#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
GAD2	2572	genome.wustl.edu	37	10	26505740	26505740	+	Start_Codon_SNP	SNP	T	T	C			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr10:26505740T>C	ENST00000376261.3	+	1	505	c.2T>C	c.(1-3)aTg>aCg	p.M1T	GAD2_ENST00000259271.3_Start_Codon_SNP_p.M1T|GAD2_ENST00000376248.1_5'Flank	NM_001134366.1	NP_001127838.1	Q05329	DCE2_HUMAN	glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa)	1					glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|cell junction (GO:0030054)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(26)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						CCAAAGCCGATGGCATCTCCG	0.682																																																	0								ENSG00000136750						58.0	60.0	59.0					10																	26505740		2203	4300	6503	GAD2	SO:0001582	initiator_codon_variant	0			-	HGNC	AJ251501	CCDS7149.1	10p13-p11.2	2003-11-11	2002-08-29		ENSG00000136750	ENSG00000136750	4.1.1.15		4093	protein-coding gene	gene with protein product		138275	"""glutamate decarboxylase 2 (pancreatic islets and brain, 65kD)"""			2039509	Standard	NM_000818		Approved	GAD65	uc001isp.2	Q05329	OTTHUMG00000017836	ENST00000376261.3:c.2T>C	10.37:g.26505740T>C	ENSP00000365437:p.Met1Thr	Somatic	0	33	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	17	27	38.64	Q9UD87	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_PyrdxlP-dep_de-COase,superfamily_PyrdxlP-dep_Trfase	p.M1T	ENST00000376261.3	37	c.2	CCDS7149.1	10	.	.	.	.	.	.	.	.	.	.	T	15.10	2.733103	0.48939	.	.	ENSG00000136750	ENST00000376261;ENST00000259271;ENST00000428517	T;T;T	0.69685	-0.42;-0.42;-0.42	4.92	4.92	0.64577	.	0.000000	0.64402	D	0.000016	T	0.80752	0.4683	.	.	.	0.80722	D	1	D;P	0.57899	0.981;0.717	D;P	0.69142	0.962;0.599	D	0.83575	0.0114	9	0.87932	D	0	-18.0697	13.5727	0.61856	0.0:0.0:0.0:1.0	.	1;1	Q4G154;Q05329	.;DCE2_HUMAN	T	1	ENSP00000365437:M1T;ENSP00000259271:M1T;ENSP00000390434:M1T	ENSP00000259271:M1T	M	+	2	0	GAD2	26545746	1.000000	0.71417	0.985000	0.45067	0.753000	0.42808	4.724000	0.61972	1.852000	0.53769	0.374000	0.22700	ATG	-	NULL		0.682	GAD2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	GAD2	protein_coding	OTTHUMT00000047255.1	T	NM_000818	-	Missense_Mutation	26505740	+1	no_errors	ENST00000259271	ensembl	human	known	74_37	missense	SNP	1.000	C
IQGAP1	8826	genome.wustl.edu	37	15	91018048	91018049	+	Intron	INS	-	-	T	rs539841859		TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr15:91018048_91018049insT	ENST00000268182.5	+	23	2908				IQGAP1_ENST00000560738.1_Intron|IQGAP1_ENST00000560020.1_3'UTR	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1						cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			GCCATAAGAGCttttttttttt	0.505																																																	0								ENSG00000140575																																			IQGAP1	SO:0001627	intron_variant	0				HGNC	D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575			6110	protein-coding gene	gene with protein product	"""RasGAP-like with IQ motifs"""	603379				8051149, 8670801	Standard	XM_005254984		Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	ENST00000268182.5:c.2784+123->T	15.37:g.91018059_91018059dupT		Somatic	0	16	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	17	19.05	A7MBM3	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000268182.5	37	NULL	CCDS10362.1	15																																																																																			-	-		0.505	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	IQGAP1	protein_coding	OTTHUMT00000313493.1	-	NM_003870			91018049	+1	no_errors	ENST00000560020	ensembl	human	known	74_37	rna	INS	0.000:0.121	T
SPEF2	79925	genome.wustl.edu	37	5	35789750	35789750	+	Intron	SNP	G	G	T			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr5:35789750G>T	ENST00000356031.3	+	31	4601				CTD-2113L7.1_ENST00000510433.1_RNA|SPEF2_ENST00000303129.4_Missense_Mutation_p.V158L|SPEF2_ENST00000440995.2_Intron	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2						axoneme assembly (GO:0035082)|brain morphogenesis (GO:0048854)|embryonic neurocranium morphogenesis (GO:0048702)|fertilization (GO:0009566)|immune system development (GO:0002520)|multicellular organismal aging (GO:0010259)|respiratory system development (GO:0060541)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|manchette (GO:0002177)|sperm midpiece (GO:0097225)				breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	37	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CAGCCAAAATGTGGTGAGGGC	0.403																																																	0								ENSG00000152582																																			SPEF2	SO:0001627	intron_variant	0			-	HGNC	AB051557	CCDS3910.1, CCDS43309.1	5p13.2	2010-05-04			ENSG00000152582	ENSG00000152582			26293	protein-coding gene	gene with protein product	"""cancer/testis antigen 122"""	610172				11214970, 16549801, 17610085	Standard	NM_024867		Approved	KPL2, FLJ23577, CT122	uc003jjo.3	Q9C093	OTTHUMG00000131111	ENST00000356031.3:c.4448-2692G>T	5.37:g.35789750G>T		Somatic	0	47	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	34	41	45.33	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_HATC_dom_C,superfamily_RNaseH-like_dom	p.V158L	ENST00000356031.3	37	c.472	CCDS43309.1	5	.	.	.	.	.	.	.	.	.	.	G	20.3	3.968232	0.74131	.	.	ENSG00000152582	ENST00000303129	T	0.41758	0.99	5.76	5.76	0.90799	.	.	.	.	.	T	0.51787	0.1695	.	.	.	0.26028	N	0.981782	D	0.89917	1.0	D	0.83275	0.996	T	0.45175	-0.9279	8	0.06365	T	0.9	.	16.8981	0.86106	0.0:0.0:1.0:0.0	.	158	Q9C093-4	.	L	158	ENSP00000303843:V158L	ENSP00000303843:V158L	V	+	1	0	SPEF2	35825507	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	4.517000	0.60503	2.726000	0.93360	0.655000	0.94253	GTG	-	NULL		0.403	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	SPEF2	protein_coding	OTTHUMT00000367199.1	G	NM_144722	-		35789750	+1	no_errors	ENST00000303129	ensembl	human	known	74_37	missense	SNP	1.000	T
CAPZA1	829	genome.wustl.edu	37	1	113202197	113202202	+	Intron	DEL	TCTCTC	TCTCTC	-	rs149635516|rs113906793	byFrequency	TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	TCTCTC	TCTCTC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr1:113202197_113202202delTCTCTC	ENST00000263168.3	+	7	1178				CAPZA1_ENST00000476936.1_Intron	NM_006135.2	NP_006126.1	P52907	CAZA1_HUMAN	capping protein (actin filament) muscle Z-line, alpha 1						actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)	actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|WASH complex (GO:0071203)	actin binding (GO:0003779)			breast(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)	9	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AATGACAGTTTCTCTCTCTCTCTTTT	0.393																																																	0								ENSG00000116489																																			CAPZA1	SO:0001627	intron_variant	0				HGNC	U56637	CCDS30805.1	1p13.2	2014-05-09			ENSG00000116489	ENSG00000116489			1488	protein-coding gene	gene with protein product		601580				7665558, 9119363	Standard	NM_006135		Approved		uc001ecj.1	P52907	OTTHUMG00000011769	ENST00000263168.3:c.507-121TCTCTC>-	1.37:g.113202203_113202208delTCTCTC		Somatic	NA	NA	NA		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	Q53FQ6|Q6FHD5	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000263168.3	37	NULL	CCDS30805.1	1																																																																																			-	-		0.393	CAPZA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CAPZA1	protein_coding	OTTHUMT00000032567.2	TCTCTC	NM_006135			113202202	+1	no_errors	ENST00000466066	ensembl	human	known	74_37	rna	DEL	0.000:0.008:0.000:0.000:0.000:0.000	-
ZNF628	89887	genome.wustl.edu	37	19	55993959	55993959	+	Missense_Mutation	SNP	T	T	C			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr19:55993959T>C	ENST00000598519.1	+	3	1952	c.1399T>C	c.(1399-1401)Tcc>Ccc	p.S467P	NAT14_ENST00000591590.1_5'Flank|ZNF628_ENST00000391718.2_Missense_Mutation_p.S463P|NAT14_ENST00000587400.1_5'Flank|NAT14_ENST00000205194.4_5'Flank			Q5EBL2	ZN628_HUMAN	zinc finger protein 628	467					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(4)|kidney(1)|lung(2)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0531)		CAAGGGCTCCTCCGGGCTGCG	0.726																																																	0								ENSG00000197483						19.0	19.0	19.0					19																	55993959		2197	4282	6479	ZNF628	SO:0001583	missense	0			-	HGNC	AF367249	CCDS33116.3	19q13.43	2013-01-08			ENSG00000197483	ENSG00000197483		"""Zinc fingers, C2H2-type"""	28054	protein-coding gene	gene with protein product	"""Zinc finger expressed in Embryonal cells and Certain adult organs"""	610671					Standard	NM_033113		Approved	ZEC, Zfp628	uc002qld.3	Q5EBL2	OTTHUMG00000150396	ENST00000598519.1:c.1399T>C	19.37:g.55993959T>C	ENSP00000469591:p.Ser467Pro	Somatic	0	54	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	21	4	84.00	Q86X34	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Znf_C2H2,smart_Znf_C2H2-like,pfscan_Znf_C2H2	p.S467P	ENST00000598519.1	37	c.1399	CCDS33116.3	19	.	.	.	.	.	.	.	.	.	.	.	14.75	2.629168	0.46944	.	.	ENSG00000197483	ENST00000391718	T	0.07908	3.15	3.48	3.48	0.39840	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.43110	U	0.000608	T	0.13927	0.0337	L	0.57536	1.79	0.40698	D	0.982456	P	0.41624	0.757	P	0.46796	0.527	T	0.01743	-1.1283	10	0.87932	D	0	-17.6648	10.2547	0.43390	0.0:0.0:0.0:1.0	.	463	Q5EBL2	ZN628_HUMAN	P	463	ENSP00000375598:S463P	ENSP00000375598:S463P	S	+	1	0	ZNF628	60685771	0.003000	0.15002	0.875000	0.34327	0.982000	0.71751	1.005000	0.29834	1.583000	0.49898	0.398000	0.26397	TCC	-	smart_Znf_C2H2-like,pfscan_Znf_C2H2		0.726	ZNF628-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ZNF628	protein_coding	OTTHUMT00000317934.2	T	XM_058964	-		55993959	+1	no_errors	ENST00000598519	ensembl	human	known	74_37	missense	SNP	0.954	C
RBAK	57786	genome.wustl.edu	37	7	5104323	5104323	+	Silent	SNP	A	A	G			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr7:5104323A>G	ENST00000353796.3	+	6	1560	c.1236A>G	c.(1234-1236)cgA>cgG	p.R412R	RBAK-RBAKDN_ENST00000396904.2_Intron|RBAK-RBAKDN_ENST00000407184.1_Intron|RBAK_ENST00000396912.1_Silent_p.R412R	NM_001204456.1	NP_001191385.1	Q9NYW8	RBAK_HUMAN	RB-associated KRAB zinc finger	412					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(2)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	10		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0916)|OV - Ovarian serous cystadenocarcinoma(56;2.44e-14)		CCTACTACCGAAAGTCTACTC	0.458																																																	0								ENSG00000146587						61.0	59.0	60.0					7																	5104323		2203	4300	6503	RBAK	SO:0001819	synonymous_variant	0			-	HGNC	AF226869	CCDS5337.1	7p22.1	2013-01-08			ENSG00000146587	ENSG00000146587		"""Zinc fingers, C2H2-type"", ""-"""	17680	protein-coding gene	gene with protein product		608191					Standard	NM_021163		Approved	ZNF769	uc003sns.1	Q9NYW8	OTTHUMG00000121155	ENST00000353796.3:c.1236A>G	7.37:g.5104323A>G		Somatic	0	37	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	16	24	40.00	A6NDF2|A8KAK4|B2RN44|B9EGS1|F8W6M7	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Znf_C2H2,pfam_Krueppel-associated_box,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	p.R412	ENST00000353796.3	37	c.1236	CCDS5337.1	7																																																																																			-	pfam_Znf_C2H2,smart_Znf_C2H2-like,pfscan_Znf_C2H2		0.458	RBAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RBAK	protein_coding	OTTHUMT00000241640.2	A	NM_021163	-		5104323	+1	no_errors	ENST00000353796	ensembl	human	known	74_37	silent	SNP	0.009	G
HLA-DRB6	3128	genome.wustl.edu	37	6	32522507	32522526	+	RNA	DEL	CACTTGGCAGGTGTAAACCT	CACTTGGCAGGTGTAAACCT	-	rs200769911|rs1064611|rs139996300	byFrequency	TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	CACTTGGCAGGTGTAAACCT	CACTTGGCAGGTGTAAACCT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr6:32522507_32522526delCACTTGGCAGGTGTAAACCT	ENST00000411500.1	-	0	680_699					NR_001298.1				major histocompatibility complex, class II, DR beta 6 (pseudogene)																		TTGGATGCTCCACTTGGCAGGTGTAAACCTCTCCACTCCG	0.527																																																	0								ENSG00000229391																																			HLA-DRB6			0				HGNC	L76566		6p21.3	2011-07-08			ENSG00000229391	ENSG00000229391		"""Histocompatibility complex"""	4954	pseudogene	pseudogene						1529427, 10436177	Standard	NR_001298		Approved		uc003obn.1		OTTHUMG00000031028		6.37:g.32522507_32522526delCACTTGGCAGGTGTAAACCT		Somatic	NA	NA	NA		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA		RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000411500.1	37	NULL		6																																																																																			-	-		0.527	HLA-DRB6-002	KNOWN	basic	processed_transcript	HLA-DRB6	pseudogene	OTTHUMT00000272900.1	CACTTGGCAGGTGTAAACCT	NR_001298			32522526	-1	no_errors	ENST00000411500	ensembl	human	known	74_37	rna	DEL	1.000:1.000:0.995:0.983:0.993:1.000:1.000:1.000:1.000:0.998:0.995:0.995:0.994:0.998:1.000:0.999:1.000:1.000:1.000:1.000	-
KHK	3795	genome.wustl.edu	37	2	27322146	27322146	+	Missense_Mutation	SNP	G	G	C			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr2:27322146G>C	ENST00000260599.6	+	6	1160	c.647G>C	c.(646-648)aGg>aCg	p.R216T	KHK_ENST00000490823.1_3'UTR|KHK_ENST00000260598.5_Missense_Mutation_p.R216T|CGREF1_ENST00000402550.1_3'UTR	NM_000221.2	NP_000212.1	P50053	KHK_HUMAN	ketohexokinase (fructokinase)	216					carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose catabolic process (GO:0006001)|regulation of glycogen metabolic process (GO:0070873)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ketohexokinase activity (GO:0004454)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGTCGTGTGAGGAAAGGGTGA	0.597																																																	0								ENSG00000138030						82.0	84.0	84.0					2																	27322146		2203	4300	6503	KHK	SO:0001583	missense	0			-	HGNC		CCDS1734.1, CCDS1735.1	2p23.3-p23.2	2008-02-05			ENSG00000138030	ENSG00000138030	2.7.1.3		6315	protein-coding gene	gene with protein product		614058				7833921	Standard	NM_000221		Approved		uc002rim.2	P50053	OTTHUMG00000097077	ENST00000260599.6:c.647G>C	2.37:g.27322146G>C	ENSP00000260599:p.Arg216Thr	Somatic	0	104	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	24	111	17.78	Q6IBK2|Q99532|Q9BRJ3|Q9UMN1	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_PfkB_dom	p.R216T	ENST00000260599.6	37	c.647	CCDS1734.1	2	.	.	.	.	.	.	.	.	.	.	G	13.81	2.347444	0.41599	.	.	ENSG00000138030	ENST00000260599;ENST00000260598;ENST00000429697	T;T;T	0.75704	-0.96;-0.96;-0.13	5.34	4.2	0.49525	Carbohydrate/purine kinase (1);	0.187786	0.56097	D	0.000032	T	0.71904	0.3395	L	0.53561	1.675	0.80722	D	1	B;P;B;P	0.41643	0.053;0.758;0.011;0.758	B;P;B;P	0.45558	0.052;0.485;0.007;0.485	T	0.68868	-0.5295	10	0.39692	T	0.17	-24.1695	9.5896	0.39537	0.133:0.0:0.867:0.0	.	216;216;216;216	Q53G56;Q6IBK2;P50053-2;P50053	.;.;.;KHK_HUMAN	T	216;216;261	ENSP00000260599:R216T;ENSP00000260598:R216T;ENSP00000404741:R261T	ENSP00000260598:R216T	R	+	2	0	KHK	27175650	1.000000	0.71417	0.997000	0.53966	0.590000	0.36582	3.684000	0.54671	0.891000	0.36235	0.462000	0.41574	AGG	-	pfam_PfkB_dom		0.597	KHK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	KHK	protein_coding	OTTHUMT00000214196.1	G		-		27322146	+1	no_errors	ENST00000260598	ensembl	human	known	74_37	missense	SNP	1.000	C
WNK1	65125	genome.wustl.edu	37	12	970296	970297	+	Frame_Shift_Ins	INS	-	-	A			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr12:970296_970297insA	ENST00000315939.6	+	7	2381_2382	c.1738_1739insA	c.(1738-1740)gaafs	p.E580fs	WNK1_ENST00000535572.1_Frame_Shift_Ins_p.E580fs|WNK1_ENST00000340908.4_Frame_Shift_Ins_p.E173fs|WNK1_ENST00000537687.1_Frame_Shift_Ins_p.E580fs|WNK1_ENST00000540360.1_3'UTR|WNK1_ENST00000530271.2_Frame_Shift_Ins_p.E580fs	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	580					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)	p.?(1)		breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			GGAGGAGCAAGAAAAAAAAAAG	0.47																																					Colon(19;451 567 6672 12618 28860)												1	Unknown(1)	skin(1)						ENSG00000060237																																			WNK1	SO:0001589	frameshift_variant	0				HGNC	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 167"""	605232	"""protein kinase, lysine deficient 1"", ""hereditary sensory neuropathy, type II"""	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.1748dupA	12.37:g.970306_970306dupA	ENSP00000313059:p.Glu580fs	Somatic	0	49	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	8	71	10.13	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Frame_Shift_Ins	INS	NA	NA	NA	NA	NA	NA	pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Kinase_OSR1/WNK_CCT,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_dom	p.K584fs	ENST00000315939.6	37	c.1738_1739	CCDS8506.1	12																																																																																			-	NULL		0.470	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	WNK1	protein_coding	OTTHUMT00000206683.1	-	NM_018979			970297	+1	no_errors	ENST00000530271	ensembl	human	known	74_37	frame_shift_ins	INS	1.000:1.000	A
GART	2618	genome.wustl.edu	37	21	34883664	34883664	+	Missense_Mutation	SNP	C	C	T	rs372288271		TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr21:34883664C>T	ENST00000381831.3	-	17	2472	c.2209G>A	c.(2209-2211)Gct>Act	p.A737T	GART_ENST00000381815.4_Missense_Mutation_p.A737T|GART_ENST00000381839.3_Missense_Mutation_p.A737T|GART_ENST00000543717.1_Missense_Mutation_p.A289T	NM_001136005.1	NP_001129477.1	P22102	PUR2_HUMAN	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	737	AIRS.				'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|glycine metabolic process (GO:0006544)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|phosphoribosylamine-glycine ligase activity (GO:0004637)|phosphoribosylformylglycinamidine cyclo-ligase activity (GO:0004641)|phosphoribosylglycinamide formyltransferase activity (GO:0004644)			NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(13)|ovary(3)|prostate(5)|urinary_tract(1)	31					Pemetrexed(DB00642)	ACAAGGACAGCGCCAACCCCA	0.547																																																	0								ENSG00000159131	C	THR/ALA,THR/ALA,THR/ALA	0,4406		0,0,2203	244.0	233.0	237.0		2209,2209,2209	5.4	1.0	21		237	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	GART	NM_000819.4,NM_001136005.1,NM_001136006.1	58,58,58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	737/1011,737/1011,737/1011	34883664	1,13005	2203	4300	6503	GART	SO:0001583	missense	0			-	HGNC	M32082	CCDS13627.1, CCDS13628.1	21q22.11	2012-10-02			ENSG00000159131	ENSG00000159131	2.1.2.2, 6.3.3.1, 6.3.4.13		4163	protein-coding gene	gene with protein product		138440		PRGS, PGFT		2050105	Standard	NM_001136005		Approved		uc002yrx.3	P22102	OTTHUMG00000065628	ENST00000381831.3:c.2209G>A	21.37:g.34883664C>T	ENSP00000371253:p.Ala737Thr	Somatic	0	107	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	81	66	54.73	A8K945|A8KA32|D3DSF3|D3DSF4|O14659|Q52M77	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_PRibGlycinamid_synth_ATP-grasp,pfam_Formyl_transf_N,pfam_PRibGlycinamide_synth_N,pfam_AIR_synth_C_dom,pfam_PRibGlycinamide_synth_C-dom,pfam_AIR_synth_N_dom,pfam_ATP-grasp_carboxylate-amine,pfam_CbamoylP_synth_lsu-like_ATP-bd,superfamily_Formyl_transf_N,superfamily_AIR_synth_C_dom,superfamily_PurM_N-like,superfamily_PreATP-grasp_dom,superfamily_Rudment_hybrid_motif,pfscan_ATP-grasp,tigrfam_PRibGlycinamide_synth,tigrfam_PurM_cligase,tigrfam_PurN_trans	p.A737T	ENST00000381831.3	37	c.2209	CCDS13627.1	21	.	.	.	.	.	.	.	.	.	.	C	29.7	5.026689	0.93518	0.0	1.16E-4	ENSG00000159131	ENST00000414353;ENST00000381815;ENST00000381831;ENST00000381839;ENST00000543717	T;T;T;T	0.17691	2.26;2.26;2.26;2.26	5.44	5.44	0.79542	AIR synthase-related protein, C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.50377	0.1612	M	0.90252	3.1	0.80722	D	1	D	0.89917	1.0	D	0.68039	0.955	T	0.57341	-0.7828	10	0.48119	T	0.1	-20.3578	19.2675	0.93996	0.0:1.0:0.0:0.0	.	737	P22102	PUR2_HUMAN	T	1;737;737;737;289	ENSP00000371236:A737T;ENSP00000371253:A737T;ENSP00000371261:A737T;ENSP00000443579:A289T	ENSP00000371236:A737T	A	-	1	0	GART	33805534	1.000000	0.71417	0.995000	0.50966	0.677000	0.39632	7.270000	0.78493	2.573000	0.86826	0.655000	0.94253	GCT	-	pfam_AIR_synth_C_dom,superfamily_AIR_synth_C_dom,tigrfam_PurM_cligase		0.547	GART-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GART	protein_coding	OTTHUMT00000140626.3	C	NM_000819	-		34883664	-1	no_errors	ENST00000381815	ensembl	human	known	74_37	missense	SNP	1.000	T
C4orf3	401152	genome.wustl.edu	37	4	120221759	120221759	+	5'UTR	SNP	C	C	G			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr4:120221759C>G	ENST00000504110.1	-	0	317				C4orf3_ENST00000399075.4_Missense_Mutation_p.A111P	NM_001001701.3	NP_001001701.2	Q8WVX3	CD003_HUMAN	chromosome 4 open reading frame 3							integral component of membrane (GO:0016021)				breast(1)|large_intestine(1)|lung(4)	6						TTGGTGTTCGCCGCACCGGAA	0.627																																																	0								ENSG00000164096						67.0	68.0	68.0					4																	120221759		692	1591	2283	C4orf3	SO:0001623	5_prime_UTR_variant	0			-	HGNC		CCDS43266.1, CCDS54798.1	4q26	2012-02-24			ENSG00000164096	ENSG00000164096			19225	protein-coding gene	gene with protein product	"""HCV F-transactivated protein 1"""						Standard	NM_001001701		Approved		uc021xrf.1	Q8WVX3	OTTHUMG00000161333	ENST00000504110.1:c.-69G>C	4.37:g.120221759C>G		Somatic	0	39	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	30	43	41.10	Q6J203	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	NULL	p.A111P	ENST00000504110.1	37	c.331	CCDS43266.1	4	.	.	.	.	.	.	.	.	.	.	C	12.94	2.088691	0.36855	.	.	ENSG00000164096	ENST00000399075	T	0.38240	1.15	4.14	2.38	0.29361	.	.	.	.	.	T	0.29190	0.0726	.	.	.	0.09310	N	1.0	.	.	.	.	.	.	T	0.33803	-0.9854	5	0.24483	T	0.36	.	6.7666	0.23571	0.0:0.5566:0.3437:0.0997	.	.	.	.	P	111	ENSP00000382026:A111P	ENSP00000382026:A111P	A	-	1	0	C4orf3	120441207	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.467000	0.22035	0.466000	0.27193	-0.122000	0.15005	GCG	-	NULL		0.627	C4orf3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C4orf3	protein_coding	OTTHUMT00000364576.3	C	NM_001001701	-		120221759	-1	no_errors	ENST00000399075	ensembl	human	known	74_37	missense	SNP	0.000	G
TP53	7157	genome.wustl.edu	37	17	7578406	7578406	+	Missense_Mutation	SNP	C	C	A	rs28934578		TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr17:7578406C>A	ENST00000269305.4	-	5	713	c.524G>T	c.(523-525)cGc>cTc	p.R175L	TP53_ENST00000359597.4_Missense_Mutation_p.R175L|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000413465.2_Missense_Mutation_p.R175L|TP53_ENST00000420246.2_Missense_Mutation_p.R175L|TP53_ENST00000455263.2_Missense_Mutation_p.R175L|TP53_ENST00000445888.2_Missense_Mutation_p.R175L	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>T	17.37:g.7578406C>A	ENSP00000269305:p.Arg175Leu	Somatic	0	43	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	42	6	87.50	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.R175L	ENST00000269305.4	37	c.524	CCDS11118.1	17	.	.	.	.	.	.	.	.	.	.	C	35	5.433431	0.96150	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99888	-7.54;-7.54;-7.54;-7.54;-7.54;-7.54;-7.54;-7.54	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	D	1	D;D;D;D;D;P;D	0.89917	1.0;0.985;1.0;1.0;0.988;0.894;1.0	D;D;D;D;D;P;D	0.97110	1.0;0.921;0.999;0.999;0.923;0.847;0.999	D	0.96278	0.9204	10	0.87932	D	0	-11.8679	17.0767	0.86588	0.0:1.0:0.0:0.0	.	136;175;175;82;175;175;175	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	L	175;175;175;175;175;175;164;82;43;82;43	ENSP00000410739:R175L;ENSP00000352610:R175L;ENSP00000269305:R175L;ENSP00000398846:R175L;ENSP00000391127:R175L;ENSP00000391478:R175L;ENSP00000425104:R43L;ENSP00000423862:R82L	ENSP00000269305:R175L	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	-		7578406	-1	no_errors	ENST00000269305	ensembl	human	known	74_37	missense	SNP	1.000	A
PIEZO2	63895	genome.wustl.edu	37	18	10773615	10773615	+	Silent	SNP	C	C	T			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr18:10773615C>T	ENST00000503781.3	-	18	2504	c.2505G>A	c.(2503-2505)ccG>ccA	p.P835P	PIEZO2_ENST00000580640.1_Silent_p.P860P|PIEZO2_ENST00000302079.6_Silent_p.P835P|PIEZO2_ENST00000383408.2_Silent_p.P123P	NM_022068.2	NP_071351.2	Q9H5I5	PIEZ2_HUMAN	piezo-type mechanosensitive ion channel component 2	835					cation transport (GO:0006812)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|regulation of membrane potential (GO:0042391)|response to mechanical stimulus (GO:0009612)	integral component of membrane (GO:0016021)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)										GGCTTCCTTCCGGGTGGGCCA	0.562																																																	0								ENSG00000154864						36.0	32.0	33.0					18																	10773615		692	1591	2283	PIEZO2	SO:0001819	synonymous_variant	0			-	HGNC	AK027056		18p11.21	2012-11-19	2011-08-31	2011-08-31	ENSG00000154864	ENSG00000154864			26270	protein-coding gene	gene with protein product		613629	"""chromosome 18 open reading frame 30"", ""chromosome 18 open reading frame 58"", ""family with sequence similarity 38, member B"""	FAM38B2, C18orf30, C18orf58, FAM38B		20813920, 21056836, 21299953	Standard	NM_022068		Approved	FLJ23403, FLJ23144, HsT748, HsT771, FLJ34907	uc002kos.2	Q9H5I5	OTTHUMG00000178507	ENST00000503781.3:c.2505G>A	18.37:g.10773615C>T		Somatic	0	36	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	15	17	46.88	B7Z812|M4GPJ9|Q6ZS91|Q8N787|Q8NAR6|Q9H5R4	Silent	SNP	NA	NA	NA	NA	NA	NA	NULL	p.P849	ENST00000503781.3	37	c.2547		18																																																																																			-	NULL		0.562	PIEZO2-003	NOVEL	basic|appris_principal	protein_coding	PIEZO2	protein_coding	OTTHUMT00000442385.4	C	NM_022068	-		10773615	-1	no_errors	ENST00000582913	ensembl	human	known	74_37	silent	SNP	0.681	T
NRXN1	9378	genome.wustl.edu	37	2	50147836	50147843	+	3'UTR	DEL	GTGTGTGT	GTGTGTGT	-	rs200264093|rs201814381|rs199597709|rs368179294|rs200969250|rs66612444		TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	GTGTGTGT	GTGTGTGT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr2:50147836_50147843delGTGTGTGT	ENST00000406316.2	-	0	7149_7156				NRXN1_ENST00000342183.5_3'UTR|NRXN1_ENST00000401710.1_3'UTR|NRXN1_ENST00000404971.1_3'UTR	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1						adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			CTGTGGATTCgtgtgtgtgtgtgtgtgt	0.394																																																	0								ENSG00000179915																																			NRXN1	SO:0001624	3_prime_UTR_variant	0				HGNC	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.*1246ACACACAC>-	2.37:g.50147844_50147851delGTGTGTGT		Somatic	NA	NA	NA		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000406316.2	37	NULL	CCDS54360.1	2																																																																																			-	-		0.394	NRXN1-001	KNOWN	basic|CCDS	protein_coding	NRXN1	protein_coding	OTTHUMT00000325291.2	GTGTGTGT				50147843	-1	no_errors	ENST00000484192	ensembl	human	known	74_37	rna	DEL	0.000:0.001:0.005:0.106:0.113:0.127:0.107:0.109	-
PDE9A	5152	genome.wustl.edu	37	21	44195538	44195538	+	3'UTR	DEL	A	A	-			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr21:44195538delA	ENST00000291539.6	+	0	1977				PDE9A_ENST00000398225.3_3'UTR|PDE9A_ENST00000398234.3_3'UTR|PDE9A_ENST00000398227.3_3'UTR|PDE9A_ENST00000328862.6_3'UTR|PDE9A_ENST00000398236.3_3'UTR|PDE9A_ENST00000398224.3_3'UTR|PDE9A_ENST00000335440.6_3'UTR|PDE9A_ENST00000398229.3_3'UTR|PDE9A_ENST00000335512.4_3'UTR|PDE9A_ENST00000380328.2_3'UTR|PDE9A_ENST00000349112.3_3'UTR|PDE9A_ENST00000398232.3_3'UTR|PDE9A_ENST00000470987.1_3'UTR|PDE9A_ENST00000539837.1_3'UTR	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A						blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|metabolic process (GO:0008152)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|large_intestine(6)|lung(8)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Caffeine(DB00201)	TCACTGATACAAAAAAAAAAA	0.398																																																	0								ENSG00000160191																																			PDE9A	SO:0001624	3_prime_UTR_variant	0				HGNC	AF048837	CCDS13690.1, CCDS33567.1, CCDS33568.1, CCDS33569.1, CCDS33570.1, CCDS33571.1, CCDS42941.1, CCDS42942.1, CCDS42943.1, CCDS42944.1, CCDS42945.1, CCDS42946.1, CCDS42947.1	21q22.3	2005-11-29			ENSG00000160191	ENSG00000160191	3.1.4.17	"""Phosphodiesterases"""	8795	protein-coding gene	gene with protein product		602973				9624146	Standard	NM_001001584		Approved		uc002zbm.3	O76083	OTTHUMG00000086825	ENST00000291539.6:c.*135A>-	21.37:g.44195538delA		Somatic	0	20	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	25	16.67	B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000291539.6	37	NULL	CCDS13690.1	21																																																																																			-	-		0.398	PDE9A-016	KNOWN	basic|CCDS	protein_coding	PDE9A	protein_coding	OTTHUMT00000195466.1	A				44195538	+1	no_errors	ENST00000460989	ensembl	human	known	74_37	rna	DEL	0.000	-
PTPRS	5802	genome.wustl.edu	37	19	5212070	5212070	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr19:5212070delG	ENST00000587303.1	-	31	5060	c.4961delC	c.(4960-4962)acafs	p.T1654fs	PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000262963.6_Frame_Shift_Del_p.T1634fs|PTPRS_ENST00000348075.2_Frame_Shift_Del_p.T1616fs|PTPRS_ENST00000372412.4_Frame_Shift_Del_p.T1655fs|PTPRS_ENST00000592099.1_Frame_Shift_Del_p.T1207fs|PTPRS_ENST00000588012.1_Frame_Shift_Del_p.T1616fs|PTPRS_ENST00000353284.2_Frame_Shift_Del_p.T1207fs|PTPRS_ENST00000357368.4_Frame_Shift_Del_p.T1654fs			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	1654					cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	GGGCACTTCTGTGTTGCCACA	0.612																																																	0								ENSG00000105426						71.0	65.0	67.0					19																	5212070		2203	4300	6503	PTPRS	SO:0001589	frameshift_variant	0				HGNC	U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.4961delC	19.37:g.5212070delG	ENSP00000467537:p.Thr1654fs	Somatic	0	53	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	39	61	39.00	O75255|O75870|Q15718|Q16341|Q2M3R7	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_Tyr_Pase_rcpt/non-rcpt,pfam_Fibronectin_type3,pfam_Ig_I-set,superfamily_Fibronectin_type3,smart_Ig_sub,smart_Ig_sub2,smart_Fibronectin_type3,smart_Tyr_Pase_rcpt/non-rcpt,smart_Tyr_Pase_cat,prints_Tyr_Pase_rcpt/non-rcpt,pfscan_Fibronectin_type3,pfscan_Tyr/Dual-sp_Pase,pfscan_Tyr_Pase_rcpt/non-rcpt,pfscan_Ig-like_dom	p.T1655fs	ENST00000587303.1	37	c.4964	CCDS45930.1	19																																																																																			-	NULL		0.612	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	PTPRS	protein_coding	OTTHUMT00000450762.2	G				5212070	-1	no_errors	ENST00000372412	ensembl	human	known	74_37	frame_shift_del	DEL	1.000	-
VPS45	11311	genome.wustl.edu	37	1	150082514	150082514	+	Intron	DEL	A	A	-			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr1:150082514delA	ENST00000369130.3	+	14	2039				VPS45_ENST00000484306.1_3'UTR|VPS45_ENST00000535106.1_Intron|VPS45_ENST00000369128.5_Intron	NM_001279354.1|NM_007259.3	NP_001266283.1|NP_009190.2	Q9NRW7	VPS45_HUMAN	vacuolar protein sorting 45 homolog (S. cerevisiae)						blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|vesicle docking involved in exocytosis (GO:0006904)	endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	21	Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			TTCCTCCACCAAAAAAAAAAG	0.303																																																	0								ENSG00000136631																																			VPS45	SO:0001627	intron_variant	0				HGNC	U35246	CCDS944.1, CCDS60244.1, CCDS72904.1	1q21.2	2008-02-05	2006-12-19	2006-12-19	ENSG00000136631	ENSG00000136631			14579	protein-coding gene	gene with protein product		610035	"""vacuolar protein sorting 45A (yeast homolog)"", ""vacuolar protein sorting 45A (yeast)"""	VPS45B, VPS45A		8996080	Standard	NM_007259		Approved	h-vps45, H1	uc001etp.3	Q9NRW7	OTTHUMG00000012511	ENST00000369130.3:c.1494-97A>-	1.37:g.150082514delA		Somatic	0	42	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	49	9.26	D3DUZ9|F5H8K1|Q15715|Q53FR8|Q5T4P6|Q9Y4Z6	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000369130.3	37	NULL	CCDS944.1	1																																																																																			-	-		0.303	VPS45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	VPS45	protein_coding	OTTHUMT00000034964.1	A	NM_007259			150082514	+1	no_errors	ENST00000484306	ensembl	human	known	74_37	rna	DEL	0.965	-
CNTNAP3	79937	genome.wustl.edu	37	9	39178156	39178156	+	Nonsense_Mutation	SNP	G	G	C			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr9:39178156G>C	ENST00000297668.6	-	5	813	c.740C>G	c.(739-741)tCa>tGa	p.S247*	CNTNAP3_ENST00000358144.2_Nonsense_Mutation_p.S159*|CNTNAP3_ENST00000323947.7_Nonsense_Mutation_p.S247*|CNTNAP3_ENST00000377653.2_5'UTR|CNTNAP3_ENST00000377656.2_Nonsense_Mutation_p.S247*|CNTNAP3_ENST00000377659.1_Nonsense_Mutation_p.S247*	NM_033655.3	NP_387504.2	Q9BZ76	CNTP3_HUMAN	contactin associated protein-like 3	247	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell recognition (GO:0008037)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	24				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		TTTTTTACCTGAATTAAGAAA	0.308																																																	0								ENSG00000106714						32.0	36.0	35.0					9																	39178156		2135	4238	6373	CNTNAP3	SO:0001587	stop_gained	0			-	HGNC	AF333769	CCDS6616.1	9q12	2008-02-05			ENSG00000106714	ENSG00000106714			13834	protein-coding gene	gene with protein product	"""cell recognition molecule CASPR3 (FLJ14195, KIAA1714)"""	610517				12093160	Standard	NM_033655		Approved	CASPR3, KIAA1714, FLJ14195, CNTNAP3A	uc004abi.3	Q9BZ76	OTTHUMG00000019954	ENST00000297668.6:c.740C>G	9.37:g.39178156G>C	ENSP00000297668:p.Ser247*	Somatic	0	151	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	117	134	46.61	B1AMA0|Q9C0E9	Nonsense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Laminin_G,pfam_Coagulation_fac_5/8-C_type_dom,superfamily_Galactose-bd-like,superfamily_ConA-like_lec_gl_sf,superfamily_Fibrinogen_a/b/g_C_dom,smart_Coagulation_fac_5/8-C_type_dom,smart_Laminin_G,smart_EG-like_dom,pfscan_EG-like_dom,pfscan_Coagulation_fac_5/8-C_type_dom,pfscan_Laminin_G	p.S247*	ENST00000297668.6	37	c.740	CCDS6616.1	9	.	.	.	.	.	.	.	.	.	.	G	39	7.871032	0.98537	.	.	ENSG00000106714	ENST00000297668;ENST00000377656;ENST00000358144;ENST00000323947;ENST00000377659;ENST00000377653	.	.	.	3.16	3.16	0.36331	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.1502	0.15005	0.2495:0.0:0.7505:0.0	.	.	.	.	X	247;247;159;247;247;159	.	ENSP00000297668:S247X	S	-	2	0	CNTNAP3	39168156	0.915000	0.31059	0.951000	0.38953	0.976000	0.68499	1.599000	0.36751	1.740000	0.51718	0.563000	0.77884	TCA	-	pfam_Laminin_G,superfamily_ConA-like_lec_gl_sf,smart_Laminin_G,pfscan_Laminin_G		0.308	CNTNAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CNTNAP3	protein_coding	OTTHUMT00000052511.1	G	NM_033655	-		39178156	-1	no_errors	ENST00000297668	ensembl	human	known	74_37	nonsense	SNP	0.967	C
ICA1	3382	genome.wustl.edu	37	7	8196567	8196585	+	Intron	DEL	AAAAAAAAAAAAAAAAAAG	AAAAAAAAAAAAAAAAAAG	-	rs544087808|rs147272214|rs73674890|rs73674888|rs73674889|rs556173262|rs398003586|rs139248933|rs77253977|rs201360539|rs200840693|rs80159917|rs71014766|rs138383936	byFrequency	TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	AAAAAAAAAAAAAAAAAAG	AAAAAAAAAAAAAAAAAAG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr7:8196567_8196585delAAAAAAAAAAAAAAAAAAG	ENST00000402384.3	-	8	1071				ICA1_ENST00000396675.3_Intron|AC007009.2_ENST00000577980.1_RNA|ICA1_ENST00000422063.2_Intron|ICA1_ENST00000406470.2_Intron|ICA1_ENST00000401396.1_Intron|ICA1_ENST00000407906.1_Frame_Shift_Del_p.SFFFFFF322fs|ICA1_ENST00000265577.7_Intron			Q05084	ICA69_HUMAN	islet cell autoantigen 1, 69kDa						neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|secretory granule membrane (GO:0030667)|synaptic vesicle membrane (GO:0030672)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|urinary_tract(1)	23		Ovarian(82;0.0612)		UCEC - Uterine corpus endometrioid carcinoma (126;0.246)		AGTaaaaaaaaaaaaaaaaaaaaaaaaagaaagaaagaa	0.37																																																	0								ENSG00000003147																																			ICA1	SO:0001627	intron_variant	0				HGNC		CCDS34602.1, CCDS64595.1	7p22	2006-12-13	2002-08-29		ENSG00000003147	ENSG00000003147			5343	protein-coding gene	gene with protein product		147625	"""islet cell autoantigen 1 (69kD)"""			7918678, 8777998	Standard	NM_001276478		Approved	ICAp69	uc003srm.3	Q05084	OTTHUMG00000152008	ENST00000402384.3:c.804+160CTTTTTTTTTTTTTTTTTT>-	7.37:g.8196567_8196585delAAAAAAAAAAAAAAAAAAG		Somatic	NA	NA	NA		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	A8K7U1|B3FTQ2|P78506|Q13824|Q96HG3	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_AH_dom,pfscan_AH_dom	p.S322fs	ENST00000402384.3	37	c.983_965	CCDS34602.1	7																																																																																			-	NULL		0.370	ICA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ICA1	protein_coding	OTTHUMT00000324793.1	AAAAAAAAAAAAAAAAAAG	NM_004968			8196585	-1	no_errors	ENST00000407906	ensembl	human	putative	74_37	frame_shift_del	DEL	0.008:0.013:0.018:0.022:0.026:0.029:0.033:0.021:0.016:0.011:0.005:0.002:0.000:0.000:0.000:0.001:0.001:0.001:0.001	-
MSH3	4437	genome.wustl.edu	37	5	79950700	79950717	+	In_Frame_Del	DEL	GCAGCGGCTGCAGCGGCC	GCAGCGGCTGCAGCGGCC	-	rs530525176|rs2431220|rs2405875|rs144776112|rs201874762|rs201906899	byFrequency	TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	GCAGCGGCTGCAGCGGCC	GCAGCGGCTGCAGCGGCC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr5:79950700_79950717delGCAGCGGCTGCAGCGGCC	ENST00000265081.6	+	1	234_251	c.154_171delGCAGCGGCTGCAGCGGCC	c.(154-171)gcagcggctgcagcggccdel	p.AAAAAA52del	DHFR_ENST00000505337.1_5'Flank|DHFR_ENST00000511032.1_5'Flank|DHFR_ENST00000439211.2_5'UTR|DHFR_ENST00000513048.1_5'Flank|DHFR_ENST00000504396.1_5'Flank	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	52	Poly-Ala.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		CCCTGGCGCTgcagcggctgcagcggccgcagcggccg	0.693								Mismatch excision repair (MMR)																													Melanoma(88;1010 1399 13793 26548 36275)												0								ENSG00000113318		,	1153,2933		197,759,1087					,		0.2		dbSNP_100	12	2199,5723		382,1435,2144	no	coding,utr-5	DHFR,MSH3	NM_002439.3,NM_000791.3	,	579,2194,3231	A1A1,A1R,RR		27.7581,28.2183,27.9147	,	,		3352,8656				MSH3	SO:0001651	inframe_deletion	0				HGNC	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.154_171delGCAGCGGCTGCAGCGGCC	5.37:g.79950700_79950717delGCAGCGGCTGCAGCGGCC	ENSP00000265081:p.Ala52_Ala57del	Somatic	NA	NA	NA		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	In_Frame_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_DNA_mismatch_repair_MutS_C,pfam_DNA_mismatch_repair_MutS_core,pfam_DNA_mmatch_repair_MutS_con_dom,pfam_DNA_mismatch_repair_MutS-lik_N,pfam_DNA_mismatch_repair_MutS_clamp,superfamily_DNA_mismatch_repair_MutS_core,superfamily_P-loop_NTPase,superfamily_DNA_mismatch_repair_MutS_N,superfamily_DNA_mmatch_repair_MutS_con_dom,smart_DNA_mismatch_repair_MutS_core,smart_DNA_mismatch_repair_MutS_C	p.AAAAAA55in_frame_del	ENST00000265081.6	37	c.154_171	CCDS34195.1	5																																																																																			-	NULL		0.693	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	MSH3	protein_coding	OTTHUMT00000369471.1	GCAGCGGCTGCAGCGGCC	NM_002439			79950717	+1	no_errors	ENST00000265081	ensembl	human	known	74_37	in_frame_del	DEL	0.640:0.607:0.574:0.541:0.508:0.474:0.440:0.406:0.372:0.338:0.304:0.271:0.238:0.205:0.172:0.140:0.107:0.075	-
VPS13B	157680	genome.wustl.edu	37	8	100880651	100880651	+	Missense_Mutation	SNP	C	C	G			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr8:100880651C>G	ENST00000358544.2	+	59	11536	c.11425C>G	c.(11425-11427)Ccc>Gcc	p.P3809A	VPS13B_ENST00000395996.1_3'UTR|VPS13B_ENST00000357162.2_Missense_Mutation_p.P3784A	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	3809					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			GTTCACAAAGCCCATCGGAGG	0.527																																					Colon(161;2205 2542 7338 31318)												0								ENSG00000132549						82.0	72.0	76.0					8																	100880651		2203	4300	6503	VPS13B	SO:0001583	missense	0			-	HGNC	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"""Cohen syndrome 1"""	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.11425C>G	8.37:g.100880651C>G	ENSP00000351346:p.Pro3809Ala	Somatic	0	76	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	56	76	42.42	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Autophagy-rel_C	p.P3809A	ENST00000358544.2	37	c.11425	CCDS6280.1	8	.	.	.	.	.	.	.	.	.	.	C	28.6	4.937155	0.92458	.	.	ENSG00000132549	ENST00000357162;ENST00000358544	D;D	0.91124	-2.77;-2.79	5.83	5.83	0.93111	Autophagy-related, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.95915	0.8670	M	0.84219	2.685	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.95655	0.8710	10	0.66056	D	0.02	.	20.1162	0.97934	0.0:1.0:0.0:0.0	.	3784;3809	Q7Z7G8-2;Q7Z7G8	.;VP13B_HUMAN	A	3784;3809	ENSP00000349685:P3784A;ENSP00000351346:P3809A	ENSP00000349685:P3784A	P	+	1	0	VPS13B	100949827	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.487000	0.81328	2.756000	0.94617	0.655000	0.94253	CCC	-	pfam_Autophagy-rel_C		0.527	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	VPS13B	protein_coding	OTTHUMT00000277138.1	C	NM_184042	-		100880651	+1	no_errors	ENST00000358544	ensembl	human	known	74_37	missense	SNP	1.000	G
MED15P1	326615	genome.wustl.edu	37	14	19499970	19499970	+	RNA	SNP	G	G	T			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr14:19499970G>T	ENST00000552968.1	-	0	599									mediator complex subunit 15 pseudogene 1																		GCAGCGAGAAGAGTCCAGGTT	0.632																																																	0								ENSG00000257853																																			MED15P1			0			-	HGNC			14q11.2	2013-06-03	2010-02-25	2010-02-25	ENSG00000257853	ENSG00000257853			19271	pseudogene	pseudogene			"""PCQAP pseudogene"", ""mediator complex subunit 15 pseudogene"""	PCQAPP, MED15P			Standard	NG_002605		Approved				OTTHUMG00000170337		14.37:g.19499970G>T		Somatic	0	27	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	6	34	15.00		RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000552968.1	37	NULL		14																																																																																			-	-		0.632	MED15P1-002	KNOWN	basic	processed_transcript	MED15P1	pseudogene	OTTHUMT00000408573.1	G	NG_002605	-		19499970	-1	no_errors	ENST00000552968	ensembl	human	known	74_37	rna	SNP	1.000	T
MTHFD1L	25902	genome.wustl.edu	37	6	151206811	151206811	+	Missense_Mutation	SNP	C	C	G			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr6:151206811C>G	ENST00000367321.3	+	6	858	c.584C>G	c.(583-585)gCc>gGc	p.A195G	MTHFD1L_ENST00000367307.4_Missense_Mutation_p.A195G	NM_001242767.1|NM_001242768.1|NM_015440.4	NP_001229696.1|NP_001229697.1|NP_056255.2	Q6UB35	C1TM_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like	195	Methylenetetrahydrofolate dehydrogenase and cyclohydrolase.				folic acid-containing compound biosynthetic process (GO:0009396)|folic acid-containing compound metabolic process (GO:0006760)|formate metabolic process (GO:0015942)|one-carbon metabolic process (GO:0006730)|oxidation-reduction process (GO:0055114)|tetrahydrofolate interconversion (GO:0035999)|tetrahydrofolate metabolic process (GO:0046653)	membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	29		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)		CGAGGGGATGCCCATGAATGT	0.408																																																	0								ENSG00000120254						146.0	149.0	148.0					6																	151206811		2203	4300	6503	MTHFD1L	SO:0001583	missense	0			-	HGNC	BC017477	CCDS5228.1, CCDS56457.1, CCDS75535.1, CCDS75536.1	6q25.1	2010-07-19	2004-12-13	2004-12-14	ENSG00000120254	ENSG00000120254	6.3.4.3		21055	protein-coding gene	gene with protein product	"""10-formyl-THF synthetase"", ""mitochondrial C1-tetrahydrofolate synthase"", ""monofunctional C1-tetrahydrofolate synthase, mitochondrial"""	611427	"""formyltetrahydrofolate synthetase domain containing 1"""	FTHFSDC1		18804703	Standard	NM_015440		Approved	DKFZP586G1517, FLJ21145	uc021zgs.1	Q6UB35	OTTHUMG00000015828	ENST00000367321.3:c.584C>G	6.37:g.151206811C>G	ENSP00000356290:p.Ala195Gly	Somatic	0	81	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	64	72	46.72	Q2TBF3|Q8WVW0|Q96HG8|Q9H789|Q9UFU8	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Formate_THF_ligase,pfam_THF_DH/CycHdrlase_NAD-bd_dom,pfam_THF_DH/CycHdrlase_cat_dom,superfamily_P-loop_NTPase,prints_THF_DH/CycHdrlase	p.A195G	ENST00000367321.3	37	c.584	CCDS5228.1	6	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.15|13.15	2.151938|2.151938	0.38021|0.38021	.|.	.|.	ENSG00000120254|ENSG00000120254	ENST00000367321;ENST00000367307;ENST00000423867;ENST00000443074;ENST00000425276|ENST00000367308	T;T;T;T;T|.	0.58060|.	0.36;0.36;0.36;0.36;0.36|.	4.75|4.75	4.75|4.75	0.60458|0.60458	Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain (1);|.	0.678882|.	0.14953|.	N|.	0.288785|.	T|T	0.19287|0.19287	0.0463|0.0463	N|N	0.17474|0.17474	0.49|0.49	0.32917|0.32917	D|D	0.51528|0.51528	B;B;P|.	0.52692|.	0.425;0.425;0.955|.	B;B;P|.	0.47470|.	0.182;0.182;0.548|.	T|T	0.07233|0.07233	-1.0783|-1.0783	10|5	0.11182|.	T|.	0.66|.	.|.	8.7966|8.7966	0.34883|0.34883	0.0:0.901:0.0:0.099|0.0:0.901:0.0:0.099	.|.	195;195;195|.	B7ZM99;Q6UB35;Q6UB35-2|.	.;C1TM_HUMAN;.|.	G|A	195;195;85;40;39|155	ENSP00000356290:A195G;ENSP00000356276:A195G;ENSP00000400776:A85G;ENSP00000415039:A40G;ENSP00000414412:A39G|.	ENSP00000356276:A195G|.	A|P	+|+	2|1	0|0	MTHFD1L|MTHFD1L	151248504|151248504	0.761000|0.761000	0.28439|0.28439	1.000000|1.000000	0.80357|0.80357	0.818000|0.818000	0.46254|0.46254	0.739000|0.739000	0.26173|0.26173	2.468000|2.468000	0.83385|0.83385	0.555000|0.555000	0.69702|0.69702	GCC|CCC	-	pfam_THF_DH/CycHdrlase_NAD-bd_dom		0.408	MTHFD1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	MTHFD1L	protein_coding	OTTHUMT00000042699.1	C	NM_015440	-		151206811	+1	no_errors	ENST00000367321	ensembl	human	known	74_37	missense	SNP	1.000	G
ANKRD28	23243	genome.wustl.edu	37	3	15838150	15838151	+	Intron	INS	-	-	T	rs397988804|rs144777884|rs34139082|rs192856159|rs201201313	byFrequency	TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr3:15838150_15838151insT	ENST00000399451.2	-	2	395				ANKRD28_ENST00000383777.1_5'Flank|ANKRD28_ENST00000497037.1_Intron	NM_001195098.1|NM_001195099.1|NM_015199.3	NP_001182027.1|NP_001182028.1|NP_056014.2	O15084	ANR28_HUMAN	ankyrin repeat domain 28							nucleus (GO:0005634)				breast(2)|endometrium(1)|large_intestine(2)|prostate(1)	6						GCACAGCTGGGTTTTTTTTTTT	0.297																																																	0								ENSG00000206560																																			ANKRD28	SO:0001627	intron_variant	0				HGNC	AY367056	CCDS46769.1, CCDS74908.1	3p25.1	2013-01-10			ENSG00000206560	ENSG00000206560		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"", ""Ankyrin repeat domain containing"""	29024	protein-coding gene	gene with protein product	"""phosphatase interactor targeting K protein"", ""protein phosphatase 6 ankyrin repeat subunit A"", ""protein phosphatase 1, regulatory subunit 65"""	611122				9205841	Standard	NM_015199		Approved	KIAA0379, PITK, PP6-ARS-A, PPP1R65	uc003caj.1	O15084	OTTHUMG00000155379	ENST00000399451.2:c.28-1337->A	3.37:g.15838161_15838161dupT		Somatic	0	8	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	6	26	18.75	B4DES5|Q1WWL4|Q29RW6|Q3B857|Q6ULS0|Q6ZT57	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000399451.2	37	NULL	CCDS46769.1	3																																																																																			-	-		0.297	ANKRD28-003	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	ANKRD28	protein_coding	OTTHUMT00000339758.1	-	NM_015199			15838151	-1	no_errors	ENST00000461696	ensembl	human	known	74_37	rna	INS	0.016:0.428	T
UBXN11	91544	genome.wustl.edu	37	1	26608812	26608889	+	In_Frame_Del	DEL	CCAGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA	CCAGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA	-	rs66614970|rs201454352|rs61775089|rs61775088|rs140364749|rs61775085|rs61775084|rs61775087|rs61775086|rs6667693|rs6672357|rs376181141|rs568953708|rs200313935|rs554923047|rs202134609|rs537852372|rs1134582|rs188535926|rs201756933|rs199707978|rs373828796|rs12354016|rs202239787|rs151149897|rs193142354|rs1134583|rs1134580|rs1134581|rs1134584	byFrequency	TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	CCAGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA	CCAGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr1:26608812_26608889delCCAGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA	ENST00000374222.1	-	16	1928_2005	c.1464_1541delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGG	c.(1462-1542)ggtcccggtcccggccccagtcccggtcccggtcccggccccagtcccggtcccggtcccggccccagtccctgtcctgga>gga	p.488_514GPGPGPSPGPGPGPSPGPGPGPSPCPG>G	UBXN11_ENST00000374217.2_In_Frame_Del_p.455_481GPGPGPSPGPGPGPSPGPGPGPSPCPG>G|UBXN11_ENST00000374221.3_In_Frame_Del_p.488_514GPGPGPSPGPGPGPSPGPGPGPSPCPG>G|UBXN11_ENST00000374223.1_In_Frame_Del_p.245_271GPGPGPSPGPGPGPSPGPGPGPSPCPG>G|UBXN11_ENST00000314675.7_In_Frame_Del_p.368_394GPGPGPSPGPGPGPSPGPGPGPSPCPG>G|UBXN11_ENST00000357089.4_In_Frame_Del_p.455_481GPGPGPSPGPGPGPSPGPGPGPSPCPG>G			Q5T124	UBX11_HUMAN	UBX domain protein 11	488	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.|Missing. {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.|P -> S (in dbSNP:rs17838088).|P -> S (in dbSNP:rs17838088). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.P503_G504insCP(1)|p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						gggactgggtccaggacagggactggggccgggaccgggaccgggactggggccgggaccgggaccgggactggggccgggaccgggaccgggacagg	0.712																																																	2	Insertion - In frame(1)|Deletion - In frame(1)	upper_aerodigestive_tract(1)|ovary(1)						ENSG00000158062																																			UBXN11	SO:0001651	inframe_deletion	0				HGNC	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1464_1541delTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCGGTCCCGGTCCCGGCCCCAGTCCCTGTCCTGG	1.37:g.26608812_26608889delCCAGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA	ENSP00000363339:p.Gly488_Pro513del	Somatic	NA	NA	NA		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	In_Frame_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_SEP_domain,superfamily_SEP_domain,pfscan_UBX	p.GPGPSPGPGPGPSPGPGPGPSPCPGP490in_frame_del	ENST00000374222.1	37	c.1541_1464	CCDS41288.1	1																																																																																			-	NULL		0.712	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	UBXN11	protein_coding	OTTHUMT00000009500.1	CCAGGACAGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGACCGGGACTGGGGCCGGGACCGGGA	NM_145345			26608889	-1	no_errors	ENST00000374221	ensembl	human	known	74_37	in_frame_del	DEL	0.001:0.001:0.001:0.001:0.001:0.001:0.002:0.002:0.128:0.145:0.146:0.148:0.148:0.149:0.149:0.149:0.149:0.149:0.148:0.141:0.128:0.126:0.131:0.132:0.128:0.134:0.156:0.169:0.174:0.173:0.168:0.156:0.134:0.097:0.084:0.080:0.075:0.071:0.065:0.060:0.054:0.049:0.042:0.024:0.015:0.010:0.006:0.004:0.004:0.008:0.005:0.003:0.002:0.004:0.007:0.010:0.014:0.019:0.018:0.000:0.000:0.000:0.001:0.002:0.005:0.007:0.007:0.000:0.001:0.000:0.000:0.000:0.000:0.000:0.025:0.015:0.007:0.001	-
DOCK2	1794	genome.wustl.edu	37	5	169188536	169188536	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr5:169188536delG	ENST00000256935.8	+	25	2541	c.2461delG	c.(2461-2463)gagfs	p.E821fs	DOCK2_ENST00000540750.1_5'UTR|DOCK2_ENST00000520908.1_Frame_Shift_Del_p.E313fs|DOCK2_ENST00000523351.1_3'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	821					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ACTCCTGTATGAGTTCTACAC	0.483																																																	0								ENSG00000134516						199.0	182.0	188.0					5																	169188536		2203	4300	6503	DOCK2	SO:0001589	frameshift_variant	0				HGNC	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"""dedicator of cyto-kinesis 2"""				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.2461delG	5.37:g.169188536delG	ENSP00000256935:p.Glu821fs	Somatic	0	54	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	47	47	50.00	Q2M3I0|Q96AK7	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_DOCK_C,pfam_SH3_2,superfamily_SH3_domain,superfamily_Cyt_c-like_dom,superfamily_ARM-type_fold,superfamily_Ferritin-like_SF,smart_SH3_domain,pfscan_SH3_domain	p.E821fs	ENST00000256935.8	37	c.2461	CCDS4371.1	5																																																																																			-	superfamily_ARM-type_fold		0.483	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DOCK2	protein_coding	OTTHUMT00000252828.2	G	NM_004946			169188536	+1	no_errors	ENST00000256935	ensembl	human	known	74_37	frame_shift_del	DEL	1.000	-
C16orf96	342346	genome.wustl.edu	37	16	4625892	4625892	+	Nonsense_Mutation	SNP	G	G	T			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr16:4625892G>T	ENST00000444310.4	+	5	1411	c.1411G>T	c.(1411-1413)Gag>Tag	p.E471*		NM_001145011.1	NP_001138483.1			chromosome 16 open reading frame 96											NS(1)|breast(1)|endometrium(6)|kidney(1)|skin(3)	12						GGGCCTTCGGGAGAGGGCCCG	0.592																																																	0								ENSG00000205832						39.0	39.0	39.0					16																	4625892		692	1591	2283	C16orf96	SO:0001587	stop_gained	0			-	HGNC		CCDS53986.1	16p13.3	2012-10-10			ENSG00000205832	ENSG00000205832			40031	protein-coding gene	gene with protein product							Standard	NM_001145011		Approved		uc010uxn.2	A6NNT2	OTTHUMG00000176519	ENST00000444310.4:c.1411G>T	16.37:g.4625892G>T	ENSP00000415027:p.Glu471*	Somatic	0	61	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	53	43	55.21		Nonsense_Mutation	SNP	NA	NA	NA	NA	NA	NA	NULL	p.E471*	ENST00000444310.4	37	c.1411	CCDS53986.1	16	.	.	.	.	.	.	.	.	.	.	G	16.21	3.058544	0.55325	.	.	ENSG00000205832	ENST00000444310	.	.	.	1.69	-0.529	0.11901	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	.	5.2303	0.15418	0.395:0.0:0.605:0.0	.	.	.	.	X	471	.	ENSP00000415027:E471X	E	+	1	0	C16orf96	4565893	0.019000	0.18553	0.000000	0.03702	0.034000	0.12701	1.065000	0.30592	-0.134000	0.11516	0.313000	0.20887	GAG	-	NULL		0.592	C16orf96-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	C16orf96	protein_coding	OTTHUMT00000432384.1	G	NM_001145011	-		4625892	+1	no_errors	ENST00000444310	ensembl	human	known	74_37	nonsense	SNP	0.004	T
HMGB1P5	10354	genome.wustl.edu	37	3	22423916	22423927	+	RNA	DEL	GAAGAAGATGAA	GAAGAAGATGAA	-	rs371395387|rs545492903|rs368921999|rs199932860	byFrequency	TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	GAAGAAGATGAA	GAAGAAGATGAA					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr3:22423916_22423927delGAAGAAGATGAA	ENST00000451497.1	+	0	481_492									high mobility group box 1 pseudogene 5																		ggaggaagatgaagaagatgaagaagaagaTG	0.387														258	0.0515176	0.0106	0.0476	5008	,	,		19267	0.0347		0.0537	False		,,,				2504	0.1247																0								ENSG00000132967																																			HMGB1P5			0				HGNC	AF076677		3p24	2011-09-21	2011-04-05	2010-10-15	ENSG00000132967	ENSG00000132967		"""High mobility group / HMG-box pseudogenes"""	4997	pseudogene	pseudogene			"""high-mobility group (nonhistone chromosomal) protein 1-like 5"", ""high-mobility group (nonhistone chromosomal) protein 1-like 5 pseudogene"", ""high-mobility group box 1-like 5 pseudogene"", ""high-mobility group box 1-like 15"", ""high-mobility group box 1 pseudogene 2"", ""high-mobility group box 1-like 5"", ""high-mobility group box 1 pseudogene 5"""	HMG1L5, HMGB1L15, HMGB1P2, HMGB1L5		9925949	Standard	NG_000897		Approved				OTTHUMG00000155591		3.37:g.22423916_22423927delGAAGAAGATGAA		Somatic	NA	NA	NA		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA		RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000451497.1	37	NULL		3																																																																																			-	-		0.387	HMGB1P5-002	KNOWN	basic	processed_transcript	HMGB1P5	pseudogene	OTTHUMT00000340803.1	GAAGAAGATGAA	NG_000897			22423927	+1	no_errors	ENST00000451497	ensembl	human	known	74_37	rna	DEL	0.989:0.992:0.991:0.998:1.000:0.999:1.000:1.000:0.999:1.000:1.000:1.000	-
TTLL1	25809	genome.wustl.edu	37	22	43435575	43435576	+	IGR	INS	-	-	AA	rs60944727|rs537490054|rs36120119|rs541681211	byFrequency	TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr22:43435575_43435576insAA	ENST00000266254.7	-	0	1645				TTLL1_ENST00000331018.7_3'UTR|AL022476.2_ENST00000443063.1_RNA	NM_012263.4	NP_036395.1	O95922	TTLL1_HUMAN	tubulin tyrosine ligase-like family, member 1						axoneme assembly (GO:0035082)|epithelial cilium movement (GO:0003351)|protein polyglutamylation (GO:0018095)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	tubulin-glutamic acid ligase activity (GO:0070740)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(1)	23		Ovarian(80;0.0694)		BRCA - Breast invasive adenocarcinoma(115;0.00461)		GGTTAAAAATTAAAAAAAAAAG	0.312																																																	0								ENSG00000230319																																			AL022476.2	SO:0001628	intergenic_variant	0				Clone_based_vega_gene	AL096886	CCDS14043.1	22q13.1	2013-02-14			ENSG00000100271	ENSG00000100271		"""Tubulin tyrosine ligase-like family"""	1312	protein-coding gene	gene with protein product		608955	"""tubulin tyrosine ligase-like 1"""	C22orf7		10591208, 11054573	Standard	NM_012263		Approved		uc003bdi.3	O95922	OTTHUMG00000150699		22.37:g.43435584_43435585dupAA		Somatic	0	8	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	3	18	14.29	B2RDS7|Q9BR27|Q9NRS9|Q9UMU0	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000266254.7	37	NULL	CCDS14043.1	22																																																																																			-	-		0.312	TTLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LOC100506679	protein_coding	OTTHUMT00000319659.1	-	NM_012263			43435576	+1	no_errors	ENST00000443063	ensembl	human	known	74_37	rna	INS	0.009:0.002	AA
TAPBPL	55080	genome.wustl.edu	37	12	6571921	6571952	+	IGR	DEL	CAAGGAGGAGCCCAGAGGAGAGTGGAGACCTT	CAAGGAGGAGCCCAGAGGAGAGTGGAGACCTT	-	rs142636658	byFrequency	TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	CAAGGAGGAGCCCAGAGGAGAGTGGAGACCTT	CAAGGAGGAGCCCAGAGGAGAGTGGAGACCTT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr12:6571921_6571952delCAAGGAGGAGCCCAGAGGAGAGTGGAGACCTT	ENST00000266556.7	+	0	1741				VAMP1_ENST00000535180.1_3'UTR|TAPBPL_ENST00000545700.1_Intron|VAMP1_ENST00000400911.3_3'UTR|VAMP1_ENST00000544432.1_5'UTR|VAMP1_ENST00000361716.3_3'UTR	NM_018009.4	NP_060479.3	Q9BX59	TPSNR_HUMAN	TAP binding protein-like						negative regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002590)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)			endometrium(2)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	6						CTGCATTAGGCAAGGAGGAGCCCAGAGGAGAGTGGAGACCTTCGAGGGGGGC	0.599																																																	0								ENSG00000139190																																			VAMP1	SO:0001628	intergenic_variant	0				HGNC	AK001005	CCDS8546.1	12p13.31	2013-01-11						"""Immunoglobulin superfamily / C1-set domain containing"""	30683	protein-coding gene	gene with protein product		607081				11920573	Standard	NM_018009		Approved	TAPBP-R, FLJ10143, TAPBPR	uc001qog.4	Q9BX59			12.37:g.6571921_6571952delCAAGGAGGAGCCCAGAGGAGAGTGGAGACCTT		Somatic	NA	NA	NA		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	Q9NWB8	RNA	DEL	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000266556.7	37	NULL	CCDS8546.1	12																																																																																			-	-		0.599	TAPBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	VAMP1	protein_coding	OTTHUMT00000399263.1	CAAGGAGGAGCCCAGAGGAGAGTGGAGACCTT	NM_018009			6571952	-1	no_errors	ENST00000544432	ensembl	human	known	74_37	rna	DEL	0.927:0.937:0.945:0.951:0.966:0.970:0.986:0.986:0.997:1.000:1.000:1.000:1.000:1.000:1.000:1.000:0.998:0.996:0.987:0.973:0.994:0.998:0.999:1.000:0.999:1.000:1.000:0.994:0.991:0.959:0.932:0.808	-
SLC7A14	57709	genome.wustl.edu	37	3	170216674	170216674	+	Splice_Site	SNP	C	C	T			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr3:170216674C>T	ENST00000231706.5	-	4	857		c.e4-1		CLDN11_ENST00000451576.1_Intron|CLDN11_ENST00000486975.1_Intron	NM_020949.2	NP_066000.2	Q8TBB6	S7A14_HUMAN	solute carrier family 7, member 14						negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	amino acid transmembrane transporter activity (GO:0015171)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(23)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(4)	53	all_cancers(22;2.41e-22)|all_epithelial(15;4.2e-27)|all_lung(20;1.17e-16)|Lung NSC(18;4.91e-16)|Ovarian(172;0.000902)|Breast(254;0.137)		Lung(28;6.23e-13)|LUSC - Lung squamous cell carcinoma(14;1.48e-12)			TCACCTTTCCCTAGAGAGGAA	0.493																																																	0								ENSG00000013293						85.0	70.0	75.0					3																	170216674		2203	4300	6503	SLC7A14	SO:0001630	splice_region_variant	0			-	HGNC	BC022968	CCDS33892.1	3q26.2	2014-06-13	2013-07-19		ENSG00000013293	ENSG00000013293		"""Solute carriers"""	29326	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 142"""	615720					Standard	NM_020949		Approved	KIAA1613, PPP1R142	uc003fgz.2	Q8TBB6	OTTHUMG00000158941	ENST00000231706.5:c.542-1G>A	3.37:g.170216674C>T		Somatic	0	46	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	27	25	51.92	B3KV33|Q9HCF9	Splice_Site	SNP	NA	NA	NA	NA	NA	NA	-	e3-1	ENST00000231706.5	37	c.542-1	CCDS33892.1	3	.	.	.	.	.	.	.	.	.	.	C	26.7	4.758208	0.89843	.	.	ENSG00000013293	ENST00000231706	.	.	.	5.78	5.78	0.91487	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.0203	0.97492	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLC7A14	171699368	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.466000	0.80914	2.730000	0.93505	0.655000	0.94253	.	-	-		0.493	SLC7A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC7A14	protein_coding	OTTHUMT00000352598.2	C	NM_020949	-	Intron	170216674	-1	no_errors	ENST00000231706	ensembl	human	known	74_37	splice_site	SNP	1.000	T
MUC4	4585	genome.wustl.edu	37	3	195513615	195513615	+	Silent	SNP	A	A	T			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr3:195513615A>T	ENST00000463781.3	-	2	5295	c.4836T>A	c.(4834-4836)ggT>ggA	p.G1612G	MUC4_ENST00000475231.1_Silent_p.G1612G|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGGTGGTGTGACCTGTAGATG	0.567																																																	0								ENSG00000145113						8.0	13.0	12.0					3																	195513615		635	1500	2135	MUC4	SO:0001819	synonymous_variant	0			-	HGNC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.4836T>A	3.37:g.195513615A>T		Somatic	0	586	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	150	707	17.48	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Nidogen_extracell_dom,pfam_AMOP,pfam_VWF_type-D,smart_Nidogen_extracell_dom,smart_AMOP,smart_VWF_type-D,smart_EG-like_dom,pfscan_AMOP,pfscan_EG-like_dom	p.G1612	ENST00000463781.3	37	c.4836	CCDS54700.1	3																																																																																			-	NULL		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	MUC4	protein_coding	OTTHUMT00000324081.6	A	NM_018406	-		195513615	-1	no_errors	ENST00000463781	ensembl	human	known	74_37	silent	SNP	0.000	T
ERBB4	2066	genome.wustl.edu	37	2	212295769	212295769	+	Missense_Mutation	SNP	A	A	T			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr2:212295769A>T	ENST00000342788.4	-	21	2854	c.2544T>A	c.(2542-2544)aaT>aaA	p.N848K	ERBB4_ENST00000436443.1_Missense_Mutation_p.N848K|ERBB4_ENST00000402597.1_Missense_Mutation_p.N838K	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	848	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	TCACTAAGACATTACGGGCTG	0.418										TSP Lung(8;0.080)																																							0								ENSG00000178568						141.0	136.0	138.0					2																	212295769		2203	4300	6503	ERBB4	SO:0001583	missense	0			-	HGNC	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"""v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"""			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.2544T>A	2.37:g.212295769A>T	ENSP00000342235:p.Asn848Lys	Somatic	0	70	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	57	60	48.72	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pirsf_Tyr_kinase_EGF/ERB/XmrK_rcpt,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_EGF_rcpt_L,pfam_Prot_kinase_dom,pfam_Furin-like_Cys-rich_dom,superfamily_Kinase-like_dom,superfamily_Growth_fac_rcpt_N_dom,smart_Furin_repeat,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom,pfscan_Prot_kinase_dom	p.N848K	ENST00000342788.4	37	c.2544	CCDS2394.1	2	.	.	.	.	.	.	.	.	.	.	A	18.50	3.638120	0.67130	.	.	ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597	D;D;D	0.86297	-2.1;-2.1;-2.1	5.04	1.32	0.21799	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.95223	0.8451	H	0.98407	4.225	0.58432	D	0.999998	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.999;0.999;1.0	D	0.93279	0.6658	10	0.87932	D	0	.	8.9189	0.35599	0.7827:0.0:0.2173:0.0	.	838;838;848;848	Q15303-4;Q15303-2;Q15303-3;Q15303	.;.;.;ERBB4_HUMAN	K	848;848;838	ENSP00000342235:N848K;ENSP00000403204:N848K;ENSP00000385565:N838K	ENSP00000342235:N848K	N	-	3	2	ERBB4	212004014	0.997000	0.39634	0.994000	0.49952	0.935000	0.57460	0.627000	0.24506	0.039000	0.15632	0.460000	0.39030	AAT	-	pirsf_Tyr_kinase_EGF/ERB/XmrK_rcpt,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom,pfscan_Prot_kinase_dom		0.418	ERBB4-001	KNOWN	basic|CCDS	protein_coding	ERBB4	protein_coding	OTTHUMT00000256597.1	A	NM_001042599	-		212295769	-1	no_errors	ENST00000342788	ensembl	human	known	74_37	missense	SNP	1.000	T
PABPC4	8761	genome.wustl.edu	37	1	40041576	40041576	+	Silent	SNP	G	G	T			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr1:40041576G>T	ENST00000372857.3	-	1	840	c.48C>A	c.(46-48)ggC>ggA	p.G16G	RP11-69E11.8_ENST00000415255.1_RNA|PABPC4_ENST00000372862.3_Silent_p.G16G|PABPC4_ENST00000372856.3_Silent_p.G16G|PABPC4_ENST00000372858.3_Silent_p.G16G	NM_003819.3	NP_003810.1	Q13310	PABP4_HUMAN	poly(A) binding protein, cytoplasmic 4 (inducible form)	16	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				blood coagulation (GO:0007596)|RNA catabolic process (GO:0006401)|RNA processing (GO:0006396)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(6)|prostate(1)|skin(3)	21	Lung NSC(20;1.55e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.89e-18)|Epithelial(16;6.17e-17)|all cancers(16;1.18e-15)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			AATGCAGGTCGCCCACGTACA	0.677																																																	0								ENSG00000090621																																			PABPC4	SO:0001819	synonymous_variant	0			-	HGNC	U33818	CCDS438.1, CCDS44114.1, CCDS44115.1	1p34.2	2013-02-12	2001-11-28		ENSG00000090621	ENSG00000090621		"""RNA binding motif (RRM) containing"""	8557	protein-coding gene	gene with protein product		603407	"""poly(A)-binding protein, cytoplasmic 4 (inducible form)"""			10543404	Standard	NM_001135653		Approved	iPABP, APP-1	uc001cdl.2	Q13310	OTTHUMG00000009097	ENST00000372857.3:c.48C>A	1.37:g.40041576G>T		Somatic	0	98	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	35	229	13.21	B1ANQ8|Q4VC03|Q6P0N3	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_RRM_dom,pfam_PABP_HYD,superfamily_PABP_HYD,smart_RRM_dom,smart_RRM_dom_euk,smart_PABP_HYD,pfscan_RRM_dom,tigrfam_PABP_1234	p.G16	ENST00000372857.3	37	c.48	CCDS438.1	1																																																																																			-	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom,tigrfam_PABP_1234		0.677	PABPC4-001	KNOWN	basic|CCDS	protein_coding	PABPC4	protein_coding	OTTHUMT00000025220.1	G	NM_001135653	-		40041576	-1	no_errors	ENST00000372858	ensembl	human	known	74_37	silent	SNP	0.957	T
MSH3	4437	genome.wustl.edu	37	5	79950742	79950750	+	In_Frame_Del	DEL	CCCCCAGCT	CCCCCAGCT	-	rs144629981|rs3045983|rs557874766|rs1047489	byFrequency	TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	CCCCCAGCT	CCCCCAGCT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr5:79950742_79950750delCCCCCAGCT	ENST00000265081.6	+	1	276_284	c.196_204delCCCCCAGCT	c.(196-204)cccccagctdel	p.PPA66del	DHFR_ENST00000505337.1_5'Flank|DHFR_ENST00000511032.1_5'Flank|DHFR_ENST00000439211.2_5'UTR|DHFR_ENST00000513048.1_5'Flank|DHFR_ENST00000504396.1_5'Flank	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	66					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		gCCCCCAGCGCCCCCAGCTCCCGCCTTCC	0.732								Mismatch excision repair (MMR)						1174	0.234425	0.2874	0.2061	5008	,	,		7173	0.0565		0.2535	False		,,,				2504	0.3466				Melanoma(88;1010 1399 13793 26548 36275)												0								ENSG00000113318		,	1105,2179		342,421,879					,	4.0	1.0		dbSNP_102	4	1941,4615		567,807,1904	no	coding,utr-5	DHFR,MSH3	NM_002439.3,NM_000791.3	,	909,1228,2783	A1A1,A1R,RR		29.6065,33.648,30.9553	,	,		3046,6794				MSH3	SO:0001651	inframe_deletion	0				HGNC	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.196_204delCCCCCAGCT	5.37:g.79950742_79950750delCCCCCAGCT	ENSP00000265081:p.Pro66_Ala68del	Somatic	NA	NA	NA		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	In_Frame_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_DNA_mismatch_repair_MutS_C,pfam_DNA_mismatch_repair_MutS_core,pfam_DNA_mmatch_repair_MutS_con_dom,pfam_DNA_mismatch_repair_MutS-lik_N,pfam_DNA_mismatch_repair_MutS_clamp,superfamily_DNA_mismatch_repair_MutS_core,superfamily_P-loop_NTPase,superfamily_DNA_mismatch_repair_MutS_N,superfamily_DNA_mmatch_repair_MutS_con_dom,smart_DNA_mismatch_repair_MutS_core,smart_DNA_mismatch_repair_MutS_C	p.PAP67in_frame_del	ENST00000265081.6	37	c.196_204	CCDS34195.1	5																																																																																			-	NULL		0.732	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	MSH3	protein_coding	OTTHUMT00000369471.1	CCCCCAGCT	NM_002439			79950750	+1	no_errors	ENST00000265081	ensembl	human	known	74_37	in_frame_del	DEL	0.890:0.802:0.715:0.628:0.541:0.455:0.369:0.282:0.196	-
OLFM3	118427	genome.wustl.edu	37	1	102462400	102462400	+	5'UTR	SNP	C	C	T			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr1:102462400C>T	ENST00000370103.4	-	0	186				OLFM3_ENST00000462354.1_5'UTR	NM_058170.2	NP_477518.2	Q96PB7	NOE3_HUMAN	olfactomedin 3						eye photoreceptor cell development (GO:0042462)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)				breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(24)|ovary(3)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	43		all_epithelial(167;1.87e-06)|all_lung(203;8.12e-05)|Lung NSC(277;0.000189)		all cancers(265;0.0843)|Epithelial(280;0.0921)|COAD - Colon adenocarcinoma(174;0.145)		CCCCTCTTTACTCTCTTTTAT	0.532																																																	0								ENSG00000118733						124.0	122.0	123.0					1																	102462400		2203	4300	6503	OLFM3	SO:0001623	5_prime_UTR_variant	0			-	HGNC	AF397392	CCDS30781.1, CCDS72832.1	1p22	2008-05-23			ENSG00000118733	ENSG00000118733			17990	protein-coding gene	gene with protein product	"""optimedin"""	607567				12019210, 16115881	Standard	NM_001288821		Approved	NOE3	uc001dug.2	Q96PB7	OTTHUMG00000010941	ENST00000370103.4:c.-28G>A	1.37:g.102462400C>T		Somatic	0	165	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	25	186	11.85	Q5T3V6|Q6IMI7|Q6IMI8|Q6IMI9|Q6IMJ1|Q8TBG1|Q96PB2|Q96PB3|Q96PB4|Q96PB5|Q96PB6	RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000370103.4	37	NULL	CCDS30781.1	1																																																																																			-	-		0.532	OLFM3-003	KNOWN	basic|CCDS	protein_coding	OLFM3	protein_coding	OTTHUMT00000030144.1	C		-		102462400	-1	no_errors	ENST00000462354	ensembl	human	known	74_37	rna	SNP	0.989	T
MIR3687-2	103504728	genome.wustl.edu	37	21	9825966	9825966	+	RNA	SNP	A	A	C	rs544334327		TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr21:9825966A>C	ENST00000577708.1	+	0	0				MIR3648_ENST00000581792.1_RNA	NR_037458.1																						GCCGCGCTCGAGGGGTCCCCG	0.816																																																	0								ENSG00000264462																																			MIR3648			0			-	HGNC																													21.37:g.9825966A>C		Somatic	0	13	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	16	35	30.77		RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000577708.1	37	NULL		21																																																																																			-	-		0.816	MIR3687-201	KNOWN	basic	miRNA	MIR3648	miRNA		A		rs1796672		9825966	+1	no_errors	ENST00000581792	ensembl	human	known	74_37	rna	SNP	0.050	C
KIAA1211	57482	genome.wustl.edu	37	4	57180576	57180577	+	In_Frame_Ins	INS	-	-	GGAGCGGAGGGAGCGGAG	rs71921617|rs138358443|rs11276076	byFrequency	TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr4:57180576_57180577insGGAGCGGAGGGAGCGGAG	ENST00000504228.1	+	6	1013_1014	c.908_909insGGAGCGGAGGGAGCGGAG	c.(907-912)gcggag>gcGGAGCGGAGGGAGCGGAGggag	p.304_305insRRERRE	KIAA1211_ENST00000541073.1_In_Frame_Ins_p.297_298insRRERRE|KIAA1211_ENST00000264229.6_In_Frame_Ins_p.304_305insRRERRE			Q6ZU35	K1211_HUMAN	KIAA1211	304	Glu-rich.									endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					TGGGAGGACGCGGAGCGGAGGG	0.733														1350	0.269569	0.2716	0.2781	5008	,	,		14300	0.0694		0.4076	False		,,,				2504	0.3252																0								ENSG00000109265			903,2311		258,387,962						-10.2	0.0		dbSNP_130	6	2065,4451		612,841,1805	no	coding	KIAA1211	NM_020722.1		870,1228,2767	A1A1,A1R,RR		31.6912,28.0958,30.5036				2968,6762				KIAA1211	SO:0001652	inframe_insertion	0				HGNC	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	Exception_encountered	4.37:g.57180576_57180577insGGAGCGGAGGGAGCGGAG	ENSP00000423366:p.Glu304_Arg305insArgArgGluArgArgGlu	Somatic	NA	NA	NA		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	Q9NTE2|Q9NTP8|Q9ULK9	In_Frame_Ins	INS	NA	NA	NA	NA	NA	NA	NULL	p.307in_frame_insERRERR	ENST00000504228.1	37	c.908_909	CCDS43230.1	4																																																																																			-	NULL		0.733	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KIAA1211	protein_coding	OTTHUMT00000362097.2	-	NM_020722			57180577	+1	no_errors	ENST00000504228	ensembl	human	known	74_37	in_frame_ins	INS	0.000:0.000	GGAGCGGAGGGAGCGGAG
MDM2	4193	genome.wustl.edu	37	12	69222659	69222659	+	Missense_Mutation	SNP	T	T	C			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr12:69222659T>C	ENST00000350057.5	+	6	539	c.539T>C	c.(538-540)aTa>aCa	p.I180T	MDM2_ENST00000360430.2_Intron|MDM2_ENST00000348801.2_Intron|MDM2_ENST00000517852.1_Intron|MDM2_ENST00000258149.5_Missense_Mutation_p.I150T|MDM2_ENST00000428863.2_Intron|MDM2_ENST00000540827.1_Intron|MDM2_ENST00000544561.1_Intron|MDM2_ENST00000258148.7_Missense_Mutation_p.I156T|MDM2_ENST00000393412.3_Intron|MDM2_ENST00000393413.3_Intron|MDM2_ENST00000462284.1_Missense_Mutation_p.I211T|MDM2_ENST00000478070.1_Intron|MDM2_ENST00000299252.4_Intron|MDM2_ENST00000393410.1_Intron|RP11-611O2.1_ENST00000544710.1_RNA|MDM2_ENST00000545204.1_Intron|MDM2_ENST00000356290.4_Intron			Q00987	MDM2_HUMAN	MDM2 proto-oncogene, E3 ubiquitin protein ligase	205	Interaction with MTBP. {ECO:0000250}.|Interaction with PYHIN1 and necessary for interaction with RFFL and RNF34. {ECO:0000269|PubMed:16479015, ECO:0000269|PubMed:18382127}.				cellular response to acid chemical (GO:0071229)|cellular response to alkaloid (GO:0071312)|cellular response to antibiotic (GO:0071236)|cellular response to estrogen stimulus (GO:0071391)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to UV-C (GO:0071494)|cellular response to vitamin B1 (GO:0071301)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment of protein localization (GO:0045184)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of protein processing (GO:0010955)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-lysine modification (GO:0018205)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein export from nucleus (GO:0046827)|protein complex assembly (GO:0006461)|protein destabilization (GO:0031648)|protein localization to nucleus (GO:0034504)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of protein catabolic process (GO:0042176)|response to antibiotic (GO:0046677)|response to carbohydrate (GO:0009743)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ether (GO:0045472)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to morphine (GO:0043278)|synaptic transmission (GO:0007268)|traversing start control point of mitotic cell cycle (GO:0007089)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(8)|prostate(1)|urinary_tract(1)	19	all_cancers(1;8.46e-121)|all_epithelial(5;3.21e-36)|Lung NSC(4;2.16e-33)|all_lung(4;3.03e-31)|Glioma(1;1.9e-09)|Breast(13;1.59e-06)|all_neural(1;1.03e-05)|Melanoma(1;0.0171)|Renal(347;0.0684)		all cancers(2;8.67e-65)|GBM - Glioblastoma multiforme(2;8.89e-62)|BRCA - Breast invasive adenocarcinoma(5;2.43e-08)|Lung(24;1.5e-05)|LUAD - Lung adenocarcinoma(15;8.5e-05)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			ATAAGGGAGATATGTTGTGAA	0.403			A		"""sarcoma, glioma, colorectal, other"""																																			Dom	yes		12	12q15	4193	Mdm2 p53 binding protein homolog		"""M, O, E, L"""	0								ENSG00000135679						180.0	171.0	174.0					12																	69222659		1914	4119	6033	MDM2	SO:0001583	missense	0			-	HGNC		CCDS8986.2, CCDS61189.1	12q13-q14	2014-06-26	2014-06-26		ENSG00000135679	ENSG00000135679			6973	protein-coding gene	gene with protein product		164785	"""mouse double minute 2, human homolog of; p53-binding protein"", ""Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse)"", ""Mdm2 p53 binding protein homolog (mouse)"""			1614537, 16905769	Standard	NM_002392		Approved	HDM2, MGC5370	uc001sui.4	Q00987	OTTHUMG00000142827	ENST00000350057.5:c.539T>C	12.37:g.69222659T>C	ENSP00000266624:p.Ile180Thr	Somatic	0	32	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	26	30	46.43	A6NL51|A8K2S6|Q13226|Q13297|Q13298|Q13299|Q13300|Q13301|Q53XW0|Q71TW9|Q8WYJ1|Q8WYJ2|Q9UGI3|Q9UMT8	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_SWIB_MDM2_domain,pfam_Znf_RanBP2,superfamily_SWIB_MDM2_domain,pirsf_p53_neg-reg_MDM_2/4,pfscan_Znf_RanBP2,pfscan_Znf_RING	p.I211T	ENST00000350057.5	37	c.632		12	.	.	.	.	.	.	.	.	.	.	T	15.13	2.742579	0.49151	.	.	ENSG00000135679	ENST00000462284;ENST00000544648;ENST00000258149;ENST00000311440;ENST00000311420;ENST00000258148;ENST00000539479;ENST00000393415;ENST00000350057	T;T;T;T;T	0.46819	1.5;0.86;0.86;0.87;1.51	4.64	4.64	0.57946	SWIB/MDM2 domain (1);	0.328417	0.32624	N	0.005860	T	0.41534	0.1163	L	0.44542	1.39	0.80722	D	1	P;P;P;P	0.40875	0.731;0.501;0.547;0.682	B;B;B;B	0.39531	0.302;0.118;0.302;0.221	T	0.30387	-0.9980	9	.	.	.	-16.4192	14.7829	0.69779	0.0:0.0:0.0:1.0	.	160;205;156;211	Q00987-9;Q00987;G3XA89;Q00987-11	.;MDM2_HUMAN;.;.	T	211;160;150;205;166;156;205;205;180	ENSP00000417281:I211T;ENSP00000258149:I150T;ENSP00000258148:I156T;ENSP00000444430:I205T;ENSP00000266624:I180T	.	I	+	2	0	MDM2	67508926	1.000000	0.71417	0.946000	0.38457	0.919000	0.55068	5.444000	0.66587	2.052000	0.61016	0.383000	0.25322	ATA	-	superfamily_SWIB_MDM2_domain,pirsf_p53_neg-reg_MDM_2/4		0.403	MDM2-033	NOVEL	basic|exp_conf	protein_coding	MDM2	protein_coding	OTTHUMT00000402665.1	T	NM_006880	-		69222659	+1	no_errors	ENST00000462284	ensembl	human	known	74_37	missense	SNP	0.919	C
ZSCAN21	7589	genome.wustl.edu	37	7	99654810	99654810	+	Nonsense_Mutation	SNP	G	G	T			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr7:99654810G>T	ENST00000292450.4	+	2	345	c.181G>T	c.(181-183)Gag>Tag	p.E61*	ZSCAN21_ENST00000477297.1_3'UTR|ZSCAN21_ENST00000456748.2_Nonsense_Mutation_p.E61*|ZSCAN21_ENST00000543588.1_Nonsense_Mutation_p.E61*	NM_145914.2	NP_666019.1	Q9Y5A6	ZSC21_HUMAN	zinc finger and SCAN domain containing 21	61	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|skin(1)	21	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			TGGACCCCGAGAGGCCCTGAG	0.587																																																	0								ENSG00000166529						65.0	67.0	67.0					7																	99654810		2203	4300	6503	ZSCAN21	SO:0001587	stop_gained	0			-	HGNC	AL136865	CCDS5681.1	7q11.1	2013-01-08	2006-10-06	2006-10-06	ENSG00000166529	ENSG00000166529		"""-"", ""Zinc fingers, C2H2-type"""	13104	protein-coding gene	gene with protein product		601261	"""zinc finger protein 38 (KOX 25)"", ""zinc finger protein 38"""	ZNF38		2288909, 2014798	Standard	NM_145914		Approved	DKFZp434L134, NY-REN-21, Zipro1	uc003uso.3	Q9Y5A6	OTTHUMG00000154583	ENST00000292450.4:c.181G>T	7.37:g.99654810G>T	ENSP00000292450:p.Glu61*	Somatic	0	46	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	58	50	53.70	A4D2A6|D6W5T9|Q9H0B5	Nonsense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Tscrpt_reg_SCAN,pfam_Znf_C2H2,superfamily_Retrov_capsid_C,smart_Tscrpt_reg_SCAN,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Tscrpt_reg_SCAN	p.E61*	ENST00000292450.4	37	c.181	CCDS5681.1	7	.	.	.	.	.	.	.	.	.	.	G	36	5.788103	0.96945	.	.	ENSG00000166529	ENST00000543588;ENST00000292450;ENST00000456748;ENST00000438937;ENST00000379635	.	.	.	4.91	4.91	0.64330	.	0.000000	0.40469	N	0.001090	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	13.7845	0.63102	0.0:0.0:1.0:0.0	.	.	.	.	X	61	.	ENSP00000292450:E61X	E	+	1	0	ZSCAN21	99492746	1.000000	0.71417	0.998000	0.56505	0.799000	0.45148	6.517000	0.73759	2.721000	0.93114	0.655000	0.94253	GAG	-	pfam_Tscrpt_reg_SCAN,superfamily_Retrov_capsid_C,smart_Tscrpt_reg_SCAN,pfscan_Tscrpt_reg_SCAN		0.587	ZSCAN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ZSCAN21	protein_coding	OTTHUMT00000336166.1	G	NM_145914	-		99654810	+1	no_errors	ENST00000292450	ensembl	human	known	74_37	nonsense	SNP	1.000	T
MSH3	4437	genome.wustl.edu	37	5	79950723	79950723	+	Frame_Shift_Del	DEL	G	G	-			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr5:79950723delG	ENST00000265081.6	+	1	257	c.177delG	c.(175-177)gcgfs	p.A62fs	DHFR_ENST00000505337.1_5'Flank|DHFR_ENST00000511032.1_5'Flank|DHFR_ENST00000439211.2_5'UTR|DHFR_ENST00000513048.1_5'Flank|DHFR_ENST00000504396.1_5'Flank	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	62	Poly-Ala.		A -> AAAA. {ECO:0000269|PubMed:8851770}.|Missing. {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8942985}.		ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		cggccgcagcggccgcagcgC	0.706								Mismatch excision repair (MMR)																													Melanoma(88;1010 1399 13793 26548 36275)												0								ENSG00000113318						5.0	6.0	6.0					5																	79950723		2054	3996	6050	MSH3	SO:0001589	frameshift_variant	0				HGNC	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.177delG	5.37:g.79950723delG	ENSP00000265081:p.Ala62fs	Somatic	0	17	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	11	38	22.45	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_DNA_mismatch_repair_MutS_C,pfam_DNA_mismatch_repair_MutS_core,pfam_DNA_mmatch_repair_MutS_con_dom,pfam_DNA_mismatch_repair_MutS-lik_N,pfam_DNA_mismatch_repair_MutS_clamp,superfamily_DNA_mismatch_repair_MutS_core,superfamily_P-loop_NTPase,superfamily_DNA_mismatch_repair_MutS_N,superfamily_DNA_mmatch_repair_MutS_con_dom,smart_DNA_mismatch_repair_MutS_core,smart_DNA_mismatch_repair_MutS_C	p.A60fs	ENST00000265081.6	37	c.177	CCDS34195.1	5																																																																																			-	NULL		0.706	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	MSH3	protein_coding	OTTHUMT00000369471.1	G	NM_002439			79950723	+1	no_errors	ENST00000265081	ensembl	human	known	74_37	frame_shift_del	DEL	0.730	-
OR51G1	79324	genome.wustl.edu	37	11	4945061	4945061	+	Missense_Mutation	SNP	T	T	C			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr11:4945061T>C	ENST00000321961.2	-	1	576	c.509A>G	c.(508-510)tAc>tGc	p.Y170C	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001005237.1	NP_001005237.1	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G, member 1	170						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(3)|skin(4)|soft_tissue(1)	25		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.58e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		GGAGTGGCAGTATTGGAAGCG	0.502																																																	0								ENSG00000176879						74.0	64.0	68.0					11																	4945061		2201	4298	6499	OR51G1	SO:0001583	missense	0			-	HGNC	AB065793	CCDS31366.1	11p15.4	2012-08-09			ENSG00000176879	ENSG00000176879		"""GPCR / Class A : Olfactory receptors"""	14738	protein-coding gene	gene with protein product				OR51G3P			Standard	NM_001005237		Approved		uc010qyr.2	Q8NGK1	OTTHUMG00000066532	ENST00000321961.2:c.509A>G	11.37:g.4945061T>C	ENSP00000322546:p.Tyr170Cys	Somatic	0	60	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	35	37	48.61	B9EGW8|Q6IFH6	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,pfscan_GPCR_Rhodpsn_7TM,prints_Olfact_rcpt,prints_GPCR_Rhodpsn	p.Y170C	ENST00000321961.2	37	c.509	CCDS31366.1	11	.	.	.	.	.	.	.	.	.	.	T	9.389	1.075131	0.20227	.	.	ENSG00000176879	ENST00000321961	T	0.00179	8.61	4.3	3.13	0.36017	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35739	U	0.003011	T	0.00552	0.0018	M	0.89414	3.03	0.31224	N	0.697074	D	0.89917	1.0	D	0.87578	0.998	T	0.16600	-1.0397	10	0.66056	D	0.02	.	7.4992	0.27507	0.4815:0.0:0.0:0.5184	.	170	Q8NGK1	O51G1_HUMAN	C	170	ENSP00000322546:Y170C	ENSP00000322546:Y170C	Y	-	2	0	OR51G1	4901637	0.000000	0.05858	0.995000	0.50966	0.057000	0.15508	-0.425000	0.07017	0.646000	0.30693	0.455000	0.32223	TAC	-	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM		0.502	OR51G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR51G1	protein_coding	OTTHUMT00000142345.1	T	NM_001005237	-		4945061	-1	no_errors	ENST00000321961	ensembl	human	known	74_37	missense	SNP	0.963	C
MSH3	4437	genome.wustl.edu	37	5	79950714	79950714	+	Frame_Shift_Del	DEL	G	G	-	rs201874762		TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr5:79950714delG	ENST00000265081.6	+	1	248	c.168delG	c.(166-168)gcgfs	p.A62fs	DHFR_ENST00000505337.1_5'Flank|DHFR_ENST00000511032.1_5'Flank|DHFR_ENST00000439211.2_5'UTR|DHFR_ENST00000513048.1_5'Flank|DHFR_ENST00000504396.1_5'Flank	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	62	Poly-Ala.		A -> AAAA. {ECO:0000269|PubMed:8851770}.|Missing. {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8942985}.		ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		cggctgcagcggccgcagcgg	0.687								Mismatch excision repair (MMR)																													Melanoma(88;1010 1399 13793 26548 36275)												0								ENSG00000113318						7.0	7.0	7.0					5																	79950714		2092	4074	6166	MSH3	SO:0001589	frameshift_variant	0				HGNC	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.168delG	5.37:g.79950714delG	ENSP00000265081:p.Ala62fs	Somatic	0	25	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	12	30	28.57	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Frame_Shift_Del	DEL	NA	NA	NA	NA	NA	NA	pfam_DNA_mismatch_repair_MutS_C,pfam_DNA_mismatch_repair_MutS_core,pfam_DNA_mmatch_repair_MutS_con_dom,pfam_DNA_mismatch_repair_MutS-lik_N,pfam_DNA_mismatch_repair_MutS_clamp,superfamily_DNA_mismatch_repair_MutS_core,superfamily_P-loop_NTPase,superfamily_DNA_mismatch_repair_MutS_N,superfamily_DNA_mmatch_repair_MutS_con_dom,smart_DNA_mismatch_repair_MutS_core,smart_DNA_mismatch_repair_MutS_C	p.A57fs	ENST00000265081.6	37	c.168	CCDS34195.1	5																																																																																			-	NULL		0.687	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	MSH3	protein_coding	OTTHUMT00000369471.1	G	NM_002439			79950714	+1	no_errors	ENST00000265081	ensembl	human	known	74_37	frame_shift_del	DEL	0.172	-
MIR663AHG	284801	genome.wustl.edu	37	20	26231957	26231957	+	IGR	SNP	G	G	A			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr20:26231957G>A								MIR663A (43043 upstream) : None (None downstream)																							cctggactccgtctgctgttt	0.607																																																	0								ENSG00000227195																																			MIR663A	SO:0001628	intergenic_variant	0			-	HGNC																													20.37:g.26231957G>A		Somatic	0	15	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	13	18	41.94		RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL		37	NULL		20																																																																																			-	-	0	0.607					MIR663A			G		-		26231957	-1	no_errors	ENST00000594130	ensembl	human	known	74_37	rna	SNP	0.046	A
TDRP	157695	genome.wustl.edu	37	8	494659	494664	+	In_Frame_Del	DEL	GGCGGC	GGCGGC	-	rs71202629	byFrequency	TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	GGCGGC	GGCGGC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr8:494659_494664delGGCGGC	ENST00000324079.6	-	1	334_339	c.94_99delGCCGCC	c.(94-99)gccgccdel	p.AA32del	TDRP_ENST00000523656.1_In_Frame_Del_p.AA32del|TDRP_ENST00000427263.2_In_Frame_Del_p.AA32del			Q86YL5	TDRP_HUMAN	testis development related protein	32	Poly-Ala.				spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.A32_A33delAA(1)									CCTGCGCCTGggcggcggcggcggcg	0.782														1130	0.225639	0.056	0.4049	5008	,	,		8817	0.1677		0.3439	False		,,,				2504	0.2658																1	Deletion - In frame(1)	upper_aerodigestive_tract(1)						ENSG00000180190			110,14,698		47,1,15,6,1,341						1.0	0.0		dbSNP_134	2	1280,14,1322		556,0,168,7,0,577	no	codingComplex	C8orf42	NM_175075.3		603,1,183,13,1,918	A1A1,A1A2,A1R,A2A2,A2R,RR		49.4648,15.0852,41.2449				1390,28,2020				TDRP	SO:0001651	inframe_deletion	0				HGNC	AY194292	CCDS47759.1, CCDS59090.1	8p23.3	2013-06-03	2013-06-03	2013-06-03	ENSG00000180190	ENSG00000180190			26951	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 42"""	C8orf42		20170638	Standard	NM_175075		Approved	INM01, TDRP1, TDRP2		Q86YL5	OTTHUMG00000163593	ENST00000324079.6:c.94_99delGCCGCC	8.37:g.494665_494670delGGCGGC	ENSP00000315111:p.Ala32_Ala33del	Somatic	NA	NA	NA		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	NA	NA	NA	B6VF03|B9EG53	In_Frame_Del	DEL	NA	NA	NA	NA	NA	NA	NULL	p.AA32in_frame_del	ENST00000324079.6	37	c.99_94	CCDS47759.1	8																																																																																			-	NULL		0.782	TDRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TDRP	protein_coding	OTTHUMT00000374442.1	GGCGGC	NM_175075			494664	-1	no_errors	ENST00000427263	ensembl	human	known	74_37	in_frame_del	DEL	0.066:0.068:0.048:0.038:0.021:0.012	-
ANKRD62	342850	genome.wustl.edu	37	18	12107409	12107409	+	Missense_Mutation	SNP	A	A	G			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr18:12107409A>G	ENST00000587848.2	+	8	1172	c.1007A>G	c.(1006-1008)aAg>aGg	p.K336R	ANKRD62_ENST00000314074.8_Missense_Mutation_p.K322R|ANKRD62_ENST00000418274.2_3'UTR			A6NC57	ANR62_HUMAN	ankyrin repeat domain 62	336										breast(2)|haematopoietic_and_lymphoid_tissue(1)	3						CACAAAATAAAGAACAGAAAA	0.348																																																	0								ENSG00000181626																																			ANKRD62	SO:0001583	missense	0			-	HGNC	BX648696	CCDS67439.1	18p11.21	2014-01-21			ENSG00000181626	ENSG00000181626		"""Ankyrin repeat domain containing"""	35241	protein-coding gene	gene with protein product							Standard	XM_003959949		Approved	DKFZp779B1634	uc031rhk.1	A6NC57	OTTHUMG00000180673	ENST00000587848.2:c.1007A>G	18.37:g.12107409A>G	ENSP00000467740:p.Lys336Arg	Somatic	0	68	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	9	93	8.82		Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom	p.K322R	ENST00000587848.2	37	c.965		18	.	.	.	.	.	.	.	.	.	.	A	3.155	-0.173287	0.06421	.	.	ENSG00000181626	ENST00000314074;ENST00000418274	T;T	0.36157	1.27;3.08	1.73	-2.87	0.05700	.	.	.	.	.	T	0.16938	0.0407	N	0.20986	0.625	0.09310	N	1	B	0.13594	0.008	B	0.04013	0.001	T	0.28332	-1.0047	9	0.15066	T	0.55	.	2.975	0.05935	0.4051:0.2503:0.3446:0.0	.	336	A6NC57	ANR62_HUMAN	R	322;58	ENSP00000326572:K322R;ENSP00000405628:K58R	ENSP00000326572:K322R	K	+	2	0	ANKRD62	12097409	0.001000	0.12720	0.000000	0.03702	0.014000	0.08584	0.089000	0.15002	-0.725000	0.04901	-0.836000	0.03065	AAG	-	NULL		0.348	ANKRD62-003	PUTATIVE	basic|appris_candidate_longest	protein_coding	ANKRD62	protein_coding	OTTHUMT00000452521.2	A	XM_001715728	-		12107409	+1	no_errors	ENST00000314074	ensembl	human	known	74_37	missense	SNP	0.000	G
NPIPB11	728888	genome.wustl.edu	37	16	29394193	29394193	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr16:29394193G>A	ENST00000524087.1	-	8	2134	c.2060C>T	c.(2059-2061)cCg>cTg	p.P687L	SNX29P2_ENST00000398878.3_lincRNA			E5RHQ5	NPB11_HUMAN	nuclear pore complex interacting protein family, member B11	687	Pro-rich.					integral component of membrane (GO:0016021)											GCTGACGCTCGGAAGGTGTCT	0.597																																																	0								ENSG00000254206																																			NPIPB11	SO:0001583	missense	0			-	HGNC			16p11.2	2013-06-11			ENSG00000254206	ENSG00000254206			37453	protein-coding gene	gene with protein product							Standard	XM_006721110		Approved			E5RHQ5	OTTHUMG00000170467	ENST00000524087.1:c.2060C>T	16.37:g.29394193G>A	ENSP00000430853:p.Pro687Leu	Somatic	0	27	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	5	36	12.20		Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	NULL	p.P687L	ENST00000524087.1	37	c.2060		16	.	.	.	.	.	.	.	.	.	.	g	9.720	1.159423	0.21454	.	.	ENSG00000254206	ENST00000524087	T	0.29917	1.55	.	.	.	.	.	.	.	.	T	0.19644	0.0472	N	0.19112	0.55	0.09310	N	1	.	.	.	.	.	.	T	0.26018	-1.0115	5	0.48119	T	0.1	.	.	.	.	.	.	.	.	L	687	ENSP00000430853:P687L	ENSP00000430853:P687L	P	-	2	0	RP11-231C14.2	29301694	.	.	0.002000	0.10522	0.002000	0.02628	.	.	0.073000	0.16731	0.074000	0.15403	CCG	-	NULL		0.597	NPIPB11-001	PUTATIVE	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NPIPB11	protein_coding	OTTHUMT00000374094.1	G	XM_002343430	-		29394193	-1	no_errors	ENST00000524087	ensembl	human	putative	74_37	missense	SNP	0.002	A
FER	2241	genome.wustl.edu	37	5	108207846	108207846	+	Missense_Mutation	SNP	G	G	C			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr5:108207846G>C	ENST00000281092.4	+	8	1240	c.856G>C	c.(856-858)Gaa>Caa	p.E286Q	FER_ENST00000438717.2_Missense_Mutation_p.E111Q|FER_ENST00000536402.1_Missense_Mutation_p.E286Q	NM_005246.2	NP_005237.2	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	286	Important for interaction with membranes containing phosphoinositides.				actin cytoskeleton reorganization (GO:0031532)|cell proliferation (GO:0008283)|cell-cell adhesion mediated by cadherin (GO:0044331)|cellular response to insulin stimulus (GO:0032869)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to reactive oxygen species (GO:0034614)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|diapedesis (GO:0050904)|extracellular matrix-cell signaling (GO:0035426)|Fc-epsilon receptor signaling pathway (GO:0038095)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular signal transduction (GO:0035556)|Kit signaling pathway (GO:0038109)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of mast cell activation involved in immune response (GO:0033007)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of fibroblast migration (GO:0010762)|regulation of lamellipodium assembly (GO:0010591)|regulation of protein phosphorylation (GO:0001932)|response to lipopolysaccharide (GO:0032496)|response to platelet-derived growth factor (GO:0036119)|substrate adhesion-dependent cell spreading (GO:0034446)|tyrosine phosphorylation of Stat3 protein (GO:0042503)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			NS(2)|biliary_tract(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	32		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		CTTACTGGAAGAAAATGAAAA	0.303																																					Colon(146;1051 1799 9836 27344 47401)												0								ENSG00000151422						65.0	65.0	65.0					5																	108207846		2200	4293	6493	FER	SO:0001583	missense	0			-	HGNC	J03358	CCDS4098.1	5q21	2013-02-14	2008-02-07		ENSG00000151422	ENSG00000151422	2.7.10.1	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""SH2 domain containing"""	3655	protein-coding gene	gene with protein product	"""phosphoprotein NCP94"", ""protein phosphatase 1, regulatory subunit 74"""	176942					Standard	NM_005246		Approved	TYK3, PPP1R74	uc003kop.1	P16591	OTTHUMG00000128751	ENST00000281092.4:c.856G>C	5.37:g.108207846G>C	ENSP00000281092:p.Glu286Gln	Somatic	0	33	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	20	36	34.48	B2RCR4|B4DSQ2|H2FLB8	Missense_Mutation	SNP	NA	NA	NA	NA	NA	NA	pirsf_Tyr_kinase_non-rcpt_Fes_subgr,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_dom,pfam_SH2,pfam_FCH_dom,superfamily_Kinase-like_dom,smart_FCH_dom,smart_SH2,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom,prints_SH2,pfscan_FCH_dom,pfscan_SH2,pfscan_Prot_kinase_dom	p.E286Q	ENST00000281092.4	37	c.856	CCDS4098.1	5	.	.	.	.	.	.	.	.	.	.	G	19.55	3.847828	0.71603	.	.	ENSG00000151422	ENST00000281092;ENST00000536402;ENST00000438717	T;T;T	0.75938	-0.95;1.8;-0.98	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.79335	0.4428	M	0.77103	2.36	0.80722	D	1	B	0.21606	0.058	B	0.28011	0.085	T	0.76222	-0.3038	10	0.72032	D	0.01	-14.9168	20.1708	0.98159	0.0:0.0:1.0:0.0	.	286	P16591	FER_HUMAN	Q	286;286;111	ENSP00000281092:E286Q;ENSP00000442627:E286Q;ENSP00000394297:E111Q	ENSP00000281092:E286Q	E	+	1	0	FER	108235745	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	9.293000	0.96082	2.761000	0.94854	0.655000	0.94253	GAA	-	pirsf_Tyr_kinase_non-rcpt_Fes_subgr		0.303	FER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FER	protein_coding	OTTHUMT00000250664.1	G	NM_005246	-		108207846	+1	no_errors	ENST00000281092	ensembl	human	known	74_37	missense	SNP	1.000	C
TPRKB	51002	genome.wustl.edu	37	2	73957880	73957881	+	Intron	INS	-	-	A	rs373860849		TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr2:73957880_73957881insA	ENST00000272424.5	-	4	371				TPRKB_ENST00000318190.7_Intron|TPRKB_ENST00000409716.2_Intron|TPRKB_ENST00000485758.1_5'UTR	NM_016058.2	NP_057142.1	Q9Y3C4	TPRKB_HUMAN	TP53RK binding protein						tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			lung(2)|ovary(1)|skin(1)	4						GAAAAAAAATGAAAAAAAAAAC	0.327																																																	0								ENSG00000144034																																			TPRKB	SO:0001627	intron_variant	0				HGNC	AY157986	CCDS1927.1	2p24.3-p24.1	2008-02-05			ENSG00000144034	ENSG00000144034			24259	protein-coding gene	gene with protein product		608680				10810093, 12659830	Standard	NM_016058		Approved	CGI-121	uc002sjn.2	Q9Y3C4	OTTHUMG00000129815	ENST00000272424.5:c.265-17->T	2.37:g.73957890_73957890dupA		Somatic	0	21	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	4	33	10.81	D6W5H6|Q8IWR6|Q8IWR7|Q9H3K4	RNA	INS	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000272424.5	37	NULL	CCDS1927.1	2																																																																																			-	-		0.327	TPRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	TPRKB	protein_coding	OTTHUMT00000252046.2	-	NM_016058			73957881	-1	no_errors	ENST00000485758	ensembl	human	putative	74_37	rna	INS	0.000:0.004	A
SH3BP5L	80851	genome.wustl.edu	37	1	249109041	249109041	+	Intron	SNP	A	A	C			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr1:249109041A>C	ENST00000366472.5	-	5	1605				SH3BP5L_ENST00000475978.1_5'UTR|SH3BP5L_ENST00000411742.2_Intron	NM_030645.1	NP_085148.1	Q7L8J4	3BP5L_HUMAN	SH3-binding domain protein 5-like											endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			TAGATGTGTGAAATCCAGCAC	0.393																																																	0								ENSG00000175137																																			SH3BP5L	SO:0001627	intron_variant	0			-	HGNC	AB051507	CCDS31126.1	1q44	2008-02-05			ENSG00000175137	ENSG00000175137			29360	protein-coding gene	gene with protein product							Standard	NM_030645		Approved	KIAA1720	uc001iew.1	Q7L8J4	OTTHUMG00000040389	ENST00000366472.5:c.376-232T>G	1.37:g.249109041A>C		Somatic	0	14	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	10	13	43.48	B4DQ94|Q96FI5|Q9BQH8|Q9C0E3	RNA	SNP	NA	NA	NA	NA	NA	NA	-	NULL	ENST00000366472.5	37	NULL	CCDS31126.1	1																																																																																			-	-		0.393	SH3BP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SH3BP5L	protein_coding	OTTHUMT00000097140.1	A	NM_030645	-		249109041	-1	no_errors	ENST00000475978	ensembl	human	known	74_37	rna	SNP	0.001	C
METTL2A	339175	genome.wustl.edu	37	17	60503814	60503814	+	Silent	SNP	C	C	T			TCGA-DX-A48U-01A-11D-A307-09	TCGA-DX-A48U-10A-01D-A307-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	acb75bde-21d7-4529-94e5-8c3d57b82a4d	5e3d2dc3-73c1-4ef0-b649-0be72a5ab634	g.chr17:60503814C>T	ENST00000311506.5	+	3	393	c.357C>T	c.(355-357)aaC>aaT	p.N119N		NM_181725.3	NP_859076.3	Q96IZ6	MET2A_HUMAN	methyltransferase like 2A	119					tRNA methylation (GO:0030488)		tRNA (cytosine) methyltransferase activity (GO:0016427)			breast(2)|central_nervous_system(1)|endometrium(1)|upper_aerodigestive_tract(2)	6			BRCA - Breast invasive adenocarcinoma(2;1.08e-10)			TCTTGGAGAACAAGAGTGAAG	0.393																																																	0								ENSG00000087995						108.0	86.0	92.0					17																	60503814		692	1591	2283	METTL2A	SO:0001819	synonymous_variant	0			-	HGNC	AK000991	CCDS45752.1	17q23.3	2012-12-20		2006-02-10	ENSG00000087995	ENSG00000087995			25755	protein-coding gene	gene with protein product						12477932	Standard	NM_181725		Approved	FLJ12760, METTL2	uc002izv.2	Q96IZ6	OTTHUMG00000164527	ENST00000311506.5:c.357C>T	17.37:g.60503814C>T		Somatic	0	126	0.00		0.7869283268765884	NA	NA	NA	WXS	Illumina HiSeq 2500	Phase_IV	tier1	90	86	51.14	A6NNC4|Q9H9G9|Q9NUI8|Q9P0B5	Silent	SNP	NA	NA	NA	NA	NA	NA	pfam_Methyltransf_12,pfam_Methyltransf_11,pfam_UbiE/COQ5_MeTrFase,pirsf_MeTrfase	p.N119	ENST00000311506.5	37	c.357	CCDS45752.1	17																																																																																			-	pirsf_MeTrfase		0.393	METTL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	METTL2A	protein_coding	OTTHUMT00000445130.1	C	NM_181725	-		60503814	+1	no_errors	ENST00000311506	ensembl	human	known	74_37	silent	SNP	0.000	T
