#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_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_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	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_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_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count
ARMC3	219681	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	23287189	23287189	+	Missense_Mutation	SNP	C	C	A			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr10:23287189C>A	ENST00000298032.5	+	11	1372	c.1288C>A	c.(1288-1290)Ccc>Acc	p.P430T	ARMC3_ENST00000409983.3_Missense_Mutation_p.P430T|RNA5SP304_ENST00000411199.1_RNA|ARMC3_ENST00000409049.3_Missense_Mutation_p.P430T|ARMC3_ENST00000376528.4_Missense_Mutation_p.P167T	NM_173081.3	NP_775104.2	Q5W041	ARMC3_HUMAN	armadillo repeat containing 3	430						extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(24)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						CATGCAGGAGCCCCTGCGCCT	0.493																																																0													73.0	59.0	64.0					10																	23287189		2203	4300	6503	SO:0001583	missense	219681			AK057389	CCDS7142.1, CCDS60499.1, CCDS60500.1, CCDS73073.1	10p12.31	2013-02-14			ENSG00000165309	ENSG00000165309		"""Armadillo repeat containing"""	30964	protein-coding gene	gene with protein product	"""cancer/testis antigen 81"""	611226					Standard	XM_005252380		Approved	FLJ32827, CT81	uc001irm.4	Q5W041	OTTHUMG00000017811	ENST00000298032.5:c.1288C>A	10.37:g.23287189C>A	ENSP00000298032:p.Pro430Thr		A0PG76|A6NH64|B4DZL3|B7ZBN6|B7ZBN7|Q8IXS5|Q8N7B0|Q96M49	Missense_Mutation	SNP	ENST00000298032.5	37	CCDS7142.1	.	.	.	.	.	.	.	.	.	.	C	6.459	0.452826	0.12283	.	.	ENSG00000165309	ENST00000298032;ENST00000409983;ENST00000376523;ENST00000409049;ENST00000376528	T;T;T;T	0.66995	-0.24;-0.24;1.33;0.69	5.57	0.869	0.19096	Armadillo-like helical (1);Armadillo-type fold (1);	0.447652	0.26163	N	0.025965	T	0.53514	0.1801	L	0.55990	1.75	0.35035	D	0.759204	B;P	0.38300	0.006;0.626	B;B	0.36186	0.005;0.219	T	0.56481	-0.7972	10	0.13853	T	0.58	-14.0538	9.4427	0.38679	0.0:0.6209:0.2381:0.141	.	430;430	Q5W041-4;Q5W041	.;ARMC3_HUMAN	T	430;430;366;430;167	ENSP00000298032:P430T;ENSP00000386943:P430T;ENSP00000387288:P430T;ENSP00000365711:P167T	ENSP00000298032:P430T	P	+	1	0	ARMC3	23327195	0.259000	0.24043	0.977000	0.42913	0.953000	0.61014	0.085000	0.14912	0.257000	0.21650	0.563000	0.77884	CCC		0.493	ARMC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047197.2	NM_173081		12	14	12	14
APBB1IP	54518	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	26802585	26802585	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr10:26802585C>T	ENST00000376236.4	+	8	1264	c.809C>T	c.(808-810)cCc>cTc	p.P270L		NM_019043.3	NP_061916.3	Q7Z5R6	AB1IP_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein	270					blood coagulation (GO:0007596)|platelet activation (GO:0030168)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(27)|skin(7)|upper_aerodigestive_tract(1)	45						TTTAAAAACCCCCAGGTAAGA	0.348																																																0													78.0	89.0	86.0					10																	26802585		2202	4298	6500	SO:0001583	missense	54518			AB085852	CCDS31167.1	10p12.1	2013-01-10			ENSG00000077420	ENSG00000077420		"""Pleckstrin homology (PH) domain containing"""	17379	protein-coding gene	gene with protein product	"""Rap1-GTP-interacting adaptor molecule"""	609036				9407065	Standard	NM_019043		Approved	INAG1, RIAM	uc001iss.3	Q7Z5R6	OTTHUMG00000017841	ENST00000376236.4:c.809C>T	10.37:g.26802585C>T	ENSP00000365411:p.Pro270Leu		Q8IWS8|Q8IYL7|Q8IZZ7	Missense_Mutation	SNP	ENST00000376236.4	37	CCDS31167.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.997019	0.93167	.	.	ENSG00000077420	ENST00000445780;ENST00000376236	T	0.64085	-0.08	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.79718	0.4494	M	0.68593	2.085	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.79526	-0.1767	10	0.87932	D	0	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	270;270	B4E100;Q7Z5R6	.;AB1IP_HUMAN	L	270	ENSP00000365411:P270L	ENSP00000365411:P270L	P	+	2	0	APBB1IP	26842591	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.445000	0.80570	2.941000	0.99782	0.655000	0.94253	CCC		0.348	APBB1IP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047270.1	NM_019043		67	94	67	94
ANO5	203859	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	22271916	22271916	+	Splice_Site	SNP	A	A	T			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr11:22271916A>T	ENST00000324559.8	+	10	1329	c.1012A>T	c.(1012-1014)Agc>Tgc	p.S338C		NM_001142649.1|NM_213599.2	NP_001136121.1|NP_998764.1	Q75V66	ANO5_HUMAN	anoctamin 5	338					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	intracellular calcium activated chloride channel activity (GO:0005229)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(12)|lung(36)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TAACACAAGCAGGTAAGTGCA	0.363																																																0													118.0	104.0	108.0					11																	22271916		2203	4300	6503	SO:0001630	splice_region_variant	203859			AL833271	CCDS31444.1	11p15.1	2014-09-17	2008-08-28	2008-08-28	ENSG00000171714	ENSG00000171714		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	27337	protein-coding gene	gene with protein product		608662	"""transmembrane protein 16E"", ""limb girdle muscular dystrophy 2L (autosomal recessive)"""	TMEM16E, LGMD2L		15067359, 20096397, 24692353	Standard	NM_213599		Approved	GDD1	uc001mqi.2	Q75V66	OTTHUMG00000166051	ENST00000324559.8:c.1013+1A>T	11.37:g.22271916A>T				Splice_Site	SNP	ENST00000324559.8	37	CCDS31444.1	.	.	.	.	.	.	.	.	.	.	A	14.87	2.664679	0.47572	.	.	ENSG00000171714	ENST00000324559	T	0.75154	-0.91	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	D	0.88336	0.6409	M	0.90542	3.125	0.54753	D	0.999988	D	0.89917	1.0	D	0.97110	1.0	D	0.90723	0.4636	10	0.87932	D	0	.	14.4249	0.67207	1.0:0.0:0.0:0.0	.	338	Q75V66	ANO5_HUMAN	C	338	ENSP00000315371:S338C	ENSP00000315371:S338C	S	+	1	0	ANO5	22228492	1.000000	0.71417	0.912000	0.35992	0.091000	0.18340	8.597000	0.90847	2.044000	0.60594	0.455000	0.32223	AGC		0.363	ANO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387615.1	NM_213599	Missense_Mutation	20	32	20	32
MARK2	2011	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	63667348	63667348	+	Silent	SNP	A	A	G			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr11:63667348A>G	ENST00000509502.2	+	8	898	c.435A>G	c.(433-435)gcA>gcG	p.A145A	MARK2_ENST00000502399.3_Silent_p.A178A|MARK2_ENST00000402010.2_Silent_p.A178A|MARK2_ENST00000513765.2_Silent_p.A145A|MARK2_ENST00000413835.2_Silent_p.A178A|MARK2_ENST00000425897.2_Silent_p.A145A|MARK2_ENST00000508192.1_Silent_p.A178A|MARK2_ENST00000361128.5_Silent_p.A178A|MARK2_ENST00000408948.3_Silent_p.A145A|MARK2_ENST00000350490.7_Silent_p.A178A|MARK2_ENST00000377809.4_Silent_p.A178A|MARK2_ENST00000315032.8_Silent_p.A178A|MARK2_ENST00000377810.3_Silent_p.A145A	NM_017490.3	NP_059672.2			MAP/microtubule affinity-regulating kinase 2											autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33						CCTCCCAGGCAGAAAACCTGC	0.498																																																0													134.0	132.0	133.0					11																	63667348		2201	4297	6498	SO:0001819	synonymous_variant	2011			BC008771	CCDS8051.1, CCDS41665.1, CCDS8051.2, CCDS53649.1, CCDS53650.1, CCDS53651.1	11q13.1	2013-06-27	2002-07-26	2002-08-01	ENSG00000072518	ENSG00000072518			3332	protein-coding gene	gene with protein product	"""ELKL motif kinase 1"", ""serine/threonine kinase"", ""protein-serine/threonine kinase"", ""Ser/Thr protein kinase PAR-1B"""	600526	"""ELKL motif kinase"""	EMK1		9730619, 10516437	Standard	NM_017490		Approved	PAR-1, Par1b, PAR-1B	uc001nxw.3	Q7KZI7	OTTHUMG00000160504	ENST00000509502.2:c.435A>G	11.37:g.63667348A>G				Silent	SNP	ENST00000509502.2	37	CCDS41665.1																																																																																				0.498	MARK2-003	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000360862.2	NM_017490		166	191	166	191
SCYL1	57410	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	65303494	65303494	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr11:65303494C>T	ENST00000270176.5	+	11	1534	c.1457C>T	c.(1456-1458)gCg>gTg	p.A486V	SCYL1_ENST00000524944.1_Missense_Mutation_p.A486V|SCYL1_ENST00000527009.1_Missense_Mutation_p.A343V|SCYL1_ENST00000525364.1_Missense_Mutation_p.A486V|SCYL1_ENST00000533862.1_Missense_Mutation_p.A486V|SCYL1_ENST00000279270.6_Missense_Mutation_p.A486V|SCYL1_ENST00000420247.2_Missense_Mutation_p.A486V	NM_020680.3	NP_065731.3	Q96KG9	NTKL_HUMAN	SCY1-like 1 (S. cerevisiae)	486					peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|protein tyrosine kinase activity (GO:0004713)			ovary(1)|skin(1)	2						TCCCGGGTTGCGGGTGTCCTG	0.597																																																0													76.0	77.0	77.0					11																	65303494		1911	4117	6028	SO:0001583	missense	57410			AF225424	CCDS41672.1, CCDS44646.1	11q11-q12	2008-07-21	2002-11-26	2002-11-29	ENSG00000142186	ENSG00000142186			14372	protein-coding gene	gene with protein product	"""teratoma-associated tyrosine kinase"", ""telomerase transcriptional elements-interacting factor"", ""telomerase regulation-associated protein"""	607982	"""N-terminal kinase-like"""	NTKL		11118629	Standard	NM_020680		Approved	HT019, P105, GKLP, NKTL, TAPK, TRAP, TEIF, MGC78454	uc001oea.1	Q96KG9	OTTHUMG00000166325	ENST00000270176.5:c.1457C>T	11.37:g.65303494C>T	ENSP00000270176:p.Ala486Val		A6NJF1|Q96G50|Q96KG8|Q96KH1|Q9HAW5|Q9HBL3|Q9NR53	Missense_Mutation	SNP	ENST00000270176.5	37	CCDS41672.1	.	.	.	.	.	.	.	.	.	.	C	35	5.551191	0.96501	.	.	ENSG00000142186	ENST00000270176;ENST00000525364;ENST00000420247;ENST00000533862;ENST00000527630;ENST00000349495;ENST00000279270;ENST00000524944;ENST00000527009	T;T;T;T;T;T;T;T	0.36699	1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24	5.46	5.46	0.80206	Armadillo-like helical (1);Armadillo-type fold (1);	0.118682	0.56097	D	0.000032	T	0.67906	0.2943	M	0.89904	3.07	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.987;0.999;0.999;0.998;0.995	T	0.74805	-0.3540	10	0.72032	D	0.01	-11.0911	16.7806	0.85562	0.0:1.0:0.0:0.0	.	486;486;486;486;486	E9PS17;Q96KG9-4;Q96KG9-6;Q96KG9-2;Q96KG9	.;.;.;.;NTKL_HUMAN	V	486;486;486;486;486;486;486;486;343	ENSP00000270176:A486V;ENSP00000431635:A486V;ENSP00000408192:A486V;ENSP00000437254:A486V;ENSP00000433450:A486V;ENSP00000279270:A486V;ENSP00000432175:A486V;ENSP00000436993:A343V	ENSP00000270176:A486V	A	+	2	0	SCYL1	65060070	1.000000	0.71417	0.985000	0.45067	0.871000	0.50021	6.864000	0.75494	2.577000	0.86979	0.462000	0.41574	GCG		0.597	SCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389159.2	NM_020680		31	55	31	55
PTPRB	5787	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	70980859	70980859	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr12:70980859G>A	ENST00000261266.5	-	7	1614	c.1585C>T	c.(1585-1587)Cga>Tga	p.R529*	PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000334414.6_Nonsense_Mutation_p.R747*|PTPRB_ENST00000551525.1_Nonsense_Mutation_p.R746*|PTPRB_ENST00000550358.1_Nonsense_Mutation_p.R747*|PTPRB_ENST00000550857.1_Nonsense_Mutation_p.R439*|PTPRB_ENST00000451516.2_Nonsense_Mutation_p.R439*|PTPRB_ENST00000538708.1_Nonsense_Mutation_p.R529*	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	529	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			ATGTATTTTCGTCCAGGCACC	0.378																																																0													126.0	118.0	121.0					12																	70980859		1879	4107	5986	SO:0001587	stop_gained	5787			X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.1585C>T	12.37:g.70980859G>A	ENSP00000261266:p.Arg529*		B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Nonsense_Mutation	SNP	ENST00000261266.5	37	CCDS44944.1	.	.	.	.	.	.	.	.	.	.	G	37	6.207881	0.97376	.	.	ENSG00000127329	ENST00000334414;ENST00000451516;ENST00000550358;ENST00000544694;ENST00000538708;ENST00000550857;ENST00000261266;ENST00000551525;ENST00000548122	.	.	.	5.12	4.14	0.48551	.	0.068792	0.53938	D	0.000058	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05721	T	0.95	.	16.4532	0.83998	0.0:0.0:0.8296:0.1704	.	.	.	.	X	747;439;747;747;529;439;529;746;626	.	ENSP00000261266:R529X	R	-	1	2	PTPRB	69267126	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.222000	0.32515	2.368000	0.80403	0.557000	0.71058	CGA		0.378	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1			58	60	58	60
MYH4	4622	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	10350515	10350515	+	Missense_Mutation	SNP	C	C	A			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr17:10350515C>A	ENST00000255381.2	-	35	5094	c.4984G>T	c.(4984-4986)Gat>Tat	p.D1662Y	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1662					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						ATGGCATCATCCAAATGTAGC	0.453																																																0													103.0	87.0	92.0					17																	10350515		2203	4300	6503	SO:0001583	missense	4622				CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"""Myosins / Myosin superfamily : Class II"""	7574	protein-coding gene	gene with protein product		160742	"""myosin, heavy polypeptide 4, skeletal muscle"""			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.4984G>T	17.37:g.10350515C>A	ENSP00000255381:p.Asp1662Tyr			Missense_Mutation	SNP	ENST00000255381.2	37	CCDS11154.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.561592	0.86335	.	.	ENSG00000141048	ENST00000255381	T	0.80304	-1.36	5.09	5.09	0.68999	Myosin tail (1);	0.000000	0.38381	U	0.001716	D	0.93009	0.7775	H	0.95365	3.66	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.94927	0.8079	10	0.87932	D	0	.	18.8453	0.92203	0.0:1.0:0.0:0.0	.	1662	Q9Y623	MYH4_HUMAN	Y	1662	ENSP00000255381:D1662Y	ENSP00000255381:D1662Y	D	-	1	0	MYH4	10291240	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.763000	0.85283	2.540000	0.85666	0.563000	0.77884	GAT		0.453	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		27	47	27	47
UTP18	51096	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	49371388	49371388	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr17:49371388G>A	ENST00000225298.7	+	12	1685	c.1628G>A	c.(1627-1629)gGc>gAc	p.G543D		NM_016001.2	NP_057085.2	Q9Y5J1	UTP18_HUMAN	UTP18 small subunit (SSU) processome component homolog (yeast)	543				GKALMYRLHHYSDF -> ARP (in Ref. 1; AAD34043). {ECO:0000305}.	rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(3)|kidney(2)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16			BRCA - Breast invasive adenocarcinoma(22;2.09e-07)			AATGAAAAGGGCAAGGCCCTG	0.333																																																0													61.0	56.0	57.0					17																	49371388		1806	4073	5879	SO:0001583	missense	51096			AF151806	CCDS42362.1	17q21.33	2013-05-21	2011-12-09	2006-05-16	ENSG00000011260	ENSG00000011260		"""WD repeat domain containing"""	24274	protein-coding gene	gene with protein product		612816	"""WD repeat domain 50"""	WDR50		10810093, 8619474, 15590835	Standard	NM_016001		Approved	CGI-48	uc002its.3	Q9Y5J1	OTTHUMG00000162370	ENST00000225298.7:c.1628G>A	17.37:g.49371388G>A	ENSP00000225298:p.Gly543Asp		Q9H4N6	Missense_Mutation	SNP	ENST00000225298.7	37	CCDS42362.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	21.0|21.0|21.0	4.088032|4.088032|4.088032	0.76642|0.76642|0.76642	.|.|.	.|.|.	ENSG00000011260|ENSG00000011260|ENSG00000011260	ENST00000508506|ENST00000508506|ENST00000225298	.|.|T	.|.|0.30981	.|.|1.51	5.2|5.2|5.2	5.2|5.2|5.2	0.72013|0.72013|0.72013	.|.|WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	.|.|0.000000	.|.|0.85682	.|.|D	.|.|0.000000	.|T|T	.|0.63522|0.63522	.|0.2518|0.2518	M|M|M	0.88181|0.88181|0.88181	2.935|2.935|2.935	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|D	.|.|0.89917	.|.|1.0	.|.|D	.|.|0.97110	.|.|1.0	.|T|T	.|0.70586|0.70586	.|-0.4831|-0.4831	.|6|10	.|0.87932|0.87932	.|D|D	.|0|0	.|-13.5073|-13.5073	17.672|17.672|17.672	0.88221|0.88221|0.88221	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	.|.|543	.|.|Q9Y5J1	.|.|UTP18_HUMAN	.|T|D	-1|519|543	.|.|ENSP00000225298:G543D	.|ENSP00000441335:A519T|ENSP00000225298:G543D	.|A|G	+|+|+	.|1|2	.|0|0	UTP18|UTP18|UTP18	46726387|46726387|46726387	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.993000|0.993000|0.993000	0.82548|0.82548|0.82548	5.469000|5.469000|5.469000	0.66749|0.66749|0.66749	2.691000|2.691000|2.691000	0.91804|0.91804|0.91804	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	.|GCA|GGC		0.333	UTP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368654.1	NM_016001		28	34	28	34
RNF213	57674	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	78320934	78320934	+	Silent	SNP	G	G	A	rs141391616	byFrequency	TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr17:78320934G>A	ENST00000582970.1	+	29	8942	c.8799G>A	c.(8797-8799)gcG>gcA	p.A2933A	RNF213_ENST00000336301.6_Silent_p.A1006A|RNF213_ENST00000508628.2_Silent_p.A2982A	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	2933					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A1006A(1)|p.A2982A(1)		NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GGTACTTTGCGTCCTTTGCCA	0.547													G|||	5	0.000998403	0.0038	0.0	5008	,	,		20308	0.0		0.0	False		,,,				2504	0.0															2	Substitution - coding silent(2)	prostate(2)						G		3,4403	6.2+/-15.9	0,3,2200	58.0	48.0	51.0		8946	-11.6	0.0	17	dbSNP_134	51	0,8600		0,0,4300	no	coding-synonymous	RNF213	NM_020914.4		0,3,6500	AA,AG,GG		0.0,0.0681,0.0231		2982/5257	78320934	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	57674			AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.8799G>A	17.37:g.78320934G>A			C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	37	CCDS58606.1																																																																																				0.547	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		30	23	30	23
MTCL1	23255	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	18	8793017	8793017	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr18:8793017C>T	ENST00000359865.3	+	8	2051	c.1909C>T	c.(1909-1911)Cct>Tct	p.P637S	SOGA2_ENST00000306285.7_5'UTR|SOGA2_ENST00000518815.1_Intron|SOGA2_ENST00000517570.1_Intron|SOGA2_ENST00000400050.3_Intron|SOGA2_ENST00000306329.11_Intron	NM_015210.3	NP_056025.2																					CCCCGTTTTACCTGAGCAGAG	0.527																																																0													95.0	105.0	102.0					18																	8793017		2203	4300	6503	SO:0001583	missense	23255																														ENST00000359865.3:c.1909C>T	18.37:g.8793017C>T	ENSP00000352927:p.Pro637Ser			Missense_Mutation	SNP	ENST00000359865.3	37	CCDS11841.1	.	.	.	.	.	.	.	.	.	.	C	9.580	1.123380	0.20959	.	.	ENSG00000168502	ENST00000306329;ENST00000359865	T	0.41065	1.01	5.36	4.46	0.54185	.	1.297080	0.05460	N	0.551114	T	0.45498	0.1345	N	0.14661	0.345	0.80722	D	1	D	0.63880	0.993	P	0.62491	0.903	T	0.40961	-0.9535	10	0.06236	T	0.91	.	15.4683	0.75419	0.1398:0.8602:0.0:0.0	.	637	Q9Y4B5-3	.	S	658;637	ENSP00000352927:P637S	ENSP00000305027:P658S	P	+	1	0	CCDC165	8783017	1.000000	0.71417	0.864000	0.33941	0.871000	0.50021	2.820000	0.48057	1.348000	0.45733	0.561000	0.74099	CCT		0.527	SOGA2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254476.1			122	141	122	141
ZNF71	58491	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	57133636	57133636	+	Silent	SNP	G	G	A			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr19:57133636G>A	ENST00000328070.6	+	3	1215	c.981G>A	c.(979-981)gtG>gtA	p.V327V		NM_021216.4	NP_067039.1	Q9NQZ8	ZNF71_HUMAN	zinc finger protein 71	327					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	26				GBM - Glioblastoma multiforme(193;0.062)|Lung(386;0.0681)|LUSC - Lung squamous cell carcinoma(496;0.18)		AGCCCTACGTGTGCGGCGAGT	0.642																																																0													84.0	77.0	79.0					19																	57133636		2203	4300	6503	SO:0001819	synonymous_variant	58491			X60074	CCDS12947.1	19q13.4	2013-01-08	2006-05-12			ENSG00000197951		"""Zinc fingers, C2H2-type"""	13141	protein-coding gene	gene with protein product		194545	"""zinc finger protein 71 (Cos26)"""			1639391	Standard	NM_021216		Approved	Cos26, EZFIT	uc002qnm.4	Q9NQZ8		ENST00000328070.6:c.981G>A	19.37:g.57133636G>A			Q15919|Q9UC09|Q9UQD3	Silent	SNP	ENST00000328070.6	37	CCDS12947.1																																																																																				0.642	ZNF71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459798.2	NM_021216		32	45	32	45
UBE4B	10277	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	10182079	10182079	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr1:10182079G>A	ENST00000253251.8	+	9	1951	c.1112G>A	c.(1111-1113)gGc>gAc	p.G371D	UBE4B_ENST00000377157.3_Missense_Mutation_p.G255D|UBE4B_ENST00000475795.1_3'UTR|UBE4B_ENST00000343090.6_Missense_Mutation_p.G500D					ubiquitination factor E4B											NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		CTCCCATATGGCTTCATTCAG	0.493																																																0													151.0	135.0	140.0					1																	10182079		2203	4300	6503	SO:0001583	missense	10277			AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"""U-box domain containing"""	12500	protein-coding gene	gene with protein product		613565	"""ubiquitination factor E4B (homologous to yeast UFD2)"", ""ubiquitination factor E4B (UFD2 homolog, yeast)"""			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.1112G>A	1.37:g.10182079G>A	ENSP00000253251:p.Gly371Asp			Missense_Mutation	SNP	ENST00000253251.8	37	CCDS110.1	.	.	.	.	.	.	.	.	.	.	G	19.55	3.847847	0.71603	.	.	ENSG00000130939	ENST00000253251;ENST00000377157;ENST00000343090	T;T;T	0.48522	0.81;0.81;0.81	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.64249	0.2581	L	0.59436	1.845	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.976;0.996	T	0.55256	-0.8169	10	0.09338	T	0.73	-28.0434	19.8879	0.96917	0.0:0.0:1.0:0.0	.	500;371	O95155;O95155-2	UBE4B_HUMAN;.	D	371;255;500	ENSP00000253251:G371D;ENSP00000366362:G255D;ENSP00000343001:G500D	ENSP00000253251:G371D	G	+	2	0	UBE4B	10104666	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.201000	0.95017	2.693000	0.91896	0.655000	0.94253	GGC		0.493	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048		13	82	13	82
EXTL1	2134	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	26361731	26361731	+	Missense_Mutation	SNP	T	T	C			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr1:26361731T>C	ENST00000374280.3	+	11	2791	c.1924T>C	c.(1924-1926)Ttc>Ctc	p.F642L		NM_004455.2	NP_004446.2	Q92935	EXTL1_HUMAN	exostosin-like glycosyltransferase 1	642					protein glycosylation (GO:0006486)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|stomach(1)|urinary_tract(1)	23		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00594)|READ - Rectum adenocarcinoma(331;0.0649)		AGCGGCAGCGTTCGGCCACAT	0.642																																																0													44.0	44.0	44.0					1																	26361731		2203	4300	6503	SO:0001583	missense	2134			U67191	CCDS271.1	1p36.1	2013-03-01	2013-03-01		ENSG00000158008	ENSG00000158008	2.4.1.224	"""Exostosin glycosyltransferase family"""	3515	protein-coding gene	gene with protein product	"""glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase"", ""alpha-N-acetylglucosaminyltransferase II"", ""glucuronyl-N-acetylglucosaminylproteoglycan alpha-1,4-N- acetylglucosaminyltransferase"", ""exostosin-L"""	601738	"""exostoses (multiple)-like 1"""			9037597	Standard	NM_004455		Approved	EXTL, MGC70794	uc001blf.3	Q92935	OTTHUMG00000007509	ENST00000374280.3:c.1924T>C	1.37:g.26361731T>C	ENSP00000363398:p.Phe642Leu		Q6GSC1	Missense_Mutation	SNP	ENST00000374280.3	37	CCDS271.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.376458	0.82682	.	.	ENSG00000158008	ENST00000374280	D	0.86627	-2.15	4.97	3.82	0.43975	EXTL2, alpha-1,4-N-acetylhexosaminyltransferase (1);	0.125439	0.53938	N	0.000054	D	0.86372	0.5917	M	0.67397	2.05	0.53688	D	0.999973	B	0.22983	0.078	B	0.33690	0.168	D	0.83373	0.0008	10	0.62326	D	0.03	-17.111	10.052	0.42221	0.0:0.0821:0.0:0.9179	.	642	Q92935	EXTL1_HUMAN	L	642	ENSP00000363398:F642L	ENSP00000363398:F642L	F	+	1	0	EXTL1	26234318	1.000000	0.71417	0.712000	0.30502	0.749000	0.42624	6.047000	0.71038	0.883000	0.36040	0.459000	0.35465	TTC		0.642	EXTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019749.1	NM_004455		49	7	49	7
ARID1A	8289	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	27101342	27101342	+	Nonsense_Mutation	SNP	G	G	T			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr1:27101342G>T	ENST00000324856.7	+	18	4995	c.4624G>T	c.(4624-4626)Gaa>Taa	p.E1542*	ARID1A_ENST00000540690.1_Intron|ARID1A_ENST00000374152.2_Nonsense_Mutation_p.E1159*|ARID1A_ENST00000457599.2_Intron	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1542					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.E1542*(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GGCCAACCACGAAGGCTCGTG	0.642			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	1	Substitution - Nonsense(1)	ovary(1)											60.0	63.0	62.0					1																	27101342		2203	4300	6503	SO:0001587	stop_gained	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.4624G>T	1.37:g.27101342G>T	ENSP00000320485:p.Glu1542*		D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Nonsense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	43|43	10.343878|10.343878	0.99388|0.99388	.|.	.|.	ENSG00000117713|ENSG00000117713	ENST00000324856;ENST00000374152|ENST00000430799	.|.	.|.	.|.	5.41|5.41	5.41|5.41	0.78517|0.78517	.|.	0.045702|.	0.85682|.	D|.	0.000000|.	.|T	.|0.75287	.|0.3829	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.72743	.|-0.4201	.|4	0.42905|.	T|.	0.14|.	-7.5866|-7.5866	19.3941|19.3941	0.94598|0.94598	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|L	1542;1159|438	.|.	ENSP00000320485:E1542X|.	E|R	+|+	1|2	0|0	ARID1A|ARID1A	26973929|26973929	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.479000|0.479000	0.33129|0.33129	9.144000|9.144000	0.94629|0.94629	2.822000|2.822000	0.97130|0.97130	0.557000|0.557000	0.71058|0.71058	GAA|CGA		0.642	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		45	7	45	7
CDC20	991	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	43824985	43824985	+	Silent	SNP	G	G	A			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr1:43824985G>A	ENST00000372462.1	+	1	302	c.99G>A	c.(97-99)aaG>aaA	p.K33K	CDC20_ENST00000310955.6_Silent_p.K33K|RP1-92O14.3_ENST00000424948.1_RNA			Q12834	CDC20_HUMAN	cell division cycle 20	33					activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell cycle (GO:0007049)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of cell proliferation (GO:0008284)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein ubiquitination (GO:0016567)|regulation of dendrite development (GO:0050773)|regulation of meiosis (GO:0040020)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|spindle (GO:0005819)	enzyme binding (GO:0019899)|protein C-terminus binding (GO:0008022)			endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	15	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GCAAAGCCAAGGAAGCCGCAG	0.677																																					Esophageal Squamous(137;1154 1759 10362 10401 46925)											0													25.0	34.0	31.0					1																	43824985		2199	4296	6495	SO:0001819	synonymous_variant	991			U05340	CCDS484.1	1p34.1	2013-01-17	2013-01-17		ENSG00000117399	ENSG00000117399		"""WD repeat domain containing"""	1723	protein-coding gene	gene with protein product		603618	"""CDC20 (cell division cycle 20, S. cerevisiae, homolog)"", ""CDC20 cell division cycle 20 homolog (S. cerevisiae)"", ""cell division cycle 20 homolog (S. cerevisiae)"""			7513050, 9353311	Standard	NM_001255		Approved	p55CDC, CDC20A	uc001cix.3	Q12834	OTTHUMG00000007420	ENST00000372462.1:c.99G>A	1.37:g.43824985G>A			B2R6Z6|D3DPJ1|Q5JUY4|Q9BW56|Q9UQI9	Silent	SNP	ENST00000372462.1	37	CCDS484.1																																																																																				0.677	CDC20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019488.1	NM_001255		5	38	5	38
SNX7	51375	hgsc.bcm.edu;ucsc.edu	37	1	99156680	99156680	+	Missense_Mutation	SNP	A	A	G	rs373963048		TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr1:99156680A>G	ENST00000306121.3	+	3	422	c.413A>G	c.(412-414)tAt>tGt	p.Y138C	SNX7_ENST00000370189.5_Missense_Mutation_p.Y74C|SNX7_ENST00000529992.1_Missense_Mutation_p.Y138C	NM_015976.4	NP_057060.2	Q9UNH6	SNX7_HUMAN	sorting nexin 7	74	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				apoptotic process (GO:0006915)|intracellular protein transport (GO:0006886)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	13		all_epithelial(167;7.64e-07)|all_lung(203;0.0006)|Lung NSC(277;0.00137)		Epithelial(280;0.0521)|all cancers(265;0.0687)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.207)|Colorectal(170;0.234)		AGGAGACGATATCAAGATTTC	0.363																																																0								A	CYS/TYR,CYS/TYR	1,4405	2.1+/-5.4	0,1,2202	98.0	94.0	95.0		413,413	6.0	0.4	1		95	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	SNX7	NM_015976.4,NM_152238.3	194,194	0,2,6501	GG,GA,AA		0.0116,0.0227,0.0154	probably-damaging,probably-damaging	138/452,138/397	99156680	2,13004	2203	4300	6503	SO:0001583	missense	51375			AF121857	CCDS755.2, CCDS756.1, CCDS756.2	1p21	2008-05-22			ENSG00000162627	ENSG00000162627		"""Sorting nexins"""	14971	protein-coding gene	gene with protein product		614904					Standard	NM_015976		Approved		uc010ouc.2	Q9UNH6	OTTHUMG00000010723	ENST00000306121.3:c.413A>G	1.37:g.99156680A>G	ENSP00000304429:p.Tyr138Cys		A8KAF3|D3DT50|Q53FQ3|Q5VT09|Q5VT10|Q86U82|Q8WVD4|Q96FW9|Q9Y3Z7	Missense_Mutation	SNP	ENST00000306121.3	37	CCDS755.2	.	.	.	.	.	.	.	.	.	.	A	19.03	3.747091	0.69418	2.27E-4	1.16E-4	ENSG00000162627	ENST00000370189;ENST00000529992;ENST00000306121;ENST00000454199	T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1	5.98	5.98	0.97165	.	0.055575	0.85682	D	0.000000	D	0.85999	0.5828	H	0.98276	4.19	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.91523	0.5236	10	0.87932	D	0	-23.7619	16.4781	0.84144	1.0:0.0:0.0:0.0	.	138;138;74	E9PNL2;Q9UNH6-3;Q9UNH6-2	.;.;.	C	74;138;138;74	ENSP00000359208:Y74C;ENSP00000434731:Y138C;ENSP00000304429:Y138C;ENSP00000388266:Y74C	ENSP00000304429:Y138C	Y	+	2	0	SNX7	98929268	1.000000	0.71417	0.404000	0.26397	0.709000	0.40893	9.339000	0.96797	2.288000	0.76882	0.528000	0.53228	TAT		0.363	SNX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029609.2			3	26	3	26
SLC27A3	11000	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	153745465	153745465	+	5'Flank	SNP	C	C	T			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr1:153745465C>T	ENST00000368661.3	+	0	0				INTS3_ENST00000476843.1_3'UTR|INTS3_ENST00000456435.1_Missense_Mutation_p.R847W|INTS3_ENST00000435409.2_Missense_Mutation_p.R987W|INTS3_ENST00000318967.2_Missense_Mutation_p.R987W|SLC27A3_ENST00000271857.2_5'Flank|INTS3_ENST00000512605.1_Missense_Mutation_p.R847W	NM_024330.1	NP_077306.1	Q5K4L6	S27A3_HUMAN	solute carrier family 27 (fatty acid transporter), member 3						fatty acid metabolic process (GO:0006631)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)	fatty-acyl-CoA synthase activity (GO:0004321)|ligase activity (GO:0016874)|nucleotide binding (GO:0000166)			NS(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	14	all_lung(78;6.47e-32)|Lung NSC(65;2.52e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			ACCCAAGAGCCGGCGAAAAGC	0.557																																																0													91.0	99.0	96.0					1																	153745465		2203	4300	6503	SO:0001631	upstream_gene_variant	65123			BC009916	CCDS1053.1	1q21.1	2013-05-22			ENSG00000143554	ENSG00000143554		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10997	protein-coding gene	gene with protein product		604193				9671728	Standard	NM_024330		Approved	FATP3, MGC4365, ACSVL3	uc001fcz.3	Q5K4L6	OTTHUMG00000037155		1.37:g.153745465C>T	Exception_encountered		Q5VUQ7|Q5VUQ8|Q5VUR3|Q6ZV16|Q8N2X7|Q8TEJ0|Q96SW5|Q9BTJ5|Q9BTY5	Missense_Mutation	SNP	ENST00000368661.3	37	CCDS1053.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.021852	0.93462	.	.	ENSG00000143624	ENST00000318967;ENST00000456435;ENST00000435409;ENST00000512605	.	.	.	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.62441	0.2428	L	0.43152	1.355	0.35465	D	0.7968	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.992;0.973;0.988	T	0.67534	-0.5646	9	0.72032	D	0.01	.	15.0624	0.71964	0.0:1.0:0.0:0.0	.	847;988;987	Q68E01-3;Q68E01;Q68E01-2	.;INT3_HUMAN;.	W	987;847;987;847	.	ENSP00000318641:R987W	R	+	1	2	INTS3	152012089	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.824000	0.55723	2.620000	0.88729	0.561000	0.74099	CGG		0.557	SLC27A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_024330		62	106	62	106
ENTPD6	955	hgsc.bcm.edu;broad.mit.edu	37	20	25201921	25201921	+	Missense_Mutation	SNP	G	G	C			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr20:25201921G>C	ENST00000376652.4	+	11	1160	c.997G>C	c.(997-999)Gag>Cag	p.E333Q	ENTPD6_ENST00000354989.5_Missense_Mutation_p.E316Q|ENTPD6_ENST00000433259.2_Intron|ENTPD6_ENST00000360031.2_Missense_Mutation_p.E332Q			O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6 (putative)	333					response to calcium ion (GO:0051592)|response to magnesium ion (GO:0032026)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity (GO:0008894)|nucleoside-triphosphatase activity (GO:0017111)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|prostate(1)|skin(1)	27						TTTCAAAGGAGAGTGGGAACA	0.517																																																0													143.0	125.0	131.0					20																	25201921		2203	4300	6503	SO:0001583	missense	955			AF039916	CCDS13170.1, CCDS46586.1	20p11.21	2010-06-24	2010-06-24		ENSG00000197586	ENSG00000197586			3368	protein-coding gene	gene with protein product		603160	"""interleukin 6 signal transducer-2"""	CD39L2, IL6ST2		9676430	Standard	NM_001247		Approved	NTPDase-6, dJ738P15.3	uc002wuj.2	O75354	OTTHUMG00000032116	ENST00000376652.4:c.997G>C	20.37:g.25201921G>C	ENSP00000365840:p.Glu333Gln		A6NCX6|D3DW49|Q5QPJ2|Q5QPJ5|Q7Z5B5|Q8N3H3|Q8TAS7|Q9UJD1	Missense_Mutation	SNP	ENST00000376652.4	37	CCDS13170.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	14.43|14.43|14.43	2.532135|2.532135|2.532135	0.45073|0.45073|0.45073	.|.|.	.|.|.	ENSG00000197586|ENSG00000197586|ENSG00000197586	ENST00000433417|ENST00000354989;ENST00000360031;ENST00000525986;ENST00000376641;ENST00000376652;ENST00000425813|ENST00000376666	.|T;T;T;T|.	.|0.11277|.	.|2.79;2.79;2.79;2.79|.	5.64|5.64|5.64	2.63|2.63|2.63	0.31362|0.31362|0.31362	.|.|.	0.303010|0.303010|.	0.40222|0.40222|.	N|N|.	0.001152|0.001152|.	T|T|T	0.56949|0.56949|0.56949	0.2020|0.2020|0.2020	L|L|L	0.52206|0.52206|0.52206	1.635|1.635|1.635	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|B;B;B;B;B;B;B|.	.|0.33549|.	.|0.299;0.169;0.417;0.1;0.345;0.036;0.036|.	.|B;B;B;B;B;B;B|.	.|0.40782|.	.|0.34;0.196;0.142;0.152;0.279;0.017;0.017|.	T|T|T	0.49466|0.49466|0.49466	-0.8937|-0.8937|-0.8937	6|10|5	.|0.37606|.	.|T|.	.|0.19|.	-29.1674|-29.1674|-29.1674	9.1399|9.1399|9.1399	0.36897|0.36897|0.36897	0.2307:0.0:0.7693:0.0|0.2307:0.0:0.7693:0.0|0.2307:0.0:0.7693:0.0	.|.|.	.|315;333;333;316;332;332;333|.	.|B4DDM7;B4DNK6;E7EP89;O75354-2;D3DW49;Q5QPJ2;O75354|.	.|.;.;.;.;.;.;ENTP6_HUMAN|.	D|Q|T	253|316;332;253;229;333;285|156	.|ENSP00000347084:E316Q;ENSP00000353131:E332Q;ENSP00000365840:E333Q;ENSP00000390646:E285Q|.	.|ENSP00000347084:E316Q|.	E|E|R	+|+|+	3|1|2	2|0|0	ENTPD6|ENTPD6|ENTPD6	25149921|25149921|25149921	0.996000|0.996000|0.996000	0.38824|0.38824|0.38824	0.954000|0.954000|0.954000	0.39281|0.39281|0.39281	0.957000|0.957000|0.957000	0.61999|0.61999|0.61999	1.249000|1.249000|1.249000	0.32839|0.32839|0.32839	0.416000|0.416000|0.416000	0.25844|0.25844|0.25844	0.561000|0.561000|0.561000	0.74099|0.74099|0.74099	GAG|GAG|AGA		0.517	ENTPD6-020	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078414.2			6	119	6	119
DIP2A	23181	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	21	47952057	47952057	+	Silent	SNP	G	G	T			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr21:47952057G>T	ENST00000417564.2	+	10	1233	c.1212G>T	c.(1210-1212)ccG>ccT	p.P404P	DIP2A_ENST00000427143.2_Silent_p.P340P|DIP2A_ENST00000466639.1_Silent_p.P361P|DIP2A_ENST00000457905.3_Silent_p.P404P|DIP2A_ENST00000318711.7_Silent_p.P405P|DIP2A_ENST00000400274.1_Silent_p.P400P|DIP2A_ENST00000435722.3_Silent_p.P404P			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	404					multicellular organismal development (GO:0007275)|negative regulation of gene expression (GO:0010629)|regulation of apoptotic process (GO:0042981)	cell surface (GO:0009986)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(22)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		TCGTGTTTCCGAATAGTGACC	0.378																																																0													176.0	167.0	170.0					21																	47952057		1936	4138	6074	SO:0001819	synonymous_variant	23181			AF490768	CCDS46655.1, CCDS46656.1, CCDS46657.1, CCDS54490.1, CCDS54491.1	21q22.3	2010-08-20	2006-01-13	2006-01-13	ENSG00000160305	ENSG00000160305			17217	protein-coding gene	gene with protein product		607711	"""chromosome 21 open reading frame 106"""	C21orf106			Standard	NM_015151		Approved	Dip2, KIAA0184	uc002zjo.2	Q14689	OTTHUMG00000090717	ENST00000417564.2:c.1212G>T	21.37:g.47952057G>T			A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Silent	SNP	ENST00000417564.2	37	CCDS46655.1																																																																																				0.378	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151		18	32	18	32
DDX17	10521	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	22	38890947	38890947	+	Missense_Mutation	SNP	T	T	C			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr22:38890947T>C	ENST00000396821.3	-	7	1084	c.985A>G	c.(985-987)Aga>Gga	p.R329G	DDX17_ENST00000381633.3_Missense_Mutation_p.R250G|DDX17_ENST00000432525.1_5'UTR	NM_001098504.1|NM_006386.4	NP_001091974|NP_006377.2	Q92841	DDX17_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 17	329	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of skeletal muscle cell differentiation (GO:2001014)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA helicase activity (GO:0003724)|RNA-dependent ATPase activity (GO:0008186)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(6)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	25	Melanoma(58;0.0286)					TCAAGCATTCTGTCAGCTTCG	0.428																																					Ovarian(55;1085 1454 6392 21425)											0													126.0	117.0	120.0					22																	38890947		2203	4300	6503	SO:0001583	missense	10521			U59321	CCDS33646.1, CCDS46706.1	22q13.1	2012-02-23	2012-02-23		ENSG00000100201	ENSG00000100201		"""DEAD-boxes"""	2740	protein-coding gene	gene with protein product		608469	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 17 (72kD)"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 17"""			8871553, 17226766	Standard	NM_006386		Approved	P72	uc003avy.4	Q92841	OTTHUMG00000151136	ENST00000396821.3:c.985A>G	22.37:g.38890947T>C	ENSP00000380033:p.Arg329Gly		B1AHM0|Q69YT1|Q6ICD6	Missense_Mutation	SNP	ENST00000396821.3	37	CCDS46706.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.005963	0.74932	.	.	ENSG00000100201	ENST00000396821;ENST00000381633;ENST00000403230;ENST00000404499	T;T;T	0.06294	3.32;3.32;3.32	5.83	3.66	0.41972	RNA helicase, ATP-dependent, DEAD-box, conserved site (1);DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.39064	0.1064	H	0.97896	4.1	0.80722	D	1	D;D;D	0.89917	0.997;1.0;1.0	D;D;D	0.85130	0.96;0.997;0.996	T	0.56842	-0.7912	10	0.87932	D	0	-14.7846	12.7282	0.57183	0.0:0.0:0.269:0.731	.	250;331;329	Q92841;Q59F66;Q92841-4	DDX17_HUMAN;.;.	G	329;250;329;331	ENSP00000380033:R329G;ENSP00000371046:R250G;ENSP00000385536:R329G	ENSP00000371046:R250G	R	-	1	2	DDX17	37220893	1.000000	0.71417	0.999000	0.59377	0.973000	0.67179	2.750000	0.47500	0.450000	0.26774	0.533000	0.62120	AGA		0.428	DDX17-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321476.2	NM_030881		53	95	53	95
EDAR	10913	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	109539871	109539871	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr2:109539871C>T	ENST00000258443.2	-	5	825	c.395G>A	c.(394-396)gGc>gAc	p.G132D	EDAR_ENST00000409271.1_Missense_Mutation_p.G132D|EDAR_ENST00000376651.1_Missense_Mutation_p.G132D	NM_022336.3	NP_071731.1	Q9UNE0	EDAR_HUMAN	ectodysplasin A receptor	132					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|epidermis development (GO:0008544)|hair follicle development (GO:0001942)|odontogenesis of dentin-containing tooth (GO:0042475)|pigmentation (GO:0043473)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|salivary gland cavitation (GO:0060662)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	16						GCAGACCATGCCATAGATGTT	0.542																																																0													178.0	148.0	158.0					2																	109539871		2203	4300	6503	SO:0001583	missense	10913			AF130988	CCDS2081.1	2q13	2013-05-22	2004-08-09		ENSG00000135960	ENSG00000135960		"""Tumor necrosis factor receptor superfamily"""	2895	protein-coding gene	gene with protein product		604095	"""ectodysplasin 1, anhidrotic receptor"""	ED3, DL		10431241, 9375732	Standard	NM_022336		Approved	ED5, EDA3, Edar, ED1R, EDA1R	uc002teq.4	Q9UNE0	OTTHUMG00000130982	ENST00000258443.2:c.395G>A	2.37:g.109539871C>T	ENSP00000258443:p.Gly132Asp		B2R9H2|B4DLC5|D3DX74|E9PC98|Q52LL5|Q9UND9	Missense_Mutation	SNP	ENST00000258443.2	37	CCDS2081.1	.	.	.	.	.	.	.	.	.	.	C	19.05	3.752084	0.69533	.	.	ENSG00000135960	ENST00000409271;ENST00000258443;ENST00000376651	D;D;D	0.89552	-2.52;-2.53;-2.52	5.24	5.24	0.73138	.	0.152498	0.64402	D	0.000015	D	0.90844	0.7124	L	0.38175	1.15	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.74674	0.984;0.96	D	0.87067	0.2157	10	0.11794	T	0.64	-40.3192	18.8226	0.92103	0.0:1.0:0.0:0.0	.	132;132	E9PC98;Q9UNE0	.;EDAR_HUMAN	D	132	ENSP00000386371:G132D;ENSP00000258443:G132D;ENSP00000365839:G132D	ENSP00000258443:G132D	G	-	2	0	EDAR	108906303	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.315000	0.59172	2.436000	0.82500	0.561000	0.74099	GGC		0.542	EDAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253595.1			54	85	54	85
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	2835	Substitution - Missense(2834)|Complex - compound substitution(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)											79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			27	44	27	44
EPHA3	2042	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	89498454	89498454	+	Missense_Mutation	SNP	G	G	T			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr3:89498454G>T	ENST00000336596.2	+	14	2651	c.2426G>T	c.(2425-2427)aGt>aTt	p.S809I	EPHA3_ENST00000494014.1_Missense_Mutation_p.S809I	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	809	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		GATGTATGGAGTTATGGGATT	0.448										TSP Lung(6;0.00050)																																						0													255.0	234.0	241.0					3																	89498454		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.2426G>T	3.37:g.89498454G>T	ENSP00000337451:p.Ser809Ile		Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.049504	0.75846	.	.	ENSG00000044524	ENST00000336596;ENST00000494014	T;T	0.78364	-1.17;-1.17	5.13	5.13	0.70059	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.92782	0.7705	H	0.98951	4.38	0.80722	D	1	D	0.71674	0.998	D	0.70487	0.969	D	0.95538	0.8609	9	.	.	.	.	15.7004	0.77538	0.0:0.1367:0.8633:0.0	.	809	P29320	EPHA3_HUMAN	I	809	ENSP00000337451:S809I;ENSP00000419190:S809I	.	S	+	2	0	EPHA3	89581144	1.000000	0.71417	1.000000	0.80357	0.788000	0.44548	7.961000	0.87903	2.396000	0.81511	0.655000	0.94253	AGT		0.448	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		54	72	54	72
HHLA2	11148	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	108074123	108074123	+	Missense_Mutation	SNP	T	T	C			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr3:108074123T>C	ENST00000357759.5	+	5	994	c.580T>C	c.(580-582)Tct>Cct	p.S194P	HHLA2_ENST00000467761.1_Missense_Mutation_p.S194P|HHLA2_ENST00000467562.1_Missense_Mutation_p.S130P|HHLA2_ENST00000491820.1_Missense_Mutation_p.S194P|HHLA2_ENST00000489514.2_Missense_Mutation_p.S194P	NM_007072.2	NP_009003.1	Q9UM44	HHLA2_HUMAN	HERV-H LTR-associating 2	194	Ig-like C1-type.				positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(14)|ovary(1)	18						GGATTCTTTTTCTATTAACAG	0.388																																																0													88.0	84.0	85.0					3																	108074123		1852	4089	5941	SO:0001583	missense	11148			AF126162	CCDS46883.1, CCDS63713.1, CCDS74975.1	3q13.13	2013-01-11			ENSG00000114455	ENSG00000114455		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	4905	protein-coding gene	gene with protein product		604371				10444326	Standard	NM_007072		Approved	B7H7	uc003dwz.3	Q9UM44	OTTHUMG00000159224	ENST00000357759.5:c.580T>C	3.37:g.108074123T>C	ENSP00000350402:p.Ser194Pro		B4DKN2|D3DN60|Q9NWQ6	Missense_Mutation	SNP	ENST00000357759.5	37	CCDS46883.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.90|13.90	2.375424|2.375424	0.42105|0.42105	.|.	.|.	ENSG00000114455|ENSG00000114455	ENST00000482099|ENST00000491820;ENST00000467562;ENST00000357759;ENST00000467761;ENST00000489514	T|T;T;T;T;T	0.04603|0.03035	3.59|4.07;4.07;4.07;4.07;4.07	5.56|5.56	-1.07|-1.07	0.09968|0.09968	.|Immunoglobulin-like (1);Immunoglobulin C1-set (1);Immunoglobulin-like fold (1);	.|1.284410	.|0.05618	.|N	.|0.579415	T|T	0.03959|0.03959	0.0111|0.0111	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	.|D;D;D	.|0.54964	.|0.969;0.969;0.969	.|P;P;P	.|0.48770	.|0.589;0.45;0.589	T|T	0.38757|0.38757	-0.9646|-0.9646	6|9	.|.	.|.	.|.	-10.2422|-10.2422	5.1187|5.1187	0.14849|0.14849	0.0:0.3285:0.1522:0.5193|0.0:0.3285:0.1522:0.5193	.|.	.|130;194;194	.|B4DKN2;C9J7D0;Q9UM44	.|.;.;HHLA2_HUMAN	S|P	96|194;130;194;194;194	ENSP00000418797:F96S|ENSP00000418284:S194P;ENSP00000418345:S130P;ENSP00000350402:S194P;ENSP00000419207:S194P;ENSP00000417856:S194P	.|.	F|S	+|+	2|1	0|0	HHLA2|HHLA2	109556813|109556813	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.005000|0.005000	0.04900|0.04900	-1.133000|-1.133000	0.03232|0.03232	-0.420000|-0.420000	0.07427|0.07427	0.533000|0.533000	0.62120|0.62120	TTC|TCT		0.388	HHLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353924.1	NM_007072		12	80	12	80
MUC4	4585	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	195515511	195515511	+	Silent	SNP	G	G	A	rs533360052		TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr3:195515511G>A	ENST00000463781.3	-	2	3399	c.2940C>T	c.(2938-2940)acC>acT	p.T980T	MUC4_ENST00000475231.1_Silent_p.T980T|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	985	Ser-rich.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGCGTAGGTGACAGGAA	0.572																																																0													93.0	89.0	90.0					3																	195515511		2196	4277	6473	SO:0001819	synonymous_variant	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.2940C>T	3.37:g.195515511G>A			O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																				0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406		10	24	10	24
ALB	213	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	74280861	74280861	+	Missense_Mutation	SNP	C	C	T	rs141343001		TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr4:74280861C>T	ENST00000503124.1	+	7	925	c.718C>T	c.(718-720)Cct>Tct	p.P240S	ALB_ENST00000509063.1_Missense_Mutation_p.P390S|ALB_ENST00000295897.4_Missense_Mutation_p.P390S|ALB_ENST00000401494.3_Missense_Mutation_p.P275S|ALB_ENST00000415165.2_Missense_Mutation_p.P198S|ALB_ENST00000505649.1_3'UTR			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)		p.P390S(1)		NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			CGCTGCAGATCCTCATGAATG	0.398																																																1	Substitution - Missense(1)	skin(1)											127.0	124.0	125.0					4																	74280861		2203	4300	6503	SO:0001583	missense	213			V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.718C>T	4.37:g.74280861C>T	ENSP00000421027:p.Pro240Ser		B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000503124.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.19|11.19	1.564304|1.564304	0.27915|0.27915	.|.	.|.	ENSG00000163631|ENSG00000163631	ENST00000295897;ENST00000415165;ENST00000329326;ENST00000503124;ENST00000509063;ENST00000401494;ENST00000430202|ENST00000511370	T;T;T;T;T|.	0.74002|.	-0.8;-0.8;-0.8;-0.8;-0.8|.	5.83|5.83	4.98|4.98	0.66077|0.66077	Serum albumin, conserved site (1);Serum albumin-like (1);Serum albumin, N-terminal (3);|.	0.133061|.	0.51477|.	D|.	0.000082|.	T|T	0.78767|0.78767	0.4335|0.4335	M|M	0.86268|0.86268	2.805|2.805	0.52501|0.52501	D|D	0.99995|0.99995	D;P;D;P;P|.	0.61080|.	0.989;0.776;0.988;0.512;0.776|.	P;P;P;B;P|.	0.57720|.	0.826;0.457;0.826;0.203;0.457|.	T|T	0.81508|0.81508	-0.0901|-0.0901	10|5	0.72032|.	D|.	0.01|.	-14.5554|-14.5554	15.4287|15.4287	0.75075|0.75075	0.0:0.8456:0.1544:0.0|0.0:0.8456:0.1544:0.0	.|.	275;198;240;390;390|.	B7WNR0;C9JKR2;D6RHD5;A6NBZ8;P02768|.	.;.;.;.;ALBU_HUMAN|.	S|F	390;198;177;240;390;275;399|234	ENSP00000295897:P390S;ENSP00000401820:P198S;ENSP00000421027:P240S;ENSP00000422784:P390S;ENSP00000384695:P275S|.	ENSP00000295897:P390S|.	P|S	+|+	1|2	0|0	ALB|ALB	74499725|74499725	0.678000|0.678000	0.27586|0.27586	0.885000|0.885000	0.34714|0.34714	0.014000|0.014000	0.08584|0.08584	1.906000|1.906000	0.39887|0.39887	1.433000|1.433000	0.47394|0.47394	0.650000|0.650000	0.86243|0.86243	CCT|TCC		0.398	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		44	7	44	7
MATR3	9782	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	138643853	138643853	+	Missense_Mutation	SNP	A	A	G			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr5:138643853A>G	ENST00000394805.3	+	2	1084	c.749A>G	c.(748-750)tAt>tGt	p.Y250C	MATR3_ENST00000504203.1_Intron|MATR3_ENST00000361059.2_Missense_Mutation_p.Y250C|MATR3_ENST00000502929.1_Missense_Mutation_p.Y250C|MATR3_ENST00000503811.1_Intron|MATR3_ENST00000509990.1_Missense_Mutation_p.Y250C|MATR3_ENST00000502499.1_Intron|MATR3_ENST00000394800.2_Missense_Mutation_p.Y250C|MATR3_ENST00000510056.1_Missense_Mutation_p.Y250C	NM_001194955.1|NM_018834.5	NP_001181884.1|NP_061322.2	P43243	MATR3_HUMAN	matrin 3	250					cell death (GO:0008219)	membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|kidney(4)|large_intestine(6)|lung(9)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GACAGTGAGTATGAGAGAATG	0.418																																																0													84.0	85.0	85.0					5																	138643853		2203	4300	6503	SO:0001583	missense	9782			M63483	CCDS4210.1, CCDS54908.1, CCDS75316.1	5q31.3	2010-08-12			ENSG00000015479	ENSG00000015479			6912	protein-coding gene	gene with protein product		164015	"""myopathy, distal 2"""	MPD2		2033075, 19344878	Standard	NM_018834		Approved	KIAA0723, MGC9105, VCPDM	uc003ldx.3	P43243	OTTHUMG00000129229	ENST00000394805.3:c.749A>G	5.37:g.138643853A>G	ENSP00000378284:p.Tyr250Cys		B7ZAV5|D3DQC3|Q9UHW0|Q9UQ27	Missense_Mutation	SNP	ENST00000394805.3	37	CCDS4210.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.99|13.99	2.402744|2.402744	0.42613|0.42613	.|.	.|.	ENSG00000015479|ENSG00000015479	ENST00000515833|ENST00000509990;ENST00000361059;ENST00000502929;ENST00000394800;ENST00000394805;ENST00000504045;ENST00000510056	.|T;T;T;T;T;T;T	.|0.80304	.|-0.89;-0.89;-0.92;-0.92;-0.89;-1.36;-0.89	5.4|5.4	5.4|5.4	0.78164|0.78164	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.83289|0.83289	0.5222|0.5222	N|N	0.24115|0.24115	0.695|0.695	0.52099|0.52099	D|D	0.999943|0.999943	.|D;D;D	.|0.76494	.|0.999;0.98;0.999	.|D;D;D	.|0.77557	.|0.99;0.96;0.99	D|D	0.86015|0.86015	0.1503|0.1503	5|10	.|0.87932	.|D	.|0	-10.4463|-10.4463	15.7064|15.7064	0.77583|0.77583	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|250;250;250	.|D6REM6;A8MXP9;P43243	.|.;.;MATR3_HUMAN	V|C	24|250	.|ENSP00000423533:Y250C;ENSP00000354346:Y250C;ENSP00000422319:Y250C;ENSP00000378279:Y250C;ENSP00000378284:Y250C;ENSP00000423290:Y250C;ENSP00000426743:Y250C	.|ENSP00000354346:Y250C	M|Y	+|+	1|2	0|0	MATR3|MATR3	138671752|138671752	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	4.602000|4.602000	0.61098|0.61098	2.171000|2.171000	0.68590|0.68590	0.459000|0.459000	0.35465|0.35465	ATG|TAT		0.418	MATR3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251324.2	NM_018834		23	64	23	64
EHMT2	10919	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	31856769	31856769	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr6:31856769C>T	ENST00000375537.4	-	10	1199	c.1193G>A	c.(1192-1194)gGg>gAg	p.G398E	EHMT2_ENST00000375528.4_Intron|EHMT2_ENST00000375530.4_Intron|EHMT2_ENST00000395728.3_Missense_Mutation_p.G455E|EHMT2_ENST00000480912.1_5'UTR	NM_006709.3	NP_006700.3	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	398					DNA methylation (GO:0006306)|DNA methylation on cytosine within a CG sequence (GO:0010424)|fertilization (GO:0009566)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ growth (GO:0035265)|peptidyl-lysine dimethylation (GO:0018027)|regulation of DNA replication (GO:0006275)|spermatid development (GO:0007286)|synaptonemal complex assembly (GO:0007130)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	21						GGAGAGGGTCCCCTCGCTGGG	0.632																																																0													13.0	15.0	15.0					6																	31856769		2202	4299	6501	SO:0001583	missense	10919			AF134726	CCDS4725.1, CCDS4726.1, CCDS75425.1	6p21.3	2013-01-10	2004-03-22	2005-06-09	ENSG00000204371	ENSG00000204371	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"", ""Ankyrin repeat domain containing"""	14129	protein-coding gene	gene with protein product		604599	"""chromosome 6 open reading frame 30"", ""HLA-B associated transcript 8"""	C6orf30, BAT8		8457211, 11316813	Standard	XM_005274833		Approved	G9A, Em:AF134726.3, NG36/G9a, KMT1C	uc003nxz.1	Q96KQ7	OTTHUMG00000031180	ENST00000375537.4:c.1193G>A	6.37:g.31856769C>T	ENSP00000364687:p.Gly398Glu		B0UZY2|Q14349|Q5JP83|Q5JQ92|Q5JQA1|Q5JQG3|Q6PK06|Q96MH5|Q96QD0|Q9UQL8|Q9Y331	Missense_Mutation	SNP	ENST00000375537.4	37	CCDS4725.1	.	.	.	.	.	.	.	.	.	.	C	12.15	1.852050	0.32699	.	.	ENSG00000204371	ENST00000395728;ENST00000375537;ENST00000442298	T;T	0.69685	-0.42;-0.41	4.61	4.61	0.57282	.	0.080699	0.50627	D	0.000102	T	0.41419	0.1158	L	0.34521	1.04	0.35837	D	0.825732	B;B	0.25667	0.131;0.049	B;B	0.28011	0.057;0.085	T	0.34551	-0.9824	10	0.17832	T	0.49	.	16.3909	0.83537	0.0:1.0:0.0:0.0	.	398;212	Q96KQ7;Q59FM7	EHMT2_HUMAN;.	E	455;398;212	ENSP00000379078:G455E;ENSP00000364687:G398E	ENSP00000364687:G398E	G	-	2	0	EHMT2	31964748	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.813000	0.55636	2.393000	0.81446	0.555000	0.69702	GGG		0.632	EHMT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076355.5	NM_006709		14	15	14	15
MTO1	25821	hgsc.bcm.edu;broad.mit.edu	37	6	74191908	74191908	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr6:74191908G>A	ENST00000370300.4	+	9	1571	c.1481G>A	c.(1480-1482)cGa>cAa	p.R494Q	MTO1_ENST00000370305.1_Missense_Mutation_p.R420Q|MTO1_ENST00000415954.2_Missense_Mutation_p.R509Q|MTO1_ENST00000498286.1_Missense_Mutation_p.R469Q	NM_012123.3|NM_133645.2	NP_036255.2|NP_598400.1	Q9Y2Z2	MTO1_HUMAN	mitochondrial tRNA translation optimization 1	494					mitochondrial tRNA wobble uridine modification (GO:0070899)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)	27						TTTACCAGCCGAGTAGAGTTC	0.527																																																0													151.0	115.0	127.0					6																	74191908		2203	4300	6503	SO:0001583	missense	25821			AF132937	CCDS4979.1, CCDS34485.1, CCDS47452.1	6q14.1	2013-05-07	2013-05-07		ENSG00000135297	ENSG00000135297			19261	protein-coding gene	gene with protein product		614667	"""mitochondrial translation optimization 1 homolog (S. cerevisiae)"""			12011058, 22608499	Standard	NM_012123		Approved		uc003pgy.4	Q9Y2Z2	OTTHUMG00000015032	ENST00000370300.4:c.1481G>A	6.37:g.74191908G>A	ENSP00000359323:p.Arg494Gln		B3KQB5|Q5SWL2|Q5SWL3|Q5SWL4|Q8NDN7|Q8WZ57|Q96FE6|Q9BS06	Missense_Mutation	SNP	ENST00000370300.4	37	CCDS4979.1	.	.	.	.	.	.	.	.	.	.	G	36	5.832867	0.97003	.	.	ENSG00000135297	ENST00000415954;ENST00000498286;ENST00000357845;ENST00000370305;ENST00000370300;ENST00000521156	.	.	.	5.48	5.48	0.80851	.	0.125717	0.52532	D	0.000067	D	0.89770	0.6811	H	0.97440	4.005	0.58432	D	0.999998	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.989;0.997;0.989;0.975	D	0.92692	0.6167	9	0.87932	D	0	-3.5456	19.7645	0.96335	0.0:0.0:1.0:0.0	.	509;372;469;494	Q9Y2Z2-6;Q9Y2Z2-2;Q9Y2Z2-4;Q9Y2Z2	.;.;.;MTO1_HUMAN	Q	509;469;372;420;494;24	.	ENSP00000350506:R372Q	R	+	2	0	MTO1	74248629	1.000000	0.71417	0.993000	0.49108	0.991000	0.79684	9.392000	0.97252	2.749000	0.94314	0.454000	0.30748	CGA		0.527	MTO1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041215.2	NM_012123		7	79	7	79
AK9	221264	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	109854548	109854548	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr6:109854548C>T	ENST00000424296.2	-	28	3552	c.3476G>A	c.(3475-3477)cGc>cAc	p.R1159H	AK9_ENST00000341338.6_Missense_Mutation_p.R238H|AK9_ENST00000355283.1_Missense_Mutation_p.R238H	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	1159	Adenylate kinase 2.				ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)										AGGAAGGAGGCGATCAAAAAT	0.383																																																0													154.0	139.0	144.0					6																	109854548		2203	4300	6503	SO:0001583	missense	221264			AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"""chromosome 6 open reading frame 224"", ""adenylate kinase domain containing 2"", ""chromosome 6 open reading frame 199"", ""adenylate kinase domain containing 1"""	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.3476G>A	6.37:g.109854548C>T	ENSP00000410186:p.Arg1159His		A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Missense_Mutation	SNP	ENST00000424296.2	37	CCDS55048.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.9|26.9	4.777801|4.777801	0.90195|0.90195	.|.	.|.	ENSG00000155085|ENSG00000155085	ENST00000491875|ENST00000424296;ENST00000355283;ENST00000341338	.|D;D;D	.|0.87029	.|-2.2;-2.2;-2.2	5.16|5.16	5.16|5.16	0.70880|0.70880	.|ATPase, AAA+ type, core (1);	.|0.106561	.|0.64402	.|N	.|0.000003	D|D	0.93579|0.93579	0.7950|0.7950	M|M	0.85542|0.85542	2.76|2.76	0.40156|0.40156	D|D	0.977004|0.977004	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|0.999;1.0	D|D	0.93478|0.93478	0.6825|0.6825	5|9	.|.	.|.	.|.	.|.	19.0135|19.0135	0.92884|0.92884	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|238;1159	.|Q5TCS8-5;Q5TCS8	.|.;AKD1_HUMAN	T|H	94|1159;238;238	.|ENSP00000410186:R1159H;ENSP00000347431:R238H;ENSP00000344637:R238H	.|.	A|R	-|-	1|2	0|0	AKD1|AKD1	109961241|109961241	0.997000|0.997000	0.39634|0.39634	0.948000|0.948000	0.38648|0.38648	0.797000|0.797000	0.45037|0.45037	3.813000|3.813000	0.55636|0.55636	2.579000|2.579000	0.87056|0.87056	0.549000|0.549000	0.68633|0.68633	GCC|CGC		0.383	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128		36	42	36	42
KIAA1244	57221	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	138657616	138657616	+	Missense_Mutation	SNP	T	T	C			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr6:138657616T>C	ENST00000251691.4	+	34	6693	c.6527T>C	c.(6526-6528)aTt>aCt	p.I2176T		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		TATGACATCATTGTGTAGCCG	0.552																																																0													88.0	77.0	81.0					6																	138657616		2203	4300	6503	SO:0001583	missense	57221			AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	21213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 33"""		"""chromosome 6 open reading frame 92"""	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.6527T>C	6.37:g.138657616T>C	ENSP00000251691:p.Ile2176Thr			Missense_Mutation	SNP	ENST00000251691.4	37	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	T	15.55	2.867262	0.51588	.	.	ENSG00000112379	ENST00000251691;ENST00000367706	T	0.21932	1.98	6.02	6.02	0.97574	.	0.102892	0.64402	D	0.000004	T	0.06917	0.0176	N	0.14661	0.345	0.48341	D	0.999635	P	0.35077	0.483	B	0.27887	0.084	T	0.10706	-1.0618	10	0.72032	D	0.01	-25.8071	16.5446	0.84426	0.0:0.0:0.0:1.0	.	2176	Q5TH69	BIG3_HUMAN	T	2176;217	ENSP00000251691:I2176T	ENSP00000251691:I2176T	I	+	2	0	KIAA1244	138699309	1.000000	0.71417	0.957000	0.39632	0.643000	0.38383	6.068000	0.71201	2.311000	0.77944	0.533000	0.62120	ATT		0.552	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		39	42	39	42
CASD1	64921	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	7	94163000	94163000	+	Missense_Mutation	SNP	A	A	G			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr7:94163000A>G	ENST00000297273.4	+	7	801	c.514A>G	c.(514-516)Aag>Gag	p.K172E		NM_022900.4	NP_075051.4	Q96PB1	CASD1_HUMAN	CAS1 domain containing 1	172						integral component of membrane (GO:0016021)				NS(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1)	31	all_cancers(62;6.71e-10)|all_epithelial(64;5e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			GTGGTCCATCAAGATTCACAA	0.294																																																0													57.0	58.0	58.0					7																	94163000		2202	4299	6501	SO:0001583	missense	64921			AF355594	CCDS5636.1	7q22	2006-03-09			ENSG00000127995	ENSG00000127995			16014	protein-coding gene	gene with protein product	"""chromosome 7 open reading frame 12"""	611686				11703667, 11528394	Standard	NM_022900		Approved	FLJ21213, FLJ21879, C7orf12	uc003uni.4	Q96PB1	OTTHUMG00000023356	ENST00000297273.4:c.514A>G	7.37:g.94163000A>G	ENSP00000297273:p.Lys172Glu		B3KW13|O14574|Q3LIE2|Q6P4R4|Q9H6T9|Q9H770	Missense_Mutation	SNP	ENST00000297273.4	37	CCDS5636.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.189327	0.78789	.	.	ENSG00000127995	ENST00000447923;ENST00000297273	T;T	0.18174	2.23;2.26	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.40619	0.1124	M	0.69823	2.125	0.58432	D	0.999999	D;D;D	0.69078	0.997;0.997;0.997	D;D;D	0.80764	0.994;0.994;0.994	T	0.13255	-1.0516	10	0.33940	T	0.23	.	15.4836	0.75548	1.0:0.0:0.0:0.0	.	172;172;172	Q8WZ77;Q96PB1;B2RAS9	.;CASD1_HUMAN;.	E	103;172	ENSP00000396261:K103E;ENSP00000297273:K172E	ENSP00000297273:K172E	K	+	1	0	CASD1	94000936	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	8.982000	0.93471	2.115000	0.64714	0.460000	0.39030	AAG		0.294	CASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255216.1	NM_022900		27	63	27	63
KLHL38	340359	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	124664667	124664667	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr8:124664667G>A	ENST00000325995.7	-	1	523	c.500C>T	c.(499-501)gCc>gTc	p.A167V	CTD-2552K11.2_ENST00000524355.1_RNA	NM_001081675.2	NP_001075144.2	Q2WGJ6	KLH38_HUMAN	kelch-like family member 38	167	BACK.									breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(16)|pancreas(1)|prostate(3)|stomach(1)	38						GGCCGATGCGGCCACCTCTGG	0.567																																																0													53.0	54.0	54.0					8																	124664667		1968	4143	6111	SO:0001583	missense	340359				CCDS43766.1	8q24.13	2013-02-22	2013-02-22		ENSG00000175946	ENSG00000175946		"""Kelch-like"", ""BTB/POZ domain containing"""	34435	protein-coding gene	gene with protein product			"""kelch-like 38 (Drosophila)"""				Standard	NM_001081675		Approved	C8ORFK36	uc003yqs.1	Q2WGJ6	OTTHUMG00000164983	ENST00000325995.7:c.500C>T	8.37:g.124664667G>A	ENSP00000321475:p.Ala167Val		A0PK12	Missense_Mutation	SNP	ENST00000325995.7	37	CCDS43766.1	.	.	.	.	.	.	.	.	.	.	G	10.75	1.438777	0.25900	.	.	ENSG00000175946	ENST00000325995	T	0.68025	-0.3	5.29	5.29	0.74685	BTB/Kelch-associated (2);	0.100336	0.64402	D	0.000002	T	0.52008	0.1708	L	0.27053	0.805	0.58432	D	0.999997	B	0.02656	0.0	B	0.09377	0.004	T	0.51949	-0.8640	10	0.02654	T	1	.	18.9124	0.92491	0.0:0.0:1.0:0.0	.	167	Q2WGJ6	KLH38_HUMAN	V	167	ENSP00000321475:A167V	ENSP00000321475:A167V	A	-	2	0	KLHL38	124733848	1.000000	0.71417	0.949000	0.38748	0.013000	0.08279	6.689000	0.74562	2.480000	0.83734	0.491000	0.48974	GCC		0.567	KLHL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381288.1			64	73	64	73
FUBP3	8939	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	9	133506050	133506050	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr9:133506050G>A	ENST00000319725.9	+	13	1228	c.1153G>A	c.(1153-1155)Ggg>Agg	p.G385R		NM_003934.1	NP_003925.1	Q96I24	FUBP3_HUMAN	far upstream element (FUSE) binding protein 3	385	KH 4. {ECO:0000255|PROSITE- ProRule:PRU00117}.				positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(10)|ovary(2)|urinary_tract(2)	21				OV - Ovarian serous cystadenocarcinoma(145;0.000279)		CCAGCAGTCAGGGGCGCACGT	0.612																																																0													49.0	53.0	52.0					9																	133506050		1987	4167	6154	SO:0001583	missense	8939			U69127	CCDS43893.1	9q34.11	2008-02-05			ENSG00000107164	ENSG00000107164			4005	protein-coding gene	gene with protein product		603536		FBP3		8940189	Standard	NM_003934		Approved		uc004bzr.1	Q96I24	OTTHUMG00000020809	ENST00000319725.9:c.1153G>A	9.37:g.133506050G>A	ENSP00000318177:p.Gly385Arg		A3KFK8|A3KFL0|Q92946|Q9BVB6	Missense_Mutation	SNP	ENST00000319725.9	37	CCDS43893.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.573366	0.86542	.	.	ENSG00000107164	ENST00000319725	T	0.50001	0.76	5.53	5.53	0.82687	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.096902	0.64402	D	0.000001	T	0.64338	0.2589	M	0.79258	2.445	0.80722	D	1	P;P	0.50943	0.94;0.94	P;P	0.52881	0.712;0.712	T	0.68273	-0.5452	10	0.62326	D	0.03	-15.1315	18.4501	0.90700	0.0:0.0:1.0:0.0	.	385;385	A3KFK8;Q96I24	.;FUBP3_HUMAN	R	385	ENSP00000318177:G385R	ENSP00000318177:G385R	G	+	1	0	FUBP3	132495871	1.000000	0.71417	0.927000	0.36925	0.918000	0.54935	6.377000	0.73145	2.592000	0.87571	0.655000	0.94253	GGG		0.612	FUBP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054666.1			38	68	38	68
USP9X	8239	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	41057788	41057788	+	Missense_Mutation	SNP	T	T	C			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chrX:41057788T>C	ENST00000324545.8	+	30	5021	c.4388T>C	c.(4387-4389)aTt>aCt	p.I1463T	USP9X_ENST00000378308.2_Missense_Mutation_p.I1463T	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	1463					axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						TAGGAATTAATTGATGATTTC	0.318																																					Ovarian(172;1807 2695 35459 49286)											0													96.0	83.0	87.0					X																	41057788		1947	4143	6090	SO:0001583	missense	8239			X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"""Ubiquitin-specific peptidases"""	12632	protein-coding gene	gene with protein product		300072	"""ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)"", ""ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)"", ""ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"""			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.4388T>C	X.37:g.41057788T>C	ENSP00000316357:p.Ile1463Thr		O75550|Q8WWT3|Q8WX12	Missense_Mutation	SNP	ENST00000324545.8	37	CCDS43930.1	.	.	.	.	.	.	.	.	.	.	T	13.33	2.205803	0.39003	.	.	ENSG00000124486	ENST00000378308;ENST00000324545	T;T	0.03181	4.02;4.02	5.04	5.04	0.67666	.	0.044884	0.85682	D	0.000000	T	0.04543	0.0124	L	0.33485	1.01	0.80722	D	1	B;B	0.16603	0.018;0.011	B;B	0.14578	0.011;0.008	T	0.37596	-0.9699	10	0.62326	D	0.03	.	14.1012	0.65056	0.0:0.0:0.0:1.0	.	1463;1463	Q93008-1;Q93008	.;USP9X_HUMAN	T	1463	ENSP00000367558:I1463T;ENSP00000316357:I1463T	ENSP00000316357:I1463T	I	+	2	0	USP9X	40942732	1.000000	0.71417	0.999000	0.59377	0.711000	0.40976	7.694000	0.84235	1.776000	0.52262	0.441000	0.28932	ATT		0.318	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652		23	2	23	2
CFTR	1080	broad.mit.edu;ucsc.edu	37	7	117304899	117304899	+	Missense_Mutation	SNP	C	C	T	rs115147093		TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr7:117304899C>T	ENST00000003084.6	+	25	4253	c.4121C>T	c.(4120-4122)gCt>gTt	p.A1374V	CFTR_ENST00000454343.1_Missense_Mutation_p.A1313V	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	1374	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	GAACCCAGTGCTCATTTGGAT	0.453									Cystic Fibrosis																																							0													217.0	183.0	194.0					7																	117304899		2203	4300	6503	SO:0001583	missense	1080	Familial Cancer Database	CF	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"""Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators"", ""ATP binding cassette transporters / subfamily C"""	1884	protein-coding gene	gene with protein product	"""ATP-binding cassette sub-family C, member 7"""	602421	"""cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"""	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.4121C>T	7.37:g.117304899C>T	ENSP00000003084:p.Ala1374Val		Q20BG8|Q20BH2|Q2I0A1|Q2I102	Missense_Mutation	SNP	ENST00000003084.6	37	CCDS5773.1	.	.	.	.	.	.	.	.	.	.	C	34	5.403853	0.96051	.	.	ENSG00000001626	ENST00000003084;ENST00000454343;ENST00000426809	D;D;D	0.91521	-2.86;-2.86;-2.86	5.78	5.78	0.91487	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.85682	D	0.000000	D	0.95242	0.8457	M	0.73372	2.23	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	D	0.94942	0.8092	10	0.87932	D	0	-16.9211	20.3754	0.98918	0.0:1.0:0.0:0.0	.	1374	P13569	CFTR_HUMAN	V	1374;1313;1344	ENSP00000003084:A1374V;ENSP00000403677:A1313V;ENSP00000389119:A1344V	ENSP00000003084:A1374V	A	+	2	0	CFTR	117092135	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.325000	0.79124	2.894000	0.99253	0.591000	0.81541	GCT		0.453	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492		67	235	67	235
KRT25	147183	broad.mit.edu;ucsc.edu	37	17	38906790	38906790	+	Silent	SNP	C	C	T			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr17:38906790C>T	ENST00000312150.4	-	6	1077	c.1017G>A	c.(1015-1017)gcG>gcA	p.A339A		NM_181534.3	NP_853512.1			keratin 25									p.A339A(2)		endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(4)	16		Breast(137;0.00526)				CCTGGATCTGCGCCAGCTGCG	0.562																																																2	Substitution - coding silent(2)	large_intestine(1)|prostate(1)											139.0	141.0	140.0					17																	38906790		2203	4300	6503	SO:0001819	synonymous_variant	147183			AK129503	CCDS11373.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000204897	ENSG00000204897		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30839	protein-coding gene	gene with protein product			"""keratin 25A"""	KRT25A		16831889	Standard	NM_181534		Approved		uc002hve.3	Q7Z3Z0	OTTHUMG00000133373	ENST00000312150.4:c.1017G>A	17.37:g.38906790C>T				Silent	SNP	ENST00000312150.4	37	CCDS11373.1																																																																																				0.562	KRT25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257218.1	NM_181534		117	159	117	159
OR4K17	390436	broad.mit.edu;ucsc.edu	37	14	20586367	20586367	+	Missense_Mutation	SNP	C	C	T	rs574115281		TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr14:20586367C>T	ENST00000315543.4	+	1	802	c.802C>T	c.(802-804)Cgt>Tgt	p.R268C		NM_001004715.1	NP_001004715.1	Q8NGC6	OR4KH_HUMAN	olfactory receptor, family 4, subfamily K, member 17	240						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(4)|lung(12)|pancreas(1)|skin(3)	21	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.77e-06)	GBM - Glioblastoma multiforme(265;0.0144)		ATCTAAAGCCCGTTCCACTTT	0.438													C|||	1	0.000199681	0.0	0.0	5008	,	,		19935	0.001		0.0	False		,,,				2504	0.0															0													139.0	131.0	133.0					14																	20586367		2203	4300	6503	SO:0001583	missense	390436				CCDS32030.1	14q11.2	2013-09-23			ENSG00000176230	ENSG00000176230		"""GPCR / Class A : Olfactory receptors"""	15355	protein-coding gene	gene with protein product							Standard	NM_001004715		Approved		uc001vwo.1	Q8NGC6	OTTHUMG00000170783	ENST00000315543.4:c.802C>T	14.37:g.20586367C>T	ENSP00000319197:p.Arg268Cys		Q6IF12	Missense_Mutation	SNP	ENST00000315543.4	37	CCDS32030.1	.	.	.	.	.	.	.	.	.	.	.	7.729	0.698766	0.15106	.	.	ENSG00000176230	ENST00000315543	T	0.00099	8.73	2.86	-0.831	0.10789	GPCR, rhodopsin-like superfamily (1);	0.875902	0.09254	U	0.827485	T	0.00144	0.0004	N	0.14661	0.345	0.09310	N	1	D	0.54397	0.966	P	0.53809	0.735	T	0.52388	-0.8582	10	0.87932	D	0	.	7.0911	0.25285	0.0:0.2847:0.0:0.7153	.	240	Q8NGC6	OR4KH_HUMAN	C	268	ENSP00000319197:R268C	ENSP00000319197:R268C	R	+	1	0	OR4K17	19656207	0.000000	0.05858	0.405000	0.26409	0.033000	0.12548	-1.102000	0.03332	-0.063000	0.13065	-0.490000	0.04691	CGT		0.438	OR4K17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410346.1			49	54	49	54
RBPJ	3516	broad.mit.edu;ucsc.edu	37	4	26422326	26422326	+	Nonsense_Mutation	SNP	C	C	T			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr4:26422326C>T	ENST00000361572.6	+	5	708	c.514C>T	c.(514-516)Cag>Tag	p.Q172*	RBPJ_ENST00000355476.3_Nonsense_Mutation_p.Q158*|RBPJ_ENST00000342295.1_Nonsense_Mutation_p.Q172*|RBPJ_ENST00000504907.1_Nonsense_Mutation_p.Q158*|RBPJ_ENST00000348160.4_Nonsense_Mutation_p.Q159*|RBPJ_ENST00000507561.1_Nonsense_Mutation_p.Q137*|RBPJ_ENST00000345843.3_Nonsense_Mutation_p.Q157*|RBPJ_ENST00000342320.4_Nonsense_Mutation_p.Q158*			Q06330	SUH_HUMAN	recombination signal binding protein for immunoglobulin kappa J region	172					angiogenesis (GO:0001525)|arterial endothelial cell fate commitment (GO:0060844)|atrioventricular canal development (GO:0036302)|auditory receptor cell fate commitment (GO:0009912)|B cell differentiation (GO:0030183)|blood vessel endothelial cell fate specification (GO:0097101)|blood vessel lumenization (GO:0072554)|blood vessel remodeling (GO:0001974)|cardiac left ventricle morphogenesis (GO:0003214)|Clara cell differentiation (GO:0060486)|defense response to bacterium (GO:0042742)|DNA recombination (GO:0006310)|dorsal aorta morphogenesis (GO:0035912)|endocardium morphogenesis (GO:0003160)|epidermal cell fate specification (GO:0009957)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|gene expression (GO:0010467)|hair follicle maturation (GO:0048820)|humoral immune response (GO:0006959)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ossification (GO:0030279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|pituitary gland development (GO:0021983)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:1901297)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of ephrin receptor signaling pathway (GO:1901189)|positive regulation of ERBB signaling pathway (GO:1901186)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription of Notch receptor target (GO:0007221)|regulation of timing of cell differentiation (GO:0048505)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|sebaceous gland development (GO:0048733)|secondary heart field specification (GO:0003139)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|recombinase activity (GO:0000150)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)	15		Breast(46;0.0503)				CAAAAAGAAGCAGTCATTGAA	0.363																																																0													63.0	58.0	60.0					4																	26422326		2203	4300	6503	SO:0001587	stop_gained	3516			L07872	CCDS3436.1, CCDS3437.1, CCDS33969.1, CCDS43219.1	4p15.2	2013-10-18	2007-02-26	2007-02-26	ENSG00000168214	ENSG00000168214			5724	protein-coding gene	gene with protein product	"""suppressor of hairless homolog (Drosophila)"""	147183	"""recombining binding protein suppressor of hairless (Drosophila)"""	IGKJRB1, RBPSUH		8406481, 9290259	Standard	NM_005349		Approved	SUH, IGKJRB, RBPJK, KBF2, RBP-J, CBF1	uc003gsb.2	Q06330	OTTHUMG00000097793	ENST00000361572.6:c.514C>T	4.37:g.26422326C>T	ENSP00000354528:p.Gln172*		B4DY22|Q5XKH9|Q6P1N3	Nonsense_Mutation	SNP	ENST00000361572.6	37	CCDS3437.1	.	.	.	.	.	.	.	.	.	.	C	37	6.331017	0.97480	.	.	ENSG00000168214	ENST00000510778;ENST00000512671;ENST00000345843;ENST00000342295;ENST00000361572;ENST00000348160;ENST00000355476;ENST00000507561;ENST00000507574;ENST00000515573;ENST00000504907;ENST00000342320;ENST00000504938	.	.	.	5.65	4.8	0.61643	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-9.0586	14.981	0.71311	0.0:0.93:0.0:0.07	.	.	.	.	X	195;172;157;172;172;159;158;137;137;137;158;158;137	.	ENSP00000345206:Q172X	Q	+	1	0	RBPJ	26031424	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.445000	0.80570	2.663000	0.90544	0.650000	0.86243	CAG		0.363	RBPJ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215046.2	NM_015874		25	2	25	2
HK1	3098	broad.mit.edu;ucsc.edu	37	10	71136763	71136763	+	Missense_Mutation	SNP	G	G	A	rs202028638		TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr10:71136763G>A	ENST00000359426.6	+	8	1053	c.949G>A	c.(949-951)Ggc>Agc	p.G317S	HK1_ENST00000494253.1_3'UTR|HK1_ENST00000360289.2_Missense_Mutation_p.G305S|HK1_ENST00000298649.3_Missense_Mutation_p.G316S|HK1_ENST00000404387.2_Missense_Mutation_p.G321S|HK1_ENST00000448642.2_Missense_Mutation_p.G352S	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	317	Hexokinase type-2 1.|Regulatory.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						GGCCAAGGAGGGCCTCTTATT	0.537																																																0													142.0	128.0	133.0					10																	71136763		2203	4300	6503	SO:0001583	missense	3098			M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	2.7.1.1		4922	protein-coding gene	gene with protein product		142600					Standard	NM_033496		Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000359426.6:c.949G>A	10.37:g.71136763G>A	ENSP00000352398:p.Gly317Ser		E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Missense_Mutation	SNP	ENST00000359426.6	37	CCDS7292.1	.	.	.	.	.	.	.	.	.	.	G	17.90	3.502527	0.64298	.	.	ENSG00000156515	ENST00000360289;ENST00000448642;ENST00000404387;ENST00000298649;ENST00000359426;ENST00000405407	D;D;D;D;D	0.96802	-4.13;-4.13;-4.13;-4.13;-4.13	4.94	2.05	0.26809	Hexokinase, C-terminal (1);	0.149827	0.64402	N	0.000012	D	0.92404	0.7589	L	0.52011	1.625	0.58432	D	0.999998	B;B;B;B;B;P	0.44690	0.001;0.005;0.0;0.001;0.004;0.841	B;B;B;B;B;B	0.36289	0.01;0.061;0.004;0.014;0.015;0.221	D	0.88120	0.2831	10	0.52906	T	0.07	-23.5565	9.5806	0.39486	0.2296:0.0:0.7704:0.0	.	317;317;316;352;321;305	A8K7J7;P19367;P19367-2;E7ENR4;P19367-3;P19367-4	.;HXK1_HUMAN;.;.;.;.	S	305;352;321;316;317;317	ENSP00000353433:G305S;ENSP00000402103:G352S;ENSP00000384774:G321S;ENSP00000298649:G316S;ENSP00000352398:G317S	ENSP00000298649:G316S	G	+	1	0	HK1	70806769	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	5.682000	0.68182	0.143000	0.18926	0.585000	0.79938	GGC		0.537	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048429.2	NM_000188		65	77	65	77
USP7	7874	broad.mit.edu;ucsc.edu	37	16	9000424	9000424	+	Silent	SNP	C	C	T			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr16:9000424C>T	ENST00000344836.4	-	13	1485	c.1287G>A	c.(1285-1287)gaG>gaA	p.E429E	USP7_ENST00000381886.4_Silent_p.E413E|USP7_ENST00000535863.1_Silent_p.E330E	NM_003470.2	NP_003461.2	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7 (herpes virus-associated)	429	USP.				maintenance of DNA methylation (GO:0010216)|multicellular organismal development (GO:0007275)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|protein deubiquitination (GO:0016579)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|transcription-coupled nucleotide-excision repair (GO:0006283)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(13)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	48						GTGGTAACTGCTCTGGGAATT	0.318																																																0													58.0	60.0	59.0					16																	9000424		2197	4300	6497	SO:0001819	synonymous_variant	7874			Z72499	CCDS32385.1, CCDS66941.1	16p13.3	2008-04-11	2005-08-08			ENSG00000187555		"""Ubiquitin-specific peptidases"""	12630	protein-coding gene	gene with protein product		602519	"""ubiquitin specific protease 7 (herpes virus-associated)"""	HAUSP		12838346, 9925944	Standard	NM_003470		Approved		uc002czl.2	Q93009		ENST00000344836.4:c.1287G>A	16.37:g.9000424C>T			A6NMY8|B7Z815|H0Y3G8	Silent	SNP	ENST00000344836.4	37	CCDS32385.1																																																																																				0.318	USP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434268.2			37	37	37	37
TARS	6897	broad.mit.edu;ucsc.edu	37	5	33445453	33445453	+	Silent	SNP	A	A	G			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr5:33445453A>G	ENST00000265112.3	+	2	392	c.81A>G	c.(79-81)caA>caG	p.Q27Q	TARS_ENST00000455217.2_Silent_p.Q27Q|TARS_ENST00000414361.2_5'UTR|TARS_ENST00000541634.1_5'UTR|TARS_ENST00000502553.1_Silent_p.Q27Q	NM_152295.4	NP_689508.3	P26639	SYTC_HUMAN	threonyl-tRNA synthetase	27					gene expression (GO:0010467)|threonyl-tRNA aminoacylation (GO:0006435)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|threonine-tRNA ligase activity (GO:0004829)			NS(1)|biliary_tract(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)	29					L-Threonine(DB00156)	AAGAGAAGCAAAAGGAAGGAG	0.423																																																0													99.0	95.0	97.0					5																	33445453		2203	4300	6503	SO:0001819	synonymous_variant	6897			AK095852	CCDS3899.1, CCDS58943.1	5p13.2	2012-10-02			ENSG00000113407	ENSG00000113407	6.1.1.3	"""Aminoacyl tRNA synthetases / Class II"""	11572	protein-coding gene	gene with protein product	"""threonine tRNA ligase 1, cytoplasmic"""	187790					Standard	NM_152295		Approved		uc011coc.3	P26639	OTTHUMG00000090683	ENST00000265112.3:c.81A>G	5.37:g.33445453A>G			A8K8I1|B4DEG8|Q96FP5|Q9BWA6	Silent	SNP	ENST00000265112.3	37	CCDS3899.1																																																																																				0.423	TARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207367.1	NM_152295		3	16	3	16
IGHV3-30	28439	broad.mit.edu;ucsc.edu	37	14	106791017	106791017	+	RNA	SNP	A	A	G			TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr14:106791017A>G	ENST00000390613.2	-	0	418									immunoglobulin heavy variable 3-30																		TCGCACAGTAATACACAGCCG	0.567																																																0													251.0	300.0	284.0					14																	106791017		2099	4231	6330			28439			M83134		14q32.33	2012-02-08			ENSG00000211953	ENSG00000270550		"""Immunoglobulins / IGH locus"""	5591	other	immunoglobulin gene							Standard	NG_001019		Approved				OTTHUMG00000152069		14.37:g.106791017A>G				RNA	SNP	ENST00000390613.2	37																																																																																					0.567	IGHV3-30-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000325163.1	NG_001019		157	1166	157	1166
TATDN2	9797	broad.mit.edu;hgsc.bcm.edu	37	3	10291133	10291135	+	In_Frame_Del	DEL	CTT	CTT	-	rs148201381		TCGA-DU-6410-01A-11D-1893-08	TCGA-DU-6410-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f978b356-f9ee-415d-b39c-a8ef1b221734	2b140fc8-fb90-4bf3-93e2-ce81a83a703a	g.chr3:10291133_10291135delCTT	ENST00000287652.4	+	2	1300_1302	c.249_251delCTT	c.(247-252)tccttc>tcc	p.F84del	RP11-438J1.1_ENST00000450534.1_In_Frame_Del_p.F27del|TATDN2_ENST00000448281.2_In_Frame_Del_p.F84del	NM_014760.3	NP_055575.3	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	84					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|DNA catabolic process (GO:0006308)|endoplasmic reticulum unfolded protein response (GO:0030968)	intracellular organelle (GO:0043229)|nucleoplasm (GO:0005654)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)	p.F84fs*19(1)		autonomic_ganglia(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(9)|pancreas(2)|prostate(1)|stomach(2)	28						CCTCCTCCTCCTTCTCCCCACAT	0.631																																																1	Deletion - Frameshift(1)	pancreas(1)								9,4239		4,1,2119						2.7	0.8			88	29,8187		11,7,4090	no	coding	TATDN2	NM_014760.3		15,8,6209	A1A1,A1R,RR		0.353,0.2119,0.3049				38,12426				SO:0001651	inframe_deletion	9797			D86972	CCDS33698.1	3p25.3	2010-11-24			ENSG00000157014	ENSG00000157014			28988	protein-coding gene	gene with protein product						9039502	Standard	NM_014760		Approved	KIAA0218	uc003bvf.3	Q93075	OTTHUMG00000155361	ENST00000287652.4:c.249_251delCTT	3.37:g.10291133_10291135delCTT	ENSP00000287652:p.Phe84del		Q3MIL9|Q5BKU0	In_Frame_Del	DEL	ENST00000287652.4	37	CCDS33698.1																																																																																				0.631	TATDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339641.1	XM_376203		61	332	61	332
