#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_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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
AADACL2	344752	genome.wustl.edu	37	3	151474973	151474973	+	Missense_Mutation	SNP	G	G	A			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr3:151474973G>A	ENST00000356517.3	+	5	906	c.797G>A	c.(796-798)aGa>aAa	p.R266K	RP11-454C18.2_ENST00000483843.2_RNA|RP11-454C18.2_ENST00000475855.1_RNA	NM_207365.3	NP_997248.2	Q6P093	ADCL2_HUMAN	arylacetamide deacetylase-like 2	266						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)	p.R244K(1)|p.R266K(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(4)|liver(1)|lung(13)|skin(2)	24			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			GCAATGAGAAGAAACCAACAC	0.393																																						dbGAP											2	Substitution - Missense(2)	breast(2)											137.0	144.0	141.0					3																	151474973		2203	4298	6501	-	-	-	SO:0001583	missense	0			BC065724	CCDS3161.2	3q25.1	2010-12-14			ENSG00000197953	ENSG00000197953			24427	protein-coding gene	gene with protein product							Standard	NM_207365		Approved	MGC72001	uc003ezc.3	Q6P093	OTTHUMG00000155914	ENST00000356517.3:c.797G>A	3.37:g.151474973G>A	ENSP00000348911:p.Arg266Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5HYJ4	Missense_Mutation	SNP	pfam_AB_hydrolase_3,pfam_CarbesteraseB,pfam_Steryl_acetyl_hydrolase,pirsf_Arylacetamide_deacetylase	p.R266K	ENST00000356517.3	37	c.797	CCDS3161.2	3	.	.	.	.	.	.	.	.	.	.	G	15.33	2.801530	0.50315	.	.	ENSG00000197953	ENST00000356517	T	0.03982	3.74	4.9	-4.85	0.03142	.	0.908518	0.09571	N	0.784178	T	0.02012	0.0063	N	0.17379	0.485	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.47471	-0.9115	10	0.05525	T	0.97	-0.7194	4.3859	0.11316	0.6131:0.1444:0.138:0.1044	.	266	Q6P093	ADCL2_HUMAN	K	266	ENSP00000348911:R266K	ENSP00000348911:R266K	R	+	2	0	AADACL2	152957663	0.010000	0.17322	0.000000	0.03702	0.903000	0.53119	0.001000	0.13038	-0.681000	0.05204	0.591000	0.81541	AGA	AADACL2	-	pirsf_Arylacetamide_deacetylase	ENSG00000197953		0.393	AADACL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AADACL2	HGNC	protein_coding	OTTHUMT00000342288.3	227	0.00	0	G	NM_207365		151474973	151474973	+1	no_errors	ENST00000356517	ensembl	human	known	69_37n	missense	81	50.30	83	SNP	0.009	A
ALX3	257	genome.wustl.edu	37	1	110603460	110603461	+	Frame_Shift_Ins	INS	-	-	C			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr1:110603460_110603461insC	ENST00000369792.4	-	4	1013_1014	c.926_927insG	c.(925-927)ggcfs	p.G309fs	RP4-773N10.4_ENST00000554749.1_RNA|RP4-773N10.4_ENST00000596959.1_RNA	NM_006492.2	NP_006483.2	O95076	ALX3_HUMAN	ALX homeobox 3	309					embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal system morphogenesis (GO:0048704)|pattern specification process (GO:0007389)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6		all_cancers(81;2.35e-05)|all_epithelial(167;7.69e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.015)|all cancers(265;0.0706)|Epithelial(280;0.0758)|Colorectal(144;0.113)|LUSC - Lung squamous cell carcinoma(189;0.135)		CAAAGCTGTGGCCCCCCAGGGT	0.619																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AF008203	CCDS819.1	1p13.3	2014-02-04	2008-11-04		ENSG00000156150	ENSG00000156150		"""Homeoboxes / PRD class"""	449	protein-coding gene	gene with protein product		606014	"""aristaless-like homeobox 3"", ""frontonasal dysplasia"""	FND		15226305, 11807986, 19409524	Standard	NM_006492		Approved		uc001dzb.3	O95076	OTTHUMG00000011650	ENST00000369792.4:c.927dupG	1.37:g.110603466_110603466dupC	ENSP00000358807:p.Gly309fs	Somatic		WXS	Illumina GAIIx	Phase_IV	O95075|Q5T8M4	Frame_Shift_Ins	INS	pfam_Homeodomain,superfamily_Homeodomain-like,smart_Homeodomain,pfscan_Homeodomain	p.H310fs	ENST00000369792.4	37	c.927_926	CCDS819.1	1																																																																																			ALX3	-	NULL	ENSG00000156150		0.619	ALX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ALX3	HGNC	protein_coding	OTTHUMT00000032232.2	31	0.00	0	-	NM_006492		110603460	110603461	-1	no_errors	ENST00000369792	ensembl	human	known	69_37n	frame_shift_ins	12	14.29	2	INS	1.000:1.000	C
ABCB10	23456	genome.wustl.edu	37	1	229663041	229663041	+	Missense_Mutation	SNP	C	C	G			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr1:229663041C>G	ENST00000344517.4	-	9	1702	c.1660G>C	c.(1660-1662)Gat>Cat	p.D554H		NM_012089.2	NP_036221.2	Q9NRK6	ABCBA_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 10	554	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)	p.D554H(1)		breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)	31	Breast(184;0.143)|Ovarian(103;0.249)	Prostate(94;0.167)				TCATGGCCATCAAGACTAATA	0.453																																						dbGAP											1	Substitution - Missense(1)	breast(1)											117.0	120.0	119.0					1																	229663041		2203	4300	6503	-	-	-	SO:0001583	missense	0			U18237	CCDS1580.1	1q32	2012-03-14			ENSG00000135776	ENSG00000135776		"""ATP binding cassette transporters / subfamily B"""	41	protein-coding gene	gene with protein product	"""ATP-binding cassette sub-family B member 10, mitochondrial"", ""ATP-binding cassette transporter 10"", ""ABC transporter 10 protein"", ""mitochondrial ATP-binding cassette 2"""	605454				7766993	Standard	NM_012089		Approved	EST20237, M-ABC2, MTABC2	uc001htp.4	Q9NRK6	OTTHUMG00000039471	ENST00000344517.4:c.1660G>C	1.37:g.229663041C>G	ENSP00000355637:p.Asp554His	Somatic		WXS	Illumina GAIIx	Phase_IV	Q13040|Q6P1Q8|Q9H3V0	Missense_Mutation	SNP	pfam_ABC_transptr_TM_dom,pfam_ABC_transporter-like,superfamily_ABC_transptrTM_dom_typ1,smart_AAA+_ATPase,pfscan_ABC_transporter-like,pfscan_ABC_transporter_type1	p.D554H	ENST00000344517.4	37	c.1660	CCDS1580.1	1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.213510	0.79352	.	.	ENSG00000135776	ENST00000344517	D	0.92099	-2.97	5.27	4.34	0.51931	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.046374	0.85682	N	0.000000	D	0.96386	0.8821	M	0.88241	2.94	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96855	0.9628	10	0.87932	D	0	-29.5795	14.0891	0.64977	0.0:0.8496:0.1504:0.0	.	554	Q9NRK6	ABCBA_HUMAN	H	554	ENSP00000355637:D554H	ENSP00000355637:D554H	D	-	1	0	ABCB10	227729664	1.000000	0.71417	0.945000	0.38365	0.998000	0.95712	4.994000	0.63901	1.183000	0.42943	0.650000	0.86243	GAT	ABCB10	-	pfam_ABC_transporter-like,smart_AAA+_ATPase,pfscan_ABC_transporter-like	ENSG00000135776		0.453	ABCB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ABCB10	HGNC	protein_coding	OTTHUMT00000095240.1	129	0.00	0	C	NM_012089		229663041	229663041	-1	no_errors	ENST00000344517	ensembl	human	known	69_37n	missense	120	14.29	20	SNP	0.998	G
AMHR2	269	genome.wustl.edu	37	12	53819509	53819509	+	Missense_Mutation	SNP	G	G	C	rs142124054		TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr12:53819509G>C	ENST00000257863.4	+	6	738	c.658G>C	c.(658-660)Ggg>Cgg	p.G220R	AMHR2_ENST00000379791.3_Missense_Mutation_p.G220R|AMHR2_ENST00000550311.1_Missense_Mutation_p.G220R	NM_001164690.1|NM_020547.2	NP_001158162.1|NP_065434.1	Q16671	AMHR2_HUMAN	anti-Mullerian hormone receptor, type II	220	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				Mullerian duct regression (GO:0001880)|negative regulation of anti-Mullerian hormone signaling pathway (GO:1902613)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	integral component of plasma membrane (GO:0005887)	anti-Mullerian hormone receptor activity (GO:1990272)|ATP binding (GO:0005524)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor activity, type II (GO:0005026)	p.G220R(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|skin(2)	34					Adenosine triphosphate(DB00171)	GGTTTGGGCCGGGCAGCTGCA	0.577																																						dbGAP											1	Substitution - Missense(1)	breast(1)											66.0	56.0	59.0					12																	53819509		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF172932	CCDS8858.1, CCDS53798.1, CCDS55829.1	12q13	2013-03-14							465	protein-coding gene	gene with protein product	"""Muellerian inhibiting substance type II receptor"""	600956				7493017	Standard	NM_001164690		Approved	MISR2, MISRII	uc001scx.2	Q16671	OTTHUMG00000170048	ENST00000257863.4:c.658G>C	12.37:g.53819509G>C	ENSP00000257863:p.Gly220Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	A0AVE1|B9EGB7|E9PGD2|F8W1D2|Q13762|Q647K2	Missense_Mutation	SNP	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Activin_rcpt,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pirsf_Anti-muellerian_hrmn_rcpt_II,pfscan_Prot_kinase_cat_dom	p.G220R	ENST00000257863.4	37	c.658	CCDS8858.1	12	.	.	.	.	.	.	.	.	.	.	G	22.9	4.354451	0.82243	.	.	ENSG00000135409	ENST00000257863;ENST00000550311;ENST00000379791	D;D;D	0.94793	-3.52;-3.52;-3.52	5.66	5.66	0.87406	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.40222	N	0.001157	D	0.97567	0.9203	M	0.89163	3.01	0.42641	D	0.993414	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.98132	1.0431	10	0.87932	D	0	.	15.6361	0.76953	0.0:0.0:1.0:0.0	.	220;220	F8W1D2;Q16671	.;AMHR2_HUMAN	R	220	ENSP00000257863:G220R;ENSP00000446661:G220R;ENSP00000369117:G220R	ENSP00000257863:G220R	G	+	1	0	AMHR2	52105776	1.000000	0.71417	0.631000	0.29282	0.947000	0.59692	5.477000	0.66799	2.840000	0.97914	0.655000	0.94253	GGG	AMHR2	-	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,pirsf_Anti-muellerian_hrmn_rcpt_II,pfscan_Prot_kinase_cat_dom	ENSG00000135409		0.577	AMHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AMHR2	HGNC	protein_coding	OTTHUMT00000407048.1	108	0.00	0	G	NM_020547		53819509	53819509	+1	no_errors	ENST00000257863	ensembl	human	known	69_37n	missense	34	60.23	53	SNP	0.814	C
ANAPC5	51433	genome.wustl.edu	37	12	121746366	121746366	+	Nonsense_Mutation	SNP	C	C	A			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr12:121746366C>A	ENST00000261819.3	-	17	2306	c.2185G>T	c.(2185-2187)Gag>Tag	p.E729*	ANAPC5_ENST00000344395.4_Nonsense_Mutation_p.E617*|ANAPC5_ENST00000441917.2_Nonsense_Mutation_p.E617*|ANAPC5_ENST00000535482.1_Nonsense_Mutation_p.E395*|ANAPC5_ENST00000544314.1_5'UTR|ANAPC5_ENST00000541887.1_Nonsense_Mutation_p.E716*	NM_016237.4	NP_057321.2	Q9UJX4	APC5_HUMAN	anaphase promoting complex subunit 5	729					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)	p.E729*(1)		breast(6)|endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(3)	31	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CGGTTCCTCTCCTGGGTCTTC	0.542																																						dbGAP											1	Substitution - Nonsense(1)	breast(1)											119.0	112.0	114.0					12																	121746366		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AF191339	CCDS9220.1, CCDS45000.1	12q24.31	2014-08-12			ENSG00000089053	ENSG00000089053		"""Anaphase promoting complex subunits"""	15713	protein-coding gene	gene with protein product		606948				9469815	Standard	NM_016237		Approved	APC5	uc001uag.3	Q9UJX4	OTTHUMG00000169157	ENST00000261819.3:c.2185G>T	12.37:g.121746366C>A	ENSP00000261819:p.Glu729*	Somatic		WXS	Illumina GAIIx	Phase_IV	E9PFB2|Q8N4H7|Q9BQD4	Nonsense_Mutation	SNP	smart_TPR_repeat	p.E729*	ENST00000261819.3	37	c.2185	CCDS9220.1	12	.	.	.	.	.	.	.	.	.	.	C	38	7.273768	0.98179	.	.	ENSG00000089053	ENST00000441917;ENST00000541887;ENST00000261819;ENST00000535482;ENST00000544314;ENST00000344395	.	.	.	5.61	5.61	0.85477	.	0.051022	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	18.6393	0.91389	0.0:1.0:0.0:0.0	.	.	.	.	X	617;716;729;395;331;617	.	ENSP00000261819:E729X	E	-	1	0	ANAPC5	120230749	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.155000	0.58131	2.646000	0.89796	0.563000	0.77884	GAG	ANAPC5	-	NULL	ENSG00000089053		0.542	ANAPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ANAPC5	HGNC	protein_coding	OTTHUMT00000402582.1	101	0.00	0	C			121746366	121746366	-1	no_errors	ENST00000261819	ensembl	human	known	69_37n	nonsense	59	44.86	48	SNP	1.000	A
AP3M1	26985	genome.wustl.edu	37	10	75884140	75884140	+	Missense_Mutation	SNP	G	G	A			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr10:75884140G>A	ENST00000355264.4	-	8	1465	c.1154C>T	c.(1153-1155)tCa>tTa	p.S385L	AP3M1_ENST00000372745.1_Missense_Mutation_p.S385L	NM_012095.4	NP_036227.1	Q9Y2T2	AP3M1_HUMAN	adaptor-related protein complex 3, mu 1 subunit	385	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|protein targeting to lysosome (GO:0006622)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	Rab GTPase binding (GO:0017137)	p.S385L(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(1)|prostate(1)|skin(1)	13	Prostate(51;0.0112)					ATCCTTACCTGAAATAGCAAG	0.393																																						dbGAP											1	Substitution - Missense(1)	breast(1)											109.0	102.0	104.0					10																	75884140		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF092092	CCDS7342.1	10q22.1-q22.3	2008-07-07			ENSG00000185009	ENSG00000185009			569	protein-coding gene	gene with protein product		610366				10024875	Standard	NM_207012		Approved		uc001jwh.3	Q9Y2T2	OTTHUMG00000018497	ENST00000355264.4:c.1154C>T	10.37:g.75884140G>A	ENSP00000347408:p.Ser385Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5JQ12|Q9H5L2	Missense_Mutation	SNP	pfam_Clathrin_mu_C,pfam_AP_mu_sigma_su,superfamily_Clathrin_mu_C,superfamily_Longin-like_dom,pirsf_Clathrin_mu,pfscan_Clathrin_mu_C,prints_Clathrin_mu	p.S385L	ENST00000355264.4	37	c.1154	CCDS7342.1	10	.	.	.	.	.	.	.	.	.	.	G	36	5.651778	0.96714	.	.	ENSG00000185009	ENST00000355264;ENST00000372745	T;T	0.45276	0.9;0.9	6.08	6.08	0.98989	Clathrin adaptor, mu subunit, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.78052	0.4223	H	0.96208	3.785	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.85130	0.993;0.997	D	0.83786	0.0228	10	0.87932	D	0	-9.355	20.6721	0.99693	0.0:0.0:1.0:0.0	.	331;385	B4DRN6;Q9Y2T2	.;AP3M1_HUMAN	L	385	ENSP00000347408:S385L;ENSP00000361831:S385L	ENSP00000347408:S385L	S	-	2	0	AP3M1	75554146	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.476000	0.97823	2.894000	0.99253	0.591000	0.81541	TCA	AP3M1	-	pfam_Clathrin_mu_C,superfamily_Clathrin_mu_C,pirsf_Clathrin_mu,pfscan_Clathrin_mu_C	ENSG00000185009		0.393	AP3M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AP3M1	HGNC	protein_coding	OTTHUMT00000048747.1	327	0.61	2	G			75884140	75884140	-1	no_errors	ENST00000355264	ensembl	human	known	69_37n	missense	136	55.41	169	SNP	1.000	A
BBC3	27113	genome.wustl.edu	37	19	47725018	47725019	+	3'UTR	INS	-	-	C			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr19:47725018_47725019insC	ENST00000439096.2	-	0	902_903				BBC3_ENST00000449228.1_Frame_Shift_Ins_p.G242fs|BBC3_ENST00000300880.7_Frame_Shift_Ins_p.G82fs|BBC3_ENST00000341983.4_3'UTR	NM_014417.4	NP_055232.1	Q9BXH1	BBC3_HUMAN	BCL2 binding component 3						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|determination of adult lifespan (GO:0008340)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of growth (GO:0045926)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein homooligomerization (GO:0032464)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|release of cytochrome c from mitochondria (GO:0001836)|release of sequestered calcium ion into cytosol (GO:0051209)|response to endoplasmic reticulum stress (GO:0034976)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)				endometrium(1)|lung(2)|skin(1)	4		all_cancers(25;1.13e-05)|all_lung(116;0.000192)|all_epithelial(76;0.000274)|Lung NSC(112;0.000446)|all_neural(266;0.0652)|Ovarian(192;0.15)		all cancers(93;0.000179)|OV - Ovarian serous cystadenocarcinoma(262;0.00029)|Epithelial(262;0.0103)|GBM - Glioblastoma multiforme(486;0.0234)		GGAGGGGCCTGCCCCCCGAGTC	0.693																																						dbGAP											0																																										-	-	-	SO:0001624	3_prime_UTR_variant	0			AF332558	CCDS12697.1, CCDS46128.1, CCDS46129.1, CCDS46130.1	19q13.3-q13.4	2014-03-07							17868	protein-coding gene	gene with protein product		605854				11463392, 11572983	Standard	NM_001127240		Approved	JFY1, PUMA	uc002pgf.4	Q96PG8		ENST00000439096.2:c.*41->G	19.37:g.47725024_47725024dupC		Somatic		WXS	Illumina GAIIx	Phase_IV	B9EGI3|O00171|Q96PG9	Frame_Shift_Ins	INS	NULL	p.R243fs	ENST00000439096.2	37	c.726_725	CCDS12697.1	19																																																																																			BBC3	-	NULL	ENSG00000105327		0.693	BBC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	BBC3	HGNC	protein_coding	OTTHUMT00000466874.1	23	0.00	0	-	NM_014417		47725018	47725019	-1	no_errors	ENST00000449228	ensembl	human	known	69_37n	frame_shift_ins	15	11.76	2	INS	1.000:1.000	C
EDRF1	26098	genome.wustl.edu	37	10	127429725	127429725	+	Missense_Mutation	SNP	G	G	A			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr10:127429725G>A	ENST00000356792.4	+	17	2558	c.2326G>A	c.(2326-2328)Gac>Aac	p.D776N	C10orf137_ENST00000337623.3_Missense_Mutation_p.D742N	NM_001202438.1	NP_001189367.1	Q3B7T1	EDRF1_HUMAN		776					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.D742N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(20)|ovary(8)|pancreas(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	61		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)				AACAAAAGAAGACCAGGAGAT	0.468																																						dbGAP											1	Substitution - Missense(1)	breast(1)											113.0	105.0	108.0					10																	127429725		2203	4300	6503	-	-	-	SO:0001583	missense	0																														ENST00000356792.4:c.2326G>A	10.37:g.127429725G>A	ENSP00000349244:p.Asp776Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RC65|Q3KR40|Q4G190|Q5VZQ4|Q8IZ74|Q9Y3W4	Missense_Mutation	SNP	NULL	p.D776N	ENST00000356792.4	37	c.2326	CCDS55733.1	10	.	.	.	.	.	.	.	.	.	.	G	35	5.447315	0.96205	.	.	ENSG00000107938	ENST00000356792;ENST00000392732;ENST00000337623;ENST00000368813	T	0.61742	0.08	5.5	5.5	0.81552	Tetratricopeptide-like helical (1);	0.046560	0.85682	D	0.000000	T	0.73102	0.3544	L	0.49778	1.585	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.993;0.999;0.998;0.996	D;P;D;D;D	0.87578	0.998;0.84;0.964;0.995;0.993	T	0.74548	-0.3629	10	0.72032	D	0.01	.	19.4119	0.94677	0.0:0.0:1.0:0.0	.	776;776;123;742;776	F8W695;Q3B7T1;Q5VZQ1;Q3B7T1-5;Q3B7T1-3	.;EDRF1_HUMAN;.;.;.	N	776;776;742;196	ENSP00000357803:D196N	ENSP00000336727:D742N	D	+	1	0	C10orf137	127419715	1.000000	0.71417	0.782000	0.31804	0.882000	0.50991	9.476000	0.97823	2.596000	0.87737	0.650000	0.86243	GAC	C10orf137	-	NULL	ENSG00000107938		0.468	C10orf137-007	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	C10orf137	HGNC	protein_coding	OTTHUMT00000388539.1	156	0.00	0	G			127429725	127429725	+1	no_errors	ENST00000356792	ensembl	human	known	69_37n	missense	108	28.76	44	SNP	1.000	A
C6orf211	79624	genome.wustl.edu	37	6	151789511	151789511	+	Missense_Mutation	SNP	C	C	A			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr6:151789511C>A	ENST00000367294.3	+	5	851	c.592C>A	c.(592-594)Ctc>Atc	p.L198I	C6orf211_ENST00000545879.1_Missense_Mutation_p.L79I	NM_024573.1	NP_078849.1	Q9H993	CF211_HUMAN	chromosome 6 open reading frame 211	198								p.L198I(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(7)	15			BRCA - Breast invasive adenocarcinoma(37;0.183)	OV - Ovarian serous cystadenocarcinoma(155;5.27e-11)		TGATCTGTCTCTCTCAGGTGG	0.348																																						dbGAP											1	Substitution - Missense(1)	breast(1)											83.0	89.0	87.0					6																	151789511		2203	4299	6502	-	-	-	SO:0001583	missense	0			AJ420548	CCDS5233.1, CCDS69224.1	6q25.1	2013-01-07			ENSG00000146476	ENSG00000146476			17872	protein-coding gene	gene with protein product							Standard	NM_001286562		Approved	FLJ12910	uc003qok.1	Q9H993	OTTHUMG00000015838	ENST00000367294.3:c.592C>A	6.37:g.151789511C>A	ENSP00000356263:p.Leu198Ile	Somatic		WXS	Illumina GAIIx	Phase_IV	Q96FC6|Q9UFY5	Missense_Mutation	SNP	pfam_DUF89,superfamily_DUF89	p.L198I	ENST00000367294.3	37	c.592	CCDS5233.1	6	.	.	.	.	.	.	.	.	.	.	C	5.528	0.282303	0.10458	.	.	ENSG00000146476	ENST00000367294;ENST00000545879	T;T	0.07688	3.17;3.17	5.69	-0.932	0.10435	Domain of unknown function DUF89 (2);	0.319335	0.30118	N	0.010362	T	0.01730	0.0055	L	0.41124	1.26	0.26707	N	0.971058	B	0.19073	0.033	B	0.32928	0.155	T	0.46679	-0.9174	10	0.22706	T	0.39	.	1.042	0.01561	0.4194:0.1886:0.1006:0.2914	.	198	Q9H993	CF211_HUMAN	I	198;79	ENSP00000356263:L198I;ENSP00000444121:L79I	ENSP00000356263:L198I	L	+	1	0	C6orf211	151831204	0.989000	0.36119	0.060000	0.19600	0.657000	0.38888	2.437000	0.44828	-0.181000	0.10619	0.561000	0.74099	CTC	C6orf211	-	pfam_DUF89,superfamily_DUF89	ENSG00000146476		0.348	C6orf211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C6orf211	HGNC	protein_coding	OTTHUMT00000042724.1	62	0.00	0	C	NM_024573		151789511	151789511	+1	no_errors	ENST00000367294	ensembl	human	known	69_37n	missense	44	44.30	35	SNP	0.401	A
CKMT2	1160	genome.wustl.edu	37	5	80562003	80562003	+	Missense_Mutation	SNP	G	G	A			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr5:80562003G>A	ENST00000424301.2	+	11	1424	c.1186G>A	c.(1186-1188)Gat>Aat	p.D396N	CKMT2-AS1_ENST00000505295.1_RNA|CKMT2-AS1_ENST00000500148.2_RNA|CKMT2-AS1_ENST00000503483.2_RNA|CKMT2-AS1_ENST00000511495.1_RNA|CKMT2-AS1_ENST00000501927.2_RNA|CKMT2_ENST00000437669.1_Missense_Mutation_p.D396N|CKMT2_ENST00000254035.4_Missense_Mutation_p.D396N|CKMT2-AS1_ENST00000512287.1_RNA|CKMT2-AS1_ENST00000502041.2_RNA	NM_001825.2	NP_001816.2	P17540	KCRS_HUMAN	creatine kinase, mitochondrial 2 (sarcomeric)	396	Phosphagen kinase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00843}.				cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|muscle contraction (GO:0006936)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)	p.D396N(1)		breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(4)|urinary_tract(1)	17		Lung NSC(167;0.00475)|all_lung(232;0.00502)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;2.29e-44)|Epithelial(54;1.05e-38)|all cancers(79;4.15e-34)	Creatine(DB00148)	TTACCTGGTGGATTGTGAAAA	0.403																																						dbGAP											1	Substitution - Missense(1)	breast(1)											183.0	190.0	188.0					5																	80562003		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS4053.1	5q14.1	2013-09-20			ENSG00000131730	ENSG00000131730	2.7.3.2		1996	protein-coding gene	gene with protein product		123295				2324105	Standard	NM_001825		Approved	SMTCK	uc003khd.4	P17540	OTTHUMG00000119013	ENST00000424301.2:c.1186G>A	5.37:g.80562003G>A	ENSP00000404203:p.Asp396Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	Q6ICS8|Q8N1E1	Missense_Mutation	SNP	pfam_ATP-guanido_PTrfase_cat,pfam_ATP-guanido_PTrfase_N,superfamily_ATP-guanido_PTrfase_N	p.D396N	ENST00000424301.2	37	c.1186	CCDS4053.1	5	.	.	.	.	.	.	.	.	.	.	G	24.2	4.506280	0.85282	.	.	ENSG00000131730	ENST00000254035;ENST00000437669;ENST00000424301	T;T;T	0.11169	2.8;2.8;2.8	5.82	5.82	0.92795	ATP:guanido phosphotransferase, catalytic domain (2);Glutamine synthetase/guanido kinase, catalytic domain (1);	0.094770	0.64402	D	0.000001	T	0.14270	0.0345	L	0.45137	1.4	0.80722	D	1	B	0.09022	0.002	B	0.11329	0.006	T	0.03008	-1.1083	10	0.56958	D	0.05	-21.201	20.0905	0.97816	0.0:0.0:1.0:0.0	.	396	P17540	KCRS_HUMAN	N	396	ENSP00000254035:D396N;ENSP00000410289:D396N;ENSP00000404203:D396N	ENSP00000254035:D396N	D	+	1	0	CKMT2	80597759	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.713000	0.98740	2.762000	0.94881	0.650000	0.86243	GAT	CKMT2	-	pfam_ATP-guanido_PTrfase_cat	ENSG00000131730		0.403	CKMT2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	CKMT2	HGNC	protein_coding	OTTHUMT00000369600.1	308	0.00	0	G	NM_001825		80562003	80562003	+1	no_errors	ENST00000254035	ensembl	human	known	69_37n	missense	138	45.70	117	SNP	1.000	A
CLCN2	1181	genome.wustl.edu	37	3	184070098	184070098	+	Missense_Mutation	SNP	C	C	T			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr3:184070098C>T	ENST00000265593.4	-	21	2464	c.2293G>A	c.(2293-2295)Gag>Aag	p.E765K	CLCN2_ENST00000423355.2_3'UTR|CLCN2_ENST00000344937.7_Missense_Mutation_p.E748K|EIF2B5_ENST00000444495.1_Intron|CLCN2_ENST00000434054.2_Missense_Mutation_p.E721K|CLCN2_ENST00000457512.1_Missense_Mutation_p.E765K	NM_004366.5	NP_004357.3	P51788	CLCN2_HUMAN	chloride channel, voltage-sensitive 2	765					cell differentiation involved in salivary gland development (GO:0060689)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|retina development in camera-type eye (GO:0060041)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|voltage-gated chloride channel activity (GO:0005247)	p.E765K(1)		breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	27	all_cancers(143;6.66e-11)|Ovarian(172;0.0339)		Epithelial(37;2.22e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Lubiprostone(DB01046)	GGGCTCATCTCGCCTTCCAGG	0.597																																						dbGAP											1	Substitution - Missense(1)	breast(1)											91.0	81.0	84.0					3																	184070098		2203	4300	6503	-	-	-	SO:0001583	missense	0			S77770	CCDS3263.1, CCDS54690.1, CCDS54691.1, CCDS54692.1	3q27.1	2013-09-19	2012-02-23		ENSG00000114859	ENSG00000114859		"""Ion channels / Chloride channels : Voltage-sensitive"""	2020	protein-coding gene	gene with protein product		600570	"""chloride channel 2"""			7795595	Standard	NM_004366		Approved	CLC2, EJM6, ClC-2	uc003foi.4	P51788	OTTHUMG00000156747	ENST00000265593.4:c.2293G>A	3.37:g.184070098C>T	ENSP00000265593:p.Glu765Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DQT9|B4DZ58|E9PBD9|E9PCD2|O14864|Q6IPA9|Q8WU13	Missense_Mutation	SNP	pfam_Cl-channel_volt-gated,pfam_Cysta_beta_synth_core,superfamily_Cl-channel_core,prints_Cl-channel_volt-gated,prints_Cl-channel-2	p.E765K	ENST00000265593.4	37	c.2293	CCDS3263.1	3	.	.	.	.	.	.	.	.	.	.	c	12.76	2.033920	0.35893	.	.	ENSG00000114859	ENST00000265593;ENST00000344937;ENST00000434054;ENST00000457512	D;D;D;D	0.87491	-2.26;-2.26;-2.26;-2.26	5.07	4.18	0.49190	.	0.440518	0.27424	N	0.019431	T	0.76814	0.4040	N	0.22421	0.69	0.80722	D	1	B;B;B;B;B	0.06786	0.001;0.0;0.001;0.001;0.001	B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.001	T	0.70525	-0.4848	10	0.38643	T	0.18	-13.3713	8.3372	0.32221	0.0:0.7485:0.0:0.2515	.	721;765;748;765;721	E9PBD9;E9PCD2;P51788-3;P51788;B4DZ58	.;.;.;CLCN2_HUMAN;.	K	765;748;721;765	ENSP00000265593:E765K;ENSP00000345056:E748K;ENSP00000400425:E721K;ENSP00000391928:E765K	ENSP00000265593:E765K	E	-	1	0	CLCN2	185552792	0.993000	0.37304	1.000000	0.80357	0.903000	0.53119	1.982000	0.40638	1.341000	0.45600	0.462000	0.41574	GAG	CLCN2	-	NULL	ENSG00000114859		0.597	CLCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CLCN2	HGNC	protein_coding	OTTHUMT00000345571.1	49	0.00	0	C			184070098	184070098	-1	no_errors	ENST00000265593	ensembl	human	known	69_37n	missense	21	26.67	8	SNP	0.958	T
COASY	80347	genome.wustl.edu	37	17	40714751	40714752	+	Frame_Shift_Ins	INS	-	-	T			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr17:40714751_40714752insT	ENST00000393818.2	+	1	567_568	c.111_112insT	c.(112-114)tatfs	p.Y38fs	COASY_ENST00000421097.2_Frame_Shift_Ins_p.Y38fs|COASY_ENST00000420359.1_Frame_Shift_Ins_p.Y38fs|COASY_ENST00000590958.1_Frame_Shift_Ins_p.Y67fs|RP11-400F19.8_ENST00000585572.1_RNA|COASY_ENST00000449624.1_Intron	NM_025233.6	NP_079509.5	Q13057	COASY_HUMAN	CoA synthase	38					cell death (GO:0008219)|coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)	ATP binding (GO:0005524)|dephospho-CoA kinase activity (GO:0004140)|pantetheine-phosphate adenylyltransferase activity (GO:0004595)	p.Y38fs*26(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)	21		all_cancers(22;1.06e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)		ATCACACACTCTATGTTCACCT	0.663																																						dbGAP											1	Insertion - Frameshift(1)	breast(1)																																								-	-	-	SO:0001589	frameshift_variant	0			AF453478	CCDS11429.1, CCDS45685.1	17q12-q21	2010-04-30	2010-04-30			ENSG00000068120	2.7.7.3		29932	protein-coding gene	gene with protein product		609855	"""Coenzyme A synthase"""			11923312, 11980892	Standard	NM_025233		Approved	DPCK, NBP, CoASY, PPAT	uc010cyj.4	Q13057		ENST00000393818.2:c.112dupT	17.37:g.40714752_40714752dupT	ENSP00000377406:p.Tyr38fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RA78|B4DLU0|Q6GS23|Q8NBM7|Q8NEW1|Q8WXD4|Q9NRM3	Frame_Shift_Ins	INS	pfam_Depp_CoAkinase,pfam_Cytidylyltransf,tigrfam_Depp_CoAkinase	p.Y66fs	ENST00000393818.2	37	c.198_199	CCDS11429.1	17																																																																																			COASY	-	NULL	ENSG00000068120		0.663	COASY-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	COASY	HGNC	protein_coding	OTTHUMT00000450409.1	22	0.00	0	-	NM_025233		40714751	40714752	+1	no_errors	ENST00000590958	ensembl	human	known	69_37n	frame_shift_ins	18	14.29	3	INS	0.915:1.000	T
COG8	84342	genome.wustl.edu	37	16	69370510	69370510	+	Silent	SNP	G	G	A			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr16:69370510G>A	ENST00000306875.4	-	2	597	c.483C>T	c.(481-483)ctC>ctT	p.L161L	RP11-343C2.9_ENST00000563634.1_Silent_p.L36L|NIP7_ENST00000254940.5_5'Flank|RP11-343C2.12_ENST00000562949.1_5'Flank|COG8_ENST00000562081.1_Silent_p.L161L|NIP7_ENST00000569637.2_5'Flank|RP11-343C2.7_ENST00000564737.1_3'UTR	NM_032382.4	NP_115758.3	Q96MW5	COG8_HUMAN	component of oligomeric golgi complex 8	161					protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)		p.L161L(1)		breast(3)|kidney(1)|large_intestine(2)|ovary(2)|skin(1)	9						AGGTGTCCATGAGCTGAGGAA	0.517																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											108.0	98.0	102.0					16																	69370510		2198	4300	6498	-	-	-	SO:0001819	synonymous_variant	0			AK025968	CCDS10876.1	16q22.1	2011-05-31			ENSG00000213380	ENSG00000213380		"""Components of oligomeric golgi complex"""	18623	protein-coding gene	gene with protein product		606979				11980916	Standard	NM_032382		Approved	FLJ22315, DOR1	uc002ewy.2	Q96MW5	OTTHUMG00000154277	ENST00000306875.4:c.483C>T	16.37:g.69370510G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q0VAK2|Q8WVV6|Q9H6F8	Missense_Mutation	SNP	pfam_Dor1	p.H142Y	ENST00000306875.4	37	c.424	CCDS10876.1	16																																																																																			COG8	-	pfam_Dor1	ENSG00000213380		0.517	COG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COG8	HGNC	protein_coding	OTTHUMT00000268948.2	118	0.00	0	G	NM_032382		69370510	69370510	-1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000562595	ensembl	human	putative	69_37n	missense	109	18.05	24	SNP	0.838	A
CXorf38	159013	genome.wustl.edu	37	X	40489945	40489945	+	Silent	SNP	C	C	T			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chrX:40489945C>T	ENST00000327877.5	-	6	908	c.882G>A	c.(880-882)caG>caA	p.Q294Q	CXorf38_ENST00000378421.1_Silent_p.Q175Q|CXorf38_ENST00000378426.1_Silent_p.Q175Q|CXorf38_ENST00000440784.2_Silent_p.Q209Q	NM_144970.2	NP_659407.1	Q8TB03	CX038_HUMAN	chromosome X open reading frame 38	294								p.Q294Q(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	12						TGTCTAGCTTCTGCATATCTT	0.463																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											186.0	139.0	155.0					X																	40489945		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AL832829	CCDS14253.1	Xp11	2008-02-05			ENSG00000185753	ENSG00000185753			28589	protein-coding gene	gene with protein product							Standard	NM_144970		Approved	MGC39350	uc004dew.3	Q8TB03	OTTHUMG00000024104	ENST00000327877.5:c.882G>A	X.37:g.40489945C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B3KW28|D3DWB5|Q5JPF5|Q8N941	Silent	SNP	NULL	p.Q294	ENST00000327877.5	37	c.882	CCDS14253.1	X																																																																																			CXorf38	-	NULL	ENSG00000185753		0.463	CXorf38-003	KNOWN	basic|appris_principal|CCDS	protein_coding	CXorf38	HGNC	protein_coding	OTTHUMT00000060685.3	294	0.00	0	C	NM_144970		40489945	40489945	-1	no_errors	ENST00000327877	ensembl	human	known	69_37n	silent	160	22.22	46	SNP	1.000	T
DACH2	117154	genome.wustl.edu	37	X	85404051	85404051	+	Missense_Mutation	SNP	C	C	G			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chrX:85404051C>G	ENST00000373125.4	+	1	427	c.427C>G	c.(427-429)Cgc>Ggc	p.R143G	DACH2_ENST00000373131.1_Missense_Mutation_p.R143G	NM_053281.3	NP_444511.1	Q96NX9	DACH2_HUMAN	dachshund family transcription factor 2	143	DACHbox-N.				development of primary female sexual characteristics (GO:0046545)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R143G(2)		breast(2)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(14)|lung(28)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	71						CGGGGTAAACCGCTGCAAACT	0.552																																						dbGAP											2	Substitution - Missense(2)	breast(2)											50.0	50.0	50.0					X																	85404051		2202	4300	6502	-	-	-	SO:0001583	missense	0			AF428101	CCDS14455.1, CCDS48140.1, CCDS55457.1	Xq21.3	2014-02-03	2014-02-03		ENSG00000126733	ENSG00000126733			16814	protein-coding gene	gene with protein product		300608	"""dachshund homolog 2 (Drosophila)"""				Standard	NM_053281		Approved		uc004eew.2	Q96NX9	OTTHUMG00000021944	ENST00000373125.4:c.427C>G	X.37:g.85404051C>G	ENSP00000362217:p.Arg143Gly	Somatic		WXS	Illumina GAIIx	Phase_IV	B1AJV3|B4DQG3|Q8NAY3|Q8ND17|Q96N55	Missense_Mutation	SNP	pfam_Transform_Ski,superfamily_DNA-bd_dom_put	p.R143G	ENST00000373125.4	37	c.427	CCDS14455.1	X	.	.	.	.	.	.	.	.	.	.	C	19.96	3.923039	0.73213	.	.	ENSG00000126733	ENST00000344497;ENST00000373131;ENST00000373125	D;D	0.84730	-1.89;-1.89	4.5	4.5	0.54988	DNA binding domain, putative (1);Transforming protein Ski (2);	0.000000	0.51477	D	0.000085	D	0.93054	0.7789	M	0.87180	2.865	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.94382	0.7605	10	0.72032	D	0.01	.	16.1211	0.81357	0.0:1.0:0.0:0.0	.	143;143	Q96NX9-2;Q96NX9	.;DACH2_HUMAN	G	143	ENSP00000362223:R143G;ENSP00000362217:R143G	ENSP00000345134:R143G	R	+	1	0	DACH2	85290707	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	6.969000	0.76092	2.071000	0.62044	0.544000	0.68410	CGC	DACH2	-	pfam_Transform_Ski,superfamily_DNA-bd_dom_put	ENSG00000126733		0.552	DACH2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	DACH2	HGNC	protein_coding	OTTHUMT00000359266.1	189	0.00	0	C	NM_053281		85404051	85404051	+1	no_errors	ENST00000373125	ensembl	human	known	69_37n	missense	116	42.86	87	SNP	1.000	G
DDB2	1643	genome.wustl.edu	37	11	47259551	47259551	+	Splice_Site	SNP	C	C	T			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr11:47259551C>T	ENST00000256996.4	+	8	1382	c.1187C>T	c.(1186-1188)tCg>tTg	p.S396L	ACP2_ENST00000525230.1_5'Flank|DDB2_ENST00000378601.3_3'UTR|DDB2_ENST00000378603.3_Splice_Site_p.S332L|DDB2_ENST00000378600.3_Splice_Site_p.S207L	NM_000107.2	NP_000098.1	Q92466	DDB2_HUMAN	damage-specific DNA binding protein 2, 48kDa	396					DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|protein autoubiquitination (GO:0051865)|protein polyubiquitination (GO:0000209)|pyrimidine dimer repair (GO:0006290)|response to UV (GO:0009411)|UV-damage excision repair (GO:0070914)	Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|nucleoplasm (GO:0005654)|protein complex (GO:0043234)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)	p.S396L(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(1)	17						GGCATCAGTTCGGTGAGGCTT	0.463			"""Mis, N"""			"""skin basal cell, skin squamous cell, melanoma"""		Direct reversal of damage;Nucleotide excision repair (NER)	Xeroderma Pigmentosum																													dbGAP	yes	Rec		Xeroderma pigmentosum (E)	11	11p12	1643	damage-specific DNA binding protein 2		E	1	Substitution - Missense(1)	breast(1)											87.0	74.0	78.0					11																	47259551		2201	4298	6499	-	-	-	SO:0001630	splice_region_variant	0	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV		CCDS7927.1, CCDS73284.1	11p12-p11	2014-09-17	2002-08-29			ENSG00000134574		"""WD repeat domain containing"""	2718	protein-coding gene	gene with protein product	"""xeroderma pigmentosum group E protein"", ""UV-damaged DNA-binding protein 2"", ""DDB p48 subunit"""	600811	"""damage-specific DNA binding protein 2 (48kD)"""			8407967, 8530102	Standard	NM_000107		Approved	DDBB, UV-DDB2, FLJ34321	uc001neb.2	Q92466		ENST00000256996.4:c.1188+1C>T	11.37:g.47259551C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B2R875|Q76E54|Q76E55|Q76E56|Q76E57	Missense_Mutation	SNP	pfam_WD40_repeat,superfamily_WD40_repeat_dom,smart_WD40_repeat,pfscan_WD40_repeat,pfscan_WD40_repeat_dom	p.S396L	ENST00000256996.4	37	c.1187	CCDS7927.1	11	.	.	.	.	.	.	.	.	.	.	C	29.4	4.999241	0.93227	.	.	ENSG00000134574	ENST00000256996;ENST00000378603;ENST00000378600	T;T;T	0.69806	-0.43;2.55;-0.31	5.94	5.04	0.67666	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.051032	0.85682	N	0.000000	T	0.80819	0.4696	M	0.71581	2.175	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;P	0.91635	0.999;0.979;0.776	T	0.83314	-0.0021	10	0.87932	D	0	-6.8412	15.0519	0.71881	0.0:0.9322:0.0:0.0678	.	332;207;396	Q92466-4;Q92466-2;Q92466	.;.;DDB2_HUMAN	L	396;332;207	ENSP00000256996:S396L;ENSP00000367866:S332L;ENSP00000367863:S207L	ENSP00000256996:S396L	S	+	2	0	DDB2	47216127	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	5.340000	0.65958	1.534000	0.49203	0.561000	0.74099	TCG	DDB2	-	superfamily_WD40_repeat_dom	ENSG00000134574		0.463	DDB2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	DDB2	HGNC	protein_coding		76	0.00	0	C	NM_000107	Missense_Mutation	47259551	47259551	+1	no_errors	ENST00000256996	ensembl	human	known	69_37n	missense	48	15.52	9	SNP	1.000	T
DHX16	8449	genome.wustl.edu	37	6	30624026	30624026	+	Frame_Shift_Del	DEL	G	G	-			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr6:30624026delG	ENST00000376442.3	-	16	2642	c.2447delC	c.(2446-2448)gcafs	p.A816fs	DHX16_ENST00000376437.5_Frame_Shift_Del_p.A335fs	NM_001164239.1|NM_003587.4	NP_001157711.1|NP_003578.2	O60231	DHX16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 16	816					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			kidney(2)|ovary(2)	4						CGGCAGCTCTGCCATCTTTCG	0.587																																						dbGAP											0													97.0	101.0	99.0					6																	30624026		1511	2709	4220	-	-	-	SO:0001589	frameshift_variant	0			AB001601	CCDS4685.1	6p21.3	2010-02-17	2003-06-13	2003-06-20	ENSG00000204560	ENSG00000204560		"""DEAH-boxes"""	2739	protein-coding gene	gene with protein product		603405	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 16"""	DDX16		9547260	Standard	NM_003587		Approved	DBP2, Prp2, PRPF2	uc003nqz.3	O60231	OTTHUMG00000031060	ENST00000376442.3:c.2447delC	6.37:g.30624026delG	ENSP00000365625:p.Ala816fs	Somatic		WXS	Illumina GAIIx	Phase_IV	O60322|Q5JP45|Q969X7|Q96QC1	Frame_Shift_Del	DEL	pfam_DUF1605,pfam_Helicase-assoc_dom,pfam_Helicase_C,pfam_DNA/RNA_helicase_DEAD/DEAH_N,smart_Helicase_ATP-bd,smart_Helicase_C,smart_Helicase-assoc_dom,pfscan_Helicase_ATP-bd,pfscan_Helicase_C	p.A816fs	ENST00000376442.3	37	c.2447	CCDS4685.1	6																																																																																			DHX16	-	pfam_Helicase-assoc_dom,smart_Helicase-assoc_dom	ENSG00000204560		0.587	DHX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DHX16	HGNC	protein_coding	OTTHUMT00000076076.2	32	0.00	0	G	NM_003587		30624026	30624026	-1	no_errors	ENST00000376442	ensembl	human	known	69_37n	frame_shift_del	38	31.58	18	DEL	1.000	-
DHX57	90957	genome.wustl.edu	37	2	39050359	39050359	+	Silent	SNP	G	G	T	rs149818203		TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr2:39050359G>T	ENST00000295373.6	-	17	3193	c.3067C>A	c.(3067-3069)Cgg>Agg	p.R1023R		NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	1023							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R1023R(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				TCAATGAGCCGAGAGAACACA	0.378																																					Melanoma(191;1090 2095 4375 23729 47341)	dbGAP											1	Substitution - coding silent(1)	breast(1)											73.0	75.0	74.0					2																	39050359		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"""DEAH-boxes"""	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.3067C>A	2.37:g.39050359G>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Nonsense_Mutation	SNP	pfam_Helicase-assoc_dom,pfam_Helicase_C,pfam_DUF1605,smart_Helicase_C,smart_Helicase-assoc_dom,pfscan_Helicase_C	p.S346*	ENST00000295373.6	37	c.1037	CCDS1800.1	2	.	.	.	.	.	.	.	.	.	.	G	8.508	0.865832	0.17250	.	.	ENSG00000163214	ENST00000452978	.	.	.	5.62	4.75	0.60458	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	.	14.7272	0.69354	0.0696:0.0:0.9304:0.0	.	.	.	.	X	346	.	ENSP00000397841:S346X	S	-	2	0	DHX57	38903863	1.000000	0.71417	1.000000	0.80357	0.846000	0.48090	7.864000	0.87037	1.373000	0.46208	0.561000	0.74099	TCG	DHX57	-	NULL	ENSG00000163214		0.378	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DHX57	HGNC	protein_coding	OTTHUMT00000219940.2	81	0.00	0	G	NM_145646		39050359	39050359	-1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000452978	ensembl	human	novel	69_37n	nonsense	100	10.71	12	SNP	1.000	T
DOCK9	23348	genome.wustl.edu	37	13	99460026	99460026	+	Missense_Mutation	SNP	A	A	C			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr13:99460026A>C	ENST00000376460.1	-	51	5525	c.5445T>G	c.(5443-5445)atT>atG	p.I1815M	DOCK9_ENST00000339416.2_Missense_Mutation_p.I1802M	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9	1816	DHR-2.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.I1816M(1)|p.I1815M(1)		breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					GTTCCTTGTAAATATACTCCT	0.418																																						dbGAP											2	Substitution - Missense(2)	breast(2)											167.0	155.0	159.0					13																	99460026		1849	4087	5936	-	-	-	SO:0001583	missense	0			AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"""Pleckstrin homology (PH) domain containing"""	14132	protein-coding gene	gene with protein product	"""zizimin1"""	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.5445T>G	13.37:g.99460026A>C	ENSP00000365643:p.Ile1815Met	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Missense_Mutation	SNP	pfam_DOCK,pfam_DUF3398,pfam_Pleckstrin_homology,superfamily_ARM-type_fold,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology	p.I1802M	ENST00000376460.1	37	c.5406	CCDS45062.1	13	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	14.98|14.98|14.98	2.698044|2.698044|2.698044	0.48307|0.48307|0.48307	.|.|.	.|.|.	ENSG00000088387|ENSG00000088387|ENSG00000088387	ENST00000419908|ENST00000376460;ENST00000357329;ENST00000376455;ENST00000400235;ENST00000428223;ENST00000400220;ENST00000339416;ENST00000376453;ENST00000451563|ENST00000400228	.|T;T|.	.|0.27720|.	.|1.95;1.65|.	5.41|5.41|5.41	2.98|2.98|2.98	0.34508|0.34508|0.34508	.|.|.	.|0.121167|.	.|0.64402|.	.|D|.	.|0.000009|.	T|T|T	0.77745|0.77745|0.77745	0.4176|0.4176|0.4176	M|M|M	0.92026|0.92026|0.92026	3.265|3.265|3.265	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|D;D;D;D;D;D|.	.|0.89917|.	.|1.0;0.993;1.0;1.0;0.997;0.999|.	.|D;D;D;D;D;D|.	.|0.85130|.	.|0.973;0.928;0.997;0.99;0.956;0.979|.	T|T|T	0.77501|0.77501|0.77501	-0.2564|-0.2564|-0.2564	5|10|5	.|0.87932|.	.|D|.	.|0|.	.|.|.	8.5118|8.5118|8.5118	0.33222|0.33222|0.33222	0.6979:0.0:0.3021:0.0|0.6979:0.0:0.3021:0.0|0.6979:0.0:0.3021:0.0	.|.|.	.|521;434;1815;1816;471;433|.	.|B7Z6H5;B7Z2J2;Q9BZ29-5;Q9BZ29;B7Z6G9;F5H1Q4|.	.|.;.;.;DOCK9_HUMAN;.;.|.	C|M|V	219|1815;1816;1808;1793;1815;723;1802;433;166|378	.|ENSP00000365643:I1815M;ENSP00000341086:I1802M|.	.|ENSP00000341086:I1802M|.	F|I|L	-|-|-	2|3|1	0|3|2	DOCK9|DOCK9|DOCK9	98258027|98258027|98258027	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.998000|0.998000|0.998000	0.95712|0.95712|0.95712	1.087000|1.087000|1.087000	0.30865|0.30865|0.30865	0.370000|0.370000|0.370000	0.24538|0.24538|0.24538	0.528000|0.528000|0.528000	0.53228|0.53228|0.53228	TTT|ATT|TTA	DOCK9	-	NULL	ENSG00000088387		0.418	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DOCK9	HGNC	protein_coding	OTTHUMT00000045566.1	282	0.35	1	A	NM_015296		99460026	99460026	-1	no_errors	ENST00000339416	ensembl	human	known	69_37n	missense	197	16.03	38	SNP	0.999	C
FAM151A	338094	genome.wustl.edu	37	1	55075435	55075435	+	Missense_Mutation	SNP	G	G	A	rs535331459		TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr1:55075435G>A	ENST00000302250.2	-	8	1424	c.1264C>T	c.(1264-1266)Cgg>Tgg	p.R422W	ACOT11_ENST00000481208.1_3'UTR|ACOT11_ENST00000371316.3_Intron|ACOT11_ENST00000343744.2_3'UTR|FAM151A_ENST00000371304.2_Intron	NM_176782.2	NP_788954.2	Q8WW52	F151A_HUMAN	family with sequence similarity 151, member A	422						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.R422W(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	12						AGGGATGGCCGGAGGGCTGCG	0.627													G|||	1	0.000199681	0.0	0.0	5008	,	,		18224	0.0		0.0	False		,,,				2504	0.001					dbGAP											1	Substitution - Missense(1)	breast(1)											41.0	45.0	43.0					1																	55075435		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK091901	CCDS594.1	1p32.3	2008-02-05	2007-12-18	2007-12-18	ENSG00000162391	ENSG00000162391			25032	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 179"""	C1orf179		17273976	Standard	NM_176782		Approved	MGC27169	uc001cxn.3	Q8WW52	OTTHUMG00000009888	ENST00000302250.2:c.1264C>T	1.37:g.55075435G>A	ENSP00000306888:p.Arg422Trp	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5VUG5|Q6DKH5|Q6UWV0|Q8NAX9|Q96KY5	Missense_Mutation	SNP	pfam_DUF2181	p.R422W	ENST00000302250.2	37	c.1264	CCDS594.1	1	.	.	.	.	.	.	.	.	.	.	G	9.212	1.031254	0.19590	.	.	ENSG00000162391	ENST00000302250	T	0.12465	2.68	4.17	2.31	0.28768	.	0.272292	0.27415	N	0.019478	T	0.10766	0.0263	L	0.41027	1.25	0.80722	D	1	B	0.22346	0.068	B	0.19946	0.027	T	0.09487	-1.0672	10	0.72032	D	0.01	-26.3526	6.674	0.23083	0.2119:0.0:0.7881:0.0	.	422	Q8WW52	F151A_HUMAN	W	422	ENSP00000306888:R422W	ENSP00000306888:R422W	R	-	1	2	FAM151A	54848023	0.970000	0.33590	1.000000	0.80357	0.438000	0.31896	0.358000	0.20216	0.723000	0.32274	-0.119000	0.15052	CGG	FAM151A	-	pfam_DUF2181	ENSG00000162391		0.627	FAM151A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM151A	HGNC	protein_coding	OTTHUMT00000027342.1	60	0.00	0	G	NM_176782		55075435	55075435	-1	no_errors	ENST00000302250	ensembl	human	known	69_37n	missense	32	11.11	4	SNP	1.000	A
FLG2	388698	genome.wustl.edu	37	1	152328629	152328629	+	Missense_Mutation	SNP	G	G	T			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr1:152328629G>T	ENST00000388718.5	-	3	1705	c.1633C>A	c.(1633-1635)Caa>Aaa	p.Q545K	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	545	Ser-rich.				establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.Q545K(1)		NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GAACCATGTTGGCCATAGCTA	0.493																																						dbGAP											1	Substitution - Missense(1)	breast(1)											276.0	278.0	277.0					1																	152328629		2203	4300	6503	-	-	-	SO:0001583	missense	0			AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"""EF-hand domain containing"""	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.1633C>A	1.37:g.152328629G>T	ENSP00000373370:p.Gln545Lys	Somatic		WXS	Illumina GAIIx	Phase_IV	Q9H4U1	Missense_Mutation	SNP	pfam_S100_Ca-bd_sub,pfscan_EF_HAND_2,prints_Filaggrin	p.Q545K	ENST00000388718.5	37	c.1633	CCDS30861.1	1	.	.	.	.	.	.	.	.	.	.	G	0.070	-1.205353	0.01568	.	.	ENSG00000143520	ENST00000388718	T	0.05139	3.49	2.79	2.79	0.32731	.	.	.	.	.	T	0.01421	0.0046	L	0.43152	1.355	0.09310	N	1	P	0.44816	0.844	B	0.37780	0.258	T	0.25012	-1.0144	9	0.06099	T	0.92	.	7.7928	0.29129	0.0:0.2608:0.7392:0.0	.	545	Q5D862	FILA2_HUMAN	K	545	ENSP00000373370:Q545K	ENSP00000373370:Q545K	Q	-	1	0	FLG2	150595253	0.022000	0.18835	0.087000	0.20705	0.136000	0.21042	1.508000	0.35769	1.564000	0.49628	0.297000	0.19635	CAA	FLG2	-	NULL	ENSG00000143520		0.493	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FLG2	HGNC	protein_coding	OTTHUMT00000034018.5	268	0.37	1	G	NM_001014342		152328629	152328629	-1	no_errors	ENST00000388718	ensembl	human	known	69_37n	missense	165	14.06	27	SNP	0.079	T
GATA3	2625	genome.wustl.edu	37	10	8115955	8115955	+	Frame_Shift_Del	DEL	A	A	-			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr10:8115955delA	ENST00000346208.3	+	6	1756	c.1301delA	c.(1300-1302)cacfs	p.H434fs	GATA3_ENST00000461472.1_3'UTR|GATA3_ENST00000379328.3_Frame_Shift_Del_p.H435fs			P23771	GATA3_HUMAN	GATA binding protein 3	434					anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|aortic valve morphogenesis (GO:0003180)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cardiac right ventricle morphogenesis (GO:0003215)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|cellular response to interferon-alpha (GO:0035457)|cellular response to interleukin-4 (GO:0071353)|cellular response to tumor necrosis factor (GO:0071356)|defense response (GO:0006952)|developmental growth (GO:0048589)|ear development (GO:0043583)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|interferon-gamma secretion (GO:0072643)|interleukin-4 secretion (GO:0072602)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lymphocyte migration (GO:0072676)|male gonad development (GO:0008584)|mast cell differentiation (GO:0060374)|mesenchymal to epithelial transition (GO:0060231)|mesonephros development (GO:0001823)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell motility (GO:2000146)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell proliferation involved in mesonephros development (GO:2000607)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation (GO:2000703)|negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation (GO:2000734)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct formation (GO:0072179)|nephric duct morphogenesis (GO:0072178)|neuron migration (GO:0001764)|norepinephrine biosynthetic process (GO:0042421)|otic vesicle development (GO:0071599)|parathyroid gland development (GO:0060017)|parathyroid hormone secretion (GO:0035898)|pharyngeal system development (GO:0060037)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of signal transduction (GO:0009967)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of thyroid hormone generation (GO:2000611)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ureteric bud formation (GO:0072107)|post-embryonic development (GO:0009791)|pro-T cell differentiation (GO:0002572)|regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043370)|regulation of cellular response to X-ray (GO:2000683)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of establishment of cell polarity (GO:2000114)|regulation of histone H3-K27 methylation (GO:0061085)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to virus (GO:0009615)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)|T cell receptor signaling pathway (GO:0050852)|T-helper 2 cell differentiation (GO:0045064)|thymic T cell selection (GO:0045061)|thymus development (GO:0048538)|TOR signaling (GO:0031929)|transcription from RNA polymerase II promoter (GO:0006366)|type IV hypersensitivity (GO:0001806)|ureter maturation (GO:0035799)|ureteric bud formation (GO:0060676)|uterus development (GO:0060065)|ventricular septum development (GO:0003281)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer sequence-specific DNA binding (GO:0001158)|HMG box domain binding (GO:0071837)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			NS(1)|breast(44)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(24)|ovary(3)|skin(2)	87						GGACCACACCACCCCTCCAGC	0.627			"""F, N, S"""		breast		"""HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE)"""																															dbGAP		Rec	yes		10	10p15	2625	GATA binding protein 3	yes	E	0													87.0	72.0	77.0					10																	8115955		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0			X55122	CCDS7083.1, CCDS31143.1	10p15	2013-01-25	2001-11-28		ENSG00000107485	ENSG00000107485		"""GATA zinc finger domain containing"""	4172	protein-coding gene	gene with protein product		131320	"""GATA-binding protein 3"""			2050118, 15087456	Standard	NM_002051		Approved	HDR	uc001ijz.3	P23771	OTTHUMG00000017640	ENST00000346208.3:c.1301delA	10.37:g.8115955delA	ENSP00000341619:p.His434fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5VWG7|Q5VWG8|Q96J16	Frame_Shift_Del	DEL	pfam_Znf_GATA,smart_Znf_GATA,pirsf_TF_GATA-1/2/3,pfscan_Znf_GATA,prints_Znf_GATA	p.H435fs	ENST00000346208.3	37	c.1304	CCDS7083.1	10																																																																																			GATA3	-	pirsf_TF_GATA-1/2/3	ENSG00000107485		0.627	GATA3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	GATA3	HGNC	protein_coding	OTTHUMT00000046719.1	72	0.00	0	A	NM_001002295		8115955	8115955	+1	no_errors	ENST00000379328	ensembl	human	known	69_37n	frame_shift_del	47	31.76	27	DEL	1.000	-
GCKR	2646	genome.wustl.edu	37	2	27722054	27722054	+	Missense_Mutation	SNP	C	C	A	rs8179207	byFrequency	TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr2:27722054C>A	ENST00000264717.2	+	6	537	c.474C>A	c.(472-474)caC>caA	p.H158Q	GCKR_ENST00000424318.2_Intron	NM_001486.3	NP_001477.2	Q14397	GCKR_HUMAN	glucokinase (hexokinase 4) regulator	158	SIS 1. {ECO:0000255|PROSITE- ProRule:PRU00797}.				carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|negative regulation of glucokinase activity (GO:0033132)|positive regulation of glucokinase activity (GO:0033133)|protein import into nucleus, translocation (GO:0000060)|regulation of glucose transport (GO:0010827)|response to fructose (GO:0009750)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|triglyceride homeostasis (GO:0070328)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	carbohydrate binding (GO:0030246)|enzyme inhibitor activity (GO:0004857)|fructose-6-phosphate binding (GO:0070095)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(2)	29	Acute lymphoblastic leukemia(172;0.155)					GTGCCTTGCACGGGATTGAGG	0.522																																						dbGAP											0													110.0	106.0	108.0					2																	27722054		2203	4300	6503	-	-	-	SO:0001583	missense	0			Z48475	CCDS1757.1	2p23	2008-05-21	2004-05-20		ENSG00000084734	ENSG00000084734			4196	protein-coding gene	gene with protein product		600842	"""glucokinase (hexokinase 4) regulatory protein"""			9570959, 8662230	Standard	NM_001486		Approved		uc002rky.3	Q14397	OTTHUMG00000128426	ENST00000264717.2:c.474C>A	2.37:g.27722054C>A	ENSP00000264717:p.His158Gln	Somatic		WXS	Illumina GAIIx	Phase_IV	A1L4C2|B4DPQ2|Q53RY6|Q99522	Missense_Mutation	SNP	NULL	p.H158Q	ENST00000264717.2	37	c.474	CCDS1757.1	2	.	.	.	.	.	.	.	.	.	.	C	7.230	0.599144	0.13939	.	.	ENSG00000084734	ENST00000264717;ENST00000453813	T;T	0.51574	0.7;0.7	4.45	-6.66	0.01789	Sugar isomerase (SIS) (1);	0.252816	0.34853	N	0.003630	T	0.17916	0.0430	N	0.02158	-0.66	0.21878	N	0.999498	B;B	0.20052	0.041;0.013	B;B	0.17098	0.017;0.004	T	0.08269	-1.0730	10	0.49607	T	0.09	-4.6759	13.9836	0.64319	0.0:0.2105:0.0:0.7895	.	158;158	A8K731;Q14397	.;GCKR_HUMAN	Q	158;130	ENSP00000264717:H158Q;ENSP00000399463:H130Q	ENSP00000264717:H158Q	H	+	3	2	GCKR	27575558	0.000000	0.05858	0.004000	0.12327	0.812000	0.45895	-4.648000	0.00203	-1.516000	0.01782	-0.258000	0.10820	CAC	GCKR	-	NULL	ENSG00000084734		0.522	GCKR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GCKR	HGNC	protein_coding	OTTHUMT00000250214.1	129	0.77	1	C	NM_001486		27722054	27722054	+1	no_errors	ENST00000264717	ensembl	human	known	69_37n	missense	77	27.10	29	SNP	0.016	A
GTF2F2	2963	genome.wustl.edu	37	13	45694817	45694817	+	Silent	SNP	G	G	A			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr13:45694817G>A	ENST00000340473.6	+	1	168	c.27G>A	c.(25-27)ttG>ttA	p.L9L	7SK_ENST00000606815.1_RNA	NM_004128.2	NP_004119.1	P13984	T2FB_HUMAN	general transcription factor IIF, polypeptide 2, 30kDa	9					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIF complex (GO:0005674)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)	p.L9L(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|prostate(1)|upper_aerodigestive_tract(1)	10		Lung NSC(96;0.00115)|Prostate(109;0.00578)|Breast(139;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.133)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000647)		AACTCGACTTGACCGGCGCCA	0.612																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											30.0	24.0	26.0					13																	45694817		2176	4243	6419	-	-	-	SO:0001819	synonymous_variant	0			X16901	CCDS9395.1	13q14	2012-01-23	2002-08-29		ENSG00000188342	ENSG00000188342		"""General transcription factors"""	4653	protein-coding gene	gene with protein product		189969	"""general transcription factor IIF, polypeptide 1 (74kD subunit)"""			8162052	Standard	NM_004128		Approved	TFIIF, BTF4, RAP30	uc001uzw.3	P13984	OTTHUMG00000016849	ENST00000340473.6:c.27G>A	13.37:g.45694817G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A6NNS5|Q5W0H3	Silent	SNP	pfam_TFIIF_beta,superfamily_TFIIF_interaction,pirsf_TFIIF-beta_subgr	p.L9	ENST00000340473.6	37	c.27	CCDS9395.1	13																																																																																			GTF2F2	-	pfam_TFIIF_beta,superfamily_TFIIF_interaction,pirsf_TFIIF-beta_subgr	ENSG00000188342		0.612	GTF2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GTF2F2	HGNC	protein_coding	OTTHUMT00000044767.2	70	0.00	0	G	NM_004128		45694817	45694817	+1	no_errors	ENST00000340473	ensembl	human	known	69_37n	silent	37	41.27	26	SNP	1.000	A
HSPG2	3339	genome.wustl.edu	37	1	22157965	22157965	+	Missense_Mutation	SNP	C	C	T			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr1:22157965C>T	ENST00000374695.3	-	83	11522	c.11443G>A	c.(11443-11445)Ggc>Agc	p.G3815S	HSPG2_ENST00000486901.1_5'Flank	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	3815	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)	p.G3815S(1)		breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	CCTATGAAGCCGCTGCTCAGC	0.642																																						dbGAP											1	Substitution - Missense(1)	breast(1)											48.0	52.0	50.0					1																	22157965		2202	4300	6502	-	-	-	SO:0001583	missense	0			M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.11443G>A	1.37:g.22157965C>T	ENSP00000363827:p.Gly3815Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	pfam_Ig_I-set,pfam_Immunoglobulin,pfam_Laminin_G,pfam_Laminin_B_type_IV,pfam_EGF_laminin,pfam_LDrepeatLR_classA_rpt,pfam_EGF-like_dom,superfamily_ConA-like_lec_gl,superfamily_LDrepeatLR_classA_rpt,smart_SEA,smart_LDrepeatLR_classA_rpt,smart_EGF-like,smart_Ig_sub,smart_Ig_sub2,smart_Ig_V-set_subgr,smart_Laminin_B_subgr,smart_EGF_laminin,smart_EGF-like_Ca-bd,smart_Laminin_G,pfscan_EG-like_dom,pfscan_Laminin_B_type_IV,pfscan_EGF_laminin,pfscan_Laminin_G,pfscan_LDrepeatLR_classA_rpt,pfscan_SEA,pfscan_Ig-like	p.G3815S	ENST00000374695.3	37	c.11443	CCDS30625.1	1	.	.	.	.	.	.	.	.	.	.	c	28.0	4.878628	0.91740	.	.	ENSG00000142798	ENST00000374695	T	0.80123	-1.34	5.26	5.26	0.73747	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.40064	N	0.001196	D	0.88100	0.6346	L	0.57536	1.79	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.88760	0.3256	10	0.62326	D	0.03	.	17.4568	0.87609	0.0:1.0:0.0:0.0	.	1755;3815	Q59EG0;P98160	.;PGBM_HUMAN	S	3815	ENSP00000363827:G3815S	ENSP00000363827:G3815S	G	-	1	0	HSPG2	22030552	1.000000	0.71417	1.000000	0.80357	0.679000	0.39708	7.301000	0.78850	2.451000	0.82905	0.450000	0.29827	GGC	HSPG2	-	pfam_Laminin_G,superfamily_ConA-like_lec_gl,smart_Laminin_G,pfscan_Laminin_G	ENSG00000142798		0.642	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HSPG2	HGNC	protein_coding	OTTHUMT00000007598.1	66	0.00	0	C	NM_005529		22157965	22157965	-1	no_errors	ENST00000374695	ensembl	human	known	69_37n	missense	53	29.33	22	SNP	1.000	T
HHAT	55733	genome.wustl.edu	37	1	210847683	210847683	+	Missense_Mutation	SNP	G	G	T	rs200853402		TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr1:210847683G>T	ENST00000367010.1	+	12	1671	c.1444G>T	c.(1444-1446)Gtg>Ttg	p.V482L	HHAT_ENST00000541565.1_Missense_Mutation_p.V345L|HHAT_ENST00000413764.2_Missense_Mutation_p.V482L|HHAT_ENST00000537898.1_Missense_Mutation_p.V417L|HHAT_ENST00000261458.3_Missense_Mutation_p.V482L|HHAT_ENST00000367009.1_Missense_Mutation_p.V172L|HHAT_ENST00000545781.1_Missense_Mutation_p.V419L|HHAT_ENST00000545154.1_Missense_Mutation_p.V483L|HHAT_ENST00000308852.6_Missense_Mutation_p.V437L	NM_001170580.1	NP_001164051.1	Q5VTY9	HHAT_HUMAN	hedgehog acyltransferase	482					multicellular organismal development (GO:0007275)|protein palmitoylation (GO:0018345)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|palmitoyltransferase activity (GO:0016409)	p.V482L(1)		breast(3)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	27				OV - Ovarian serous cystadenocarcinoma(81;0.0136)|all cancers(67;0.161)|KIRC - Kidney renal clear cell carcinoma(1967;0.215)		CTACTCCCACGTGGGCATTGC	0.587																																						dbGAP											1	Substitution - Missense(1)	breast(1)											129.0	104.0	112.0					1																	210847683		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK001586	CCDS1495.1, CCDS53471.1, CCDS53472.1, CCDS53473.1	1q32	2008-02-05			ENSG00000054392	ENSG00000054392			18270	protein-coding gene	gene with protein product		605743				11160356	Standard	NM_001170587		Approved	FLJ10724, MART-2, MART2, Skn, ski, rasp, sit, GUP2	uc009xcx.3	Q5VTY9	OTTHUMG00000036447	ENST00000367010.1:c.1444G>T	1.37:g.210847683G>T	ENSP00000355977:p.Val482Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	B7Z4D5|B7Z5I1|B7Z868|B7ZA75|D3DT91|F5H444|Q17RZ7|Q4G0K3|Q5CZ95|Q5TGI2|Q9NVH9|Q9Y3N8	Missense_Mutation	SNP	pfam_MBOAT_fam	p.V483L	ENST00000367010.1	37	c.1447	CCDS1495.1	1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.529023	0.85706	.	.	ENSG00000054392	ENST00000413764;ENST00000541565;ENST00000545154;ENST00000537898;ENST00000545781;ENST00000261458;ENST00000308852;ENST00000367010;ENST00000367009	T;T;T;T;T;T;T;T;T	0.49432	2.14;0.83;2.09;2.13;2.06;2.14;2.14;2.14;0.78	5.51	5.51	0.81932	.	.	.	.	.	T	0.49355	0.1552	N	0.21142	0.635	0.39951	D	0.974535	P;D;P;P;P	0.56035	0.956;0.974;0.924;0.956;0.956	P;P;P;P;P	0.55087	0.59;0.768;0.491;0.59;0.59	T	0.50406	-0.8832	9	0.48119	T	0.1	.	16.499	0.84253	0.0:0.0:1.0:0.0	.	437;483;345;417;482	B7Z2U8;F5H444;B7Z4D5;B7Z5I1;Q5VTY9	.;.;.;.;HHAT_HUMAN	L	482;345;483;417;419;482;437;482;172	ENSP00000416845:V482L;ENSP00000444995:V345L;ENSP00000438468:V483L;ENSP00000442625:V417L;ENSP00000439229:V419L;ENSP00000261458:V482L;ENSP00000308628:V437L;ENSP00000355977:V482L;ENSP00000355976:V172L	ENSP00000261458:V482L	V	+	1	0	HHAT	208914306	1.000000	0.71417	0.984000	0.44739	0.953000	0.61014	4.899000	0.63245	2.736000	0.93811	0.655000	0.94253	GTG	HHAT	-	NULL	ENSG00000054392		0.587	HHAT-004	KNOWN	basic|appris_principal|CCDS	protein_coding	HHAT	HGNC	protein_coding	OTTHUMT00000088662.1	79	0.00	0	G	NM_018194		210847683	210847683	+1	no_errors	ENST00000545154	ensembl	human	known	69_37n	missense	60	22.08	17	SNP	0.996	T
IPCEF1	26034	genome.wustl.edu	37	6	154521037	154521038	+	Frame_Shift_Del	DEL	TG	TG	-	rs574726765	byFrequency	TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	TG	TG					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr6:154521037_154521038delTG	ENST00000265198.4	-	10	826_827	c.671_672delCA	c.(670-672)acafs	p.T224fs	IPCEF1_ENST00000519091.1_5'UTR|IPCEF1_ENST00000422970.2_Frame_Shift_Del_p.T225fs|IPCEF1_ENST00000367220.4_Frame_Shift_Del_p.T225fs|OPRM1_ENST00000337049.4_Intron|IPCEF1_ENST00000519344.1_Frame_Shift_Del_p.T196fs	NM_001130700.1|NM_015553.2	NP_001124172.1|NP_056368.1	Q8WWN9	ICEF1_HUMAN	interaction protein for cytohesin exchange factors 1	224	Ser-rich.				oxidation-reduction process (GO:0055114)|oxygen transport (GO:0015671)|positive regulation of GTP catabolic process (GO:0033126)|response to oxidative stress (GO:0006979)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	oxygen transporter activity (GO:0005344)|peroxidase activity (GO:0004601)	p.T224fs*2(1)		breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	12						AACTGTTAACTGTGTCAGGCAA	0.47																																						dbGAP											1	Deletion - Frameshift(1)	breast(1)																																								-	-	-	SO:0001589	frameshift_variant	0			AB007863	CCDS5245.1, CCDS47509.1	6q25.2	2013-01-10			ENSG00000074706	ENSG00000074706		"""Pleckstrin homology (PH) domain containing"""	21204	protein-coding gene	gene with protein product	"""phosphoinositide binding protein PIP3-E"""					11804589, 19756519	Standard	NM_001130699		Approved	PIP3-E, KIAA0403	uc021zhc.1	Q8WWN9	OTTHUMG00000015872	ENST00000265198.4:c.671_672delCA	6.37:g.154521039_154521040delTG	ENSP00000265198:p.Thr224fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K1K2|B7ZL78|B7ZL80|O43153|Q5HYL8	Frame_Shift_Del	DEL	pfam_Pleckstrin_homology,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology	p.T225fs	ENST00000265198.4	37	c.675_674	CCDS5245.1	6																																																																																			IPCEF1	-	NULL	ENSG00000074706		0.470	IPCEF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	IPCEF1	HGNC	protein_coding	OTTHUMT00000042789.2	191	0.00	0	TG	NM_001130699		154521037	154521038	-1	no_errors	ENST00000367220	ensembl	human	known	69_37n	frame_shift_del	126	12.41	18	DEL	0.000:0.000	-
ISLR2	57611	genome.wustl.edu	37	15	74426742	74426742	+	Silent	SNP	C	C	T			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr15:74426742C>T	ENST00000361742.3	+	4	2416	c.1647C>T	c.(1645-1647)ggC>ggT	p.G549G	ISLR2_ENST00000419208.1_Silent_p.G549G|ISLR2_ENST00000445793.1_Silent_p.G549G|ISLR2_ENST00000565540.1_Silent_p.G549G|ISLR2_ENST00000435464.1_Silent_p.G549G|ISLR2_ENST00000565159.1_Silent_p.G549G|ISLR2_ENST00000453268.2_Silent_p.G549G|ISLR2_ENST00000561975.1_Intron	NM_001130136.1|NM_020851.2	NP_001123608.1|NP_065902.1	Q6UXK2	ISLR2_HUMAN	immunoglobulin superfamily containing leucine-rich repeat 2	549					positive regulation of axon extension (GO:0045773)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G549G(1)		breast(3)|endometrium(6)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	36						TAGAGGAAGGCGTCAACGCCT	0.706																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											11.0	13.0	13.0					15																	74426742		2176	4256	6432	-	-	-	SO:0001819	synonymous_variant	0				CCDS10259.1	15q24.1	2013-01-11			ENSG00000167178	ENSG00000167178		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29286	protein-coding gene	gene with protein product		614179				10819331, 12975309	Standard	NM_001130136		Approved	KIAA1465	uc010bjf.3	Q6UXK2	OTTHUMG00000137624	ENST00000361742.3:c.1647C>T	15.37:g.74426742C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A8K352|Q9P263	Silent	SNP	pfam_Leu-rich_rpt,superfamily_Fibronectin_type3,smart_Leu-rich_rpt_typical-subtyp,smart_Cys-rich_flank_reg_C,pfscan_Ig-like	p.G549	ENST00000361742.3	37	c.1647	CCDS10259.1	15																																																																																			ISLR2	-	superfamily_Fibronectin_type3	ENSG00000167178		0.706	ISLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ISLR2	HGNC	protein_coding	OTTHUMT00000269046.1	13	0.00	0	C	NM_020851		74426742	74426742	+1	no_errors	ENST00000361742	ensembl	human	known	69_37n	silent	8	50.00	8	SNP	0.988	T
KIF1C	10749	genome.wustl.edu	37	17	4925966	4925966	+	Missense_Mutation	SNP	C	C	T			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr17:4925966C>T	ENST00000320785.5	+	22	2947	c.2590C>T	c.(2590-2592)Cgc>Tgc	p.R864C	AC109333.10_ENST00000438266.1_RNA	NM_006612.5	NP_006603.2	O43896	KIF1C_HUMAN	kinesin family member 1C	864					ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)|poly(A) RNA binding (GO:0044822)	p.R864C(1)		NS(2)|breast(4)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|skin(1)|urinary_tract(3)	30						CCTGCGGGACCGCATGCTCCG	0.637																																					Melanoma(96;1023 1447 10250 19259 33730)	dbGAP											1	Substitution - Missense(1)	breast(1)											22.0	23.0	22.0					17																	4925966		2202	4300	6502	-	-	-	SO:0001583	missense	0			U91329	CCDS11065.1	17p13.2	2014-03-03			ENSG00000129250	ENSG00000129250		"""Kinesins"""	6317	protein-coding gene	gene with protein product		603060	"""spastic ataxia 2 (autosomal recessive)"""	SAX2		9685376, 24319291, 24482476	Standard	NM_006612		Approved	SPAX2, SPG58	uc002gan.2	O43896	OTTHUMG00000099451	ENST00000320785.5:c.2590C>T	17.37:g.4925966C>T	ENSP00000320821:p.Arg864Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	D3DTL6|O75186|Q5U618	Missense_Mutation	SNP	pfam_Kinesin_motor_dom,pfam_FHA_dom,superfamily_SMAD_FHA_domain,smart_Kinesin_motor_dom,pfscan_Kinesin_motor_dom,prints_Kinesin_motor_dom	p.R864C	ENST00000320785.5	37	c.2590	CCDS11065.1	17	.	.	.	.	.	.	.	.	.	.	C	21.6	4.178189	0.78564	.	.	ENSG00000129250	ENST00000320785	T	0.75154	-0.91	4.67	4.67	0.58626	.	.	.	.	.	T	0.70263	0.3204	L	0.39898	1.24	0.47123	D	0.999325	D	0.76494	0.999	P	0.48677	0.586	T	0.73591	-0.3934	9	0.87932	D	0	.	10.1938	0.43043	0.1983:0.8017:0.0:0.0	.	864	O43896	KIF1C_HUMAN	C	864	ENSP00000320821:R864C	ENSP00000320821:R864C	R	+	1	0	KIF1C	4866690	0.012000	0.17670	1.000000	0.80357	0.999000	0.98932	0.739000	0.26173	2.436000	0.82500	0.655000	0.94253	CGC	KIF1C	-	NULL	ENSG00000129250		0.637	KIF1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KIF1C	HGNC	protein_coding	OTTHUMT00000216916.1	84	0.00	0	C			4925966	4925966	+1	no_errors	ENST00000320785	ensembl	human	known	69_37n	missense	13	63.89	23	SNP	1.000	T
KCNJ12	3768	genome.wustl.edu	37	17	21319341	21319341	+	Silent	SNP	C	C	T	rs569037483	byFrequency	TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr17:21319341C>T	ENST00000583088.1	+	3	1582	c.687C>T	c.(685-687)cgC>cgT	p.R229R	KCNJ12_ENST00000331718.5_Silent_p.R229R	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	229					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)	p.R229R(2)		NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	CCCATGTGCGCGCGCAGCTCA	0.642										Prostate(3;0.18)			.|||	4	0.000798722	0.0	0.0	5008	,	,		38914	0.004		0.0	False		,,,				2504	0.0					dbGAP											2	Substitution - coding silent(2)	breast(1)|endometrium(1)											87.0	70.0	76.0					17																	21319341		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.687C>T	17.37:g.21319341C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	O43401|Q15756|Q8NG63	Silent	SNP	pfam_K_chnl_inward-rec_Kir_Cr2,pfam_K_chnl_inward-rec_Kir_N,superfamily_Ig_E-set,pirsf_K_chnl_inward-rec_Kir,prints_K_chnl_inward-rec_Kir_Cr2,prints_K_chnl_inward-rec_Kir2.2	p.R229	ENST00000583088.1	37	c.687	CCDS11219.1	17																																																																																			KCNJ12	-	pfam_K_chnl_inward-rec_Kir_Cr2,superfamily_Ig_E-set,pirsf_K_chnl_inward-rec_Kir	ENSG00000184185		0.642	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KCNJ12	HGNC	protein_coding	OTTHUMT00000255060.2	37	0.00	0	C	NM_021012		21319341	21319341	+1	no_errors	ENST00000331718	ensembl	human	known	69_37n	silent	20	33.33	10	SNP	0.231	T
LENG9	94059	genome.wustl.edu	37	19	54973945	54973946	+	Frame_Shift_Ins	INS	-	-	C			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr19:54973945_54973946insC	ENST00000333834.4	-	1	948_949	c.830_831insG	c.(829-831)ggcfs	p.G277fs		NM_198988.1	NP_945339.2	Q96B70	LENG9_HUMAN	leukocyte receptor cluster (LRC) member 9	277							catalytic activity (GO:0003824)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)	11	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.134)		GTGCTTCCTTGCCCCCCAGCAA	0.663																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AF211976		19q13.4	2014-05-06			ENSG00000182909	ENSG00000275183			16306	protein-coding gene	gene with protein product						10941842	Standard	NM_198988		Approved		uc010yez.2	Q96B70	OTTHUMG00000188273	ENST00000333834.4:c.831dupG	19.37:g.54973951_54973951dupC	ENSP00000331647:p.Gly277fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B2VAM3	Frame_Shift_Ins	INS	superfamily_RNA_ligase/cNuc_Pdiesterase,smart_Znf_CCCH	p.K278fs	ENST00000333834.4	37	c.831_830	CCDS12895.2	19																																																																																			LENG9	-	NULL	ENSG00000182909		0.663	LENG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LENG9	HGNC	protein_coding	OTTHUMT00000140806.3	8	0.00	0	-	NM_198988		54973945	54973946	-1	no_errors	ENST00000333834	ensembl	human	known	69_37n	frame_shift_ins	8	20.00	2	INS	0.000:0.000	C
LINC00200	399706	genome.wustl.edu	37	10	1206562	1206562	+	lincRNA	SNP	C	C	T			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr10:1206562C>T	ENST00000425630.1	+	0	293					NR_015376.2				long intergenic non-protein coding RNA 200																		CTCCGTACATCACACCCATAT	0.547																																						dbGAP											0													104.0	91.0	95.0					10																	1206562		692	1591	2283	-	-	-			0			AK097673		10p15.3	2012-10-12	2011-08-11	2011-08-11	ENSG00000229205	ENSG00000229205		"""Long non-coding RNAs"""	30974	non-coding RNA	RNA, long non-coding			"""chromosome 10 open reading frame 139"", ""non-protein coding RNA 200"""	C10orf139, NCRNA00200			Standard	NR_015376		Approved	FLJ40354	uc010qag.1		OTTHUMG00000017539		10.37:g.1206562C>T		Somatic		WXS	Illumina GAIIx	Phase_IV		RNA	SNP	-	NULL	ENST00000425630.1	37	NULL		10																																																																																			LINC00200	-	-	ENSG00000229205		0.547	LINC00200-001	KNOWN	basic	lincRNA	LINC00200	HGNC	lincRNA	OTTHUMT00000046417.2	65	0.00	0	C	NR_015376		1206562	1206562	+1	no_errors	ENST00000425630	ensembl	human	known	69_37n	rna	50	16.67	10	SNP	0.001	T
MAP3K1	4214	genome.wustl.edu	37	5	56168740	56168740	+	Nonsense_Mutation	SNP	C	C	T			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr5:56168740C>T	ENST00000399503.3	+	9	1594	c.1594C>T	c.(1594-1596)Cga>Tga	p.R532*		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	532					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)	p.R369*(1)|p.R532*(1)		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)		GGCTGGATCACGAAGGAATCA	0.458																																						dbGAP											2	Substitution - Nonsense(2)	breast(2)											79.0	75.0	77.0					5																	56168740		1882	4104	5986	-	-	-	SO:0001587	stop_gained	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.1594C>T	5.37:g.56168740C>T	ENSP00000382423:p.Arg532*	Somatic		WXS	Illumina GAIIx	Phase_IV		Nonsense_Mutation	SNP	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.R532*	ENST00000399503.3	37	c.1594	CCDS43318.1	5	.	.	.	.	.	.	.	.	.	.	C	38	6.921236	0.97936	.	.	ENSG00000095015	ENST00000399503	.	.	.	5.97	5.97	0.96955	.	0.060770	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.4238	0.99064	0.0:1.0:0.0:0.0	.	.	.	.	X	532	.	ENSP00000382423:R532X	R	+	1	2	MAP3K1	56204497	1.000000	0.71417	0.882000	0.34594	0.951000	0.60555	6.268000	0.72552	2.834000	0.97654	0.650000	0.86243	CGA	MAP3K1	-	NULL	ENSG00000095015		0.458	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	MAP3K1	HGNC	protein_coding	OTTHUMT00000132309.2	233	0.00	0	C	XM_042066		56168740	56168740	+1	no_errors	ENST00000399503	ensembl	human	novel	69_37n	nonsense	105	41.67	75	SNP	0.998	T
MAP3K1	4214	genome.wustl.edu	37	5	56170880	56170880	+	Frame_Shift_Del	DEL	G	G	-			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr5:56170880delG	ENST00000399503.3	+	10	1708	c.1708delG	c.(1708-1710)ggcfs	p.G570fs		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	570					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)	p.G570fs*10(1)|p.G407fs*10(1)		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)		GGAACTCGTTGGCTGCTTATT	0.448																																						dbGAP											2	Deletion - Frameshift(2)	breast(2)											163.0	155.0	157.0					5																	56170880		1879	4126	6005	-	-	-	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.1708delG	5.37:g.56170880delG	ENSP00000382423:p.Gly570fs	Somatic		WXS	Illumina GAIIx	Phase_IV		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.G570fs	ENST00000399503.3	37	c.1708	CCDS43318.1	5																																																																																			MAP3K1	-	superfamily_ARM-type_fold	ENSG00000095015		0.448	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	MAP3K1	HGNC	protein_coding	OTTHUMT00000132309.2	206	0.00	0	G	XM_042066		56170880	56170880	+1	no_errors	ENST00000399503	ensembl	human	novel	69_37n	frame_shift_del	124	26.44	46	DEL	1.000	-
MUC4	4585	genome.wustl.edu	37	3	195507062	195507062	+	Missense_Mutation	SNP	C	C	T	rs199822551	byFrequency	TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr3:195507062C>T	ENST00000463781.3	-	2	11848	c.11389G>A	c.(11389-11391)Gac>Aac	p.D3797N	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D3797N	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGAAGTGTCGGTGACAGGA	0.607													.|||	549	0.109625	0.0575	0.1239	5008	,	,		9468	0.0556		0.2028	False		,,,				2504	0.1299					dbGAP											0													7.0	7.0	7.0					3																	195507062		641	1482	2123	-	-	-	SO:0001583	missense	0			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11389G>A	3.37:g.195507062C>T	ENSP00000417498:p.Asp3797Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	pfam_Nidogen_extracell_dom,pfam_AMOP,pfam_VWF_type-D,smart_Nidogen_extracell_dom,smart_AMOP,smart_VWF_type-D,smart_EGF-like,pfscan_AMOP,pfscan_EG-like_dom	p.D3797N	ENST00000463781.3	37	c.11389	CCDS54700.1	3	.	.	.	.	.	.	.	.	.	.	c	8.329	0.826143	0.16749	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31247	1.51;1.5	.	.	.	.	0.282130	0.14041	U	0.345384	T	0.13586	0.0329	N	0.19112	0.55	0.09310	N	0.999991	B	0.26975	0.165	B	0.06405	0.002	T	0.19516	-1.0303	8	.	.	.	.	3.5985	0.08016	2.0E-4:0.5013:0.4982:2.0E-4	.	3669	E7ESK3	.	N	3797	ENSP00000417498:D3797N;ENSP00000420243:D3797N	.	D	-	1	0	MUC4	196991841	0.000000	0.05858	0.054000	0.19295	0.055000	0.15305	0.157000	0.16402	0.064000	0.16427	0.064000	0.15345	GAC	MUC4	-	NULL	ENSG00000145113		0.607	MUC4-001	KNOWN	basic|CCDS	protein_coding	MUC4	HGNC	protein_coding	OTTHUMT00000324081.6	11	0.00	0	C	NM_018406		195507062	195507062	-1	no_errors	ENST00000463781	ensembl	human	known	69_37n	missense	21	30.00	9	SNP	0.860	T
MUC4	4585	genome.wustl.edu	37	3	195510156	195510156	+	Silent	SNP	G	G	A	rs201141296	byFrequency	TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr3:195510156G>A	ENST00000463781.3	-	2	8754	c.8295C>T	c.(8293-8295)caC>caT	p.H2765H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.H2765H	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.H2765H(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGGGTGGCGTGACCTGTGG	0.572													.|||	185	0.0369409	0.0129	0.0447	5008	,	,		4806	0.0298		0.0437	False		,,,				2504	0.0644					dbGAP											1	Substitution - coding silent(1)	prostate(1)											28.0	17.0	21.0					3																	195510156		686	1527	2213	-	-	-	SO:0001819	synonymous_variant	0			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8295C>T	3.37:g.195510156G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	pfam_Nidogen_extracell_dom,pfam_AMOP,pfam_VWF_type-D,smart_Nidogen_extracell_dom,smart_AMOP,smart_VWF_type-D,smart_EGF-like,pfscan_AMOP,pfscan_EG-like_dom	p.H2765	ENST00000463781.3	37	c.8295	CCDS54700.1	3																																																																																			MUC4	-	NULL	ENSG00000145113		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	MUC4	HGNC	protein_coding	OTTHUMT00000324081.6	12	0.00	0	G	NM_018406		195510156	195510156	-1	no_errors	ENST00000463781	ensembl	human	known	69_37n	silent	24	32.56	14	SNP	0.035	A
NBPF1	55672	genome.wustl.edu	37	1	16899669	16899669	+	Silent	SNP	C	C	T	rs373211172		TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr1:16899669C>T	ENST00000430580.2	-	22	3305	c.2418G>A	c.(2416-2418)gaG>gaA	p.E806E	NBPF1_ENST00000420031.2_Silent_p.E24E|NBPF1_ENST00000432949.1_Silent_p.E264E|NBPF1_ENST00000287968.8_3'UTR	NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	806	NBPF 4. {ECO:0000255|PROSITE- ProRule:PRU00647}.|Poly-Glu.					cytoplasm (GO:0005737)									UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		CTTCCTCTTCCTCATCATCAC	0.383																																						dbGAP											0													3.0	2.0	2.0					1																	16899669		574	1351	1925	-	-	-	SO:0001819	synonymous_variant	0			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481		"""neuroblastoma breakpoint family"""	26088	protein-coding gene	gene with protein product		610501				11214970, 16079250	Standard	NM_017940		Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.2418G>A	1.37:g.16899669C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q8N4E8|Q9C0H0	RNA	SNP	-	NULL	ENST00000430580.2	37	NULL		1																																																																																			NBPF1	-	-	ENSG00000219481		0.383	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NBPF1	HGNC	protein_coding	OTTHUMT00000106436.3	28	0.00	0	C	NM_017940		16899669	16899669	-1	no_errors	ENST00000287968	ensembl	human	known	69_37n	rna	56	12.50	8	SNP	0.002	T
NCOR2	9612	genome.wustl.edu	37	12	124816874	124816874	+	Missense_Mutation	SNP	G	G	C	rs377394425		TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr12:124816874G>C	ENST00000405201.1	-	43	6895	c.6895C>G	c.(6895-6897)Cct>Gct	p.P2299A	NCOR2_ENST00000404121.2_Missense_Mutation_p.P1860A|NCOR2_ENST00000356219.3_Missense_Mutation_p.P2306A|NCOR2_ENST00000404621.1_Missense_Mutation_p.P2289A|NCOR2_ENST00000429285.2_Missense_Mutation_p.P2289A|NCOR2_ENST00000397355.1_Missense_Mutation_p.P2290A			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	2310					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)	p.P2299A(1)|p.R2306G(1)		breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		CTGTATTCAGGCTCATTCCGG	0.612											OREG0022237	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										dbGAP											2	Substitution - Missense(2)	breast(2)											120.0	117.0	118.0					12																	124816874		1964	4152	6116	-	-	-	SO:0001583	missense	0			U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"""nuclear receptor co-repressor 2"""			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.6895C>G	12.37:g.124816874G>C	ENSP00000384018:p.Pro2299Ala	Somatic	1537	WXS	Illumina GAIIx	Phase_IV	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	pfam_SANT/Myb,superfamily_Homeodomain-like,smart_SANT/Myb,pfscan_Myb-like_dom	p.P2306A	ENST00000405201.1	37	c.6916	CCDS41858.2	12	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.205|9.205	1.029505|1.029505	0.19512|0.19512	.|.	.|.	ENSG00000196498|ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000447675;ENST00000429285|ENST00000418829;ENST00000443451;ENST00000440337	T;T;T;T;T;T|.	0.16897|.	2.31;2.6;2.31;2.6;2.31;2.57|.	4.4|4.4	4.4|4.4	0.53042|0.53042	.|.	0.299519|.	0.31685|.	N|.	0.007239|.	T|T	0.34513|0.34513	0.0900|0.0900	L|L	0.29908|0.29908	0.895|0.895	0.25903|0.25903	N|N	0.983321|0.983321	P;B;B|.	0.36027|.	0.533;0.178;0.112|.	B;B;B|.	0.32928|.	0.083;0.155;0.05|.	T|T	0.17806|0.17806	-1.0357|-1.0357	10|5	0.12430|.	T|.	0.62|.	-13.6125|-13.6125	9.4317|9.4317	0.38615|0.38615	0.0:0.1431:0.689:0.168|0.0:0.1431:0.689:0.168	.|.	2290;2299;2310|.	C9J239;C9JFD3;Q9Y618|.	.;.;NCOR2_HUMAN|.	A|R	2299;2289;2306;2290;2298;1860;391;2289|6;170;89	ENSP00000384018:P2299A;ENSP00000384202:P2289A;ENSP00000348551:P2306A;ENSP00000380513:P2290A;ENSP00000385618:P1860A;ENSP00000400281:P2289A|.	ENSP00000348551:P2306A|.	P|S	-|-	1|3	0|2	NCOR2|NCOR2	123382827|123382827	1.000000|1.000000	0.71417|0.71417	0.930000|0.930000	0.37139|0.37139	0.834000|0.834000	0.47266|0.47266	1.880000|1.880000	0.39628|0.39628	1.981000|1.981000	0.57761|0.57761	0.462000|0.462000	0.41574|0.41574	CCT|AGC	NCOR2	-	NULL	ENSG00000196498		0.612	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	NCOR2	HGNC	protein_coding	OTTHUMT00000318173.2	35	0.00	0	G	NM_006312		124816874	124816874	-1	no_errors	ENST00000356219	ensembl	human	known	69_37n	missense	27	20.59	7	SNP	0.990	C
NEFM	4741	genome.wustl.edu	37	8	24774763	24774763	+	Missense_Mutation	SNP	G	G	C			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr8:24774763G>C	ENST00000221166.5	+	3	2177	c.1395G>C	c.(1393-1395)gaG>gaC	p.E465D	GS1-72M22.1_ENST00000607058.1_RNA|NEFM_ENST00000521540.1_3'UTR|NEFM_ENST00000437366.2_Missense_Mutation_p.E465D|NEFM_ENST00000518131.1_Missense_Mutation_p.E465D|NEFM_ENST00000433454.2_Missense_Mutation_p.E89D			P07197	NFM_HUMAN	neurofilament, medium polypeptide	465	Tail.				axon cargo transport (GO:0008088)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|regulation of axon diameter (GO:0031133)	axon (GO:0030424)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)|neuromuscular junction (GO:0031594)	microtubule binding (GO:0008017)|structural constituent of cytoskeleton (GO:0005200)	p.E465D(1)		breast(3)|endometrium(7)|kidney(4)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|urinary_tract(1)	36		Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)		TGGAGGATGAGAAGTCAGAAA	0.453																																						dbGAP											1	Substitution - Missense(1)	breast(1)											72.0	72.0	72.0					8																	24774763		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC002421	CCDS6046.1, CCDS47831.1	8p21	2013-01-16	2008-09-19	2006-11-20	ENSG00000104722	ENSG00000104722		"""Intermediate filaments type IV"""	7734	protein-coding gene	gene with protein product		162250	"""neurofilament, medium polypeptide 150kDa"""	NEF3		1348579	Standard	NM_001105541		Approved	NFM, NF-M	uc003xed.4	P07197	OTTHUMG00000131990	ENST00000221166.5:c.1395G>C	8.37:g.24774763G>C	ENSP00000221166:p.Glu465Asp	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DGN2|E9PBF7|Q4QRK6	Missense_Mutation	SNP	pfam_F,pfam_Intermed_filament_DNA-bd,superfamily_Prefoldin,prints_Keratin_I	p.E465D	ENST00000221166.5	37	c.1395	CCDS6046.1	8	.	.	.	.	.	.	.	.	.	.	G	11.72	1.722331	0.30503	.	.	ENSG00000104722	ENST00000221166;ENST00000518131;ENST00000437366;ENST00000433454	D;D;D;D	0.94793	-1.83;-1.82;-1.9;-3.52	4.8	0.965	0.19661	.	0.000000	0.47455	D	0.000226	D	0.91549	0.7331	M	0.69823	2.125	0.42323	D	0.99226	B;B	0.24963	0.006;0.115	B;B	0.22386	0.008;0.039	D	0.85299	0.1072	10	0.37606	T	0.19	.	8.6943	0.34287	0.3929:0.0:0.6071:0.0	.	465;465	E7EMV2;P07197	.;NFM_HUMAN	D	465;465;465;89	ENSP00000221166:E465D;ENSP00000427872:E465D;ENSP00000410137:E465D;ENSP00000412295:E89D	ENSP00000221166:E465D	E	+	3	2	NEFM	24830668	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	0.508000	0.22692	0.193000	0.20303	0.467000	0.42956	GAG	NEFM	-	NULL	ENSG00000104722		0.453	NEFM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NEFM	HGNC	protein_coding	OTTHUMT00000254954.2	121	0.00	0	G	NM_005382		24774763	24774763	+1	no_errors	ENST00000221166	ensembl	human	known	69_37n	missense	58	51.67	62	SNP	0.998	C
NEFM	4741	genome.wustl.edu	37	8	24775733	24775733	+	Missense_Mutation	SNP	G	G	A			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr8:24775733G>A	ENST00000221166.5	+	3	3147	c.2365G>A	c.(2365-2367)Gat>Aat	p.D789N	NEFM_ENST00000521540.1_Intron|NEFM_ENST00000437366.2_Missense_Mutation_p.D750N|NEFM_ENST00000518131.1_Intron|NEFM_ENST00000433454.2_Missense_Mutation_p.D413N			P07197	NFM_HUMAN	neurofilament, medium polypeptide	789	Tail.				axon cargo transport (GO:0008088)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|regulation of axon diameter (GO:0031133)	axon (GO:0030424)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)|neuromuscular junction (GO:0031594)	microtubule binding (GO:0008017)|structural constituent of cytoskeleton (GO:0005200)	p.D789N(1)		breast(3)|endometrium(7)|kidney(4)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|urinary_tract(1)	36		Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)		ggaagggagtgataaaggtgc	0.527																																						dbGAP											1	Substitution - Missense(1)	breast(1)											49.0	35.0	40.0					8																	24775733		2186	4275	6461	-	-	-	SO:0001583	missense	0			BC002421	CCDS6046.1, CCDS47831.1	8p21	2013-01-16	2008-09-19	2006-11-20	ENSG00000104722	ENSG00000104722		"""Intermediate filaments type IV"""	7734	protein-coding gene	gene with protein product		162250	"""neurofilament, medium polypeptide 150kDa"""	NEF3		1348579	Standard	NM_001105541		Approved	NFM, NF-M	uc003xed.4	P07197	OTTHUMG00000131990	ENST00000221166.5:c.2365G>A	8.37:g.24775733G>A	ENSP00000221166:p.Asp789Asn	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DGN2|E9PBF7|Q4QRK6	Missense_Mutation	SNP	pfam_F,pfam_Intermed_filament_DNA-bd,superfamily_Prefoldin,prints_Keratin_I	p.D789N	ENST00000221166.5	37	c.2365	CCDS6046.1	8	.	.	.	.	.	.	.	.	.	.	G	10.67	1.416864	0.25552	.	.	ENSG00000104722	ENST00000221166;ENST00000437366;ENST00000433454	D;D;D	0.94650	-1.95;-1.82;-3.48	4.07	4.07	0.47477	.	0.295363	0.23698	N	0.045453	D	0.91050	0.7184	L	0.52011	1.625	0.21416	N	0.999698	B	0.30482	0.281	B	0.30179	0.112	D	0.85372	0.1114	10	0.54805	T	0.06	.	9.3398	0.38074	0.1045:0.0:0.8955:0.0	.	789	P07197	NFM_HUMAN	N	789;750;413	ENSP00000221166:D789N;ENSP00000410137:D750N;ENSP00000412295:D413N	ENSP00000221166:D789N	D	+	1	0	NEFM	24831638	0.983000	0.35010	0.095000	0.20976	0.061000	0.15899	4.582000	0.60957	1.974000	0.57490	0.411000	0.27672	GAT	NEFM	-	NULL	ENSG00000104722		0.527	NEFM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NEFM	HGNC	protein_coding	OTTHUMT00000254954.2	224	0.00	0	G	NM_005382		24775733	24775733	+1	no_errors	ENST00000221166	ensembl	human	known	69_37n	missense	89	52.66	99	SNP	0.163	A
NFRKB	4798	genome.wustl.edu	37	11	129762649	129762649	+	Silent	SNP	T	T	C			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr11:129762649T>C	ENST00000446488.3	-	2	199	c.96A>G	c.(94-96)ggA>ggG	p.G32G	NFRKB_ENST00000526940.1_Silent_p.G32G|NFRKB_ENST00000524746.1_Silent_p.G32G|NFRKB_ENST00000524794.1_Silent_p.G45G|NFRKB_ENST00000304521.5_Silent_p.G32G	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	32					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protease binding (GO:0002020)	p.G45G(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(13)|ovary(4)|skin(3)|urinary_tract(1)	32	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)		CTCTGGTGCCTCCCAGGAGGC	0.527																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											176.0	146.0	156.0					11																	129762649		2201	4297	6498	-	-	-	SO:0001819	synonymous_variant	0				CCDS8483.1, CCDS44770.1	11q24-q25	2011-07-06			ENSG00000170322	ENSG00000170322		"""INO80 complex subunits"""	7802	protein-coding gene	gene with protein product	"""nuclear factor related to kappa B binding protein"", ""DNA-binding protein R kappa B"", ""INO80 complex subunit G"""	164013				1427843	Standard	NM_006165		Approved	DKFZp547B2013, INO80G	uc001qfg.3	Q6P4R8	OTTHUMG00000165761	ENST00000446488.3:c.96A>G	11.37:g.129762649T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	Q12869|Q15312|Q9H048	Silent	SNP	NULL	p.G45	ENST00000446488.3	37	c.135	CCDS44770.1	11																																																																																			NFRKB	-	NULL	ENSG00000170322		0.527	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NFRKB	HGNC	protein_coding	OTTHUMT00000386063.2	333	0.60	2	T	NM_006165		129762649	129762649	-1	no_errors	ENST00000524794	ensembl	human	known	69_37n	silent	338	18.31	76	SNP	0.423	C
NINL	22981	genome.wustl.edu	37	20	25507207	25507207	+	Missense_Mutation	SNP	T	T	G			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr20:25507207T>G	ENST00000278886.6	-	2	90	c.17A>C	c.(16-18)aAc>aCc	p.N6T	NINL_ENST00000422516.1_Missense_Mutation_p.N6T	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	6					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)	p.N6T(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						GACATAGTGGTTCTCTTCTTC	0.567																																						dbGAP											1	Substitution - Missense(1)	breast(1)											122.0	117.0	118.0					20																	25507207		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"""EF-hand domain containing"""	29163	protein-coding gene	gene with protein product	"""ninein-like protein"""	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.17A>C	20.37:g.25507207T>G	ENSP00000278886:p.Asn6Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Missense_Mutation	SNP	pfam_EF-hand,smart_EF_hand_Ca-bd,pfscan_EF_HAND_2	p.N6T	ENST00000278886.6	37	c.17	CCDS33452.1	20	.	.	.	.	.	.	.	.	.	.	T	7.533	0.659074	0.14645	.	.	ENSG00000101004	ENST00000278886;ENST00000422516	T;T	0.34072	1.38;1.38	5.25	-1.26	0.09376	.	0.463788	0.24113	N	0.041424	T	0.27098	0.0664	L	0.60455	1.87	0.09310	N	1	P;P	0.40731	0.617;0.728	B;B	0.30943	0.121;0.122	T	0.19321	-1.0309	10	0.66056	D	0.02	-9.9934	11.477	0.50304	0.0:0.5217:0.0:0.4783	.	6;6	Q9Y2I6-2;Q9Y2I6	.;NINL_HUMAN	T	6	ENSP00000278886:N6T;ENSP00000410431:N6T	ENSP00000278886:N6T	N	-	2	0	NINL	25455207	0.995000	0.38212	0.001000	0.08648	0.044000	0.14063	0.299000	0.19138	-0.299000	0.08909	-0.408000	0.06270	AAC	NINL	-	NULL	ENSG00000101004		0.567	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NINL	HGNC	protein_coding	OTTHUMT00000078445.3	100	0.99	1	T	NM_025176		25507207	25507207	-1	no_errors	ENST00000278886	ensembl	human	known	69_37n	missense	69	31.00	31	SNP	0.048	G
PAX2	5076	genome.wustl.edu	37	10	102509528	102509529	+	Frame_Shift_Ins	INS	-	-	G	rs75462234|rs77453353		TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr10:102509528_102509529insG	ENST00000428433.1	+	2	619_620	c.69_70insG	c.(70-72)gggfs	p.G24fs	PAX2_ENST00000355243.3_Frame_Shift_Ins_p.G24fs|PAX2_ENST00000370296.2_Frame_Shift_Ins_p.G24fs|PAX2_ENST00000553492.1_Intron|PAX2_ENST00000556085.1_Frame_Shift_Ins_p.G23fs|PAX2_ENST00000361791.3_Frame_Shift_Ins_p.G24fs	NM_003987.3|NM_003990.3	NP_003978|NP_003981.2	Q02962	PAX2_HUMAN	paired box 2	24	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.		G -> E (probable disease-associated mutation found in a patient with renal hypodysplasia). {ECO:0000269|PubMed:21380624}.		aging (GO:0007568)|axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cell fate determination (GO:0001709)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucose stimulus (GO:0071333)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cochlea development (GO:0090102)|cochlea morphogenesis (GO:0090103)|glial cell differentiation (GO:0010001)|inner ear morphogenesis (GO:0042472)|mesenchymal to epithelial transition (GO:0060231)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesodermal cell fate specification (GO:0007501)|mesonephric duct development (GO:0072177)|mesonephric tubule formation (GO:0072172)|mesonephros development (GO:0001823)|metanephric collecting duct development (GO:0072205)|metanephric distal convoluted tubule development (GO:0072221)|metanephric epithelium development (GO:0072207)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchyme development (GO:0072075)|metanephric nephron tubule formation (GO:0072289)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic process involved in metanephric collecting duct development (GO:1900215)|negative regulation of apoptotic process involved in metanephric nephron tubule development (GO:1900218)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of cytolysis (GO:0045918)|negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis (GO:0072305)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|negative regulation of programmed cell death (GO:0043069)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct formation (GO:0072179)|neural tube closure (GO:0001843)|optic chiasma development (GO:0061360)|optic cup morphogenesis involved in camera-type eye development (GO:0002072)|optic nerve development (GO:0021554)|optic nerve morphogenesis (GO:0021631)|optic nerve structural organization (GO:0021633)|pancreas development (GO:0031016)|paramesonephric duct development (GO:0061205)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of metanephric DCT cell differentiation (GO:2000594)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of optic nerve formation (GO:2000597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric field specification (GO:0039003)|pronephros development (GO:0048793)|protein kinase B signaling (GO:0043491)|reactive oxygen species metabolic process (GO:0072593)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of metanephros size (GO:0035566)|response to nutrient levels (GO:0031667)|retinal pigment epithelium development (GO:0003406)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|ureter development (GO:0072189)|ureter maturation (GO:0035799)|ureter morphogenesis (GO:0072197)|urogenital system development (GO:0001655)|vestibulocochlear nerve formation (GO:0021650)|visual perception (GO:0007601)	centriolar satellite (GO:0034451)|lysosome (GO:0005764)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|protein complex (GO:0043234)|protein-DNA complex (GO:0032993)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|superoxide-generating NADPH oxidase activity (GO:0016175)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	18		Colorectal(252;0.234)		Epithelial(162;1.32e-08)|all cancers(201;7.32e-07)		TGAACCAGCTCGGGGGGGTGTT	0.663																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0				CCDS7499.1, CCDS41561.1	10q24.31	2011-06-20	2007-07-12		ENSG00000075891	ENSG00000075891		"""Paired boxes"", ""Homeoboxes / PRD class"""	8616	protein-coding gene	gene with protein product		167409	"""paired box gene 2"""			8431641, 7981748	Standard	NM_003990		Approved		uc001krk.4	Q02962	OTTHUMG00000018913	ENST00000428433.1:c.76dupG	10.37:g.102509535_102509535dupG	ENSP00000396259:p.Gly24fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q15105|Q15110|Q15837|Q5SZP2|Q5SZP3	Frame_Shift_Ins	INS	pfam_Paired_dom,pfam_Pax2_C,superfamily_Homeodomain-like,smart_Paired_dom,prints_Paired_dom,pfscan_Paired_dom	p.V25fs	ENST00000428433.1	37	c.69_70	CCDS53569.1	10																																																																																			PAX2	-	pfam_Paired_dom,superfamily_Homeodomain-like,smart_Paired_dom,prints_Paired_dom,pfscan_Paired_dom	ENSG00000075891		0.663	PAX2-202	KNOWN	basic|CCDS	protein_coding	PAX2	HGNC	protein_coding		26	0.00	0	-			102509528	102509529	+1	no_errors	ENST00000370296	ensembl	human	known	69_37n	frame_shift_ins	22	15.38	4	INS	1.000:1.000	G
PCDHA9	9752	genome.wustl.edu	37	5	140229589	140229589	+	Silent	SNP	G	G	A			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr5:140229589G>A	ENST00000532602.1	+	1	2542	c.1509G>A	c.(1507-1509)tcG>tcA	p.S503S	PCDHA6_ENST00000527624.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA9_ENST00000378122.3_Silent_p.S503S|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	503	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S503S(2)		breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGAGCGCTCGCTGTCGAGCT	0.672																																					Melanoma(55;1800 1972 14909)	dbGAP											2	Substitution - coding silent(2)	breast(2)											61.0	67.0	65.0					5																	140229589		2196	4271	6467	-	-	-	SO:0001819	synonymous_variant	0			AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"""Cadherins / Protocadherins : Clustered"""	8675	other	complex locus constituent	"""KIAA0345-like 5"""	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.1509G>A	5.37:g.140229589G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	O15053|Q2M3S5	Silent	SNP	pfam_Cadherin,pfam_Cadherin_N,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin,prints_Cadherin	p.S503	ENST00000532602.1	37	c.1509	CCDS54920.1	5																																																																																			PCDHA9	-	pfam_Cadherin,superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin	ENSG00000204961		0.672	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PCDHA9	HGNC	protein_coding	OTTHUMT00000372896.2	23	0.00	0	G	NM_031857		140229589	140229589	+1	no_errors	ENST00000532602	ensembl	human	known	69_37n	silent	5	70.59	12	SNP	0.770	A
PEBP1	5037	genome.wustl.edu	37	12	118574086	118574086	+	Silent	SNP	G	G	C	rs11554100		TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr12:118574086G>C	ENST00000261313.2	+	1	424	c.72G>C	c.(70-72)ccG>ccC	p.P24P		NM_002567.2	NP_002558.1	P30086	PEBP1_HUMAN	phosphatidylethanolamine binding protein 1	24						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|phosphatidylethanolamine binding (GO:0008429)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|serine-type endopeptidase inhibitor activity (GO:0004867)			ovary(1)	1	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CGCAGCACCCGCTGCATGTCA	0.716																																					NSCLC(44;94 1357 12187 49467)	dbGAP											0													9.0	11.0	10.0					12																	118574086		1946	3646	5592	-	-	-	SO:0001819	synonymous_variant	0			X85033	CCDS9187.1	12q24	2009-06-16	2006-02-16	2006-02-16	ENSG00000089220	ENSG00000089220			8630	protein-coding gene	gene with protein product	"""Raf kinase inhibitory protein"", ""hippocampal cholinergic neurostimulating peptide"""	604591	"""prostatic binding protein"""	PBP		15782137	Standard	NM_002567		Approved	RKIP, HCNP, PEBP	uc001twu.1	P30086	OTTHUMG00000168860	ENST00000261313.2:c.72G>C	12.37:g.118574086G>C		Somatic		WXS	Illumina GAIIx	Phase_IV	B2R4S1	Silent	SNP	pfam_PtdEtn-bd_prot_PEBP,superfamily_PtdEtn-bd_prot_PEBP	p.P24	ENST00000261313.2	37	c.72	CCDS9187.1	12																																																																																			PEBP1	-	pfam_PtdEtn-bd_prot_PEBP,superfamily_PtdEtn-bd_prot_PEBP	ENSG00000089220		0.716	PEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PEBP1	HGNC	protein_coding	OTTHUMT00000401405.1	21	0.00	0	G	NM_002567		118574086	118574086	+1	no_errors	ENST00000261313	ensembl	human	known	69_37n	silent	6	40.00	4	SNP	0.994	C
PLCG2	5336	genome.wustl.edu	37	16	81902858	81902858	+	Silent	SNP	C	C	A			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr16:81902858C>A	ENST00000359376.3	+	6	733	c.519C>A	c.(517-519)atC>atA	p.I173I		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	173					B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.I173I(2)		NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						TGCCCCTGATCAACTTTAAAG	0.458																																						dbGAP											2	Substitution - coding silent(2)	breast(2)											217.0	208.0	211.0					16																	81902858		1903	4133	6036	-	-	-	SO:0001819	synonymous_variant	0				CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"""SH2 domain containing"""	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.519C>A	16.37:g.81902858C>A		Somatic		WXS	Illumina GAIIx	Phase_IV	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Silent	SNP	pfam_PLipase_C_PInositol-sp_X_dom,pfam_SH2,pfam_PLipase_C_Pinositol-sp_Y,pfam_SH3_domain,pfam_C2_Ca-dep,pfam_PLipase_C_EF-hand-like,pfam_SH3_2,superfamily_PLC-like_Pdiesterase_TIM-brl,superfamily_C2_Ca/lipid-bd_dom_CaLB,superfamily_SH3_domain,smart_Pleckstrin_homology,smart_PLipase_C_PInositol-sp_X_dom,smart_SH2,smart_SH3_domain,smart_PLipase_C_Pinositol-sp_Y,smart_C2_Ca-dep,pirsf_PLC-gamma,prints_Pinositol_PLipase_C,prints_SH2,prints_SH3_domain,pfscan_C2_membr_targeting,pfscan_Pleckstrin_homology,pfscan_SH2,pfscan_SH3_domain,pfscan_PLipase_C_PInositol-sp_X_dom,pfscan_PLipase_C_Pinositol-sp_Y	p.I173	ENST00000359376.3	37	c.519	CCDS42204.1	16																																																																																			PLCG2	-	pirsf_PLC-gamma	ENSG00000197943		0.458	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PLCG2	HGNC	protein_coding	OTTHUMT00000432429.1	86	0.00	0	C			81902858	81902858	+1	no_errors	ENST00000359376	ensembl	human	known	69_37n	silent	31	26.19	11	SNP	1.000	A
PLG	5340	genome.wustl.edu	37	6	161173261	161173261	+	Missense_Mutation	SNP	G	G	A			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr6:161173261G>A	ENST00000308192.9	+	18	2303	c.2240G>A	c.(2239-2241)gGg>gAg	p.G747E		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	747	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.G747E(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	CTCTGTGCTGGGCATTTGGCC	0.502																																						dbGAP											1	Substitution - Missense(1)	breast(1)											82.0	81.0	81.0					6																	161173261		2203	4300	6503	-	-	-	SO:0001583	missense	0			M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.2240G>A	6.37:g.161173261G>A	ENSP00000308938:p.Gly747Glu	Somatic		WXS	Illumina GAIIx	Phase_IV	Q15146|Q5TEH4|Q6PA00	Missense_Mutation	SNP	pirsf_Pept_S1A_plasmin,pfam_Kringle,pfam_Peptidase_S1_S6,pfam_PAN-1_domain,pfam_Peptidase_S1A_nudel,superfamily_Pept_cys/ser_Trypsin-like,superfamily_Kringle-like,smart_Pan_app,smart_Kringle,smart_Peptidase_S1_S6,prints_Peptidase_S1A,pfscan_Pan_app,pfscan_Kringle,pfscan_Peptidase_S1_S6	p.G747E	ENST00000308192.9	37	c.2240	CCDS5279.1	6	.	.	.	.	.	.	.	.	.	.	.	15.42	2.827854	0.50845	.	.	ENSG00000122194	ENST00000308192;ENST00000316325	D	0.90324	-2.65	3.38	3.38	0.38709	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.39985	U	0.001217	D	0.94879	0.8345	M	0.91510	3.215	0.58432	D	0.99999	D	0.76494	0.999	D	0.87578	0.998	D	0.94164	0.7417	10	0.30078	T	0.28	.	14.6685	0.68926	0.0:0.0:1.0:0.0	.	747	P00747	PLMN_HUMAN	E	747;147	ENSP00000308938:G747E	ENSP00000308938:G747E	G	+	2	0	PLG	161093251	1.000000	0.71417	0.012000	0.15200	0.717000	0.41224	9.032000	0.93736	1.582000	0.49881	0.411000	0.27672	GGG	PLG	-	pirsf_Pept_S1A_plasmin,pfam_Peptidase_S1_S6,superfamily_Pept_cys/ser_Trypsin-like,smart_Peptidase_S1_S6,pfscan_Peptidase_S1_S6	ENSG00000122194		0.502	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PLG	HGNC	protein_coding	OTTHUMT00000042959.2	143	0.00	0	G	NM_000301		161173261	161173261	+1	no_errors	ENST00000308192	ensembl	human	known	69_37n	missense	138	13.66	22	SNP	0.004	A
POLG	5428	genome.wustl.edu	37	15	89870412	89870412	+	Silent	SNP	C	C	T			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr15:89870412C>T	ENST00000268124.5	-	7	1752	c.1419G>A	c.(1417-1419)ctG>ctA	p.L473L	POLG_ENST00000442287.2_Silent_p.L473L	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma	473					aging (GO:0007568)|base-excision repair, gap-filling (GO:0006287)|cell death (GO:0008219)|DNA metabolic process (GO:0006259)|DNA-dependent DNA replication (GO:0006261)|mitochondrial DNA replication (GO:0006264)	extracellular vesicular exosome (GO:0070062)|gamma DNA polymerase complex (GO:0005760)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|exonuclease activity (GO:0004527)|protease binding (GO:0002020)	p.L473L(1)		breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(3)|urinary_tract(2)	33	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			CTCCTGAGAGCAGCTGGCAGG	0.612								DNA polymerases (catalytic subunits)																													Colon(73;648 1203 11348 18386 27782)	dbGAP											1	Substitution - coding silent(1)	breast(1)											91.0	89.0	90.0					15																	89870412		2200	4299	6499	-	-	-	SO:0001819	synonymous_variant	0			X98093	CCDS10350.1	15q24	2014-09-17			ENSG00000140521	ENSG00000140521		"""DNA polymerases"""	9179	protein-coding gene	gene with protein product		174763				9465903	Standard	NM_002693		Approved	POLG1, POLGA	uc002bnr.4	P54098	OTTHUMG00000149646	ENST00000268124.5:c.1419G>A	15.37:g.89870412C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q8NFM2|Q92515	Silent	SNP	pirsf_DNA-dir_DNA_pol_A_mt_sub,pfam_DNA-dir_DNA_pol_A_palm_dom,superfamily_RNaseH-like_dom,smart_DNA-dir_DNA_pol_A_palm_dom,prints_DNA-dir_DNA_pol_A_mt	p.L473	ENST00000268124.5	37	c.1419	CCDS10350.1	15																																																																																			POLG	-	pirsf_DNA-dir_DNA_pol_A_mt_sub	ENSG00000140521		0.612	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	POLG	HGNC	protein_coding	OTTHUMT00000312854.2	36	0.00	0	C	NM_002693		89870412	89870412	-1	no_errors	ENST00000268124	ensembl	human	known	69_37n	silent	74	13.95	12	SNP	1.000	T
PPL	5493	genome.wustl.edu	37	16	4944499	4944500	+	Frame_Shift_Ins	INS	-	-	G	rs147027769|rs552407353		TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr16:4944499_4944500insG	ENST00000345988.2	-	12	1451_1452	c.1362_1363insC	c.(1360-1365)cccacafs	p.T455fs	PPL_ENST00000590782.2_Frame_Shift_Ins_p.T453fs	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	455					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)	p.T455fs*4(1)		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						TCAGGGTCTGTGGGGGGGATCA	0.609																																						dbGAP											1	Insertion - Frameshift(1)	large_intestine(1)								16,4248		0,16,2116						5.2	1.0			76	3,8251		0,3,4124	no	frameshift	PPL	NM_002705.4		0,19,6240	A1A1,A1R,RR		0.0363,0.3752,0.1518				19,12499				-	-	-	SO:0001589	frameshift_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.1363dupC	16.37:g.4944506_4944506dupG	ENSP00000340510:p.Thr455fs	Somatic		WXS	Illumina GAIIx	Phase_IV	O60314|O60454|Q14C98	Frame_Shift_Ins	INS	pfam_Plectin_repeat,smart_Spectrin/alpha-actinin,smart_Plectin_repeat	p.T454fs	ENST00000345988.2	37	c.1363_1362	CCDS10526.1	16																																																																																			PPL	-	smart_Spectrin/alpha-actinin	ENSG00000118898		0.609	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PPL	HGNC	protein_coding	OTTHUMT00000251715.1	29	0.00	0	-	NM_002705		4944499	4944500	-1	no_errors	ENST00000345988	ensembl	human	known	69_37n	frame_shift_ins	26	13.33	4	INS	0.994:0.933	G
PRKAR1A	5573	genome.wustl.edu	37	17	66521903	66521903	+	Silent	SNP	T	T	C			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr17:66521903T>C	ENST00000589228.1	+	7	686	c.558T>C	c.(556-558)gtT>gtC	p.V186V	PRKAR1A_ENST00000588188.2_Silent_p.V186V|PRKAR1A_ENST00000536854.2_Silent_p.V186V|PRKAR1A_ENST00000586397.1_Silent_p.V186V|PRKAR1A_ENST00000392711.1_Silent_p.V186V|PRKAR1A_ENST00000358598.2_Silent_p.V186V	NM_001276289.1|NM_001278433.1	NP_001263218.1|NP_001265362.1	P10644	KAP0_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, alpha	186					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cardiac muscle cell proliferation (GO:0060038)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|female meiotic division (GO:0007143)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm formation (GO:0001707)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sarcomere organization (GO:0045214)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)	p.V186V(1)		adrenal_gland(4)|breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(8)|soft_tissue(2)|stomach(2)|testis(1)|thyroid(2)|upper_aerodigestive_tract(1)	31	Breast(10;1.64e-13)					AGGTCTATGTTAACAATGAAT	0.383			"""T, Mis, N, F, S"""	RET	papillary thyroid	"""myxoma, endocrine, papillary thyroid"""			Primary Pigmented Nodular Adrenocortical Disease, Familial;Carney Complex;Cardiac Myxomas, Familial Clustering of																												Ovarian(167;637 1670 33025 39608 46699 51856)	dbGAP	yes	"""Dom, Rec"""	yes	Carney complex	17	17q23-q24	5573	"""protein kinase, cAMP-dependent, regulatory, type I, alpha (tissue specific extinguisher 1)"""		"""E, M"""	1	Substitution - coding silent(1)	breast(1)											122.0	121.0	122.0					17																	66521903		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2;Carney syndrome, NAME syndrome, LAMB syndrome, Familial Myxoma syndrome;		CCDS11678.1, CCDS62307.1	17q24.2	2014-09-17	2012-07-31		ENSG00000108946	ENSG00000108946	2.7.11.1		9388	protein-coding gene	gene with protein product	"""Carney complex type 1"""	188830	"""tissue specific extinguisher 1"""	PRKAR1, TSE1		3479018, 10973256	Standard	NM_212471		Approved	CNC1	uc002jhg.4	P10644	OTTHUMG00000180128	ENST00000589228.1:c.558T>C	17.37:g.66521903T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	K7ER48|Q567S7	Nonstop_Mutation	SNP	pfam_cNMP-bd_dom,pfam_cAMP_dep_PK_reg_su_I/II_a/b,superfamily_cNMP-bd-like,superfamily_cAMP_dep_PK_reg_su_I/II_a/b,smart_cAMP_dep_PK_reg_su_I/II_a/b,smart_cNMP-bd_dom,pirsf_cAMP_dep_PK_reg_su,pfscan_cNMP-bd_dom,prints_cAMP/cGMP_kin	p.*186Q	ENST00000589228.1	37	c.556	CCDS11678.1	17																																																																																			PRKAR1A	-	pfam_cNMP-bd_dom,superfamily_cNMP-bd-like,smart_cNMP-bd_dom,pirsf_cAMP_dep_PK_reg_su,pfscan_cNMP-bd_dom,prints_cAMP/cGMP_kin	ENSG00000108946		0.383	PRKAR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PRKAR1A	HGNC	protein_coding	OTTHUMT00000449884.1	168	0.00	0	T			66521903	66521903	+1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000588188	ensembl	human	putative	69_37n	nonstop	159	15.43	29	SNP	1.000	C
PTEN	5728	genome.wustl.edu	37	10	89692794	89692794	+	Missense_Mutation	SNP	A	A	T	rs121909238		TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr10:89692794A>T	ENST00000371953.3	+	5	1635	c.278A>T	c.(277-279)cAt>cTt	p.H93L		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	93	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.		H -> R (in MCEPHAS). {ECO:0000269|PubMed:15805158}.|H -> Y (in CWS1).		activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(5)|p.R55fs*1(5)|p.H93R(3)|p.Y27fs*1(2)|p.Q87_P96del(1)|p.N82_P95del(1)|p.F56fs*2(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		TTTGAAGACCATAACCCACCA	0.338		31	"""D, Mis, N, F, S"""		"""glioma,  prostate, endometrial"""	"""harmartoma, glioma,  prostate, endometrial"""			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												dbGAP	yes	Rec	yes	"""Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"""	10	10q23.3	5728	phosphatase and tensin homolog gene		"""L, E, M, O"""	55	Whole gene deletion(37)|Deletion - Frameshift(8)|Unknown(5)|Substitution - Missense(3)|Deletion - In frame(2)	prostate(16)|central_nervous_system(12)|lung(6)|skin(6)|haematopoietic_and_lymphoid_tissue(4)|endometrium(3)|breast(3)|ovary(3)|soft_tissue(1)|urinary_tract(1)	GRCh37	CM051214	PTEN	M	rs121909238						111.0	102.0	105.0					10																	89692794		2203	4300	6503	-	-	-	SO:0001583	missense	0	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	9588	protein-coding gene	gene with protein product	"""mutated in multiple advanced cancers 1"""	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.278A>T	10.37:g.89692794A>T	ENSP00000361021:p.His93Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	pfam_Tensin_phosphatase_C2-dom,pfam_Dual-sp_phosphatase_cat-dom,pfam_Tyr_Pase_rcpt/non-rcpt,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_Tyr_Pase_cat,pirsf_Bifunc_PIno_P3_Pase/Pase_PTEN,pfscan_Tyr/Dual-specificity_Pase,pfscan_Phosphatase_tensin-typ,pfscan_Tensin_phosphatase_C2-dom	p.H93L	ENST00000371953.3	37	c.278	CCDS31238.1	10	.	.	.	.	.	.	.	.	.	.	A	26.3	4.725392	0.89298	.	.	ENSG00000171862	ENST00000371953	D	0.98762	-5.12	5.07	5.07	0.68467	Phosphatase tensin type (1);Dual specificity phosphatase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.99190	0.9719	M	0.88640	2.97	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99331	1.0909	9	.	.	.	-6.7727	14.8406	0.70220	1.0:0.0:0.0:0.0	.	93	P60484	PTEN_HUMAN	L	93	ENSP00000361021:H93L	.	H	+	2	0	PTEN	89682774	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.914000	0.92735	1.880000	0.54463	0.533000	0.62120	CAT	PTEN	-	pfam_Dual-sp_phosphatase_cat-dom,pfam_Tyr_Pase_rcpt/non-rcpt,smart_Tyr_Pase_cat,pirsf_Bifunc_PIno_P3_Pase/Pase_PTEN,pfscan_Phosphatase_tensin-typ	ENSG00000171862		0.338	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PTEN	HGNC	protein_coding	OTTHUMT00000049241.1	271	0.00	0	A	NM_000314		89692794	89692794	+1	no_errors	ENST00000371953	ensembl	human	known	69_37n	missense	44	61.06	69	SNP	1.000	T
RAD18	56852	genome.wustl.edu	37	3	8932110	8932110	+	Missense_Mutation	SNP	G	G	A			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr3:8932110G>A	ENST00000264926.2	-	12	1464	c.1348C>T	c.(1348-1350)Ctt>Ttt	p.L450F		NM_020165.3	NP_064550.3	Q9NS91	RAD18_HUMAN	RAD18 E3 ubiquitin protein ligase	450					DNA repair (GO:0006281)|negative regulation of DNA recombination (GO:0045910)|protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|spermatogenesis (GO:0007283)	chromatin (GO:0000785)|nucleus (GO:0005634)|replication fork (GO:0005657)|XY body (GO:0001741)	damaged DNA binding (GO:0003684)|ligase activity (GO:0016874)|polyubiquitin binding (GO:0031593)|ubiquitin protein ligase binding (GO:0031625)|Y-form DNA binding (GO:0000403)|zinc ion binding (GO:0008270)	p.L450F(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)|skin(3)	15				OV - Ovarian serous cystadenocarcinoma(96;0.0552)		TCTTCTAAAAGATCTCTTATG	0.348								Rad6 pathway																														dbGAP											1	Substitution - Missense(1)	breast(1)											123.0	119.0	120.0					3																	8932110		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS2571.1	3p25-p24	2014-08-04	2014-08-04		ENSG00000070950	ENSG00000070950		"""RING-type (C3HC4) zinc fingers"""	18278	protein-coding gene	gene with protein product		605256	"""RAD18 homolog (S. cerevisiae)"""			10884424, 10908344	Standard	NM_020165		Approved	RNF73	uc003brd.3	Q9NS91	OTTHUMG00000090545	ENST00000264926.2:c.1348C>T	3.37:g.8932110G>A	ENSP00000264926:p.Leu450Phe	Somatic		WXS	Illumina GAIIx	Phase_IV	Q58F55|Q9NRT6	Missense_Mutation	SNP	pfam_SAP_DNA-bd,pfam_Znf_C3HC4_RING-type,smart_Znf_RING,smart_Znf_Rad18_put,smart_SAP_DNA-bd,pfscan_Znf_RING,pfscan_SAP_DNA-bd	p.L450F	ENST00000264926.2	37	c.1348	CCDS2571.1	3	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.39|15.39	2.820837|2.820837	0.50633|0.50633	.|.	.|.	ENSG00000070950|ENSG00000070950	ENST00000264926;ENST00000429790|ENST00000427329	T|.	0.35973|.	1.28|.	5.06|5.06	-0.19|-0.19	0.13256|0.13256	.|.	0.582210|.	0.15651|.	N|.	0.251389|.	T|T	0.50326|0.50326	0.1609|0.1609	M|M	0.66939|0.66939	2.045|2.045	0.09310|0.09310	N|N	1|1	D|.	0.56035|.	0.974|.	P|.	0.51135|.	0.66|.	T|T	0.46062|0.46062	-0.9218|-0.9218	10|5	0.59425|.	D|.	0.04|.	6.8465|6.8465	9.0751|9.0751	0.36515|0.36515	0.0:0.1355:0.3086:0.5559|0.0:0.1355:0.3086:0.5559	.|.	450|.	Q9NS91|.	RAD18_HUMAN|.	F|F	450;67|86	ENSP00000264926:L450F|.	ENSP00000264926:L450F|.	L|S	-|-	1|2	0|0	RAD18|RAD18	8907110|8907110	0.999000|0.999000	0.42202|0.42202	0.125000|0.125000	0.21846|0.21846	0.963000|0.963000	0.63663|0.63663	2.116000|2.116000	0.41930|0.41930	-0.222000|-0.222000	0.09958|0.09958	-0.311000|-0.311000	0.09066|0.09066	CTT|TCT	RAD18	-	NULL	ENSG00000070950		0.348	RAD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RAD18	HGNC	protein_coding	OTTHUMT00000207071.2	262	0.00	0	G	NM_020165		8932110	8932110	-1	no_errors	ENST00000264926	ensembl	human	known	69_37n	missense	104	30.67	46	SNP	0.059	A
RBM10	8241	genome.wustl.edu	37	X	47044963	47044963	+	Silent	SNP	C	C	T			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chrX:47044963C>T	ENST00000377604.3	+	20	3031	c.2289C>T	c.(2287-2289)ctC>ctT	p.L763L	RBM10_ENST00000345781.6_Silent_p.L686L|RBM10_ENST00000329236.7_Silent_p.L685L	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	763					3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)	p.L763L(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						CCTGTCTGCTCTGCCGACGCC	0.657																																					Melanoma(171;120 2705 19495 39241)	dbGAP											1	Substitution - coding silent(1)	breast(1)											31.0	24.0	26.0					X																	47044963		2198	4293	6491	-	-	-	SO:0001819	synonymous_variant	0			U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"""Zinc fingers, RAN-binding domain containing"", ""G patch domain containing"", ""RNA binding motif (RRM) containing"""	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.2289C>T	X.37:g.47044963C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Silent	SNP	pfam_G_patch_dom,pfam_RRM_dom,pfam_Znf_RanBP2,smart_RRM_dom,smart_Znf_RanBP2,smart_G_patch_dom,pfscan_Znf_RanBP2,pfscan_Znf_C2H2,pfscan_G_patch_dom,pfscan_RRM_dom	p.L763	ENST00000377604.3	37	c.2289	CCDS14274.1	X																																																																																			RBM10	-	pfscan_Znf_C2H2	ENSG00000182872		0.657	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	RBM10	HGNC	protein_coding	OTTHUMT00000056381.1	44	0.00	0	C	NM_005676		47044963	47044963	+1	no_errors	ENST00000377604	ensembl	human	known	69_37n	silent	65	18.75	15	SNP	0.978	T
RIF1	55183	genome.wustl.edu	37	2	152285358	152285358	+	Missense_Mutation	SNP	C	C	T			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr2:152285358C>T	ENST00000243326.5	+	8	1330	c.847C>T	c.(847-849)Cgt>Tgt	p.R283C	RIF1_ENST00000428287.2_Missense_Mutation_p.R283C|RIF1_ENST00000433166.2_Missense_Mutation_p.R252C|RIF1_ENST00000453091.2_Missense_Mutation_p.R283C|RIF1_ENST00000430328.2_Missense_Mutation_p.R283C|RIF1_ENST00000444746.2_Missense_Mutation_p.R283C			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)	p.R283C(1)		NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		ACTTGGATTTCGTAGTGGAGC	0.318																																						dbGAP											1	Substitution - Missense(1)	breast(1)											99.0	100.0	99.0					2																	152285358		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"""RAP1 interacting factor homolog (yeast)"""			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.847C>T	2.37:g.152285358C>T	ENSP00000243326:p.Arg283Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	A0AVS0|Q9NS16	Missense_Mutation	SNP	pfam_Rif1_N,superfamily_ARM-type_fold	p.R283C	ENST00000243326.5	37	c.847	CCDS2194.1	2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.4|24.4	4.529440|4.529440	0.85706|0.85706	.|.	.|.	ENSG00000080345|ENSG00000080345	ENST00000444746;ENST00000453091;ENST00000428287;ENST00000433166;ENST00000243326;ENST00000430328|ENST00000414861	T;T;T;T;T;T|.	0.65916|.	-0.18;-0.18;-0.18;0.73;-0.18;-0.18|.	5.84|5.84	5.84|5.84	0.93424|0.93424	Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.53818|0.53818	0.1820|0.1820	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;0.999|.	T|T	0.47947|0.47947	-0.9077|-0.9077	10|5	0.87932|.	D|.	0|.	-11.9028|-11.9028	14.5703|14.5703	0.68205|0.68205	0.1463:0.8537:0.0:0.0|0.1463:0.8537:0.0:0.0	.|.	283;283|.	Q5UIP0;Q5UIP0-2|.	RIF1_HUMAN;.|.	C|L	283;283;283;252;283;283|274	ENSP00000390181:R283C;ENSP00000414615:R283C;ENSP00000415691:R283C;ENSP00000396865:R252C;ENSP00000243326:R283C;ENSP00000416123:R283C|.	ENSP00000243326:R283C|.	R|S	+|+	1|2	0|0	RIF1|RIF1	151993604|151993604	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	5.600000|5.600000	0.67599|0.67599	2.760000|2.760000	0.94817|0.94817	0.591000|0.591000	0.81541|0.81541	CGT|TCG	RIF1	-	pfam_Rif1_N,superfamily_ARM-type_fold	ENSG00000080345		0.318	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	RIF1	HGNC	protein_coding	OTTHUMT00000254836.3	379	0.00	0	C			152285358	152285358	+1	no_errors	ENST00000243326	ensembl	human	known	69_37n	missense	187	13.36	29	SNP	1.000	T
RPS6KA1	6195	genome.wustl.edu	37	1	26885310	26885311	+	Frame_Shift_Ins	INS	-	-	C			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr1:26885310_26885311insC	ENST00000374168.2	+	14	1251_1252	c.1097_1098insC	c.(1096-1101)atccccfs	p.IP366fs	RPS6KA1_ENST00000530003.1_Frame_Shift_Ins_p.IP350fs|RPS6KA1_ENST00000526792.1_Frame_Shift_Ins_p.IP274fs|RPS6KA1_ENST00000531382.1_Frame_Shift_Ins_p.IP375fs|RPS6KA1_ENST00000374166.4_Frame_Shift_Ins_p.IP355fs|RPS6KA1_ENST00000374162.2_Frame_Shift_Ins_p.IP274fs	NM_002953.3	NP_002944.2	Q15418	KS6A1_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 1	366	AGC-kinase C-terminal.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of hepatic stellate cell activation (GO:2000491)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|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)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			lung(1)	1		all_cancers(24;2.49e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00571)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.12e-50)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-29)|Colorectal(126;1.4e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000537)|KIRC - Kidney renal clear cell carcinoma(1967;0.000759)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0361)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.161)|LUSC - Lung squamous cell carcinoma(448;0.234)		TCCCCAGGCATCCCCCCCAGCG	0.673																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			BC014966	CCDS284.1, CCDS30649.1	1p	2011-04-05	2002-08-29		ENSG00000117676	ENSG00000117676			10430	protein-coding gene	gene with protein product		601684	"""ribosomal protein S6 kinase, 90kD, polypeptide 1"""			8141249	Standard	NM_001006665		Approved	RSK, RSK1, HU-1	uc001bms.1	Q15418	OTTHUMG00000004003	ENST00000374168.2:c.1104dupC	1.37:g.26885317_26885317dupC	ENSP00000363283:p.Ile366fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NGG4|A8K9K7|B2RDY8|B7Z5J0|Q5SVM5|Q5SVM8|Q5SVM9|Q96C05|Q9BQK2	Frame_Shift_Ins	INS	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_LipoPS_kinase,pfam_Pkinase_C,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_AGC-kinase_C,pirsf_Ribosomal_S6_kinase_II,pfscan_Prot_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom	p.S378fs	ENST00000374168.2	37	c.1124_1125	CCDS284.1	1																																																																																			RPS6KA1	-	pfam_Pkinase_C,smart_AGC-kinase_C,pirsf_Ribosomal_S6_kinase_II	ENSG00000117676		0.673	RPS6KA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RPS6KA1	HGNC	protein_coding	OTTHUMT00000011431.1	28	0.00	0	-	NM_002953		26885310	26885311	+1	no_errors	ENST00000531382	ensembl	human	known	69_37n	frame_shift_ins	17	26.09	6	INS	1.000:0.993	C
RUSC1	23623	genome.wustl.edu	37	1	155295022	155295023	+	Intron	INS	-	-	G			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr1:155295022_155295023insG	ENST00000368352.5	+	4	1684				RUSC1_ENST00000368354.3_Intron|RUSC1-AS1_ENST00000443642.1_RNA|RUSC1_ENST00000462780.1_3'UTR|RUSC1_ENST00000368349.4_Intron|RUSC1_ENST00000368347.4_Intron|RUSC1_ENST00000292254.4_Intron|RUSC1-AS1_ENST00000450199.1_RNA	NM_001105203.1	NP_001098673.1	Q9BVN2	RUSC1_HUMAN	RUN and SH3 domain containing 1						positive regulation of signal transduction (GO:0009967)|protein polyubiquitination (GO:0000209)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(2)|skin(1)|urinary_tract(1)	21	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;1.55e-10)|all cancers(21;4.15e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)			TGGAGCTCCGCGGGGGGTGCGG	0.629											OREG0013860	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			AB026894	CCDS1112.1, CCDS41410.1, CCDS41411.1, CCDS41412.1	1q21-q22	2011-04-28			ENSG00000160753	ENSG00000160753			17153	protein-coding gene	gene with protein product						10760598	Standard	NM_001105203		Approved	NESCA	uc001fkj.2	Q9BVN2	OTTHUMG00000013910	ENST00000368352.5:c.1533+53->G	1.37:g.155295028_155295028dupG		Somatic	1769	WXS	Illumina GAIIx	Phase_IV	B3KWM9|Q5T9U9|Q5T9V0|Q5T9V1|Q5T9V2|Q9UPY4|Q9Y4T5	RNA	INS	-	NULL	ENST00000368352.5	37	NULL	CCDS41410.1	1																																																																																			RUSC1	-	-	ENSG00000160753		0.629	RUSC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	RUSC1	HGNC	protein_coding	OTTHUMT00000039071.1	54	0.00	0	-			155295022	155295023	+1	no_errors	ENST00000462780	ensembl	human	known	69_37n	rna	27	10.00	3	INS	0.001:0.001	G
SMCR8	140775	genome.wustl.edu	37	17	18221216	18221216	+	Frame_Shift_Del	DEL	A	A	-			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr17:18221216delA	ENST00000406438.3	+	1	2593	c.2113delA	c.(2113-2115)aggfs	p.R705fs	TOP3A_ENST00000582230.1_5'Flank|TOP3A_ENST00000542570.1_5'Flank|TOP3A_ENST00000321105.5_5'Flank	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	705						nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21						GCATAAAAAGAGGGCTGGCCA	0.572																																						dbGAP											0													71.0	62.0	65.0					17																	18221216		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0			AF467440	CCDS11195.2	17p11.2	2014-06-12			ENSG00000176994	ENSG00000176994			17921	protein-coding gene	gene with protein product						11997338, 23248642	Standard	NM_144775		Approved	FLJ34716	uc002gsy.4	Q8TEV9	OTTHUMG00000059394	ENST00000406438.3:c.2113delA	17.37:g.18221216delA	ENSP00000385025:p.Arg705fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A5PKZ5|Q3ZCN0|Q6PJL3	Frame_Shift_Del	DEL	pfam_Folliculin	p.R705fs	ENST00000406438.3	37	c.2113	CCDS11195.2	17																																																																																			SMCR8	-	NULL	ENSG00000176994		0.572	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SMCR8	HGNC	protein_coding	OTTHUMT00000132065.2	50	0.00	0	A	NM_144775		18221216	18221216	+1	no_errors	ENST00000406438	ensembl	human	known	69_37n	frame_shift_del	32	36.84	21	DEL	1.000	-
SLC38A10	124565	genome.wustl.edu	37	17	79226469	79226469	+	Missense_Mutation	SNP	C	C	A			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr17:79226469C>A	ENST00000374759.3	-	13	1854	c.1471G>T	c.(1471-1473)Gtg>Ttg	p.V491L	SLC38A10_ENST00000288439.5_Missense_Mutation_p.V491L	NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	491					amino acid transport (GO:0006865)|bone development (GO:0060348)|sodium ion transport (GO:0006814)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			GCCTCGCCCACAGGCACAGCA	0.607																																						dbGAP											0													47.0	40.0	42.0					17																	79226469		2198	4295	6493	-	-	-	SO:0001583	missense	0			BC014642	CCDS11780.1, CCDS42397.1	17q25.3	2013-05-22			ENSG00000157637	ENSG00000157637		"""Solute carriers"""	28237	protein-coding gene	gene with protein product							Standard	XM_005257019		Approved	MGC15523, PP1744	uc002jzz.1	Q9HBR0	OTTHUMG00000168049	ENST00000374759.3:c.1471G>T	17.37:g.79226469C>A	ENSP00000363891:p.Val491Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	Q6ZRC5|Q8NA99|Q96C66	Missense_Mutation	SNP	pfam_AA_transpt_TM	p.V491L	ENST00000374759.3	37	c.1471	CCDS42397.1	17	.	.	.	.	.	.	.	.	.	.	C	11.04	1.520978	0.27211	.	.	ENSG00000157637	ENST00000374759;ENST00000288439	T;T	0.10477	3.03;2.87	4.26	-8.52	0.00920	.	2.980960	0.00769	N	0.001198	T	0.05364	0.0142	N	0.14661	0.345	0.09310	N	0.999999	B;B	0.12013	0.005;0.0	B;B	0.11329	0.006;0.002	T	0.24905	-1.0147	10	0.30854	T	0.27	-6.2294	4.8332	0.13451	0.0899:0.4139:0.3033:0.1928	.	491;491	Q9HBR0-2;Q9HBR0	.;S38AA_HUMAN	L	491	ENSP00000363891:V491L;ENSP00000288439:V491L	ENSP00000288439:V491L	V	-	1	0	SLC38A10	76841064	0.000000	0.05858	0.001000	0.08648	0.068000	0.16541	-0.773000	0.04689	-2.122000	0.00824	-1.073000	0.02249	GTG	SLC38A10	-	NULL	ENSG00000157637		0.607	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	SLC38A10	HGNC	protein_coding	OTTHUMT00000397747.1	11	0.00	0	C	NM_138570		79226469	79226469	-1	no_errors	ENST00000374759	ensembl	human	known	69_37n	missense	10	37.50	6	SNP	0.013	A
SP100	6672	genome.wustl.edu	37	2	231367806	231367806	+	Missense_Mutation	SNP	G	G	C			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr2:231367806G>C	ENST00000264052.5	+	20	2101	c.1746G>C	c.(1744-1746)ttG>ttC	p.L582F	SP100_ENST00000340126.4_Missense_Mutation_p.L582F|SP100_ENST00000409112.1_Missense_Mutation_p.L582F	NM_003113.3	NP_003104.2	P23497	SP100_HUMAN	SP100 nuclear antigen	582					cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cellular component movement (GO:0051271)|negative regulation of DNA binding (GO:0043392)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of Fas signaling pathway (GO:1902044)|response to cytokine (GO:0034097)|response to interferon-gamma (GO:0034341)|response to retinoic acid (GO:0032526)|response to type I interferon (GO:0034340)|retinoic acid receptor signaling pathway (GO:0048384)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear periphery (GO:0034399)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.L582F(2)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(4)|upper_aerodigestive_tract(1)	25		Renal(207;0.0112)|all_lung(227;0.0335)|all_hematologic(139;0.0749)|Lung NSC(271;0.142)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		CTAGACCTTTGAAAAGAAGAA	0.284																																						dbGAP											2	Substitution - Missense(2)	breast(2)											76.0	79.0	78.0					2																	231367806		2203	4299	6502	-	-	-	SO:0001583	missense	0			AF056322	CCDS2477.1, CCDS42832.1, CCDS56170.1, CCDS56171.1, CCDS56172.1, CCDS56173.1	2q37.1	2013-01-28	2005-11-30		ENSG00000067066	ENSG00000067066		"""Zinc fingers, PHD-type"""	11206	protein-coding gene	gene with protein product		604585	"""nuclear antigen Sp100"""			2258622, 8695863	Standard	NM_001080391		Approved		uc002vqu.1	P23497	OTTHUMG00000133203	ENST00000264052.5:c.1746G>C	2.37:g.231367806G>C	ENSP00000264052:p.Leu582Phe	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DDX5|B8ZZD8|E7EUA7|E9PH61|F8WFE2|O75450|Q13343|Q8TE34|Q96F70|Q96T24|Q96T95|Q9NP33|Q9UE32	Missense_Mutation	SNP	pfam_Sp100,pfam_SAND_dom,pfam_Bromodomain,superfamily_SAND_dom-like,superfamily_Bromodomain,superfamily_Znf_FYVE_PHD,smart_SAND_dom,smart_Znf_PHD,smart_Bromodomain,pfscan_Znf_PHD-finger,pfscan_SAND_dom	p.L582F	ENST00000264052.5	37	c.1746	CCDS2477.1	2	.	.	.	.	.	.	.	.	.	.	G	14.39	2.520860	0.44866	.	.	ENSG00000067066	ENST00000264052;ENST00000409112;ENST00000340126;ENST00000414648	T;T;T	0.80033	2.31;-1.33;0.25	4.32	0.437	0.16555	.	0.439657	0.14474	N	0.317387	T	0.77585	0.4152	L	0.27053	0.805	0.18873	N	0.999986	D;D;D	0.69078	0.995;0.997;0.991	D;P;P	0.66497	0.944;0.881;0.881	T	0.64575	-0.6375	10	0.49607	T	0.09	.	3.9968	0.09561	0.3068:0.1862:0.5069:0.0	.	582;582;582	P23497-4;P23497;E7EUA7	.;SP100_HUMAN;.	F	582;582;582;65	ENSP00000264052:L582F;ENSP00000386427:L582F;ENSP00000343023:L582F	ENSP00000264052:L582F	L	+	3	2	SP100	231076050	0.018000	0.18449	0.002000	0.10522	0.682000	0.39822	0.292000	0.19011	0.066000	0.16515	0.563000	0.77884	TTG	SP100	-	NULL	ENSG00000067066		0.284	SP100-001	KNOWN	basic|CCDS	protein_coding	SP100	HGNC	protein_coding	OTTHUMT00000256914.2	207	0.00	0	G	NM_003113		231367806	231367806	+1	no_errors	ENST00000340126	ensembl	human	known	69_37n	missense	39	43.48	30	SNP	0.002	C
STK31	56164	genome.wustl.edu	37	7	23871977	23871977	+	Missense_Mutation	SNP	G	G	C			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr7:23871977G>C	ENST00000355870.3	+	24	3171	c.3052G>C	c.(3052-3054)Gat>Cat	p.D1018H	STK31_ENST00000433467.2_Missense_Mutation_p.D995H|STK31_ENST00000428484.1_Missense_Mutation_p.D995H|STK31_ENST00000405627.3_3'UTR|STK31_ENST00000354639.3_Missense_Mutation_p.D995H	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	1018	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						AGCCAACTTTGATTGTTAAAT	0.313																																						dbGAP											0													52.0	59.0	57.0					7																	23871977		2203	4299	6502	-	-	-	SO:0001583	missense	0			AF285599	CCDS5386.1, CCDS43556.1, CCDS59049.1	7p15.3	2014-04-23			ENSG00000196335	ENSG00000196335		"""Tudor domain containing"""	11407	protein-coding gene	gene with protein product		605790				11279525	Standard	NM_031414		Approved	TDRD8, SgK396	uc003sws.5	Q9BXU1	OTTHUMG00000023053	ENST00000355870.3:c.3052G>C	7.37:g.23871977G>C	ENSP00000348132:p.Asp1018His	Somatic		WXS	Illumina GAIIx	Phase_IV	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Missense_Mutation	SNP	pfam_Tudor,pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Tudor,smart_Ser/Thr_dual-sp_kinase_dom,pfscan_Tudor,pfscan_Prot_kinase_cat_dom	p.D1018H	ENST00000355870.3	37	c.3052	CCDS5386.1	7	.	.	.	.	.	.	.	.	.	.	G	11.23	1.577067	0.28092	.	.	ENSG00000196335	ENST00000355870;ENST00000433467;ENST00000354639;ENST00000428484	T;T;T;T	0.73363	-0.74;0.66;-0.73;-0.73	4.82	2.92	0.33932	Protein kinase, catalytic domain (1);	0.588311	0.16127	N	0.228375	T	0.51736	0.1692	N	0.08118	0	0.09310	N	1	P;P	0.40476	0.718;0.718	B;B	0.39379	0.298;0.298	T	0.47636	-0.9102	10	0.87932	D	0	.	5.2968	0.15756	0.1046:0.0:0.6913:0.2041	.	995;1018	B4DZ06;Q9BXU1	.;STK31_HUMAN	H	1018;995;995;995	ENSP00000348132:D1018H;ENSP00000411852:D995H;ENSP00000346660:D995H;ENSP00000406146:D995H	ENSP00000346660:D995H	D	+	1	0	STK31	23838502	0.996000	0.38824	0.104000	0.21259	0.456000	0.32438	1.359000	0.34113	1.097000	0.41459	0.313000	0.20887	GAT	STK31	-	pfscan_Prot_kinase_cat_dom	ENSG00000196335		0.313	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	STK31	HGNC	protein_coding	OTTHUMT00000214036.2	93	0.00	0	G	NM_031414		23871977	23871977	+1	no_errors	ENST00000355870	ensembl	human	known	69_37n	missense	67	35.58	37	SNP	0.045	C
TMEM247	388946	genome.wustl.edu	37	2	46707888	46707888	+	Frame_Shift_Del	DEL	G	G	-			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr2:46707888delG	ENST00000434431.1	+	2	462	c.462delG	c.(460-462)gagfs	p.E154fs		NM_001145051.2	NP_001138523.1	A6NEH6	TM247_HUMAN	transmembrane protein 247	154						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											TGCAGCAAGAGGCGGCGCCCC	0.682																																						dbGAP											0										59,2867		9,41,1413	15.0	19.0	18.0			1.5	0.0	2	dbSNP_130	19	233,5079		9,215,2432	no	frameshift	LOC388946	NM_001145051.2		18,256,3845	A1A1,A1R,RR		4.3863,2.0164,3.5445			46707888	292,7946	690	1589	2279	-	-	-	SO:0001589	frameshift_variant	0				CCDS56117.1	2p21	2012-04-11			ENSG00000187600	ENSG00000187600			42967	protein-coding gene	gene with protein product							Standard	NM_001145051		Approved		uc010yod.3	A6NEH6	OTTHUMG00000153137	ENST00000434431.1:c.462delG	2.37:g.46707888delG	ENSP00000388684:p.Glu154fs	Somatic		WXS	Illumina GAIIx	Phase_IV		Frame_Shift_Del	DEL	NULL	p.A155fs	ENST00000434431.1	37	c.462	CCDS56117.1	2																																																																																			TMEM247	-	NULL	ENSG00000187600		0.682	TMEM247-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	TMEM247	HGNC	protein_coding	OTTHUMT00000329726.1	28	0.00	0	G	NM_001145051		46707888	46707888	+1	no_stop_codon:bad_bp_length_for_coding_region	ENST00000434431	ensembl	human	known	69_37n	frame_shift_del	16	15.79	3	DEL	0.083	-
TMPRSS6	164656	genome.wustl.edu	37	22	37485669	37485669	+	Missense_Mutation	SNP	C	C	G			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr22:37485669C>G	ENST00000346753.3	-	7	928	c.812G>C	c.(811-813)cGa>cCa	p.R271P	TMPRSS6_ENST00000381792.2_Missense_Mutation_p.R262P|TMPRSS6_ENST00000442782.2_Missense_Mutation_p.R271P|TMPRSS6_ENST00000406856.1_Missense_Mutation_p.R262P|TMPRSS6_ENST00000406725.1_Missense_Mutation_p.R262P	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	271	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.		R -> Q (in IRIDA; does not affect activity). {ECO:0000269|PubMed:20232450}.		angiogenesis (GO:0001525)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|intracellular signal transduction (GO:0035556)|iron ion homeostasis (GO:0055072)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(5)|central_nervous_system(4)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)	40						CATGGCCAGTCGGTCCCGGCA	0.662																																						dbGAP											0													24.0	24.0	24.0					22																	37485669		2202	4300	6502	-	-	-	SO:0001583	missense	0			AY055383	CCDS13941.1, CCDS74856.1, CCDS74857.1	22q13.1	2010-04-13			ENSG00000187045	ENSG00000187045		"""Serine peptidases / Transmembrane"""	16517	protein-coding gene	gene with protein product		609862					Standard	NM_001289000		Approved	FLJ30744	uc003aqs.1	Q8IU80	OTTHUMG00000150541	ENST00000346753.3:c.812G>C	22.37:g.37485669C>G	ENSP00000334962:p.Arg271Pro	Somatic		WXS	Illumina GAIIx	Phase_IV	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Missense_Mutation	SNP	pirsf_Pept_S1A_matriptase-2,pfam_Peptidase_S1_S6,pfam_LDrepeatLR_classA_rpt,pfam_SEA,pfam_Peptidase_S1A_nudel,superfamily_Pept_cys/ser_Trypsin-like,superfamily_CUB,superfamily_LDrepeatLR_classA_rpt,smart_LDrepeatLR_classA_rpt,smart_Peptidase_S1_S6,prints_Peptidase_S1A,pfscan_CUB,pfscan_LDrepeatLR_classA_rpt,pfscan_Peptidase_S1_S6	p.R262P	ENST00000346753.3	37	c.785	CCDS13941.1	22	.	.	.	.	.	.	.	.	.	.	C	19.82	3.899269	0.72754	.	.	ENSG00000187045	ENST00000381792;ENST00000346753;ENST00000406725;ENST00000406856;ENST00000442782	T;T;T;T;T	0.59502	0.26;0.26;0.26;0.26;0.26	4.37	4.37	0.52481	CUB (1);	0.000000	0.85682	D	0.000000	T	0.67915	0.2944	L	0.36672	1.1	0.54753	D	0.999983	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.986;0.968	T	0.70241	-0.4926	10	0.49607	T	0.09	.	17.2674	0.87090	0.0:1.0:0.0:0.0	.	271;262;271	Q8IU80-2;Q8IU80-5;Q8IU80	.;.;TMPS6_HUMAN	P	262;271;262;262;271	ENSP00000371211:R262P;ENSP00000334962:R271P;ENSP00000385453:R262P;ENSP00000384964:R262P;ENSP00000397691:R271P	ENSP00000334962:R271P	R	-	2	0	TMPRSS6	35815615	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.108000	0.64609	2.126000	0.65437	0.462000	0.41574	CGA	TMPRSS6	-	pirsf_Pept_S1A_matriptase-2,superfamily_CUB	ENSG00000187045		0.662	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	TMPRSS6	HGNC	protein_coding	OTTHUMT00000318822.1	21	0.00	0	C	NM_153609		37485669	37485669	-1	no_errors	ENST00000381792	ensembl	human	known	69_37n	missense	14	33.33	7	SNP	1.000	G
TMTC2	160335	genome.wustl.edu	37	12	83526091	83526091	+	Missense_Mutation	SNP	G	G	C			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr12:83526091G>C	ENST00000321196.3	+	12	3141	c.2434G>C	c.(2434-2436)Gat>Cat	p.D812H	TMTC2_ENST00000549919.1_Missense_Mutation_p.D806H	NM_152588.1	NP_689801.1	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat containing 2	812					calcium ion homeostasis (GO:0055074)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)		p.D812H(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|urinary_tract(1)	39						CAAGCCAGACGATGTCATCAC	0.537																																						dbGAP											1	Substitution - Missense(1)	breast(1)											100.0	81.0	88.0					12																	83526091		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK074634	CCDS9025.1	12q21.31	2014-06-09			ENSG00000179104	ENSG00000179104		"""Tetratricopeptide (TTC) repeat domain containing"""	25440	protein-coding gene	gene with protein product		615856				24764305	Standard	NM_152588		Approved	DKFZp762A217	uc001szt.3	Q8N394	OTTHUMG00000169736	ENST00000321196.3:c.2434G>C	12.37:g.83526091G>C	ENSP00000322300:p.Asp812His	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RCU7|Q8N2K8	Missense_Mutation	SNP	pfam_TPR-1,pfam_TPR_2,pfam_DUF1736,pfam_TPR-4,smart_TPR_repeat,pfscan_TPR_repeat,pfscan_TPR-contain_dom	p.D812H	ENST00000321196.3	37	c.2434	CCDS9025.1	12	.	.	.	.	.	.	.	.	.	.	G	14.66	2.600868	0.46423	.	.	ENSG00000179104	ENST00000321196;ENST00000549919;ENST00000546590	T;T	0.65178	-0.14;-0.14	5.33	5.33	0.75918	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.69278	0.3093	L	0.28274	0.84	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.67715	-0.5599	10	0.33940	T	0.23	-15.3046	18.0042	0.89205	0.0:0.0:1.0:0.0	.	812	Q8N394	TMTC2_HUMAN	H	812;806;567	ENSP00000322300:D812H;ENSP00000447609:D806H	ENSP00000322300:D812H	D	+	1	0	TMTC2	82050222	1.000000	0.71417	0.811000	0.32455	0.265000	0.26407	9.804000	0.99143	2.512000	0.84698	0.655000	0.94253	GAT	TMTC2	-	pfam_TPR-1,pfam_TPR_2,smart_TPR_repeat,pfscan_TPR_repeat,pfscan_TPR-contain_dom	ENSG00000179104		0.537	TMTC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	TMTC2	HGNC	protein_coding	OTTHUMT00000405663.1	89	0.00	0	G	NM_152588		83526091	83526091	+1	no_errors	ENST00000321196	ensembl	human	known	69_37n	missense	71	21.11	19	SNP	1.000	C
UBE4A	9354	genome.wustl.edu	37	11	118239367	118239367	+	Missense_Mutation	SNP	A	A	G			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr11:118239367A>G	ENST00000431736.2	+	3	215	c.143A>G	c.(142-144)gAt>gGt	p.D48G	UBE4A_ENST00000252108.3_Missense_Mutation_p.D48G					ubiquitination factor E4A									p.D48G(1)		autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(7)|liver(2)|lung(14)|ovary(3)|prostate(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	56	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		GCTAGCCCAGATGACTCGGAT	0.423																																						dbGAP											1	Substitution - Missense(1)	breast(1)											200.0	202.0	202.0					11																	118239367		2200	4296	6496	-	-	-	SO:0001583	missense	0			D50916	CCDS8396.1, CCDS55790.1	11q23.3	2013-01-28	2011-05-19					"""U-box domain containing"""	12499	protein-coding gene	gene with protein product		603753	"""ubiquitination factor E4A (homologous to yeast UFD2)"", ""ubiquitination factor E4A (UFD2 homolog, yeast)"""			10089879	Standard	NM_004788		Approved	UBOX2, UFD2, KIAA0126, E4	uc001psv.3	Q14139	OTTHUMG00000168100	ENST00000431736.2:c.143A>G	11.37:g.118239367A>G	ENSP00000387362:p.Asp48Gly	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_Ub_conjug_fac_E4_core,pfam_Ubox_domain,smart_Ubox_domain	p.D48G	ENST00000431736.2	37	c.143	CCDS8396.1	11	.	.	.	.	.	.	.	.	.	.	A	16.69	3.193451	0.58017	.	.	ENSG00000110344	ENST00000252108;ENST00000431736	T;T	0.39997	1.05;1.05	5.18	5.18	0.71444	.	0.107942	0.64402	D	0.000006	T	0.36276	0.0961	L	0.38175	1.15	0.80722	D	1	B;B	0.25667	0.131;0.103	B;B	0.28011	0.039;0.085	T	0.13202	-1.0518	10	0.34782	T	0.22	-13.6223	15.1999	0.73126	1.0:0.0:0.0:0.0	.	48;48	Q14139;Q14139-2	UBE4A_HUMAN;.	G	48	ENSP00000252108:D48G;ENSP00000387362:D48G	ENSP00000252108:D48G	D	+	2	0	UBE4A	117744577	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.084000	0.71335	2.186000	0.69663	0.533000	0.62120	GAT	UBE4A	-	NULL	ENSG00000110344		0.423	UBE4A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	UBE4A	HGNC	protein_coding	OTTHUMT00000398143.1	142	0.00	0	A	NM_004788		118239367	118239367	+1	no_errors	ENST00000431736	ensembl	human	known	69_37n	missense	56	41.24	40	SNP	1.000	G
USP11	8237	genome.wustl.edu	37	X	47092577	47092577	+	Silent	SNP	C	C	T			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chrX:47092577C>T	ENST00000218348.3	+	1	264	c.264C>T	c.(262-264)ggC>ggT	p.G88G	USP11_ENST00000377107.2_Silent_p.G45G	NM_004651.3	NP_004642.2	P51784	UBP11_HUMAN	ubiquitin specific peptidase 11	88	DUSP. {ECO:0000255|PROSITE- ProRule:PRU00613}.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)	p.G88G(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|ovary(3)|pancreas(1)|stomach(1)	40						TAGAAAACGGCGAGAGTGGGC	0.687																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											10.0	10.0	10.0					X																	47092577		2151	4237	6388	-	-	-	SO:0001819	synonymous_variant	0			U44839	CCDS14277.1	Xp11.23	2008-02-05	2005-08-08		ENSG00000102226	ENSG00000102226		"""Ubiquitin-specific peptidases"""	12609	protein-coding gene	gene with protein product		300050	"""ubiquitin specific protease 11"""			12838346	Standard	XM_005272674		Approved	UHX1	uc004dhp.3	P51784	OTTHUMG00000021437	ENST00000218348.3:c.264C>T	X.37:g.47092577C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B2RTX1|Q8IUG6|Q9BWE1	Silent	SNP	pfam_Peptidase_C19,pfam_Pept_C19_DUSP,smart_Pept_C19_DUSP,pfscan_Peptidase_C19	p.G88	ENST00000218348.3	37	c.264	CCDS14277.1	X																																																																																			USP11	-	NULL	ENSG00000102226		0.687	USP11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	USP11	HGNC	protein_coding		27	0.00	0	C	NM_004651		47092577	47092577	+1	no_errors	ENST00000218348	ensembl	human	known	69_37n	silent	27	18.18	6	SNP	0.234	T
WAS	7454	genome.wustl.edu	37	X	48547798	48547798	+	Silent	SNP	G	G	A			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chrX:48547798G>A	ENST00000376701.4	+	11	1503	c.1428G>A	c.(1426-1428)aaG>aaA	p.K476K		NM_000377.2	NP_000368.1	P42768	WASP_HUMAN	Wiskott-Aldrich syndrome	476			K -> E (in WAS). {ECO:0000269|PubMed:8528198}.		actin filament polymerization (GO:0030041)|actin filament-based movement (GO:0030048)|actin polymerization or depolymerization (GO:0008154)|blood coagulation (GO:0007596)|defense response (GO:0006952)|endosomal transport (GO:0016197)|epidermis development (GO:0008544)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|protein complex assembly (GO:0006461)|regulation of catalytic activity (GO:0050790)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|vesicle membrane (GO:0012506)	identical protein binding (GO:0042802)|phospholipase binding (GO:0043274)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|small GTPase regulator activity (GO:0005083)	p.K476K(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	28		all_lung(315;1.27e-10)				TGATGCAGAAGAGAAGCAGAG	0.642			"""Mis, N, F, S"""			lymphoma																																dbGAP		X-linked recessive		Wiskott-Aldrich syndrome	X	Xp11.23-p11.22	7454	Wiskott-Aldrich syndrome		L	1	Substitution - coding silent(1)	breast(1)											33.0	33.0	33.0					X																	48547798		2202	4300	6502	-	-	-	SO:0001819	synonymous_variant	0			AF115548	CCDS14303.1	Xp11.4-p11.21	2014-09-17	2012-07-12		ENSG00000015285	ENSG00000015285			12731	protein-coding gene	gene with protein product	"""eczema-thrombocytopenia"""	300392	"""thrombocytopenia 1 (X-linked)"", ""Wiskott-Aldrich syndrome (eczema-thrombocytopenia)"""	IMD2, THC		7795648	Standard	NM_000377		Approved	WASP	uc004dkm.4	P42768	OTTHUMG00000034483	ENST00000376701.4:c.1428G>A	X.37:g.48547798G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q9BU11|Q9UNJ9	Silent	SNP	pfam_EVH1,pfam_PAK_box_Rho-bd,pfam_WH2_dom,superfamily_WASP_C,smart_EVH1,smart_PAK_box_Rho-bd,smart_WH2_dom,pfscan_PAK_box_Rho-bd,pfscan_EVH1,pfscan_WH2_dom	p.K476	ENST00000376701.4	37	c.1428	CCDS14303.1	X																																																																																			WAS	-	superfamily_WASP_C	ENSG00000015285		0.642	WAS-007	KNOWN	basic|appris_principal|CCDS	protein_coding	WAS	HGNC	protein_coding	OTTHUMT00000083379.1	159	0.00	0	G	NM_000377		48547798	48547798	+1	no_errors	ENST00000376701	ensembl	human	known	69_37n	silent	328	18.20	73	SNP	1.000	A
TBC1D31	93594	genome.wustl.edu	37	8	124162367	124162367	+	Splice_Site	SNP	G	G	A			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr8:124162367G>A	ENST00000287380.1	+	21	3156	c.3066G>A	c.(3064-3066)caG>caA	p.Q1022Q	TBC1D31_ENST00000327098.5_Splice_Site_p.Q926Q|TBC1D31_ENST00000378080.2_3'UTR|TBC1D31_ENST00000521676.1_Splice_Site_p.Q899Q|TBC1D31_ENST00000518805.1_Splice_Site_p.Q576Q|TBC1D31_ENST00000309336.3_Splice_Site_p.Q957Q|TBC1D31_ENST00000522420.1_Splice_Site_p.Q917Q	NM_145647.3	NP_663622.2	Q96DN5	TBC31_HUMAN	TBC1 domain family, member 31	1022						centrosome (GO:0005813)	Rab GTPase activator activity (GO:0005097)	p.Q1022Q(1)									CCTCAACACAGAGTAAGTTGA	0.343																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											69.0	63.0	65.0					8																	124162367		2203	4300	6503	-	-	-	SO:0001630	splice_region_variant	0			AK094612	CCDS6338.1, CCDS47916.1	8q24.13	2013-07-10	2013-07-10	2013-07-10	ENSG00000156787	ENSG00000156787		"""WD repeat domain containing"""	30888	protein-coding gene	gene with protein product			"""WD repeat domain 67"""	WDR67		12477932	Standard	NM_001145088		Approved	MGC21654, Gm85	uc003ypp.2	Q96DN5	OTTHUMG00000165081	ENST00000287380.1:c.3067+1G>A	8.37:g.124162367G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B7ZL19|Q2M2J9|Q3MIR6|Q8TBP9	Silent	SNP	pfam_Rab-GTPase-TBC_dom,pfam_WD40_repeat,superfamily_WD40_repeat_dom,superfamily_Rab-GTPase-TBC_dom,smart_WD40_repeat,pfscan_Rab-GTPase-TBC_dom,pfscan_WD40_repeat_dom	p.Q1022	ENST00000287380.1	37	c.3066	CCDS6338.1	8																																																																																			WDR67	-	NULL	ENSG00000156787		0.343	TBC1D31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	WDR67	HGNC	protein_coding	OTTHUMT00000381721.1	106	0.00	0	G	NM_145647	Silent	124162367	124162367	+1	no_errors	ENST00000287380	ensembl	human	known	69_37n	silent	71	22.58	21	SNP	0.000	A
WHAMMP3	339005	genome.wustl.edu	37	15	23201529	23201529	+	RNA	SNP	G	G	C			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr15:23201529G>C	ENST00000400153.2	-	0	923					NR_003521.1		Q1A5X7	WHAL1_HUMAN	WAS protein homolog associated with actin, golgi membranes and microtubules pseudogene 3																		AATTCACTGTGATATCTTGAA	0.393																																						dbGAP											0																																										-	-	-			0			BC048987		15q11.2	2014-03-20	2011-06-24	2011-06-24	ENSG00000187667	ENSG00000276141			27892	pseudogene	pseudogene			"""WAS protein homology region 2 domain containing 1-like 1"", ""WAS protein homolog associated with actin, golgi membranes and microtubules-like 1"", ""WAS protein homolog associated with actin, golgi membranes and microtubules-like 1 (pseudogene)"""	WHDC1L1, WHAMML1		18226259	Standard	NR_003521		Approved		uc001yvg.3	Q1A5X7	OTTHUMG00000171921		15.37:g.23201529G>C		Somatic		WXS	Illumina GAIIx	Phase_IV	Q1A5X8|Q52M16|Q52M18	RNA	SNP	-	NULL	ENST00000400153.2	37	NULL		15																																																																																			WHAMMP3	-	-	ENSG00000187667		0.393	WHAMMP3-001	KNOWN	basic	processed_transcript	WHAMMP3	HGNC	pseudogene	OTTHUMT00000415907.1	52	0.00	0	G	NR_003521		23201529	23201529	-1	no_errors	ENST00000400153	ensembl	human	known	69_37n	rna	38	24.00	12	SNP	1.000	C
ZAN	7455	genome.wustl.edu	37	7	100365499	100365499	+	RNA	SNP	C	C	T	rs545917447		TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr7:100365499C>T	ENST00000348028.3	+	0	5071				ZAN_ENST00000443370.1_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000542585.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000427578.1_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R1636W(2)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			TGCACAAGGCCGGGTGACCAT	0.577																																						dbGAP											2	Substitution - Missense(2)	breast(2)																																								-	-	-			0			U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"""zonadhesin"""			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100365499C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Missense_Mutation	SNP	pfam_VWF_type-D,pfam_MAM_dom,pfam_Unchr_dom_Cys-rich,pfam_TIL_dom,superfamily_ConA-like_lec_gl,superfamily_TIL_dom,smart_MAM_dom,smart_VWC_out,smart_VWF_type-D,smart_Unchr_dom_Cys-rich,smart_EGF-like,pfscan_EG-like_dom,pfscan_MAM_dom	p.R1636W	ENST00000348028.3	37	c.4906		7	.	.	.	.	.	.	.	.	.	.	C	19.84	3.901866	0.72754	.	.	ENSG00000146839	ENST00000546292;ENST00000538115;ENST00000542585;ENST00000546213	T;T;T;T	0.60299	0.2;0.2;0.2;0.2	4.57	3.67	0.42095	von Willebrand factor, type D domain (3);	0.885934	0.09367	N	0.811871	T	0.76176	0.3951	M	0.87971	2.92	0.21719	N	0.999576	D;D	0.76494	0.999;0.999	P;P	0.60886	0.809;0.88	T	0.62205	-0.6903	10	0.87932	D	0	.	10.5823	0.45263	0.1935:0.8065:0.0:0.0	.	1636;1636	F5H0T8;Q9Y493	.;ZAN_HUMAN	W	1636;1636;1636;213	ENSP00000445943:R1636W;ENSP00000445091:R1636W;ENSP00000444427:R1636W;ENSP00000441117:R213W	ENSP00000423579:R1636W	R	+	1	2	ZAN	100203435	0.000000	0.05858	0.139000	0.22197	0.010000	0.07245	-0.021000	0.12504	1.208000	0.43306	0.655000	0.94253	CGG	ZAN	-	pfam_VWF_type-D,smart_VWF_type-D	ENSG00000146839		0.577	ZAN-006	KNOWN	basic	polymorphic_pseudogene	ZAN	HGNC	polymorphic_pseudogene	OTTHUMT00000347214.1	65	0.00	0	C	NM_003386		100365499	100365499	+1	no_errors	ENST00000546292	ensembl	human	known	69_37n	missense	137	14.29	23	SNP	0.683	T
ZFHX3	463	genome.wustl.edu	37	16	72993144	72993144	+	Missense_Mutation	SNP	C	C	T			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr16:72993144C>T	ENST00000268489.5	-	2	1573	c.901G>A	c.(901-903)Gcg>Acg	p.A301T	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	301					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.A301T(1)		NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				TCATGCACCGCGTGGGTCACA	0.493																																						dbGAP											1	Substitution - Missense(1)	breast(1)											88.0	78.0	81.0					16																	72993144		2198	4300	6498	-	-	-	SO:0001583	missense	0			D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.901G>A	16.37:g.72993144C>T	ENSP00000268489:p.Ala301Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	pfam_Homeodomain,superfamily_Homeodomain-like,superfamily_Adenylate_cyclase-assoc_CAP_N,smart_Znf_C2H2-like,smart_Znf_U1,smart_Homeodomain,pfscan_Homeodomain,pfscan_Znf_C2H2	p.A301T	ENST00000268489.5	37	c.901	CCDS10908.1	16	.	.	.	.	.	.	.	.	.	.	C	15.66	2.897836	0.52227	.	.	ENSG00000140836	ENST00000268489	D	0.91011	-2.77	4.51	4.51	0.55191	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.000000	0.48286	D	0.000181	D	0.94918	0.8357	M	0.75085	2.285	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.95251	0.8360	10	0.56958	D	0.05	.	17.5869	0.87984	0.0:1.0:0.0:0.0	.	301	Q15911	ZFHX3_HUMAN	T	301	ENSP00000268489:A301T	ENSP00000268489:A301T	A	-	1	0	ZFHX3	71550645	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.398000	0.79919	2.235000	0.73313	0.491000	0.48974	GCG	ZFHX3	-	smart_Znf_C2H2-like	ENSG00000140836		0.493	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZFHX3	HGNC	protein_coding	OTTHUMT00000269008.1	87	0.00	0	C	NM_006885		72993144	72993144	-1	no_errors	ENST00000268489	ensembl	human	known	69_37n	missense	24	25.00	8	SNP	1.000	T
ZNF192P1	651302	genome.wustl.edu	37	6	28135014	28135014	+	RNA	SNP	G	G	A			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chr6:28135014G>A	ENST00000440790.2	+	0	1117					NR_103448.1				zinc finger protein 192 pseudogene 1																		AGATCTCAACGCTTATTCATC	0.438																																						dbGAP											0													84.0	80.0	81.0					6																	28135014		692	1591	2283	-	-	-			0					6p22.1	2012-10-05	2011-08-31	2011-08-31	ENSG00000226314	ENSG00000226314			18777	pseudogene	pseudogene	"""zinc finger protein 389, pseudogene"""		"""zinc finger protein 389"""	ZNF389			Standard	NR_103448		Approved	dJ265C24.4, ZNF389P	uc021yrq.2		OTTHUMG00000014513		6.37:g.28135014G>A		Somatic		WXS	Illumina GAIIx	Phase_IV		RNA	SNP	-	NULL	ENST00000440790.2	37	NULL		6																																																																																			ZNF192P1	-	-	ENSG00000226314		0.438	ZNF192P1-001	KNOWN	basic	processed_transcript	ZNF192P1	HGNC	pseudogene	OTTHUMT00000040181.1	179	0.00	0	G			28135014	28135014	+1	no_errors	ENST00000440790	ensembl	human	known	69_37n	rna	170	19.72	42	SNP	0.000	A
ZNF75D	7626	genome.wustl.edu	37	X	134427818	134427818	+	Silent	SNP	G	G	A			TCGA-B6-A0IO-01A-11W-A050-09	TCGA-B6-A0IO-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	648cee86-f2e7-45a0-abf2-0ab0037e2eee	ffcf5f3e-608f-4d7d-ac3a-b79a45325ff4	g.chrX:134427818G>A	ENST00000370766.3	-	3	2958	c.249C>T	c.(247-249)caC>caT	p.H83H	ZNF75D_ENST00000494295.1_Intron|ZNF75D_ENST00000370764.1_Silent_p.H83H	NM_007131.3	NP_009062.2	P51815	ZN75D_HUMAN	zinc finger protein 75D	83	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.H83H(1)		autonomic_ganglia(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(14)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						GCTCTTTTGAGTGGATCTCTG	0.507																																						dbGAP											1	Substitution - coding silent(1)	breast(1)											79.0	70.0	73.0					X																	134427818		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			S43109	CCDS14648.1, CCDS55503.1	Xq26	2013-01-09	2008-06-11	2008-06-11	ENSG00000186376	ENSG00000186376		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13145	protein-coding gene	gene with protein product		314997	"""zinc finger protein 75 (D8C6)"""	ZNF82, ZNF75		1505955	Standard	XM_005262469		Approved	ZKSCAN24, D8C6, ZSCAN28	uc004eyo.3	P51815	OTTHUMG00000022482	ENST00000370766.3:c.249C>T	X.37:g.134427818G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	A6NK62|B3KRI7|Q5JPG0|Q6LDE0	Silent	SNP	pfam_Tscrpt_reg_SCAN,pfam_Znf_C2H2,pfam_Krueppel-associated_box,superfamily_Retrov_capsid_C,superfamily_Krueppel-associated_box,smart_Tscrpt_reg_SCAN,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box,pfscan_Tscrpt_reg_SCAN	p.H83	ENST00000370766.3	37	c.249	CCDS14648.1	X																																																																																			ZNF75D	-	pfam_Tscrpt_reg_SCAN,superfamily_Retrov_capsid_C,smart_Tscrpt_reg_SCAN,pfscan_Tscrpt_reg_SCAN	ENSG00000186376		0.507	ZNF75D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ZNF75D	HGNC	protein_coding	OTTHUMT00000058415.1	82	0.00	0	G	NM_007131		134427818	134427818	-1	no_errors	ENST00000370766	ensembl	human	known	69_37n	silent	73	13.10	11	SNP	0.135	A
