#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	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_default_gene_name	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_name_source	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_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
ANAPC15	25906	genome.wustl.edu	37	11	71818495	71818495	+	IGR	SNP	G	G	A			TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr11:71818495G>A	ENST00000227618.4	-	0	886				LRTOMT_ENST00000419228.1_Intron|LRTOMT_ENST00000439209.1_Intron|LRTOMT_ENST00000307198.7_Intron|LRTOMT_ENST00000435085.1_Intron|ANAPC15_ENST00000543015.1_5'Flank|ANAPC15_ENST00000502597.2_Nonsense_Mutation_p.Q74*|ANAPC15_ENST00000543050.1_Nonsense_Mutation_p.Q159*	NM_001278487.1|NM_001278491.1|NM_014042.2	NP_001265416.1|NP_001265420.1|NP_054761.1	P60006	APC15_HUMAN	anaphase promoting complex subunit 15						mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)	anaphase-promoting complex (GO:0005680)|intracellular (GO:0005622)											tggaagttctgagttggccag	0.478																																																	0																																										SO:0001628	intergenic_variant	25906			AL080071	CCDS8210.1, CCDS60880.1	11q13.4	2012-10-17	2012-05-31	2012-05-31	ENSG00000110200	ENSG00000110200		"""Anaphase promoting complex subunits"""	24531	protein-coding gene	gene with protein product		614717	"""chromosome 11 open reading frame 51"""	C11orf51		21926987	Standard	NM_014042		Approved	HSPC020, DKFZP564M082, APC15	uc001orw.3	P60006	OTTHUMG00000167865		11.37:g.71818495G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	G3V1Q3|Q9CXK2|Q9Y269	Nonsense_Mutation	SNP	NULL	p.Q159*	ENST00000227618.4	37	c.475	CCDS8210.1	11	.	.	.	.	.	.	.	.	.	.	G	17.56	3.420920	0.62622	.	.	ENSG00000110200	ENST00000502597;ENST00000543050	.	.	.	3.31	0.534	0.17127	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	6.2519	0.20850	0.6477:0.0:0.3523:0.0	.	.	.	.	X	74;159	.	ENSP00000441774:Q74X	Q	-	1	0	C11orf51	71496143	0.006000	0.16342	0.000000	0.03702	0.620000	0.37586	-0.150000	0.10189	0.094000	0.17404	0.462000	0.41574	CAG	ANAPC15	-	NULL		0.478	ANAPC15-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	ANAPC15	HGNC	protein_coding	OTTHUMT00000396695.1	G	NM_014042		71818495	-1	no_errors	ENST00000543050	ensembl	human	putative	70_37	nonsense	SNP	0.001	A
CDH23	64072	genome.wustl.edu	37	10	73269694	73269694	+	Intron	SNP	G	G	A			TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr10:73269694G>A	ENST00000224721.6	+	3	150				CDH23_ENST00000398809.4_Intron|CDH23_ENST00000398842.3_Intron|CDH23-AS1_ENST00000428918.1_RNA|CDH23_ENST00000299366.7_Intron|CDH23_ENST00000461841.3_Intron	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23						calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						TCCCAGATGCGCCAGGGCCTT	0.562																																																	0																																										SO:0001627	intron_variant	414246			AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.146-145G>A	10.37:g.73269694G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	RNA	SNP	-	NULL	ENST00000224721.6	37	NULL		10																																																																																			CDH23-AS1	-	-		0.562	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	CDH23-AS1	HGNC	protein_coding	OTTHUMT00000051227.4	G	NM_052836		73269694	-1	no_errors	ENST00000428918	ensembl	human	known	70_37	rna	SNP	0.000	A
CNOT2	4848	genome.wustl.edu	37	12	70729334	70729334	+	Missense_Mutation	SNP	G	G	T			TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr12:70729334G>T	ENST00000418359.3	+	9	1217	c.766G>T	c.(766-768)Gct>Tct	p.A256S	CNOT2_ENST00000551483.1_5'UTR|CNOT2_ENST00000229195.3_Missense_Mutation_p.A256S	NM_001199302.1	NP_001186231.1	Q9NZN8	CNOT2_HUMAN	CCR4-NOT transcription complex, subunit 2	256					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription from RNA polymerase II promoter (GO:0006366)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription corepressor binding (GO:0001226)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|pancreas(2)|urinary_tract(1)	20	Renal(347;0.236)		GBM - Glioblastoma multiforme(1;4.77e-09)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)			GGCTGGAAGAGCTCCTTATGG	0.413																																																	0													116.0	108.0	111.0					12																	70729334		2203	4300	6503	SO:0001583	missense	4848			AF180473	CCDS31857.1	12q15	2008-05-14				ENSG00000111596			7878	protein-coding gene	gene with protein product		604909		NOT2		10637334	Standard	NM_014515		Approved	CDC36, NOT2H	uc001svv.3	Q9NZN8		ENST00000418359.3:c.766G>T	12.37:g.70729334G>T	ENSP00000412091:p.Ala256Ser	Somatic		WXS	Illumina HiSeq	Phase_IV	Q9H3E0|Q9NSX5|Q9NWR6|Q9P028	Missense_Mutation	SNP	pfam_NOT	p.A256S	ENST00000418359.3	37	c.766	CCDS31857.1	12	.	.	.	.	.	.	.	.	.	.	G	17.30	3.355063	0.61293	.	.	ENSG00000111596	ENST00000552231;ENST00000229195;ENST00000418359;ENST00000550160;ENST00000552915;ENST00000552483;ENST00000548159;ENST00000551043;ENST00000550155	T;T;T;T;T;T;T;T;T	0.73469	-0.75;-0.75;-0.75;-0.75;-0.75;-0.75;-0.75;-0.75;-0.75	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.65873	0.2733	L	0.43152	1.355	0.80722	D	1	B	0.14805	0.011	B	0.10450	0.005	T	0.62450	-0.6852	10	0.02654	T	1	-4.7429	19.268	0.93997	0.0:0.0:1.0:0.0	.	256	Q9NZN8	CNOT2_HUMAN	S	256;256;256;119;195;110;247;256;66	ENSP00000450318:A256S;ENSP00000229195:A256S;ENSP00000412091:A256S;ENSP00000448490:A119S;ENSP00000447497:A195S;ENSP00000450077:A110S;ENSP00000449659:A247S;ENSP00000449260:A256S;ENSP00000448499:A66S	ENSP00000229195:A256S	A	+	1	0	CNOT2	69015601	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.974000	0.88039	2.622000	0.88805	0.650000	0.86243	GCT	CNOT2	-	NULL		0.413	CNOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CNOT2	HGNC	protein_coding	OTTHUMT00000404260.1	G			70729334	+1	no_errors	ENST00000229195	ensembl	human	known	70_37	missense	SNP	1.000	T
DCAF12L1	139170	genome.wustl.edu	37	X	125686155	125686155	+	Missense_Mutation	SNP	T	T	C			TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chrX:125686155T>C	ENST00000371126.1	-	1	679	c.437A>G	c.(436-438)gAc>gGc	p.D146G		NM_178470.4	NP_848565.2	Q5VU92	DC121_HUMAN	DDB1 and CUL4 associated factor 12-like 1	146										breast(1)|central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(39)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68						GCCCTGTTGGTCCTGGGCCAG	0.632																																																	0													94.0	82.0	86.0					X																	125686155		2203	4300	6503	SO:0001583	missense	139170			BC035674	CCDS14610.1	Xq25	2013-01-09	2009-07-17	2009-07-17	ENSG00000198889	ENSG00000198889		"""WD repeat domain containing"""	29395	protein-coding gene	gene with protein product			"""WD repeat domain 40B"""	WDR40B		12477932	Standard	NM_178470		Approved	KIAA1892L	uc004eul.3	Q5VU92	OTTHUMG00000022353	ENST00000371126.1:c.437A>G	X.37:g.125686155T>C	ENSP00000360167:p.Asp146Gly	Somatic		WXS	Illumina HiSeq	Phase_IV	Q8IYK3	Missense_Mutation	SNP	pfam_WD40_repeat,superfamily_WD40_repeat_dom,smart_WD40_repeat,pfscan_WD40_repeat,pfscan_WD40_repeat_dom	p.D146G	ENST00000371126.1	37	c.437	CCDS14610.1	X	.	.	.	.	.	.	.	.	.	.	T	0.134	-1.109875	0.01813	.	.	ENSG00000198889	ENST00000371126	T	0.29655	1.56	3.49	-4.42	0.03579	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	.	.	.	.	T	0.08223	0.0205	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25363	-1.0134	9	0.20519	T	0.43	.	2.0774	0.03628	0.1049:0.2691:0.1939:0.4321	.	146	Q5VU92	DC121_HUMAN	G	146	ENSP00000360167:D146G	ENSP00000360167:D146G	D	-	2	0	DCAF12L1	125513836	0.710000	0.27896	0.000000	0.03702	0.004000	0.04260	0.929000	0.28844	-1.191000	0.02695	-0.802000	0.03209	GAC	DCAF12L1	-	superfamily_WD40_repeat_dom		0.632	DCAF12L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DCAF12L1	HGNC	protein_coding	OTTHUMT00000058186.1	T	NM_178470		125686155	-1	no_errors	ENST00000371126	ensembl	human	known	70_37	missense	SNP	0.001	C
DIP2B	57609	genome.wustl.edu	37	12	51138529	51138529	+	Silent	SNP	G	G	A	rs546140546	byFrequency	TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr12:51138529G>A	ENST00000301180.5	+	38	4672	c.4638G>A	c.(4636-4638)ccG>ccA	p.P1546P	Y_RNA_ENST00000363558.1_RNA	NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)	1546						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(15)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	60						GTGTCATCCCGATCAACTCCA	0.532													G|||	2	0.000399361	0.0	0.0	5008	,	,		19143	0.0		0.0	False		,,,				2504	0.002																0													142.0	113.0	123.0					12																	51138529		2203	4300	6503	SO:0001819	synonymous_variant	57609			AB040896	CCDS31799.1	12q13.12	2012-10-02	2006-01-13		ENSG00000066084	ENSG00000066084			29284	protein-coding gene	gene with protein product		611379					Standard	XM_005269044		Approved	KIAA1463, FLJ34278	uc001rwv.3	Q9P265	OTTHUMG00000169475	ENST00000301180.5:c.4638G>A	12.37:g.51138529G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	Q6B011|Q8N1L5|Q8NB38	Silent	SNP	pfam_AMP-dep_Synth/Lig,pfam_DMAP1-bd	p.P1546	ENST00000301180.5	37	c.4638	CCDS31799.1	12																																																																																			DIP2B	-	NULL		0.532	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	DIP2B	HGNC	protein_coding	OTTHUMT00000404243.1	G	NM_173602		51138529	+1	no_errors	ENST00000301180	ensembl	human	known	70_37	silent	SNP	0.734	A
POLR2J2	246721	genome.wustl.edu	37	7	102313428	102313428	+	5'Flank	SNP	G	G	A	rs369917945		TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr7:102313428G>A	ENST00000476151.1	-	0	0				POLR2J2_ENST00000358438.5_5'Flank|POLR2J2_ENST00000591000.1_5'Flank|POLR2J2_ENST00000333432.6_5'Flank			Q9GZM3	RPB1B_HUMAN	polymerase (RNA) II (DNA directed) polypeptide J2						transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			skin(1)	1						ttagcagaccgggaaagggag	0.577																																																	0																																										SO:0001631	upstream_gene_variant	0				CCDS43627.1	7q22.1	2014-08-12			ENSG00000228049	ENSG00000267645		"""RNA polymerase subunits"""	23208	protein-coding gene	gene with protein product		609881				15586814	Standard	NM_032959		Approved	RPB11b1	uc010lij.2	Q9GZM3	OTTHUMG00000150388		7.37:g.102313428G>A	Exception_encountered	Somatic		WXS	Illumina HiSeq	Phase_IV	F6W009|Q9H1A8	Silent	SNP	NULL	p.P127	ENST00000476151.1	37	c.381	CCDS43627.1	7																																																																																			AC105052.1	-	NULL		0.577	POLR2J2-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	ENSG00000205233	Clone_based_ensembl_gene	protein_coding	OTTHUMT00000453068.1	G			102313428	-1	no_errors	ENST00000542270	ensembl	human	known	70_37	silent	SNP	0.000	A
GLUD1P2	100381203	genome.wustl.edu	37	10	48968566	48968566	+	RNA	SNP	A	A	G	rs201727873		TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr10:48968566A>G	ENST00000594520.1	+	0	723									glutamate dehydrogenase 1 pseudogene 2																		ACAGGATAACAAACTGGAAAA	0.318																																																	0																																												0			X66313, X66315, X66319		10q11.22	2013-02-15	2010-01-18	2010-01-18	ENSG00000227781				4337	pseudogene	pseudogene			"""glutamate dehydrogenase pseudogene 2"""	GLUDP2		8486350	Standard			Approved				OTTHUMG00000018156		10.37:g.48968566A>G		Somatic		WXS	Illumina HiSeq	Phase_IV		RNA	SNP	-	NULL	ENST00000594520.1	37	NULL		10																																																																																			GLUDP2	-	-		0.318	GLUD1P2-003	KNOWN	basic	processed_transcript	ENSG00000227781	Clone_based_vega_gene	pseudogene	OTTHUMT00000461126.1	A	NG_016765		48968566	+1	no_errors	ENST00000438010	ensembl	human	known	70_37	rna	SNP	0.999	G
EPHA3	2042	genome.wustl.edu	37	3	89391151	89391151	+	Missense_Mutation	SNP	C	C	G			TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr3:89391151C>G	ENST00000336596.2	+	5	1442	c.1217C>G	c.(1216-1218)aCc>aGc	p.T406S	EPHA3_ENST00000452448.2_Missense_Mutation_p.T406S|EPHA3_ENST00000494014.1_Missense_Mutation_p.T406S	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	406	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		ACTAACTACACCTTTGAGATT	0.517										TSP Lung(6;0.00050)																																							0													94.0	77.0	83.0					3																	89391151		2203	4300	6503	SO:0001583	missense	2042			M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3387	protein-coding gene	gene with protein product		179611	"""EphA3"""	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.1217C>G	3.37:g.89391151C>G	ENSP00000337451:p.Thr406Ser	Somatic		WXS	Illumina HiSeq	Phase_IV	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	pirsf_Tyr_kinase_ephrin_rcpt,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Ephrin_rcpt_lig-bd_dom,pfam_Prot_kinase_cat_dom,pfam_Fibronectin_type3,pfam_SAM_2,pfam_SAM_type1,pfam_Tyr-kin_ephrin_A/B_rcpt-like,superfamily_Galactose-bd-like,superfamily_Kinase-like_dom,superfamily_Fibronectin_type3,superfamily_SAM/pointed,superfamily_Growth_fac_rcpt,smart_Ephrin_rcpt_lig-bd_dom,smart_Fibronectin_type3,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_SAM,prints_Ser-Thr/Tyr_kinase_cat_dom,pfscan_Fibronectin_type3,pfscan_SAM,pfscan_Prot_kinase_cat_dom	p.T406S	ENST00000336596.2	37	c.1217	CCDS2922.1	3	.	.	.	.	.	.	.	.	.	.	C	19.11	3.764184	0.69878	.	.	ENSG00000044524	ENST00000336596;ENST00000452448;ENST00000494014	T;T;T	0.57752	0.38;0.38;0.38	5.66	5.66	0.87406	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.71500	0.3347	M	0.65320	2	0.80722	D	1	D;B	0.76494	0.999;0.385	D;B	0.79108	0.992;0.118	T	0.68198	-0.5472	9	.	.	.	.	20.1253	0.97977	0.0:1.0:0.0:0.0	.	406;406	P29320;P29320-2	EPHA3_HUMAN;.	S	406	ENSP00000337451:T406S;ENSP00000399926:T406S;ENSP00000419190:T406S	.	T	+	2	0	EPHA3	89473841	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.814000	0.62627	2.832000	0.97577	0.655000	0.94253	ACC	EPHA3	-	pirsf_Tyr_kinase_ephrin_rcpt,pfam_Fibronectin_type3,superfamily_Fibronectin_type3,smart_Fibronectin_type3,pfscan_Fibronectin_type3		0.517	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EPHA3	HGNC	protein_coding	OTTHUMT00000352995.1	C	NM_005233		89391151	+1	no_errors	ENST00000336596	ensembl	human	known	70_37	missense	SNP	1.000	G
FAT3	120114	genome.wustl.edu	37	11	92532414	92532414	+	Missense_Mutation	SNP	G	G	A			TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr11:92532414G>A	ENST00000298047.6	+	9	6252	c.6235G>A	c.(6235-6237)Gac>Aac	p.D2079N	FAT3_ENST00000409404.2_Missense_Mutation_p.D2079N|FAT3_ENST00000525166.1_Missense_Mutation_p.D1929N			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2079	Cadherin 18. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				AGACATAAATGACAATTCTCC	0.493										TCGA Ovarian(4;0.039)																																							0													72.0	77.0	76.0					11																	92532414		1983	4165	6148	SO:0001583	missense	120114			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.6235G>A	11.37:g.92532414G>A	ENSP00000298047:p.Asp2079Asn	Somatic		WXS	Illumina HiSeq	Phase_IV	B5MDB0|Q96AU6	Missense_Mutation	SNP	pfam_Cadherin,pfam_Laminin_G,pfam_EGF-like_Ca-bd,superfamily_ConA-like_lec_gl_sf,superfamily_Cadherin-like,smart_Cadherin,smart_EG-like_dom,smart_Laminin_G,smart_EGF-like_Ca-bd,pfscan_EG-like_dom,pfscan_Laminin_G,pfscan_Cadherin,prints_Cadherin	p.D2079N	ENST00000298047.6	37	c.6235		11	.	.	.	.	.	.	.	.	.	.	G	24.1	4.491252	0.84962	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.71579	-0.58;-0.58;-0.58	5.9	5.9	0.94986	.	.	.	.	.	D	0.89121	0.6625	M	0.93375	3.41	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90882	0.4754	9	0.87932	D	0	.	20.2822	0.98520	0.0:0.0:1.0:0.0	.	2079	Q8TDW7-3	.	N	2079;2079;1929	ENSP00000298047:D2079N;ENSP00000387040:D2079N;ENSP00000432586:D1929N	ENSP00000298047:D2079N	D	+	1	0	FAT3	92172062	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.787000	0.99055	2.806000	0.96561	0.655000	0.94253	GAC	FAT3	-	superfamily_Cadherin-like,smart_Cadherin,pfscan_Cadherin		0.493	FAT3-201	KNOWN	basic	protein_coding	FAT3	HGNC	protein_coding		G	NM_001008781		92532414	+1	no_errors	ENST00000298047	ensembl	human	known	70_37	missense	SNP	1.000	A
FREM3	166752	genome.wustl.edu	37	4	144617512	144617512	+	Silent	SNP	A	A	T			TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr4:144617512A>T	ENST00000329798.5	-	1	4316	c.4317T>A	c.(4315-4317)ggT>ggA	p.G1439G		NM_001168235.1	NP_001161707.1	P0C091	FREM3_HUMAN	FRAS1 related extracellular matrix 3	1439					cell adhesion (GO:0007155)|cell communication (GO:0007154)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|prostate(1)	8						TCACTCTGGCACCTTCTATCA	0.468																																																	0													312.0	245.0	265.0					4																	144617512		692	1591	2283	SO:0001819	synonymous_variant	166752			BX091796	CCDS54808.1	4q31.21	2011-06-09			ENSG00000183090	ENSG00000183090			25172	protein-coding gene	gene with protein product		608946				15345741	Standard	NM_001168235		Approved		uc021xsj.1	P0C091	OTTHUMG00000161577	ENST00000329798.5:c.4317T>A	4.37:g.144617512A>T		Somatic		WXS	Illumina HiSeq	Phase_IV		Silent	SNP	pfam_Calx_beta,superfamily_Cadherin-like,smart_Calx_beta	p.G1439	ENST00000329798.5	37	c.4317	CCDS54808.1	4																																																																																			FREM3	-	NULL		0.468	FREM3-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	FREM3	HGNC	protein_coding	OTTHUMT00000365391.1	A	XM_094074		144617512	-1	no_errors	ENST00000329798	ensembl	human	putative	70_37	silent	SNP	0.023	T
GABRB3	2562	genome.wustl.edu	37	15	26806135	26806135	+	Missense_Mutation	SNP	G	G	T			TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr15:26806135G>T	ENST00000311550.5	-	8	1135	c.1024C>A	c.(1024-1026)Ctt>Att	p.L342I	GABRB3_ENST00000541819.2_Missense_Mutation_p.L398I|GABRB3_ENST00000400188.3_Missense_Mutation_p.L271I|GABRB3_ENST00000299267.4_Missense_Mutation_p.L342I|GABRB3_ENST00000545868.1_Missense_Mutation_p.L257I	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	342					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|GABA-gated chloride ion channel activity (GO:0022851)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TTTTCTGCAAGCTTCTTCTGC	0.517																																																	0													180.0	191.0	187.0					15																	26806135		2203	4300	6503	SO:0001583	missense	2562				CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4083	protein-coding gene	gene with protein product	"""GABA(A) receptor, beta 3"""	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.1024C>A	15.37:g.26806135G>T	ENSP00000308725:p.Leu342Ile	Somatic		WXS	Illumina HiSeq	Phase_IV	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Missense_Mutation	SNP	pfam_Neurotrans-gated_channel_TM,pfam_Neur_chan_lig-bd,superfamily_Neur_chan_lig-bd,superfamily_Neurotrans-gated_channel_TM,prints_GABAA_rcpt,prints_GABAAb_rcpt,prints_Neur_channel,prints_GABBAg_rcpt,tigrfam_Neur_channel	p.L342I	ENST00000311550.5	37	c.1024	CCDS10019.1	15	.	.	.	.	.	.	.	.	.	.	G	15.43	2.831652	0.50845	.	.	ENSG00000166206	ENST00000311550;ENST00000541819;ENST00000299267;ENST00000400188;ENST00000545868	D;D;D;D;D	0.85773	-2.03;-2.03;-2.03;-2.03;-2.03	5.19	4.27	0.50696	Neurotransmitter-gated ion-channel transmembrane domain (2);	.	.	.	.	T	0.79393	0.4438	L	0.39467	1.215	0.53688	D	0.999973	B;B;B	0.16396	0.017;0.004;0.009	B;B;B	0.18263	0.021;0.007;0.008	T	0.75169	-0.3412	9	0.37606	T	0.19	.	13.2454	0.60020	0.078:0.0:0.922:0.0	.	398;342;342	F5H7N0;P28472-2;P28472	.;.;GBRB3_HUMAN	I	342;398;342;271;257	ENSP00000308725:L342I;ENSP00000442408:L398I;ENSP00000299267:L342I;ENSP00000383049:L271I;ENSP00000439169:L257I	ENSP00000299267:L342I	L	-	1	0	GABRB3	24357228	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.439000	0.52878	2.416000	0.81992	0.655000	0.94253	CTT	GABRB3	-	pfam_Neurotrans-gated_channel_TM,superfamily_Neurotrans-gated_channel_TM,prints_GABBAg_rcpt,tigrfam_Neur_channel		0.517	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	GABRB3	HGNC	protein_coding	OTTHUMT00000251352.2	G			26806135	-1	no_errors	ENST00000299267	ensembl	human	known	70_37	missense	SNP	1.000	T
HIVEP1	3096	genome.wustl.edu	37	6	12164277	12164277	+	Silent	SNP	G	G	A			TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr6:12164277G>A	ENST00000379388.2	+	9	8072	c.7740G>A	c.(7738-7740)gaG>gaA	p.E2580E	HIVEP1_ENST00000541134.1_Silent_p.E445E	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	2580					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				AAGCATGCGAGACACAACCCA	0.522																																																	0													73.0	80.0	78.0					6																	12164277		2035	4195	6230	SO:0001819	synonymous_variant	3096			J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"""Zinc fingers, C2H2-type"""	4920	protein-coding gene	gene with protein product		194540	"""human immunodeficiency virus type I enhancer-binding protein 1"", ""zinc finger protein 40"""	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.7740G>A	6.37:g.12164277G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	B2RTU3|Q14122|Q5MPB1|Q5VW60	Silent	SNP	smart_Znf_C2H2-like,pfscan_Znf_C2H2	p.E2580	ENST00000379388.2	37	c.7740	CCDS43426.1	6																																																																																			HIVEP1	-	NULL		0.522	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HIVEP1	HGNC	protein_coding	OTTHUMT00000039870.2	G	NM_002114		12164277	+1	no_errors	ENST00000379388	ensembl	human	known	70_37	silent	SNP	0.000	A
KDR	3791	genome.wustl.edu	37	4	55973990	55973990	+	Silent	SNP	C	C	T	rs41279537		TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr4:55973990C>T	ENST00000263923.4	-	10	1621	c.1326G>A	c.(1324-1326)acG>acA	p.T442T		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	442	Ig-like C2-type 5.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TACATGTCAGCGTTTGAGTGG	0.512			Mis		"""NSCLC, angiosarcoma"""					TSP Lung(20;0.16)																														Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	0													241.0	202.0	215.0					4																	55973990		2203	4300	6503	SO:0001819	synonymous_variant	3791			AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.1326G>A	4.37:g.55973990C>T		Somatic		WXS	Illumina HiSeq	Phase_IV	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Silent	SNP	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Ig_I-set,pfam_Prot_kinase_cat_dom,pfam_Ig_V-set,pfam_Immunoglobulin,pfam_CD80_C2-set,superfamily_Kinase-like_dom,smart_Ig_sub,smart_Ig_sub2,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom,pfscan_Ig-like,prints_Tyr_kinase_VEGFR2_rcpt,prints_Tyr_kinase_VEGFR_rcpt_N	p.T442	ENST00000263923.4	37	c.1326	CCDS3497.1	4																																																																																			KDR	-	smart_Ig_sub,smart_Ig_sub2,pfscan_Ig-like,prints_Tyr_kinase_VEGFR_rcpt_N		0.512	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KDR	HGNC	protein_coding	OTTHUMT00000250645.1	C			55973990	-1	no_errors	ENST00000263923	ensembl	human	known	70_37	silent	SNP	0.000	T
MAP3K9	4293	genome.wustl.edu	37	14	71197432	71197432	+	Missense_Mutation	SNP	G	G	A			TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr14:71197432G>A	ENST00000554752.2	-	12	2979	c.2980C>T	c.(2980-2982)Cgg>Tgg	p.R994W	MAP3K9_ENST00000381250.4_Missense_Mutation_p.R971W|MAP3K9_ENST00000555993.2_Missense_Mutation_p.R1008W|MAP3K9_ENST00000554146.1_Missense_Mutation_p.R722W|MAP3K9_ENST00000553414.1_Missense_Mutation_p.R727W	NM_001284230.1	NP_001271159.1	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase 9	994					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		ATP binding (GO:0005524)|JUN kinase kinase kinase activity (GO:0004706)|MAP kinase kinase activity (GO:0004708)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		GGACGCGGCCGAGGCAGAAAC	0.627																																					GBM(114;411 1587 13539 28235 50070)												0													46.0	49.0	48.0					14																	71197432		2203	4300	6503	SO:0001583	missense	4293			AF251442	CCDS32112.1, CCDS61485.1, CCDS61488.1, CCDS73650.1	14q24.2	2012-10-02			ENSG00000006432	ENSG00000006432		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6861	protein-coding gene	gene with protein product		600136		MLK1			Standard	NM_001284231		Approved	PRKE1, MEKK9	uc001xml.3	P80192	OTTHUMG00000171249	ENST00000554752.2:c.2980C>T	14.37:g.71197432G>A	ENSP00000451612:p.Arg994Trp	Somatic		WXS	Illumina HiSeq	Phase_IV	A3KN85|Q0D2G7|Q6EH31|Q9H2N5	Missense_Mutation	SNP	pirsf_MAPKKK9/10/11,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_cat_dom,pfam_SH3_2,pfam_SH3_domain,superfamily_Kinase-like_dom,superfamily_SH3_domain,superfamily_Regulat_G_prot_signal_superfam,smart_SH3_domain,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom,prints_SH3_domain,pfscan_SH3_domain,pfscan_Prot_kinase_cat_dom	p.R1008W	ENST00000554752.2	37	c.3022		14	.	.	.	.	.	.	.	.	.	.	G	15.91	2.972002	0.53614	.	.	ENSG00000006432	ENST00000554752;ENST00000005198;ENST00000553414;ENST00000381250;ENST00000554146;ENST00000542284	D;D;D;D	0.85556	-1.68;-2.0;-1.7;-1.74	4.84	3.93	0.45458	.	0.054353	0.64402	D	0.000001	D	0.89918	0.6854	L	0.57536	1.79	0.48830	D	0.999718	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.965;0.994;0.998	D	0.90446	0.4435	10	0.87932	D	0	.	12.3629	0.55213	0.0:0.0:0.5715:0.4285	.	722;994;1008;727	G3V4P9;P80192;P80192-4;G3V347	.;M3K9_HUMAN;.;.	W	994;1008;727;971;722;710	ENSP00000451612:R994W;ENSP00000451038:R727W;ENSP00000370649:R971W;ENSP00000451921:R722W	ENSP00000005198:R1008W	R	-	1	2	MAP3K9	70267185	0.998000	0.40836	1.000000	0.80357	0.669000	0.39330	2.587000	0.46128	1.240000	0.43803	0.655000	0.94253	CGG	MAP3K9	-	pirsf_MAPKKK9/10/11		0.627	MAP3K9-001	KNOWN	basic	protein_coding	MAP3K9	HGNC	protein_coding	OTTHUMT00000412550.2	G			71197432	-1	no_errors	ENST00000555993	ensembl	human	known	70_37	missense	SNP	0.953	A
MAPK1	5594	genome.wustl.edu	37	22	22127164	22127164	+	Missense_Mutation	SNP	C	C	T			TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr22:22127164C>T	ENST00000215832.6	-	7	1152	c.964G>A	c.(964-966)Gag>Aag	p.E322K	MAPK1_ENST00000544786.1_Missense_Mutation_p.E278K|MAPK1_ENST00000398822.3_Missense_Mutation_p.E322K	NM_002745.4	NP_002736.3	P28482	MK01_HUMAN	mitogen-activated protein kinase 1	322					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|caveolin-mediated endocytosis (GO:0072584)|cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|chemotaxis (GO:0006935)|cytosine metabolic process (GO:0019858)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|labyrinthine layer blood vessel development (GO:0060716)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mammary gland epithelial cell proliferation (GO:0033598)|MAPK cascade (GO:0000165)|MAPK import into nucleus (GO:0000189)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell differentiation (GO:0045596)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|Ras protein signal transduction (GO:0007265)|regulation of cytoskeleton organization (GO:0051493)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of protein stability (GO:0031647)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of stress-activated MAPK cascade (GO:0032872)|response to epidermal growth factor (GO:0070849)|response to estrogen (GO:0043627)|response to exogenous dsRNA (GO:0043330)|response to stress (GO:0006950)|response to toxic substance (GO:0009636)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perikaryon (GO:0043204)|protein complex (GO:0043234)|pseudopodium (GO:0031143)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MAP kinase activity (GO:0004707)|phosphatase binding (GO:0019902)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)	p.E322K(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Colorectal(54;0.105)	all_lung(157;3.89e-05)		READ - Rectum adenocarcinoma(21;0.0689)	Arsenic trioxide(DB01169)|Isoprenaline(DB01064)	GCTCTTACCTCGTCACTCGGG	0.478																																																	1	Substitution - Missense(1)	cervix(1)											165.0	132.0	143.0					22																	22127164		2203	4300	6503	SO:0001583	missense	5594			M84489	CCDS13795.1	22q11.2	2014-09-17			ENSG00000100030	ENSG00000100030	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinases"""	6871	protein-coding gene	gene with protein product		176948		PRKM2, PRKM1			Standard	NM_138957		Approved	ERK, ERK2, p41mapk, MAPK2	uc002zvn.3	P28482	OTTHUMG00000030508	ENST00000215832.6:c.964G>A	22.37:g.22127164C>T	ENSP00000215832:p.Glu322Lys	Somatic		WXS	Illumina HiSeq	Phase_IV	A8CZ64	Missense_Mutation	SNP	pfam_Prot_kinase_cat_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_cat_dom,prints_MAPK_ERK1/2,prints_MAPK_ERK3/4	p.E322K	ENST00000215832.6	37	c.964	CCDS13795.1	22	.	.	.	.	.	.	.	.	.	.	C	35	5.567659	0.96540	.	.	ENSG00000100030	ENST00000215832;ENST00000415911;ENST00000398822;ENST00000544786	T;T;T	0.46063	0.88;0.88;0.88	4.9	4.9	0.64082	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.79275	0.4418	H	0.98388	4.22	0.80722	D	1	D;D	0.89917	0.999;1.0	P;D	0.83275	0.905;0.996	D	0.87609	0.2502	10	0.87932	D	0	-8.3311	18.6384	0.91386	0.0:1.0:0.0:0.0	.	278;322	A8CZ64;P28482	.;MK01_HUMAN	K	322;310;322;278	ENSP00000215832:E322K;ENSP00000381803:E322K;ENSP00000440842:E278K	ENSP00000215832:E322K	E	-	1	0	MAPK1	20457164	1.000000	0.71417	0.999000	0.59377	0.862000	0.49288	7.564000	0.82326	2.706000	0.92434	0.655000	0.94253	GAG	MAPK1	-	superfamily_Kinase-like_dom,prints_MAPK_ERK1/2		0.478	MAPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	MAPK1	HGNC	protein_coding	OTTHUMT00000075396.2	C			22127164	-1	no_errors	ENST00000215832	ensembl	human	known	70_37	missense	SNP	1.000	T
GLIDR	389741	genome.wustl.edu	37	9	66553736	66553736	+	lincRNA	SNP	C	C	T	rs17852433		TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr9:66553736C>T	ENST00000305709.5	+	0	349				RP11-262H14.3_ENST00000445604.2_lincRNA	NR_015363.1																						GTCCGTTTTCCGCTGCCGCTG	0.582																																																	0																																												0																															9.37:g.66553736C>T		Somatic		WXS	Illumina HiSeq	Phase_IV		RNA	SNP	-	NULL	ENST00000305709.5	37	NULL		9	.	.	.	.	.	.	.	.	.	.	.	5.414	0.261494	0.10239	.	.	ENSG00000170161	ENST00000305709	.	.	.	.	.	.	.	.	.	.	.	T	0.48822	0.1521	.	.	.	.	.	.	.	.	.	.	.	.	T	0.59150	-0.7508	2	0.87932	D	0	.	.	.	.	rs17852433	.	.	.	L	63	.	ENSP00000303136:P63L	P	+	2	0	RP11-262H14.4	66293556	0.040000	0.19996	0.106000	0.21319	0.108000	0.19459	0.239000	0.18023	0.149000	0.19098	0.152000	0.16155	CCG	RP11-262H14.4	-	-		0.582	RP11-262H14.4-001	KNOWN	basic	lincRNA	MGC21881	Clone_based_vega_gene	lincRNA	OTTHUMT00000037077.1	C			66553736	+1	no_errors	ENST00000305709	ensembl	human	known	70_37	rna	SNP	0.118	T
MT-CO1	4512	genome.wustl.edu	37	M	3179	3179	+	5'Flank	SNP	G	G	A			TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chrM:3179G>A	ENST00000361624.2	+	0	0				MT-TV_ENST00000387342.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-RNR1_ENST00000389680.2_RNA|MT-TC_ENST00000387405.1_RNA|MT-ND2_ENST00000361453.3_5'Flank|MT-TL1_ENST00000386347.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-ND1_ENST00000361390.2_5'Flank|MT-TI_ENST00000387365.1_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-TW_ENST00000387382.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-TF_ENST00000387314.1_RNA			P00395	COX1_HUMAN	mitochondrially encoded cytochrome c oxidase I						aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex IV (GO:0005751)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(4)|endometrium(25)|kidney(19)|lung(3)|prostate(3)	54						CCCCCGTAAATGATATCATCT	0.433																																																	0																																										SO:0001631	upstream_gene_variant	100616263					mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198804	ENSG00000198804		"""Mitochondrial respiratory chain complex / Complex IV"""	7419	protein-coding gene	gene with protein product		516030	"""cytochrome c oxidase I"""	MTCO1		7219534	Standard			Approved	COX1, COI		P00395			M.37:g.3179G>A	Exception_encountered	Somatic		WXS	Illumina HiSeq	Phase_IV	Q34770	RNA	SNP	-	NULL	ENST00000361624.2	37	NULL		MT																																																																																			MIR4485	-	-		0.433	MT-CO1-201	KNOWN	basic|appris_principal	protein_coding	MIR4485	HGNC	protein_coding		G	YP_003024028		3179	+1	no_errors	ENST00000387347	ensembl	human	known	70_37	rna	SNP	NULL	A
MYO15A	51168	genome.wustl.edu	37	17	18067132	18067132	+	Missense_Mutation	SNP	T	T	C			TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr17:18067132T>C	ENST00000205890.5	+	60	10105	c.9767T>C	c.(9766-9768)aTc>aCc	p.I3256T	MYO15A_ENST00000451725.2_Missense_Mutation_p.I148T|MYO15A_ENST00000418233.3_Missense_Mutation_p.I520T	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	3256	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.|Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					GAATATGTTATCTTCGTTGTC	0.587																																																	0													76.0	79.0	78.0					17																	18067132		2045	4197	6242	SO:0001583	missense	51168			AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.9767T>C	17.37:g.18067132T>C	ENSP00000205890:p.Ile3256Thr	Somatic		WXS	Illumina HiSeq	Phase_IV	B4DFC7	Missense_Mutation	SNP	pfam_Myosin_head_motor_dom,pfam_MyTH4_dom,pfam_SH3_2,pfam_FERM_central,pfam_IQ_motif_EF-hand-BS,superfamily_FERM_central,superfamily_SH3_domain,smart_Myosin_head_motor_dom,smart_IQ_motif_EF-hand-BS,smart_MyTH4_dom,smart_SH3_domain,smart_Band_41_domain,pfscan_FERM_domain,pfscan_IQ_motif_EF-hand-BS,pfscan_MyTH4_dom,prints_Myosin_head_motor_dom	p.I3256T	ENST00000205890.5	37	c.9767	CCDS42271.1	17	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.1|23.1	4.376398|4.376398	0.82682|0.82682	.|.	.|.	ENSG00000091536|ENSG00000091536	ENST00000205890;ENST00000418233;ENST00000451725|ENST00000445289	D;D|.	0.97642|.	-2.45;-4.47|.	4.94|4.94	4.94|4.94	0.65067|0.65067	Band 4.1 domain (1);FERM domain (1);|.	.|.	.|.	.|.	.|.	T|T	0.64832|0.64832	0.2634|0.2634	L|L	0.50333|0.50333	1.59|1.59	0.50313|0.50313	D|D	0.999862|0.999862	P;P;P;D;D;D|D	0.58970|0.61080	0.949;0.839;0.871;0.979;0.983;0.984|0.989	P;B;P;P;P;P|P	0.53266|0.55087	0.621;0.432;0.623;0.702;0.722;0.632|0.768	T|T	0.68093|0.68093	-0.5500|-0.5500	9|8	0.62326|0.59425	D|D	0.03|0.04	.|.	14.7596|14.7596	0.69596|0.69596	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	148;245;520;3256;178;263|5	B4DQJ3;B4DLV9;B4DFC7;Q9UKN7;Q7Z382;Q8TCK0|B4DMU9	.;.;.;MYO15_HUMAN;.;.|.	T|P	3256;245;148|5	ENSP00000205890:I3256T;ENSP00000409098:I148T|.	ENSP00000205890:I3256T|ENSP00000401827:S5P	I|S	+|+	2|1	0|0	MYO15A|MYO15A	18007857|18007857	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.890000|0.890000	0.51754|0.51754	7.573000|7.573000	0.82421|0.82421	2.078000|2.078000	0.62432|0.62432	0.459000|0.459000	0.35465|0.35465	ATC|TCT	MYO15A	-	smart_Band_41_domain,pfscan_FERM_domain		0.587	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MYO15A	HGNC	protein_coding	OTTHUMT00000132048.1	T	NM_016239		18067132	+1	no_errors	ENST00000205890	ensembl	human	known	70_37	missense	SNP	1.000	C
NBPF1	55672	genome.wustl.edu	37	1	16889985	16889985	+	3'UTR	SNP	T	T	C	rs6603880	byFrequency	TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr1:16889985T>C	ENST00000430580.2	-	0	4760					NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1							cytoplasm (GO:0005737)									UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		ATCCCTCCTGTGTTAAAGATG	0.428																																																	0																																										SO:0001624	3_prime_UTR_variant	55672			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481		"""neuroblastoma breakpoint family"""	26088	protein-coding gene	gene with protein product		610501				11214970, 16079250	Standard	NM_017940		Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.*453A>G	1.37:g.16889985T>C		Somatic		WXS	Illumina HiSeq	Phase_IV	Q8N4E8|Q9C0H0	RNA	SNP	-	NULL	ENST00000430580.2	37	NULL		1																																																																																			NBPF1	-	-		0.428	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NBPF1	HGNC	protein_coding	OTTHUMT00000106436.3	T	NM_017940		16889985	-1	no_errors	ENST00000401007	ensembl	human	known	70_37	rna	SNP	0.040	C
NDST3	9348	genome.wustl.edu	37	4	119163280	119163280	+	Missense_Mutation	SNP	A	A	G			TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr4:119163280A>G	ENST00000296499.5	+	12	2778	c.2375A>G	c.(2374-2376)cAt>cGt	p.H792R		NM_004784.2	NP_004775.1	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	792	Heparan sulfate N-sulfotransferase 3.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	54						GTCTTGCCTCATTATAATTAC	0.318																																																	0													104.0	109.0	108.0					4																	119163280		2203	4300	6503	SO:0001583	missense	9348			AF074924	CCDS3708.1	4q26	2008-08-04			ENSG00000164100	ENSG00000164100		"""Sulfotransferases, membrane-bound"""	7682	protein-coding gene	gene with protein product		603950				9915799	Standard	NM_004784		Approved	HSST3	uc003ibx.3	O95803	OTTHUMG00000132959	ENST00000296499.5:c.2375A>G	4.37:g.119163280A>G	ENSP00000296499:p.His792Arg	Somatic		WXS	Illumina HiSeq	Phase_IV	B4DI67|Q4W5C1|Q4W5D0|Q6UWC5|Q9UP21	Missense_Mutation	SNP	pfam_Heparan_SO4_deacetylase,pfam_Sulfotransferase_dom	p.H792R	ENST00000296499.5	37	c.2375	CCDS3708.1	4	.	.	.	.	.	.	.	.	.	.	A	12.52	1.963917	0.34659	.	.	ENSG00000164100	ENST00000296499	D	0.81739	-1.53	5.73	5.73	0.89815	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	T	0.67562	0.2906	N	0.12920	0.275	0.80722	D	1	B	0.06786	0.001	B	0.12837	0.008	T	0.62412	-0.6860	10	0.21014	T	0.42	.	16.0239	0.80528	1.0:0.0:0.0:0.0	.	792	O95803	NDST3_HUMAN	R	792	ENSP00000296499:H792R	ENSP00000296499:H792R	H	+	2	0	NDST3	119382728	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.766000	0.62279	2.179000	0.69175	0.533000	0.62120	CAT	NDST3	-	pfam_Sulfotransferase_dom		0.318	NDST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NDST3	HGNC	protein_coding	OTTHUMT00000256517.4	A	NM_004784		119163280	+1	no_errors	ENST00000296499	ensembl	human	known	70_37	missense	SNP	1.000	G
NOTCH3	4854	genome.wustl.edu	37	19	15299079	15299079	+	Nonsense_Mutation	SNP	G	G	A			TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr19:15299079G>A	ENST00000263388.2	-	9	1534	c.1459C>T	c.(1459-1461)Cga>Tga	p.R487*		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	487	EGF-like 12; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			CCATTGACTCGGTCCTTGCAG	0.592																																																	0													44.0	38.0	40.0					19																	15299079		2203	4300	6503	SO:0001587	stop_gained	4854			U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"""Ankyrin repeat domain containing"""	7883	protein-coding gene	gene with protein product		600276	"""Notch (Drosophila) homolog 3"", ""Notch homolog 3 (Drosophila)"""	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.1459C>T	19.37:g.15299079G>A	ENSP00000263388:p.Arg487*	Somatic		WXS	Illumina HiSeq	Phase_IV	Q9UEB3|Q9UPL3|Q9Y6L8	Nonsense_Mutation	SNP	pfam_EG-like_dom,pfam_EGF-like_Ca-bd,pfam_Ankyrin_rpt,pfam_Notch_dom,pfam_Notch_NODP_dom,pfam_Notch_NOD_dom,pfam_EGF_extracell,pfam_DUF3454_notch,superfamily_Ankyrin_rpt-contain_dom,superfamily_Notch_dom,smart_EG-like_dom,smart_EGF-like_Ca-bd,smart_Notch_dom,smart_Ankyrin_rpt,pirsf_Notch,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,pfscan_EG-like_dom,pfscan_Notch_dom,prints_Notch_3,prints_Notch_dom	p.R487*	ENST00000263388.2	37	c.1459	CCDS12326.1	19	.	.	.	.	.	.	.	.	.	.	g	39	7.372655	0.98241	.	.	ENSG00000074181	ENST00000263388;ENST00000539383	.	.	.	5.04	-0.00534	0.14018	.	0.000000	0.30126	N	0.010347	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15952	T	0.53	.	9.9283	0.41505	0.0:0.1034:0.198:0.6986	.	.	.	.	X	487;489	.	ENSP00000263388:R487X	R	-	1	2	NOTCH3	15160079	0.000000	0.05858	0.993000	0.49108	0.971000	0.66376	0.141000	0.16076	0.066000	0.16515	0.556000	0.70494	CGA	NOTCH3	-	pfam_EG-like_dom,smart_EGF-like_Ca-bd,smart_EG-like_dom,pirsf_Notch,pfscan_EG-like_dom		0.592	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NOTCH3	HGNC	protein_coding	OTTHUMT00000465714.1	G	NM_000435		15299079	-1	no_errors	ENST00000263388	ensembl	human	known	70_37	nonsense	SNP	0.967	A
PTPRE	5791	genome.wustl.edu	37	10	129883836	129883836	+	3'UTR	SNP	C	C	T			TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr10:129883836C>T	ENST00000254667.3	+	0	5048				PTPRE_ENST00000306042.5_3'UTR	NM_006504.4	NP_006495.1	P23469	PTPRE_HUMAN	protein tyrosine phosphatase, receptor type, E						negative regulation of insulin receptor signaling pathway (GO:0046627)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of mast cell activation (GO:0033003)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	22		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)			Alendronate(DB00630)	GAGCCTGACACCTGTGTTTCA	0.303																																					Colon(52;977 1184 20575 41685)												0																																										SO:0001624	3_prime_UTR_variant	5791			AF406557	CCDS7657.1, CCDS7658.1	10q26	2011-06-09			ENSG00000132334	ENSG00000132334		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9669	protein-coding gene	gene with protein product		600926				8595895	Standard	NM_130435		Approved	PTPE	uc001lkb.3	P23469	OTTHUMG00000019254	ENST00000254667.3:c.*2666C>T	10.37:g.129883836C>T		Somatic		WXS	Illumina HiSeq	Phase_IV	Q13345|Q5VWH3|Q5VWH4|Q96KQ6	RNA	SNP	-	NULL	ENST00000254667.3	37	NULL	CCDS7657.1	10																																																																																			PTPRE	-	-		0.303	PTPRE-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	PTPRE	HGNC	protein_coding	OTTHUMT00000050990.1	C			129883836	+1	no_errors	ENST00000479896	ensembl	human	known	70_37	rna	SNP	0.929	T
RBFOX1	54715	genome.wustl.edu	37	16	7629836	7629836	+	Missense_Mutation	SNP	A	A	G			TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr16:7629836A>G	ENST00000550418.1	+	6	1316	c.328A>G	c.(328-330)Acg>Gcg	p.T110A	RBFOX1_ENST00000552089.1_Missense_Mutation_p.T145A|RBFOX1_ENST00000535565.2_Intron|RBFOX1_ENST00000340209.4_Missense_Mutation_p.T115A|RBFOX1_ENST00000355637.4_Missense_Mutation_p.T130A|RBFOX1_ENST00000422070.4_Missense_Mutation_p.T153A|RBFOX1_ENST00000311745.5_Missense_Mutation_p.T130A|RBFOX1_ENST00000547338.1_Missense_Mutation_p.T110A|RBFOX1_ENST00000547372.1_Missense_Mutation_p.T153A|RBFOX1_ENST00000436368.2_Missense_Mutation_p.T130A|RBFOX1_ENST00000553186.1_Missense_Mutation_p.T110A	NM_018723.3	NP_061193.2	Q9NWB1	RFOX1_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 1	110					mRNA processing (GO:0006397)|neuromuscular process controlling balance (GO:0050885)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	nucleotide binding (GO:0000166)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|lung(17)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)	55						TTCTGAAAACACGGAAAACAA	0.512																																					Ovarian(157;934 2567 15163 39509)												0													150.0	137.0	141.0					16																	7629836		2197	4300	6497	SO:0001583	missense	54715			AF107203	CCDS10531.1, CCDS10532.1, CCDS45405.1, CCDS55983.1, CCDS55984.1	16p13.3	2013-02-12			ENSG00000078328	ENSG00000078328		"""RNA binding motif (RRM) containing"""	18222	protein-coding gene	gene with protein product	"""ataxin 2-binding protein 1"", ""hexaribonucleotide binding protein 1"""	605104				10814712, 16260614	Standard	NM_018723		Approved	A2BP1, FOX-1, HRNBP1	uc002cyy.2	Q9NWB1	OTTHUMG00000129551	ENST00000550418.1:c.328A>G	16.37:g.7629836A>G	ENSP00000450031:p.Thr110Ala	Somatic		WXS	Illumina HiSeq	Phase_IV	Q7Z7I7|Q8TAE3|Q8TAF2|Q8WYB2|Q9NS20	Missense_Mutation	SNP	pfam_Fox-1_C_dom,pfam_RRM_dom,smart_RRM_dom,pirsf_RNA-bd_Fox-1,pfscan_RRM_dom	p.T153A	ENST00000550418.1	37	c.457	CCDS55983.1	16	.	.	.	.	.	.	.	.	.	.	A	14.70	2.612575	0.46631	.	.	ENSG00000078328	ENST00000547605;ENST00000550418;ENST00000553186;ENST00000547372;ENST00000422070;ENST00000552089;ENST00000551752;ENST00000547338;ENST00000436368;ENST00000311745;ENST00000355637;ENST00000352951;ENST00000340209	T;T;T;T;T;T;T;T;T;T;T;T	0.34072	1.38;1.38;1.38;1.38;1.38;1.38;1.38;1.38;1.38;1.38;1.38;1.38	5.39	4.29	0.51040	Nucleotide-binding, alpha-beta plait (1);	0.055129	0.64402	D	0.000001	T	0.51381	0.1671	L	0.54323	1.7	0.47009	D	0.999286	B;B;D;B;D;B;B;B	0.71674	0.113;0.069;0.998;0.029;0.992;0.002;0.012;0.057	B;B;D;B;D;B;B;B	0.80764	0.07;0.032;0.994;0.022;0.984;0.01;0.01;0.113	T	0.41161	-0.9524	10	0.29301	T	0.29	-5.3434	11.7568	0.51880	0.8681:0.0:0.0:0.1318	.	130;153;130;130;130;110;110;153	F8WAC5;B7Z1U7;Q9NWB1-2;Q9NWB1-4;Q9NWB1-5;Q9NWB1-3;Q9NWB1;F8VZG9	.;.;.;.;.;.;RFOX1_HUMAN;.	A	109;110;110;153;153;145;110;110;130;130;130;130;115	ENSP00000450402:T109A;ENSP00000450031:T110A;ENSP00000447753:T110A;ENSP00000446842:T153A;ENSP00000391269:T153A;ENSP00000448496:T145A;ENSP00000447281:T110A;ENSP00000447717:T110A;ENSP00000402745:T130A;ENSP00000309117:T130A;ENSP00000347855:T130A;ENSP00000344196:T115A	ENSP00000309117:T130A	T	+	1	0	RBFOX1	7569837	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.373000	0.52394	0.872000	0.35775	0.533000	0.62120	ACG	RBFOX1	-	pirsf_RNA-bd_Fox-1		0.512	RBFOX1-003	KNOWN	basic|CCDS	protein_coding	RBFOX1	HGNC	protein_coding	OTTHUMT00000409492.2	A	NM_145891		7629836	+1	no_errors	ENST00000547372	ensembl	human	known	70_37	missense	SNP	1.000	G
RBM27	54439	genome.wustl.edu	37	5	145665548	145665548	+	Silent	SNP	C	C	T			TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr5:145665548C>T	ENST00000265271.5	+	21	3304	c.3138C>T	c.(3136-3138)gaC>gaT	p.D1046D	RBM27_ENST00000506502.1_Intron	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	1046					mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTGATGATGACGATGAAGATG	0.338																																																	0													142.0	124.0	129.0					5																	145665548		1568	3582	5150	SO:0001819	synonymous_variant	54439			AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"""Zinc fingers, CCCH-type domain containing"", ""RNA binding motif (RRM) containing"""	29243	protein-coding gene	gene with protein product	"""acidic rich RS domain containing 1"""					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.3138C>T	5.37:g.145665548C>T		Somatic		WXS	Illumina HiSeq	Phase_IV	Q8IYW9	Silent	SNP	pfam_PWI,pfam_Znf_CCCH,smart_RRM_dom,pfscan_RRM_dom	p.D1046	ENST00000265271.5	37	c.3138	CCDS43378.1	5																																																																																			RBM27	-	NULL		0.338	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RBM27	HGNC	protein_coding	OTTHUMT00000373420.1	C	XM_291128		145665548	+1	no_errors	ENST00000265271	ensembl	human	known	70_37	silent	SNP	0.855	T
SEMA5B	54437	genome.wustl.edu	37	3	122641210	122641210	+	Missense_Mutation	SNP	C	C	T			TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr3:122641210C>T	ENST00000357599.3	-	11	1743	c.1357G>A	c.(1357-1359)Gag>Aag	p.E453K	SEMA5B_ENST00000195173.4_Missense_Mutation_p.E453K|SEMA5B_ENST00000451055.2_Missense_Mutation_p.E507K	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	453	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		TGCACGGCCTCGCTCATCAGG	0.667																																																	0													39.0	37.0	38.0					3																	122641210		2203	4300	6503	SO:0001583	missense	54437			AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"""Semaphorins"""	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.1357G>A	3.37:g.122641210C>T	ENSP00000350215:p.Glu453Lys	Somatic		WXS	Illumina HiSeq	Phase_IV	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Missense_Mutation	SNP	pfam_Semaphorin/CD100_Ag,pfam_Thrombospondin_1_rpt,superfamily_Semaphorin/CD100_Ag,superfamily_Thrombospondin_1_rpt,superfamily_Plexin-like_fold,smart_Semaphorin/CD100_Ag,smart_Plexin-like,smart_Thrombospondin_1_rpt,pfscan_Semaphorin/CD100_Ag,pfscan_Thrombospondin_1_rpt	p.E507K	ENST00000357599.3	37	c.1519	CCDS35491.1	3	.	.	.	.	.	.	.	.	.	.	C	36	5.794819	0.96952	.	.	ENSG00000082684	ENST00000357599;ENST00000195173;ENST00000418793;ENST00000451055;ENST00000393583	T;T;T;T	0.23147	1.92;1.92;1.92;1.92	5.29	5.29	0.74685	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.054309	0.64402	D	0.000001	T	0.34861	0.0912	L	0.46885	1.475	0.80722	D	1	P;D;D	0.55800	0.94;0.973;0.973	B;P;P	0.49887	0.396;0.625;0.625	T	0.03384	-1.1042	10	0.54805	T	0.06	.	18.0865	0.89458	0.0:1.0:0.0:0.0	.	395;453;453	D3YTI7;B5ME80;Q9P283	.;.;SEM5B_HUMAN	K	453;453;395;507;453	ENSP00000350215:E453K;ENSP00000195173:E453K;ENSP00000389588:E507K;ENSP00000377208:E453K	ENSP00000195173:E453K	E	-	1	0	SEMA5B	124123900	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.600000	0.82769	2.759000	0.94783	0.591000	0.81541	GAG	SEMA5B	-	pfam_Semaphorin/CD100_Ag,superfamily_Semaphorin/CD100_Ag,smart_Semaphorin/CD100_Ag,pfscan_Semaphorin/CD100_Ag		0.667	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	SEMA5B	HGNC	protein_coding	OTTHUMT00000277165.1	C	NM_001031702		122641210	-1	no_errors	ENST00000451055	ensembl	human	known	70_37	missense	SNP	1.000	T
SKOR1	390598	genome.wustl.edu	37	15	68125560	68125560	+	Missense_Mutation	SNP	G	G	A			TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr15:68125560G>A	ENST00000380035.2	+	8	2826	c.2768G>A	c.(2767-2769)cGg>cAg	p.R923Q	SKOR1_ENST00000554054.1_Missense_Mutation_p.R895Q|SKOR1_ENST00000389002.1_Missense_Mutation_p.R879Q|RP11-34F13.3_ENST00000558889.1_RNA|SKOR1_ENST00000554240.1_Missense_Mutation_p.R884Q|SKOR1_ENST00000341418.5_Missense_Mutation_p.R826Q|RP11-34F13.2_ENST00000502156.1_lincRNA			P84550	SKOR1_HUMAN	SKI family transcriptional corepressor 1	923					negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)			endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(7)|urinary_tract(1)	23						GACCAGGAGCGGAAGGCGCGC	0.607																																																	0													57.0	53.0	55.0					15																	68125560		2200	4298	6498	SO:0001583	missense	390598				CCDS58374.1	15q23	2011-08-04	2010-06-23	2010-06-23	ENSG00000188779	ENSG00000188779		"""SKI transcriptional corepressors"""	21326	protein-coding gene	gene with protein product	"""transcriptional corepressor CORL1"", ""functional smad suppressing element 15"", ""corepressor for LBX1"""	611273	"""Lbxcor1 homolog (mouse)"""	LBXCOR1		15528197	Standard	NM_001258024		Approved	CORL1, FUSSEL15	uc031qsn.1	P84550		ENST00000380035.2:c.2768G>A	15.37:g.68125560G>A	ENSP00000369374:p.Arg923Gln	Somatic		WXS	Illumina HiSeq	Phase_IV	A6NIP4|A6NJY0|Q2VWA5	Missense_Mutation	SNP	pfam_Transform_Ski,pfam_c-SKI_SMAD4-bd_dom,superfamily_DNA-bd_dom_put,superfamily_SAND_dom-like	p.R923Q	ENST00000380035.2	37	c.2768		15	.	.	.	.	.	.	.	.	.	.	G	27.5	4.835404	0.91117	.	.	ENSG00000188779	ENST00000341418;ENST00000554240;ENST00000554054;ENST00000380035;ENST00000389002	T;T;T;T;T	0.77489	-1.1;-1.06;-1.06;-1.07;-1.06	5.34	5.34	0.76211	.	0.000000	0.64402	D	0.000001	D	0.82467	0.5043	L	0.29908	0.895	0.33176	D	0.548989	D	0.89917	1.0	D	0.72982	0.979	D	0.86445	0.1769	10	0.72032	D	0.01	-23.6603	17.9801	0.89138	0.0:0.0:1.0:0.0	.	879	P84550-3	.	Q	826;884;895;923;879	ENSP00000343200:R826Q;ENSP00000451193:R884Q;ENSP00000452361:R895Q;ENSP00000369374:R923Q;ENSP00000373654:R879Q	ENSP00000343200:R826Q	R	+	2	0	SKOR1	65912614	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.972000	0.88022	2.655000	0.90218	0.462000	0.41574	CGG	SKOR1	-	NULL		0.607	SKOR1-003	KNOWN	not_organism_supported|basic|appris_candidate_longest	protein_coding	SKOR1	HGNC	protein_coding	OTTHUMT00000410832.1	G	NM_001031807		68125560	+1	no_errors	ENST00000380035	ensembl	human	known	70_37	missense	SNP	1.000	A
SPATA31E1	286234	genome.wustl.edu	37	9	90502270	90502270	+	Missense_Mutation	SNP	G	G	C			TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr9:90502270G>C	ENST00000325643.5	+	4	2934	c.2868G>C	c.(2866-2868)agG>agC	p.R956S		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	956					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											ACAAGGGCAGGGGGTGTTCTC	0.622																																																	0													42.0	43.0	42.0					9																	90502270		2203	4299	6502	SO:0001583	missense	286234			AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 79"", ""family with sequence similarity 75, member E1"""	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.2868G>C	9.37:g.90502270G>C	ENSP00000322640:p.Arg956Ser	Somatic		WXS	Illumina HiSeq	Phase_IV	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	NULL	p.R956S	ENST00000325643.5	37	c.2868	CCDS6676.1	9	.	.	.	.	.	.	.	.	.	.	g	9.537	1.112355	0.20795	.	.	ENSG00000177992	ENST00000325643	T	0.03663	3.85	2.46	1.38	0.22167	.	0.592097	0.14577	N	0.311140	T	0.08223	0.0205	M	0.68317	2.08	0.09310	N	1	D	0.55385	0.971	P	0.53062	0.717	T	0.23476	-1.0187	10	0.32370	T	0.25	.	6.2614	0.20901	0.0:0.0:0.5998:0.4002	.	956	Q6ZUB1	CI079_HUMAN	S	956	ENSP00000322640:R956S	ENSP00000322640:R956S	R	+	3	2	C9orf79	89692090	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-1.084000	0.03393	0.420000	0.25954	0.557000	0.71058	AGG	SPATA31E1	-	NULL		0.622	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SPATA31E1	HGNC	protein_coding	OTTHUMT00000052954.2	G	NM_178828		90502270	+1	no_errors	ENST00000325643	ensembl	human	known	70_37	missense	SNP	0.001	C
TNS1	7145	genome.wustl.edu	37	2	218712887	218712889	+	In_Frame_Del	DEL	GCT	GCT	-	rs375721540|rs574153391		TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	GCT	GCT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr2:218712887_218712889delGCT	ENST00000171887.4	-	17	2428_2430	c.1976_1978delAGC	c.(1975-1980)cagcct>cct	p.Q659del	TNS1_ENST00000480665.1_5'Flank|TNS1_ENST00000430930.1_In_Frame_Del_p.Q659del|TNS1_ENST00000419504.1_In_Frame_Del_p.Q659del	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	659	Gln-rich.				cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		GGTGGGCGAGgctgctgctgctg	0.66																																																	0																																										SO:0001651	inframe_deletion	7145			AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	11973	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 155"""	600076	"""tensin"", ""matrix-remodelling associated 6"""	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.1976_1978delAGC	2.37:g.218712896_218712898delGCT	ENSP00000171887:p.Gln659del	Somatic		WXS	Illumina HiSeq	Phase_IV	Q4ZG71|Q6IPI5	In_Frame_Del	DEL	pfam_PTB,pfam_Tensin_phosphatase_C2-dom,pfam_SH2,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_Tyr_Pase_cat,smart_SH2,smart_PTyr_interaction_dom,pfscan_SH2,pfscan_Phosphatase_tensin-typ,pfscan_Tensin_phosphatase_C2-dom	p.Q659in_frame_del	ENST00000171887.4	37	c.1978_1976	CCDS2407.1	2																																																																																			TNS1	-	NULL		0.660	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	TNS1	HGNC	protein_coding	OTTHUMT00000256672.2	GCT	NM_022648		218712889	-1	no_errors	ENST00000171887	ensembl	human	known	70_37	in_frame_del	DEL	1.000:1.000:0.994	-
USP43	124739	genome.wustl.edu	37	17	9615324	9615324	+	Missense_Mutation	SNP	G	G	A			TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr17:9615324G>A	ENST00000285199.7	+	14	2306	c.2210G>A	c.(2209-2211)cGg>cAg	p.R737Q	USP43_ENST00000570475.1_Missense_Mutation_p.R732Q|USP43_ENST00000570827.2_3'UTR	NM_001267576.1|NM_153210.4	NP_001254505.1|NP_694942.3	Q70EL4	UBP43_HUMAN	ubiquitin specific peptidase 43	737					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	26						TGGCTCTTACGGCTCGGGAGC	0.637																																																	0													26.0	29.0	28.0					17																	9615324		1988	4147	6135	SO:0001583	missense	124739			AK055188	CCDS45610.1, CCDS58516.1	17p12	2005-08-08	2005-08-08			ENSG00000154914		"""Ubiquitin-specific peptidases"""	20072	protein-coding gene	gene with protein product			"""ubiquitin specific protease 43"""			12838346	Standard	NM_153210		Approved	FLJ30626	uc010cod.4	Q70EL4		ENST00000285199.7:c.2210G>A	17.37:g.9615324G>A	ENSP00000285199:p.Arg737Gln	Somatic		WXS	Illumina HiSeq	Phase_IV	A6NDT9|B7ZLT9|B7ZVX5|Q8N2C5|Q96DQ6	Missense_Mutation	SNP	pfam_Peptidase_C19,pfscan_Peptidase_C19	p.R737Q	ENST00000285199.7	37	c.2210	CCDS45610.1	17	.	.	.	.	.	.	.	.	.	.	G	18.00	3.524854	0.64747	.	.	ENSG00000154914	ENST00000285199	T	0.15603	2.41	4.9	4.9	0.64082	.	0.572466	0.14770	U	0.299468	T	0.40171	0.1106	M	0.63843	1.955	0.50467	D	0.999876	D;D;D;D	0.76494	0.997;0.997;0.999;0.999	P;P;P;D	0.70227	0.733;0.896;0.885;0.968	T	0.12760	-1.0535	10	0.87932	D	0	-28.0757	15.6088	0.76696	0.0:0.0:1.0:0.0	.	732;426;737;249	B7ZVX5;Q70EL4-3;Q70EL4;Q70EL4-2	.;.;UBP43_HUMAN;.	Q	737	ENSP00000285199:R737Q	ENSP00000285199:R737Q	R	+	2	0	USP43	9556049	1.000000	0.71417	0.479000	0.27329	0.043000	0.13939	8.227000	0.89787	2.543000	0.85770	0.561000	0.74099	CGG	USP43	-	NULL		0.637	USP43-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	USP43	HGNC	protein_coding	OTTHUMT00000439855.3	G	NM_153210		9615324	+1	no_errors	ENST00000285199	ensembl	human	known	70_37	missense	SNP	0.998	A
VPS52	6293	genome.wustl.edu	37	6	33239435	33239435	+	Silent	SNP	G	G	A			TCGA-EA-A5ZD-01A-11D-A28B-09	TCGA-EA-A5ZD-10A-01D-A28E-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	7fd39abc-ea1a-42b8-8cc1-90ec3de41c86	b8a74f15-4ec7-45dd-809b-4460c734ee33	g.chr6:33239435G>A	ENST00000445902.2	-	1	236	c.18C>T	c.(16-18)acC>acT	p.T6T	VPS52_ENST00000478934.1_Intron|RPS18_ENST00000474973.1_5'Flank|RPS18_ENST00000439602.2_5'Flank|VPS52_ENST00000482399.1_Silent_p.T6T|VPS52_ENST00000436044.2_Intron	NM_022553.4	NP_072047.4	Q8N1B4	VPS52_HUMAN	vacuolar protein sorting 52 homolog (S. cerevisiae)	6					ectodermal cell differentiation (GO:0010668)|embryonic ectodermal digestive tract development (GO:0048611)|protein transport (GO:0015031)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(8)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	28						CAGCCGCCATGGTCGCAGCGG	0.667																																																	0													15.0	18.0	17.0					6																	33239435		2202	4295	6497	SO:0001819	synonymous_variant	6293			AJ223319	CCDS4770.2	6p21.3	2010-02-17	2006-12-19	2003-09-05	ENSG00000223501	ENSG00000223501			10518	protein-coding gene	gene with protein product		603443	"""SAC2 suppressor of actin mutations 2-like (yeast)"", ""vacuolar protein sorting 52 (yeast)"""	SACM2L		9790748	Standard	NM_022553		Approved	ARE1	uc003odm.1	Q8N1B4	OTTHUMG00000031276	ENST00000445902.2:c.18C>T	6.37:g.33239435G>A		Somatic		WXS	Illumina HiSeq	Phase_IV	A2BF38|B0UZZ4|B4DNI9|Q53GR4|Q5JPA0|Q5SQW1|Q8IUN6|Q9NPT5	Silent	SNP	pfam_Vps52,pfam_Exocyst_Exoc1	p.T6	ENST00000445902.2	37	c.18	CCDS4770.2	6																																																																																			VPS52	-	NULL		0.667	VPS52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	VPS52	HGNC	protein_coding	OTTHUMT00000076598.2	G	NM_022553		33239435	-1	no_errors	ENST00000445902	ensembl	human	known	70_37	silent	SNP	0.995	A
