#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
ABCA8	10351	genome.wustl.edu	37	17	66925817	66925817	+	Missense_Mutation	SNP	C	C	A			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr17:66925817C>A	ENST00000269080.2	-	7	961	c.824G>T	c.(823-825)gGt>gTt	p.G275V	ABCA8_ENST00000430352.2_Missense_Mutation_p.G275V|ABCA8_ENST00000586539.1_Missense_Mutation_p.G275V	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	275					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					GAAGATGAAACCAGCATAGAG	0.383																																						dbGAP											0													85.0	80.0	81.0					17																	66925817		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"""ATP binding cassette transporters / subfamily A"""	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.824G>T	17.37:g.66925817C>A	ENSP00000269080:p.Gly275Val	Somatic		WXS	Illumina GAIIx	Phase_IV	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	pfam_ABC_transporter-like,smart_AAA+_ATPase,pfscan_ABC_transporter-like	p.G275V	ENST00000269080.2	37	c.824	CCDS11680.1	17	.	.	.	.	.	.	.	.	.	.	C	10.07	1.248806	0.22880	.	.	ENSG00000141338	ENST00000269080;ENST00000430352;ENST00000541225	D;D	0.86097	-2.07;-2.07	4.75	1.46	0.22682	.	0.398001	0.20946	N	0.082838	T	0.76241	0.3960	L	0.27053	0.805	0.21220	N	0.999757	B;B;B;B;B	0.24675	0.071;0.109;0.002;0.011;0.029	B;B;B;B;B	0.37451	0.106;0.25;0.006;0.059;0.084	T	0.61192	-0.7112	10	0.17369	T	0.5	.	8.0578	0.30614	0.4847:0.3707:0.1446:0.0	.	214;275;275;275;275	F5H6Z4;A1L3U3;B4DJ11;C9JQE6;O94911	.;.;.;.;ABCA8_HUMAN	V	275;275;214	ENSP00000269080:G275V;ENSP00000402814:G275V	ENSP00000269080:G275V	G	-	2	0	ABCA8	64437412	0.000000	0.05858	0.068000	0.19968	0.986000	0.74619	-0.583000	0.05807	0.250000	0.21479	0.591000	0.81541	GGT	ABCA8	-	NULL	ENSG00000141338		0.383	ABCA8-001	KNOWN	basic|CCDS	protein_coding	ABCA8	HGNC	protein_coding	OTTHUMT00000450172.1	336	0.00	0	C	NM_007168		66925817	66925817	-1	no_errors	ENST00000430352	ensembl	human	known	69_37n	missense	217	28.85	88	SNP	0.025	A
ANKRD20A4	728747	genome.wustl.edu	37	9	69421983	69421983	+	Missense_Mutation	SNP	G	G	C			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr9:69421983G>C	ENST00000357336.3	+	14	1728	c.1447G>C	c.(1447-1449)Gtt>Ctt	p.V483L		NM_001098805.1	NP_001092275.1	Q4UJ75	A20A4_HUMAN	ankyrin repeat domain 20 family, member A4	483										breast(1)|large_intestine(1)|liver(1)|lung(9)|pancreas(2)|skin(2)	16						TGAACCAACTGTTCAGTCACT	0.279																																						dbGAP											0																																										-	-	-	SO:0001583	missense	0				CCDS43828.1	9q21.11	2013-01-10			ENSG00000172014	ENSG00000172014		"""Ankyrin repeat domain containing"""	31982	protein-coding gene	gene with protein product							Standard	NM_001098805		Approved	OTTHUMG00000066855	uc004afn.3	Q4UJ75	OTTHUMG00000066855	ENST00000357336.3:c.1447G>C	9.37:g.69421983G>C	ENSP00000349891:p.Val483Leu	Somatic		WXS	Illumina GAIIx	Phase_IV		Missense_Mutation	SNP	pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,prints_Ankyrin_rpt	p.V483L	ENST00000357336.3	37	c.1447	CCDS43828.1	9	.	.	.	.	.	.	.	.	.	.	G	0.006	-2.106205	0.00356	.	.	ENSG00000172014	ENST00000357336	T	0.14144	2.53	2.26	1.3	0.21679	.	.	.	.	.	T	0.05273	0.0140	N	0.12527	0.23	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.43376	-0.9395	9	0.02654	T	1	.	4.462	0.11671	0.2504:0.49:0.2596:0.0	.	483	Q4UJ75	A20A4_HUMAN	L	483	ENSP00000349891:V483L	ENSP00000349891:V483L	V	+	1	0	ANKRD20A4	68711803	0.000000	0.05858	0.002000	0.10522	0.011000	0.07611	-0.043000	0.12043	0.254000	0.21573	0.184000	0.17185	GTT	ANKRD20A4	-	NULL	ENSG00000172014		0.279	ANKRD20A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ANKRD20A4	HGNC	protein_coding	OTTHUMT00000143287.3	32	0.00	0	G	NM_001098805		69421983	69421983	+1	no_errors	ENST00000357336	ensembl	human	known	69_37n	missense	29	19.44	7	SNP	0.004	C
ARMCX1	51309	genome.wustl.edu	37	X	100808906	100808907	+	Frame_Shift_Ins	INS	-	-	T			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chrX:100808906_100808907insT	ENST00000372829.3	+	4	1364_1365	c.993_994insT	c.(994-996)tttfs	p.F332fs		NM_016608.1	NP_057692.1	Q9P291	ARMX1_HUMAN	armadillo repeat containing, X-linked 1	332						integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(2)|ovary(3)|pancreas(1)|urinary_tract(1)	19						CTTTTCCAGACTTTTTTGCTTT	0.391																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AB039670	CCDS14487.1	Xq21.33-q22.2	2014-03-21			ENSG00000126947	ENSG00000126947		"""Armadillo repeat containing"""	18073	protein-coding gene	gene with protein product		300362				11162520, 16221301, 22569362	Standard	NM_016608		Approved	ALEX1, GASP7	uc004ehv.3	Q9P291	OTTHUMG00000022033	ENST00000372829.3:c.999dupT	X.37:g.100808912_100808912dupT	ENSP00000361917:p.Phe332fs	Somatic		WXS	Illumina GAIIx	Phase_IV	Q53HK2|Q9H2Q0	Frame_Shift_Ins	INS	pfam_ARM-rpt_dom,superfamily_ARM-type_fold,smart_Armadillo,pfscan_Armadillo	p.A333fs	ENST00000372829.3	37	c.993_994	CCDS14487.1	X																																																																																			ARMCX1	-	pfam_ARM-rpt_dom,superfamily_ARM-type_fold	ENSG00000126947		0.391	ARMCX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ARMCX1	HGNC	protein_coding	OTTHUMT00000057561.1	417	0.00	0	-	NM_016608		100808906	100808907	+1	no_errors	ENST00000372829	ensembl	human	known	69_37n	frame_shift_ins	408	18.07	90	INS	0.997:0.998	T
BMX	660	genome.wustl.edu	37	X	15540601	15540601	+	Nonsense_Mutation	SNP	C	C	T			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chrX:15540601C>T	ENST00000357607.2	+	7	831	c.643C>T	c.(643-645)Caa>Taa	p.Q215*	BMX_ENST00000342014.6_Nonsense_Mutation_p.Q215*|BMX_ENST00000348343.6_Nonsense_Mutation_p.Q215*			P51813	BMX_HUMAN	BMX non-receptor tyrosine kinase	215					apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to stress (GO:0006950)|signal transduction (GO:0007165)	cytosol (GO:0005829)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(14)|ovary(2)|urinary_tract(3)	30	Hepatocellular(33;0.183)					CAGTCTAGCGCAATATGACAG	0.438																																						dbGAP											0													126.0	104.0	111.0					X																	15540601		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AF045459	CCDS14168.1	Xp22.2	2013-05-14			ENSG00000102010	ENSG00000102010		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	1079	protein-coding gene	gene with protein product	"""BTK-like on X chromosome"""	300101				7970727	Standard	NM_203281		Approved	ETK, PSCTK3	uc004cwx.4	P51813	OTTHUMG00000021180	ENST00000357607.2:c.643C>T	X.37:g.15540601C>T	ENSP00000350224:p.Gln215*	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NIH9|O60564|Q12871	Nonsense_Mutation	SNP	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_cat_dom,pfam_SH2,pfam_Pleckstrin_homology,pfam_Znf_Btk_motif,superfamily_Kinase-like_dom,smart_Pleckstrin_homology,smart_Znf_Btk_motif,smart_SH2,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom,prints_SH2,prints_Znf_Btk_motif,pfscan_Pleckstrin_homology,pfscan_SH2,pfscan_Znf_Btk_motif,pfscan_Prot_kinase_cat_dom	p.Q215*	ENST00000357607.2	37	c.643	CCDS14168.1	X	.	.	.	.	.	.	.	.	.	.	C	17.28	3.350806	0.61183	.	.	ENSG00000102010	ENST00000357607;ENST00000348343;ENST00000342014	.	.	.	2.63	1.73	0.24493	.	0.420242	0.22606	N	0.057898	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	.	6.1136	0.20114	0.2993:0.7007:0.0:0.0	.	.	.	.	X	215	.	ENSP00000340082:Q215X	Q	+	1	0	BMX	15450522	0.612000	0.27000	0.005000	0.12908	0.117000	0.20001	0.183000	0.16919	0.502000	0.28037	0.292000	0.19580	CAA	BMX	-	NULL	ENSG00000102010		0.438	BMX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	BMX	HGNC	protein_coding	OTTHUMT00000055877.1	631	0.31	2	C	NM_001721		15540601	15540601	+1	no_errors	ENST00000342014	ensembl	human	known	69_37n	nonsense	432	33.64	219	SNP	0.005	T
C4orf6	10141	genome.wustl.edu	37	4	5528055	5528055	+	Silent	SNP	A	A	G			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr4:5528055A>G	ENST00000195455.2	+	2	454	c.279A>G	c.(277-279)caA>caG	p.Q93Q	C4orf6_ENST00000515342.1_3'UTR	NM_005750.2	NP_005741.1	Q99440	CD006_HUMAN	chromosome 4 open reading frame 6	93					nervous system development (GO:0007399)					large_intestine(1)|prostate(1)	2						CAGTGCATCAATGAAGGTAAC	0.423																																						dbGAP											0													88.0	82.0	84.0					4																	5528055		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			D82070	CCDS3381.1	4p16	2012-02-24			ENSG00000082929	ENSG00000082929			13716	protein-coding gene	gene with protein product						9016955	Standard	NM_005750		Approved	aC1	uc003gii.3	Q99440	OTTHUMG00000125492	ENST00000195455.2:c.279A>G	4.37:g.5528055A>G		Somatic		WXS	Illumina GAIIx	Phase_IV	Q17R65	Missense_Mutation	SNP	NULL	p.M81V	ENST00000195455.2	37	c.241	CCDS3381.1	4	.	.	.	.	.	.	.	.	.	.	A	1.792	-0.479310	0.04383	.	.	ENSG00000082929	ENST00000505296	.	.	.	1.51	0.314	0.15847	.	.	.	.	.	T	0.22126	0.0533	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.23904	-1.0175	4	.	.	.	.	3.2671	0.06869	0.7624:0.0:0.2376:0.0	.	.	.	.	V	81	.	.	M	+	1	0	C4orf6	5578956	0.001000	0.12720	0.018000	0.16275	0.091000	0.18340	-0.128000	0.10531	0.076000	0.16826	0.379000	0.24179	ATG	C4orf6	-	NULL	ENSG00000082929		0.423	C4orf6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C4orf6	HGNC	protein_coding	OTTHUMT00000246818.1	126	0.00	0	A	NM_005750		5528055	5528055	+1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000505296	ensembl	human	novel	69_37n	missense	93	34.04	48	SNP	0.024	G
CCDC88A	55704	genome.wustl.edu	37	2	55549817	55549818	+	Frame_Shift_Ins	INS	-	-	T			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr2:55549817_55549818insT	ENST00000436346.1	-	18	3849_3850	c.3008_3009insA	c.(3007-3009)aatfs	p.N1003fs	CCDC88A_ENST00000336838.6_Frame_Shift_Ins_p.N1002fs|AC012358.8_ENST00000599352.1_RNA|CCDC88A_ENST00000413716.2_Frame_Shift_Ins_p.N1002fs|AC012358.8_ENST00000608103.1_RNA|AC012358.8_ENST00000599475.1_RNA|AC012358.8_ENST00000600219.1_RNA|AC012358.8_ENST00000594078.1_RNA|CCDC88A_ENST00000263630.8_Frame_Shift_Ins_p.N1003fs	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	1003					activation of protein kinase B activity (GO:0032148)|cell migration (GO:0016477)|DNA replication (GO:0006260)|lamellipodium assembly (GO:0030032)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell proliferation (GO:0042127)|regulation of DNA replication (GO:0006275)|regulation of neuron projection development (GO:0010975)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|microtubule binding (GO:0008017)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)|protein kinase B binding (GO:0043422)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(22)|lung(23)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	69						GAGCTTCATAATTTTTTTTCAC	0.351																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AB033038, AF112218	CCDS33203.1, CCDS46288.1, CCDS58710.1	2p16.3	2013-03-13	2007-05-31	2007-05-31	ENSG00000115355	ENSG00000115355			25523	protein-coding gene	gene with protein product	"""Galpha-interacting vesicle-associated protein"", ""Akt-phosphorylation enhancer"", ""girdin"", ""girders of actin filaments"""	609736	"""KIAA1212"""	KIAA1212		15749703, 15753085	Standard	NM_001135597		Approved	FLJ10392, APE, GIV, HkRP1, GRDN	uc002ryv.2	Q3V6T2	OTTHUMG00000151915	ENST00000436346.1:c.3009dupA	2.37:g.55549825_55549825dupT	ENSP00000410608:p.Asn1003fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	Frame_Shift_Ins	INS	pfam_HOOK,superfamily_Prefoldin,superfamily_t-SNARE	p.N1003fs	ENST00000436346.1	37	c.3009_3008		2																																																																																			CCDC88A	-	NULL	ENSG00000115355		0.351	CCDC88A-203	KNOWN	basic	protein_coding	CCDC88A	HGNC	protein_coding		107	0.00	0	-	NM_017571		55549817	55549818	-1	no_errors	ENST00000436346	ensembl	human	known	69_37n	frame_shift_ins	93	20.51	24	INS	1.000:1.000	T
CTC1	80169	genome.wustl.edu	37	17	8141861	8141861	+	Missense_Mutation	SNP	C	C	G			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr17:8141861C>G	ENST00000315684.8	-	3	291	c.284G>C	c.(283-285)tGg>tCg	p.W95S	CTC1_ENST00000581671.1_5'UTR	NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	95					bone marrow development (GO:0048539)|cellular response to DNA damage stimulus (GO:0006974)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organism growth (GO:0035264)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|replicative senescence (GO:0090399)|spleen development (GO:0048536)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)|thymus development (GO:0048538)	nuclear chromosome, telomeric region (GO:0000784)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|skin(4)	29						CTCTTGGGCCCAGGCCTGGTA	0.567																																						dbGAP											0													88.0	89.0	89.0					17																	8141861		2021	4177	6198	-	-	-	SO:0001583	missense	0			AL831955	CCDS42259.1	17p13.1	2011-02-21	2011-02-21	2011-02-21	ENSG00000178971	ENSG00000178971			26169	protein-coding gene	gene with protein product	"""conserved telomere maintenance component 1"", ""alpha accessory factor 132"", ""conserved telomere capping protein 1"""	613129	"""tmp494178"", ""chromosome 17 open reading frame 68"""	C17orf68		19854130, 19854131	Standard	NM_025099		Approved	FLJ22170, AAF132	uc002gkq.4	Q2NKJ3		ENST00000315684.8:c.284G>C	17.37:g.8141861C>G	ENSP00000313759:p.Trp95Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Missense_Mutation	SNP	NULL	p.W95S	ENST00000315684.8	37	c.284	CCDS42259.1	17	.	.	.	.	.	.	.	.	.	.	C	17.40	3.380776	0.61845	.	.	ENSG00000178971	ENST00000315684;ENST00000449476	D;D	0.86432	-2.12;-2.12	5.94	4.95	0.65309	.	0.076403	0.56097	D	0.000029	D	0.91616	0.7351	M	0.70595	2.14	0.58432	D	0.999998	D	0.61080	0.989	D	0.63957	0.92	D	0.92132	0.5713	10	0.72032	D	0.01	-9.1169	12.2694	0.54697	0.1695:0.8305:0.0:0.0	.	95	Q2NKJ3	CTC1_HUMAN	S	95	ENSP00000313759:W95S;ENSP00000396018:W95S	ENSP00000313759:W95S	W	-	2	0	CTC1	8082586	1.000000	0.71417	0.922000	0.36590	0.767000	0.43475	4.899000	0.63245	1.462000	0.47948	0.561000	0.74099	TGG	CTC1	-	NULL	ENSG00000178971		0.567	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	CTC1	HGNC	protein_coding	OTTHUMT00000442012.1	95	0.00	0	C	NM_025099		8141861	8141861	-1	no_errors	ENST00000315684	ensembl	human	known	69_37n	missense	94	14.55	16	SNP	0.987	G
CYP11B1	1584	genome.wustl.edu	37	8	143959174	143959174	+	Intron	SNP	T	T	C	rs75717953	byFrequency	TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr8:143959174T>C	ENST00000292427.4	-	3	428				CYP11B1_ENST00000517471.1_Intron|CYP11B1_ENST00000377675.3_Splice_Site_p.R203G	NM_000497.3	NP_000488.3	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 1						aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|glucocorticoid biosynthetic process (GO:0006704)|glucose homeostasis (GO:0042593)|immune response (GO:0006955)|mineralocorticoid biosynthetic process (GO:0006705)|regulation of blood pressure (GO:0008217)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(36)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	67	all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Cimetidine(DB00501)|Clotrimazole(DB00257)|Etomidate(DB00292)|Fluconazole(DB00196)|Hydrocortisone(DB00741)|Ketoconazole(DB01026)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Miconazole(DB01110)|Mitotane(DB00648)|Phenytoin(DB00252)|Spironolactone(DB00421)	CATCCTCACCTACAGCCAGAG	0.557									Familial Hyperaldosteronism type I																													dbGAP											0													61.0	58.0	59.0					8																	143959174		876	1991	2867	-	-	-	SO:0001627	intron_variant	0	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	D16153	CCDS6392.1, CCDS34953.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000160882	ENSG00000160882	1.14.15.4	"""Cytochrome P450s"""	2591	protein-coding gene	gene with protein product	"""steroid 11-beta-monooxygenase"""	610613	"""cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 1"""	CYP11B		1303253	Standard	XM_005250807		Approved	P450C11, FHI, CPN1	uc003yxi.3	P15538	OTTHUMG00000164637	ENST00000292427.4:c.396-536A>G	8.37:g.143959174T>C		Somatic		WXS	Illumina GAIIx	Phase_IV	Q14095|Q4VAQ8|Q4VAQ9|Q9UML2	Missense_Mutation	SNP	pfam_Cyt_P450,superfamily_Cyt_P450,prints_Cyt_P450_E_grp-IV,prints_Cyt_P450_E_grp-I,prints_Cyt_P450_B,prints_Cyt_P450	p.R203G	ENST00000292427.4	37	c.607	CCDS6392.1	8	.	.	.	.	.	.	.	.	.	.	.	5.217	0.225576	0.09916	.	.	ENSG00000160882	ENST00000377675	T	0.68181	-0.31	1.6	-3.2	0.05156	.	.	.	.	.	T	0.46151	0.1378	.	.	.	0.19300	N	0.99998	B	0.02656	0.0	B	0.01281	0.0	T	0.12708	-1.0537	8	0.42905	T	0.14	.	1.1804	0.01844	0.156:0.3861:0.2612:0.1967	.	203	Q4VAR0	.	G	203	ENSP00000366903:R203G	ENSP00000366903:R203G	R	-	1	2	CYP11B1	143956176	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.158000	0.10070	-2.403000	0.00577	-1.307000	0.01316	AGG	CYP11B1	-	superfamily_Cyt_P450	ENSG00000160882		0.557	CYP11B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CYP11B1	HGNC	protein_coding	OTTHUMT00000379475.2	40	0.00	0	T			143959174	143959174	-1	no_errors	ENST00000377675	ensembl	human	novel	69_37n	missense	31	22.50	9	SNP	0.000	C
ERBB4	2066	genome.wustl.edu	37	2	212248393	212248393	+	Missense_Mutation	SNP	G	G	A			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr2:212248393G>A	ENST00000342788.4	-	28	4184	c.3874C>T	c.(3874-3876)Cca>Tca	p.P1292S	ERBB4_ENST00000436443.1_Missense_Mutation_p.P1276S|ERBB4_ENST00000402597.1_Missense_Mutation_p.P1282S	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	1292					cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	ACAGTGCCTGGCTTCAGGGAG	0.493										TSP Lung(8;0.080)																												dbGAP											0													72.0	75.0	74.0					2																	212248393		2203	4300	6503	-	-	-	SO:0001583	missense	0			L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"""v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"""			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.3874C>T	2.37:g.212248393G>A	ENSP00000342235:p.Pro1292Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	pirsf_Tyr_kinase_EGF/ERB/XmrK_rcpt,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_EGF_rcpt_L,pfam_Prot_kinase_cat_dom,pfam_Furin-like_Cys-rich_dom,superfamily_Kinase-like_dom,superfamily_Growth_fac_rcpt,smart_Furin_repeat,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom	p.P1292S	ENST00000342788.4	37	c.3874	CCDS2394.1	2	.	.	.	.	.	.	.	.	.	.	G	12.50	1.957457	0.34565	.	.	ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597	T;T;T	0.74737	-0.86;-0.87;-0.86	5.41	5.41	0.78517	.	0.066860	0.64402	D	0.000010	T	0.71962	0.3402	L	0.44542	1.39	0.49582	D	0.999808	P;B;B;B	0.36909	0.573;0.017;0.017;0.01	B;B;B;B	0.38378	0.272;0.007;0.007;0.003	T	0.74665	-0.3589	10	0.72032	D	0.01	.	19.39	0.94576	0.0:0.0:1.0:0.0	.	1266;1282;1276;1292	Q15303-4;Q15303-2;Q15303-3;Q15303	.;.;.;ERBB4_HUMAN	S	1292;1276;1282	ENSP00000342235:P1292S;ENSP00000403204:P1276S;ENSP00000385565:P1282S	ENSP00000342235:P1292S	P	-	1	0	ERBB4	211956638	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.878000	0.63093	2.812000	0.96745	0.557000	0.71058	CCA	ERBB4	-	pirsf_Tyr_kinase_EGF/ERB/XmrK_rcpt	ENSG00000178568		0.493	ERBB4-001	KNOWN	basic|CCDS	protein_coding	ERBB4	HGNC	protein_coding	OTTHUMT00000256597.1	129	0.00	0	G	NM_001042599		212248393	212248393	-1	no_errors	ENST00000342788	ensembl	human	known	69_37n	missense	75	28.57	30	SNP	1.000	A
AMER1	139285	genome.wustl.edu	37	X	63411447	63411447	+	Missense_Mutation	SNP	G	G	A			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chrX:63411447G>A	ENST00000330258.3	-	2	1992	c.1720C>T	c.(1720-1722)Cgg>Tgg	p.R574W	AMER1_ENST00000374869.3_Missense_Mutation_p.R574W|AMER1_ENST00000403336.1_Missense_Mutation_p.R574W	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	574					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)									TGCTCCCGCCGAAGCTCCCAA	0.592																																						dbGAP											67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)											58.0	56.0	57.0					X																	63411447		2203	4300	6503	-	-	-	SO:0001583	missense	0			AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"""-"""	26837	protein-coding gene	gene with protein product	"""Wilms Tumor on the X"", ""adenomatous polyposis coli membrane recruitment 1"""	300647	"""family with sequence similarity 123B"""	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.1720C>T	X.37:g.63411447G>A	ENSP00000329117:p.Arg574Trp	Somatic		WXS	Illumina GAIIx	Phase_IV	A2IB86|Q8N885	Missense_Mutation	SNP	pfam_Uncharacterised_FAM123	p.R574W	ENST00000330258.3	37	c.1720	CCDS14377.2	X	.	.	.	.	.	.	.	.	.	.	G	11.25	1.581975	0.28180	.	.	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	T;T;T	0.51325	0.74;0.71;0.74	5.21	2.44	0.29823	.	0.439092	0.19690	N	0.108287	T	0.39009	0.1062	L	0.54323	1.7	0.09310	N	1	B	0.20988	0.05	B	0.15052	0.012	T	0.37776	-0.9691	10	0.87932	D	0	-1.166	6.2648	0.20919	0.1658:0.0:0.6847:0.1495	.	574	Q5JTC6	F123B_HUMAN	W	574	ENSP00000364003:R574W;ENSP00000329117:R574W;ENSP00000384722:R574W	ENSP00000329117:R574W	R	-	1	2	FAM123B	63328172	0.994000	0.37717	0.105000	0.21289	0.386000	0.30323	3.887000	0.56197	0.270000	0.21984	-0.192000	0.12808	CGG	FAM123B	-	NULL	ENSG00000184675		0.592	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM123B	HGNC	protein_coding	OTTHUMT00000316584.1	142	0.00	0	G	NM_152424		63411447	63411447	-1	no_errors	ENST00000330258	ensembl	human	known	69_37n	missense	121	25.31	41	SNP	0.035	A
FAT2	2196	genome.wustl.edu	37	5	150948304	150948304	+	Silent	SNP	C	C	T			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr5:150948304C>T	ENST00000261800.5	-	1	201	c.189G>A	c.(187-189)gcG>gcA	p.A63A		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	63	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ACTGTGGCTCCGCGAGGTAGA	0.488																																						dbGAP											0													162.0	164.0	163.0					5																	150948304		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.189G>A	5.37:g.150948304C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	O75091|Q9NSR7	Silent	SNP	pfam_Cadherin,pfam_Laminin_G,superfamily_Cadherin-like,superfamily_ConA-like_lec_gl,smart_Cadherin,smart_Laminin_G,smart_EGF-like_Ca-bd,smart_EGF-like,pfscan_EG-like_dom,pfscan_Laminin_G,pfscan_Cadherin,prints_Cadherin	p.A63	ENST00000261800.5	37	c.189	CCDS4317.1	5																																																																																			FAT2	-	superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin	ENSG00000086570		0.488	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAT2	HGNC	protein_coding	OTTHUMT00000252434.1	237	0.00	0	C	NM_001447		150948304	150948304	-1	no_errors	ENST00000261800	ensembl	human	known	69_37n	silent	117	36.07	66	SNP	0.000	T
FCHO1	23149	genome.wustl.edu	37	19	17881246	17881248	+	In_Frame_Del	DEL	GTG	GTG	-			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	GTG	GTG					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr19:17881246_17881248delGTG	ENST00000596536.1	+	8	632_634	c.349_351delGTG	c.(349-351)gtgdel	p.V118del	FCHO1_ENST00000597512.1_In_Frame_Del_p.V125del|FCHO1_ENST00000389133.4_In_Frame_Del_p.V118del|FCHO1_ENST00000594202.1_In_Frame_Del_p.V118del|FCHO1_ENST00000595033.1_In_Frame_Del_p.V68del|FCHO1_ENST00000252771.7_In_Frame_Del_p.V118del|FCHO1_ENST00000600676.1_In_Frame_Del_p.V118del|FCHO1_ENST00000596951.1_In_Frame_Del_p.V118del|FCHO1_ENST00000539407.1_In_Frame_Del_p.V118del	NM_015122.2	NP_055937.1	O14526	FCHO1_HUMAN	FCH domain only 1	118	Mediates membrane-binding.				clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	AP-2 adaptor complex binding (GO:0035612)			NS(2)|breast(1)|large_intestine(6)|liver(1)|lung(12)	22						CAAGGAGGAAGTGGTGAGCACCT	0.571																																						dbGAP											0																																										-	-	-	SO:0001651	inframe_deletion	0			AB006628	CCDS32955.1, CCDS59365.1, CCDS59366.1	19p13.12	2008-02-05				ENSG00000130475			29002	protein-coding gene	gene with protein product		613437				12477932	Standard	NM_001161357		Approved	KIAA0290	uc002nhg.3	O14526		ENST00000596536.1:c.349_351delGTG	19.37:g.17881249_17881251delGTG	ENSP00000470731:p.Val118del	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NHE6|A8K5U5|B4E120|Q05C93|Q8IW22	In_Frame_Del	DEL	pfam_Muniscin_C-term_mu_dom,pfam_FCH,superfamily_Clathrin_mu_C,smart_FCH,pfscan_FCH	p.V118in_frame_del	ENST00000596536.1	37	c.349_351	CCDS32955.1	19																																																																																			FCHO1	-	NULL	ENSG00000130475		0.571	FCHO1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	FCHO1	HGNC	protein_coding	OTTHUMT00000466946.2	21	0.00	0	GTG	NM_015122		17881246	17881248	+1	no_errors	ENST00000252771	ensembl	human	known	69_37n	in_frame_del	30	18.92	7	DEL	0.843:0.631:0.438	-
FMNL3	91010	genome.wustl.edu	37	12	50052270	50052270	+	Missense_Mutation	SNP	G	G	A			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr12:50052270G>A	ENST00000293590.5	-	6	793	c.560C>T	c.(559-561)cCc>cTc	p.P187L	FMNL3_ENST00000335154.5_Missense_Mutation_p.P187L|FMNL3_ENST00000550488.1_Missense_Mutation_p.P187L|FMNL3_ENST00000352151.5_Intron			Q8IVF7	FMNL3_HUMAN	formin-like 3	187	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)|cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)	GTPase activating protein binding (GO:0032794)			breast(4)|endometrium(7)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|stomach(1)	39						GTTGGTGAAGGGGGCCGACAG	0.612																																						dbGAP											0													56.0	65.0	62.0					12																	50052270		2132	4233	6365	-	-	-	SO:0001583	missense	0			AK128195	CCDS41780.1, CCDS44874.1	12q13.12	2006-04-10							23698	protein-coding gene	gene with protein product						12684686	Standard	NM_198900		Approved	DKFZp762B245, MGC45819, WBP3	uc001ruv.1	Q8IVF7	OTTHUMG00000169651	ENST00000293590.5:c.560C>T	12.37:g.50052270G>A	ENSP00000293590:p.Pro187Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	B0JZA7|Q6ZRJ1	Missense_Mutation	SNP	pfam_FH2_actin-bd,pfam_Drf_FH3,pfam_Drf_GTPase-bd,superfamily_FH2_actin-bd,superfamily_ARM-type_fold,smart_Actin-bd_FH2/DRF_autoreg	p.P187L	ENST00000293590.5	37	c.560		12	.	.	.	.	.	.	.	.	.	.	G	16.19	3.052562	0.55218	.	.	ENSG00000161791	ENST00000335154;ENST00000550488;ENST00000293590	T;T;T	0.80480	-1.38;-1.37;-1.36	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	T	0.78413	0.4279	M	0.70595	2.14	0.58432	D	0.999996	B	0.33807	0.426	B	0.28139	0.086	T	0.77099	-0.2713	10	0.27785	T	0.31	.	17.409	0.87480	0.0:0.0:1.0:0.0	.	187	Q8IVF7-3	.	L	187	ENSP00000335655:P187L;ENSP00000447479:P187L;ENSP00000293590:P187L	ENSP00000293590:P187L	P	-	2	0	FMNL3	48338537	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	3.867000	0.56047	2.507000	0.84556	0.467000	0.42956	CCC	FMNL3	-	superfamily_ARM-type_fold	ENSG00000161791		0.612	FMNL3-201	KNOWN	basic	protein_coding	FMNL3	HGNC	protein_coding		48	0.00	0	G	NM_175736		50052270	50052270	-1	no_errors	ENST00000293590	ensembl	human	known	69_37n	missense	34	39.29	22	SNP	1.000	A
FOXA1	3169	genome.wustl.edu	37	14	38061222	38061222	+	Missense_Mutation	SNP	T	T	A			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr14:38061222T>A	ENST00000250448.2	-	2	828	c.767A>T	c.(766-768)aAc>aTc	p.N256I	FOXA1_ENST00000540786.1_Missense_Mutation_p.N223I|FOXA1_ENST00000545425.2_5'UTR	NM_004496.3	NP_004487.2	P55317	FOXA1_HUMAN	forkhead box A1	256					anatomical structure formation involved in morphogenesis (GO:0048646)|chromatin remodeling (GO:0006338)|dorsal/ventral neural tube patterning (GO:0021904)|epithelial cell maturation involved in prostate gland development (GO:0060743)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|epithelial-mesenchymal signaling involved in prostate gland development (GO:0060738)|glucose homeostasis (GO:0042593)|hormone metabolic process (GO:0042445)|lung epithelial cell differentiation (GO:0060487)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron fate specification (GO:0048665)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland epithelium morphogenesis (GO:0060740)|prostate gland stromal morphogenesis (GO:0060741)|response to estradiol (GO:0032355)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)	microvillus (GO:0005902)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(1)|large_intestine(2)|lung(3)|prostate(12)	19	Breast(36;0.0954)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;5.41e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.0454)|LUSC - Lung squamous cell carcinoma(13;0.0917)|all cancers(34;0.0925)|BRCA - Breast invasive adenocarcinoma(188;0.239)	GBM - Glioblastoma multiforme(112;0.0222)		GTAGCAGCCGTTCTCGAACAT	0.692																																						dbGAP											0													22.0	23.0	22.0					14																	38061222		2203	4300	6503	-	-	-	SO:0001583	missense	0			U39840	CCDS9665.1	14q12-q13	2008-04-10		2002-09-20	ENSG00000129514	ENSG00000129514		"""Forkhead boxes"""	5021	protein-coding gene	gene with protein product		602294	"""hepatocyte nuclear factor 3, alpha"""	HNF3A		9119385, 8652662	Standard	NM_004496		Approved		uc001wuf.4	P55317	OTTHUMG00000140253	ENST00000250448.2:c.767A>T	14.37:g.38061222T>A	ENSP00000250448:p.Asn256Ile	Somatic		WXS	Illumina GAIIx	Phase_IV	B2R9H6|B7ZAP5|Q9H2A0	Missense_Mutation	SNP	pfam_TF_fork_head,pfam_Fork-head_N,pfam_Forkhead_box_C,smart_TF_fork_head,pfscan_TF_fork_head,prints_TF_fork_head	p.N256I	ENST00000250448.2	37	c.767	CCDS9665.1	14	.	.	.	.	.	.	.	.	.	.	T	23.2	4.390343	0.82902	.	.	ENSG00000129514	ENST00000250448;ENST00000540786	D;D	0.95885	-3.84;-3.84	3.92	3.92	0.45320	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.052618	0.64402	D	0.000001	D	0.97554	0.9199	H	0.95187	3.635	0.80722	D	1	D	0.56521	0.976	P	0.54499	0.754	D	0.98107	1.0418	10	0.87932	D	0	.	11.8486	0.52399	0.0:0.0:0.0:1.0	.	256	P55317	FOXA1_HUMAN	I	256;223	ENSP00000250448:N256I;ENSP00000440178:N223I	ENSP00000250448:N256I	N	-	2	0	FOXA1	37130973	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.697000	0.84279	1.648000	0.50643	0.329000	0.21502	AAC	FOXA1	-	pfam_TF_fork_head,smart_TF_fork_head,pfscan_TF_fork_head	ENSG00000129514		0.692	FOXA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FOXA1	HGNC	protein_coding	OTTHUMT00000276735.1	21	0.00	0	T			38061222	38061222	-1	no_errors	ENST00000250448	ensembl	human	known	69_37n	missense	18	18.18	4	SNP	1.000	A
GPR133	283383	genome.wustl.edu	37	12	131622702	131622703	+	Frame_Shift_Ins	INS	-	-	A			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr12:131622702_131622703insA	ENST00000261654.5	+	24	3016_3017	c.2457_2458insA	c.(2458-2460)aaafs	p.K820fs	GPR133_ENST00000376682.4_Frame_Shift_Ins_p.K506fs|GPR133_ENST00000543617.1_Frame_Shift_Ins_p.K339fs|GPR133_ENST00000540207.1_3'UTR|GPR133_ENST00000535015.1_Frame_Shift_Ins_p.K852fs	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	820					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(2)|endometrium(6)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|pancreas(6)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	67	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		CCTTCAAGCACAAAACCAAGGT	0.594																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			AY278561	CCDS9272.1	12q24.33	2014-08-08			ENSG00000111452	ENSG00000111452		"""-"", ""GPCR / Class B : Orphans"""	19893	protein-coding gene	gene with protein product		613639					Standard	NM_198827		Approved	DKFZp434B1272, PGR25	uc001uit.4	Q6QNK2	OTTHUMG00000168339	ENST00000261654.5:c.2461dupA	12.37:g.131622706_131622706dupA	ENSP00000261654:p.Lys820fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Frame_Shift_Ins	INS	pfam_GPCR_2_secretin-like,pfam_GPS_dom,superfamily_ConA-like_lec_gl,smart_GPS_dom,pfscan_GPS_dom,pfscan_GPCR_2-like,prints_GPCR_2_secretin-like	p.T820fs	ENST00000261654.5	37	c.2457_2458	CCDS9272.1	12																																																																																			GPR133	-	NULL	ENSG00000111452		0.594	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GPR133	HGNC	protein_coding	OTTHUMT00000399356.1	44	0.00	0	-	NM_198827		131622702	131622703	+1	no_errors	ENST00000261654	ensembl	human	known	69_37n	frame_shift_ins	16	11.11	2	INS	1.000:1.000	A
GTF2IRD1	9569	genome.wustl.edu	37	7	73961494	73961494	+	Silent	SNP	G	G	A			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr7:73961494G>A	ENST00000265755.3	+	17	2187	c.1794G>A	c.(1792-1794)ccG>ccA	p.P598P	GTF2IRD1_ENST00000476977.1_Silent_p.P598P|GTF2IRD1_ENST00000455841.2_Silent_p.P630P|GTF2IRD1_ENST00000424337.2_Silent_p.P598P|GTF2IRD1_ENST00000489094.1_3'UTR	NM_005685.3|NM_016328.2	NP_005676.3|NP_057412.1	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1	598					multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transition between slow and fast fiber (GO:0014886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(19)|ovary(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						TGATGCACCCGGAGGAGCTGT	0.617																																						dbGAP											0													78.0	69.0	72.0					7																	73961494		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF151354	CCDS5571.1, CCDS47613.1, CCDS56492.1	7q11.23	2008-04-18	2002-01-14		ENSG00000006704	ENSG00000006704			4661	protein-coding gene	gene with protein product	"""binding factor for early enhancer"""	604318	"""GTF2I repeat domain-containing 1"""	WBSCR11		9774679, 10198167	Standard	NM_016328		Approved	MusTRD1, RBAP2, GTF3, WBSCR12, BEN, Cream1	uc010lbq.3	Q9UHL9	OTTHUMG00000023782	ENST00000265755.3:c.1794G>A	7.37:g.73961494G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	O95444|Q6DSU6|Q75MX7|Q86UM3|Q8WVC4|Q9UHK8|Q9UI91	Silent	SNP	pfam_GTF2I,superfamily_GTF2I,pirsf_TF_II-I,pfscan_GTF2I	p.P598	ENST00000265755.3	37	c.1794	CCDS5571.1	7																																																																																			GTF2IRD1	-	pfam_GTF2I,superfamily_GTF2I,pirsf_TF_II-I,pfscan_GTF2I	ENSG00000006704		0.617	GTF2IRD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	GTF2IRD1	HGNC	protein_coding	OTTHUMT00000252654.2	28	0.00	0	G	NM_016328		73961494	73961494	+1	no_errors	ENST00000265755	ensembl	human	known	69_37n	silent	30	16.22	6	SNP	0.291	A
GTF3C1	2975	genome.wustl.edu	37	16	27506805	27506805	+	Silent	SNP	G	G	A			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr16:27506805G>A	ENST00000356183.4	-	15	2374	c.2359C>T	c.(2359-2361)Ctg>Ttg	p.L787L	GTF3C1_ENST00000561623.1_Silent_p.L787L	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	787					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						GAACGCCCCAGTCCGGGAACT	0.498																																						dbGAP											0													17.0	18.0	18.0					16																	27506805		2193	4298	6491	-	-	-	SO:0001819	synonymous_variant	0			U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"""General transcription factors"""	4664	protein-coding gene	gene with protein product		603246	"""general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"""			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.2359C>T	16.37:g.27506805G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Silent	SNP	pfam_TFIIIC_Bblock-bd	p.L787	ENST00000356183.4	37	c.2359	CCDS32414.1	16																																																																																			GTF3C1	-	NULL	ENSG00000077235		0.498	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GTF3C1	HGNC	protein_coding	OTTHUMT00000433856.1	22	0.00	0	G	NM_001520		27506805	27506805	-1	no_errors	ENST00000356183	ensembl	human	known	69_37n	silent	20	16.67	4	SNP	1.000	A
HERC1	8925	genome.wustl.edu	37	15	63944671	63944671	+	Missense_Mutation	SNP	C	C	T	rs373098342		TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr15:63944671C>T	ENST00000443617.2	-	52	10447	c.10360G>A	c.(10360-10362)Gta>Ata	p.V3454I		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	3454					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.V3454I(2)		NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						ACATTCCATACGCGGATGGTG	0.373																																						dbGAP											2	Substitution - Missense(2)	large_intestine(2)											114.0	111.0	112.0					15																	63944671		1948	4140	6088	-	-	-	SO:0001583	missense	0			U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"""WD repeat domain containing"""	4867	protein-coding gene	gene with protein product		605109	"""hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"""			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.10360G>A	15.37:g.63944671C>T	ENSP00000390158:p.Val3454Ile	Somatic		WXS	Illumina GAIIx	Phase_IV	Q8IW65	Missense_Mutation	SNP	pfam_Reg_chr_condens,pfam_HECT,pfam_WD40_repeat,pfam_SPRY_rcpt,superfamily_Reg_csome_cond/b-lactamase_inh,superfamily_HECT,superfamily_WD40_repeat_dom,superfamily_ConA-like_lec_gl,superfamily_UBA-like,superfamily_ARM-type_fold,smart_SPla/RYanodine_receptor_subgr,smart_WD40_repeat,smart_HECT,pfscan_B30.2/SPRY,pfscan_HECT,pfscan_Reg_chr_condens,pfscan_WD40_repeat,pfscan_WD40_repeat_dom,prints_Reg_chr_condens	p.V3454I	ENST00000443617.2	37	c.10360	CCDS45277.1	15	.	.	.	.	.	.	.	.	.	.	C	25.2	4.614974	0.87359	.	.	ENSG00000103657	ENST00000443617	T	0.59772	0.24	5.98	5.98	0.97165	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.64402	D	0.000003	T	0.40619	0.1124	N	0.05608	-0.01	0.54753	D	0.999983	B	0.30104	0.268	B	0.24006	0.05	T	0.25710	-1.0124	10	0.33940	T	0.23	.	20.4434	0.99119	0.0:1.0:0.0:0.0	.	3454	Q15751	HERC1_HUMAN	I	3454	ENSP00000390158:V3454I	ENSP00000390158:V3454I	V	-	1	0	HERC1	61731724	0.999000	0.42202	0.894000	0.35097	0.994000	0.84299	4.031000	0.57267	2.838000	0.97847	0.655000	0.94253	GTA	HERC1	-	pfam_WD40_repeat,superfamily_WD40_repeat_dom,smart_WD40_repeat,pfscan_WD40_repeat,pfscan_WD40_repeat_dom	ENSG00000103657		0.373	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HERC1	HGNC	protein_coding	OTTHUMT00000418523.1	53	0.00	0	C	NM_003922		63944671	63944671	-1	no_errors	ENST00000443617	ensembl	human	known	69_37n	missense	33	40.00	22	SNP	0.997	T
IGFBP7	3490	genome.wustl.edu	37	4	57907076	57907077	+	Frame_Shift_Ins	INS	-	-	G			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr4:57907076_57907077insG	ENST00000295666.4	-	2	531_532	c.498_499insC	c.(496-501)cccaagfs	p.K167fs	IGFBP7_ENST00000512512.1_5'UTR|IGFBP7_ENST00000537922.1_Frame_Shift_Ins_p.K167fs	NM_001553.2	NP_001544.1	Q16270	IBP7_HUMAN	insulin-like growth factor binding protein 7	167	Ig-like C2-type.				cell adhesion (GO:0007155)|cellular response to hormone stimulus (GO:0032870)|embryo implantation (GO:0007566)|inner ear development (GO:0048839)|negative regulation of cell proliferation (GO:0008285)|regulation of cell growth (GO:0001558)|regulation of steroid biosynthetic process (GO:0050810)|response to cortisol (GO:0051414)|response to heat (GO:0009408)|response to retinoic acid (GO:0032526)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(1)|lung(3)	5	Glioma(25;0.08)|all_neural(26;0.181)				"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	CAGATGTCCTTGGGGGGCGTCA	0.505																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			S75725	CCDS3512.1	4q12	2013-01-11			ENSG00000163453	ENSG00000163453		"""Immunoglobulin superfamily / I-set domain containing"""	5476	protein-coding gene	gene with protein product		602867				7694637, 7980422	Standard	NM_001553		Approved	MAC25, IGFBP-7, PSF, FSTL2	uc003hcn.3	Q16270	OTTHUMG00000128772	ENST00000295666.4:c.499dupC	4.37:g.57907082_57907082dupG	ENSP00000295666:p.Lys167fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B4E1N2|B7Z9W7|Q07822|Q53YE6|Q9UCA8	Frame_Shift_Ins	INS	pfam_Ig_I-set,pfam_Kazal-type_dom,pfam_Prot_inh_Kazal,pfam_IGFBP-like,smart_IGFBP-like,smart_Prot_inh_Kazal,smart_Ig_sub,pirsf_IGFBP_rP_mac25,pfscan_Ig-like	p.K166fs	ENST00000295666.4	37	c.499_498	CCDS3512.1	4																																																																																			IGFBP7	-	pfam_Ig_I-set,smart_Ig_sub,pirsf_IGFBP_rP_mac25,pfscan_Ig-like	ENSG00000163453		0.505	IGFBP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	IGFBP7	HGNC	protein_coding	OTTHUMT00000250693.1	78	0.00	0	-			57907076	57907077	-1	no_errors	ENST00000295666	ensembl	human	known	69_37n	frame_shift_ins	62	10.14	7	INS	1.000:1.000	G
LPA	4018	genome.wustl.edu	37	6	161007564	161007564	+	Missense_Mutation	SNP	G	G	A	rs201200716		TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr6:161007564G>A	ENST00000316300.5	-	25	4090	c.4046C>T	c.(4045-4047)aCg>aTg	p.T1349M	LPA_ENST00000447678.1_Missense_Mutation_p.T1349M			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3857	Kringle 12. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	TGGACATTGCGTCAGGTTGCA	0.522																																						dbGAP											0													134.0	135.0	135.0					6																	161007564		2168	4284	6452	-	-	-	SO:0001583	missense	0			X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.4046C>T	6.37:g.161007564G>A	ENSP00000321334:p.Thr1349Met	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5VTD7|Q9UD88	Missense_Mutation	SNP	pfam_Kringle,pfam_Peptidase_S1_S6,pfam_Peptidase_S1A_nudel,superfamily_Pept_cys/ser_Trypsin-like,superfamily_Kringle-like,smart_Kringle,smart_Peptidase_S1_S6,prints_Peptidase_S1A,pfscan_Kringle,pfscan_Peptidase_S1_S6	p.T1349M	ENST00000316300.5	37	c.4046	CCDS43523.1	6	.	.	.	.	.	.	.	.	.	.	g	13.44	2.236416	0.39498	.	.	ENSG00000198670	ENST00000316300;ENST00000447678	T;T	0.62941	-0.01;-0.01	2.39	-4.03	0.04021	Kringle (4);Kringle-like fold (1);	.	.	.	.	T	0.50463	0.1617	L	0.46670	1.46	0.09310	N	0.999999	D	0.71674	0.998	D	0.79784	0.993	T	0.46020	-0.9221	9	0.54805	T	0.06	.	5.0802	0.14653	0.0:0.1932:0.2003:0.6065	.	3857	P08519	APOA_HUMAN	M	1349	ENSP00000321334:T1349M;ENSP00000395608:T1349M	ENSP00000321334:T1349M	T	-	2	0	LPA	160927554	0.002000	0.14202	0.316000	0.25252	0.413000	0.31143	-0.365000	0.07573	-1.024000	0.03338	0.436000	0.28706	ACG	LPA	-	pfam_Kringle,superfamily_Kringle-like,smart_Kringle,pfscan_Kringle	ENSG00000198670		0.522	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LPA	HGNC	protein_coding	OTTHUMT00000042957.1	341	0.00	0	G	NM_005577		161007564	161007564	-1	no_errors	ENST00000316300	ensembl	human	known	69_37n	missense	210	34.78	112	SNP	0.337	A
MED12	9968	genome.wustl.edu	37	X	70340011	70340011	+	Missense_Mutation	SNP	C	C	T			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chrX:70340011C>T	ENST00000374080.3	+	4	576	c.544C>T	c.(544-546)Cct>Tct	p.P182S	MED12_ENST00000374102.1_Missense_Mutation_p.P182S|MED12_ENST00000333646.6_Missense_Mutation_p.P182S			Q93074	MED12_HUMAN	mediator complex subunit 12	182					androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					ACATGTTGACCCTTTCATGGG	0.478			"""M, S"""		uterine leiomyoma		Opitz-Kaveggia Syndrome																															dbGAP		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	0													108.0	100.0	103.0					X																	70340011		2024	4159	6183	-	-	-	SO:0001583	missense	0			U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"""trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)"", ""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)"", ""FG syndrome 1"""	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.544C>T	X.37:g.70340011C>T	ENSP00000363193:p.Pro182Ser	Somatic		WXS	Illumina GAIIx	Phase_IV	O15410|O75557|Q9UHV6|Q9UND7	Missense_Mutation	SNP	pfam_Mediator_Med12_LCEWAV,pfam_Mediator_Med12_catenin-bd,pfam_Mediator_Med12	p.P182S	ENST00000374080.3	37	c.544	CCDS43970.1	X	.	.	.	.	.	.	.	.	.	.	.	16.62	3.174631	0.57692	.	.	ENSG00000184634	ENST00000333646;ENST00000536756;ENST00000374102;ENST00000374080;ENST00000430072	T;T;T;T	0.59502	0.26;0.27;0.27;0.26	5.09	5.09	0.68999	.	0.060784	0.64402	D	0.000002	T	0.73040	0.3536	M	0.62266	1.93	0.58432	D	0.999999	B;D;D;B	0.89917	0.132;1.0;0.998;0.434	B;D;D;B	0.80764	0.144;0.994;0.951;0.114	T	0.74748	-0.3560	10	0.54805	T	0.06	-16.0548	15.7852	0.78297	0.0:1.0:0.0:0.0	.	182;29;182;182	F5H3Y1;Q7Z3Z5;Q93074-3;Q93074	.;.;.;MED12_HUMAN	S	182;182;182;182;150	ENSP00000333125:P182S;ENSP00000363215:P182S;ENSP00000363193:P182S;ENSP00000414203:P150S	ENSP00000333125:P182S	P	+	1	0	MED12	70256736	1.000000	0.71417	0.998000	0.56505	0.774000	0.43823	7.434000	0.80377	2.348000	0.79779	0.600000	0.82982	CCT	MED12	-	NULL	ENSG00000184634		0.478	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	MED12	HGNC	protein_coding	OTTHUMT00000057105.1	276	0.00	0	C	NM_005120		70340011	70340011	+1	no_errors	ENST00000333646	ensembl	human	known	69_37n	missense	128	31.91	60	SNP	1.000	T
MTUS2	23281	genome.wustl.edu	37	13	29600217	29600217	+	Missense_Mutation	SNP	G	G	T			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr13:29600217G>T	ENST00000431530.3	+	1	1470	c.1412G>T	c.(1411-1413)aGt>aTt	p.S471I		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	461						cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						CGGTTGGGCAGTGGGAATAAG	0.502																																						dbGAP											0													80.0	85.0	84.0					13																	29600217		1956	4139	6095	-	-	-	SO:0001583	missense	0			AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"""+TIP of 150 kDa"", ""cardiac zipper protein"""		"""KIAA0774"""	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000431530.3:c.1412G>T	13.37:g.29600217G>T	ENSP00000392057:p.Ser471Ile	Somatic		WXS	Illumina GAIIx	Phase_IV	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Missense_Mutation	SNP	NULL	p.S471I	ENST00000431530.3	37	c.1412	CCDS45022.1	13	.	.	.	.	.	.	.	.	.	.	g	9.688	1.151183	0.21371	.	.	ENSG00000132938	ENST00000431530	T	0.12569	2.67	5.26	1.26	0.21427	.	0.877927	0.09849	N	0.747889	T	0.12135	0.0295	L	0.51422	1.61	0.09310	N	1	P	0.40834	0.73	B	0.37304	0.246	T	0.21861	-1.0233	9	.	.	.	.	6.1828	0.20480	0.1791:0.4645:0.3564:0.0	.	461	Q5JR59	MTUS2_HUMAN	I	471	ENSP00000392057:S471I	.	S	+	2	0	MTUS2	28498217	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-0.145000	0.10265	0.196000	0.20367	0.655000	0.94253	AGT	MTUS2	-	NULL	ENSG00000132938		0.502	MTUS2-002	KNOWN	basic|CCDS	protein_coding	MTUS2	HGNC	protein_coding	OTTHUMT00000044336.3	197	0.00	0	G	XM_166270		29600217	29600217	+1	no_errors	ENST00000431530	ensembl	human	known	69_37n	missense	101	32.21	48	SNP	0.000	T
PIP5K1A	8394	genome.wustl.edu	37	1	151204807	151204807	+	Frame_Shift_Del	DEL	G	G	-			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr1:151204807delG	ENST00000368888.4	+	6	874	c.452delG	c.(451-453)cggfs	p.R151fs	PIP5K1A_ENST00000441902.2_Frame_Shift_Del_p.R139fs|PIP5K1A_ENST00000414290.2_5'Flank|PIP5K1A_ENST00000368890.4_Frame_Shift_Del_p.R138fs|PIP5K1A_ENST00000409426.1_Frame_Shift_Del_p.R139fs	NM_001135638.1	NP_001129110.1	Q99755	PI51A_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, alpha	151	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				actin cytoskeleton reorganization (GO:0031532)|activation of Rac GTPase activity (GO:0032863)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|fibroblast migration (GO:0010761)|focal adhesion assembly (GO:0048041)|glycerophospholipid metabolic process (GO:0006650)|keratinocyte differentiation (GO:0030216)|phagocytosis (GO:0006909)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|protein targeting to plasma membrane (GO:0072661)|ruffle assembly (GO:0097178)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|kinase binding (GO:0019900)			breast(1)|central_nervous_system(1)|ovary(1)|skin(1)|stomach(1)	5	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.181)			CGCTACTTCCGGGAGCTATTT	0.502																																					Pancreas(80;36 1443 2325 16095 21302)	dbGAP											0													165.0	154.0	158.0					1																	151204807		2203	4300	6503	-	-	-	SO:0001589	frameshift_variant	0			U78575	CCDS990.1, CCDS44219.1, CCDS44220.1, CCDS44221.1	1q21.3	2010-04-08			ENSG00000143398	ENSG00000143398			8994	protein-coding gene	gene with protein product		603275				8955136, 10828584	Standard	NM_003557		Approved		uc001exj.3	Q99755	OTTHUMG00000012351	ENST00000368888.4:c.452delG	1.37:g.151204807delG	ENSP00000357883:p.Arg151fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K4Q0|B4DIN0|Q99754|Q99756	Frame_Shift_Del	DEL	pfam_PInositol-4-P-5-kinase_core,smart_PInositol-4P-5-kinase_core_sub	p.E152fs	ENST00000368888.4	37	c.452	CCDS44219.1	1																																																																																			PIP5K1A	-	smart_PInositol-4P-5-kinase_core_sub	ENSG00000143398		0.502	PIP5K1A-003	KNOWN	basic|CCDS	protein_coding	PIP5K1A	HGNC	protein_coding	OTTHUMT00000034425.2	220	0.00	0	G	NM_003557		151204807	151204807	+1	no_errors	ENST00000368888	ensembl	human	known	69_37n	frame_shift_del	392	11.89	54	DEL	1.000	-
PLA2G4E	123745	genome.wustl.edu	37	15	42284983	42284983	+	Silent	SNP	G	G	A			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr15:42284983G>A	ENST00000399518.3	-	13	1908	c.1422C>T	c.(1420-1422)acC>acT	p.T474T	CTD-2382E5.1_ENST00000499478.2_RNA|PLA2G4E_ENST00000413860.2_Silent_p.T445T	NM_001206670.1	NP_001193599.1	Q3MJ16	PA24E_HUMAN	phospholipase A2, group IVE	462	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|stomach(1)	16		all_cancers(109;8.09e-13)|all_epithelial(112;2.03e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.0273)		OV - Ovarian serous cystadenocarcinoma(18;7.61e-18)|GBM - Glioblastoma multiforme(94;3.07e-06)		AGTCTGTAAAGGTGACCCTGT	0.622																																						dbGAP											0													48.0	51.0	50.0					15																	42284983		1912	4121	6033	-	-	-	SO:0001819	synonymous_variant	0				CCDS55962.1	15q15.1	2008-09-19			ENSG00000188089	ENSG00000188089	3.1.1.4		24791	protein-coding gene	gene with protein product						15866882	Standard	NM_001206670		Approved	FLJ45651	uc021sjp.1	Q3MJ16	OTTHUMG00000130371	ENST00000399518.3:c.1422C>T	15.37:g.42284983G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	Q6ZSC0	Silent	SNP	pfam_LysoPLipase_cat_dom,pfam_C2_Ca-dep,superfamily_Acyl_Trfase/lysoPLipase,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_C2_Ca-dep,smart_LysoPLipase_cat_dom,pfscan_C2_membr_targeting,pfscan_LysoPLipase_cat_dom	p.T445	ENST00000399518.3	37	c.1335	CCDS55962.1	15																																																																																			PLA2G4E	-	pfam_LysoPLipase_cat_dom,superfamily_Acyl_Trfase/lysoPLipase,smart_LysoPLipase_cat_dom,pfscan_LysoPLipase_cat_dom	ENSG00000188089		0.622	PLA2G4E-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	PLA2G4E	HGNC	protein_coding	OTTHUMT00000252738.2	51	0.00	0	G	NM_198442		42284983	42284983	-1	no_errors	ENST00000413860	ensembl	human	known	69_37n	silent	24	25.00	8	SNP	0.992	A
PSIP1	11168	genome.wustl.edu	37	9	15474030	15474032	+	In_Frame_Del	DEL	CTT	CTT	-	rs148785652		TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	CTT	CTT					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr9:15474030_15474032delCTT	ENST00000380733.4	-	9	1176_1178	c.833_835delAAG	c.(832-837)gaagga>gga	p.E278del	PSIP1_ENST00000380715.1_In_Frame_Del_p.E278del|PSIP1_ENST00000397519.2_In_Frame_Del_p.E278del|PSIP1_ENST00000380716.4_In_Frame_Del_p.E278del|PSIP1_ENST00000380738.4_In_Frame_Del_p.E278del			O75475	PSIP1_HUMAN	PC4 and SFRS1 interacting protein 1	278					establishment of integrated proviral latency (GO:0075713)|mRNA 5'-splice site recognition (GO:0000395)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to heat (GO:0009408)|response to oxidative stress (GO:0006979)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear heterochromatin (GO:0005720)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription coactivator activity (GO:0001105)|supercoiled DNA binding (GO:0097100)			breast(2)|endometrium(2)|kidney(1)|lung(3)|prostate(1)	9				GBM - Glioblastoma multiforme(50;2.38e-06)		TGATCATCTCCTTCTTCTTCAGA	0.296																																						dbGAP											0									,,	3,4259		0,3,2128					,,	3.5	1.0			98	4,8248		1,2,4123	no	coding,coding,coding	PSIP1	NM_033222.3,NM_021144.3,NM_001128217.1	,,	1,5,6251	A1A1,A1R,RR		0.0485,0.0704,0.0559	,,	,,		7,12507				-	-	-	SO:0001651	inframe_deletion	0			AF098482	CCDS6479.1, CCDS6480.1	9p22.2	2008-02-05	2004-02-24		ENSG00000164985	ENSG00000164985			9527	protein-coding gene	gene with protein product		603620	"""PC4 and SFRS1 interacting protein 2"""	PSIP2		9822615, 9885563	Standard	NM_033222		Approved	p52, LEDGF, p75	uc003zlw.4	O75475	OTTHUMG00000021021	ENST00000380733.4:c.833_835delAAG	9.37:g.15474036_15474038delCTT	ENSP00000370109:p.Glu278del	Somatic		WXS	Illumina GAIIx	Phase_IV	D3DRI9|O00256|O95368|Q6P391|Q86YB9|Q9NZI3|Q9UER6	In_Frame_Del	DEL	pfam_LEDGF,pfam_PWWP,smart_PWWP,prints_Treacle-like_TCS,pfscan_PWWP	p.E278in_frame_del	ENST00000380733.4	37	c.835_833	CCDS6479.1	9																																																																																			PSIP1	-	prints_Treacle-like_TCS	ENSG00000164985		0.296	PSIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	PSIP1	HGNC	protein_coding	OTTHUMT00000055445.1	447	0.00	0	CTT	NM_033222		15474030	15474032	-1	no_errors	ENST00000380733	ensembl	human	known	69_37n	in_frame_del	358	24.31	115	DEL	1.000:0.993:1.000	-
RTKN2	219790	genome.wustl.edu	37	10	63964752	63964752	+	Missense_Mutation	SNP	A	A	T			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr10:63964752A>T	ENST00000373789.3	-	10	1146	c.1050T>A	c.(1048-1050)gaT>gaA	p.D350E	RTKN2_ENST00000315289.2_Missense_Mutation_p.D152E|RTKN2_ENST00000395265.1_Missense_Mutation_p.D371E	NM_145307.2	NP_660350.2	Q8IZC4	RTKN2_HUMAN	rhotekin 2	350	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(12;0.0297)|all_hematologic(501;0.215)					TTTTCTTGGCATCCTTATCCA	0.338																																						dbGAP											0													96.0	98.0	97.0					10																	63964752		2203	4300	6503	-	-	-	SO:0001583	missense	0			BC025765	CCDS7263.1, CCDS73140.1	10q21.3	2013-01-10	2007-12-14	2007-12-14	ENSG00000182010	ENSG00000182010		"""Pleckstrin homology (PH) domain containing"""	19364	protein-coding gene	gene with protein product			"""pleckstrin homology domain containing, family K member 1"""	PLEKHK1		15504364	Standard	NM_001282941		Approved	Em:AC024597.2, bA531F24.1, FLJ39352	uc001jlw.3	Q8IZC4	OTTHUMG00000018299	ENST00000373789.3:c.1050T>A	10.37:g.63964752A>T	ENSP00000362894:p.Asp350Glu	Somatic		WXS	Illumina GAIIx	Phase_IV	Q3ZCR1|Q68DZ6|Q8N8K1|Q8TAV2	Missense_Mutation	SNP	pfam_Pleckstrin_homology,superfamily_HR1_rho-bd,smart_HR1_rho-bd,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology	p.D350E	ENST00000373789.3	37	c.1050	CCDS7263.1	10	.	.	.	.	.	.	.	.	.	.	A	16.33	3.093215	0.56075	.	.	ENSG00000182010	ENST00000315289;ENST00000395265;ENST00000373789	T;T;T	0.79845	-1.31;-1.31;-0.88	5.11	3.96	0.45880	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.314618	0.32120	N	0.006554	T	0.82130	0.4970	L	0.52905	1.665	0.32825	D	0.503285	B;D	0.56746	0.243;0.977	B;P	0.57283	0.134;0.817	D	0.84781	0.0773	10	0.49607	T	0.09	-3.6428	7.9238	0.29861	0.813:0.0:0.187:0.0	.	152;350	Q5SVY4;Q8IZC4	.;RTKN2_HUMAN	E	152;371;350	ENSP00000325379:D152E;ENSP00000378682:D371E;ENSP00000362894:D350E	ENSP00000325379:D152E	D	-	3	2	RTKN2	63634758	0.980000	0.34600	0.997000	0.53966	0.757000	0.42996	2.059000	0.41384	1.938000	0.56188	0.528000	0.53228	GAT	RTKN2	-	pfam_Pleckstrin_homology,smart_Pleckstrin_homology,pfscan_Pleckstrin_homology	ENSG00000182010		0.338	RTKN2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	RTKN2	HGNC	protein_coding	OTTHUMT00000091618.1	123	0.00	0	A	NM_145307		63964752	63964752	-1	no_errors	ENST00000373789	ensembl	human	known	69_37n	missense	101	33.11	50	SNP	0.358	T
TBC1D2	55357	genome.wustl.edu	37	9	100983164	100983164	+	Frame_Shift_Del	DEL	G	G	-			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr9:100983164delG	ENST00000375064.1	-	6	1363	c.1325delC	c.(1324-1326)gctfs	p.A443fs	TBC1D2_ENST00000375066.5_Frame_Shift_Del_p.A443fs|TBC1D2_ENST00000342112.5_Frame_Shift_Del_p.A225fs|TBC1D2_ENST00000493589.2_Intron	NM_001267571.1	NP_001254500.1	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2	443					positive regulation of Rab GTPase activity (GO:0032851)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)	cadherin binding (GO:0045296)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.55e-37)		CCTGTTGGCAGCGTCGGGGCG	0.632																																						dbGAP											0													61.0	73.0	69.0					9																	100983164		2202	4299	6501	-	-	-	SO:0001589	frameshift_variant	0			AY026527	CCDS35080.1, CCDS59137.1, CCDS75865.1	9q22.32	2011-11-30			ENSG00000095383	ENSG00000095383			18026	protein-coding gene	gene with protein product	"""prostate antigen recognized and identified by SEREX"""	609871					Standard	NM_018421		Approved	PARIS1, TBC1D2A, Armus	uc011lvb.2	Q9BYX2	OTTHUMG00000020343	ENST00000375064.1:c.1325delC	9.37:g.100983164delG	ENSP00000364205:p.Ala443fs	Somatic		WXS	Illumina GAIIx	Phase_IV	B3KWD1|B4DQ05|B9A6J7|Q59EU0|Q5TBQ5|Q6IPC7|Q7L1K8|Q8WYT1|Q9H6A2|Q9NSH4	Frame_Shift_Del	DEL	pfam_Rab-GTPase-TBC_dom,superfamily_Rab-GTPase-TBC_dom,smart_Pleckstrin_homology,smart_Rab-GTPase-TBC_dom,pfscan_Pleckstrin_homology,pfscan_Rab-GTPase-TBC_dom	p.A442fs	ENST00000375064.1	37	c.1325		9																																																																																			TBC1D2	-	NULL	ENSG00000095383		0.632	TBC1D2-001	KNOWN	basic|appris_principal	protein_coding	TBC1D2	HGNC	protein_coding	OTTHUMT00000053366.1	25	0.00	0	G	NM_018421		100983164	100983164	-1	no_errors	ENST00000375066	ensembl	human	known	69_37n	frame_shift_del	16	30.43	7	DEL	0.000	-
THBS1	7057	genome.wustl.edu	37	15	39883401	39883402	+	Frame_Shift_Ins	INS	-	-	CA			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr15:39883401_39883402insCA	ENST00000260356.5	+	15	2428_2429	c.2263_2264insCA	c.(2263-2265)ccafs	p.P755fs	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	755					activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		GGACAACTGTCCATTCCATTAC	0.446																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0				CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.2264_2265dupCA	15.37:g.39883402_39883403dupCA	ENSP00000260356:p.Pro755fs	Somatic		WXS	Illumina GAIIx	Phase_IV	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Frame_Shift_Ins	INS	pfam_Thrombospondin_C,pfam_Thrombospondin_1_rpt,pfam_VWF_C,pfam_Thrombospondin_3-like_rpt,pfam_EGF-like_Ca-bd,superfamily_ConA-like_lec_gl,superfamily_Thrombospondin_1_rpt,smart_Laminin_G,smart_VWF_C,smart_Thrombospondin_1_rpt,smart_EGF-like_Ca-bd,smart_EGF-like,pfscan_EG-like_dom,pfscan_Thrombospondin_1_rpt,pfscan_VWF_C	p.F756fs	ENST00000260356.5	37	c.2263_2264	CCDS32194.1	15																																																																																			THBS1	-	NULL	ENSG00000137801		0.446	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	THBS1	HGNC	protein_coding	OTTHUMT00000257831.2	146	0.00	0	-	NM_003246		39883401	39883402	+1	no_errors	ENST00000260356	ensembl	human	known	69_37n	frame_shift_ins	82	20.39	21	INS	1.000:0.999	CA
TMEM161B	153396	genome.wustl.edu	37	5	87494931	87494931	+	Missense_Mutation	SNP	C	C	A	rs554989470		TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr5:87494931C>A	ENST00000296595.6	-	10	1075	c.951G>T	c.(949-951)tgG>tgT	p.W317C	TMEM161B_ENST00000512429.1_Missense_Mutation_p.W306C|TMEM161B_ENST00000511218.1_Intron|TMEM161B_ENST00000515293.1_5'Flank|TMEM161B_ENST00000506536.1_Missense_Mutation_p.W135C|TMEM161B_ENST00000514135.1_Missense_Mutation_p.W317C	NM_153354.3	NP_699185.1	Q8NDZ6	T161B_HUMAN	transmembrane protein 161B	317						integral component of membrane (GO:0016021)				endometrium(4)|large_intestine(3)|lung(9)|skin(3)|upper_aerodigestive_tract(1)	20		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)		GGATTATTAACCAGAGTCGCA	0.413													C|||	1	0.000199681	0.0	0.0014	5008	,	,		16244	0.0		0.0	False		,,,				2504	0.0					dbGAP											0													53.0	49.0	50.0					5																	87494931		2203	4299	6502	-	-	-	SO:0001583	missense	0			BC037287	CCDS4065.1, CCDS75269.1, CCDS75270.1	5q14.3	2008-02-05			ENSG00000164180	ENSG00000164180			28483	protein-coding gene	gene with protein product						12477932	Standard	NM_001289008		Approved	MGC33214	uc003kjc.3	Q8NDZ6	OTTHUMG00000131323	ENST00000296595.6:c.951G>T	5.37:g.87494931C>A	ENSP00000296595:p.Trp317Cys	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5CZH7|Q6UWQ6	Missense_Mutation	SNP	pfam_Transmembrane_161A/B	p.W317C	ENST00000296595.6	37	c.951	CCDS4065.1	5	.	.	.	.	.	.	.	.	.	.	C	24.5	4.534250	0.85812	.	.	ENSG00000164180	ENST00000514135;ENST00000296595;ENST00000506536;ENST00000512429	.	.	.	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.78065	0.4225	M	0.64404	1.975	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.72921	-0.4145	9	0.32370	T	0.25	-13.9372	20.2956	0.98549	0.0:1.0:0.0:0.0	.	317	Q8NDZ6	T161B_HUMAN	C	317;317;135;306	.	ENSP00000296595:W317C	W	-	3	0	TMEM161B	87530687	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.818000	0.86416	2.805000	0.96524	0.460000	0.39030	TGG	TMEM161B	-	pfam_Transmembrane_161A/B	ENSG00000164180		0.413	TMEM161B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TMEM161B	HGNC	protein_coding	OTTHUMT00000254094.1	38	0.00	0	C	NM_153354		87494931	87494931	-1	no_errors	ENST00000296595	ensembl	human	known	69_37n	missense	48	33.33	24	SNP	1.000	A
VSIG1	340547	genome.wustl.edu	37	X	107320387	107320387	+	Missense_Mutation	SNP	A	A	G			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chrX:107320387A>G	ENST00000217957.5	+	7	1057	c.940A>G	c.(940-942)Acc>Gcc	p.T314A	VSIG1_ENST00000415430.3_Missense_Mutation_p.T350A	NM_182607.4	NP_872413.1	Q86XK7	VSIG1_HUMAN	V-set and immunoglobulin domain containing 1	314						integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	17						TGGCCCTGATACCATCCAAGA	0.517																																						dbGAP											0													111.0	99.0	103.0					X																	107320387		2203	4300	6503	-	-	-	SO:0001583	missense	0			BX648658	CCDS14535.1, CCDS55474.1	Xq22.3	2013-01-29			ENSG00000101842	ENSG00000101842		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	28675	protein-coding gene	gene with protein product		300620				12477932	Standard	NM_182607		Approved	MGC44287	uc011msk.2	Q86XK7	OTTHUMG00000022175	ENST00000217957.5:c.940A>G	X.37:g.107320387A>G	ENSP00000217957:p.Thr314Ala	Somatic		WXS	Illumina GAIIx	Phase_IV	C9J4P2|Q6MZS4	Missense_Mutation	SNP	pfam_Ig_V-set,smart_Ig_sub,smart_Ig_sub2,smart_Ig_V-set_subgr,pfscan_Ig-like	p.T350A	ENST00000217957.5	37	c.1048	CCDS14535.1	X	.	.	.	.	.	.	.	.	.	.	A	7.802	0.713919	0.15306	.	.	ENSG00000101842	ENST00000415430;ENST00000217957	T;T	0.75589	-0.95;-0.71	4.14	-1.41	0.08941	.	5.571950	0.00166	N	0.000001	T	0.52517	0.1739	N	0.17474	0.49	0.09310	N	1	B;B	0.12013	0.005;0.001	B;B	0.06405	0.002;0.001	T	0.42155	-0.9468	10	0.06891	T	0.86	.	3.3207	0.07049	0.4169:0.0:0.386:0.1971	.	350;314	C9J4P2;Q86XK7	.;VSIG1_HUMAN	A	350;314	ENSP00000402219:T350A;ENSP00000217957:T314A	ENSP00000217957:T314A	T	+	1	0	VSIG1	107207043	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.871000	0.04223	-0.377000	0.07930	0.417000	0.27973	ACC	VSIG1	-	NULL	ENSG00000101842		0.517	VSIG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	VSIG1	HGNC	protein_coding	OTTHUMT00000057858.1	421	0.24	1	A	NM_182607		107320387	107320387	+1	no_errors	ENST00000415430	ensembl	human	known	69_37n	missense	281	31.31	129	SNP	0.000	G
UPF3B	65109	genome.wustl.edu	37	X	118986832	118986832	+	Silent	SNP	G	G	A			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chrX:118986832G>A	ENST00000276201.2	-	1	129	c.60C>T	c.(58-60)gcC>gcT	p.A20A	UPF3B_ENST00000345865.2_Silent_p.A20A	NM_080632.2	NP_542199.1	Q9BZI7	REN3B_HUMAN	UPF3 regulator of nonsense transcripts homolog B (yeast)	20					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|prostate(1)	30						CTGTGGCCCCGGCGGGGGTTA	0.617																																						dbGAP											0													117.0	114.0	115.0					X																	118986832		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF318576	CCDS14587.1, CCDS14588.1	Xq25-q26	2014-01-31			ENSG00000125351	ENSG00000125351			20439	protein-coding gene	gene with protein product		300298	"""mental retardation, X-linked 62"""	MRX62		11113196, 11163187, 19238151	Standard	NM_023010		Approved	RENT3B, UPF3X, HUPF3B	uc004erz.2	Q9BZI7	OTTHUMG00000022282	ENST00000276201.2:c.60C>T	X.37:g.118986832G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	D3DWI3|D3DWI4|Q0VAK8|Q9H1J0	Silent	SNP	pfam_Nonsense_mediated_decay_UPF3	p.A20	ENST00000276201.2	37	c.60	CCDS14588.1	X																																																																																			UPF3B	-	NULL	ENSG00000125351		0.617	UPF3B-001	KNOWN	basic|CCDS	protein_coding	UPF3B	HGNC	protein_coding	OTTHUMT00000058068.1	125	0.00	0	G			118986832	118986832	-1	no_errors	ENST00000276201	ensembl	human	known	69_37n	silent	114	33.71	60	SNP	0.000	A
ZNF142	7701	genome.wustl.edu	37	2	219514141	219514141	+	Missense_Mutation	SNP	T	T	C			TCGA-A8-A08A-01A-11W-A019-09	TCGA-A8-A08A-10A-01W-A021-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	0257d030-6d78-452c-9dcc-79fe50533543	47f8d355-c16e-49ea-919c-9924b1a9c375	g.chr2:219514141T>C	ENST00000449707.1	-	6	911	c.490A>G	c.(490-492)Atg>Gtg	p.M164V	ZNF142_ENST00000411696.2_Missense_Mutation_p.M164V	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	164					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(7)|endometrium(7)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38		Renal(207;0.0474)		Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		TCTGGACACATATGGGTCTTG	0.532											OREG0015202	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									Colon(170;867 1942 8995 15834 18053)	dbGAP											0													31.0	31.0	31.0					2																	219514141		1934	4148	6082	-	-	-	SO:0001583	missense	0			U09849	CCDS42817.1	2q35	2013-01-08	2006-06-13		ENSG00000115568	ENSG00000115568		"""Zinc fingers, C2H2-type"""	12927	protein-coding gene	gene with protein product		604083	"""zinc finger protein 142 (clone pHZ-49)"""				Standard	NM_001105537		Approved	KIAA0236, pHZ-49	uc002vin.4	P52746	OTTHUMG00000154736	ENST00000449707.1:c.490A>G	2.37:g.219514141T>C	ENSP00000408643:p.Met164Val	Somatic	2259	WXS	Illumina GAIIx	Phase_IV	Q92510	Missense_Mutation	SNP	pfam_Znf_C2H2,smart_Znf_C2H2-like,pfscan_Znf_C2H2	p.M164V	ENST00000449707.1	37	c.490	CCDS42817.1	2	.	.	.	.	.	.	.	.	.	.	T	13.04	2.118122	0.37339	.	.	ENSG00000115568	ENST00000449707;ENST00000411696	T;T	0.26518	1.73;1.73	5.65	5.65	0.86999	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.213387	0.56097	D	0.000025	T	0.32734	0.0839	L	0.31664	0.95	0.35578	D	0.806044	B;D	0.53312	0.116;0.959	B;P	0.55011	0.036;0.766	T	0.27673	-1.0067	10	0.34782	T	0.22	-16.8816	16.0399	0.80667	0.0:0.0:0.0:1.0	.	164;1	P52746;A8MWU9	ZN142_HUMAN;.	V	164	ENSP00000408643:M164V;ENSP00000398798:M164V	ENSP00000398798:M164V	M	-	1	0	ZNF142	219222385	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.901000	0.56303	2.371000	0.80710	0.533000	0.62120	ATG	ZNF142	-	smart_Znf_C2H2-like,pfscan_Znf_C2H2	ENSG00000115568		0.532	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF142	HGNC	protein_coding	OTTHUMT00000336833.1	26	0.00	0	T	NM_005081		219514141	219514141	-1	no_errors	ENST00000411696	ensembl	human	known	69_37n	missense	16	38.46	10	SNP	1.000	C
