939G>A	ENST00000358273.4	+	15	2096	c.1713G>A	c.(1711-1713)tgG>tgA	p.W571*	NF1_ENST00000431387.4_Nonsense_Mutation_p.W571*|NF1_ENST00000356175.3_Nonsense_Mutation_p.W571*	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	571					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		AAACATTTTGGGAGATTAGGT	0.279			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												dbGAP	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	12	Whole gene deletion(8)|Unknown(4)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)	GRCh37	CM080451	NF1	M							58.0	56.0	56.0					17																	29548939		2202	4298	6500	-	-	-	SO:0001587	stop_gained	0	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.1713G>A	17.37:g.29548939G>A	ENSP00000351015:p.Trp571*		O00662|Q14284|Q14930|Q14931|Q9UMK3	Nonsense_Mutation	SNP	pfam_RasGAP,superfamily_Rho_GTPase_activation_prot,superfamily_ARM-type_fold,superfamily_CRAL-TRIO_dom,smart_RasGAP,smart_CRAL-TRIO_dom,pfscan_CRAL-TRIO_dom,pfscan_RasGAP	p.W571*	ENST00000358273.4	37	c.1713	CCDS42292.1	17	.	.	.	.	.	.	.	.	.	.	G	40	8.013207	0.98610	.	.	ENSG00000196712	ENST00000431387;ENST00000358273;ENST00000356175;ENST00000456735	.	.	.	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.0022	0.97423	0.0:0.0:1.0:0.0	.	.	.	.	X	571;571;571;237	.	ENSP00000348498:W571X	W	+	3	0	NF1	26573065	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.434000	0.97515	2.738000	0.93877	0.655000	0.94253	TGG	NF1	-	superfamily_ARM-type_fold	ENSG00000196712		0.279	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NF1	HGNC	protein_coding	OTTHUMT00000256351.2	46	0.00	0	G	NM_000267		29548939	29548939	+1	no_errors	ENST00000358273	ensembl	human	known	69_37n	nonsense	259	12.50	37	SNP	1.000	A
PCLO	27445	genome.wustl.edu	37	7	82791690	82791691	+	Frame_Shift_Ins	INS	-	-	G	rs370346756	byFrequency	TCGA-A2-A04Q-01A-21W-A050-09	TCGA-A2-A04Q-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	02eb17d4-9e9e-4e32-96b0-90ccdda3f167	41482042-a515-4e00-985b-f18952dfcbf3	g.chr7:82791690_82791691insG	ENST00000333891.9	-	1	555_556	c.218_219insC	c.(217-219)ccgfs	p.P73fs	PCLO_ENST00000423517.2_Frame_Shift_Ins_p.P73fs	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.Q186E(1)|p.P73R(1)		breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CCGCAGCGGCCGGGGGGACGCT	0.604																																						dbGAP											2	Substitution - Missense(2)	upper_aerodigestive_tract(2)																																								-	-	-	SO:0001589	frameshift_variant	0			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.219dupC	7.37:g.82791696_82791696dupG	ENSP00000334319:p.Pro73fs			Frame_Shift_Ins	INS	pfam_Znf_piccolo,pfam_C2_Ca-dep,pfam_PDZ,superfamily_C2_Ca/lipid-bd_dom_CaLB,superfamily_PDZ,superfamily_Znf_FYVE_PHD,smart_PDZ,smart_C2_Ca-dep,pfscan_C2_membr_targeting,pfscan_PDZ	p.A74fs	ENST00000333891.9	37	c.219_218	CCDS47630.1	7																																																																																			PCLO	-	NULL	ENSG00000186472		0.604	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	PCLO	HGNC	protein_coding	OTTHUMT00000337368.5	27	0.00	0	-	NM_014510		82791690	82791691	-1	no_errors	ENST00000333891	ensembl	human	known	69_37n	frame_shift_ins	23	11.54	3	INS	0.999:0.998	G
SH3PXD2A	9644	genome.wustl.edu	37	10	105484097	105484098	+	Frame_Shift_Ins	INS	-	-	G	rs149867987		TCGA-A2-A04Q-01A-21W-A050-09	TCGA-A2-A04Q-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	02eb17d4-9e9e-4e32-96b0-90ccdda3f167	41482042-a515-4e00-985b-f18952dfcbf3	g.chr10:105484097_105484098insG	ENST00000369774.4	-	5	604_605	c.328_329insC	c.(328-330)cacfs	p.H110fs	SH3PXD2A_ENST00000355946.2_Frame_Shift_Ins_p.H110fs			Q5TCZ1	SPD2A_HUMAN	SH3 and PX domains 2A	110	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(18)|ovary(1)|skin(1)|urinary_tract(1)	38		Colorectal(252;0.0815)|Breast(234;0.131)		Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119)		CTGTGAGATGTGGGGGGGCAGC	0.535																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AB007878	CCDS31278.1	10q25.1	2006-02-13	2006-02-13	2006-02-13	ENSG00000107957	ENSG00000107957			23664	protein-coding gene	gene with protein product	"""five SH3 domains"""		"""SH3 multiple domains 1"""	SH3MD1		9687503	Standard	XM_005270297		Approved	FISH, KIAA0418	uc001kxj.1	Q5TCZ1	OTTHUMG00000018997	ENST00000369774.4:c.329dupC	10.37:g.105484104_105484104dupG	ENSP00000358789:p.His110fs		D3DR98|O43302|Q5TCZ2|Q5TDQ8	Frame_Shift_Ins	INS	pfam_SH3_domain,pfam_SH3_2,pfam_Phox,superfamily_Phox,superfamily_SH3_domain,smart_Phox,smart_SH3_domain,pfscan_Phox,pfscan_SH3_domain	p.H110fs	ENST00000369774.4	37	c.329_328		10																																																																																			SH3PXD2A	-	pfam_Phox,superfamily_Phox,smart_Phox,pfscan_Phox	ENSG00000107957		0.535	SH3PXD2A-001	KNOWN	basic	protein_coding	SH3PXD2A	HGNC	protein_coding	OTTHUMT00000050178.1	44	0.00	0	-	NM_014631		105484097	105484098	-1	no_errors	ENST00000369774	ensembl	human	known	69_37n	frame_shift_ins	40	11.11	5	INS	1.000:0.989	G
SVEP1	79987	genome.wustl.edu	37	9	113191597	113191597	+	Missense_Mutation	SNP	G	G	T	rs76469101	byFrequency	TCGA-A2-A04Q-01A-21W-A050-09	TCGA-A2-A04Q-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	02eb17d4-9e9e-4e32-96b0-90ccdda3f167	41482042-a515-4e00-985b-f18952dfcbf3	g.chr9:113191597G>T	ENST00000401783.2	-	35	5969	c.5633C>A	c.(5632-5634)aCt>aAt	p.T1878N	SVEP1_ENST00000374469.1_Missense_Mutation_p.T1855N|SVEP1_ENST00000297826.5_5'Flank	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1878	Sushi 8. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						ACCGGCCAGAGTATATCCTTT	0.373																																						dbGAP											0													31.0	29.0	30.0					9																	113191597		1826	4082	5908	-	-	-	SO:0001583	missense	0			AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.5633C>A	9.37:g.113191597G>T	ENSP00000384917:p.Thr1878Asn		Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	pfam_Sushi_SCR_CCP,pfam_EGF-like_dom,pfam_Tyr-kin_ephrin_A/B_rcpt-like,pfam_Hyalin,pfam_VWF_A,pfam_Pentaxin,pfam_EGF_extracell,pfam_EGF-like_Ca-bd,superfamily_ConA-like_lec_gl,superfamily_Complement_control_module,superfamily_Growth_fac_rcpt,smart_VWF_A,smart_Sushi_SCR_CCP,smart_EGF-like_Ca-bd,smart_EGF-like,smart_Pentaxin,pfscan_EG-like_dom,pfscan_Hyalin,pfscan_Sushi_SCR_CCP,pfscan_VWF_A,prints_Pentaxin	p.T1878N	ENST00000401783.2	37	c.5633	CCDS48004.1	9	.	.	.	.	.	.	.	.	.	.	G	4.604	0.112245	0.08831	.	.	ENSG00000165124	ENST00000401783;ENST00000374469	T;T	0.64803	-0.12;-0.12	5.17	0.493	0.16878	Complement control module (2);Sushi/SCR/CCP (3);	0.564203	0.19954	N	0.102353	T	0.37892	0.1020	N	0.26130	0.795	0.09310	N	0.99999	B	0.12630	0.006	B	0.12156	0.007	T	0.07424	-1.0773	10	0.20046	T	0.44	.	1.835	0.03138	0.1462:0.1919:0.3544:0.3075	.	1878	Q4LDE5	SVEP1_HUMAN	N	1878;1855	ENSP00000384917:T1878N;ENSP00000363593:T1855N	ENSP00000363593:T1855N	T	-	2	0	SVEP1	112231418	0.001000	0.12720	0.220000	0.23810	0.893000	0.52053	-0.099000	0.11007	0.282000	0.22254	0.650000	0.86243	ACT	SVEP1	-	pfam_Sushi_SCR_CCP,superfamily_Complement_control_module,smart_Sushi_SCR_CCP,pfscan_Sushi_SCR_CCP	ENSG00000165124		0.373	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	SVEP1	HGNC	protein_coding		44	0.00	0	G			113191597	113191597	-1	no_errors	ENST00000401783	ensembl	human	known	69_37n	missense	83	14.43	14	SNP	0.002	T
TEKT1	83659	genome.wustl.edu	37	17	6733605	6733605	+	Silent	SNP	T	T	G			TCGA-A2-A04Q-01A-21W-A050-09	TCGA-A2-A04Q-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	02eb17d4-9e9e-4e32-96b0-90ccdda3f167	41482042-a515-4e00-985b-f18952dfcbf3	g.chr17:6733605T>G	ENST00000338694.2	-	2	220	c.91A>C	c.(91-93)Agg>Cgg	p.R31R	TEKT1_ENST00000535086.1_5'UTR	NM_053285.1	NP_444515.1	Q969V4	TEKT1_HUMAN	tektin 1	31						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)	20		Myeloproliferative disorder(207;0.0255)				GATCGGGACCTTTGAGCGTCT	0.473																																						dbGAP											0													106.0	98.0	100.0					17																	6733605		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0				CCDS11083.1	17p13.2	2011-05-23			ENSG00000167858	ENSG00000167858			15534	protein-coding gene	gene with protein product		609002				11606253	Standard	NM_053285		Approved		uc002gdt.3	Q969V4	OTTHUMG00000102063	ENST00000338694.2:c.91A>C	17.37:g.6733605T>G			D3DTM7	Silent	SNP	pfam_Tektin,prints_Tektin	p.R31	ENST00000338694.2	37	c.91	CCDS11083.1	17																																																																																			TEKT1	-	pfam_Tektin	ENSG00000167858		0.473	TEKT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TEKT1	HGNC	protein_coding	OTTHUMT00000219867.2	59	0.00	0	T	NM_053285		6733605	6733605	-1	no_errors	ENST00000338694	ensembl	human	known	69_37n	silent	96	14.29	16	SNP	0.728	G
