#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
APTX	54840	genome.wustl.edu	37	9	33001567	33001567	+	Missense_Mutation	SNP	C	C	A			TCGA-A8-A082-01A-11W-A019-09	TCGA-A8-A082-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	575d25ea-eae7-423a-9464-d3b2806bf9eb	576b6dc6-351b-4a61-b6e4-fbfda702de27	g.chr9:33001567C>A	ENST00000379819.1	-	1	35	c.36G>T	c.(34-36)tgG>tgT	p.W12C	APTX_ENST00000476858.1_Missense_Mutation_p.W12C|APTX_ENST00000397172.3_Missense_Mutation_p.W12C|APTX_ENST00000379825.2_Missense_Mutation_p.W12C|APTX_ENST00000309615.3_Missense_Mutation_p.W12C|APTX_ENST00000379813.3_5'UTR|APTX_ENST00000463596.1_5'Flank			Q7Z2E3	APTX_HUMAN	aprataxin	12	Interactions with ADPRT and NCL.				cell death (GO:0008219)|cellular response to DNA damage stimulus (GO:0006974)|dephosphorylation (GO:0016311)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA ligation (GO:0006266)|double-strand break repair (GO:0006302)|polynucleotide 3' dephosphorylation (GO:0098506)|regulation of protein stability (GO:0031647)|response to hydrogen peroxide (GO:0042542)|single strand break repair (GO:0000012)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA 5'-adenosine monophosphate hydrolase activity (GO:0033699)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|phosphoglycolate phosphatase activity (GO:0008967)|phosphoprotein binding (GO:0051219)|polynucleotide 3'-phosphatase activity (GO:0046403)|protein N-terminus binding (GO:0047485)			endometrium(1)|lung(1)|ovary(2)|prostate(2)	6			LUSC - Lung squamous cell carcinoma(29;0.0302)	GBM - Glioblastoma multiforme(74;0.105)		CGCCTTACCTCCAGAAGTCGG	0.612								Editing and processing nucleases																														dbGAP											0													104.0	80.0	88.0					9																	33001567		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK000164	CCDS47956.1, CCDS56568.1, CCDS75827.1	9p13.3	2014-01-28	2003-04-03		ENSG00000137074	ENSG00000137074			15984	protein-coding gene	gene with protein product		606350	"""ataxia 1, early onset with hypoalbuminemia"""	AXA1		11586299, 11586300	Standard	NM_175069		Approved	FLJ20157, AOA, AOA1, EAOH, EOAHA	uc003zry.3	Q7Z2E3	OTTHUMG00000019759	ENST00000379819.1:c.36G>T	9.37:g.33001567C>A	ENSP00000369147:p.Trp12Cys		A8MTN4|D3DRK9|D3DRL0|Q0P662|Q5T781|Q5T782|Q5T784|Q6JV81|Q6JV82|Q6JV85|Q7Z2F3|Q7Z336|Q7Z5R5|Q7Z6V7|Q7Z6V8|Q9NXM5	Missense_Mutation	SNP	pfam_Histidine_triad_HIT,superfamily_HIT-like,superfamily_SMAD_FHA_domain,pfscan_Histidine_triad_HIT	p.W12C	ENST00000379819.1	37	c.36		9	.	.	.	.	.	.	.	.	.	.	C	4.482	0.089421	0.08632	.	.	ENSG00000137074	ENST00000379825;ENST00000309615;ENST00000397172;ENST00000379819;ENST00000476858;ENST00000344355;ENST00000379812;ENST00000473221	T;T;T;T;D;T;D	0.91464	1.97;1.97;1.97;1.97;-2.85;1.97;-2.36	3.99	2.08	0.27032	.	3.277280	0.00819	N	0.001563	T	0.80138	0.4568	N	0.02011	-0.69	0.37618	D	0.921199	B	0.22480	0.07	B	0.25405	0.06	T	0.64833	-0.6314	10	0.48119	T	0.1	-2.1894	8.9449	0.35753	0.4038:0.5962:0.0:0.0	.	12	Q5T782	.	C	12	ENSP00000369153:W12C;ENSP00000311547:W12C;ENSP00000380357:W12C;ENSP00000369147:W12C;ENSP00000419042:W12C;ENSP00000369140:W12C;ENSP00000419020:W12C	ENSP00000311547:W12C	W	-	3	0	APTX	32991567	0.048000	0.20356	0.424000	0.26647	0.045000	0.14185	-0.048000	0.11944	0.600000	0.29862	0.655000	0.94253	TGG	APTX	-	superfamily_SMAD_FHA_domain	ENSG00000137074		0.612	APTX-003	KNOWN	basic|appris_candidate_longest	protein_coding	APTX	HGNC	protein_coding	OTTHUMT00000052028.2	53	0.00	0	C	NM_017692		33001567	33001567	-1	no_errors	ENST00000379819	ensembl	human	known	69_37n	missense	61	29.89	26	SNP	0.439	A
ARHGEF15	22899	genome.wustl.edu	37	17	8224297	8224298	+	Frame_Shift_Ins	INS	-	-	C			TCGA-A8-A082-01A-11W-A019-09	TCGA-A8-A082-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	575d25ea-eae7-423a-9464-d3b2806bf9eb	576b6dc6-351b-4a61-b6e4-fbfda702de27	g.chr17:8224297_8224298insC	ENST00000361926.3	+	16	2622_2623	c.2512_2513insC	c.(2512-2514)gccfs	p.A838fs	ARHGEF15_ENST00000421050.1_Frame_Shift_Ins_p.A838fs|AC135178.7_ENST00000458568.1_RNA	NM_173728.3	NP_776089.2	O94989	ARHGF_HUMAN	Rho guanine nucleotide exchange factor (GEF) 15	838					negative regulation of synapse maturation (GO:2000297)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|regulation of catalytic activity (GO:0050790)|retina vasculature morphogenesis in camera-type eye (GO:0061299)	cytoplasm (GO:0005737)|dendrite (GO:0030425)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(9)|large_intestine(5)|lung(11)|ovary(5)|prostate(3)|skin(2)|urinary_tract(1)	37						CACCCCCAATGCCCCCCCACCC	0.574																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AB020722	CCDS11139.1	17p13.1	2011-11-16			ENSG00000198844	ENSG00000198844		"""Rho guanine nucleotide exchange factors"""	15590	protein-coding gene	gene with protein product	"""Rho guanine exchange factor (GEF) 15"""	608504				10048485	Standard	NM_173728		Approved	KIAA0915, Vsm-RhoGEF, ARGEF15, FLJ13791, MGC44868	uc002glc.3	O94989	OTTHUMG00000108187	ENST00000361926.3:c.2519dupC	17.37:g.8224304_8224304dupC	ENSP00000355026:p.Ala838fs		A8K6G1|Q8N449|Q9H8B4	Frame_Shift_Ins	INS	pfam_DH-domain,superfamily_DH-domain,smart_DH-domain,pfscan_DH-domain	p.P841fs	ENST00000361926.3	37	c.2512_2513	CCDS11139.1	17																																																																																			ARHGEF15	-	NULL	ENSG00000198844		0.574	ARHGEF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ARHGEF15	HGNC	protein_coding	OTTHUMT00000226993.2	43	0.00	0	-	NM_173728		8224297	8224298	+1	no_errors	ENST00000361926	ensembl	human	known	69_37n	frame_shift_ins	46	11.54	6	INS	0.000:0.001	C
BPTF	2186	genome.wustl.edu	37	17	65925453	65925453	+	Splice_Site	SNP	C	C	T			TCGA-A8-A082-01A-11W-A019-09	TCGA-A8-A082-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	575d25ea-eae7-423a-9464-d3b2806bf9eb	576b6dc6-351b-4a61-b6e4-fbfda702de27	g.chr17:65925453C>T	ENST00000321892.4	+	19	6439	c.6378C>T	c.(6376-6378)ggC>ggT	p.G2126G	BPTF_ENST00000424123.3_Splice_Site_p.G1987G|BPTF_ENST00000306378.6_Splice_Site_p.G2000G|BPTF_ENST00000335221.5_Splice_Site_p.G2126G			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2126					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.G2000G(1)|p.G2126G(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			TTTTTTAAGGCGTTGTTCAAG	0.428																																						dbGAP											2	Substitution - coding silent(2)	lung(2)											79.0	78.0	78.0					17																	65925453		2203	4300	6503	-	-	-	SO:0001630	splice_region_variant	0			AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"""Zinc fingers, PHD-type"""	3581	protein-coding gene	gene with protein product		601819	"""fetal Alzheimer antigen"""	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.6377-1C>T	17.37:g.65925453C>T			Q6NX67|Q7Z7D6|Q9UIG2	Missense_Mutation	SNP	NULL	p.R217C	ENST00000321892.4	37	c.649		17																																																																																			BPTF	-	NULL	ENSG00000171634		0.428	BPTF-201	KNOWN	basic	protein_coding	BPTF	HGNC	protein_coding		76	0.00	0	C	NM_182641, NM_004459	Silent	65925453	65925453	+1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000582467	ensembl	human	novel	69_37n	missense	41	41.33	31	SNP	0.966	T
C11orf63	79864	genome.wustl.edu	37	11	122828073	122828073	+	Silent	SNP	G	G	A	rs199645772		TCGA-A8-A082-01A-11W-A019-09	TCGA-A8-A082-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	575d25ea-eae7-423a-9464-d3b2806bf9eb	576b6dc6-351b-4a61-b6e4-fbfda702de27	g.chr11:122828073G>A	ENST00000531316.1	+	7	2105	c.2013G>A	c.(2011-2013)acG>acA	p.T671T	C11orf63_ENST00000227349.2_Silent_p.T671T			Q6NUN7	CK063_HUMAN	chromosome 11 open reading frame 63	671					axoneme assembly (GO:0035082)|brain development (GO:0007420)|cerebrospinal fluid secretion (GO:0033326)|ciliary basal body organization (GO:0032053)			p.T671T(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(13)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	47		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.018)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.34e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0311)		CTGAACAGACGCAAAAATTAA	0.378																																						dbGAP											1	Substitution - coding silent(1)	large_intestine(1)											99.0	88.0	92.0					11																	122828073		2202	4299	6501	-	-	-	SO:0001819	synonymous_variant	0			BC068507	CCDS8438.1, CCDS8439.1	11q24.1	2012-05-25			ENSG00000109944	ENSG00000109944			26288	protein-coding gene	gene with protein product						12477932	Standard	NM_024806		Approved	FLJ23554	uc001pym.4	Q6NUN7	OTTHUMG00000166027	ENST00000531316.1:c.2013G>A	11.37:g.122828073G>A			A8K6G0|Q96GB5|Q9H5D6	Silent	SNP	NULL	p.T671	ENST00000531316.1	37	c.2013	CCDS8438.1	11																																																																																			C11orf63	-	NULL	ENSG00000109944		0.378	C11orf63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	C11orf63	HGNC	protein_coding	OTTHUMT00000387511.1	266	0.00	0	G	NM_024806		122828073	122828073	+1	no_errors	ENST00000227349	ensembl	human	known	69_37n	silent	72	62.56	122	SNP	0.983	A
COL27A1	85301	genome.wustl.edu	37	9	116930472	116930472	+	Missense_Mutation	SNP	C	C	G			TCGA-A8-A082-01A-11W-A019-09	TCGA-A8-A082-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	575d25ea-eae7-423a-9464-d3b2806bf9eb	576b6dc6-351b-4a61-b6e4-fbfda702de27	g.chr9:116930472C>G	ENST00000356083.3	+	3	1028	c.637C>G	c.(637-639)Ctc>Gtc	p.L213V		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	213	Laminin G-like.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						TGAAGGTGCTCTCTGCCAGTT	0.577																																						dbGAP											0													72.0	67.0	69.0					9																	116930472		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"""Collagens"""	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.637C>G	9.37:g.116930472C>G	ENSP00000348385:p.Leu213Val		Q66K43|Q96JF7	Missense_Mutation	SNP	pfam_Collagen,pfam_Fib_collagen_C,superfamily_ConA-like_lec_gl,smart_Laminin_G,smart_Fib_collagen_C	p.L213V	ENST00000356083.3	37	c.637	CCDS6802.1	9	.	.	.	.	.	.	.	.	.	.	C	12.91	2.080123	0.36662	.	.	ENSG00000196739	ENST00000356083;ENST00000357257;ENST00000374106;ENST00000451716	T;T	0.03801	3.8;3.8	5.12	4.2	0.49525	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G, thrombospondin-type, N-terminal (1);	.	.	.	.	T	0.02970	0.0088	N	0.14661	0.345	0.35071	D	0.762512	B;P	0.38020	0.009;0.615	B;B	0.29267	0.007;0.1	T	0.54807	-0.8238	9	0.29301	T	0.29	.	12.8135	0.57652	0.0:0.7925:0.2075:0.0	.	213;160	Q8IZC6;Q5T1U7	CORA1_HUMAN;.	V	213;213;160;160	ENSP00000348385:L213V;ENSP00000391328:L160V	ENSP00000348385:L213V	L	+	1	0	COL27A1	115970293	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	2.902000	0.48703	2.360000	0.80028	0.555000	0.69702	CTC	COL27A1	-	superfamily_ConA-like_lec_gl,smart_Laminin_G	ENSG00000196739		0.577	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL27A1	HGNC	protein_coding	OTTHUMT00000053763.1	56	0.00	0	C	NM_032888		116930472	116930472	+1	no_errors	ENST00000356083	ensembl	human	known	69_37n	missense	38	32.14	18	SNP	1.000	G
COL7A1	1294	genome.wustl.edu	37	3	48612870	48612871	+	Frame_Shift_Ins	INS	-	-	G	rs375047225		TCGA-A8-A082-01A-11W-A019-09	TCGA-A8-A082-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	575d25ea-eae7-423a-9464-d3b2806bf9eb	576b6dc6-351b-4a61-b6e4-fbfda702de27	g.chr3:48612870_48612871insG	ENST00000328333.8	-	73	6188_6189	c.6081_6082insC	c.(6079-6084)cccgggfs	p.G2028fs	COL7A1_ENST00000454817.1_Frame_Shift_Ins_p.G1996fs	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2028	Triple-helical region.		G -> A (in DDEB). {ECO:0000269|PubMed:11142768}.|G -> R (in DDEB and EBP). {ECO:0000269|PubMed:10836608, ECO:0000269|PubMed:11142768}.		cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.G2028W(1)|p.P2029fs*177(1)		NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CCGGAAGGCCCGGGGGGGCCCC	0.718																																						dbGAP											2	Substitution - Missense(1)|Deletion - Frameshift(1)	urinary_tract(1)|large_intestine(1)	GRCh37	CD961934|CI031897|CM001106|CM071636	COL7A1	D|I|M																																				-	-	-	SO:0001589	frameshift_variant	0			L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"""Collagens"", ""Fibronectin type III domain containing"""	2214	protein-coding gene	gene with protein product	"""collagen VII, alpha-1 polypeptide"", ""LC collagen"""	120120	"""epidermolysis bullosa, dystrophic, dominant and recessive"""	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.6082dupC	3.37:g.48612877_48612877dupG	ENSP00000332371:p.Gly2028fs		Q14054|Q16507	Frame_Shift_Ins	INS	pfam_Collagen,pfam_Fibronectin_type3,pfam_VWF_A,pfam_Prot_inh_Kunz-m,superfamily_Fibronectin_type3,superfamily_Prot_inh_Kunz-m,smart_VWF_A,smart_Fibronectin_type3,pfscan_Fibronectin_type3,pfscan_VWF_A,pfscan_Prot_inh_Kunz-m,prints_Prot_inh_Kunz-m	p.G2027fs	ENST00000328333.8	37	c.6082_6081	CCDS2773.1	3																																																																																			COL7A1	-	pfam_Collagen	ENSG00000114270		0.718	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL7A1	HGNC	protein_coding	OTTHUMT00000257519.1	16	0.00	0	-	NM_000094		48612870	48612871	-1	no_errors	ENST00000328333	ensembl	human	known	69_37n	frame_shift_ins	15	11.76	2	INS	1.000:0.981	G
CPA4	51200	genome.wustl.edu	37	7	129939179	129939179	+	Nonsense_Mutation	SNP	C	C	T	rs546291221		TCGA-A8-A082-01A-11W-A019-09	TCGA-A8-A082-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	575d25ea-eae7-423a-9464-d3b2806bf9eb	576b6dc6-351b-4a61-b6e4-fbfda702de27	g.chr7:129939179C>T	ENST00000222482.4	+	3	248	c.220C>T	c.(220-222)Cag>Tag	p.Q74*	CPA4_ENST00000493259.1_Intron|CPA4_ENST00000445470.2_Nonsense_Mutation_p.Q74*	NM_016352.3	NP_057436.2	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4	74					histone acetylation (GO:0016573)	extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Melanoma(18;0.0435)					TGTCAGTCTGCAGGCATTTAA	0.502																																						dbGAP											0													142.0	127.0	132.0					7																	129939179		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AF095719	CCDS5818.1, CCDS55163.1	7q32	2008-07-18			ENSG00000128510	ENSG00000128510			15740	protein-coding gene	gene with protein product	"""carboxypeptidase A3"""	607635				10383164, 10860668	Standard	NM_016352		Approved	CPA3	uc003vpr.3	Q9UI42	OTTHUMG00000157825	ENST00000222482.4:c.220C>T	7.37:g.129939179C>T	ENSP00000222482:p.Gln74*		B7Z576|Q86UY9	Nonsense_Mutation	SNP	pfam_Peptidase_M14,pfam_Prot_inh_M14A,superfamily_Prot_inh_propept,smart_Peptidase_M14,prints_Peptidase_M14	p.Q74*	ENST00000222482.4	37	c.220	CCDS5818.1	7	.	.	.	.	.	.	.	.	.	.	C	17.40	3.379948	0.61845	.	.	ENSG00000128510	ENST00000445470;ENST00000222482;ENST00000492072;ENST00000473956	.	.	.	6.11	4.14	0.48551	.	0.802567	0.11990	N	0.509954	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	.	8.4766	0.33016	0.1634:0.7517:0.0:0.0849	.	.	.	.	X	74	.	ENSP00000222482:Q74X	Q	+	1	0	CPA4	129726415	0.083000	0.21467	0.889000	0.34880	0.667000	0.39255	0.824000	0.27379	1.590000	0.49995	0.655000	0.94253	CAG	CPA4	-	pfam_Prot_inh_M14A,superfamily_Prot_inh_propept	ENSG00000128510		0.502	CPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CPA4	HGNC	protein_coding	OTTHUMT00000349725.1	147	0.00	0	C	NM_016352		129939179	129939179	+1	no_errors	ENST00000222482	ensembl	human	known	69_37n	nonsense	86	36.96	51	SNP	0.572	T
CROCCP2	84809	genome.wustl.edu	37	1	16946407	16946407	+	lincRNA	SNP	T	T	G	rs10796418		TCGA-A8-A082-01A-11W-A019-09	TCGA-A8-A082-10A-01W-A021-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	575d25ea-eae7-423a-9464-d3b2806bf9eb	576b6dc6-351b-4a61-b6e4-fbfda702de27	g.chr1:16946407T>G	ENST00000412962.1	-	0	1112				RP5-1182A14.5_ENST00000607700.1_lincRNA			Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2						centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)											AGCAATCTCCTCACTCAGCTG	0.672																																						dbGAP											0																																										-	-	-			0			AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908			28170	pseudogene	pseudogene			"""ciliary rootlet coiled-coil, rootletin-like 1"""	CROCCL1		12477932	Standard	NR_026752		Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884		1.37:g.16946407T>G			Q8NF65|Q96FR5|Q9BRE8	RNA	SNP	-	NULL	ENST00000412962.1	37	NULL		1																																																																																			CROCCP2	-	-	ENSG00000215908		0.672	CROCCP2-003	KNOWN	basic	lincRNA	CROCCP2	HGNC	lincRNA	OTTHUMT00000092784.1	15	0.00	0	T	NR_026752.1		16946407	16946407	-1	no_errors	ENST00000412962	ensembl	human	known	69_37n	rna	12	25.00	4	SNP	1.000	G
RTP5	285093	genome.wustl.edu	37	2	242814374	242814375	+	Frame_Shift_Ins	INS	-	-	C	rs35989328		TCGA-A8-A082-01A-11W-A019-09	TCGA-A8-A082-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	575d25ea-eae7-423a-9464-d3b2806bf9eb	576b6dc6-351b-4a61-b6e4-fbfda702de27	g.chr2:242814374_242814375insC	ENST00000343216.3	+	2	695_696	c.667_668insC	c.(667-669)gccfs	p.A223fs		NM_173821.2	NP_776182.2																					TGAGGGCCCTGCCCCCCCTGCG	0.658																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0																														ENST00000343216.3:c.674dupC	2.37:g.242814381_242814381dupC	ENSP00000345374:p.Ala223fs			Frame_Shift_Ins	INS	NULL	p.A226fs	ENST00000343216.3	37	c.667_668	CCDS42843.1	2																																																																																			CXXC11	-	NULL	ENSG00000188011		0.658	CXXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CXXC11	HGNC	protein_coding	OTTHUMT00000322310.1	13	0.00	0	-			242814374	242814375	+1	no_errors	ENST00000343216	ensembl	human	known	69_37n	frame_shift_ins	11	26.67	4	INS	0.000:0.000	C
ENPP3	5169	genome.wustl.edu	37	6	132054845	132054845	+	Missense_Mutation	SNP	G	G	C	rs535729818		TCGA-A8-A082-01A-11W-A019-09	TCGA-A8-A082-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	575d25ea-eae7-423a-9464-d3b2806bf9eb	576b6dc6-351b-4a61-b6e4-fbfda702de27	g.chr6:132054845G>C	ENST00000414305.1	+	22	2399	c.2071G>C	c.(2071-2073)Ggc>Cgc	p.G691R	ENPP3_ENST00000358229.5_Intron|ENPP3_ENST00000357639.3_Missense_Mutation_p.G691R			O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 3	691	Nuclease.				immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		TATCACCCACGGCTTCCTCTA	0.478																																						dbGAP											0													109.0	107.0	108.0					6																	132054845		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF005632	CCDS5148.1	6q22	2010-06-23			ENSG00000154269	ENSG00000154269	3.1.4.1, 3.6.1.9	"""CD molecules"""	3358	protein-coding gene	gene with protein product		602182		PDNP3		9344668	Standard	NM_005021		Approved	PD-IBETA, gp130RB13-6, B10, CD203c	uc003qcv.3	O14638	OTTHUMG00000016292	ENST00000414305.1:c.2071G>C	6.37:g.132054845G>C	ENSP00000406261:p.Gly691Arg		Q5JTL3	Missense_Mutation	SNP	pfam_Phosphodiest/P_Trfase,pfam_Somatomedin_B_dom,pfam_DNA/RNA_non-sp_Endonuclease,superfamily_Alkaline_phosphatase_core,smart_Somatomedin_B_dom,smart_DNA/RNA_non-sp_Endonuclease,smart_Extracellular_endonuc_su_A,pfscan_Somatomedin_B_dom	p.G691R	ENST00000414305.1	37	c.2071	CCDS5148.1	6	.	.	.	.	.	.	.	.	.	.	G	17.03	3.284776	0.59867	.	.	ENSG00000154269	ENST00000414305;ENST00000357639	D;D	0.97138	-4.26;-4.26	5.91	5.91	0.95273	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.000000	0.64402	D	0.000001	D	0.98369	0.9458	M	0.88640	2.97	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.98779	1.0731	10	0.87932	D	0	-17.339	11.5406	0.50665	0.1374:0.0:0.8626:0.0	.	691	O14638	ENPP3_HUMAN	R	691	ENSP00000406261:G691R;ENSP00000350265:G691R	ENSP00000350265:G691R	G	+	1	0	ENPP3	132096538	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.209000	0.65208	2.805000	0.96524	0.460000	0.39030	GGC	ENPP3	-	pfam_DNA/RNA_non-sp_Endonuclease,smart_DNA/RNA_non-sp_Endonuclease,smart_Extracellular_endonuc_su_A	ENSG00000154269		0.478	ENPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENPP3	HGNC	protein_coding	OTTHUMT00000043627.2	125	0.00	0	G			132054845	132054845	+1	no_errors	ENST00000357639	ensembl	human	known	69_37n	missense	100	37.11	59	SNP	1.000	C
FOXA1	3169	genome.wustl.edu	37	14	38061240	38061240	+	Missense_Mutation	SNP	G	G	A			TCGA-A8-A082-01A-11W-A019-09	TCGA-A8-A082-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	575d25ea-eae7-423a-9464-d3b2806bf9eb	576b6dc6-351b-4a61-b6e4-fbfda702de27	g.chr14:38061240G>A	ENST00000250448.2	-	2	810	c.749C>T	c.(748-750)tCc>tTc	p.S250F	FOXA1_ENST00000540786.1_Missense_Mutation_p.S217F|FOXA1_ENST00000545425.2_5'UTR	NM_004496.3	NP_004487.2	P55317	FOXA1_HUMAN	forkhead box A1	250					anatomical structure formation involved in morphogenesis (GO:0048646)|chromatin remodeling (GO:0006338)|dorsal/ventral neural tube patterning (GO:0021904)|epithelial cell maturation involved in prostate gland development (GO:0060743)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|epithelial-mesenchymal signaling involved in prostate gland development (GO:0060738)|glucose homeostasis (GO:0042593)|hormone metabolic process (GO:0042445)|lung epithelial cell differentiation (GO:0060487)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate specification (GO:0048665)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland epithelium morphogenesis (GO:0060740)|prostate gland stromal morphogenesis (GO:0060741)|response to estradiol (GO:0032355)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)	microvillus (GO:0005902)|nucleus (GO:0005634)	DNA binding (GO:0003677)|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)			breast(1)|endometrium(1)|large_intestine(2)|lung(3)|prostate(12)	19	Breast(36;0.0954)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;5.41e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.0454)|LUSC - Lung squamous cell carcinoma(13;0.0917)|all cancers(34;0.0925)|BRCA - Breast invasive adenocarcinoma(188;0.239)	GBM - Glioblastoma multiforme(112;0.0222)		CATGTTGCCGGAGTCCGGGTG	0.677																																						dbGAP											0													29.0	28.0	29.0					14																	38061240		2203	4300	6503	-	-	-	SO:0001583	missense	0			U39840	CCDS9665.1	14q12-q13	2008-04-10		2002-09-20	ENSG00000129514	ENSG00000129514		"""Forkhead boxes"""	5021	protein-coding gene	gene with protein product		602294	"""hepatocyte nuclear factor 3, alpha"""	HNF3A		9119385, 8652662	Standard	NM_004496		Approved		uc001wuf.4	P55317	OTTHUMG00000140253	ENST00000250448.2:c.749C>T	14.37:g.38061240G>A	ENSP00000250448:p.Ser250Phe		B2R9H6|B7ZAP5|Q9H2A0	Missense_Mutation	SNP	pfam_TF_fork_head,pfam_Fork-head_N,pfam_Forkhead_box_C,smart_TF_fork_head,pfscan_TF_fork_head,prints_TF_fork_head	p.S250F	ENST00000250448.2	37	c.749	CCDS9665.1	14	.	.	.	.	.	.	.	.	.	.	G	24.0	4.480686	0.84747	.	.	ENSG00000129514	ENST00000250448;ENST00000540786	D;D	0.95788	-3.81;-3.81	3.88	3.88	0.44766	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.85682	D	0.000000	D	0.96269	0.8783	L	0.42632	1.34	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96852	0.9626	10	0.87932	D	0	.	14.7467	0.69494	0.0:0.0:1.0:0.0	.	250	P55317	FOXA1_HUMAN	F	250;217	ENSP00000250448:S250F;ENSP00000440178:S217F	ENSP00000250448:S250F	S	-	2	0	FOXA1	37130991	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.596000	0.82721	1.996000	0.58369	0.400000	0.26472	TCC	FOXA1	-	pfam_TF_fork_head,smart_TF_fork_head,pfscan_TF_fork_head	ENSG00000129514		0.677	FOXA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FOXA1	HGNC	protein_coding	OTTHUMT00000276735.1	20	0.00	0	G			38061240	38061240	-1	no_errors	ENST00000250448	ensembl	human	known	69_37n	missense	13	33.33	7	SNP	1.000	A
GDAP1	54332	genome.wustl.edu	37	8	75276279	75276279	+	Missense_Mutation	SNP	G	G	A			TCGA-A8-A082-01A-11W-A019-09	TCGA-A8-A082-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	575d25ea-eae7-423a-9464-d3b2806bf9eb	576b6dc6-351b-4a61-b6e4-fbfda702de27	g.chr8:75276279G>A	ENST00000220822.7	+	6	834	c.754G>A	c.(754-756)Gct>Act	p.A252T	GDAP1_ENST00000434412.2_Missense_Mutation_p.A184T|GDAP1_ENST00000521096.1_3'UTR	NM_001040875.2|NM_018972.2	NP_001035808.1|NP_061845.2	Q8TB36	GDAP1_HUMAN	ganglioside induced differentiation associated protein 1	252	GST C-terminal.				cell death (GO:0008219)|mitochondrial fission (GO:0000266)|protein targeting to mitochondrion (GO:0006626)|response to retinoic acid (GO:0032526)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	Breast(64;0.00769)	Myeloproliferative disorder(644;0.0122)	BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.104)|all cancers(69;0.234)			CGTCTCACTCGCTGTCACATT	0.498																																						dbGAP											0													71.0	69.0	70.0					8																	75276279		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS34911.1, CCDS47877.1	8q13.3	2014-09-17	2012-02-09						15968	protein-coding gene	gene with protein product		606598	"""Charcot-Marie-Tooth neuropathy 4A"""	CMT4A		8268915, 11743579	Standard	NM_018972		Approved	CMT4	uc003yah.3	Q8TB36		ENST00000220822.7:c.754G>A	8.37:g.75276279G>A	ENSP00000220822:p.Ala252Thr		A8K957|E7FJF3|E7FJF4	Missense_Mutation	SNP	pfam_Glutathione_S-Trfase_N,pfam_GST_C,superfamily_Thioredoxin-like_fold,superfamily_Glutathione-S-Trfase_C-like	p.A252T	ENST00000220822.7	37	c.754	CCDS34911.1	8	.	.	.	.	.	.	.	.	.	.	G	28.1	4.889113	0.91889	.	.	ENSG00000104381	ENST00000220822;ENST00000434412	D;D	0.94537	-3.45;-3.45	4.99	4.99	0.66335	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.94324	0.8176	L	0.42529	1.33	0.58432	D	0.999996	D	0.62365	0.991	P	0.55667	0.781	D	0.91604	0.5297	10	0.14656	T	0.56	-13.0359	18.8301	0.92135	0.0:0.0:1.0:0.0	.	252	Q8TB36	GDAP1_HUMAN	T	252;184	ENSP00000220822:A252T;ENSP00000417006:A184T	ENSP00000220822:A252T	A	+	1	0	GDAP1	75438834	1.000000	0.71417	0.969000	0.41365	0.809000	0.45718	9.092000	0.94157	2.767000	0.95098	0.655000	0.94253	GCT	GDAP1	-	pfam_GST_C,superfamily_Glutathione-S-Trfase_C-like	ENSG00000104381		0.498	GDAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GDAP1	HGNC	protein_coding	OTTHUMT00000379061.1	110	0.00	0	G	NM_018972		75276279	75276279	+1	no_errors	ENST00000220822	ensembl	human	known	69_37n	missense	75	57.78	104	SNP	1.000	A
LECT1	11061	genome.wustl.edu	37	13	53313765	53313766	+	Splice_Site	INS	-	-	G	rs370653677		TCGA-A8-A082-01A-11W-A019-09	TCGA-A8-A082-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	575d25ea-eae7-423a-9464-d3b2806bf9eb	576b6dc6-351b-4a61-b6e4-fbfda702de27	g.chr13:53313765_53313766insG	ENST00000377962.3	-	1	149_150	c.71_72insC	c.(70-72)ccg>ccCg	p.P24fs	LECT1_ENST00000448904.2_Splice_Site_p.P24fs			O75829	LECT1_HUMAN	leukocyte cell derived chemotaxin 1	24					cartilage development (GO:0051216)|endothelial cell morphogenesis (GO:0001886)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|proteoglycan metabolic process (GO:0006029)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)		p.P24fs*6(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|urinary_tract(1)	15		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.38e-08)		CGGTACTCACCGGGGGGCTGCA	0.594																																						dbGAP											1	Deletion - Frameshift(1)	large_intestine(1)							,	4,4260		0,4,2128					,	2.8	1.0			114	2,8252		0,2,4125	no	frameshift-near-splice,frameshift-near-splice	LECT1	NM_007015.2,NM_001011705.1	,	0,6,6253	A1A1,A1R,RR		0.0242,0.0938,0.0479	,	,		6,12512				-	-	-	SO:0001630	splice_region_variant	0			AB006000	CCDS9437.1, CCDS45051.1	13q14.3	2012-10-10			ENSG00000136110	ENSG00000136110		"""BRICHOS domain containing"""	17005	protein-coding gene	gene with protein product	"""BRICHOS domain containing 3"""	605147	"""multiple myeloma tumor suppressor 1"""	MYETS1		9731231, 10103018	Standard	XM_006719760		Approved	CHM-I, CHM1, chondromodulin, BRICD3	uc001vhf.2	O75829	OTTHUMG00000016980	ENST00000377962.3:c.72+1->C	13.37:g.53313771_53313771dupG			Q5TAM4|Q8TAY6|Q9UM18	Frame_Shift_Ins	INS	pfam_BRICHOS_dom,pfscan_BRICHOS_dom	p.A25fs	ENST00000377962.3	37	c.72_71	CCDS9437.1	13																																																																																			LECT1	-	NULL	ENSG00000136110		0.594	LECT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	LECT1	HGNC	protein_coding	OTTHUMT00000045110.3	27	0.00	0	-		Frame_Shift_Ins	53313765	53313766	-1	no_errors	ENST00000377962	ensembl	human	known	69_37n	frame_shift_ins	10	23.08	3	INS	1.000:1.000	G
MAP3K1	4214	genome.wustl.edu	37	5	56183311	56183311	+	Frame_Shift_Del	DEL	A	A	-			TCGA-A8-A082-01A-11W-A019-09	TCGA-A8-A082-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	575d25ea-eae7-423a-9464-d3b2806bf9eb	576b6dc6-351b-4a61-b6e4-fbfda702de27	g.chr5:56183311delA	ENST00000399503.3	+	18	4221	c.4221delA	c.(4219-4221)ggafs	p.G1407fs		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	1407	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		AGTTTCAGGGACAATTACTGG	0.423																																						dbGAP											0													220.0	199.0	205.0					5																	56183311		1898	4123	6021	-	-	-	SO:0001589	frameshift_variant	0			U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.4221delA	5.37:g.56183311delA	ENSP00000382423:p.Gly1407fs			Frame_Shift_Del	DEL	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Znf_RING,pfscan_Znf_SWIM,pfscan_Prot_kinase_cat_dom	p.Q1408fs	ENST00000399503.3	37	c.4221	CCDS43318.1	5																																																																																			MAP3K1	-	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	ENSG00000095015		0.423	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	MAP3K1	HGNC	protein_coding	OTTHUMT00000132309.2	335	0.00	0	A	XM_042066		56183311	56183311	+1	no_errors	ENST00000399503	ensembl	human	novel	69_37n	frame_shift_del	228	32.28	112	DEL	1.000	-
MGA	23269	genome.wustl.edu	37	15	41988487	41988487	+	Missense_Mutation	SNP	C	C	G			TCGA-A8-A082-01A-11W-A019-09	TCGA-A8-A082-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	575d25ea-eae7-423a-9464-d3b2806bf9eb	576b6dc6-351b-4a61-b6e4-fbfda702de27	g.chr15:41988487C>G	ENST00000570161.1	+	2	1279	c.1279C>G	c.(1279-1281)Cta>Gta	p.L427V	MGA_ENST00000219905.7_Missense_Mutation_p.L427V|MGA_ENST00000566586.1_Missense_Mutation_p.L427V|MGA_ENST00000545763.1_Missense_Mutation_p.L427V|MGA_ENST00000389936.4_Missense_Mutation_p.L427V|MGA_ENST00000568630.1_3'UTR			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Maltase.				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)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	AGAGAAACAGCTAAAGAGGCA	0.433																																						dbGAP											0													79.0	75.0	76.0					15																	41988487		1902	4122	6024	-	-	-	SO:0001583	missense	0			AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.1279C>G	15.37:g.41988487C>G	ENSP00000457035:p.Leu427Val		Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	pfam_TF_T-box,pfam_HLH_DNA-bd,superfamily_p53-like_TF_DNA-bd,superfamily_HLH_DNA-bd,smart_TF_T-box,smart_HLH_DNA-bd,prints_TF_T-box,pfscan_HLH_DNA-bd,pfscan_TF_T-box	p.L427V	ENST00000570161.1	37	c.1279	CCDS55959.1	15	.	.	.	.	.	.	.	.	.	.	C	15.75	2.926853	0.52759	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	D;D;D	0.89681	-2.52;-2.55;-2.44	5.53	3.63	0.41609	.	1.793160	0.02420	N	0.082473	D	0.93684	0.7982	L	0.59436	1.845	0.28156	N	0.929198	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.94	T	0.79045	-0.1964	10	0.87932	D	0	.	9.8688	0.41162	0.0:0.7879:0.0:0.2121	.	427;427	F5H7K2;E7ENI0	.;.	V	427	ENSP00000219905:L427V;ENSP00000374586:L427V;ENSP00000442467:L427V	ENSP00000219905:L427V	L	+	1	2	MGA	39775779	0.981000	0.34729	0.931000	0.37212	0.934000	0.57294	0.885000	0.28227	1.329000	0.45376	0.561000	0.74099	CTA	MGA	-	NULL	ENSG00000174197		0.433	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	MGA	HGNC	protein_coding	OTTHUMT00000420229.1	377	0.00	0	C	NM_001164273.1		41988487	41988487	+1	no_errors	ENST00000219905	ensembl	human	known	69_37n	missense	293	35.75	163	SNP	0.964	G
MMP9	4318	genome.wustl.edu	37	20	44640290	44640290	+	Missense_Mutation	SNP	G	G	A			TCGA-A8-A082-01A-11W-A019-09	TCGA-A8-A082-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	575d25ea-eae7-423a-9464-d3b2806bf9eb	576b6dc6-351b-4a61-b6e4-fbfda702de27	g.chr20:44640290G>A	ENST00000372330.3	+	6	920	c.901G>A	c.(901-903)Gcc>Acc	p.A301T	RP11-465L10.10_ENST00000535913.1_RNA	NM_004994.2	NP_004985.2	P14780	MMP9_HUMAN	matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)	301	Fibronectin type-II 2. {ECO:0000255|PROSITE-ProRule:PRU00479}.				collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|macrophage differentiation (GO:0030225)|negative regulation of cation channel activity (GO:2001258)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of receptor binding (GO:1900122)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|identical protein binding (GO:0042802)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|large_intestine(14)|liver(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	46		Myeloproliferative disorder(115;0.0122)			Captopril(DB01197)|Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017)	ATCCTACTCCGCCTGCACCAC	0.627											OREG0025989	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										dbGAP											0													88.0	81.0	83.0					20																	44640290		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS13390.1	20q12-q13	2008-01-07	2005-08-08		ENSG00000100985	ENSG00000100985	3.4.24.35		7176	protein-coding gene	gene with protein product		120361	"""matrix metalloproteinase 9 (gelatinase B, 92kD gelatinase, 92kD type IV collagenase)"", ""matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)"""	CLG4B		2158484	Standard	NM_004994		Approved		uc002xqz.3	P14780	OTTHUMG00000033044	ENST00000372330.3:c.901G>A	20.37:g.44640290G>A	ENSP00000361405:p.Ala301Thr	925	B2R7V9|Q3LR70|Q8N725|Q9H4Z1|Q9UCJ9|Q9UCL1|Q9UDK2	Missense_Mutation	SNP	pfam_Pept_M10_metallopeptidase,pfam_FN_type2_col-bd,pfam_Hemopexin/matrixin_repeat,pfam_PT,pfam_Peptidoglycan-bd-like,superfamily_Hemopexin/matrixin,superfamily_Kringle-like,superfamily_Peptidoglycan-bd-like,smart_Peptidase_Metallo,smart_FN_type2_col-bd,smart_Hemopexin/matrixin_repeat,pfscan_FN_type2_col-bd,prints_Pept_M10A_matrixin	p.A301T	ENST00000372330.3	37	c.901	CCDS13390.1	20	.	.	.	.	.	.	.	.	.	.	G	10.28	1.306807	0.23821	.	.	ENSG00000100985	ENST00000372330	T	0.48836	0.8	4.3	2.34	0.29019	Peptidase M10, metallopeptidase (1);Fibronectin, type II, collagen-binding (5);Kringle-like fold (1);Peptidase, metallopeptidase (1);	0.403771	0.29730	N	0.011343	T	0.25717	0.0626	N	0.12831	0.26	0.09310	N	1	B	0.12013	0.005	B	0.04013	0.001	T	0.13953	-1.0490	10	0.33940	T	0.23	.	7.9881	0.30224	0.2811:0.0:0.7189:0.0	.	301	P14780	MMP9_HUMAN	T	301	ENSP00000361405:A301T	ENSP00000361405:A301T	A	+	1	0	MMP9	44073697	0.000000	0.05858	0.701000	0.30321	0.579000	0.36224	-0.091000	0.11146	0.576000	0.29452	0.561000	0.74099	GCC	MMP9	-	pfam_Pept_M10_metallopeptidase,pfam_FN_type2_col-bd,superfamily_Kringle-like,smart_Peptidase_Metallo,smart_FN_type2_col-bd,pfscan_FN_type2_col-bd	ENSG00000100985		0.627	MMP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MMP9	HGNC	protein_coding	OTTHUMT00000080337.1	71	0.00	0	G			44640290	44640290	+1	no_errors	ENST00000372330	ensembl	human	known	69_37n	missense	57	25.61	21	SNP	0.036	A
NAA11	84779	genome.wustl.edu	37	4	80246828	80246828	+	Silent	SNP	C	C	T			TCGA-A8-A082-01A-11W-A019-09	TCGA-A8-A082-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	575d25ea-eae7-423a-9464-d3b2806bf9eb	576b6dc6-351b-4a61-b6e4-fbfda702de27	g.chr4:80246828C>T	ENST00000286794.4	-	1	376	c.204G>A	c.(202-204)ccG>ccA	p.P68P	NAA11_ENST00000513733.1_5'Flank	NM_032693.2	NP_116082.1	Q9BSU3	NAA11_HUMAN	N(alpha)-acetyltransferase 11, NatA catalytic subunit	68	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				N-terminal protein amino acid acetylation (GO:0006474)	NatA complex (GO:0031415)|nucleus (GO:0005634)	peptide alpha-N-acetyltransferase activity (GO:0004596)	p.P68P(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|pancreas(1)|skin(2)	23						TATGGCCATGCGGGACATCAT	0.582																																						dbGAP											1	Substitution - coding silent(1)	lung(1)											111.0	111.0	111.0					4																	80246828		2177	4289	6466	-	-	-	SO:0001819	synonymous_variant	0				CCDS47084.1	4q21.23	2010-05-07	2010-01-14	2010-01-14		ENSG00000156269	2.3.1.88	"""N(alpha)-acetyltransferase subunits"""	28125	protein-coding gene	gene with protein product			"""ARD1 homolog B (S. cerevisiae)"""	ARD1B		16638120, 19660095	Standard	NM_032693		Approved	ARD2, hARD2	uc003hlt.4	Q9BSU3		ENST00000286794.4:c.204G>A	4.37:g.80246828C>T			Q66K19|Q6P479	Silent	SNP	pfam_GNAT_dom,pfam_FR47,superfamily_Acyl_CoA_acyltransferase,pfscan_GNAT_dom	p.P68	ENST00000286794.4	37	c.204	CCDS47084.1	4																																																																																			NAA11	-	pfam_GNAT_dom,pfam_FR47,superfamily_Acyl_CoA_acyltransferase,pfscan_GNAT_dom	ENSG00000156269		0.582	NAA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NAA11	HGNC	protein_coding	OTTHUMT00000362922.1	128	0.00	0	C			80246828	80246828	-1	no_errors	ENST00000286794	ensembl	human	known	69_37n	silent	73	39.17	47	SNP	0.615	T
OAS2	4939	genome.wustl.edu	37	12	113435383	113435383	+	Missense_Mutation	SNP	C	C	T	rs200589437		TCGA-A8-A082-01A-11W-A019-09	TCGA-A8-A082-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	575d25ea-eae7-423a-9464-d3b2806bf9eb	576b6dc6-351b-4a61-b6e4-fbfda702de27	g.chr12:113435383C>T	ENST00000342315.4	+	4	900	c.686C>T	c.(685-687)aCg>aTg	p.T229M	RP1-71H24.1_ENST00000552784.1_RNA|OAS2_ENST00000392583.2_Missense_Mutation_p.T229M	NM_016817.2	NP_058197.2	P29728	OAS2_HUMAN	2'-5'-oligoadenylate synthetase 2, 69/71kDa	229	OAS domain 1.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|nucleobase-containing compound metabolic process (GO:0006139)|protein glycosylation (GO:0006486)|protein myristoylation (GO:0018377)|purine nucleotide biosynthetic process (GO:0006164)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						GAGCTGCTTACGGTGTATGCC	0.507													C|||	1	0.000199681	0.0	0.0014	5008	,	,		22710	0.0		0.0	False		,,,				2504	0.0				Pancreas(199;709 2232 18410 33584 35052)	dbGAP											0													120.0	106.0	111.0					12																	113435383		2203	4300	6503	-	-	-	SO:0001583	missense	0			M87284	CCDS31906.1, CCDS41839.1, CCDS44982.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111335			8087	protein-coding gene	gene with protein product		603350	"""2'-5'-oligoadenylate synthetase 2 (69-71 kD)"""			9790745	Standard	NM_002535		Approved		uc001tuj.3	P29728	OTTHUMG00000169802	ENST00000342315.4:c.686C>T	12.37:g.113435383C>T	ENSP00000342278:p.Thr229Met		A8K9T1|Q6PJ33|Q86XX8	Missense_Mutation	SNP	pfam_2-5-oligoAdlate_synth_1_dom2/C,pfam_Nucleotidyltransferase,pfscan_2-5-oligoadenylate_synth_N	p.T229M	ENST00000342315.4	37	c.686	CCDS31906.1	12	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	11.58	1.680599	0.29872	.	.	ENSG00000111335	ENST00000342315;ENST00000392583;ENST00000552756	T;T;T	0.56444	0.46;0.46;0.46	4.06	4.06	0.47325	-oligoadenylate synthetase 1, domain 2/C-terminal (2);-5&apos (2);2&apos (2);	0.000000	0.37483	U	0.002072	T	0.75831	0.3903	M	0.91561	3.22	0.43360	D	0.995435	D;D	0.89917	1.0;1.0	D;D	0.78314	0.991;0.979	T	0.81263	-0.1012	10	0.87932	D	0	-15.5079	11.9132	0.52751	0.0:1.0:0.0:0.0	.	229;229	P29728;P29728-2	OAS2_HUMAN;.	M	229;229;154	ENSP00000342278:T229M;ENSP00000376362:T229M;ENSP00000446977:T154M	ENSP00000342278:T229M	T	+	2	0	OAS2	111919766	0.198000	0.23374	0.013000	0.15412	0.024000	0.10985	3.926000	0.56491	2.247000	0.74100	0.460000	0.39030	ACG	OAS2	-	pfam_2-5-oligoAdlate_synth_1_dom2/C	ENSG00000111335		0.507	OAS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	OAS2	HGNC	protein_coding	OTTHUMT00000405937.1	235	0.00	0	C			113435383	113435383	+1	no_errors	ENST00000342315	ensembl	human	known	69_37n	missense	196	40.66	135	SNP	0.000	T
PCED1A	64773	genome.wustl.edu	37	20	2816203	2816204	+	Frame_Shift_Ins	INS	-	-	C	rs371156741		TCGA-A8-A082-01A-11W-A019-09	TCGA-A8-A082-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	575d25ea-eae7-423a-9464-d3b2806bf9eb	576b6dc6-351b-4a61-b6e4-fbfda702de27	g.chr20:2816203_2816204insC	ENST00000360652.2	-	8	1771_1772	c.1269_1270insG	c.(1267-1272)gggcccfs	p.P424fs	PCED1A_ENST00000356872.3_Frame_Shift_Ins_p.P373fs	NM_022760.4	NP_073597.2	Q9H1Q7	PED1A_HUMAN	PC-esterase domain containing 1A	424																	TGCCTGCAGGGCCCCCCCATTC	0.624																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AK026029	CCDS13035.1, CCDS59442.1	20p13	2012-06-11	2012-06-11	2012-06-11	ENSG00000132635	ENSG00000132635			16212	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 81"", ""family with sequence similarity 113, member A"""	C20orf81, FAM113A		20056006	Standard	NM_022760		Approved	bA12M19.1, FLJ22376	uc002wgz.2	Q9H1Q7	OTTHUMG00000031716	ENST00000360652.2:c.1270dupG	20.37:g.2816210_2816210dupC	ENSP00000353868:p.Pro424fs		Q5JUA5|Q5JUA6|Q6PK19|Q86WF5|Q96CG7|Q9H1Q6|Q9H6D1	Frame_Shift_Ins	INS	superfamily_Esterase_SGNH_hydro-type	p.P423fs	ENST00000360652.2	37	c.1270_1269	CCDS13035.1	20																																																																																			PCED1A	-	NULL	ENSG00000132635		0.624	PCED1A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	PCED1A	HGNC	protein_coding	OTTHUMT00000077676.2	47	0.00	0	-	NM_022760		2816203	2816204	-1	no_errors	ENST00000360652	ensembl	human	known	69_37n	frame_shift_ins	29	12.12	4	INS	0.660:0.001	C
POLD1	5424	genome.wustl.edu	37	19	50906369	50906370	+	Frame_Shift_Ins	INS	-	-	G			TCGA-A8-A082-01A-11W-A019-09	TCGA-A8-A082-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	575d25ea-eae7-423a-9464-d3b2806bf9eb	576b6dc6-351b-4a61-b6e4-fbfda702de27	g.chr19:50906369_50906370insG	ENST00000440232.2	+	9	1083_1084	c.1030_1031insG	c.(1030-1032)tggfs	p.W344fs	POLD1_ENST00000595904.1_Frame_Shift_Ins_p.W344fs|POLD1_ENST00000599857.1_Frame_Shift_Ins_p.W344fs	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	344					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		GGGCCTGCGCTGGGGGGAGCCG	0.688								DNA polymerases (catalytic subunits)																														dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0				CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"""DNA polymerases"""	9175	protein-coding gene	gene with protein product	"""CDC2 homolog (S. cerevisiae)"""	174761	"""polymerase (DNA directed), delta 1, catalytic subunit (125kD)"""	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.1036dupG	19.37:g.50906375_50906375dupG	ENSP00000406046:p.Trp344fs		Q8NER3|Q96H98	Frame_Shift_Ins	INS	pfam_DNA-dir_DNA_pol_B_multi_dom,pfam_DNA-dir_DNA_pol_B_exonuc,superfamily_RNaseH-like_dom,smart_DNA-dir_DNA_pol_B,prints_DNA-dir_DNA_pol_B,tigrfam_DNA-dir_DNA_pol_B_pol2	p.E346fs	ENST00000440232.2	37	c.1030_1031	CCDS12795.1	19																																																																																			POLD1	-	pfam_DNA-dir_DNA_pol_B_exonuc,superfamily_RNaseH-like_dom,smart_DNA-dir_DNA_pol_B	ENSG00000062822		0.688	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	POLD1	HGNC	protein_coding	OTTHUMT00000464732.1	8	0.00	0	-			50906369	50906370	+1	no_errors	ENST00000440232	ensembl	human	known	69_37n	frame_shift_ins	4	33.33	2	INS	1.000:1.000	G
PPL	5493	genome.wustl.edu	37	16	4937211	4937211	+	Silent	SNP	G	G	A			TCGA-A8-A082-01A-11W-A019-09	TCGA-A8-A082-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	575d25ea-eae7-423a-9464-d3b2806bf9eb	576b6dc6-351b-4a61-b6e4-fbfda702de27	g.chr16:4937211G>A	ENST00000345988.2	-	21	2621	c.2532C>T	c.(2530-2532)gcC>gcT	p.A844A	PPL_ENST00000590782.2_Silent_p.A842A	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	844					keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						CAGTGAACTTGGCGGCAAGTG	0.483																																						dbGAP											0													145.0	145.0	145.0					16																	4937211		2197	4300	6497	-	-	-	SO:0001819	synonymous_variant	0			AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.2532C>T	16.37:g.4937211G>A			O60314|O60454|Q14C98	Silent	SNP	pfam_Plectin_repeat,smart_Spectrin/alpha-actinin,smart_Plectin_repeat	p.A844	ENST00000345988.2	37	c.2532	CCDS10526.1	16																																																																																			PPL	-	smart_Spectrin/alpha-actinin	ENSG00000118898		0.483	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PPL	HGNC	protein_coding	OTTHUMT00000251715.1	128	0.00	0	G	NM_002705		4937211	4937211	-1	no_errors	ENST00000345988	ensembl	human	known	69_37n	silent	65	36.89	38	SNP	1.000	A
SLC13A4	26266	genome.wustl.edu	37	7	135376383	135376383	+	Missense_Mutation	SNP	G	G	A			TCGA-A8-A082-01A-11W-A019-09	TCGA-A8-A082-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	575d25ea-eae7-423a-9464-d3b2806bf9eb	576b6dc6-351b-4a61-b6e4-fbfda702de27	g.chr7:135376383G>A	ENST00000354042.4	-	12	1920	c.1231C>T	c.(1231-1233)Cgt>Tgt	p.R411C	C7orf73_ENST00000422968.1_3'UTR	NM_012450.2	NP_036582.2	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 4	411					sodium ion transmembrane transport (GO:0035725)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	24						GCATCAGTACGGTAGCCTTTC	0.493																																						dbGAP											0													77.0	68.0	71.0					7																	135376383		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF169301	CCDS5840.1	7q33	2013-07-18	2013-07-18		ENSG00000164707	ENSG00000164707		"""Solute carriers"""	15827	protein-coding gene	gene with protein product	"""sulphate transporter 1"""	604309	"""solute carrier family 13 (sodium/sulphate symporters), member 4"""			10535998	Standard	NM_012450		Approved	SUT-1, SUT1	uc003vta.3	Q9UKG4	OTTHUMG00000155539	ENST00000354042.4:c.1231C>T	7.37:g.135376383G>A	ENSP00000297282:p.Arg411Cys		A4D1Q4|Q8N631	Missense_Mutation	SNP	pfam_Na/sul_symport,pfam_Cit_transptr-like_dom,pfam_DctM	p.R411C	ENST00000354042.4	37	c.1231	CCDS5840.1	7	.	.	.	.	.	.	.	.	.	.	G	9.692	1.152230	0.21371	.	.	ENSG00000164707	ENST00000354042	T	0.02763	4.17	5.69	4.81	0.61882	.	0.101143	0.64402	D	0.000004	T	0.03827	0.0108	L	0.57536	1.79	0.80722	D	1	P;B	0.38535	0.635;0.344	B;B	0.35114	0.196;0.091	T	0.44112	-0.9349	10	0.54805	T	0.06	.	7.5034	0.27530	0.0835:0.0:0.7521:0.1643	.	280;411	Q59HF0;Q9UKG4	.;S13A4_HUMAN	C	411	ENSP00000297282:R411C	ENSP00000297282:R411C	R	-	1	0	SLC13A4	135026923	1.000000	0.71417	1.000000	0.80357	0.015000	0.08874	2.739000	0.47409	1.409000	0.46915	-0.136000	0.14681	CGT	SLC13A4	-	pfam_Na/sul_symport	ENSG00000164707		0.493	SLC13A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC13A4	HGNC	protein_coding	OTTHUMT00000340558.1	67	0.00	0	G	NM_012450		135376383	135376383	-1	no_errors	ENST00000354042	ensembl	human	known	69_37n	missense	52	35.00	28	SNP	1.000	A
SLC9A6	10479	genome.wustl.edu	37	X	135080645	135080646	+	Frame_Shift_Ins	INS	-	-	T			TCGA-A8-A082-01A-11W-A019-09	TCGA-A8-A082-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	575d25ea-eae7-423a-9464-d3b2806bf9eb	576b6dc6-351b-4a61-b6e4-fbfda702de27	g.chrX:135080645_135080646insT	ENST00000370698.3	+	4	547_548	c.512_513insT	c.(511-516)cattttfs	p.HF171fs	SLC9A6_ENST00000370701.1_Frame_Shift_Ins_p.HF151fs|SLC9A6_ENST00000370695.4_Frame_Shift_Ins_p.HF203fs	NM_006359.2	NP_006350.1	Q92581	SL9A6_HUMAN	solute carrier family 9, subfamily A (NHE6, cation proton antiporter 6), member 6	171					axon extension (GO:0048675)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|dendrite extension (GO:0097484)|dendritic spine development (GO:0060996)|ion transport (GO:0006811)|neuron projection morphogenesis (GO:0048812)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon terminus (GO:0043679)|axonal spine (GO:0044308)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|synapse (GO:0045202)	sodium:proton antiporter activity (GO:0015385)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(18)|ovary(2)|upper_aerodigestive_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					TGTCAGAGACATTTTTTTCGAA	0.297																																						dbGAP											0			GRCh37	CD082200	SLC9A6	D																																				-	-	-	SO:0001589	frameshift_variant	0			AF030409	CCDS14654.1, CCDS44003.1, CCDS55504.1	Xq26.3	2013-05-22	2012-03-22		ENSG00000198689	ENSG00000198689		"""Solute carriers"""	11079	protein-coding gene	gene with protein product		300231	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 6"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 6"""			9507001	Standard	NM_001042537		Approved	NHE6, KIAA0267	uc004ezk.3	Q92581	OTTHUMG00000022498	ENST00000370698.3:c.519dupT	X.37:g.135080652_135080652dupT	ENSP00000359732:p.His171fs		A6NIQ9|A8K160|B4DU30|B7ZAE0|Q3ZCW7|Q5JPP8|Q5JPP9|Q86VS0	Frame_Shift_Ins	INS	pfam_Cation/H_exchanger,prints_Na/H_exchanger_6,prints_NaH_exchanger,tigrfam_NaH_exchanger	p.R206fs	ENST00000370698.3	37	c.608_609	CCDS14654.1	X																																																																																			SLC9A6	-	pfam_Cation/H_exchanger,prints_NaH_exchanger,tigrfam_NaH_exchanger	ENSG00000198689		0.297	SLC9A6-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	SLC9A6	HGNC	protein_coding	OTTHUMT00000058450.1	214	0.00	0	-	NM_006359		135080645	135080646	+1	no_errors	ENST00000370695	ensembl	human	known	69_37n	frame_shift_ins	153	23.50	47	INS	1.000:1.000	T
TBX18	9096	genome.wustl.edu	37	6	85446535	85446535	+	Silent	SNP	C	C	T			TCGA-A8-A082-01A-11W-A019-09	TCGA-A8-A082-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	575d25ea-eae7-423a-9464-d3b2806bf9eb	576b6dc6-351b-4a61-b6e4-fbfda702de27	g.chr6:85446535C>T	ENST00000369663.5	-	8	2029	c.1692G>A	c.(1690-1692)acG>acA	p.T564T	TBX18_ENST00000606784.1_Intron	NM_001080508.1	NP_001073977.1	O95935	TBX18_HUMAN	T-box 18	564					anterior/posterior axis specification (GO:0009948)|cochlea morphogenesis (GO:0090103)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060829)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation involved in ureter development (GO:2000729)|sensory perception of sound (GO:0007605)|sinoatrial node development (GO:0003163)|smooth muscle cell differentiation (GO:0051145)|somitogenesis (GO:0001756)|ureter development (GO:0072189)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|liver(1)|lung(31)|ovary(2)|pancreas(3)|prostate(6)|skin(3)	61		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)		TCTGCCGATCCGTCATGGTCC	0.522																																						dbGAP											0													57.0	61.0	60.0					6																	85446535		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AJ010278	CCDS34495.1	6q14.1-q15	2012-12-19			ENSG00000112837	ENSG00000112837		"""T-boxes"""	11595	protein-coding gene	gene with protein product		604613				9888994, 16688725, 23242162	Standard	NM_001080508		Approved		uc003pkl.2	O95935	OTTHUMG00000015129	ENST00000369663.5:c.1692G>A	6.37:g.85446535C>T			A2RU13|Q7Z6U4|Q9UJI6	Silent	SNP	pfam_TF_T-box,superfamily_p53-like_TF_DNA-bd,smart_TF_T-box,pfscan_TF_T-box,prints_TF_T-box	p.T564	ENST00000369663.5	37	c.1692	CCDS34495.1	6																																																																																			TBX18	-	NULL	ENSG00000112837		0.522	TBX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TBX18	HGNC	protein_coding	OTTHUMT00000041378.2	115	0.00	0	C	NM_001080508		85446535	85446535	-1	no_errors	ENST00000369663	ensembl	human	known	69_37n	silent	61	39.00	39	SNP	0.007	T
UTP14A	10813	genome.wustl.edu	37	X	129059021	129059021	+	Silent	SNP	A	A	G			TCGA-A8-A082-01A-11W-A019-09	TCGA-A8-A082-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	575d25ea-eae7-423a-9464-d3b2806bf9eb	576b6dc6-351b-4a61-b6e4-fbfda702de27	g.chrX:129059021A>G	ENST00000394422.3	+	12	1627	c.1599A>G	c.(1597-1599)ttA>ttG	p.L533L	UTP14A_ENST00000371051.5_Silent_p.L479L|RP4-537K23.4_ENST00000432062.1_RNA|UTP14A_ENST00000425117.2_Silent_p.L481L|UTP14A_ENST00000371042.3_Silent_p.L365L	NM_006649.3	NP_006640.2	Q9BVJ6	UT14A_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein, homolog A (yeast)	533					rRNA processing (GO:0006364)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(16)|ovary(3)|urinary_tract(1)	32						GACCTGTGTTAGAAGGGCAGC	0.473																																						dbGAP											0													106.0	107.0	107.0					X																	129059021		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF039694	CCDS14615.1, CCDS55489.1	Xq26.1	2009-01-15	2004-06-01	2004-06-01	ENSG00000156697	ENSG00000156697			10665	protein-coding gene	gene with protein product		300508	"""serologically defined colon cancer antigen 16"""	SDCCAG16		9610721, 16354793	Standard	NM_006649		Approved	NY-CO-16	uc004euz.3	Q9BVJ6	OTTHUMG00000022378	ENST00000394422.3:c.1599A>G	X.37:g.129059021A>G			A8K7A3|A8MVQ1|B4DQ08|E9PEL7|Q5JYF1	Silent	SNP	pfam_SSU_processome_Utp14	p.L533	ENST00000394422.3	37	c.1599	CCDS14615.1	X																																																																																			UTP14A	-	pfam_SSU_processome_Utp14	ENSG00000156697		0.473	UTP14A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	UTP14A	HGNC	protein_coding	OTTHUMT00000058221.1	295	0.00	0	A	NM_006649		129059021	129059021	+1	no_errors	ENST00000394422	ensembl	human	known	69_37n	silent	276	11.25	35	SNP	0.006	G
