#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
AKR1C4	1109	genome.wustl.edu	37	10	5254676	5254676	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A1FG-01A-11D-A13L-09	TCGA-BH-A1FG-11B-12D-A13O-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	311f2f1a-75c8-4fee-b31d-0815d71a3173	e0c48952-a56b-4c97-89b7-7bc9d7acde38	g.chr10:5254676G>A	ENST00000380448.1	+	8	921	c.668G>A	c.(667-669)cGa>cAa	p.R223Q	AKR1C4_ENST00000263126.1_Missense_Mutation_p.R223Q			P17516	AK1C4_HUMAN	aldo-keto reductase family 1, member C4	223					androgen metabolic process (GO:0008209)|bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular response to jasmonic acid stimulus (GO:0071395)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|bile acid transmembrane transporter activity (GO:0015125)|chlordecone reductase activity (GO:0047743)|electron carrier activity (GO:0009055)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|retinal dehydrogenase activity (GO:0001758)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(2)|stomach(2)|urinary_tract(1)	18						GGAACCCAACGACATAAACTA	0.393																																						dbGAP											0													75.0	69.0	71.0					10																	5254676		2203	4300	6503	-	-	-	SO:0001583	missense	0			M33375	CCDS7064.1	10p15.1	2012-12-04	2012-12-04		ENSG00000198610	ENSG00000198610	1.1.1.225	"""Aldo-keto reductases"""	387	protein-coding gene	gene with protein product	"""chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4"""	600451	"""aldo-keto reductase family 1, member C4 (chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4)"""	CHDR		7789999	Standard	NM_001818		Approved	DD4, HAKRA, C11, 3-alpha-HSD, CDR, MGC22581	uc001ihw.2	P17516	OTTHUMG00000017591	ENST00000380448.1:c.668G>A	10.37:g.5254676G>A	ENSP00000369814:p.Arg223Gln	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5T6A3|Q8WW84|Q9NS54	Missense_Mutation	SNP	pfam_NADP_OxRdtase_dom,superfamily_NADP_OxRdtase_dom,prints_Aldo/keto_reductase_subgr	p.R223Q	ENST00000380448.1	37	c.668	CCDS7064.1	10	.	.	.	.	.	.	.	.	.	.	G	15.89	2.965217	0.53507	.	.	ENSG00000198610	ENST00000380448;ENST00000263126	T;T	0.23754	1.89;1.89	3.13	0.892	0.19230	NADP-dependent oxidoreductase domain (3);	0.000000	0.51477	D	0.000088	T	0.25791	0.0628	N	0.21240	0.645	0.09310	N	0.999991	D	0.71674	0.998	P	0.57283	0.817	T	0.07597	-1.0764	10	0.72032	D	0.01	.	8.3396	0.32235	0.0:0.0:0.5821:0.4179	.	223	P17516	AK1C4_HUMAN	Q	223	ENSP00000369814:R223Q;ENSP00000263126:R223Q	ENSP00000263126:R223Q	R	+	2	0	AKR1C4	5244676	0.006000	0.16342	0.001000	0.08648	0.106000	0.19336	1.473000	0.35387	0.256000	0.21614	0.313000	0.20887	CGA	AKR1C4	-	pfam_NADP_OxRdtase_dom,superfamily_NADP_OxRdtase_dom	ENSG00000198610		0.393	AKR1C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AKR1C4	HGNC	protein_coding	OTTHUMT00000046543.2	101	0.00	0	G	NM_001818		5254676	5254676	+1	no_errors	ENST00000263126	ensembl	human	known	69_37n	missense	57	13.64	9	SNP	0.155	A
GPR98	84059	genome.wustl.edu	37	5	89986809	89986809	+	Missense_Mutation	SNP	A	A	T			TCGA-BH-A1FG-01A-11D-A13L-09	TCGA-BH-A1FG-11B-12D-A13O-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	311f2f1a-75c8-4fee-b31d-0815d71a3173	e0c48952-a56b-4c97-89b7-7bc9d7acde38	g.chr5:89986809A>T	ENST00000405460.2	+	31	6998	c.6902A>T	c.(6901-6903)cAa>cTa	p.Q2301L		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	2301	Calx-beta 16. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GAAACCATTCAAACCTTGTTG	0.483																																						dbGAP											0													127.0	123.0	125.0					5																	89986809		1961	4151	6112	-	-	-	SO:0001583	missense	0			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.6902A>T	5.37:g.89986809A>T	ENSP00000384582:p.Gln2301Leu	Somatic		WXS	Illumina GAIIx	Phase_IV	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	pfam_Calx_beta,pfam_EPTP,pfam_GPCR_2_secretin-like,pfam_GPS_dom,superfamily_ConA-like_lec_gl,superfamily_Gal_Oxase/kelch_b-propeller,smart_Calx_beta,pfscan_EAR,pfscan_GPS_dom,pfscan_GPCR_2-like	p.Q2301L	ENST00000405460.2	37	c.6902	CCDS47246.1	5	.	.	.	.	.	.	.	.	.	.	A	21.1	4.104984	0.77096	.	.	ENSG00000164199	ENST00000405460;ENST00000296619	T	0.27557	1.66	5.94	5.94	0.96194	Na-Ca exchanger/integrin-beta4 (1);	0.046639	0.85682	D	0.000000	T	0.29423	0.0733	N	0.19112	0.55	0.80722	D	1	D	0.55605	0.972	P	0.50970	0.655	T	0.06110	-1.0845	10	0.59425	D	0.04	.	11.434	0.50058	0.9303:0.0:0.0697:0.0	.	2301	Q8WXG9	GPR98_HUMAN	L	2301	ENSP00000384582:Q2301L	ENSP00000296619:Q2301L	Q	+	2	0	GPR98	90022565	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.352000	0.66028	2.265000	0.75225	0.482000	0.46254	CAA	GPR98	-	smart_Calx_beta	ENSG00000164199		0.483	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GPR98	HGNC	protein_coding	OTTHUMT00000369993.2	122	0.00	0	A	NM_032119		89986809	89986809	+1	no_errors	ENST00000405460	ensembl	human	known	69_37n	missense	45	39.19	29	SNP	1.000	T
KHDC3L	154288	genome.wustl.edu	37	6	74072569	74072569	+	Silent	SNP	G	G	T			TCGA-BH-A1FG-01A-11D-A13L-09	TCGA-BH-A1FG-11B-12D-A13O-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	311f2f1a-75c8-4fee-b31d-0815d71a3173	e0c48952-a56b-4c97-89b7-7bc9d7acde38	g.chr6:74072569G>T	ENST00000370367.3	+	1	170	c.117G>T	c.(115-117)ctG>ctT	p.L39L		NM_001017361.2	NP_001017361.1	Q587J8	KHD3L_HUMAN	KH domain containing 3-like, subcortical maternal complex member	39							RNA binding (GO:0003723)										CTGAGTTCCTGAAGAATCCGA	0.562																																						dbGAP											0													101.0	97.0	99.0					6																	74072569		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AB211062	CCDS34484.1	6q13	2012-06-25	2012-06-25	2012-06-25	ENSG00000203908	ENSG00000203908			33699	protein-coding gene	gene with protein product	"""ES cell associated transcript 1"""	611687	"""chromosome 6 open reading frame 221"""	C6orf221		21885028	Standard	NM_001017361		Approved	ECAT1	uc003pgt.4	Q587J8	OTTHUMG00000015024	ENST00000370367.3:c.117G>T	6.37:g.74072569G>T		Somatic		WXS	Illumina GAIIx	Phase_IV	B2RNW7	Silent	SNP	NULL	p.L39	ENST00000370367.3	37	c.117	CCDS34484.1	6																																																																																			KHDC3L	-	NULL	ENSG00000203908		0.562	KHDC3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KHDC3L	HGNC	protein_coding	OTTHUMT00000041202.3	76	0.00	0	G	NM_001017361		74072569	74072569	+1	no_errors	ENST00000370367	ensembl	human	known	69_37n	silent	33	10.81	4	SNP	0.003	T
LILRA4	23547	genome.wustl.edu	37	19	54849483	54849483	+	Missense_Mutation	SNP	C	C	T			TCGA-BH-A1FG-01A-11D-A13L-09	TCGA-BH-A1FG-11B-12D-A13O-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	311f2f1a-75c8-4fee-b31d-0815d71a3173	e0c48952-a56b-4c97-89b7-7bc9d7acde38	g.chr19:54849483C>T	ENST00000291759.4	-	4	435	c.379G>A	c.(379-381)Gca>Aca	p.A127T	AC008984.2_ENST00000507363.1_RNA	NM_012276.3	NP_036408.3	P59901	LIRA4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 4	127	Ig-like C2-type 2.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)		p.A127T(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	32	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0565)		CTTGGCAGTGCGGACAGGGTG	0.572																																						dbGAP											1	Substitution - Missense(1)	central_nervous_system(1)											47.0	50.0	49.0					19																	54849483		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF041261	CCDS12890.1	19q13.4	2013-01-11			ENSG00000239961	ENSG00000239961		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15503	protein-coding gene	gene with protein product		607517				10941842	Standard	NM_012276		Approved	ILT7, CD85g	uc002qfj.3	P59901	OTTHUMG00000065355	ENST00000291759.4:c.379G>A	19.37:g.54849483C>T	ENSP00000291759:p.Ala127Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	Q32MC4	Missense_Mutation	SNP	smart_Ig_sub,smart_Ig_sub2,pirsf_A1B_glyco/leuk_Ig-like_rcpt,pfscan_Ig-like	p.A127T	ENST00000291759.4	37	c.379	CCDS12890.1	19	.	.	.	.	.	.	.	.	.	.	.	10.50	1.368934	0.24771	.	.	ENSG00000239961	ENST00000291759	T	0.03272	3.99	2.65	0.334	0.15948	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.429774	0.20036	N	0.100608	T	0.12390	0.0301	M	0.83483	2.645	0.09310	N	1	D	0.76494	0.999	D	0.66497	0.944	T	0.08046	-1.0741	10	0.87932	D	0	.	3.1054	0.06340	0.262:0.5852:0.0:0.1528	.	127	P59901	LIRA4_HUMAN	T	127	ENSP00000291759:A127T	ENSP00000291759:A127T	A	-	1	0	LILRA4	59541295	0.909000	0.30893	0.030000	0.17652	0.001000	0.01503	1.355000	0.34068	0.165000	0.19558	-0.251000	0.11542	GCA	LILRA4	-	pirsf_A1B_glyco/leuk_Ig-like_rcpt,pfscan_Ig-like	ENSG00000239961		0.572	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LILRA4	HGNC	protein_coding	OTTHUMT00000140229.2	42	0.00	0	C	NM_012276		54849483	54849483	-1	no_errors	ENST00000291759	ensembl	human	known	69_37n	missense	13	43.48	10	SNP	0.035	T
MAMLD1	10046	genome.wustl.edu	37	X	149613879	149613879	+	Splice_Site	SNP	G	G	A			TCGA-BH-A1FG-01A-11D-A13L-09	TCGA-BH-A1FG-11B-12D-A13O-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	311f2f1a-75c8-4fee-b31d-0815d71a3173	e0c48952-a56b-4c97-89b7-7bc9d7acde38	g.chrX:149613879G>A	ENST00000370401.2	+	2	406		c.e2+1		MAMLD1_ENST00000426613.2_Splice_Site|MAMLD1_ENST00000468306.1_Intron|MAMLD1_ENST00000262858.5_Splice_Site|MAMLD1_ENST00000432680.2_Splice_Site			Q13495	MAMD1_HUMAN	mastermind-like domain containing 1						male gonad development (GO:0008584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(3)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)	37	Acute lymphoblastic leukemia(192;6.56e-05)					CCAGGAATCGGTCAGACAATG	0.463																																						dbGAP											0													46.0	45.0	45.0					X																	149613879		1863	4086	5949	-	-	-	SO:0001630	splice_region_variant	0			U46023	CCDS14693.2, CCDS55525.1, CCDS55526.1	Xq28	2008-02-05	2008-01-03	2008-01-03	ENSG00000013619	ENSG00000013619			2568	protein-coding gene	gene with protein product		300120	"""chromosome X open reading frame 6"""	CXorf6		9169146, 17086185, 18162467	Standard	NM_001177465		Approved	CG1, F18	uc011mxu.2	Q13495	OTTHUMG00000024157	ENST00000370401.2:c.96+1G>A	X.37:g.149613879G>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B2RCQ4|B4DG93|B9EGA5	Splice_Site	SNP	-	e1+1	ENST00000370401.2	37	c.96+1	CCDS14693.2	X	.	.	.	.	.	.	.	.	.	.	G	14.33	2.504329	0.44558	.	.	ENSG00000013619	ENST00000370401;ENST00000432680;ENST00000358892;ENST00000262858;ENST00000426613	.	.	.	5.64	4.69	0.59074	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.2123	0.48806	0.0:0.0:0.8034:0.1966	.	.	.	.	.	-1	.	.	.	+	.	.	MAMLD1	149364537	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	2.105000	0.41825	2.345000	0.79718	0.513000	0.50165	.	MAMLD1	-	-	ENSG00000013619		0.463	MAMLD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	MAMLD1	HGNC	protein_coding	OTTHUMT00000060844.2	98	0.00	0	G	NM_005491	Intron	149613879	149613879	+1	no_errors	ENST00000432680	ensembl	human	known	69_37n	splice_site	32	43.86	25	SNP	1.000	A
NBEA	26960	genome.wustl.edu	37	13	35785239	35785239	+	Silent	SNP	G	G	C			TCGA-BH-A1FG-01A-11D-A13L-09	TCGA-BH-A1FG-11B-12D-A13O-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	311f2f1a-75c8-4fee-b31d-0815d71a3173	e0c48952-a56b-4c97-89b7-7bc9d7acde38	g.chr13:35785239G>C	ENST00000400445.3	+	33	6105	c.5571G>C	c.(5569-5571)gtG>gtC	p.V1857V	NBEA_ENST00000540320.1_Silent_p.V1857V|NBEA_ENST00000379939.2_Silent_p.V1854V|NBEA_ENST00000310336.4_Silent_p.V1857V	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1857					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		CTAGTTTTGTGAATGGTGCTA	0.373																																						dbGAP											0													52.0	50.0	51.0					13																	35785239		1839	4017	5856	-	-	-	SO:0001819	synonymous_variant	0			AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"""A-kinase anchor proteins"", ""WD repeat domain containing"""	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.5571G>C	13.37:g.35785239G>C		Somatic		WXS	Illumina GAIIx	Phase_IV	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Silent	SNP	pfam_BEACH_dom,pfam_DUF1088,pfam_WD40_repeat,superfamily_BEACH_dom,superfamily_ConA-like_lec_gl,superfamily_WD40_repeat_dom,superfamily_ARM-type_fold,smart_WD40_repeat,pfscan_BEACH_dom,pfscan_WD40_repeat_dom	p.V1857	ENST00000400445.3	37	c.5571	CCDS45026.1	13																																																																																			NBEA	-	NULL	ENSG00000172915		0.373	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NBEA	HGNC	protein_coding		147	0.00	0	G	NM_015678		35785239	35785239	+1	no_errors	ENST00000310336	ensembl	human	known	69_37n	silent	70	38.60	44	SNP	1.000	C
PPP2R2A	5520	genome.wustl.edu	37	8	26227655	26227655	+	Missense_Mutation	SNP	T	T	A			TCGA-BH-A1FG-01A-11D-A13L-09	TCGA-BH-A1FG-11B-12D-A13O-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	311f2f1a-75c8-4fee-b31d-0815d71a3173	e0c48952-a56b-4c97-89b7-7bc9d7acde38	g.chr8:26227655T>A	ENST00000380737.3	+	10	1399	c.1070T>A	c.(1069-1071)gTc>gAc	p.V357D	PPP2R2A_ENST00000315985.7_Missense_Mutation_p.V367D	NM_002717.3	NP_002708.1	P63151	2ABA_HUMAN	protein phosphatase 2, regulatory subunit B, alpha	357					G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|response to morphine (GO:0043278)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			kidney(1)|large_intestine(2)|ovary(1)	4		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		CACAGTGTTGTCATGACTGGA	0.378																																						dbGAP											0													66.0	61.0	63.0					8																	26227655		2202	4300	6502	-	-	-	SO:0001583	missense	0			M64929	CCDS34867.1, CCDS55213.1	8p21.2	2013-01-10	2010-04-14		ENSG00000221914	ENSG00000221914	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""WD repeat domain containing"""	9304	protein-coding gene	gene with protein product	"""PP2A subunit B isoform alpha"""	604941	"""protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), alpha isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B, alpha isoform"""			1849734	Standard	NM_001177591		Approved	PR52A, PR55A, B55A		P63151	OTTHUMG00000163850	ENST00000380737.3:c.1070T>A	8.37:g.26227655T>A	ENSP00000370113:p.Val357Asp	Somatic		WXS	Illumina GAIIx	Phase_IV	B2RBU8|B4E1T7|P50409|Q00007	Missense_Mutation	SNP	pfam_WD40_repeat,superfamily_WD40_repeat_dom,smart_WD40_repeat,pirsf_PP2A_PR55,prints_PP2A_PR55	p.V357D	ENST00000380737.3	37	c.1070	CCDS34867.1	8	.	.	.	.	.	.	.	.	.	.	T	16.65	3.181558	0.57800	.	.	ENSG00000221914	ENST00000380737;ENST00000524169;ENST00000315985	T;T;T	0.73047	1.34;-0.71;1.34	5.34	5.34	0.76211	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.64402	U	0.000002	T	0.78848	0.4348	M	0.72118	2.19	0.80722	D	1	D;D;P	0.54397	0.966;0.961;0.929	P;P;P	0.53146	0.529;0.719;0.516	T	0.82039	-0.0655	10	0.87932	D	0	-19.0399	15.7739	0.78193	0.0:0.0:0.0:1.0	.	367;357;358	B4E1T7;P63151;Q6ZP32	.;2ABA_HUMAN;.	D	357;136;367	ENSP00000370113:V357D;ENSP00000430320:V136D;ENSP00000325074:V367D	ENSP00000325074:V367D	V	+	2	0	PPP2R2A	26283572	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	7.448000	0.80631	2.367000	0.80283	0.528000	0.53228	GTC	PPP2R2A	-	superfamily_WD40_repeat_dom,smart_WD40_repeat,pirsf_PP2A_PR55,prints_PP2A_PR55	ENSG00000221914		0.378	PPP2R2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PPP2R2A	HGNC	protein_coding	OTTHUMT00000375954.2	62	0.00	0	T	NM_002717		26227655	26227655	+1	no_errors	ENST00000380737	ensembl	human	known	69_37n	missense	11	68.57	24	SNP	1.000	A
PRDM16	63976	genome.wustl.edu	37	1	3328646	3328646	+	Missense_Mutation	SNP	G	G	A	rs568518616		TCGA-BH-A1FG-01A-11D-A13L-09	TCGA-BH-A1FG-11B-12D-A13O-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	311f2f1a-75c8-4fee-b31d-0815d71a3173	e0c48952-a56b-4c97-89b7-7bc9d7acde38	g.chr1:3328646G>A	ENST00000270722.5	+	9	1934	c.1885G>A	c.(1885-1887)Gtg>Atg	p.V629M	PRDM16_ENST00000378398.3_Missense_Mutation_p.V630M|PRDM16_ENST00000378391.2_Missense_Mutation_p.V629M|PRDM16_ENST00000442529.2_Missense_Mutation_p.V629M|PRDM16_ENST00000511072.1_Missense_Mutation_p.V630M|PRDM16_ENST00000514189.1_Missense_Mutation_p.V630M|PRDM16_ENST00000441472.2_Missense_Mutation_p.V629M|PRDM16_ENST00000512462.1_3'UTR			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	629					brown fat cell differentiation (GO:0050873)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurogenesis (GO:0022008)|palate development (GO:0060021)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular respiration (GO:0043457)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(3)	59	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		GGACAGCGACGTGGACAGCGA	0.687			T	EVI1	"""MDS, AML"""								G|||	1	0.000199681	0.0	0.0	5008	,	,		13245	0.0		0.001	False		,,,				2504	0.0					dbGAP		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	0													61.0	72.0	68.0					1																	3328646		2159	4236	6395	-	-	-	SO:0001583	missense	0			AF294278	CCDS41236.1, CCDS44048.1, CCDS41236.2, CCDS44048.2	1p36.23-p33	2013-01-08			ENSG00000142611	ENSG00000142611		"""Zinc fingers, C2H2-type"""	14000	protein-coding gene	gene with protein product	"""MDS1/EVI1-like"", ""PR-domain zinc finger protein 16"", ""transcription factor MEL1"""	605557				11050005	Standard	NM_199454		Approved	MEL1, PFM13, KIAA1675, MGC166915	uc001akf.3	Q9HAZ2	OTTHUMG00000000581	ENST00000270722.5:c.1885G>A	1.37:g.3328646G>A	ENSP00000270722:p.Val629Met	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Missense_Mutation	SNP	pfam_Znf_C2H2,pfam_Znf_BED_prd,smart_SET_dom,smart_Znf_C2H2-like,pfscan_SET_dom,pfscan_Znf_C2H2	p.V629M	ENST00000270722.5	37	c.1885	CCDS41236.2	1	.	.	.	.	.	.	.	.	.	.	G	12.95	2.092564	0.36952	.	.	ENSG00000142611	ENST00000511072;ENST00000378398;ENST00000441472;ENST00000442529;ENST00000378391;ENST00000514189;ENST00000270722;ENST00000512462;ENST00000408992;ENST00000509860	T;T;T;T;T;T;T;T;T	0.05717	3.42;3.44;3.45;3.45;3.44;3.44;3.45;3.41;3.4	5.09	3.1	0.35709	.	0.502419	0.15820	N	0.243027	T	0.10508	0.0257	L	0.60455	1.87	0.23628	N	0.997255	P;P;P;P	0.52692	0.814;0.883;0.955;0.918	B;B;B;B	0.43052	0.122;0.326;0.406;0.175	T	0.07539	-1.0767	10	0.62326	D	0.03	.	14.9164	0.70801	0.0:0.2721:0.7279:0.0	.	629;629;629;629	Q9HAZ2;Q9HAZ2-2;F8WEV3;D3YTA5	PRD16_HUMAN;.;.;.	M	630;630;629;629;629;630;629;445;445;438	ENSP00000426975:V630M;ENSP00000367651:V630M;ENSP00000407968:V629M;ENSP00000405253:V629M;ENSP00000367643:V629M;ENSP00000421400:V630M;ENSP00000270722:V629M;ENSP00000422504:V445M;ENSP00000425796:V438M	ENSP00000270722:V629M	V	+	1	0	PRDM16	3318506	0.982000	0.34865	0.994000	0.49952	0.974000	0.67602	3.943000	0.56621	0.477000	0.27464	0.603000	0.83216	GTG	PRDM16	-	NULL	ENSG00000142611		0.687	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PRDM16	HGNC	protein_coding	OTTHUMT00000001382.3	13	0.00	0	G	NM_022114		3328646	3328646	+1	no_errors	ENST00000270722	ensembl	human	known	69_37n	missense	3	62.50	5	SNP	1.000	A
RAB40A	142684	genome.wustl.edu	37	X	102755501	102755501	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A1FG-01A-11D-A13L-09	TCGA-BH-A1FG-11B-12D-A13O-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	311f2f1a-75c8-4fee-b31d-0815d71a3173	e0c48952-a56b-4c97-89b7-7bc9d7acde38	g.chrX:102755501G>A	ENST00000372633.1	-	1	2302	c.184C>T	c.(184-186)Cgg>Tgg	p.R62W	RAB40A_ENST00000304236.1_Missense_Mutation_p.R62W|LL0XNC01-250H12.3_ENST00000445990.1_RNA			Q8WXH6	RB40A_HUMAN	RAB40A, member RAS oncogene family	62					protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|skin(1)	12						AGCTTCACCCGCTGGCCGTCC	0.582																																						dbGAP											0													94.0	83.0	87.0					X																	102755501		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF132748	CCDS35357.1	Xq22.1	2009-08-25			ENSG00000172476	ENSG00000172476		"""RAB, member RAS oncogene"""	18283	protein-coding gene	gene with protein product						11697911	Standard	NM_080879		Approved	RAR2A, Rar-2	uc004ekk.3	Q8WXH6	OTTHUMG00000022100	ENST00000372633.1:c.184C>T	X.37:g.102755501G>A	ENSP00000361716:p.Arg62Trp	Somatic		WXS	Illumina GAIIx	Phase_IV	O00407|Q17RQ5|Q6DK06|Q8TF06	Missense_Mutation	SNP	pfam_Small_GTPase,pfam_MIRO-like,pfam_SOCS_C,pfam_Small_GTPase_ARF/SAR,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho,smart_Ran_GTPase,smart_SOCS_C,prints_Small_GTPase,pfscan_SOCS_C,tigrfam_Small_GTP-bd_dom	p.R62W	ENST00000372633.1	37	c.184	CCDS35357.1	X	.	.	.	.	.	.	.	.	.	.	.	19.09	3.759880	0.69763	.	.	ENSG00000172476	ENST00000372633;ENST00000304236	T;T	0.77877	-1.13;-1.13	0.848	0.848	0.18966	Small GTP-binding protein domain (1);	0.000000	0.42548	U	0.000686	D	0.85927	0.5811	M	0.85197	2.74	0.54753	D	0.99998	D	0.89917	1.0	D	0.87578	0.998	D	0.84699	0.0727	10	0.87932	D	0	.	7.3213	0.26529	1.0E-4:0.0:0.9999:0.0	.	62	Q8WXH6	RB40A_HUMAN	W	62	ENSP00000361716:R62W;ENSP00000305648:R62W	ENSP00000305648:R62W	R	-	1	2	RAB40A	102642157	0.479000	0.25925	0.851000	0.33527	0.757000	0.42996	0.526000	0.22971	0.702000	0.31825	0.284000	0.19432	CGG	RAB40A	-	pfam_Small_GTPase,pfam_MIRO-like,pfam_Small_GTPase_ARF/SAR,smart_Small_GTPase_Ras,smart_Small_GTPase_Rab_type,smart_Small_GTPase_Rho,smart_Ran_GTPase,prints_Small_GTPase,tigrfam_Small_GTP-bd_dom	ENSG00000172476		0.582	RAB40A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	RAB40A	HGNC	protein_coding	OTTHUMT00000057714.1	101	0.00	0	G			102755501	102755501	-1	no_errors	ENST00000304236	ensembl	human	known	69_37n	missense	54	12.90	8	SNP	1.000	A
RASAL1	8437	genome.wustl.edu	37	12	113553739	113553739	+	Splice_Site	SNP	C	C	A			TCGA-BH-A1FG-01A-11D-A13L-09	TCGA-BH-A1FG-11B-12D-A13O-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	311f2f1a-75c8-4fee-b31d-0815d71a3173	e0c48952-a56b-4c97-89b7-7bc9d7acde38	g.chr12:113553739C>A	ENST00000261729.5	-	10	1164	c.849G>T	c.(847-849)gaG>gaT	p.E283D	RASAL1_ENST00000418411.2_5'UTR|RASAL1_ENST00000446861.3_Splice_Site_p.E283D|RASAL1_ENST00000546530.1_Splice_Site_p.E283D|RASAL1_ENST00000548055.1_Splice_Site_p.E283D			O95294	RASL1_HUMAN	RAS protein activator like 1 (GAP1 like)	283					intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|phospholipid binding (GO:0005543)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(3)|prostate(2)|skin(2)	43						ACGCACCCACCTCTGCTGGCC	0.637																																						dbGAP											0													76.0	80.0	79.0					12																	113553739		2203	4300	6503	-	-	-	SO:0001630	splice_region_variant	0			AF086713	CCDS9165.1, CCDS55888.1, CCDS55889.1, CCDS73529.1	12q23-q24	2013-01-10			ENSG00000111344	ENSG00000111344		"""Pleckstrin homology (PH) domain containing"""	9873	protein-coding gene	gene with protein product		604118				9751798	Standard	NM_001193520		Approved	RASAL	uc001tul.3	O95294	OTTHUMG00000169705	ENST00000261729.5:c.849+1G>T	12.37:g.113553739C>A		Somatic		WXS	Illumina GAIIx	Phase_IV	B7ZKM4|C9JFK5|F8VQX1|Q52M03|Q59H24|Q96CC7	Missense_Mutation	SNP	pfam_RasGAP,pfam_C2_Ca-dep,pfam_Znf_Btk_motif,pfam_Pleckstrin_homology,superfamily_Rho_GTPase_activation_prot,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_C2_Ca-dep,smart_RasGAP,smart_Pleckstrin_homology,smart_Znf_Btk_motif,pfscan_C2_membr_targeting,pfscan_Pleckstrin_homology,pfscan_Znf_Btk_motif,pfscan_RasGAP	p.E283D	ENST00000261729.5	37	c.849	CCDS9165.1	12	.	.	.	.	.	.	.	.	.	.	C	25.2	4.610456	0.87258	.	.	ENSG00000111344	ENST00000546530;ENST00000261729;ENST00000446861;ENST00000548055	T;T;T;T	0.69561	-0.41;-0.33;-0.31;-0.4	4.99	4.99	0.66335	Rho GTPase activation protein (1);Ras GTPase-activating protein (1);	0.193253	0.42682	D	0.000661	T	0.68311	0.2987	M	0.61703	1.905	0.38394	D	0.945489	P;P;P;P;P;P;P	0.52061	0.917;0.839;0.95;0.917;0.696;0.749;0.95	B;B;P;B;P;B;P	0.48334	0.37;0.37;0.574;0.37;0.457;0.269;0.574	T	0.71941	-0.4440	9	.	.	.	.	12.5249	0.56081	0.1671:0.8329:0.0:0.0	.	283;283;283;295;283;283;283	B7ZKM4;B4DG06;F8VRH9;Q59H24;F8VQX1;O95294;O95294-2	.;.;.;.;.;RASL1_HUMAN;.	D	283	ENSP00000450244:E283D;ENSP00000261729:E283D;ENSP00000395920:E283D;ENSP00000448510:E283D	.	E	-	3	2	RASAL1	112038122	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	2.832000	0.48152	2.467000	0.83353	0.491000	0.48974	GAG	RASAL1	-	superfamily_Rho_GTPase_activation_prot,smart_RasGAP	ENSG00000111344		0.637	RASAL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	RASAL1	HGNC	protein_coding	OTTHUMT00000405522.2	27	0.00	0	C	NM_004658	Missense_Mutation	113553739	113553739	-1	no_errors	ENST00000546530	ensembl	human	known	69_37n	missense	10	44.44	8	SNP	1.000	A
RNA5-8SP6	100873336	genome.wustl.edu	37	Y	10037843	10037843	+	RNA	SNP	C	C	T			TCGA-BH-A1FG-01A-11D-A13L-09	TCGA-BH-A1FG-11B-12D-A13O-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	311f2f1a-75c8-4fee-b31d-0815d71a3173	e0c48952-a56b-4c97-89b7-7bc9d7acde38	g.chrY:10037843C>T	ENST00000515896.1	+	0	80									RNA, 5.8S ribosomal pseudogene 6																		AATTGCAGGACACATTGATCA	0.512																																						dbGAP											0																																										-	-	-			0					Yp11.2	2012-08-07	2012-08-07	2012-08-07	ENSG00000251705	ENSG00000251705			41960	pseudogene	RNA, pseudogene			"""RNA, 5.8S ribosomal 6"""	RN5-8S6			Standard	NG_033474		Approved						Y.37:g.10037843C>T		Somatic		WXS	Illumina GAIIx	Phase_IV		RNA	SNP	-	NULL	ENST00000515896.1	37	NULL		Y																																																																																			RNA5-8SP6	-	-	ENSG00000251705		0.512	RNA5-8SP6-201	KNOWN	basic	rRNA	RNA5-8SP6	HGNC	rRNA		29	0.00	0	C			10037843	10037843	+1	no_errors	ENST00000515896	ensembl	human	known	69_37n	rna	22	15.38	4	SNP	1.000	T
RPLP0	6175	genome.wustl.edu	37	12	120635133	120635133	+	Missense_Mutation	SNP	C	C	T			TCGA-BH-A1FG-01A-11D-A13L-09	TCGA-BH-A1FG-11B-12D-A13O-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	311f2f1a-75c8-4fee-b31d-0815d71a3173	e0c48952-a56b-4c97-89b7-7bc9d7acde38	g.chr12:120635133C>T	ENST00000551150.1	-	6	1099	c.784G>A	c.(784-786)Gct>Act	p.A262T	RPLP0_ENST00000546989.1_Missense_Mutation_p.A226T|RPLP0_ENST00000552292.1_Missense_Mutation_p.A52T|RPLP0_ENST00000313104.5_Missense_Mutation_p.A200T|RPLP0_ENST00000228306.4_Missense_Mutation_p.A262T|RPLP0_ENST00000392514.4_Missense_Mutation_p.A262T|GCN1L1_ENST00000300648.6_5'Flank|RPLP0_ENST00000550296.1_5'Flank			P05388	RLA0_HUMAN	ribosomal protein, large, P0	262					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosome biogenesis (GO:0042254)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ACCTTTTCAGCAAGTGGGAAG	0.483																																						dbGAP											0													94.0	78.0	83.0					12																	120635133		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB007187	CCDS9193.1	12q24.2	2011-07-29			ENSG00000089157	ENSG00000089157		"""L ribosomal proteins"""	10371	protein-coding gene	gene with protein product	"""acidic ribosomal phosphoprotein P0"""	180510				9582194	Standard	NM_053275		Approved	PRLP0, P0, L10E, RPP0, LP0	uc001txq.3	P05388	OTTHUMG00000169317	ENST00000551150.1:c.784G>A	12.37:g.120635133C>T	ENSP00000449328:p.Ala262Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	Q3B7A4|Q9BVK4	Missense_Mutation	SNP	pfam_Ribosomal_L10/acidic_P0,pfam_Ribosomal_60S	p.A262T	ENST00000551150.1	37	c.784	CCDS9193.1	12	.	.	.	.	.	.	.	.	.	.	C	33	5.248858	0.95305	.	.	ENSG00000089157	ENST00000392514;ENST00000551150;ENST00000552292;ENST00000313104;ENST00000546989;ENST00000228306;ENST00000546990;ENST00000547211	.	.	.	5.56	3.66	0.41972	.	0.000000	0.85682	U	0.000000	T	0.79724	0.4495	M	0.88640	2.97	0.80722	D	1	D;D	0.89917	1.0;0.99	D;P	0.74348	0.983;0.817	T	0.80390	-0.1402	9	0.56958	D	0.05	.	10.5187	0.44905	0.1331:0.7962:0.0:0.0708	.	200;262	Q3B7A4;P05388	.;RLA0_HUMAN	T	262;262;52;200;226;262;213;242	.	ENSP00000339027:A262T	A	-	1	0	RPLP0	119119516	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.972000	0.56838	0.647000	0.30713	0.655000	0.94253	GCT	RPLP0	-	pfam_Ribosomal_60S	ENSG00000089157		0.483	RPLP0-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	RPLP0	HGNC	protein_coding	OTTHUMT00000403448.3	53	0.00	0	C	NM_053275		120635133	120635133	-1	no_errors	ENST00000228306	ensembl	human	known	69_37n	missense	29	34.09	15	SNP	1.000	T
SPDYE1	285955	genome.wustl.edu	37	7	44043475	44043475	+	Silent	SNP	C	C	T	rs369507758		TCGA-BH-A1FG-01A-11D-A13L-09	TCGA-BH-A1FG-11B-12D-A13O-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	311f2f1a-75c8-4fee-b31d-0815d71a3173	e0c48952-a56b-4c97-89b7-7bc9d7acde38	g.chr7:44043475C>T	ENST00000258704.3	+	3	648	c.511C>T	c.(511-513)Ctg>Ttg	p.L171L	RP5-1165K10.2_ENST00000454572.1_RNA|AC004951.6_ENST00000447643.1_lincRNA|POLR2J4_ENST00000427076.1_RNA	NM_001099435.2|NM_175064.2	NP_001092905.2|NP_778234.2	Q8NFV5	SPDE1_HUMAN	speedy/RINGO cell cycle regulator family member E1	171										endometrium(1)|kidney(4)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	11						TAAAAGATTCCTGGCCTGGGA	0.542																																						dbGAP											0													4.0	4.0	4.0					7																	44043475		1263	2925	4188	-	-	-	SO:0001819	synonymous_variant	0			AF412027	CCDS5475.1	7q11.23	2013-05-08	2013-05-08	2009-02-17	ENSG00000136206	ENSG00000136206		"""Speedy homologs"""	16408	protein-coding gene	gene with protein product	"""Speedy E"""		"""Williams Beuren syndrome chromosome region 19"", ""speedy homolog E1 (Xenopus laevis)"""	WBSCR19		12073013	Standard	NM_175064		Approved	Ringo1, SPDYE	uc003tjf.3	Q8NFV5	OTTHUMG00000128985	ENST00000258704.3:c.511C>T	7.37:g.44043475C>T		Somatic		WXS	Illumina GAIIx	Phase_IV	Q9NTH5	Silent	SNP	pfam_Cell_cycle_regulatory_Spy1	p.L171	ENST00000258704.3	37	c.511	CCDS5475.1	7																																																																																			SPDYE1	-	pfam_Cell_cycle_regulatory_Spy1	ENSG00000136206		0.542	SPDYE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SPDYE1	HGNC	protein_coding	OTTHUMT00000250974.1	46	0.00	0	C	NM_175064		44043475	44043475	+1	no_errors	ENST00000258704	ensembl	human	known	69_37n	silent	33	13.16	5	SNP	0.412	T
TMEM214	54867	genome.wustl.edu	37	2	27262671	27262671	+	Missense_Mutation	SNP	G	G	A			TCGA-BH-A1FG-01A-11D-A13L-09	TCGA-BH-A1FG-11B-12D-A13O-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	311f2f1a-75c8-4fee-b31d-0815d71a3173	e0c48952-a56b-4c97-89b7-7bc9d7acde38	g.chr2:27262671G>A	ENST00000238788.9	+	14	1650	c.1588G>A	c.(1588-1590)Gcc>Acc	p.A530T	TMEM214_ENST00000404032.3_Missense_Mutation_p.A485T	NM_017727.4	NP_060197.4	Q6NUQ4	TM214_HUMAN	transmembrane protein 214	530					apoptotic process (GO:0006915)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						ACAAGCGTGTGCCAAGCTCTA	0.587																																						dbGAP											0													148.0	146.0	147.0					2																	27262671		2066	4200	6266	-	-	-	SO:0001583	missense	0				CCDS42664.1, CCDS46242.1	2p23.3	2013-06-19			ENSG00000119777	ENSG00000119777			25983	protein-coding gene	gene with protein product						23661706	Standard	NM_001083590		Approved	FLJ20254	uc002ria.4	Q6NUQ4	OTTHUMG00000151999	ENST00000238788.9:c.1588G>A	2.37:g.27262671G>A	ENSP00000238788:p.Ala530Thr	Somatic		WXS	Illumina GAIIx	Phase_IV	A6NNF2|B3KUI9|B5MCD8|D6W547|Q53SW1|Q69YH4|Q8NC45|Q8WZ37|Q9NXH2	Missense_Mutation	SNP	pfam_DUF2359_TMEM214	p.A530T	ENST00000238788.9	37	c.1588	CCDS42664.1	2	.	.	.	.	.	.	.	.	.	.	G	11.00	1.510785	0.27036	.	.	ENSG00000119777	ENST00000238788;ENST00000404032;ENST00000537397;ENST00000444135	T;T;T	0.44083	0.93;0.93;0.93	5.69	0.621	0.17643	.	0.394849	0.30320	N	0.009900	T	0.20740	0.0499	L	0.28115	0.83	0.09310	N	1	B;B	0.13594	0.008;0.002	B;B	0.11329	0.005;0.006	T	0.11518	-1.0584	10	0.18276	T	0.48	-0.149	1.656	0.02782	0.3932:0.1298:0.3438:0.1331	.	485;530	Q6NUQ4-2;Q6NUQ4	.;TM214_HUMAN	T	530;485;270;190	ENSP00000238788:A530T;ENSP00000384417:A485T;ENSP00000392442:A190T	ENSP00000238788:A530T	A	+	1	0	TMEM214	27116175	0.170000	0.23016	0.002000	0.10522	0.932000	0.56968	0.352000	0.20113	-0.170000	0.10816	0.561000	0.74099	GCC	TMEM214	-	pfam_DUF2359_TMEM214	ENSG00000119777		0.587	TMEM214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TMEM214	HGNC	protein_coding	OTTHUMT00000324748.1	106	0.00	0	G	NM_017727		27262671	27262671	+1	no_errors	ENST00000238788	ensembl	human	known	69_37n	missense	44	25.42	15	SNP	0.041	A
TNFSF4	7292	genome.wustl.edu	37	1	173155705	173155705	+	Missense_Mutation	SNP	C	C	T			TCGA-BH-A1FG-01A-11D-A13L-09	TCGA-BH-A1FG-11B-12D-A13O-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	311f2f1a-75c8-4fee-b31d-0815d71a3173	e0c48952-a56b-4c97-89b7-7bc9d7acde38	g.chr1:173155705C>T	ENST00000281834.3	-	3	638	c.502G>A	c.(502-504)Gga>Aga	p.G168R	TNFSF4_ENST00000367718.1_Missense_Mutation_p.G118R|TNFSF4_ENST00000488053.1_5'Flank	NM_003326.3	NP_003317.1	P23510	TNFL4_HUMAN	tumor necrosis factor (ligand) superfamily, member 4	168					acute inflammatory response (GO:0002526)|CD4-positive, alpha-beta T cell costimulation (GO:0035783)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nitrogen dioxide (GO:0035714)|cellular response to prostaglandin E stimulus (GO:0071380)|chemokine (C-C motif) ligand 11 production (GO:0071954)|cholesterol metabolic process (GO:0008203)|defense response to nematode (GO:0002215)|immune response (GO:0006955)|memory T cell activation (GO:0035709)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of regulatory T cell differentiation (GO:0045590)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell activation (GO:0050871)|positive regulation of CD4-positive, alpha-beta T cell costimulation (GO:1900281)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of cell proliferation (GO:0008284)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-4-dependent isotype switching to IgE isotypes (GO:2000572)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of memory T cell activation (GO:2000568)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T-helper 2 cell activation (GO:2000570)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of type 2 immune response (GO:0002830)|regulation of adaptive immune response (GO:0002819)|regulation of inflammatory response (GO:0050727)|response to nitrogen dioxide (GO:0035713)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation (GO:0042098)|T-helper 2 cell activation (GO:0035712)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor binding (GO:0005102)|tumor necrosis factor receptor superfamily binding (GO:0032813)			breast(2)|central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(3)|skin(1)|urinary_tract(1)	12						ATCAGTTCTCCGCCATTCACA	0.458																																						dbGAP											0													82.0	75.0	78.0					1																	173155705		2203	4300	6503	-	-	-	SO:0001583	missense	0			D90224	CCDS1306.1, CCDS72985.1	1q25	2008-07-31	2008-07-31		ENSG00000117586	ENSG00000117586		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11934	protein-coding gene	gene with protein product		603594	"""tax-transcriptionally activated glycoprotein 1, 34kD"""	TXGP1		1996093, 8076595	Standard	XM_005245475		Approved	OX-40L, gp34, CD252	uc001giw.3	P23510	OTTHUMG00000034838	ENST00000281834.3:c.502G>A	1.37:g.173155705C>T	ENSP00000281834:p.Gly168Arg	Somatic		WXS	Illumina GAIIx	Phase_IV	Q5JZA5|Q8IV74|Q9HCN9	Missense_Mutation	SNP	pfam_TNF,superfamily_Tumour_necrosis_fac-like,smart_TNF	p.G168R	ENST00000281834.3	37	c.502	CCDS1306.1	1	.	.	.	.	.	.	.	.	.	.	C	18.55	3.647846	0.67358	.	.	ENSG00000117586	ENST00000367718;ENST00000281834;ENST00000545292	D;D	0.94457	-3.43;-3.43	5.38	5.38	0.77491	Tumour necrosis factor (2);Tumour necrosis factor-like (1);	0.092760	0.47455	D	0.000237	D	0.96386	0.8821	M	0.69823	2.125	0.40310	D	0.978702	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96596	0.9441	10	0.87932	D	0	-18.1674	14.5119	0.67794	0.0:1.0:0.0:0.0	.	168;118	P23510;Q8IV74	TNFL4_HUMAN;.	R	118;168;118	ENSP00000356691:G118R;ENSP00000281834:G168R	ENSP00000281834:G168R	G	-	1	0	TNFSF4	171422328	0.951000	0.32395	0.993000	0.49108	0.504000	0.33889	3.235000	0.51328	2.802000	0.96397	0.655000	0.94253	GGA	TNFSF4	-	pfam_TNF,superfamily_Tumour_necrosis_fac-like,smart_TNF	ENSG00000117586		0.458	TNFSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TNFSF4	HGNC	protein_coding	OTTHUMT00000084271.1	48	0.00	0	C			173155705	173155705	-1	no_errors	ENST00000281834	ensembl	human	known	69_37n	missense	23	23.33	7	SNP	0.930	T
TRIP12	9320	genome.wustl.edu	37	2	230663600	230663601	+	Frame_Shift_Del	DEL	GA	GA	-			TCGA-BH-A1FG-01A-11D-A13L-09	TCGA-BH-A1FG-11B-12D-A13O-09	GA	GA					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	311f2f1a-75c8-4fee-b31d-0815d71a3173	e0c48952-a56b-4c97-89b7-7bc9d7acde38	g.chr2:230663600_230663601delGA	ENST00000283943.5	-	22	3425_3426	c.3247_3248delTC	c.(3247-3249)tccfs	p.S1083fs	TRIP12_ENST00000389045.3_Frame_Shift_Del_p.S813fs|TRIP12_ENST00000543084.1_3'UTR|TRIP12_ENST00000389044.4_Frame_Shift_Del_p.S1131fs	NM_001284214.1|NM_004238.1	NP_001271143.1|NP_004229.1	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	1083					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		CCTATTATTGGAGATGGTATCC	0.455																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827			12306	protein-coding gene	gene with protein product		604506				7776974	Standard	XM_005246961		Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000283943.5:c.3247_3248delTC	2.37:g.230663602_230663603delGA	ENSP00000283943:p.Ser1083fs	Somatic		WXS	Illumina GAIIx	Phase_IV	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	Frame_Shift_Del	DEL	pfam_HECT,superfamily_HECT,superfamily_ARM-type_fold,smart_HECT,pfscan_HECT,pfscan_WWE-dom	p.S1083fs	ENST00000283943.5	37	c.3248_3247	CCDS33391.1	2																																																																																			TRIP12	-	NULL	ENSG00000153827		0.455	TRIP12-001	KNOWN	basic|CCDS	protein_coding	TRIP12	HGNC	protein_coding	OTTHUMT00000331861.3	127	0.00	0	GA	NM_004238		230663600	230663601	-1	no_errors	ENST00000283943	ensembl	human	known	69_37n	frame_shift_del	72	20.65	19	DEL	1.000:1.000	-
WDR47	22911	genome.wustl.edu	37	1	109553818	109553818	+	Missense_Mutation	SNP	A	A	C			TCGA-BH-A1FG-01A-11D-A13L-09	TCGA-BH-A1FG-11B-12D-A13O-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	311f2f1a-75c8-4fee-b31d-0815d71a3173	e0c48952-a56b-4c97-89b7-7bc9d7acde38	g.chr1:109553818A>C	ENST00000369962.3	-	5	1072	c.850T>G	c.(850-852)Ttg>Gtg	p.L284V	WDR47_ENST00000369965.4_Missense_Mutation_p.L284V|WDR47_ENST00000361054.3_Missense_Mutation_p.L256V|WDR47_ENST00000357672.3_Missense_Mutation_p.L256V|WDR47_ENST00000400794.3_Missense_Mutation_p.L291V			O94967	WDR47_HUMAN	WD repeat domain 47	284					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)		AGAGGAGTCAAAAGATCAGCA	0.408																																						dbGAP											0													245.0	259.0	254.0					1																	109553818		2203	4296	6499	-	-	-	SO:0001583	missense	0			AB020700	CCDS30787.1, CCDS44186.1, CCDS44187.1	1p13.3	2013-01-09			ENSG00000085433	ENSG00000085433		"""WD repeat domain containing"""	29141	protein-coding gene	gene with protein product		615734				10048485	Standard	NM_014969		Approved	KIAA0893	uc001dwl.3	O94967	OTTHUMG00000011734	ENST00000369962.3:c.850T>G	1.37:g.109553818A>C	ENSP00000358979:p.Leu284Val	Somatic		WXS	Illumina GAIIx	Phase_IV	A8MX09|Q5TYV7|Q5TYV8|Q5TYV9|Q8IXT7|Q8IYU9	Missense_Mutation	SNP	pfam_WD40_repeat,superfamily_WD40_repeat_dom,smart_LisH_dimerisation,smart_CTLH_C,smart_WD40_repeat,pfscan_LisH_dimerisation,pfscan_CTLH_C,pfscan_WD40_repeat,pfscan_WD40_repeat_dom	p.L291V	ENST00000369962.3	37	c.871	CCDS44187.1	1	.	.	.	.	.	.	.	.	.	.	A	13.73	2.323417	0.41096	.	.	ENSG00000085433	ENST00000400794;ENST00000369962;ENST00000361054;ENST00000369965;ENST00000357672	T;T;T;T;T	0.54479	0.57;0.6;0.59;0.57;0.59	5.46	1.28	0.21552	.	0.000000	0.64402	D	0.000003	T	0.40322	0.1112	L	0.27053	0.805	0.48185	D	0.999607	D;D;D;D	0.69078	0.996;0.997;0.997;0.996	D;D;D;D	0.78314	0.986;0.991;0.991;0.986	T	0.18366	-1.0339	10	0.23302	T	0.38	-1.307	10.5488	0.45077	0.6535:0.0:0.3465:0.0	.	256;291;284;284	O94967-2;A8MX09;O94967;O94967-3	.;.;WDR47_HUMAN;.	V	291;284;256;284;256	ENSP00000383599:L291V;ENSP00000358979:L284V;ENSP00000354339:L256V;ENSP00000358982:L284V;ENSP00000350301:L256V	ENSP00000350301:L256V	L	-	1	2	WDR47	109355341	1.000000	0.71417	0.996000	0.52242	0.992000	0.81027	2.650000	0.46665	0.325000	0.23359	0.460000	0.39030	TTG	WDR47	-	NULL	ENSG00000085433		0.408	WDR47-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	WDR47	HGNC	protein_coding	OTTHUMT00000032414.2	78	0.00	0	A	NM_014969		109553818	109553818	-1	no_errors	ENST00000400794	ensembl	human	known	69_37n	missense	62	12.68	9	SNP	0.995	C
WDR54	84058	genome.wustl.edu	37	2	74652076	74652076	+	Silent	SNP	A	A	G			TCGA-BH-A1FG-01A-11D-A13L-09	TCGA-BH-A1FG-11B-12D-A13O-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	311f2f1a-75c8-4fee-b31d-0815d71a3173	e0c48952-a56b-4c97-89b7-7bc9d7acde38	g.chr2:74652076A>G	ENST00000348227.4	+	7	697	c.609A>G	c.(607-609)acA>acG	p.T203T	WDR54_ENST00000461531.1_3'UTR|WDR54_ENST00000409791.1_Silent_p.T151T	NM_032118.2	NP_115494.1	Q9H977	WDR54_HUMAN	WD repeat domain 54	203										breast(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	9						CAGAATTCACATTATTGACCC	0.527																																						dbGAP											0													191.0	157.0	169.0					2																	74652076		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AK023015	CCDS1940.1	2p13.1	2013-01-09			ENSG00000005448	ENSG00000005448		"""WD repeat domain containing"""	25770	protein-coding gene	gene with protein product						12477932	Standard	NM_032118		Approved	FLJ12953	uc002slb.3	Q9H977	OTTHUMG00000129951	ENST00000348227.4:c.609A>G	2.37:g.74652076A>G		Somatic		WXS	Illumina GAIIx	Phase_IV	D6W5I3|Q53H85|Q86V45	Silent	SNP	pfam_WD40_repeat,superfamily_WD40_repeat_dom,smart_WD40_repeat,pfscan_WD40_repeat,pfscan_WD40_repeat_dom	p.T203	ENST00000348227.4	37	c.609	CCDS1940.1	2																																																																																			WDR54	-	superfamily_WD40_repeat_dom,smart_WD40_repeat,pfscan_WD40_repeat_dom	ENSG00000005448		0.527	WDR54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	WDR54	HGNC	protein_coding	OTTHUMT00000252213.1	70	0.00	0	A	NM_032118		74652076	74652076	+1	no_errors	ENST00000348227	ensembl	human	known	69_37n	silent	50	25.00	17	SNP	0.420	G
YIPF6	286451	genome.wustl.edu	37	X	67741223	67741223	+	Silent	SNP	A	A	G			TCGA-BH-A1FG-01A-11D-A13L-09	TCGA-BH-A1FG-11B-12D-A13O-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none	1		Illumina GAIIx	311f2f1a-75c8-4fee-b31d-0815d71a3173	e0c48952-a56b-4c97-89b7-7bc9d7acde38	g.chrX:67741223A>G	ENST00000462683.1	+	5	1062	c.318A>G	c.(316-318)caA>caG	p.Q106Q	YIPF6_ENST00000374622.2_Silent_p.Q63Q	NM_173834.3	NP_776195.2	Q96EC8	YIPF6_HUMAN	Yip1 domain family, member 6	106					intestinal epithelial cell development (GO:0060576)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|urinary_tract(1)	7						GAATGCTGCAAAGAGACTCTG	0.418																																						dbGAP											0													117.0	101.0	106.0					X																	67741223		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			BC012469	CCDS14389.1, CCDS56604.1	Xq13.1	2008-02-05			ENSG00000181704	ENSG00000181704		"""Yip1 domain family"""	28304	protein-coding gene	gene with protein product						12477932	Standard	NM_173834		Approved	MGC21416, FinGER6	uc004dwz.3	Q96EC8	OTTHUMG00000021745	ENST00000462683.1:c.318A>G	X.37:g.67741223A>G		Somatic		WXS	Illumina GAIIx	Phase_IV	B4E1U7|G5E997|Q5JP08	Silent	SNP	pfam_Yip1	p.Q106	ENST00000462683.1	37	c.318	CCDS14389.1	X																																																																																			YIPF6	-	pfam_Yip1	ENSG00000181704		0.418	YIPF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	YIPF6	HGNC	protein_coding	OTTHUMT00000057016.1	170	0.00	0	A	NM_173834		67741223	67741223	+1	no_errors	ENST00000462683	ensembl	human	known	69_37n	silent	89	42.95	67	SNP	0.981	G
