#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_ENSG_ID	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_Ens_Gene	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GMAF	i_HGNC	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_Normal_Alt_Count	i_Normal_Ref_Count	i_Normal_VAF	i_ORegAnno_bin	i_PurityEst	i_RNA_Tum_Ref_count	i_RNA_Tum_VAF	i_RNA_Tum_Var_count	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Tier	i_Tumor_Alt_Count	i_Tumor_Ref_Count	i_Tumor_VAF	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_WGS_Norm_Ref_count	i_WGS_Norm_VAF	i_WGS_Norm_Var_count	i_WGS_Tum_Ref_count	i_WGS_Tum_VAF	i_WGS_Tum_Var_count	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	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_deletion_substructures	i_domain	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	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_rs_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
CHD6	84181	genome.wustl.edu	37	20	40102151	40102151	+	Silent	SNP	G	G	T			TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr20:40102151G>T	ENST00000373233.3	-	17	2652	c.2475C>A	c.(2473-2475)acC>acA	p.T825T	CHD6_ENST00000309279.7_Intron	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	825	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				TTCGCTCATAGGTGTATCTGA	0.512																																																	0								ENSG00000124177						71.0	64.0	66.0					20																	40102151		2203	4300	6503	CHD6	SO:0001819	synonymous_variant	0			-	HGNC	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.2475C>A	20.37:g.40102151G>T		Somatic	0	34	0.00		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	26	13.33	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_SNF2_N,pfam_Chromo_domain,pfam_Helicase_C,pfam_Helicase/UvrB_dom,pfam_BRK_domain,pfam_DNA/RNA_helicase_DEAD/DEAH_N,superfamily_P-loop_NTPase,superfamily_Chromodomain-like,smart_Chromo_domain/shadow,smart_Helicase_ATP-bd,smart_Helicase_C,smart_BRK_domain,pfscan_Helicase_ATP-bd,pfscan_Helicase_C,pfscan_Chromo_domain/shadow	p.T825	ENST00000373233.3	37	c.2475	CCDS13317.1	20																																																																																			-	pfam_Helicase_C,superfamily_P-loop_NTPase,smart_Helicase_C,pfscan_Helicase_C		0.512	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CHD6	protein_coding	OTTHUMT00000079270.1	G		-		40102151	-1	no_errors	ENST00000373233	ensembl	human	known	74_37	silent	SNP	1.000	T
GAPVD1	26130	genome.wustl.edu	37	9	128025963	128025989	+	Intron	DEL	CAGCACTCCATCTGTAGGTATGTCTGT	CAGCACTCCATCTGTAGGTATGTCTGT	-	rs551743640|rs71374244|rs143312600	byFrequency	TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	CAGCACTCCATCTGTAGGTATGTCTGT	CAGCACTCCATCTGTAGGTATGTCTGT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr9:128025963_128025989delCAGCACTCCATCTGTAGGTATGTCTGT	ENST00000495955.1	+	1	92				GAPVD1_ENST00000394083.2_Intron|GAPVD1_ENST00000394104.2_Intron|GAPVD1_ENST00000469528.1_3'UTR|GAPVD1_ENST00000394105.2_Intron|GAPVD1_ENST00000394084.1_Intron|GAPVD1_ENST00000297933.6_Intron|GAPVD1_ENST00000265956.4_Intron|GAPVD1_ENST00000470056.1_Intron			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1						endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of protein transport (GO:0051223)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	GTPase activating protein binding (GO:0032794)|GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						CTAAGTGGCACAGCACTCCATCTGTAGGTATGTCTGTCAGCACTCCA	0.564														2105	0.420327	0.4516	0.3818	5008	,	,		19587	0.4454		0.3777	False		,,,				2504	0.4233																0								ENSG00000165219																																			GAPVD1	SO:0001627	intron_variant	0				HGNC		CCDS65130.1, CCDS65131.1, CCDS65132.1	9q34.11	2008-02-05			ENSG00000165219	ENSG00000165219			23375	protein-coding gene	gene with protein product		611714					Standard	XM_005251901		Approved	DKFZP434C212, KIAA1521	uc004bpr.3	Q14C86	OTTHUMG00000020678	ENST00000495955.1:c.-199+1725CAGCACTCCATCTGTAGGTATGTCTGT>-	9.37:g.128025963_128025989delCAGCACTCCATCTGTAGGTATGTCTGT		Somatic	NA	NA	NA		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Splice_Site	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000495955.1	37	c.NULL		9																																																																																			-	-		0.564	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	GAPVD1	protein_coding	OTTHUMT00000355644.1	CAGCACTCCATCTGTAGGTATGTCTGT				128025989	+1	no_errors	ENST00000469528	ensembl	human	known	74_37	splice_site_del	DEL	1.000:1.000:1.000:1.000:1.000:0.999:0.996:0.980:0.970:0.963:0.961:0.959:0.952:0.948:0.947:0.950:0.961:0.966:0.966:0.969:0.974:0.982:0.984:0.985:0.984:0.985:0.993	-
MUC5B	727897	genome.wustl.edu	37	11	1265292	1265292	+	Silent	SNP	G	G	A	rs60084884	byFrequency	TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr11:1265292G>A	ENST00000529681.1	+	31	7240	c.7182G>A	c.(7180-7182)ggG>ggA	p.G2394G	MUC5B_ENST00000447027.1_Silent_p.G2397G|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2394	7 X Cys-rich subdomain repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		AGCAGGTGGGGAAGTTCAAGA	0.627													g|||	251	0.0501198	0.0817	0.0403	5008	,	,		19083	0.002		0.0388	False		,,,				2504	0.0757																0								ENSG00000117983	G		88,1378		1,86,646	4.0	6.0	5.0		7182	-1.7	0.0	11		5	142,4258		6,130,2064	no	coding-synonymous	MUC5B	NM_002458.2		7,216,2710	AA,AG,GG		3.2273,6.0027,3.9209		2394/5763	1265292	230,5636	733	2200	2933	MUC5B	SO:0001819	synonymous_variant	0			-	HGNC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.7182G>A	11.37:g.1265292G>A		Somatic	0	17	0.00		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	12	14	46.15	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_VWF_type-D,pfam_Unchr_dom_Cys-rich,pfam_TIL_dom,pfam_VWF_C,superfamily_TIL_dom,smart_VWF_type-D,smart_Unchr_dom_Cys-rich,smart_VWC_out,smart_VWF_C,smart_Cys_knot_C,pfscan_Cys_knot_C,pfscan_VWF_C	p.G2397	ENST00000529681.1	37	c.7191	CCDS44515.2	11																																																																																			-	NULL		0.627	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	MUC5B	protein_coding	OTTHUMT00000390041.2	G	XM_001126093	-		1265292	+1	no_errors	ENST00000447027	ensembl	human	known	74_37	silent	SNP	0.000	A
KRTAP4-5	85289	genome.wustl.edu	37	17	39305800	39305814	+	In_Frame_Del	DEL	TGGATTCACAGCAAT	TGGATTCACAGCAAT	-	rs141998775|rs377168597		TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	TGGATTCACAGCAAT	TGGATTCACAGCAAT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr17:39305800_39305814delTGGATTCACAGCAAT	ENST00000343246.4	-	1	240_254	c.206_220delATTGCTGTGAATCCA	c.(205-222)tattgctgtgaatccagc>tgc	p.69_74YCCESS>C		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	69	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			cggcagcagctggattcacagcaataggggcggca	0.665																																																	0								ENSG00000198271																																			KRTAP4-5	SO:0001651	inframe_deletion	0				HGNC	AJ406937	CCDS32650.1	17q21.2	2013-06-25			ENSG00000198271	ENSG00000198271		"""Keratin associated proteins"""	18899	protein-coding gene	gene with protein product						11279113	Standard	NM_033188		Approved	KAP4.5	uc002hwb.3	Q9BYR2	OTTHUMG00000133638	ENST00000343246.4:c.206_220delATTGCTGTGAATCCA	17.37:g.39305800_39305814delTGGATTCACAGCAAT	ENSP00000340546:p.Tyr69_Ser74delinsCys	Somatic	NA	NA	NA		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA		In_Frame_Del	DEL	NA	NA	NA	NA	NA	NA	NULL	p.YCCESS69in_frame_delC	ENST00000343246.4	37	c.220_206	CCDS32650.1	17																																																																																			-	NULL		0.665	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KRTAP4-5	protein_coding	OTTHUMT00000257783.1	TGGATTCACAGCAAT				39305814	-1	no_errors	ENST00000343246	ensembl	human	known	74_37	in_frame_del	DEL	0.689:0.524:0.472:0.042:0.004:0.003:0.006:0.126:0.849:0.943:0.982:0.981:0.896:0.000:0.000	-
APBA2	321	genome.wustl.edu	37	15	29393906	29393906	+	Missense_Mutation	SNP	G	G	T			TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr15:29393906G>T	ENST00000558402.1	+	11	2042	c.1443G>T	c.(1441-1443)caG>caT	p.Q481H	APBA2_ENST00000558330.1_Missense_Mutation_p.Q469H|APBA2_ENST00000561069.1_Missense_Mutation_p.Q481H|APBA2_ENST00000558259.1_Missense_Mutation_p.Q481H|APBA2_ENST00000411764.1_Missense_Mutation_p.Q469H			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	481	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		CAGCCTCTCAGGACTGCATCG	0.577																																																	0								ENSG00000034053						86.0	62.0	71.0					15																	29393906		2203	4300	6503	APBA2	SO:0001583	missense	0			-	HGNC	AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"""X11-like"", ""amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"""	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.1443G>T	15.37:g.29393906G>T	ENSP00000453293:p.Gln481His	Somatic	0	26	0.00		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	37	9.76	E9PGI4|O60571|Q5XKC0	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_PTB/PI_dom,pfam_PDZ,superfamily_PDZ,smart_PTB/PI_dom,smart_PDZ,pfscan_PDZ,pfscan_PTB/PI_dom	p.Q481H	ENST00000558402.1	37	c.1443	CCDS10022.1	15	.	.	.	.	.	.	.	.	.	.	G	17.98	3.519651	0.64634	.	.	ENSG00000034053	ENST00000411764;ENST00000219865;ENST00000382938	T	0.55760	0.5	4.47	-0.63	0.11530	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.133176	0.50627	D	0.000118	T	0.62429	0.2427	L	0.55481	1.735	0.58432	D	0.999997	D;D;D;D	0.76494	0.997;0.998;0.999;0.999	D;D;D;D	0.91635	0.972;0.986;0.999;0.979	T	0.62267	-0.6890	10	0.87932	D	0	.	10.3879	0.44152	0.4494:0.0:0.5506:0.0	.	469;173;469;481	Q5XKC0;Q6ZVB1;E9PGI4;Q99767	.;.;.;APBA2_HUMAN	H	469;481;173	ENSP00000409312:Q469H	ENSP00000219865:Q481H	Q	+	3	2	APBA2	27181198	1.000000	0.71417	0.971000	0.41717	0.976000	0.68499	0.729000	0.26028	0.002000	0.14630	-0.150000	0.13652	CAG	-	pfam_PTB/PI_dom,smart_PTB/PI_dom,pfscan_PTB/PI_dom		0.577	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	APBA2	protein_coding	OTTHUMT00000251362.3	G	NM_005503	-		29393906	+1	no_errors	ENST00000558259	ensembl	human	known	74_37	missense	SNP	0.998	T
PLXNB3	5365	genome.wustl.edu	37	X	153033837	153033837	+	Missense_Mutation	SNP	G	G	T			TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chrX:153033837G>T	ENST00000361971.5	+	4	1334	c.1220G>T	c.(1219-1221)gGg>gTg	p.G407V	PLXNB3_ENST00000538282.1_Missense_Mutation_p.G60V|U52111.14_ENST00000434284.1_RNA|PLXNB3_ENST00000538543.1_Intron|PLXNB3_ENST00000538776.1_Missense_Mutation_p.G60V|U52111.14_ENST00000416854.1_RNA|PLXNB3_ENST00000538966.1_Missense_Mutation_p.G430V	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	407	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)			central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					CAGGCAGATGGGCACATGATA	0.697																																																	0								ENSG00000198753						39.0	37.0	38.0					X																	153033837		2202	4297	6499	PLXNB3	SO:0001583	missense	0			-	HGNC	AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"""Plexins"""	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.1220G>T	X.37:g.153033837G>T	ENSP00000355378:p.Gly407Val	Somatic	0	17	0.00		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	14	22.22	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Plexin_cytoplasmic_RasGAP_dom,pfam_IPT,pfam_Plexin_repeat,pfam_Semap_dom,superfamily_Semap_dom,superfamily_Rho_GTPase_activation_prot,superfamily_Ig_E-set,superfamily_Plexin-like_fold,smart_Semap_dom,smart_Plexin-like_fold,smart_IPT,pfscan_Semap_dom	p.G430V	ENST00000361971.5	37	c.1289	CCDS14729.1	X	.	.	.	.	.	.	.	.	.	.	G	16.11	3.030184	0.54790	.	.	ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776;ENST00000538282	T;T;T;T	0.11495	2.77;2.77;3.46;3.46	4.83	4.83	0.62350	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.283230	0.32987	N	0.005408	T	0.34366	0.0895	M	0.83118	2.625	0.58432	D	0.999992	D;D;D;D	0.89917	0.999;1.0;0.999;0.999	D;D;D;D	0.85130	0.973;0.997;0.984;0.991	T	0.12091	-1.0561	10	0.59425	D	0.04	.	11.9485	0.52942	0.0:0.1716:0.8284:0.0	.	60;89;430;407	B7Z3H9;B7Z9A5;F5H773;Q9ULL4	.;.;.;PLXB3_HUMAN	V	430;407;60;60	ENSP00000442736:G430V;ENSP00000355378:G407V;ENSP00000445569:G60V;ENSP00000441919:G60V	ENSP00000355378:G407V	G	+	2	0	PLXNB3	152687031	1.000000	0.71417	0.849000	0.33467	0.471000	0.32888	3.242000	0.51384	2.113000	0.64589	0.513000	0.50165	GGG	-	pfam_Semap_dom,superfamily_Semap_dom,smart_Semap_dom,pfscan_Semap_dom		0.697	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	PLXNB3	protein_coding	OTTHUMT00000061063.1	G		-		153033837	+1	no_errors	ENST00000538966	ensembl	human	known	74_37	missense	SNP	0.996	T
LRRC48	83450	genome.wustl.edu	37	17	17896105	17896105	+	Silent	SNP	C	C	T			TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr17:17896105C>T	ENST00000399187.1	+	6	689	c.471C>T	c.(469-471)tgC>tgT	p.C157C	LRRC48_ENST00000411504.2_Silent_p.C157C|LRRC48_ENST00000313838.8_Silent_p.C157C|LRRC48_ENST00000584166.1_Silent_p.C157C|LRRC48_ENST00000399182.1_Silent_p.C157C	NM_031294.3	NP_112584.3	Q9H069	LRC48_HUMAN	leucine rich repeat containing 48	157						cytoplasm (GO:0005737)				breast(1)|large_intestine(2)|lung(2)|pancreas(1)|urinary_tract(1)	7	all_neural(463;0.228)					GGTTCAAGTGCCTGCGGACGC	0.532																																																	0								ENSG00000171962						58.0	59.0	59.0					17																	17896105		2036	4172	6208	LRRC48	SO:0001819	synonymous_variant	0			-	HGNC	AK093317	CCDS45622.1, CCDS45623.1	17p11.2	2014-07-18			ENSG00000171962	ENSG00000171962			25384	protein-coding gene	gene with protein product						11997338, 23354437	Standard	NM_001130090		Approved	DKFZP586M1120	uc021trk.1	Q9H069	OTTHUMG00000059355	ENST00000399187.1:c.471C>T	17.37:g.17896105C>T		Somatic	0	46	0.00		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	47	9.62	A8KAE6|Q86SF9|Q86W73|Q8IWG0	Silent	SNP	NA	NA	NA	NA	NA	NA	NULL	p.C157	ENST00000399187.1	37	c.471	CCDS45622.1	17																																																																																			-	NULL		0.532	LRRC48-001	KNOWN	non_canonical_conserved|non_canonical_U12|basic|appris_principal|CCDS	protein_coding	LRRC48	protein_coding	OTTHUMT00000131945.3	C	NM_031294	-		17896105	+1	no_errors	ENST00000313838	ensembl	human	known	74_37	silent	SNP	0.739	T
FREM3	166752	genome.wustl.edu	37	4	144614357	144614358	+	Splice_Site	INS	-	-	A			TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr4:144614357_144614358insA	ENST00000329798.5	-	2	5185		c.e2-2			NM_001168235.1	NP_001161707.1	P0C091	FREM3_HUMAN	FRAS1 related extracellular matrix 3						cell adhesion (GO:0007155)|cell communication (GO:0007154)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|prostate(1)	8						CAATGTCAGCTAAAAAAAAAGC	0.337																																																	0								ENSG00000183090																																			FREM3	SO:0001630	splice_region_variant	0				HGNC	BX091796	CCDS54808.1	4q31.21	2011-06-09			ENSG00000183090	ENSG00000183090			25172	protein-coding gene	gene with protein product		608946				15345741	Standard	NM_001168235		Approved		uc021xsj.1	P0C091	OTTHUMG00000161577	ENST00000329798.5:c.5186-2->T	4.37:g.144614366_144614366dupA		Somatic	0	30	0.00		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	41	8.89		Splice_Site	INS	NA	NA	NA	NA	NA	NA	-	e2-2	ENST00000329798.5	37	c.5186-3_5186-2	CCDS54808.1	4																																																																																			-	-		0.337	FREM3-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	FREM3	protein_coding	OTTHUMT00000365391.1	-	XM_094074		Intron	144614358	-1	no_errors	ENST00000329798	ensembl	human	putative	74_37	splice_site_ins	INS	1.000:0.000	A
RCVRN	5957	genome.wustl.edu	37	17	9801316	9801317	+	3'UTR	INS	-	-	GTGTGTGCGC	rs531533066|rs376748693	byFrequency	TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr17:9801316_9801317insGTGTGTGCGC	ENST00000226193.5	-	0	1138_1139				RCVRN_ENST00000570909.3_5'UTR	NM_002903.2	NP_002894.1	P35243	RECO_HUMAN	recoverin						phototransduction, visible light (GO:0007603)|positive regulation of guanylate cyclase activity (GO:0031284)|regulation of calcium ion transport (GO:0051924)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|visual perception (GO:0007601)	dendrite (GO:0030425)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)			endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|upper_aerodigestive_tract(1)	12						tgtgtgtgtgtgcgcgcgcgtg	0.589																																																	0								ENSG00000109047																																			RCVRN	SO:0001624	3_prime_UTR_variant	0				HGNC	BC001720	CCDS11151.1	17p13.1	2013-01-10		2006-09-26	ENSG00000109047	ENSG00000109047		"""EF-hand domain containing"""	9937	protein-coding gene	gene with protein product		179618		RCV1		1387789, 12507501, 1467959, 12789533	Standard	NM_002903		Approved		uc002gme.1	P35243	OTTHUMG00000130268	ENST00000226193.5:c.*96->GCGCACACAC	17.37:g.9801316_9801317insGTGTGTGCGC		Somatic	NA	NA	NA		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	Q53XL0	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000226193.5	37	NULL	CCDS11151.1	17																																																																																			-	-		0.589	RCVRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RCVRN	protein_coding	OTTHUMT00000252600.2	-	NM_002903			9801317	-1	no_errors	ENST00000570909	ensembl	human	putative	74_37	rna	INS	0.000:0.000	GTGTGTGCGC
GRIP1	23426	genome.wustl.edu	37	12	67072671	67072671	+	Missense_Mutation	SNP	G	G	C			TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr12:67072671G>C	ENST00000398016.3	-	1	82	c.14C>G	c.(13-15)tCt>tGt	p.S5C	GRIP1_ENST00000359742.4_Missense_Mutation_p.S5C|GRIP1_ENST00000286445.7_Missense_Mutation_p.S5C	NM_021150.3	NP_066973.2	Q96DT0	LEG12_HUMAN	glutamate receptor interacting protein 1	79					intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)			NS(3)|breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(19)|ovary(2)|prostate(2)|skin(1)	50			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		GCATTTAAAAGAGACAGCTAT	0.463																																																	0								ENSG00000155974						109.0	104.0	106.0					12																	67072671		1952	4154	6106	GRIP1	SO:0001583	missense	0			-	HGNC	AJ133439	CCDS41807.1	12q13.13	2008-05-02			ENSG00000155974	ENSG00000155974			18708	protein-coding gene	gene with protein product		604597				10197531	Standard	NM_021150		Approved		uc001stk.3	Q9Y3R0	OTTHUMG00000169019	ENST00000398016.3:c.14C>G	12.37:g.67072671G>C	ENSP00000381098:p.Ser5Cys	Somatic	0	41	0.00		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	51	8.93	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_PDZ,superfamily_PDZ,smart_PDZ,pfscan_PDZ	p.S5C	ENST00000398016.3	37	c.14	CCDS41807.1	12	.	.	.	.	.	.	.	.	.	.	G	17.51	3.407165	0.62399	.	.	ENSG00000155974	ENST00000398016;ENST00000359742;ENST00000286445;ENST00000538211;ENST00000545666	T;T;T;T;T	0.34472	1.88;1.85;1.87;1.89;1.36	5.61	5.61	0.85477	.	0.287831	0.34555	N	0.003878	T	0.44726	0.1307	N	0.14661	0.345	0.38248	D	0.941512	D;D	0.76494	0.999;0.999	D;D	0.76071	0.987;0.987	T	0.44590	-0.9318	9	.	.	.	-10.9598	19.6209	0.95654	0.0:0.0:1.0:0.0	.	5;5	F5H4N6;Q9Y3R0-3	.;.	C	5	ENSP00000381098:S5C;ENSP00000352780:S5C;ENSP00000286445:S5C;ENSP00000446047:S5C;ENSP00000439124:S5C	.	S	-	2	0	GRIP1	65358938	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.111000	0.77077	2.643000	0.89663	0.462000	0.41574	TCT	-	NULL		0.463	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GRIP1	protein_coding	OTTHUMT00000401975.2	G		-		67072671	-1	no_errors	ENST00000359742	ensembl	human	known	74_37	missense	SNP	1.000	C
BMF	90427	genome.wustl.edu	37	15	40400420	40400421	+	Intron	INS	-	-	ACACACAC	rs140876953|rs143336176|rs58924044	byFrequency	TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr15:40400420_40400421insACACACAC	ENST00000354670.4	-	2	230				BMF_ENST00000431415.3_5'Flank|BMF_ENST00000397573.1_5'Flank|BMF_ENST00000220446.4_5'Flank|BMF_ENST00000558057.1_5'UTR|BMF_ENST00000561282.1_5'Flank|BMF_ENST00000561360.1_5'Flank|BMF_ENST00000558774.1_Intron|BMF_ENST00000559701.1_Intron	NM_001003940.1	NP_001003940.1	Q96LC9	BMF_HUMAN	Bcl2 modifying factor						anoikis (GO:0043276)|apoptotic process (GO:0006915)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of apoptotic signaling pathway (GO:2001234)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of protein homooligomerization (GO:0032464)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(2)|lung(1)|ovary(1)	6		all_cancers(109;4.18e-18)|all_epithelial(112;6.15e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.29e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0516)		AGTGACTAGGAacacacacaca	0.589																																																	0								ENSG00000104081																																			BMF	SO:0001627	intron_variant	0				HGNC	BC060783	CCDS10052.1, CCDS32196.1, CCDS45223.1	15q14	2014-03-07			ENSG00000104081	ENSG00000104081			24132	protein-coding gene	gene with protein product		606266				11546872	Standard	NM_001003943		Approved	FLJ00065	uc001zkw.4	Q96LC9	OTTHUMG00000129875	ENST00000354670.4:c.4+38->GTGTGTGT	15.37:g.40400421_40400428dupACACACAC		Somatic	NA	NA	NA		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	Q2M396|Q6NT30|Q6NT56|Q6P9F6|Q7Z7D4|Q7Z7D5|Q9H7K7	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000354670.4	37	NULL	CCDS10052.1	15																																																																																			-	-		0.589	BMF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	BMF	protein_coding	OTTHUMT00000252119.1	-	NM_033503			40400421	-1	no_errors	ENST00000558057	ensembl	human	known	74_37	rna	INS	0.000:0.001	ACACACAC
GMPPB	29925	genome.wustl.edu	37	3	49755642	49755643	+	3'UTR	INS	-	-	CAGCGGCGG	rs576080161|rs543098573	byFrequency	TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr3:49755642_49755643insCAGCGGCGG	ENST00000480687.1	-	0	4741_4742				RNF123_ENST00000327697.6_Intron|AMIGO3_ENST00000535833.1_In_Frame_Ins_p.418_419insCRR|AMIGO3_ENST00000320431.7_In_Frame_Ins_p.418_419insCRR|RNF123_ENST00000497099.1_3'UTR|RNF123_ENST00000433785.1_Intron			Q9Y5P6	GMPPB_HUMAN	GDP-mannose pyrophosphorylase B						cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|mannose-1-phosphate guanylyltransferase activity (GO:0004475)			endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GTGTTTGGGGCcagcggcggca	0.693																																																	0								ENSG00000176020																																			AMIGO3	SO:0001624	3_prime_UTR_variant	0				HGNC	AF135421	CCDS2802.1, CCDS2803.1	3p21.31	2008-02-05			ENSG00000173540	ENSG00000173540	2.7.7.22		22932	protein-coding gene	gene with protein product		615320					Standard	NM_013334		Approved	KIAA1851	uc003cxl.1	Q9Y5P6	OTTHUMG00000158151	ENST00000480687.1:c.*3543->CCGCCGCTG	3.37:g.49755643_49755651dupCAGCGGCGG		Somatic	NA	NA	NA		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	A8K6N5|Q9H7U3	In_Frame_Ins	INS	NA	NA	NA	NA	NA	NA	pfam_Leu-rich_rpt,smart_Leu-rich_rpt_typical-subtyp,smart_Ig_sub,smart_Ig_sub2,pfscan_Ig-like_dom	p.419in_frame_insCRR	ENST00000480687.1	37	c.1257_1256	CCDS2803.1	3																																																																																			-	NULL		0.693	GMPPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AMIGO3	protein_coding	OTTHUMT00000350291.1	-	NM_013334			49755643	-1	no_errors	ENST00000320431	ensembl	human	known	74_37	in_frame_ins	INS	0.999:0.938	CAGCGGCGG
SLC13A4	26266	genome.wustl.edu	37	7	135377097	135377097	+	Silent	SNP	G	G	C			TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr7:135377097G>C	ENST00000354042.4	-	11	1883	c.1194C>G	c.(1192-1194)gtC>gtG	p.V398V	C7orf73_ENST00000422968.1_3'UTR	NM_012450.2	NP_036582.2	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 4	398					sodium ion transmembrane transport (GO:0035725)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	24						CCCAGCCAGGGACAAAGCCAG	0.438																																																	0								ENSG00000164707						65.0	75.0	71.0					7																	135377097		2203	4300	6503	SLC13A4	SO:0001819	synonymous_variant	0			-	HGNC	AF169301	CCDS5840.1	7q33	2013-07-18	2013-07-18		ENSG00000164707	ENSG00000164707		"""Solute carriers"""	15827	protein-coding gene	gene with protein product	"""sulphate transporter 1"""	604309	"""solute carrier family 13 (sodium/sulphate symporters), member 4"""			10535998	Standard	NM_012450		Approved	SUT-1, SUT1	uc003vta.3	Q9UKG4	OTTHUMG00000155539	ENST00000354042.4:c.1194C>G	7.37:g.135377097G>C		Somatic	0	82	0.00		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	19	122	13.48	A4D1Q4|Q8N631	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Na/sul_symport,pfam_Cit_transptr-like_dom,pfam_DctM	p.V398	ENST00000354042.4	37	c.1194	CCDS5840.1	7																																																																																			-	pfam_Na/sul_symport		0.438	SLC13A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC13A4	protein_coding	OTTHUMT00000340558.1	G	NM_012450	-		135377097	-1	no_errors	ENST00000354042	ensembl	human	known	74_37	silent	SNP	0.997	C
BCL11A	53335	genome.wustl.edu	37	2	60687039	60687039	+	3'UTR	SNP	G	G	T			TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr2:60687039G>T	ENST00000335712.6	-	0	3235				BCL11A_ENST00000537768.1_Intron|BCL11A_ENST00000477659.1_5'UTR|BCL11A_ENST00000359629.5_Intron|BCL11A_ENST00000538214.1_Intron|BCL11A_ENST00000356842.4_Intron	NM_022893.3	NP_075044.2	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A (zinc finger protein)						B cell differentiation (GO:0030183)|negative regulation of axon extension (GO:0030517)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein homooligomerization (GO:0032463)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of dendrite development (GO:0050773)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription corepressor activity (GO:0003714)			NS(1)|breast(6)|central_nervous_system(6)|endometrium(4)|kidney(1)|large_intestine(8)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	59			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			TACATGATATGTATTACAGAA	0.358			T	IGH@	B-CLL																																			Dom	yes		2	2p13	53335	B-cell CLL/lymphoma 11A		L	0								ENSG00000119866																																			BCL11A	SO:0001624	3_prime_UTR_variant	0			-	HGNC	AJ404611	CCDS1861.1, CCDS1862.1, CCDS46295.1	2p16.1	2013-01-08	2002-05-08		ENSG00000119866	ENSG00000119866		"""Zinc fingers, C2H2-type"""	13221	protein-coding gene	gene with protein product		606557	"""ecotropic viral integration site 9"""	EVI9		11719382, 18245381	Standard	NM_018014		Approved	BCL11A-XL, BCL11A-L, BCL11A-S, CTIP1, HBFQTL5, ZNF856	uc002sae.1	Q9H165	OTTHUMG00000129420	ENST00000335712.6:c.*500C>A	2.37:g.60687039G>T		Somatic	0	33	0.00		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	43	8.51	D6W5D7|Q86W14|Q8WU92|Q96JL6|Q9H163|Q9H164|Q9H3G9|Q9NWA7	RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000335712.6	37	NULL	CCDS1862.1	2																																																																																			-	-		0.358	BCL11A-001	KNOWN	basic|CCDS	protein_coding	BCL11A	protein_coding	OTTHUMT00000251579.2	G	NM_022893	-		60687039	-1	no_errors	ENST00000477659	ensembl	human	known	74_37	rna	SNP	1.000	T
PHF23	79142	genome.wustl.edu	37	17	7140765	7140765	+	Missense_Mutation	SNP	T	T	C			TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr17:7140765T>C	ENST00000320316.3	-	3	324	c.98A>G	c.(97-99)gAt>gGt	p.D33G	PHF23_ENST00000454255.2_Missense_Mutation_p.D29G|PHF23_ENST00000571362.1_Missense_Mutation_p.D33G|DVL2_ENST00000005340.5_5'Flank|PHF23_ENST00000570753.1_5'UTR|PHF23_ENST00000576955.1_5'UTR	NM_001284518.1|NM_024297.2	NP_001271447.1|NP_077273.2	Q9BUL5	PHF23_HUMAN	PHD finger protein 23	33							zinc ion binding (GO:0008270)			breast(4)|kidney(2)|large_intestine(6)|lung(3)	15						TTTGTTGAAATCCTCAATTGT	0.453																																																	0								ENSG00000040633						135.0	140.0	139.0					17																	7140765		1898	4139	6037	PHF23	SO:0001583	missense	0			-	HGNC	AK122791	CCDS42250.1, CCDS67143.1, CCDS67144.1	17p13.1	2014-08-13			ENSG00000040633	ENSG00000040633		"""Zinc fingers, PHD-type"""	28428	protein-coding gene	gene with protein product		612910					Standard	NM_024297		Approved	MGC2941, FLJ16355	uc002gfa.3	Q9BUL5	OTTHUMG00000177972	ENST00000320316.3:c.98A>G	17.37:g.7140765T>C	ENSP00000322579:p.Asp33Gly	Somatic	0	78	0.00		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	8	85	8.60	A1DZ74|B3KVH8|B4DLK6|D3DTN4|Q8IZK0|Q96HG7|Q9H5X0	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Znf_PHD-finger,superfamily_Znf_FYVE_PHD,smart_Znf_PHD	p.D33G	ENST00000320316.3	37	c.98	CCDS42250.1	17	.	.	.	.	.	.	.	.	.	.	T	27.1	4.803065	0.90623	.	.	ENSG00000040633	ENST00000320316;ENST00000454255;ENST00000043410	T;T	0.60424	0.19;0.23	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	T	0.70404	0.3220	L	0.52905	1.665	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.994	T	0.73541	-0.3950	10	0.87932	D	0	-9.1676	12.7759	0.57448	0.0:0.0:0.0:1.0	.	33;33	B4DLK6;Q9BUL5	.;PHF23_HUMAN	G	33;29;33	ENSP00000322579:D33G;ENSP00000414607:D29G	ENSP00000043410:D33G	D	-	2	0	PHF23	7081489	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.358000	0.79466	1.898000	0.54952	0.455000	0.32223	GAT	-	NULL		0.453	PHF23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PHF23	protein_coding	OTTHUMT00000440047.1	T	NM_024297	-		7140765	-1	no_errors	ENST00000320316	ensembl	human	known	74_37	missense	SNP	1.000	C
AMZ1	155185	genome.wustl.edu	37	7	2741852	2741906	+	Intron	DEL	TGTGTGCTACTCTGCCCCAGCCAGGCTGGCATTTTGCAGCCATGCAGCCTGGCTC	TGTGTGCTACTCTGCCCCAGCCAGGCTGGCATTTTGCAGCCATGCAGCCTGGCTC	-	rs798471|rs540419422|rs191436847|rs10624226|rs33915832|rs35358739|rs10694020|rs397762646	byFrequency	TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	TGTGTGCTACTCTGCCCCAGCCAGGCTGGCATTTTGCAGCCATGCAGCCTGGCTC	TGTGTGCTACTCTGCCCCAGCCAGGCTGGCATTTTGCAGCCATGCAGCCTGGCTC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr7:2741852_2741906delTGTGTGCTACTCTGCCCCAGCCAGGCTGGCATTTTGCAGCCATGCAGCCTGGCTC	ENST00000312371.4	+	3	672				AMZ1_ENST00000407112.1_Intron	NM_133463.1	NP_597720.1	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1								metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	16		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;5.03e-14)		CCTGCACCCTTGTGTGCTACTCTGCCCCAGCCAGGCTGGCATTTTGCAGCCATGCAGCCTGGCTCTGTGTCCTGC	0.624																																																	0								ENSG00000174945																																			AMZ1	SO:0001627	intron_variant	0				HGNC	AB075830	CCDS34589.1, CCDS64582.1	7p22.3	2008-01-17			ENSG00000174945	ENSG00000174945			22231	protein-coding gene	gene with protein product	"""archaemetzincin-1"""	615168				15972818	Standard	NM_133463		Approved	KIAA1950	uc003smr.1	Q400G9	OTTHUMG00000152111	ENST00000312371.4:c.305-450TGTGTGCTACTCTGCCCCAGCCAGGCTGGCATTTTGCAGCCATGCAGCCTGGCTC>-	7.37:g.2741852_2741906delTGTGTGCTACTCTGCCCCAGCCAGGCTGGCATTTTGCAGCCATGCAGCCTGGCTC		Somatic	NA	NA	NA		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	B3KRS0|Q8TF51	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000312371.4	37	NULL	CCDS34589.1	7																																																																																			-	-		0.624	AMZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AMZ1	protein_coding	OTTHUMT00000325244.1	TGTGTGCTACTCTGCCCCAGCCAGGCTGGCATTTTGCAGCCATGCAGCCTGGCTC	NM_133463			2741906	+1	no_errors	ENST00000485540	ensembl	human	known	74_37	rna	DEL	0.000:0.000:0.001:0.002:0.002:0.003:0.004:0.003:0.001:0.000:0.000:0.004:0.003:0.003:0.002:0.002:0.002:0.003:0.003:0.001:0.005:0.071:0.077:0.080:0.076:0.071:0.067:0.056:0.014:0.004:0.001:0.002:0.002:0.000:0.001:0.002:0.003:0.004:0.005:0.002:0.002:0.002:0.002:0.002:0.002:0.003:0.000:0.001:0.001:0.000:0.000:0.000:0.001:0.000:0.000	-
ARFGEF2	10564	genome.wustl.edu	37	20	47626792	47626792	+	Missense_Mutation	SNP	C	C	T			TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr20:47626792C>T	ENST00000371917.4	+	27	3608	c.3608C>T	c.(3607-3609)gCg>gTg	p.A1203V		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	1203					endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)	p.A1203V(1)		breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			CGGGACATGGCGATCCGCTGC	0.537																																					Esophageal Squamous(176;1738 1974 26285 33069 35354)												1	Substitution - Missense(1)	endometrium(1)						ENSG00000124198						123.0	111.0	115.0					20																	47626792		2203	4300	6503	ARFGEF2	SO:0001583	missense	0			-	HGNC	AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"""A-kinase anchor proteins"""	15853	protein-coding gene	gene with protein product	"""Brefeldin A-inhibited guanine nucleotide-exchange protein 2"""	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.3608C>T	20.37:g.47626792C>T	ENSP00000360985:p.Ala1203Val	Somatic	0	30	0.00		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	26	13.33	Q5TFT9|Q9NTS1	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Sec7_dom,pfam_DUF1981_Sec7_assoc,superfamily_Sec7_dom,superfamily_ARM-type_fold,smart_Sec7_dom,pfscan_Sec7_dom	p.A1203V	ENST00000371917.4	37	c.3608	CCDS13411.1	20	.	.	.	.	.	.	.	.	.	.	C	8.985	0.976386	0.18736	.	.	ENSG00000124198	ENST00000371917	T	0.74632	-0.86	5.33	4.23	0.50019	Domain of unknown function DUF1981, SEC7 associated (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.059297	0.64402	N	0.000003	T	0.21801	0.0525	N	0.00006	-3.2	0.28184	N	0.928024	B	0.02656	0.0	B	0.01281	0.0	T	0.46048	-0.9219	10	0.02654	T	1	.	11.2531	0.49037	0.0:0.0717:0.0:0.9283	.	1203	Q9Y6D5	BIG2_HUMAN	V	1203	ENSP00000360985:A1203V	ENSP00000360985:A1203V	A	+	2	0	ARFGEF2	47060199	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.256000	0.72473	0.979000	0.38497	-0.238000	0.12139	GCG	-	pfam_DUF1981_Sec7_assoc,superfamily_ARM-type_fold		0.537	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ARFGEF2	protein_coding	OTTHUMT00000079627.1	C	NM_006420	-		47626792	+1	no_errors	ENST00000371917	ensembl	human	known	74_37	missense	SNP	1.000	T
COL4A3	1285	genome.wustl.edu	37	2	228104874	228104874	+	Missense_Mutation	SNP	C	C	T			TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr2:228104874C>T	ENST00000396578.3	+	3	322	c.160C>T	c.(160-162)Cct>Tct	p.P54S	AC097662.2_ENST00000606119.1_RNA|AC097662.2_ENST00000437673.1_RNA|AC097662.2_ENST00000439598.2_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	54	Triple-helical region.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|collagen catabolic process (GO:0030574)|endothelial cell apoptotic process (GO:0072577)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|sensory perception of sound (GO:0007605)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metalloendopeptidase inhibitor activity (GO:0008191)|structural molecule activity (GO:0005198)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		GAAGGGCTTTCCTGGACCCCC	0.502																																																	0								ENSG00000169031						51.0	53.0	52.0					2																	228104874		1889	4125	6014	COL4A3	SO:0001583	missense	0			-	HGNC		CCDS42829.1	2q36-q37	2014-09-17			ENSG00000169031	ENSG00000169031		"""Collagens"""	2204	protein-coding gene	gene with protein product	"""tumstatin"""	120070				1737849	Standard	NM_000091		Approved		uc002vom.2	Q01955	OTTHUMG00000149891	ENST00000396578.3:c.160C>T	2.37:g.228104874C>T	ENSP00000379823:p.Pro54Ser	Somatic	0	35	0.00		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	43	8.51	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Collagen,pfam_Collagen_VI_NC,superfamily_C-type_lectin_fold,smart_Collagen_VI_NC	p.P54S	ENST00000396578.3	37	c.160	CCDS42829.1	2	.	.	.	.	.	.	.	.	.	.	C	17.53	3.412277	0.62511	.	.	ENSG00000169031	ENST00000396578;ENST00000328380;ENST00000335583;ENST00000396574;ENST00000315699	D	0.97665	-4.48	5.87	5.87	0.94306	.	0.112285	0.41097	D	0.000960	D	0.98099	0.9373	M	0.79614	2.46	0.36485	D	0.86806	D;D;D;D	0.89917	0.999;0.999;1.0;0.999	D;D;D;D	0.91635	0.967;0.982;0.999;0.995	D	0.99271	1.0893	10	0.21014	T	0.42	.	15.7708	0.78167	0.0:1.0:0.0:0.0	.	54;54;54;54	Q01955-5;Q01955-4;Q01955-2;Q01955	.;.;.;CO4A3_HUMAN	S	54	ENSP00000379823:P54S	ENSP00000323334:P54S	P	+	1	0	COL4A3	227813118	0.530000	0.26330	0.447000	0.26932	0.402000	0.30811	1.140000	0.31516	2.792000	0.96026	0.650000	0.86243	CCT	-	pfam_Collagen		0.502	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL4A3	protein_coding	OTTHUMT00000331409.2	C	NM_000091	-		228104874	+1	no_errors	ENST00000396578	ensembl	human	known	74_37	missense	SNP	0.853	T
PLIN4	729359	genome.wustl.edu	37	19	4499633	4499647	+	IGR	DEL	AGCTGGCCGGGGAGG	AGCTGGCCGGGGAGG	-	rs62131000|rs72100503|rs587644307|rs34068770|rs62131001	byFrequency	TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	AGCTGGCCGGGGAGG	AGCTGGCCGGGGAGG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr19:4499633_4499647delAGCTGGCCGGGGAGG	ENST00000301286.3	-	0	6341				HDGFRP2_ENST00000301284.4_In_Frame_Del_p.LAGEE585del|HDGFRP2_ENST00000586684.1_In_Frame_Del_p.LAGEE585del	NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4							cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						gccgaggagaagctggccggggaggagctggccgg	0.679														2593	0.517772	0.5091	0.4971	5008	,	,		9107	0.5476		0.5209	False		,,,				2504	0.5102																0								ENSG00000167674		,	2387,77		1193,1,38					,	3.1	0.0		dbSNP_130	25	5941,203		2952,37,83	no	coding,coding	HDGFRP2	NM_032631.2,NM_001001520.1	,	4145,38,121	A1A1,A1R,RR		3.304,3.125,3.2528	,	,		8328,280				HDGFRP2	SO:0001628	intergenic_variant	0				Uniprot_gn	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571		19.37:g.4499633_4499647delAGCTGGCCGGGGAGG		Somatic	NA	NA	NA		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	A6NEI2	In_Frame_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_LEDGF,pfam_PWWP_dom,smart_PWWP_dom,pfscan_PWWP_dom	p.EELAG578in_frame_del	ENST00000301286.3	37	c.1721_1735	CCDS45927.1	19																																																																																			-	NULL		0.679	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	HDGFRP2	protein_coding	OTTHUMT00000395095.1	AGCTGGCCGGGGAGG	XM_170901			4499647	+1	no_errors	ENST00000301284	ensembl	human	known	74_37	in_frame_del	DEL	0.074:0.085:0.097:0.108:0.119:0.130:0.141:0.151:0.162:0.172:0.183:0.193:0.203:0.213:0.223	-
ZNF28	7576	genome.wustl.edu	37	19	53303182	53303182	+	Missense_Mutation	SNP	T	T	C	rs142391659		TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr19:53303182T>C	ENST00000457749.2	-	4	2035	c.1916A>G	c.(1915-1917)gAg>gGg	p.E639G	ZNF28_ENST00000438150.2_Missense_Mutation_p.E586G|ZNF28_ENST00000360272.4_Missense_Mutation_p.E586G|ZNF28_ENST00000414252.2_Missense_Mutation_p.E586G	NM_006969.3	NP_008900.3	P17035	ZNF28_HUMAN	zinc finger protein 28	639					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|liver(1)|lung(10)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)		CTTGCCACACTCATTACACTT	0.428																																																	0								ENSG00000198538						193.0	181.0	185.0					19																	53303182		2203	4300	6503	ZNF28	SO:0001583	missense	0			-	HGNC	X52355	CCDS33093.1, CCDS33093.2	19q13.41	2013-01-08	2006-05-10		ENSG00000198538	ENSG00000198538		"""Zinc fingers, C2H2-type"", ""-"""	13073	protein-coding gene	gene with protein product			"""zinc finger protein 28 (KOX 24)"""				Standard	NR_036599		Approved	KOX24, DKFZp781D0275	uc002qad.3	P17035	OTTHUMG00000154564	ENST00000457749.2:c.1916A>G	19.37:g.53303182T>C	ENSP00000397693:p.Glu639Gly	Somatic	0	48	0.00		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	57	8.06	A8KAK9|B4E3G0|B9EIK7|Q5H9V1|Q5HYM9|Q6ZML9|Q6ZN56	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Znf_C2H2,pfam_Krueppel-associated_box,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	p.E639G	ENST00000457749.2	37	c.1916	CCDS33093.2	19	.	.	.	.	.	.	.	.	.	.	-	10.84	1.465403	0.26335	.	.	ENSG00000198538	ENST00000438150;ENST00000457749;ENST00000360272;ENST00000414252	T;T;T;T	0.35789	1.29;1.29;1.29;1.29	1.81	0.634	0.17718	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.40546	0.1121	L	0.47716	1.5	0.09310	N	1	D	0.60575	0.988	P	0.55615	0.78	T	0.22695	-1.0209	9	0.72032	D	0.01	.	5.8153	0.18490	0.2376:0.0:0.0:0.7624	.	639	P17035	ZNF28_HUMAN	G	586;639;586;586	ENSP00000412143:E586G;ENSP00000397693:E639G;ENSP00000353410:E586G;ENSP00000444965:E586G	ENSP00000353410:E586G	E	-	2	0	ZNF28	57994994	0.000000	0.05858	0.024000	0.17045	0.568000	0.35870	-0.093000	0.11111	-0.035000	0.13691	0.248000	0.18094	GAG	-	pfam_Znf_C2H2,smart_Znf_C2H2-like,pfscan_Znf_C2H2		0.428	ZNF28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF28	protein_coding	OTTHUMT00000336038.2	T	NM_006969	rs142391659		53303182	-1	no_errors	ENST00000457749	ensembl	human	known	74_37	missense	SNP	0.006	C
POTEE	445582	genome.wustl.edu	37	2	132022031	132022031	+	Silent	SNP	C	C	T			TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr2:132022031C>T	ENST00000356920.5	+	15	3097	c.3003C>T	c.(3001-3003)ggC>ggT	p.G1001G	PLEKHB2_ENST00000404460.1_Intron|PLEKHB2_ENST00000303908.3_Intron|POTEE_ENST00000358087.5_3'UTR	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	1001	Actin-like.				retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)											TGCTGTCTGGCGGCACCACCA	0.537																																																	0								ENSG00000188219						1.0	1.0	1.0					2																	132022031		335	417	752	POTEE	SO:0001819	synonymous_variant	0			-	HGNC	AY462868	CCDS46414.1	2q21.1	2014-04-10	2008-11-26	2008-11-26	ENSG00000188219	ENSG00000188219		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33895	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 2"""	608914	"""ANKRD26-like family C, member 1A"""	A26C1A			Standard	NM_001083538		Approved	POTE2, POTE-2, A26C1, POTE2gamma, CT104.2	uc002tsn.2	Q6S8J3	OTTHUMG00000186974	ENST00000356920.5:c.3003C>T	2.37:g.132022031C>T		Somatic	0	19	0.00		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	11	29.41	Q6S8J4|Q6S8J5|Q6S8J8	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Actin-related,pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,smart_Actin-related,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,prints_Actin-related	p.G1001	ENST00000356920.5	37	c.3003	CCDS46414.1	2																																																																																			-	pfam_Actin-related,smart_Actin-related		0.537	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	POTEE	protein_coding		C	NM_001083538	-		132022031	+1	no_errors	ENST00000356920	ensembl	human	known	74_37	silent	SNP	1.000	T
MLXIP	22877	genome.wustl.edu	37	12	122614518	122614518	+	Missense_Mutation	SNP	G	G	T			TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr12:122614518G>T	ENST00000319080.7	+	6	901	c.769G>T	c.(769-771)Ggg>Tgg	p.G257W	MLXIP_ENST00000538698.1_5'Flank					MLX interacting protein											NS(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;0.0659)		OV - Ovarian serous cystadenocarcinoma(86;0.000599)|Epithelial(86;0.00102)|BRCA - Breast invasive adenocarcinoma(302;0.233)		GCACAAGCACGGGGATGGATG	0.542																																					Esophageal Squamous(105;787 1493 16200 18566 52466)												0								ENSG00000175727						68.0	70.0	69.0					12																	122614518		2077	4220	6297	MLXIP	SO:0001583	missense	0			-	HGNC	AB020674	CCDS73540.1	12q21.31	2013-05-21				ENSG00000175727		"""Basic helix-loop-helix proteins"""	17055	protein-coding gene	gene with protein product		608090				10048485, 11073985	Standard	XM_006719290		Approved	MONDOA, KIAA0867, MIR, bHLHe36	uc001ubq.3	Q9HAP2		ENST00000319080.7:c.769G>T	12.37:g.122614518G>T	ENSP00000312834:p.Gly257Trp	Somatic	0	36	0.00		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	42	8.70		Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_bHLH_dom,superfamily_bHLH_dom,smart_bHLH_dom,pfscan_bHLH_dom	p.G257W	ENST00000319080.7	37	c.769		12	.	.	.	.	.	.	.	.	.	.	G	13.35	2.209512	0.39003	.	.	ENSG00000175727	ENST00000319080;ENST00000535430	T;T	0.33438	2.4;1.41	5.19	0.0971	0.14493	.	0.567049	0.19489	N	0.113040	T	0.45776	0.1359	.	.	.	0.40161	D	0.977062	D;D	0.89917	1.0;0.988	D;P	0.83275	0.996;0.708	T	0.32214	-0.9915	9	0.37606	T	0.19	-6.7613	5.5304	0.16980	0.3305:0.2424:0.427:0.0	.	257;257	Q9HAP2-3;Q9HAP2	.;MLXIP_HUMAN	W	257;8	ENSP00000312834:G257W;ENSP00000438206:G8W	ENSP00000312834:G257W	G	+	1	0	MLXIP	121180471	0.936000	0.31750	0.045000	0.18777	0.458000	0.32498	1.197000	0.32211	-0.287000	0.09064	-1.036000	0.02392	GGG	-	NULL		0.542	MLXIP-001	KNOWN	basic|appris_principal	protein_coding	MLXIP	protein_coding	OTTHUMT00000401718.2	G	NM_014938	-		122614518	+1	no_errors	ENST00000319080	ensembl	human	known	74_37	missense	SNP	0.007	T
VRTN	55237	genome.wustl.edu	37	14	74824312	74824312	+	Missense_Mutation	SNP	C	C	T	rs377542755		TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr14:74824312C>T	ENST00000256362.4	+	2	1067	c.826C>T	c.(826-828)Cgt>Tgt	p.R276C		NM_018228.2	NP_060698.2	Q9H8Y1	VRTN_HUMAN	vertebrae development associated	276					transposition, DNA-mediated (GO:0006313)		sequence-specific DNA binding (GO:0043565)|transposase activity (GO:0004803)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(15)|ovary(5)|prostate(2)|skin(1)|urinary_tract(1)	41						GCTGCTCAACCGTGAACCTGG	0.652																																																	0								ENSG00000133980	C	CYS/ARG	0,4406		0,0,2203	44.0	42.0	42.0		826	3.4	0.1	14		42	1,8599	1.2+/-3.3	0,1,4299	no	missense	VRTN	NM_018228.2	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	276/703	74824312	1,13005	2203	4300	6503	VRTN	SO:0001583	missense	0			-	HGNC	AK001673	CCDS9830.1	14q24.2	2012-12-07	2012-12-07	2010-10-20	ENSG00000133980	ENSG00000133980			20223	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 115"", ""vertebrae development homolog (pig)"""	C14orf115		21232157	Standard	NM_018228		Approved	FLJ10811, vertnin	uc001xpw.4	Q9H8Y1	OTTHUMG00000171208	ENST00000256362.4:c.826C>T	14.37:g.74824312C>T	ENSP00000256362:p.Arg276Cys	Somatic	0	43	0.00		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	6	59	9.23	Q9NVC7	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Transposase_8	p.R276C	ENST00000256362.4	37	c.826	CCDS9830.1	14	.	.	.	.	.	.	.	.	.	.	C	12.22	1.873727	0.33069	0.0	1.16E-4	ENSG00000133980	ENST00000256362	T	0.46819	0.86	5.2	3.39	0.38822	.	0.791785	0.11486	N	0.559193	T	0.42607	0.1210	N	0.14661	0.345	0.45554	D	0.998508	D	0.76494	0.999	P	0.57846	0.828	T	0.33979	-0.9847	10	0.87932	D	0	-6.7824	4.9155	0.13844	0.2107:0.6157:0.0:0.1736	.	276	Q9H8Y1	VRTN_HUMAN	C	276	ENSP00000256362:R276C	ENSP00000256362:R276C	R	+	1	0	VRTN	73894065	1.000000	0.71417	0.050000	0.19076	0.047000	0.14425	5.128000	0.64733	0.780000	0.33566	0.561000	0.74099	CGT	-	pfam_Transposase_8		0.652	VRTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	VRTN	protein_coding	OTTHUMT00000412339.1	C	NM_018228	-		74824312	+1	no_errors	ENST00000256362	ensembl	human	known	74_37	missense	SNP	0.846	T
LRRC71	149499	genome.wustl.edu	37	1	156904654	156904654	+	IGR	DEL	A	A	-	rs561157526		TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr1:156904654delA	ENST00000337428.7	+	0	1959				MIR765_ENST00000390226.1_RNA|ARHGEF11_ENST00000487682.1_5'UTR|ARHGEF11_ENST00000368194.3_3'UTR	NM_144702.2	NP_653303.2	Q8N4P6	LRC71_HUMAN	leucine rich repeat containing 71											endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|stomach(1)	12						AACTTTTCTTAAAAAAAAAAT	0.308																																																	0								ENSG00000132694																																			ARHGEF11	SO:0001628	intergenic_variant	0				HGNC	BC033790	CCDS44249.1	1q23.1	2011-02-14	2011-02-14	2011-02-14	ENSG00000160838	ENSG00000160838			26556	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 92"""	C1orf92		14702039	Standard	NM_144702		Approved	FLJ32884	uc001fqm.2	Q8N4P6	OTTHUMG00000041298		1.37:g.156904654delA		Somatic	0	21	0.00		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	11	21.43	Q96M24	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000337428.7	37	NULL	CCDS44249.1	1																																																																																			-	-		0.308	LRRC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ARHGEF11	protein_coding	OTTHUMT00000098961.1	A	NM_144702			156904654	-1	no_errors	ENST00000487682	ensembl	human	known	74_37	rna	DEL	0.863	-
SP100	6672	genome.wustl.edu	37	2	231334496	231334496	+	Intron	DEL	A	A	-	rs372197214		TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr2:231334496delA	ENST00000264052.5	+	15	1700				SP100_ENST00000409897.1_Intron|SP100_ENST00000341950.4_Frame_Shift_Del_p.L450fs|SP100_ENST00000409341.1_Intron|SP100_ENST00000409112.1_Intron|SP100_ENST00000427101.2_Intron|SP100_ENST00000409824.1_Intron|SP100_ENST00000340126.4_Intron	NM_003113.3	NP_003104.2	P23497	SP100_HUMAN	SP100 nuclear antigen						cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cellular component movement (GO:0051271)|negative regulation of DNA binding (GO:0043392)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of Fas signaling pathway (GO:1902044)|response to cytokine (GO:0034097)|response to interferon-gamma (GO:0034341)|response to retinoic acid (GO:0032526)|response to type I interferon (GO:0034340)|retinoic acid receptor signaling pathway (GO:0048384)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear periphery (GO:0034399)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(4)|upper_aerodigestive_tract(1)	25		Renal(207;0.0112)|all_lung(227;0.0335)|all_hematologic(139;0.0749)|Lung NSC(271;0.142)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		TCCCAAAGTTAAAAAAAAAAA	0.363																																																	0								ENSG00000067066																																			SP100	SO:0001627	intron_variant	0				HGNC	AF056322	CCDS2477.1, CCDS42832.1, CCDS56170.1, CCDS56171.1, CCDS56172.1, CCDS56173.1	2q37.1	2013-01-28	2005-11-30		ENSG00000067066	ENSG00000067066		"""Zinc fingers, PHD-type"""	11206	protein-coding gene	gene with protein product		604585	"""nuclear antigen Sp100"""			2258622, 8695863	Standard	NM_001080391		Approved		uc002vqu.1	P23497	OTTHUMG00000133203	ENST00000264052.5:c.1346-234A>-	2.37:g.231334496delA		Somatic	0	13	0.00		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	22	15.38	B4DDX5|B8ZZD8|E7EUA7|E9PH61|F8WFE2|O75450|Q13343|Q8TE34|Q96F70|Q96T24|Q96T95|Q9NP33|Q9UE32	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_Sp100	p.K453fs	ENST00000264052.5	37	c.1350	CCDS2477.1	2																																																																																			-	NULL		0.363	SP100-001	KNOWN	basic|CCDS	protein_coding	SP100	protein_coding	OTTHUMT00000256914.2	A	NM_003113			231334496	+1	no_errors	ENST00000341950	ensembl	human	known	74_37	frame_shift_del	DEL	0.007	-
PARP1	142	genome.wustl.edu	37	1	226549885	226549886	+	Intron	INS	-	-	T	rs368063214		TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr1:226549885_226549886insT	ENST00000366794.5	-	22	2992				PARP1_ENST00000490921.1_Intron	NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1						base-excision repair (GO:0006284)|cellular response to insulin stimulus (GO:0032869)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|gene expression (GO:0010467)|macrophage differentiation (GO:0030225)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein ADP-ribosylation (GO:0006471)|protein autoprocessing (GO:0016540)|protein poly-ADP-ribosylation (GO:0070212)|regulation of growth rate (GO:0040009)|signal transduction involved in regulation of gene expression (GO:0023019)|telomere maintenance (GO:0000723)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NAD binding (GO:0051287)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		TGTGGTCtttcttttttttttt	0.47								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																																									0								ENSG00000143799																																			PARP1	SO:0001627	intron_variant	0				HGNC	BC037545	CCDS1554.1	1q41-q42	2010-02-16	2008-07-28	2004-08-26	ENSG00000143799	ENSG00000143799	2.4.2.30	"""Poly (ADP-ribose) polymerases"""	270	protein-coding gene	gene with protein product		173870	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)"", ""poly (ADP-ribose) polymerase family, member 1"""	PPOL, ADPRT		10964595	Standard	NM_001618		Approved	PARP	uc001hqd.4	P09874	OTTHUMG00000037556	ENST00000366794.5:c.2849-101->A	1.37:g.226549896_226549896dupT		Somatic	0	31	0.00		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	31	8.82	B1ANJ4|Q8IUZ9	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000366794.5	37	NULL	CCDS1554.1	1																																																																																			-	-		0.470	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PARP1	protein_coding	OTTHUMT00000091519.1	-	NM_001618			226549886	-1	no_errors	ENST00000491816	ensembl	human	known	74_37	rna	INS	0.002:0.004	T
AMBRA1	55626	genome.wustl.edu	37	11	46568608	46568609	+	Intron	INS	-	-	A	rs545025314		TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr11:46568608_46568609insA	ENST00000458649.2	-	4	797				AMBRA1_ENST00000314845.3_Intron|AMBRA1_ENST00000528950.1_Intron|AMBRA1_ENST00000298834.3_Intron|AMBRA1_ENST00000534300.1_Intron|AMBRA1_ENST00000533727.1_Intron|AMBRA1_ENST00000426438.1_Intron			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1						autophagy (GO:0006914)|cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neural tube development (GO:0021915)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|phagocytic vesicle (GO:0045335)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	39				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		gactccgtctcaaaaaaaaaaa	0.465																																																	0								ENSG00000110497																																			AMBRA1	SO:0001627	intron_variant	0				HGNC	AB051523	CCDS31475.1, CCDS58132.1, CCDS73281.1	11p11.2	2013-01-09			ENSG00000110497	ENSG00000110497		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	25990	protein-coding gene	gene with protein product	"""WD repeat domain 94"", ""DDB1 and CUL4 associated factor 3"""	611359				17622796, 17603510, 17589504	Standard	NM_001267782		Approved	FLJ20294, KIAA1736, WDR94, DCAF3	uc001ncv.3	Q9C0C7	OTTHUMG00000166500	ENST00000458649.2:c.378+53->T	11.37:g.46568619_46568619dupA		Somatic	0	22	0.00		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	26	13.33	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000458649.2	37	NULL		11																																																																																			-	-		0.465	AMBRA1-005	KNOWN	basic	protein_coding	AMBRA1	protein_coding	OTTHUMT00000390103.1	-	NM_017749			46568609	-1	no_errors	ENST00000524783	ensembl	human	known	74_37	rna	INS	0.032:0.881	A
DPH5	51611	genome.wustl.edu	37	1	101456193	101456193	+	Intron	DEL	A	A	-			TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr1:101456193delA	ENST00000370109.3	-	8	747				AC093157.1_ENST00000593496.1_Frame_Shift_Del_p.K65fs|DPH5_ENST00000370105.3_Intron|DPH5_ENST00000488176.1_Intron|DPH5_ENST00000342173.7_Intron|DPH5_ENST00000427040.2_Intron	NM_001077394.1|NM_001077395.1|NM_015958.2	NP_001070862.1|NP_001070863.1|NP_057042.2	Q9H2P9	DPH5_HUMAN	diphthamide biosynthesis 5						peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)		diphthine synthase activity (GO:0004164)			endometrium(2)|large_intestine(1)|lung(4)	7		all_epithelial(167;3.1e-06)|all_lung(203;0.000414)|Lung NSC(277;0.000946)		Epithelial(280;0.0385)|all cancers(265;0.043)|COAD - Colon adenocarcinoma(174;0.151)|Colorectal(144;0.173)|Lung(183;0.198)		AACTGCTATTAAAAAAAAAAG	0.413																																																	0								ENSG00000269175		,,	118,28,3432		2,0,114,1,26,1646	39.0	39.0	39.0		,,	0.1	0.9	1		41	13,69,7776		1,0,11,0,69,3848	no	intron,intron,intron	DPH5	NM_015958.2,NM_001077395.1,NM_001077394.1	,,	3,0,125,1,95,5494	A1A1,A1A2,A1R,A2A2,A2R,RR		1.0435,4.0805,1.9937	,,	,,	101456193	131,97,11208	1860	4106	5966	AC093157.1	SO:0001627	intron_variant	0				Clone_based_ensembl_gene	AF132964	CCDS41358.1, CCDS41359.1	1p21.2	2013-05-02	2013-05-02		ENSG00000117543	ENSG00000117543			24270	protein-coding gene	gene with protein product		611075	"""DPH5 homolog (S. cerevisiae)"""			15485916, 23486472	Standard	NM_015958		Approved	CGI-30	uc001dtt.2	Q9H2P9	OTTHUMG00000010829	ENST00000370109.3:c.635-6T>-	1.37:g.101456193delA		Somatic	0	23	0.00		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	24	17.24	A8JZY6|D3DT62|Q9P017|Q9P0I4|Q9Y319	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	NULL	p.R66fs	ENST00000370109.3	37	c.187	CCDS41358.1	1																																																																																			-	NULL		0.413	DPH5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ENSG00000269175	protein_coding	OTTHUMT00000029881.1	A	NM_015958			101456193	+1	no_errors	ENST00000593496	ensembl	human	known	74_37	frame_shift_del	DEL	0.002	-
OR4L1	122742	genome.wustl.edu	37	14	20528449	20528467	+	Frame_Shift_Del	DEL	CATAGATTTGCTCACTGAC	CATAGATTTGCTCACTGAC	-	rs145273733|rs111945603|rs112516164|rs75613488|rs139767954|rs112425920|rs33965693|rs112192573|rs200018603|rs201521851	byFrequency	TCGA-QQ-A8VD-01A-42D-A38Z-09	TCGA-QQ-A8VD-10A-01D-A38Z-09	CATAGATTTGCTCACTGAC	CATAGATTTGCTCACTGAC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	076d23f5-8017-4f0b-b9a1-462386d9e1ed	34a49c5e-6a61-43d0-82b6-2b597c3cbab8	g.chr14:20528449_20528467delCATAGATTTGCTCACTGAC	ENST00000315683.1	+	1	246_264	c.246_264delCATAGATTTGCTCACTGAC	c.(244-264)atcatagatttgctcactgacfs	p.IIDLLTD82fs		NM_001004717.1	NP_001004717.1	Q8NH43	OR4L1_HUMAN	olfactory receptor, family 4, subfamily L, member 1	82						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L85F(1)|p.I83fs*10(1)		central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(16)|ovary(2)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		CCAAGATGATCATAGATTTGCTCACTGACCACAAGACCA	0.466														2665	0.532149	0.4849	0.5562	5008	,	,		20575	0.5734		0.3837	False		,,,				2504	0.6892																2	Substitution - Missense(1)|Deletion - Frameshift(1)	upper_aerodigestive_tract(1)|lung(1)						ENSG00000176246																																			OR4L1	SO:0001589	frameshift_variant	0				HGNC		CCDS32029.1	14q11.2	2013-09-23			ENSG00000176246	ENSG00000176246		"""GPCR / Class A : Olfactory receptors"""	15356	protein-coding gene	gene with protein product				OR4L2P			Standard	NM_001004717		Approved		uc001vwn.1	Q8NH43	OTTHUMG00000169492	ENST00000315683.1:c.246_264delCATAGATTTGCTCACTGAC	14.37:g.20528449_20528467delCATAGATTTGCTCACTGAC	ENSP00000319217:p.Ile82fs	Somatic	NA	NA	NA		0.512518232618712	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	Q6IEZ5	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,prints_Olfact_rcpt,prints_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM	p.I83fs	ENST00000315683.1	37	c.246_264	CCDS32029.1	14																																																																																			-	pfam_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,pfscan_GPCR_Rhodpsn_7TM		0.466	OR4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR4L1	protein_coding	OTTHUMT00000404381.1	CATAGATTTGCTCACTGAC				20528467	+1	no_errors	ENST00000315683	ensembl	human	known	74_37	frame_shift_del	DEL	0.310:0.063:0.001:0.001:0.010:0.035:0.041:0.029:0.169:0.162:0.267:0.267:0.008:0.000:0.000:0.000:0.000:0.001:0.002	-
