#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
ABCC5	10057	genome.wustl.edu	37	3	183646535	183646535	+	Splice_Site	SNP	A	A	G			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr3:183646535A>G	ENST00000334444.6	-	27	4173	c.3933T>C	c.(3931-3933)tgT>tgC	p.C1311C	ABCC5_ENST00000265586.6_Splice_Site_p.C1268C	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	1311	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	CTTCACTTACACATTCTTTCA	0.527																																																	0								ENSG00000114770						118.0	123.0	121.0					3																	183646535		2057	4191	6248	ABCC5	SO:0001630	splice_region_variant	0			-	HGNC	AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770		"""ATP binding cassette transporters / subfamily C"""	56	protein-coding gene	gene with protein product		605251				8894702, 9827529	Standard	XM_005247058		Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000334444.6:c.3933+1T>C	3.37:g.183646535A>G		Somatic	0	32	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	33	10.81	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_ABC_transptr_TM_dom,pfam_ABC_transporter-like,superfamily_ABC1_TM_dom,superfamily_P-loop_NTPase,smart_AAA+_ATPase,pfscan_ABC_transporter-like,pfscan_ABC1_TM_dom	p.C1311	ENST00000334444.6	37	c.3933	CCDS43176.1	3																																																																																			-	pfam_ABC_transporter-like,superfamily_P-loop_NTPase,smart_AAA+_ATPase,pfscan_ABC_transporter-like		0.527	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ABCC5	protein_coding	OTTHUMT00000346350.1	A	NM_005688	-	Silent	183646535	-1	no_errors	ENST00000334444	ensembl	human	known	74_37	silent	SNP	1.000	G
MYO3A	53904	genome.wustl.edu	37	10	26310463	26310463	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr10:26310463C>T	ENST00000265944.5	+	8	783	c.617C>T	c.(616-618)aCt>aTt	p.T206I	MYO3A_ENST00000543632.1_Missense_Mutation_p.T206I|MYO3A_ENST00000376302.1_Missense_Mutation_p.T206I	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	206	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						TTGGATACCACTTATGACGCC	0.443																																																	0								ENSG00000095777						196.0	166.0	176.0					10																	26310463		2203	4300	6503	MYO3A	SO:0001583	missense	0			-	HGNC	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.617C>T	10.37:g.26310463C>T	ENSP00000265944:p.Thr206Ile	Somatic	0	43	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	32	18	64.00	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Myosin_head_motor_dom,pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_IQ_motif_EF-hand-BS,superfamily_P-loop_NTPase,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_Myosin_head_motor_dom,smart_IQ_motif_EF-hand-BS,pfscan_IQ_motif_EF-hand-BS,pfscan_Prot_kinase_dom,prints_Myosin_head_motor_dom	p.T206I	ENST00000265944.5	37	c.617	CCDS7148.1	10	.	.	.	.	.	.	.	.	.	.	C	24.7	4.555042	0.86231	.	.	ENSG00000095777	ENST00000265944;ENST00000376302;ENST00000543632	T;T;T	0.66099	-0.19;-0.19;-0.19	6.03	5.07	0.68467	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.187775	0.56097	D	0.000032	T	0.56062	0.1960	N	0.16266	0.395	0.53688	D	0.99997	P;P;P;B	0.46064	0.551;0.606;0.872;0.431	B;B;P;B	0.48524	0.178;0.272;0.58;0.234	T	0.62062	-0.6933	10	0.72032	D	0.01	.	16.1309	0.81436	0.1341:0.8659:0.0:0.0	.	206;206;206;206	F5H0U9;Q0VD65;Q8NEV4;Q4G0X2	.;.;MYO3A_HUMAN;.	I	206	ENSP00000265944:T206I;ENSP00000365479:T206I;ENSP00000445909:T206I	ENSP00000265944:T206I	T	+	2	0	MYO3A	26350469	0.999000	0.42202	1.000000	0.80357	0.991000	0.79684	4.023000	0.57211	2.861000	0.98227	0.655000	0.94253	ACT	-	pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_dom		0.443	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MYO3A	protein_coding	OTTHUMT00000047259.1	C	NM_017433	-		26310463	+1	no_errors	ENST00000265944	ensembl	human	known	74_37	missense	SNP	1.000	T
VTN	7448	genome.wustl.edu	37	17	26696630	26696630	+	Missense_Mutation	SNP	G	G	T			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr17:26696630G>T	ENST00000226218.4	-	3	1045	c.427C>A	c.(427-429)Cat>Aat	p.H143N	VTN_ENST00000438614.1_5'Flank|SARM1_ENST00000457710.3_5'Flank|CTB-96E2.2_ENST00000555059.2_5'Flank|SARM1_ENST00000379061.4_Intron|CTB-96E2.3_ENST00000591482.1_RNA|VTN_ENST00000536498.1_5'UTR|TMEM199_ENST00000509083.1_Intron	NM_000638.3	NP_000629.3	P04004	VTNC_HUMAN	vitronectin	143					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|innate immune response (GO:0045087)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endopeptidase activity (GO:0010951)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein binding (GO:0032092)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of wound healing (GO:0090303)|regulation of complement activation (GO:0030449)|smooth muscle cell-matrix adhesion (GO:0061302)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|blood microparticle (GO:0072562)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			kidney(2)|large_intestine(7)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	13	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Abciximab(DB00054)	CTCCCTGGATGAAGGGTCTCA	0.612																																																	0								ENSG00000109072						38.0	38.0	38.0					17																	26696630		2203	4300	6503	VTN	SO:0001583	missense	0			-	HGNC	BC005046	CCDS11229.1	17q11.2	2014-08-08	2006-02-10		ENSG00000109072	ENSG00000109072		"""Endogenous ligands"""	12724	protein-coding gene	gene with protein product	"""serum spreading factor"", ""somatomedin B"", ""complement S-protein"""	193190	"""vitronectin (serum spreading factor, somatomedin B, complement S-protein)"""			2447940	Standard	NM_000638		Approved	VN	uc002hbc.3	P04004	OTTHUMG00000132500	ENST00000226218.4:c.427C>A	17.37:g.26696630G>T	ENSP00000226218:p.His143Asn	Somatic	0	28	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	27	12.90	B2R7G0|P01141|Q9BSH7	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Hemopexin-like_repeat,pfam_Somatomedin_B_dom,superfamily_Hemopexin-like_dom,smart_Somatomedin_B_dom,smart_Hemopexin-like_repeat,pfscan_Somatomedin_B_dom,prints_Somatomedin_B_chordata	p.H143N	ENST00000226218.4	37	c.427	CCDS11229.1	17	.	.	.	.	.	.	.	.	.	.	G	7.085	0.571046	0.13623	.	.	ENSG00000255604	ENST00000226218	T	0.03951	3.75	5.79	-1.77	0.07982	.	1.188450	0.05656	N	0.585945	T	0.02047	0.0064	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47302	-0.9128	10	0.16420	T	0.52	-0.8684	4.5133	0.11923	0.1608:0.3753:0.3402:0.1237	.	143	P04004	VTNC_HUMAN	N	143	ENSP00000226218:H143N	ENSP00000226218:H143N	H	-	1	0	AC002094.1	23720757	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.942000	0.03921	0.051000	0.15978	-0.270000	0.10280	CAT	-	NULL		0.612	VTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	VTN	protein_coding	OTTHUMT00000255680.2	G	NM_000638	-		26696630	-1	no_errors	ENST00000226218	ensembl	human	known	74_37	missense	SNP	0.000	T
FTH1P3	2498	genome.wustl.edu	37	5	17353803	17353804	+	lincRNA	INS	-	-	T	rs77011080|rs373084262		TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr5:17353803_17353804insT	ENST00000511821.1	+	0	0				FTH1P10_ENST00000401830.3_RNA																							TATCTCTTCACTTTTTTTTTTT	0.342																																																	0								ENSG00000223361																																			FTH1P10			0				HGNC																													5.37:g.17353814_17353814dupT		Somatic	0	22	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	7	32	17.95		RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000511821.1	37	NULL		5																																																																																			-	-		0.342	CTD-2139B15.2-001	KNOWN	basic	lincRNA	FTH1P10	lincRNA	OTTHUMT00000366261.1	-				17353804	-1	no_errors	ENST00000401830	ensembl	human	known	74_37	rna	INS	0.002:0.004	T
SEH1L	81929	genome.wustl.edu	37	18	12986927	12986929	+	3'UTR	DEL	TCC	TCC	-			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	TCC	TCC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr18:12986927_12986929delTCC	ENST00000262124.11	+	0	2886_2888				RP11-773H22.4_ENST00000588211.1_RNA|SEH1L_ENST00000399892.2_In_Frame_Del_p.P385del	NM_031216.3	NP_112493.2	Q96EE3	SEH1_HUMAN	SEH1-like (S. cerevisiae)						attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation (GO:0051315)|carbohydrate metabolic process (GO:0005975)|cytokine production involved in inflammatory response (GO:0002534)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-positive bacterium (GO:0050830)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore organization (GO:0006999)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	11						CCCAGCTCCTtcctcctcctcct	0.522																																																	0								ENSG00000085415																																			SEH1L	SO:0001624	3_prime_UTR_variant	0				HGNC	BC012430	CCDS32791.1, CCDS45832.1	18p11.21	2013-01-10				ENSG00000085415		"""WD repeat domain containing"""	30379	protein-coding gene	gene with protein product	"""sec13 like protein"", ""nucleoporin Seh1"""	609263				12196509, 14517296	Standard	XM_005258152		Approved	SEH1A, SEH1B, Seh1, SEC13L	uc002krq.3	Q96EE3		ENST00000262124.11:c.*1678TCC>-	18.37:g.12986936_12986938delTCC		Somatic	0	25	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	25	13.79	A8K5B1|Q8NFU6|Q96MH3|Q9C069	In_Frame_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_WD40_repeat,superfamily_WD40_repeat_dom,smart_WD40_repeat,pfscan_WD40_repeat,pfscan_WD40_repeat_dom,prints_G-protein_beta_WD-40_rep	p.P383in_frame_del	ENST00000262124.11	37	c.1137_1139	CCDS45832.1	18																																																																																			-	NULL		0.522	SEH1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SEH1L	protein_coding	OTTHUMT00000458254.1	TCC	NM_031216			12986929	+1	no_errors	ENST00000399892	ensembl	human	known	74_37	in_frame_del	DEL	0.997:1.000:1.000	-
DBNDD2	55861	genome.wustl.edu	37	20	44038638	44038640	+	In_Frame_Del	DEL	CCT	CCT	-			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	CCT	CCT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr20:44038638_44038640delCCT	ENST00000372720.3	+	4	869_871	c.638_640delCCT	c.(637-642)acctcc>acc	p.S219del	DBNDD2_ENST00000372723.3_In_Frame_Del_p.S121del|DBNDD2_ENST00000372712.2_In_Frame_Del_p.S121del|TP53TG5_ENST00000494455.1_5'Flank|DBNDD2_ENST00000372722.3_3'UTR|DBNDD2_ENST00000372717.1_3'UTR|DBNDD2_ENST00000372710.3_In_Frame_Del_p.S223del|SYS1-DBNDD2_ENST00000452133.1_3'UTR|DBNDD2_ENST00000360981.4_In_Frame_Del_p.S121del|SYS1-DBNDD2_ENST00000475242.1_3'UTR|DBNDD2_ENST00000357275.2_In_Frame_Del_p.S121del	NM_018478.3	NP_060948.3	Q9BQY9	DBND2_HUMAN	dysbindin (dystrobrevin binding protein 1) domain containing 2	219	Poly-Ser.				negative regulation of protein kinase activity (GO:0006469)	cytoplasm (GO:0005737)				breast(1)|lung(2)	3		Myeloproliferative disorder(115;0.0122)				ACATCTAGGAcctcctcctcctc	0.567																																																	0								ENSG00000244274		,,,,,,,,	41,2,3581		10,0,21,0,2,1779					,,,,,,,,	4.5	1.0		dbSNP_126	47	104,7,7269		32,0,40,1,5,3612	no	codingComplex,codingComplex,codingComplex,utr-3,codingComplex,utr-3,codingComplex,utr-3,codingComplex	DBNDD2	NM_018478.3,NM_001197140.1,NM_001197139.1,NM_001048226.2,NM_001048225.2,NM_001048224.2,NM_001048223.2,NM_001048222.2,NM_001048221.2	,,,,,,,,	42,0,61,1,7,5391	A1A1,A1A2,A1R,A2A2,A2R,RR		1.5041,1.1865,1.3995	,,,,,,,,	,,,,,,,,		145,9,10850				DBNDD2	SO:0001651	inframe_deletion	0				HGNC	AF220191	CCDS42880.1, CCDS42881.1, CCDS56193.1, CCDS56194.1	20q13.12	2007-07-23	2006-04-04	2006-04-04	ENSG00000244274	ENSG00000244274			15881	protein-coding gene	gene with protein product		611453	"""chromosome 20 open reading frame 35"""	C20orf35			Standard	NM_001048225		Approved	HSMNP1	uc002xof.3	Q9BQY9	OTTHUMG00000032576	ENST00000372720.3:c.638_640delCCT	20.37:g.44038647_44038649delCCT	ENSP00000361805:p.Ser219del	Somatic	0	16	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	2	20	9.09	Q331S6|Q5QPV4|Q5QPV6|Q9BQZ0|Q9BVL1|Q9H1F6|Q9NWZ0|Q9NY07|Q9NZ31	In_Frame_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_Dysbindin	p.S217in_frame_del	ENST00000372720.3	37	c.638_640	CCDS56193.1	20																																																																																			-	pfam_Dysbindin		0.567	DBNDD2-001	KNOWN	basic|CCDS	protein_coding	DBNDD2	protein_coding	OTTHUMT00000079438.1	CCT	NM_018478			44038640	+1	no_errors	ENST00000372720	ensembl	human	known	74_37	in_frame_del	DEL	0.980:0.959:0.969	-
KIAA0100	9703	genome.wustl.edu	37	17	26961805	26961805	+	Missense_Mutation	SNP	G	G	T			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr17:26961805G>T	ENST00000528896.2	-	16	2874	c.2800C>A	c.(2800-2802)Ctc>Atc	p.L934I	KIAA0100_ENST00000544884.1_Missense_Mutation_p.L791I|KIAA0100_ENST00000389003.3_Missense_Mutation_p.L791I|RP11-192H23.7_ENST00000583787.1_RNA|RP11-192H23.7_ENST00000577814.1_RNA	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	934						extracellular region (GO:0005576)		p.L934I(1)		breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					GAGGCATAGAGCTCCTCAATT	0.522																																																	1	Substitution - Missense(1)	endometrium(1)						ENSG00000007202						179.0	189.0	186.0					17																	26961805		2203	4300	6503	KIAA0100	SO:0001583	missense	0			-	HGNC	D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"""cancer/testis antigen 101"", ""breast cancer overexpressed gene 1"""	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.2800C>A	17.37:g.26961805G>T	ENSP00000436773:p.Leu934Ile	Somatic	0	58	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	40	9.09	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_FMP27_C,pfam_FMP27_N,pfam_FMP27_GFWDK_dom	p.L934I	ENST00000528896.2	37	c.2800	CCDS32595.1	17	.	.	.	.	.	.	.	.	.	.	G	24.6	4.552130	0.86127	.	.	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	T;T	0.32988	1.43;1.45	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.56093	0.1962	M	0.62266	1.93	0.80722	D	1	D	0.69078	0.997	D	0.78314	0.991	T	0.51180	-0.8738	10	0.52906	T	0.07	.	20.2651	0.98459	0.0:0.0:1.0:0.0	.	934	Q14667	K0100_HUMAN	I	934;904;934;791	ENSP00000436773:L934I;ENSP00000446443:L791I	ENSP00000005905:L934I	L	-	1	0	KIAA0100	23985932	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.256000	0.95535	2.796000	0.96246	0.563000	0.77884	CTC	-	NULL		0.522	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KIAA0100	protein_coding	OTTHUMT00000390571.3	G	NM_014680	-		26961805	-1	no_errors	ENST00000528896	ensembl	human	known	74_37	missense	SNP	1.000	T
DNAH3	55567	genome.wustl.edu	37	16	21108691	21108691	+	Missense_Mutation	SNP	C	C	G			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr16:21108691C>G	ENST00000261383.3	-	18	2649	c.2650G>C	c.(2650-2652)Gag>Cag	p.E884Q	DNAH3_ENST00000415178.1_Missense_Mutation_p.E884Q	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	884	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		ATCCATTCCTCTGACTTGATG	0.478																																																	0								ENSG00000158486						219.0	174.0	189.0					16																	21108691		2201	4300	6501	DNAH3	SO:0001583	missense	0			-	HGNC	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.2650G>C	16.37:g.21108691C>G	ENSP00000261383:p.Glu884Gln	Somatic	0	37	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	14	24	36.84	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Dynein_heavy_dom,pfam_Dynein_heavy_dom-2,pfam_ATPase_dyneun-rel_AAA,superfamily_P-loop_NTPase,superfamily_Prefoldin,smart_AAA+_ATPase	p.E884Q	ENST00000261383.3	37	c.2650	CCDS10594.1	16	.	.	.	.	.	.	.	.	.	.	C	13.25	2.179988	0.38511	.	.	ENSG00000158486	ENST00000261383;ENST00000415178	T;T	0.61510	0.1;0.1	5.26	5.26	0.73747	Dynein heavy chain, domain-2 (1);	0.064020	0.64402	D	0.000008	T	0.56292	0.1975	L	0.52011	1.625	0.58432	D	0.999999	P	0.41232	0.743	B	0.40506	0.331	T	0.56263	-0.8008	10	0.36615	T	0.2	.	18.824	0.92109	0.0:1.0:0.0:0.0	.	884	Q8TD57	DYH3_HUMAN	Q	884	ENSP00000261383:E884Q;ENSP00000394245:E884Q	ENSP00000261383:E884Q	E	-	1	0	DNAH3	21016192	0.999000	0.42202	0.959000	0.39883	0.185000	0.23345	4.572000	0.60886	2.627000	0.88993	0.650000	0.86243	GAG	-	pfam_Dynein_heavy_dom-2,superfamily_P-loop_NTPase		0.478	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DNAH3	protein_coding	OTTHUMT00000207361.1	C	NM_017539	-		21108691	-1	no_errors	ENST00000261383	ensembl	human	known	74_37	missense	SNP	0.999	G
PDIA3	2923	genome.wustl.edu	37	15	44065171	44065171	+	3'UTR	SNP	G	G	T			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr15:44065171G>T	ENST00000300289.5	+	0	3421				RP11-296A16.1_ENST00000417761.2_3'UTR|ELL3_ENST00000319359.3_3'UTR|ELL3_ENST00000497465.1_5'UTR	NM_005313.4	NP_005304.3	P30101	PDIA3_HUMAN	protein disulfide isomerase family A, member 3						antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein N-linked glycosylation via asparagine (GO:0018279)|protein retention in ER lumen (GO:0006621)|proteolysis (GO:0006508)|response to endoplasmic reticulum stress (GO:0034976)|signal transduction (GO:0007165)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|phospholipase C activity (GO:0004629)|poly(A) RNA binding (GO:0044822)|protein disulfide isomerase activity (GO:0003756)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(9)|ovary(2)|skin(1)	17		all_cancers(109;2.61e-15)|all_epithelial(112;1.12e-12)|Lung NSC(122;2.17e-08)|all_lung(180;2.45e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.48e-07)		CAAACCTCAAGAACCTAGAGC	0.428																																																	0								ENSG00000128886																																			ELL3	SO:0001624	3_prime_UTR_variant	0			-	HGNC		CCDS10101.1	15q15	2009-11-20	2005-06-29	2005-03-03	ENSG00000167004	ENSG00000167004	5.3.4.1	"""Protein disulfide isomerases"""	4606	protein-coding gene	gene with protein product		602046	"""glucose regulated protein, 58kDa"", ""protein disulfide isomerase-associated 3"""	GRP58		8974399	Standard	NM_005313		Approved	P58, ERp61, ERp57, ERp60, GRP57, PI-PLC, HsT17083	uc001zsu.3	P30101	OTTHUMG00000044444	ENST00000300289.5:c.*1755G>T	15.37:g.44065171G>T		Somatic	0	35	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	40	9.09	Q13453|Q14255|Q8IYF8|Q9UMU7	RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000300289.5	37	NULL	CCDS10101.1	15																																																																																			-	-		0.428	PDIA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ELL3	protein_coding	OTTHUMT00000103532.3	G	NM_005313	-		44065171	-1	no_errors	ENST00000497465	ensembl	human	known	74_37	rna	SNP	0.006	T
TMED10	10972	genome.wustl.edu	37	14	75601711	75601712	+	Splice_Site	INS	-	-	A	rs200389497	byFrequency	TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr14:75601711_75601712insA	ENST00000303575.4	-	5	590		c.e5-2		TMED10_ENST00000557670.1_Splice_Site|RP11-950C14.7_ENST00000556236.1_RNA	NM_006827.5	NP_006818.3	P49755	TMEDA_HUMAN	transmembrane emp24-like trafficking protein 10 (yeast)						beta-amyloid formation (GO:0034205)|cargo loading into vesicle (GO:0035459)|COPI coating of Golgi vesicle (GO:0048205)|COPI-coated vesicle budding (GO:0035964)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|kidney development (GO:0001822)|protein oligomerization (GO:0051259)|regulated secretory pathway (GO:0045055)|response to acid chemical (GO:0001101)|response to alkaloid (GO:0043279)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle targeting, to, from or within Golgi (GO:0048199)	cis-Golgi network (GO:0005801)|COPI-coated vesicle (GO:0030137)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|gamma-secretase complex (GO:0070765)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network transport vesicle (GO:0030140)|zymogen granule membrane (GO:0042589)	syntaxin binding (GO:0019905)			endometrium(1)|large_intestine(5)|lung(3)	9				BRCA - Breast invasive adenocarcinoma(234;0.0126)		TTGTTGACTCTAAAAAAAAACA	0.426																																																	0								ENSG00000170348																																			TMED10	SO:0001630	splice_region_variant	0				HGNC	AL832012, X97442	CCDS9840.1	14q24.3	2008-08-11			ENSG00000170348	ENSG00000170348			16998	protein-coding gene	gene with protein product		605406				7596406, 8663407	Standard	NM_006827		Approved	TMP21, P24(DELTA)	uc001xrm.1	P49755		ENST00000303575.4:c.539-2->T	14.37:g.75601720_75601720dupA		Somatic	0	38	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	27	10.00	B2R605|Q15602|Q16536|Q86TC2|Q86TS5	Splice_Site	INS	NA	NA	NA	NA	NA	NA	-	e5-2	ENST00000303575.4	37	c.539-3_539-2	CCDS9840.1	14																																																																																			-	-		0.426	TMED10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TMED10	protein_coding	OTTHUMT00000415034.1	-	NM_006827		Intron	75601712	-1	no_errors	ENST00000303575	ensembl	human	known	74_37	splice_site_ins	INS	1.000:0.961	A
CES1P1	51716	genome.wustl.edu	37	16	55803899	55803899	+	RNA	SNP	G	G	A			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr16:55803899G>A	ENST00000571348.1	+	0	474					NR_003276.2		Q9UKY3	CES1P_HUMAN	carboxylesterase 1 pseudogene 1						anatomical structure morphogenesis (GO:0009653)|metabolic process (GO:0008152)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)										CACGGAGGGGGGCTGATGGTG	0.572																																																	0								ENSG00000228695																																			CES1P1			0			-	HGNC	AF106005		16q12.2	2013-07-10	2010-10-12	2010-10-12	ENSG00000228695	ENSG00000228695			18546	pseudogene	pseudogene			"""carboxylesterase 4-like"", ""carboxylesterase 4, pseudogene"""	CES4		10452915, 20931200	Standard	NR_003276		Approved	PCE-3, CESR, CES1A3	uc010cce.3	Q9UKY3	OTTHUMG00000154668		16.37:g.55803899G>A		Somatic	0	14	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	11	26.67	A2RRL8|B9ZVS2	RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000571348.1	37	NULL		16																																																																																			-	-		0.572	CES1P1-003	KNOWN	basic	processed_transcript	CES1P1	pseudogene	OTTHUMT00000440035.1	G	NR_003276	-		55803899	+1	no_errors	ENST00000571348	ensembl	human	known	74_37	rna	SNP	0.860	A
SDHAP1	255812	genome.wustl.edu	37	3	195687221	195687221	+	RNA	SNP	A	A	G	rs62282781		TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr3:195687221A>G	ENST00000427841.1	-	0	2325					NR_003264.2				succinate dehydrogenase complex, subunit A, flavoprotein pseudogene 1																		gctggagcccaggaggtggag	0.522																																					Ovarian(67;1158 1227 12109 20189 43170)												0								ENSG00000185485																																			SDHAP1			0			-	HGNC	BC071730		3q29	2009-12-02	2006-11-21	2009-12-02	ENSG00000185485	ENSG00000185485			32455	pseudogene	pseudogene			"""succinate dehydrogenase complex, subunit A, flavoprotein-like 1"""	SDHAL1, SDHALP1			Standard	NR_003264		Approved		uc003fvy.3		OTTHUMG00000155716		3.37:g.195687221A>G		Somatic	0	14	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	8	38.46		RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000427841.1	37	NULL		3																																																																																			-	-		0.522	SDHAP1-002	KNOWN	basic	processed_transcript	SDHAP1	pseudogene	OTTHUMT00000341367.1	A		rs62282781		195687221	-1	no_errors	ENST00000427149	ensembl	human	known	74_37	rna	SNP	0.009	G
MIR200A	406983	genome.wustl.edu	37	1	1103249	1103249	+	lincRNA	SNP	C	C	T			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr1:1103249C>T	ENST00000606993.1	+	0	0				MIR200B_ENST00000384997.1_RNA|MIR429_ENST00000362106.1_RNA|MIR200A_ENST00000384875.1_RNA																							CCTCCCGGGCCCCTGTGAGCA	0.662																																																	0								ENSG00000207607						22.0	25.0	24.0					1																	1103249		1556	3569	5125	MIR200A			0			-	HGNC																													1.37:g.1103249C>T		Somatic	0	111	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	60	9	86.96		RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000606993.1	37	NULL		1																																																																																			-	-		0.662	RP11-465B22.8-001	KNOWN	basic	lincRNA	MIR200A	lincRNA	OTTHUMT00000470776.1	C		-		1103249	+1	no_errors	ENST00000384875	ensembl	human	known	74_37	rna	SNP	1.000	T
AC023490.2	0	genome.wustl.edu	37	22	20378616	20378628	+	lincRNA	DEL	GGGATCCGGGGGT	GGGATCCGGGGGT	-			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	GGGATCCGGGGGT	GGGATCCGGGGGT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr22:20378616_20378628delGGGATCCGGGGGT	ENST00000426653.1	+	0	666_678				AC023490.1_ENST00000438669.1_lincRNA																							ggaagggggcgggatccgggggtggggtgaggt	0.704																																																	0								ENSG00000235704																																			AC023490.2			0				Clone_based_vega_gene																													22.37:g.20378616_20378628delGGGATCCGGGGGT		Somatic	NA	NA	NA		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA		RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000426653.1	37	NULL		22																																																																																			-	-		0.704	AC023490.2-001	KNOWN	basic|exp_conf	lincRNA	ENSG00000235704	lincRNA	OTTHUMT00000322210.1	GGGATCCGGGGGT				20378628	+1	no_errors	ENST00000426653	ensembl	human	known	74_37	rna	DEL	0.009:0.014:0.006:0.004:0.011:0.028:0.217:0.219:0.178:0.177:0.193:0.194:0.213	-
SPERT	220082	genome.wustl.edu	37	13	46277722	46277722	+	Intron	SNP	C	C	T			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr13:46277722C>T	ENST00000310521.1	+	2	236				SPERT_ENST00000378966.3_Missense_Mutation_p.A15V	NM_152719.1	NP_689932.1	Q8NA61	SPERT_HUMAN	spermatid associated							cytoplasmic membrane-bounded vesicle (GO:0016023)				NS(1)|central_nervous_system(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	15		Breast(56;0.000819)|Lung NSC(96;0.00227)|Prostate(109;0.00703)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;7.26e-05)		GAATCCAATGCAGAGGTAACT	0.473																																																	0								ENSG00000174015																																			SPERT	SO:0001627	intron_variant	0			-	HGNC	AK093129	CCDS9399.1, CCDS66540.1	13q14.13	2010-03-23			ENSG00000174015	ENSG00000174015			30720	protein-coding gene	gene with protein product	"""spermatid flower-like structure protein"", ""testis specific leucine zipper protein nurit"", ""chibby homolog 2 (Drosophila)"""					12204287, 20096028	Standard	NM_001286341		Approved	NURIT, CBY2	uc001van.1	Q8NA61	OTTHUMG00000016861	ENST00000310521.1:c.156+732C>T	13.37:g.46277722C>T		Somatic	0	46	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	29	12.12	A8K8I5|Q8NHV2	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	NULL	p.A15V	ENST00000310521.1	37	c.44	CCDS9399.1	13	.	.	.	.	.	.	.	.	.	.	C	6.494	0.459343	0.12342	.	.	ENSG00000174015	ENST00000378966	T	0.46451	0.87	4.42	0.771	0.18504	.	.	.	.	.	T	0.29223	0.0727	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.25222	-1.0138	8	0.59425	D	0.04	.	6.3912	0.21587	0.0:0.584:0.0:0.416	.	15	Q8NA61-2	.	V	15	ENSP00000368249:A15V	ENSP00000368249:A15V	A	+	2	0	SPERT	45175723	0.003000	0.15002	0.278000	0.24718	0.115000	0.19883	-0.275000	0.08525	0.245000	0.21373	-0.157000	0.13467	GCA	-	NULL		0.473	SPERT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SPERT	protein_coding	OTTHUMT00000044786.2	C	NM_152719	-		46277722	+1	no_errors	ENST00000378966	ensembl	human	putative	74_37	missense	SNP	0.157	T
GCK	2645	genome.wustl.edu	37	7	44187337	44187337	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr7:44187337C>T	ENST00000403799.3	-	7	1244	c.775G>A	c.(775-777)Gcc>Acc	p.A259T	GCK_ENST00000395796.3_Missense_Mutation_p.A258T|GCK_ENST00000437084.1_Missense_Mutation_p.A242T|GCK_ENST00000345378.2_Missense_Mutation_p.A260T	NM_000162.3	NP_000153.1	P35557	HXK4_HUMAN	glucokinase (hexokinase 4)	259	Hexokinase type-2.		A -> T (in MODY2). {ECO:0000269|PubMed:9662401}.		calcium ion import (GO:0070509)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|cellular response to glucose starvation (GO:0042149)|cellular response to insulin stimulus (GO:0032869)|cellular response to leptin stimulus (GO:0044320)|detection of glucose (GO:0051594)|endocrine pancreas development (GO:0031018)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|NADP metabolic process (GO:0006739)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of gluconeogenesis (GO:0045721)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of insulin secretion (GO:0032024)|positive regulation of phosphorylation (GO:0042327)|regulation of glucose transport (GO:0010827)|regulation of glycolytic process (GO:0006110)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transport (GO:0043266)|second-messenger-mediated signaling (GO:0019932)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|secretory granule (GO:0030141)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|magnesium ion binding (GO:0000287)			central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(17)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	37						TCCCCGAAGGCGCCCCACTCG	0.642																																																	0			GRCh37	CM980894	GCK	M		ENSG00000106633						72.0	71.0	71.0					7																	44187337		2203	4300	6503	GCK	SO:0001583	missense	0			-	HGNC	AF041014	CCDS5479.1, CCDS5480.1, CCDS5481.1	7p15.3-p15.1	2008-02-07	2008-02-07		ENSG00000106633	ENSG00000106633	2.7.1.2, 2.7.1.1		4195	protein-coding gene	gene with protein product		138079	"""maturity onset diabetes of the young 2"""	MODY2		1740341, 1502186	Standard	NM_033507		Approved	HK4	uc003tkk.1	P35557	OTTHUMG00000022903	ENST00000403799.3:c.775G>A	7.37:g.44187337C>T	ENSP00000384247:p.Ala259Thr	Somatic	0	48	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	37	9.76	A4D2J2|A4D2J3|Q05810	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Hexokinase_C,pfam_Hexokinase_N,prints_Hexokinase	p.A260T	ENST00000403799.3	37	c.778	CCDS5479.1	7	.	.	.	.	.	.	.	.	.	.	C	36	5.650711	0.96714	.	.	ENSG00000106633	ENST00000403799;ENST00000395796;ENST00000345378;ENST00000437084	D;D;D;D	0.96802	-4.13;-4.13;-4.13;-4.13	5.23	5.23	0.72850	Hexokinase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.97387	0.9145	M	0.92412	3.305	0.80722	D	1	P;P;P	0.49961	0.922;0.93;0.904	P;P;B	0.45167	0.472;0.449;0.341	D	0.98638	1.0674	10	0.87932	D	0	-21.9406	18.3902	0.90479	0.0:1.0:0.0:0.0	.	259;260;258	P35557;P35557-2;P35557-3	HXK4_HUMAN;.;.	T	259;258;260;242	ENSP00000384247:A259T;ENSP00000379142:A258T;ENSP00000223366:A260T;ENSP00000402840:A242T	ENSP00000223366:A260T	A	-	1	0	GCK	44153862	1.000000	0.71417	0.969000	0.41365	0.763000	0.43281	7.739000	0.84976	2.444000	0.82710	0.561000	0.74099	GCC	-	pfam_Hexokinase_C		0.642	GCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GCK	protein_coding	OTTHUMT00000251069.2	C		-		44187337	-1	no_errors	ENST00000345378	ensembl	human	known	74_37	missense	SNP	1.000	T
CROCCP2	84809	genome.wustl.edu	37	1	16945182	16945184	+	lincRNA	DEL	AAT	AAT	-	rs374889577|rs71803374	byFrequency	TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	AAT	AAT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr1:16945182_16945184delAAT	ENST00000412962.1	-	0	2335_2337				RP5-1182A14.5_ENST00000607700.1_lincRNA			Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2						centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)											TACTGATGAAAATAATAACAGAT	0.325														915	0.182708	0.1906	0.2853	5008	,	,		89095	0.0278		0.2157	False		,,,				2504	0.2249																0								ENSG00000215908																																			CROCCP2			0				HGNC	AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908			28170	pseudogene	pseudogene			"""ciliary rootlet coiled-coil, rootletin-like 1"""	CROCCL1		12477932	Standard	NR_026752		Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884		1.37:g.16945185_16945187delAAT		Somatic	0	17	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	10	28.57	Q8NF65|Q96FR5|Q9BRE8	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000412962.1	37	NULL		1																																																																																			-	-		0.325	CROCCP2-003	KNOWN	basic	lincRNA	CROCCP2	lincRNA	OTTHUMT00000092784.1	AAT	NR_026752.1			16945184	-1	no_errors	ENST00000412962	ensembl	human	known	74_37	rna	DEL	0.016:0.018:0.018	-
PAPSS2	9060	genome.wustl.edu	37	10	89419638	89419639	+	5'UTR	INS	-	-	GCT	rs540045493|rs368634218|rs540138599	byFrequency	TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr10:89419638_89419639insGCT	ENST00000361175.4	+	0	269_270				PAPSS2_ENST00000427144.2_5'Flank|RP11-57C13.3_ENST00000354527.2_RNA|RP11-57C13.6_ENST00000438082.1_lincRNA|PAPSS2_ENST00000456849.1_5'UTR	NM_004670.3	NP_004661.2	O95340	PAPS2_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 2						3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|blood coagulation (GO:0007596)|bone development (GO:0060348)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	adenylylsulfate kinase activity (GO:0004020)|ATP binding (GO:0005524)|nucleotidyltransferase activity (GO:0016779)|sulfate adenylyltransferase (ATP) activity (GO:0004781)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|stomach(1)	20		Melanoma(5;0.019)|Colorectal(252;0.123)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00164)|Colorectal(12;0.000323)|COAD - Colon adenocarcinoma(12;0.00124)		GTCCGGCAgccgctgctgctgc	0.708														1002	0.20008	0.2852	0.1628	5008	,	,		8101	0.0585		0.2435	False		,,,				2504	0.2127																0								ENSG00000196566																																			RP11-57C13.3	SO:0001623	5_prime_UTR_variant	0				Clone_based_vega_gene	AF091242	CCDS7385.1, CCDS44453.1	10q24	2008-02-07			ENSG00000198682	ENSG00000198682	2.7.7.4, 2.7.1.25		8604	protein-coding gene	gene with protein product		603005				9771708	Standard	NM_004670		Approved	ATPSK2	uc001kex.3	O95340	OTTHUMG00000018683	ENST00000361175.4:c.-100->GCT	10.37:g.89419645_89419647dupGCT		Somatic	0	11	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	4	55.56	Q9BZL2|Q9P0G6|Q9UHM1|Q9UKD3|Q9UP30	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000361175.4	37	NULL	CCDS7385.1	10																																																																																			-	-		0.708	PAPSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000196566	protein_coding	OTTHUMT00000049229.1	-				89419639	-1	no_errors	ENST00000354527	ensembl	human	known	74_37	rna	INS	0.000:0.000	GCT
AL021920.1	0	genome.wustl.edu	37	1	17007767	17007767	+	RNA	SNP	G	G	A			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr1:17007767G>A	ENST00000584111.1	+	0	18																											AAGTTATGGGGGCTTCTGTAG	0.448																																																	0								ENSG00000264742																																			AL021920.1			0			-	Clone_based_ensembl_gene																													1.37:g.17007767G>A		Somatic	0	120	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	10	53	15.87		RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000584111.1	37	NULL		1																																																																																			-	-		0.448	AL021920.1-201	NOVEL	basic	miRNA	ENSG00000264742	miRNA		G		-		17007767	+1	no_errors	ENST00000584111	ensembl	human	novel	74_37	rna	SNP	0.190	A
TELO2	9894	genome.wustl.edu	37	16	1550652	1550652	+	Missense_Mutation	SNP	G	G	T			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr16:1550652G>T	ENST00000262319.6	+	9	1512	c.1233G>T	c.(1231-1233)gaG>gaT	p.E411D		NM_016111.3	NP_057195.2	Q9Y4R8	TELO2_HUMAN	telomere maintenance 2	411					regulation of TOR signaling (GO:0032006)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	protein complex binding (GO:0032403)			NS(1)|endometrium(1)|kidney(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	19		Hepatocellular(780;0.219)				TCGTGGCAGAGGTCGTTAGTG	0.697																																																	0								ENSG00000100726						38.0	42.0	40.0					16																	1550652		2198	4299	6497	TELO2	SO:0001583	missense	0			-	HGNC	AL080126	CCDS32363.1	16p13.3	2013-08-06	2013-08-06		ENSG00000100726	ENSG00000100726			29099	protein-coding gene	gene with protein product		611140	"""TEL2, telomere maintenance 2, homolog (S. cerevisiae)"""			9734811, 11230166, 12670948	Standard	NM_016111		Approved	KIAA0683, hCLK2, TEL2	uc002cly.3	Q9Y4R8	OTTHUMG00000044471	ENST00000262319.6:c.1233G>T	16.37:g.1550652G>T	ENSP00000262319:p.Glu411Asp	Somatic	0	32	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	22	15.38	D3DU73|O75168|Q7LDV4|Q9BR21	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Telomere_length_regulation_dom,superfamily_ARM-type_fold	p.E411D	ENST00000262319.6	37	c.1233	CCDS32363.1	16	.	.	.	.	.	.	.	.	.	.	g	13.97	2.397211	0.42512	.	.	ENSG00000100726	ENST00000437914;ENST00000262319	D	0.84944	-1.92	4.79	-0.243	0.13035	.	0.047821	0.85682	N	0.000000	D	0.90373	0.6987	M	0.84326	2.69	0.43959	D	0.996638	D	0.89917	1.0	D	0.91635	0.999	D	0.86844	0.2019	10	0.44086	T	0.13	-28.9035	8.9679	0.35887	0.441:0.0:0.559:0.0	.	411	Q9Y4R8	TELO2_HUMAN	D	25;411	ENSP00000262319:E411D	ENSP00000262319:E411D	E	+	3	2	TELO2	1490653	1.000000	0.71417	0.193000	0.23327	0.007000	0.05969	1.465000	0.35299	-0.306000	0.08818	0.651000	0.88453	GAG	-	NULL		0.697	TELO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TELO2	protein_coding	OTTHUMT00000103602.2	G	NM_016111	-		1550652	+1	no_errors	ENST00000262319	ensembl	human	known	74_37	missense	SNP	0.755	T
ALX3	257	genome.wustl.edu	37	1	110603286	110603287	+	3'UTR	INS	-	-	GGTGCTTCCTCCGTGGTGTCCAGGCAGG	rs139173949|rs4520416|rs144523285	byFrequency	TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr1:110603286_110603287insGGTGCTTCCTCCGTGGTGTCCAGGCAGG	ENST00000369792.4	-	0	1187_1188				RP4-773N10.4_ENST00000596959.1_RNA|RP4-773N10.4_ENST00000554749.1_RNA	NM_006492.2	NP_006483.2	O95076	ALX3_HUMAN	ALX homeobox 3						embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal system morphogenesis (GO:0048704)|pattern specification process (GO:0007389)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6		all_cancers(81;2.35e-05)|all_epithelial(167;7.69e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.015)|all cancers(265;0.0706)|Epithelial(280;0.0758)|Colorectal(144;0.113)|LUSC - Lung squamous cell carcinoma(189;0.135)		TTGGAGGCAGAGGTGGGCTGGG	0.589														3605	0.719848	0.7927	0.6599	5008	,	,		20548	0.7629		0.5666	False		,,,				2504	0.7771																0								ENSG00000258634																																			RP4-773N10.4	SO:0001624	3_prime_UTR_variant	0				Clone_based_vega_gene	AF008203	CCDS819.1	1p13.3	2014-02-04	2008-11-04		ENSG00000156150	ENSG00000156150		"""Homeoboxes / PRD class"""	449	protein-coding gene	gene with protein product		606014	"""aristaless-like homeobox 3"", ""frontonasal dysplasia"""	FND		15226305, 11807986, 19409524	Standard	NM_006492		Approved		uc001dzb.3	O95076	OTTHUMG00000011650	ENST00000369792.4:c.*69->CCTGCCTGGACACCACGGAGGAAGCACC	1.37:g.110603286_110603287insGGTGCTTCCTCCGTGGTGTCCAGGCAGG		Somatic	NA	NA	NA		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	O95075|Q5T8M4	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000369792.4	37	NULL	CCDS819.1	1																																																																																			-	-		0.589	ALX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000258634	protein_coding	OTTHUMT00000032232.2	-	NM_006492			110603287	+1	no_errors	ENST00000554749	ensembl	human	known	74_37	rna	INS	0.324:0.902	GGTGCTTCCTCCGTGGTGTCCAGGCAGG
RASAL2	9462	genome.wustl.edu	37	1	178063820	178063820	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr1:178063820C>T	ENST00000367649.3	+	1	545	c.193C>T	c.(193-195)Cgg>Tgg	p.R65W	RASAL2-AS1_ENST00000421505.1_lincRNA|RASAL2_ENST00000448150.3_Missense_Mutation_p.R47W			Q9UJF2	NGAP_HUMAN	RAS protein activator like 2	0	PH.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Ras GTPase activator activity (GO:0005099)			biliary_tract(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(2)|lung(25)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54						GAGCTGGGTCCGGGTGTACGG	0.577																																																	0								ENSG00000075391						46.0	38.0	41.0					1																	178063820		2203	4300	6503	RASAL2	SO:0001583	missense	0			-	HGNC	AF047711	CCDS1321.1, CCDS1322.1, CCDS1321.2	1q25	2013-01-10			ENSG00000075391	ENSG00000075391		"""Pleckstrin homology (PH) domain containing"""	9874	protein-coding gene	gene with protein product	"""Ras GTPase activating protein-like"", ""Ras protein activator like 1"""	606136				9877179	Standard	NM_004841		Approved	nGAP	uc001glq.3	Q9UJF2	OTTHUMG00000035022	ENST00000367649.3:c.193C>T	1.37:g.178063820C>T	ENSP00000356621:p.Arg65Trp	Somatic	0	34	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	13	13	50.00	F8W755|O95174|Q2TB22|Q5TFU9	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_DUF3498,pfam_RasGAP,pfam_Pleckstrin_homology,pfam_C2_dom,superfamily_Rho_GTPase_activation_prot,superfamily_C2_dom,superfamily_PP1_inhibitor,smart_Pleckstrin_homology,smart_C2_dom,smart_RasGAP,pfscan_Pleckstrin_homology,pfscan_RasGAP	p.R65W	ENST00000367649.3	37	c.193	CCDS1321.2	1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344018	0.61073	.	.	ENSG00000075391	ENST00000448150;ENST00000367649	T;T	0.21543	2.03;2.0	4.53	4.53	0.55603	.	0.133249	0.32015	N	0.006717	T	0.26521	0.0648	L	0.36672	1.1	0.46521	D	0.999089	D	0.58620	0.983	P	0.51016	0.656	T	0.02156	-1.1204	10	0.62326	D	0.03	.	14.5484	0.68050	0.0:1.0:0.0:0.0	.	65	F8W755	.	W	47;65	ENSP00000407768:R47W;ENSP00000356621:R65W	ENSP00000356621:R65W	R	+	1	2	RASAL2	176330443	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	4.253000	0.58791	2.224000	0.72417	0.491000	0.48974	CGG	-	smart_Pleckstrin_homology		0.577	RASAL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	RASAL2	protein_coding	OTTHUMT00000352415.1	C	NM_170692	-		178063820	+1	no_errors	ENST00000367649	ensembl	human	known	74_37	missense	SNP	1.000	T
TMEM132D	121256	genome.wustl.edu	37	12	129694177	129694177	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr12:129694177G>A	ENST00000422113.2	-	5	1657	c.1331C>T	c.(1330-1332)aCg>aTg	p.T444M	RP11-669N7.3_ENST00000542578.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	444					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		CGTCTTCCCCGTGAGGATGGC	0.592																																																	0								ENSG00000151952						93.0	74.0	80.0					12																	129694177		2203	4300	6503	TMEM132D	SO:0001583	missense	0			-	HGNC	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 153"""	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.1331C>T	12.37:g.129694177G>A	ENSP00000408581:p.Thr444Met	Somatic	0	49	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	17	26	39.53	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	NULL	p.T444M	ENST00000422113.2	37	c.1331	CCDS9266.1	12	.	.	.	.	.	.	.	.	.	.	G	24.2	4.499800	0.85176	.	.	ENSG00000151952	ENST00000422113	T	0.17691	2.26	5.3	5.3	0.74995	.	0.000000	0.64402	D	0.000002	T	0.47820	0.1466	M	0.88640	2.97	0.58432	D	0.999999	D	0.89917	1.0	D	0.74674	0.984	T	0.54873	-0.8228	9	.	.	.	-23.1339	14.6727	0.68956	0.0:0.0:0.8542:0.1458	.	444	Q14C87	T132D_HUMAN	M	444	ENSP00000408581:T444M	.	T	-	2	0	TMEM132D	128260130	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	7.321000	0.79088	2.446000	0.82766	0.655000	0.94253	ACG	-	NULL		0.592	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TMEM132D	protein_coding	OTTHUMT00000399592.1	G	NM_133448	-		129694177	-1	no_errors	ENST00000422113	ensembl	human	known	74_37	missense	SNP	1.000	A
DNMT3A	1788	genome.wustl.edu	37	2	25469935	25469935	+	Silent	SNP	G	G	T			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr2:25469935G>T	ENST00000264709.3	-	9	1444	c.1107C>A	c.(1105-1107)atC>atA	p.I369I	DNMT3A_ENST00000321117.5_Silent_p.I369I|DNMT3A_ENST00000402667.1_Silent_p.I146I|DNMT3A_ENST00000474887.1_5'Flank|DNMT3A_ENST00000380746.4_Silent_p.I180I	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	369	Interaction with DNMT1 and DNMT3B.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGACCTCGTAGATGGCTTTGC	0.602			"""Mis, F, N, S"""		AML																																			Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	0								ENSG00000119772						130.0	91.0	104.0					2																	25469935		2203	4300	6503	DNMT3A	SO:0001819	synonymous_variant	0			-	HGNC		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.1107C>A	2.37:g.25469935G>T		Somatic	0	51	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	57	8.06	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_PWWP_dom,pfam_C5_MeTfrase,superfamily_Znf_FYVE_PHD,smart_PWWP_dom,pfscan_PWWP_dom	p.I369	ENST00000264709.3	37	c.1107	CCDS33157.1	2																																																																																			-	NULL		0.602	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	DNMT3A	protein_coding	OTTHUMT00000211587.1	G	NM_022552	-		25469935	-1	no_errors	ENST00000264709	ensembl	human	known	74_37	silent	SNP	1.000	T
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-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	CATAGATTTGCTCACTGAC	CATAGATTTGCTCACTGAC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	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		0.5898141783798939	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	-
ITGA6	3655	genome.wustl.edu	37	2	173355768	173355768	+	Missense_Mutation	SNP	G	G	T			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr2:173355768G>T	ENST00000264106.6	+	22	3016	c.2813G>T	c.(2812-2814)aGa>aTa	p.R938I	AC093818.1_ENST00000442417.1_RNA|ITGA6_ENST00000375221.2_Missense_Mutation_p.R938I|ITGA6_ENST00000409080.1_Missense_Mutation_p.R899I|ITGA6_ENST00000264107.7_Missense_Mutation_p.R899I|ITGA6_ENST00000409532.1_Missense_Mutation_p.R780I|ITGA6_ENST00000343713.4_Missense_Mutation_p.R894I			P23229	ITA6_HUMAN	integrin, alpha 6	938					amelogenesis (GO:0097186)|blood coagulation (GO:0007596)|brown fat cell differentiation (GO:0050873)|cell adhesion mediated by integrin (GO:0033627)|cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|cellular response to extracellular stimulus (GO:0031668)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|nail development (GO:0035878)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|renal system development (GO:0072001)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|external side of plasma membrane (GO:0009897)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha6-beta4 complex (GO:0034676)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	44			OV - Ovarian serous cystadenocarcinoma(117;0.0979)			CACAACTCAAGAAAGAAACGG	0.308																																																	0								ENSG00000091409						87.0	108.0	101.0					2																	173355768		2199	4299	6498	ITGA6	SO:0001583	missense	0			-	HGNC		CCDS2249.1, CCDS46451.1	2q31.1	2010-09-20			ENSG00000091409	ENSG00000091409		"""CD molecules"", ""Integrins"""	6142	protein-coding gene	gene with protein product		147556					Standard	NM_001079818		Approved	CD49f	uc002uhp.1	P23229	OTTHUMG00000132277	ENST00000264106.6:c.2813G>T	2.37:g.173355768G>T	ENSP00000264106:p.Arg938Ile	Somatic	0	42	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	43	8.51	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Integrin_alpha-2,pfam_FG-GAP,smart_Int_alpha_beta-p,prints_Integrin_alpha	p.R938I	ENST00000264106.6	37	c.2813		2	.	.	.	.	.	.	.	.	.	.	G	24.3	4.511588	0.85389	.	.	ENSG00000091409	ENST00000409532;ENST00000264107;ENST00000264106;ENST00000375221;ENST00000343713;ENST00000409080;ENST00000442250;ENST00000458358;ENST00000416789	T;T;T;T;T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.73976	0.3656	M	0.89095	3.005	0.80722	D	1	D;D;D;D	0.89917	1.0;0.995;1.0;1.0	D;D;D;D	0.97110	0.998;0.965;0.998;1.0	T	0.79443	-0.1801	10	0.87932	D	0	.	16.3226	0.82956	0.0:0.0:1.0:0.0	.	894;923;899;899	P23229-4;P23229-9;G5E9H1;P23229-2	.;.;.;.	I	780;899;938;938;894;899;938;894;66	ENSP00000386614:R780I;ENSP00000264107:R899I;ENSP00000264106:R938I;ENSP00000364369:R938I;ENSP00000341078:R894I;ENSP00000386896:R899I;ENSP00000406694:R938I;ENSP00000394169:R894I;ENSP00000388435:R66I	ENSP00000264106:R938I	R	+	2	0	ITGA6	173064014	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	4.934000	0.63491	2.534000	0.85438	0.460000	0.39030	AGA	-	pfam_Integrin_alpha-2		0.308	ITGA6-201	KNOWN	basic	protein_coding	ITGA6	protein_coding		G		-		173355768	+1	no_errors	ENST00000264106	ensembl	human	known	74_37	missense	SNP	1.000	T
ZNF134	7693	genome.wustl.edu	37	19	58132422	58132422	+	Missense_Mutation	SNP	G	G	T			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr19:58132422G>T	ENST00000396161.5	+	3	1245	c.935G>T	c.(934-936)gGa>gTa	p.G312V		NM_003435.3	NP_003426.3	P52741	ZN134_HUMAN	zinc finger protein 134	312					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)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(3)|prostate(1)	11		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		ATTCACACTGGAGAAAATCCT	0.423																																																	0								ENSG00000213762						127.0	130.0	129.0					19																	58132422		2202	4300	6502	ZNF134	SO:0001583	missense	0			-	HGNC	U09412	CCDS42638.1	19q13.4	2013-01-08	2006-06-13			ENSG00000213762		"""Zinc fingers, C2H2-type"""	12918	protein-coding gene	gene with protein product		604076	"""zinc finger protein 134 (clone pHZ-15)"""			7557990	Standard	NM_003435		Approved	pHZ-15	uc002qpn.2	P52741		ENST00000396161.5:c.935G>T	19.37:g.58132422G>T	ENSP00000379464:p.Gly312Val	Somatic	0	37	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	33	10.81	Q9Y4B2	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Znf_C2H2,smart_Znf_C2H2-like,pfscan_Znf_C2H2	p.G312V	ENST00000396161.5	37	c.935	CCDS42638.1	19	.	.	.	.	.	.	.	.	.	.	G	19.94	3.919383	0.73098	.	.	ENSG00000213762	ENST00000418193;ENST00000541849;ENST00000396161	T	0.01599	4.74	4.45	4.45	0.53987	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09862	0.0242	M	0.69523	2.12	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.00926	-1.1512	9	0.87932	D	0	.	16.3388	0.83075	0.0:0.0:1.0:0.0	.	312	P52741	ZN134_HUMAN	V	379;232;312	ENSP00000379464:G312V	ENSP00000379464:G312V	G	+	2	0	ZNF134	62824234	0.991000	0.36638	1.000000	0.80357	0.998000	0.95712	2.093000	0.41710	2.458000	0.83093	0.561000	0.74099	GGA	-	pfscan_Znf_C2H2		0.423	ZNF134-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZNF134	protein_coding	OTTHUMT00000466808.1	G	NM_003435	-		58132422	+1	no_errors	ENST00000396161	ensembl	human	known	74_37	missense	SNP	1.000	T
LNX1	84708	genome.wustl.edu	37	4	54327211	54327212	+	Splice_Site	INS	-	-	A	rs60909872|rs150358881|rs572804300|rs397939876	byFrequency	TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr4:54327211_54327212insA	ENST00000263925.7	-	11	2366		c.e11-2		FIP1L1_ENST00000507166.1_Intron|LNX1_ENST00000306888.2_Splice_Site	NM_001126328.2	NP_001119800.1	Q8TBB1	LNX1_HUMAN	ligand of numb-protein X 1, E3 ubiquitin protein ligase						protein homooligomerization (GO:0051260)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.?(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|endometrium(3)|large_intestine(11)|lung(6)|ovary(3)|urinary_tract(4)	32	all_neural(26;0.153)		GBM - Glioblastoma multiforme(3;8.2e-46)|LUSC - Lung squamous cell carcinoma(32;0.0134)			TCACCACATCTAAAAAAAAAAA	0.332																																																	1	Unknown(1)	ovary(1)						ENSG00000072201																																			LNX1	SO:0001630	splice_region_variant	0				HGNC	AF237782	CCDS3492.1, CCDS47057.1	4q12	2013-01-09	2012-02-23	2005-11-04	ENSG00000072201	ENSG00000072201		"""RING-type (C3HC4) zinc fingers"""	6657	protein-coding gene	gene with protein product		609732	"""ligand of numb-protein X"", ""ligand of numb-protein X 1"""	LNX		11521506, 11782429	Standard	NM_032622		Approved	MPDZ, PDZRN2	uc003hag.5	Q8TBB1	OTTHUMG00000102099	ENST00000263925.7:c.2052-2->T	4.37:g.54327222_54327222dupA		Somatic	0	28	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	17	22.73	Q4W5K7|Q8N4C2|Q96MJ7|Q9BY20	Splice_Site	INS	NA	NA	NA	NA	NA	NA	-	e10-2	ENST00000263925.7	37	c.2052-3_2052-2	CCDS47057.1	4																																																																																			-	-		0.332	LNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LNX1	protein_coding	OTTHUMT00000219934.2	-			Intron	54327212	-1	no_errors	ENST00000263925	ensembl	human	known	74_37	splice_site_ins	INS	0.694:0.015	A
FAM196B	100131897	genome.wustl.edu	37	5	169309787	169309787	+	Silent	SNP	A	A	G			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr5:169309787A>G	ENST00000377365.3	-	2	2497	c.1116T>C	c.(1114-1116)aaT>aaC	p.N372N	DOCK2_ENST00000256935.8_Intron|FAM196B_ENST00000523970.1_5'Flank|DOCK2_ENST00000540750.1_Intron|DOCK2_ENST00000523351.1_Intron|DOCK2_ENST00000520908.1_Intron	NM_001129891.1	NP_001123363.1	A6NMK8	F196B_HUMAN	family with sequence similarity 196, member B	372										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(1)|skin(1)	5						TTCCTGGACAATTTGGAAACT	0.478																																																	0								ENSG00000204767						106.0	90.0	95.0					5																	169309787		692	1591	2283	FAM196B	SO:0001819	synonymous_variant	0			-	HGNC		CCDS47336.1	5q35.1	2010-02-17	2009-09-11	2009-09-11	ENSG00000204767	ENSG00000204767			37271	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 57"""	C5orf57			Standard	NM_001129891		Approved		uc003mag.2	A6NMK8	OTTHUMG00000163083	ENST00000377365.3:c.1116T>C	5.37:g.169309787A>G		Somatic	0	55	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	7	61	10.29		Silent	SNP	NA	NA	NA	NA	NA	NA	NULL	p.N372	ENST00000377365.3	37	c.1116	CCDS47336.1	5																																																																																			-	NULL		0.478	FAM196B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM196B	protein_coding	OTTHUMT00000371629.1	A	NM_001129891	-		169309787	-1	no_errors	ENST00000377365	ensembl	human	known	74_37	silent	SNP	0.000	G
POMC	5443	genome.wustl.edu	37	2	25384456	25384457	+	In_Frame_Ins	INS	-	-	GCTGCTGCT	rs10654394	byFrequency	TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr2:25384456_25384457insGCTGCTGCT	ENST00000405623.1	-	3	752_753	c.297_298insAGCAGCAGC	c.(295-300)ggcgca>ggcAGCAGCAGCgca	p.99_100GA>GSSSA	POMC_ENST00000380794.1_In_Frame_Ins_p.99_100GA>GSSSA|RP11-509E16.1_ENST00000567599.1_lincRNA|POMC_ENST00000264708.3_In_Frame_Ins_p.99_100GA>GSSSA|POMC_ENST00000395826.2_In_Frame_Ins_p.99_100GA>GSSSA			P01189	COLI_HUMAN	proopiomelanocortin	99			Missing. {ECO:0000269|PubMed:11244459, ECO:0000269|PubMed:7828531, ECO:0000269|PubMed:9768693}.		cell-cell signaling (GO:0007267)|cellular pigmentation (GO:0033059)|cellular protein metabolic process (GO:0044267)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|negative regulation of tumor necrosis factor production (GO:0032720)|neuropeptide signaling pathway (GO:0007218)|peptide hormone processing (GO:0016486)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of appetite (GO:0032098)|regulation of blood pressure (GO:0008217)|regulation of corticosterone secretion (GO:2000852)|regulation of glycogen metabolic process (GO:0070873)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|peroxisomal matrix (GO:0005782)|secretory granule (GO:0030141)|secretory granule lumen (GO:0034774)	G-protein coupled receptor binding (GO:0001664)|hormone activity (GO:0005179)|receptor binding (GO:0005102)|type 1 melanocortin receptor binding (GO:0070996)|type 3 melanocortin receptor binding (GO:0031781)|type 4 melanocortin receptor binding (GO:0031782)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(5)|ovary(1)	12	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Loperamide(DB00836)	TTCTGCCCTGCgccgctgctgc	0.728																																					Colon(110;1515 1566 8452 10082 43216)												0			GRCh37	CI042901|CI984063	POMC	I	rs10654394	ENSG00000115138																																			POMC	SO:0001652	inframe_insertion	0				HGNC		CCDS1717.1	2p23	2013-02-25	2008-07-31		ENSG00000115138	ENSG00000115138		"""Endogenous ligands"""	9201	protein-coding gene	gene with protein product	"""adrenocorticotropin"", ""beta-lipotropin"", ""alpha-melanocyte stimulating hormone"", ""beta-melanocyte stimulating hormone"", ""beta-endorphin"", ""adrenocorticotropic hormone"", ""opiomelanocortin prepropeptide"""	176830				6254047, 9620771	Standard	NM_001035256		Approved	MSH, POC, CLIP, ACTH, NPP, LPH	uc002rfz.1	P01189	OTTHUMG00000094764	ENST00000405623.1:c.297_298insAGCAGCAGC	2.37:g.25384456_25384457insGCTGCTGCT	ENSP00000384092:p.Gly99_Ala100insSerSerSer	Somatic	NA	NA	NA		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	P78442|Q53T23|Q9UD39|Q9UD40	In_Frame_Ins	INS	NA	NA	NA	NA	NA	NA	pfam_Mcrtin_ACTH_cent,pfam_Melanocortin_N,pfam_Opioid_neuropept,prints_Mcortin_ACTH	p.99in_frame_insSSS	ENST00000405623.1	37	c.298_297	CCDS1717.1	2																																																																																			-	NULL		0.728	POMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	POMC	protein_coding	OTTHUMT00000211573.3	-	NM_001035256			25384457	-1	no_errors	ENST00000264708	ensembl	human	known	74_37	in_frame_ins	INS	0.404:0.522	GCTGCTGCT
GSTA4	2941	genome.wustl.edu	37	6	52849261	52849261	+	Splice_Site	SNP	C	C	A			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr6:52849261C>A	ENST00000370959.1	-	5	532		c.e5+1		GSTA4_ENST00000370960.1_Splice_Site|GSTA4_ENST00000486559.1_Splice_Site|GSTA4_ENST00000541324.1_Splice_Site			O15217	GSTA4_HUMAN	glutathione S-transferase alpha 4						glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	glutathione transferase activity (GO:0004364)|protein homodimerization activity (GO:0042803)			endometrium(1)|lung(3)|skin(2)|urinary_tract(1)	7	Lung NSC(77;0.103)				Glutathione(DB00143)	CTGCCACCTACCTTTTCAAAC	0.418																																																	0								ENSG00000170899						108.0	96.0	100.0					6																	52849261		2203	4300	6503	GSTA4	SO:0001630	splice_region_variant	0			-	HGNC	AF020918	CCDS4948.1	6p12.2	2012-06-21	2008-11-26		ENSG00000170899	ENSG00000170899	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4629	protein-coding gene	gene with protein product		605450	"""glutathione S-transferase A4"""			9480897	Standard	NM_001512		Approved		uc003pbf.3	O15217	OTTHUMG00000014868	ENST00000370959.1:c.414+1G>T	6.37:g.52849261C>A		Somatic	0	208	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	90	20	81.82	B2RD15|Q5T7Q8|Q6P4G1|Q9BX18|Q9H414	Splice_Site	SNP	NA	NA	NA	NA	NA	NA	-	e4+1	ENST00000370959.1	37	c.414+1	CCDS4948.1	6	.	.	.	.	.	.	.	.	.	.	C	22.4	4.284616	0.80803	.	.	ENSG00000170899	ENST00000370963;ENST00000541324;ENST00000370960;ENST00000370959;ENST00000457564	.	.	.	5.05	5.05	0.67936	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.3562	0.90358	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GSTA4	52957220	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.088000	0.71371	2.507000	0.84556	0.557000	0.71058	.	-	-		0.418	GSTA4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	GSTA4	protein_coding	OTTHUMT00000040946.1	C	NM_001512	-	Intron	52849261	-1	no_errors	ENST00000370959	ensembl	human	known	74_37	splice_site	SNP	1.000	A
PRRC2C	23215	genome.wustl.edu	37	1	171511148	171511149	+	Frame_Shift_Ins	INS	-	-	A			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr1:171511148_171511149insA	ENST00000338920.4	+	16	4774_4775	c.4537_4538insA	c.(4537-4539)gaafs	p.E1513fs	PRRC2C_ENST00000392078.3_Frame_Shift_Ins_p.E1515fs|PRRC2C_ENST00000426496.2_Frame_Shift_Ins_p.E1513fs|PRRC2C_ENST00000367742.3_Frame_Shift_Ins_p.E1515fs	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	1513					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										AGAGAGGGATGAAAAAAAAAAT	0.391																																																	0								ENSG00000117523																																			PRRC2C	SO:0001589	frameshift_variant	0				HGNC	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"""BAT2 domain containing 1"", ""HLA-B associated transcript 2-like 2"""	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.4547dupA	1.37:g.171511158_171511158dupA	ENSP00000343629:p.Glu1513fs	Somatic	0	28	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	24	17.24	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Frame_Shift_Ins	INS	NA	NA	NA	NA	NA	NA	pfam_BAT2_N	p.N1518fs	ENST00000338920.4	37	c.4543_4544	CCDS1296.2	1																																																																																			-	NULL		0.391	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	PRRC2C	protein_coding	OTTHUMT00000314826.4	-	NM_015172			171511149	+1	no_errors	ENST00000392078	ensembl	human	known	74_37	frame_shift_ins	INS	1.000:1.000	A
ANKRD20A2	441430	genome.wustl.edu	37	9	42366347	42366347	+	5'Flank	SNP	G	G	C	rs200984588		TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr9:42366347G>C	ENST00000377601.2	+	0	0				RP11-216M21.7_ENST00000450520.1_RNA	NM_001012421.1	NP_001012421.1	Q5SQ80	A20A2_HUMAN	ankyrin repeat domain 20 family, member A2											large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	4						ttgaatattagaaaataatga	0.284																																																	0								ENSG00000233207																																			RP11-216M21.7	SO:0001631	upstream_gene_variant	0			-	Clone_based_vega_gene		CCDS35028.1	9p12	2013-01-10			ENSG00000183148	ENSG00000183148		"""Ankyrin repeat domain containing"""	31979	protein-coding gene	gene with protein product							Standard	XM_005272519		Approved			Q5SQ80	OTTHUMG00000058641		9.37:g.42366347G>C	Exception_encountered	Somatic	0	19	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	23	17.86		RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000377601.2	37	NULL	CCDS35028.1	9																																																																																			-	-		0.284	ANKRD20A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000233207	protein_coding	OTTHUMT00000129794.1	G	NM_001012421	rs200984588		42366347	-1	no_errors	ENST00000450520	ensembl	human	known	74_37	rna	SNP	0.081	C
HES3	390992	genome.wustl.edu	37	1	6305511	6305511	+	Missense_Mutation	SNP	G	G	T			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr1:6305511G>T	ENST00000377898.3	+	4	570	c.505G>T	c.(505-507)Ggg>Tgg	p.G169W		NM_001024598.3	NP_001019769.1	Q5TGS1	HES3_HUMAN	hes family bHLH transcription factor 3	169	Pro-rich.				hindbrain morphogenesis (GO:0021575)|in utero embryonic development (GO:0001701)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oculomotor nerve development (GO:0021557)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of timing of neuron differentiation (GO:0060164)|transcription, DNA-templated (GO:0006351)|trochlear nerve development (GO:0021558)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription factor binding (GO:0008134)			lung(2)|skin(1)	3	Ovarian(185;0.0634)	all_cancers(23;2.48e-32)|all_epithelial(116;1.14e-17)|all_lung(118;2.85e-06)|all_neural(13;3.68e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;3.77e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00475)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;1.2e-37)|GBM - Glioblastoma multiforme(13;3.2e-29)|OV - Ovarian serous cystadenocarcinoma(86;2.52e-19)|Colorectal(212;1.19e-07)|COAD - Colon adenocarcinoma(227;1.3e-05)|Kidney(185;4.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000871)|BRCA - Breast invasive adenocarcinoma(365;0.00105)|STAD - Stomach adenocarcinoma(132;0.00308)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.241)		CGAGAGTCCCGGGCTGGGCCT	0.697																																																	0								ENSG00000173673						7.0	9.0	8.0					1																	6305511		1657	3748	5405	HES3	SO:0001583	missense	0			-	HGNC		CCDS41238.1	1p36.31	2013-10-17	2013-10-17		ENSG00000173673	ENSG00000173673		"""Basic helix-loop-helix proteins"""	26226	protein-coding gene	gene with protein product		609971	"""hairy and enhancer of split 3 (Drosophila)"""				Standard	NM_001024598		Approved	bHLHb43	uc009vly.2	Q5TGS1	OTTHUMG00000001271	ENST00000377898.3:c.505G>T	1.37:g.6305511G>T	ENSP00000367130:p.Gly169Trp	Somatic	0	80	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	29	12.12	Q5TGS0	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_bHLH_dom,superfamily_bHLH_dom,smart_bHLH_dom,pfscan_bHLH_dom	p.G169W	ENST00000377898.3	37	c.505	CCDS41238.1	1	.	.	.	.	.	.	.	.	.	.	G	15.85	2.955231	0.53293	.	.	ENSG00000173673	ENST00000377898	T	0.32753	1.44	2.9	1.95	0.26073	.	2.454950	0.02007	N	0.046722	T	0.39937	0.1097	N	0.19112	0.55	0.09310	N	1	D	0.76494	0.999	D	0.73708	0.981	T	0.30621	-0.9972	10	0.66056	D	0.02	-6.1494	5.1074	0.14790	0.1755:0.0:0.8245:0.0	.	169	Q5TGS1	HES3_HUMAN	W	169	ENSP00000367130:G169W	ENSP00000367130:G169W	G	+	1	0	HES3	6228098	0.250000	0.23951	0.008000	0.14137	0.326000	0.28443	1.472000	0.35376	0.766000	0.33244	0.289000	0.19496	GGG	-	NULL		0.697	HES3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	HES3	protein_coding	OTTHUMT00000003716.3	G	NM_001024598	-		6305511	+1	no_errors	ENST00000377898	ensembl	human	known	74_37	missense	SNP	0.007	T
ENPP1	5167	genome.wustl.edu	37	6	132211605	132211605	+	Frame_Shift_Del	DEL	T	T	-			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr6:132211605delT	ENST00000360971.2	+	25	2752	c.2732delT	c.(2731-2733)attfs	p.I911fs		NM_006208.2	NP_006199.2	P22413	ENPP1_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 1	911	Nuclease.				3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|ATP catabolic process (GO:0006200)|biomineral tissue development (GO:0031214)|bone remodeling (GO:0046849)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to insulin stimulus (GO:0032869)|generation of precursor metabolites and energy (GO:0006091)|immune response (GO:0006955)|inorganic diphosphate transport (GO:0030505)|negative regulation of cell growth (GO:0030308)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of ossification (GO:0030279)|negative regulation of protein autophosphorylation (GO:0031953)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)|regulation of bone mineralization (GO:0030500)|riboflavin metabolic process (GO:0006771)|sequestering of triglyceride (GO:0030730)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|insulin receptor binding (GO:0005158)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|protein homodimerization activity (GO:0042803)|scavenger receptor activity (GO:0005044)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(22)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	46	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)	GTTTCAGACATTTTAAAGTTG	0.358																																					Colon(104;336 1535 5856 11019 33782)												0								ENSG00000197594						98.0	94.0	95.0					6																	132211605		2203	4300	6503	ENPP1	SO:0001589	frameshift_variant	0				HGNC	M57736	CCDS5150.2	6q22-q23	2008-02-07			ENSG00000197594	ENSG00000197594	3.1.4.1, 3.6.1.9		3356	protein-coding gene	gene with protein product		173335		NPPS, M6S1, PDNP1		1315502	Standard	NM_006208		Approved	PC-1, PCA1	uc011ecf.2	P22413	OTTHUMG00000015572	ENST00000360971.2:c.2732delT	6.37:g.132211605delT	ENSP00000354238:p.Ile911fs	Somatic	0	42	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	40	9.09	Q5T9R6|Q9NPZ3|Q9P1P6|Q9UP61|Q9Y6K3	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_Phosphodiest/P_Trfase,pfam_Somatomedin_B_dom,pfam_DNA/RNA_non-sp_Endonuclease,superfamily_Alkaline_phosphatase_core,smart_Somatomedin_B_dom,smart_DNA/RNA_non-sp_Endonuclease,smart_Extracellular_endonuc_su_A,pfscan_Somatomedin_B_dom,prints_Somatomedin_B_chordata	p.L912fs	ENST00000360971.2	37	c.2732	CCDS5150.2	6																																																																																			-	NULL		0.358	ENPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENPP1	protein_coding	OTTHUMT00000042238.2	T				132211605	+1	no_errors	ENST00000360971	ensembl	human	known	74_37	frame_shift_del	DEL	1.000	-
CTSE	1510	genome.wustl.edu	37	1	206327295	206327295	+	Intron	DEL	A	A	-			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr1:206327295delA	ENST00000358184.2	+	6	780				CTSE_ENST00000361052.3_Intron|CTSE_ENST00000432969.2_Intron|CTSE_ENST00000468617.1_Intron|CTSE_ENST00000360218.2_Intron	NM_001910.3	NP_001901.1	P14091	CATE_HUMAN	cathepsin E						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|digestion (GO:0007586)|protein autoprocessing (GO:0016540)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(2)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|skin(3)	16			BRCA - Breast invasive adenocarcinoma(75;0.0754)			ACCTTGTGTCAAAAAGGCCCA	0.483																																																	0								ENSG00000196188																																			CTSE	SO:0001627	intron_variant	0				HGNC	BC042537	CCDS73012.1, CCDS73013.1	1q32.1	2008-02-05			ENSG00000196188	ENSG00000196188	3.4.23.5	"""Cathepsins"""	2530	protein-coding gene	gene with protein product		116890				2369841, 2674141	Standard	NM_001910		Approved		uc001hdu.3	P14091	OTTHUMG00000036121	ENST00000358184.2:c.663-179A>-	1.37:g.206327295delA		Somatic	0	27	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	2	22	8.33	Q5TZ01|Q5TZ02|Q9NY58|Q9UCE3|Q9UCE4	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000358184.2	37	NULL	CCDS1462.1	1																																																																																			-	-		0.483	CTSE-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	CTSE	protein_coding	OTTHUMT00000087998.1	A	NM_001910			206327295	+1	no_errors	ENST00000486757	ensembl	human	putative	74_37	rna	DEL	0.000	-
HLA-DRB1	3123	genome.wustl.edu	37	6	32548628	32548628	+	Missense_Mutation	SNP	G	G	A	rs34624872	byFrequency	TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr6:32548628G>A	ENST00000360004.5	-	4	763	c.658C>T	c.(658-660)Cgg>Tgg	p.R220W		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	220	Beta-2.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						GATTCAGACCGTGCTCCTGAG	0.483										Multiple Myeloma(14;0.17)																																							0								ENSG00000196126						77.0	86.0	83.0					6																	32548628		1511	2709	4220	HLA-DRB1	SO:0001583	missense	0			-	HGNC	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.658C>T	6.37:g.32548628G>A	ENSP00000353099:p.Arg220Trp	Somatic	1	133	0.75		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	9	35	20.45	P01914|Q9MYF5	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_MHC_II_b_N,pfam_Ig_C1-set,superfamily_MHC_I/II-like_Ag-recog,smart_MHC_II_b_N,smart_Ig_C1-set,pfscan_Ig-like_dom	p.R220W	ENST00000360004.5	37	c.658	CCDS47409.1	6	.	.	.	.	.	.	.	.	.	.	.	12.70	2.016010	0.35606	.	.	ENSG00000196126	ENST00000360004	T	0.00635	6.06	3.98	3.98	0.46160	Immunoglobulin-like fold (3);	0.849923	0.10912	N	0.620484	T	0.00580	0.0019	L	0.56769	1.78	0.24665	N	0.993446	B;B;D	0.71674	0.007;0.007;0.998	B;B;P	0.47430	0.0;0.001;0.547	T	0.53995	-0.8359	10	0.66056	D	0.02	.	10.0825	0.42399	0.0:0.2056:0.7944:0.0	rs34624872	220;220;220	P04229;Q29974;P01911	2B11_HUMAN;2B1G_HUMAN;2B1F_HUMAN	W	220	ENSP00000353099:R220W	ENSP00000353099:R220W	R	-	1	2	HLA-DRB1	32656606	0.013000	0.17824	0.747000	0.31113	0.149000	0.21700	1.804000	0.38873	1.943000	0.56356	0.453000	0.30009	CGG	-	NULL		0.483	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HLA-DRB1	protein_coding	OTTHUMT00000076393.3	G	NM_002124	rs34624872		32548628	-1	no_errors	ENST00000360004	ensembl	human	known	74_37	missense	SNP	0.988	A
F5	2153	genome.wustl.edu	37	1	169510957	169510957	+	Missense_Mutation	SNP	T	T	C			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr1:169510957T>C	ENST00000367797.3	-	13	3572	c.3371A>G	c.(3370-3372)gAg>gGg	p.E1124G	F5_ENST00000367796.3_Missense_Mutation_p.E1129G	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	1124	B.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	ATAGTGTTCCTCTGGGGGCAC	0.478																																																	0								ENSG00000198734						151.0	155.0	154.0					1																	169510957		2203	4300	6503	F5	SO:0001583	missense	0			-	HGNC	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.3371A>G	1.37:g.169510957T>C	ENSP00000356771:p.Glu1124Gly	Somatic	0	105	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	44	65	40.37	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Coagulation_fac_5/8-C_type_dom,pfam_Cu-oxidase_3,superfamily_Galactose-bd-like,superfamily_Cupredoxin,smart_Coagulation_fac_5/8-C_type_dom,pfscan_Coagulation_fac_5/8-C_type_dom	p.E1124G	ENST00000367797.3	37	c.3371	CCDS1281.1	1	.	.	.	.	.	.	.	.	.	.	T	10.84	1.462770	0.26248	.	.	ENSG00000198734	ENST00000367797;ENST00000367796	T;T	0.22539	1.95;1.95	4.93	2.45	0.29901	.	0.694656	0.13436	N	0.388075	T	0.09335	0.0230	M	0.68952	2.095	0.25285	N	0.989405	B	0.12630	0.006	B	0.09377	0.004	T	0.07616	-1.0763	9	0.49607	T	0.09	-7.8335	6.5337	0.22341	0.0:0.0888:0.1556:0.7555	.	1124	P12259	FA5_HUMAN	G	1124;1129	ENSP00000356771:E1124G;ENSP00000356770:E1129G	ENSP00000356770:E1129G	E	-	2	0	F5	167777581	0.001000	0.12720	0.186000	0.23195	0.557000	0.35523	0.681000	0.25320	0.850000	0.35239	0.446000	0.29264	GAG	-	NULL		0.478	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	F5	protein_coding	OTTHUMT00000083712.1	T	NM_000130	-		169510957	-1	no_errors	ENST00000367797	ensembl	human	known	74_37	missense	SNP	0.277	C
UBE3B	89910	genome.wustl.edu	37	12	109968375	109968375	+	Missense_Mutation	SNP	G	G	T			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr12:109968375G>T	ENST00000342494.3	+	26	3429	c.2834G>T	c.(2833-2835)gGt>gTt	p.G945V	UBE3B_ENST00000434735.2_Missense_Mutation_p.G945V|UBE3B_ENST00000535089.1_Missense_Mutation_p.G32V	NM_130466.3	NP_569733.2	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B	945	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(3)|endometrium(6)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|urinary_tract(2)	45						TACTACGGTGGTTTCCATGGA	0.493																																																	0								ENSG00000151148						144.0	128.0	134.0					12																	109968375		2203	4300	6503	UBE3B	SO:0001583	missense	0			-	HGNC	BC032301	CCDS9129.1, CCDS58277.1	12q24.12	2004-03-02			ENSG00000151148	ENSG00000151148			13478	protein-coding gene	gene with protein product		608047					Standard	NM_130466		Approved		uc001toq.4	Q7Z3V4	OTTHUMG00000169254	ENST00000342494.3:c.2834G>T	12.37:g.109968375G>T	ENSP00000340596:p.Gly945Val	Somatic	0	27	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	38	9.52	A5D8Z3|Q05BX9|Q659F7|Q7Z7Q1|Q9BXZ4	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_HECT,pfam_IQ_motif_EF-hand-BS,superfamily_HECT,superfamily_P-loop_NTPase,smart_IQ_motif_EF-hand-BS,smart_HECT,pfscan_HECT,pfscan_IQ_motif_EF-hand-BS	p.G945V	ENST00000342494.3	37	c.2834	CCDS9129.1	12	.	.	.	.	.	.	.	.	.	.	G	27.6	4.845395	0.91197	.	.	ENSG00000151148	ENST00000434735;ENST00000342494;ENST00000538070;ENST00000535089	T;T;D	0.86097	0.45;0.45;-2.07	5.56	5.56	0.83823	HECT (4);	0.000000	0.85682	D	0.000000	D	0.93993	0.8076	M	0.89534	3.04	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.94798	0.7968	10	0.87932	D	0	-18.7058	18.5098	0.90911	0.0:0.0:1.0:0.0	.	240;945	F5H2J2;Q7Z3V4	.;UBE3B_HUMAN	V	945;945;240;32	ENSP00000391529:G945V;ENSP00000340596:G945V;ENSP00000442276:G32V	ENSP00000340596:G945V	G	+	2	0	UBE3B	108452758	1.000000	0.71417	0.860000	0.33809	0.760000	0.43138	9.338000	0.96553	2.626000	0.88956	0.655000	0.94253	GGT	-	pfam_HECT,superfamily_HECT,smart_HECT,pfscan_HECT		0.493	UBE3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	UBE3B	protein_coding	OTTHUMT00000403119.1	G	NM_183415	-		109968375	+1	no_errors	ENST00000342494	ensembl	human	known	74_37	missense	SNP	1.000	T
YEATS2	55689	genome.wustl.edu	37	3	183520323	183520324	+	Intron	INS	-	-	TA	rs11276625|rs74710373	byFrequency	TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr3:183520323_183520324insTA	ENST00000305135.5	+	26	3697				AC131160.1_ENST00000401347.1_RNA	NM_018023.4	NP_060493.3	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2						chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|mitotic spindle (GO:0072686)	TBP-class protein binding (GO:0017025)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3)	49	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			atatacacgtgtatatacacac	0.332														2148	0.428914	0.2602	0.4568	5008	,	,		21295	0.5228		0.4642	False		,,,				2504	0.5041																0								ENSG00000216166																																			AC131160.1	SO:0001627	intron_variant	0				Clone_based_ensembl_gene	AB033023	CCDS43175.1	3q27.3	2004-08-18			ENSG00000163872	ENSG00000163872			25489	protein-coding gene	gene with protein product		613373				10574462	Standard	NM_018023		Approved	FLJ10201, FLJ12841, FLJ13308, KIAA1197	uc003fly.2	Q9ULM3	OTTHUMG00000156898	ENST00000305135.5:c.3503-720->TA	3.37:g.183520328_183520329dupTA		Somatic	0	11	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	6	11	35.29	A7E2B9|D3DNS9|Q641P6|Q9NW96	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000305135.5	37	NULL	CCDS43175.1	3																																																																																			-	-		0.332	YEATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ENSG00000216166	protein_coding	OTTHUMT00000346507.2	-	NM_018023			183520324	-1	no_errors	ENST00000401347	ensembl	human	novel	74_37	rna	INS	0.000:0.000	TA
TTLL5	23093	genome.wustl.edu	37	14	76420882	76420882	+	3'UTR	DEL	T	T	-			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr14:76420882delT	ENST00000298832.9	+	0	4144					NM_015072.4	NP_055887.3	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5						fertilization (GO:0009566)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|sperm motility (GO:0030317)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)			NS(2)|breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(3)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	50				BRCA - Breast invasive adenocarcinoma(234;0.029)		GTCCATAGTATTTTTTTTTTT	0.463																																																	0								ENSG00000119685																																			TTLL5	SO:0001624	3_prime_UTR_variant	0				HGNC	AF107885	CCDS32124.1	14q24.3	2014-09-09	2005-07-29	2005-07-29	ENSG00000119685	ENSG00000119685		"""Tubulin tyrosine ligase-like family"""	19963	protein-coding gene	gene with protein product		612268	"""KIAA0998"""	KIAA0998		15890843	Standard	NM_015072		Approved		uc001xrx.3	Q6EMB2	OTTHUMG00000171611	ENST00000298832.9:c.*93T>-	14.37:g.76420882delT		Somatic	0	25	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	33	10.81	B9EGH8|B9EGH9|Q9BUB0|Q9H0G4|Q9H7W2|Q9P1V5|Q9UPZ4	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000298832.9	37	NULL	CCDS32124.1	14																																																																																			-	-		0.463	TTLL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TTLL5	protein_coding	OTTHUMT00000414453.1	T	NM_015072			76420882	+1	no_errors	ENST00000554972	ensembl	human	known	74_37	rna	DEL	0.005	-
TP53	7157	genome.wustl.edu	37	17	7578406	7578406	+	Missense_Mutation	SNP	C	C	T	rs28934578		TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr17:7578406C>T	ENST00000269305.4	-	5	713	c.524G>A	c.(523-525)cGc>cAc	p.R175H	TP53_ENST00000455263.2_Missense_Mutation_p.R175H|TP53_ENST00000359597.4_Missense_Mutation_p.R175H|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000420246.2_Missense_Mutation_p.R175H|TP53_ENST00000413465.2_Missense_Mutation_p.R175H|TP53_ENST00000445888.2_Missense_Mutation_p.R175H	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	175	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> C (in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; reduces interaction with ZNF385A; dbSNP:rs28934578). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:8825920}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in a sporadic cancer; somatic mutation).|R -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R175H(847)|p.R43H(36)|p.R82H(36)|p.R175L(19)|p.0?(8)|p.R175P(6)|p.R174fs*24(3)|p.R175_E180delRCPHHE(3)|p.V173fs*59(2)|p.R174fs*1(2)|p.V157_C176del20(1)|p.V173fs*69(1)|p.E171fs*61(1)|p.V173fs*23(1)|p.R174_H178>S(1)|p.V172_E180delVVRRCPHHE(1)|p.R174_H179delRRCPHH(1)|p.E171fs*1(1)|p.R175_H178>X(1)|p.R175fs*5(1)|p.R42fs*24(1)|p.R174_C176delRRC(1)|p.H168fs*69(1)|p.R174fs*70(1)|p.E171_H179delEVVRRCPHH(1)|p.R81fs*24(1)|p.R174_E180>K(1)|p.R174fs*3(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTGGGGGCAGCGCCTCACAAC	0.652	R175H(AU565_BREAST)|R175H(CAL33_UPPER_AERODIGESTIVE_TRACT)|R175H(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|R175H(HCC1395_BREAST)|R175H(HUCCT1_BILIARY_TRACT)|R175H(KLE_ENDOMETRIUM)|R175H(KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R175H(LS123_LARGE_INTESTINE)|R175H(NCIH196_LUNG)|R175H(RKN_OVARY)|R175H(SKBR3_BREAST)|R175H(SKUT1_SOFT_TISSUE)|R175H(TYKNU_OVARY)	111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)		yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	980	Substitution - Missense(944)|Deletion - Frameshift(17)|Whole gene deletion(8)|Deletion - In frame(8)|Complex - deletion inframe(3)	large_intestine(350)|breast(103)|upper_aerodigestive_tract(74)|stomach(70)|central_nervous_system(69)|oesophagus(67)|ovary(58)|lung(40)|haematopoietic_and_lymphoid_tissue(39)|urinary_tract(22)|prostate(17)|liver(14)|pancreas(11)|endometrium(10)|biliary_tract(10)|bone(9)|kidney(4)|cervix(4)|skin(3)|vulva(2)|soft_tissue(2)|penis(1)|adrenal_gland(1)	GRCh37	CM062017|CM951224	TP53	M	rs28934578	ENSG00000141510						50.0	50.0	50.0					17																	7578406		2203	4300	6503	TP53	SO:0001583	missense	0	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	-	HGNC	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.524G>A	17.37:g.7578406C>T	ENSP00000269305:p.Arg175His	Somatic	0	30	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	17	2	89.47	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_p53_DNA-bd,pfam_p53_tetrameristn,pfam_p53_transactivation_domain,superfamily_p53-like_TF_DNA-bd,superfamily_p53_tetrameristn,prints_p53_tumour_suppressor	p.R175H	ENST00000269305.4	37	c.524	CCDS11118.1	17	.	.	.	.	.	.	.	.	.	.	C	31	5.079737	0.94050	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99889	-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55;-7.55	5.41	5.41	0.78517	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.101149	0.64402	D	0.000008	D	0.99908	0.9956	M	0.92784	3.345	0.80722	A	1	D;P;D;D;P;B;D	0.89917	0.999;0.578;1.0;0.998;0.632;0.213;0.999	D;B;D;D;B;B;D	0.91635	0.985;0.26;0.999;0.921;0.378;0.144;0.939	D	0.96278	0.9204	9	0.87932	D	0	-11.8679	17.0767	0.86588	0.0:1.0:0.0:0.0	rs28934578	136;175;175;82;175;175;175	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	H	175;175;175;175;175;175;164;82;43;82;43	ENSP00000410739:R175H;ENSP00000352610:R175H;ENSP00000269305:R175H;ENSP00000398846:R175H;ENSP00000391127:R175H;ENSP00000391478:R175H;ENSP00000425104:R43H;ENSP00000423862:R82H	ENSP00000269305:R175H	R	-	2	0	TP53	7519131	1.000000	0.71417	0.989000	0.46669	0.795000	0.44927	6.042000	0.70996	2.702000	0.92279	0.655000	0.94253	CGC	-	pfam_p53_DNA-bd,superfamily_p53-like_TF_DNA-bd,prints_p53_tumour_suppressor		0.652	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TP53	protein_coding	OTTHUMT00000367397.1	C	NM_000546	rs28934578		7578406	-1	no_errors	ENST00000269305	ensembl	human	known	74_37	missense	SNP	1.000	T
SPPL2C	162540	genome.wustl.edu	37	17	43924079	43924079	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr17:43924079G>A	ENST00000329196.5	+	1	1824	c.1807G>A	c.(1807-1809)Ggc>Agc	p.G603S	MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000579244.1_RNA|MAPT-AS1_ENST00000581125.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	603						endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										TAGCTCCGAGGGCTGGAGTGA	0.572																																																	0								ENSG00000185294						119.0	101.0	107.0					17																	43924079		2203	4300	6503	SPPL2C	SO:0001583	missense	0			-	HGNC		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.1807G>A	17.37:g.43924079G>A	ENSP00000332488:p.Gly603Ser	Somatic	0	32	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	7	21	25.00	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Peptidase_A22B_SPP,pfam_Protease-assoc_domain,smart_Preselin/SPP	p.G603S	ENST00000329196.5	37	c.1807	CCDS32673.1	17	.	.	.	.	.	.	.	.	.	.	G	15.58	2.874324	0.51695	.	.	ENSG00000185294	ENST00000329196	T	0.10192	2.9	4.68	2.69	0.31865	.	0.154448	0.30302	N	0.009925	T	0.07458	0.0188	L	0.29908	0.895	0.30555	N	0.765105	B	0.27882	0.192	B	0.23150	0.044	T	0.09335	-1.0679	10	0.62326	D	0.03	-41.243	7.1956	0.25851	0.2007:0.0:0.7993:0.0	.	603	Q8IUH8	IMP5_HUMAN	S	603	ENSP00000332488:G603S	ENSP00000332488:G603S	G	+	1	0	AC217771.1	41279859	1.000000	0.71417	0.999000	0.59377	0.245000	0.25701	4.109000	0.57824	0.684000	0.31448	0.655000	0.94253	GGC	-	NULL		0.572	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SPPL2C	protein_coding	OTTHUMT00000441156.1	G	NM_175882	-		43924079	+1	no_errors	ENST00000329196	ensembl	human	known	74_37	missense	SNP	1.000	A
CCDC7	79741	genome.wustl.edu	37	10	33140795	33140795	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr10:33140795C>T	ENST00000375030.2	+	21	2180	c.1562C>T	c.(1561-1563)aCa>aTa	p.T521I	C10orf68_ENST00000375028.3_Missense_Mutation_p.T566I|C10orf68_ENST00000375025.4_Missense_Mutation_p.T626I			Q9H943	CJ068_HUMAN		562										breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(4)	29						ATTTATAGAACATATAGGGCT	0.343																																																	0								ENSG00000150076						135.0	147.0	143.0					10																	33140795		2203	4299	6502	C10orf68	SO:0001583	missense	0			-	HGNC																												ENST00000375030.2:c.1562C>T	10.37:g.33140795C>T	ENSP00000364170:p.Thr521Ile	Somatic	0	43	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	6	44	12.00	B0QZ71|Q08AN7|Q8N7T7	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	NULL	p.T626I	ENST00000375030.2	37	c.1877		10	.	.	.	.	.	.	.	.	.	.	.	7.400	0.632497	0.14322	.	.	ENSG00000150076	ENST00000302316;ENST00000375030;ENST00000375028;ENST00000375025;ENST00000375037	T;T;T;T	0.28895	1.61;1.6;1.59;1.59	3.17	-2.98	0.05513	.	.	.	.	.	T	0.17746	0.0426	L	0.36672	1.1	0.09310	N	1	B;B;B;B	0.25667	0.012;0.131;0.131;0.021	B;B;B;B	0.22601	0.007;0.027;0.04;0.016	T	0.29792	-1.0000	9	0.66056	D	0.02	.	0.6371	0.00804	0.1743:0.2598:0.1723:0.3936	.	543;562;566;521	B4DX58;Q9H943;A2A3B4;A2A3D6	.;CJ068_HUMAN;.;.	I	562;521;566;626;538	ENSP00000303710:T562I;ENSP00000364170:T521I;ENSP00000364168:T566I;ENSP00000364165:T626I	ENSP00000303710:T562I	T	+	2	0	C10orf68	33180801	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.859000	0.01657	-0.673000	0.05259	-0.143000	0.13931	ACA	-	NULL		0.343	C10orf68-001	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	C10orf68	protein_coding	OTTHUMT00000313999.2	C		-		33140795	+1	no_errors	ENST00000375025	ensembl	human	known	74_37	missense	SNP	0.000	T
IRF2BP2	359948	genome.wustl.edu	37	1	234742799	234742800	+	3'UTR	INS	-	-	AT	rs142351268|rs531493187		TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr1:234742799_234742800insAT	ENST00000366609.3	-	0	1877_1878				IRF2BP2_ENST00000366610.3_3'UTR|RP4-781K5.2_ENST00000436039.1_RNA|IRF2BP2_ENST00000491430.1_5'Flank	NM_182972.2	NP_892017.2	Q7Z5L9	I2BP2_HUMAN	interferon regulatory factor 2 binding protein 2						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11	Ovarian(103;0.0303)	all_cancers(173;0.0236)|Prostate(94;0.0115)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)|Epithelial(3;6.2e-05)			CCTTGTCTTGGATATATATATA	0.292																																																	0								ENSG00000228830																																			RP4-781K5.2	SO:0001624	3_prime_UTR_variant	0				Clone_based_vega_gene	AY278023	CCDS1602.1, CCDS41475.1	1q42.3	2008-02-05			ENSG00000168264	ENSG00000168264			21729	protein-coding gene	gene with protein product		615332				12799427	Standard	NM_182972		Approved	IRF-2BP2	uc001hwg.3	Q7Z5L9	OTTHUMG00000037981	ENST00000366609.3:c.*84->AT	1.37:g.234742808_234742809dupAT		Somatic	0	27	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	15	16.67	B1AM35|B1AM36|Q6P083|Q7Z5L8|Q8N351|Q8WUH8	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000366609.3	37	NULL	CCDS1602.1	1																																																																																			-	-		0.292	IRF2BP2-002	NOVEL	basic|CCDS	protein_coding	ENSG00000228830	protein_coding	OTTHUMT00000092705.1	-	NM_182972			234742800	+1	no_errors	ENST00000436039	ensembl	human	known	74_37	rna	INS	1.000:1.000	AT
HCFC1	3054	genome.wustl.edu	37	X	153230115	153230115	+	Missense_Mutation	SNP	C	C	A			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chrX:153230115C>A	ENST00000310441.7	-	2	1222	c.256G>T	c.(256-258)Ggc>Tgc	p.G86C	HCFC1_ENST00000354233.3_Missense_Mutation_p.G86C|HCFC1_ENST00000461098.1_5'Flank|HCFC1_ENST00000369984.4_Missense_Mutation_p.G86C	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	86					cell cycle (GO:0007049)|chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein stabilization (GO:0050821)|regulation of protein complex assembly (GO:0043254)|regulation of transcription, DNA-templated (GO:0006355)|release from viral latency (GO:0019046)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|membrane (GO:0016020)|mitochondrion (GO:0005739)|MLL1 complex (GO:0071339)|MLL5-L complex (GO:0070688)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CACACGAAGCCATAGGCTGCA	0.582											OREG0003629	type=REGULATORY REGION|Gene=HCFC1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																																					0								ENSG00000172534						97.0	107.0	104.0					X																	153230115		2149	4222	6371	HCFC1	SO:0001583	missense	0			-	HGNC		CCDS44020.1	Xq28	2014-06-12	2014-06-09		ENSG00000172534	ENSG00000172534			4839	protein-coding gene	gene with protein product	"""VP16-accessory protein"", ""protein phosphatase 1, regulatory subunit 89"""	300019	"""mental retardation, X-linked 3"", ""host cell factor C1 (VP16-accessory protein)"""	HFC1, MRX3		8392914, 23000143	Standard	XM_005274664		Approved	HCF-1, HCF1, CFF, VCAF, MGC70925, PPP1R89	uc004fjp.3	P51610	OTTHUMG00000024222	ENST00000310441.7:c.256G>T	X.37:g.153230115C>A	ENSP00000309555:p.Gly86Cys	Somatic	0	34	0.00	1754	0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	32	11.11	Q6P4G5	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Kelch_2,pfam_Kelch_1,superfamily_Fibronectin_type3,smart_Fibronectin_type3	p.G86C	ENST00000310441.7	37	c.256	CCDS44020.1	X	.	.	.	.	.	.	.	.	.	.	C	27.5	4.835451	0.91117	.	.	ENSG00000172534	ENST00000310441;ENST00000369984;ENST00000354233	T;T;T	0.68624	-0.33;-0.33;-0.34	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.79209	0.4407	L	0.55990	1.75	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.81202	-0.1040	10	0.87932	D	0	.	16.9947	0.86363	0.0:1.0:0.0:0.0	.	86	P51610	HCFC1_HUMAN	C	86	ENSP00000309555:G86C;ENSP00000359001:G86C;ENSP00000346174:G86C	ENSP00000309555:G86C	G	-	1	0	HCFC1	152883309	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.398000	0.79919	2.276000	0.75962	0.468000	0.43344	GGC	-	NULL		0.582	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HCFC1	protein_coding	OTTHUMT00000061099.4	C	NM_005334	-		153230115	-1	no_errors	ENST00000310441	ensembl	human	known	74_37	missense	SNP	1.000	A
FAM134A	79137	genome.wustl.edu	37	2	220045810	220045810	+	Missense_Mutation	SNP	G	G	T			TCGA-DX-A48J-01A-21D-A307-09	TCGA-DX-A48J-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c31d841a-1b54-4e64-bde0-e458668a7f88	130d56bf-7533-4fbc-bea1-bc8973a3b123	g.chr2:220045810G>T	ENST00000430297.2	+	6	803	c.667G>T	c.(667-669)Gtg>Ttg	p.V223L	CNPPD1_ENST00000409789.1_5'Flank	NM_024293.4	NP_077269.3	Q8NC44	F134A_HUMAN	family with sequence similarity 134, member A	223						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)	19		Renal(207;0.0915)		Epithelial(149;8.92e-07)|all cancers(144;0.000151)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GTGGCCCCTGGTGGTTTATCA	0.522																																																	0								ENSG00000144567						133.0	128.0	130.0					2																	220045810		2203	4300	6503	FAM134A	SO:0001583	missense	0			-	HGNC	AK074983	CCDS2434.1	2q36.1	2008-02-05	2007-05-01	2007-05-01	ENSG00000144567	ENSG00000144567			28450	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 17"""	C2orf17			Standard	NM_024293		Approved	MGC3035	uc002vjw.4	Q8NC44	OTTHUMG00000154577	ENST00000430297.2:c.667G>T	2.37:g.220045810G>T	ENSP00000395249:p.Val223Leu	Somatic	0	85	0.00		0.5898141783798939	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	30	38	44.12	Q6P1P5|Q9H0K7	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Reticulon	p.V223L	ENST00000430297.2	37	c.667	CCDS2434.1	2	.	.	.	.	.	.	.	.	.	.	G	29.1	4.980531	0.92982	.	.	ENSG00000144567	ENST00000458520;ENST00000430297;ENST00000452022;ENST00000443518	T;T;T	0.41758	0.99;1.06;0.99	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.48040	0.1478	L	0.45698	1.435	0.80722	D	1	P;P	0.48230	0.907;0.711	P;P	0.50405	0.64;0.507	T	0.24083	-1.0170	10	0.19147	T	0.46	-17.3832	19.0001	0.92830	0.0:0.0:1.0:0.0	.	16;223	E7EUL4;Q8NC44	.;F134A_HUMAN	L	16;223;16;16	ENSP00000403898:V16L;ENSP00000395249:V223L;ENSP00000391284:V16L	ENSP00000395249:V223L	V	+	1	0	FAM134A	219754054	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.857000	0.99534	2.476000	0.83614	0.655000	0.94253	GTG	-	pfam_Reticulon		0.522	FAM134A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FAM134A	protein_coding	OTTHUMT00000336147.2	G	NM_024293	-		220045810	+1	no_errors	ENST00000430297	ensembl	human	known	74_37	missense	SNP	1.000	T
