#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
FAM76B	143684	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	95512812	95512812	+	Missense_Mutation	SNP	C	C	G			TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chr11:95512812C>G	ENST00000358780.5	-	7	963	c.651G>C	c.(649-651)aaG>aaC	p.K217N	FAM76B_ENST00000536839.1_Missense_Mutation_p.K217N	NM_144664.4	NP_653265.3	Q5HYJ3	FA76B_HUMAN	family with sequence similarity 76, member B	217						nuclear membrane (GO:0031965)|nucleus (GO:0005634)				breast(1)|kidney(1)|lung(1)	3		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TGGGCTTTTTCTTTGGAGTTT	0.308																																																0													126.0	121.0	123.0					11																	95512812		1792	4063	5855	SO:0001583	missense	143684				CCDS41700.1	11q21	2008-02-05			ENSG00000077458	ENSG00000077458			28492	protein-coding gene	gene with protein product						12477932	Standard	NM_144664		Approved	MGC33371	uc001pfn.2	Q5HYJ3	OTTHUMG00000167739	ENST00000358780.5:c.651G>C	11.37:g.95512812C>G	ENSP00000351631:p.Lys217Asn		Q6PIU3|Q8TC53	Missense_Mutation	SNP	ENST00000358780.5	37	CCDS41700.1	.	.	.	.	.	.	.	.	.	.	C	16.98	3.272360	0.59649	.	.	ENSG00000077458	ENST00000358780;ENST00000536839	.	.	.	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.57242	0.2040	L	0.48642	1.525	0.80722	D	1	B	0.27732	0.187	B	0.24155	0.051	T	0.52298	-0.8594	9	0.25106	T	0.35	1.3526	19.5534	0.95331	0.0:1.0:0.0:0.0	.	217	Q5HYJ3	FA76B_HUMAN	N	217	.	ENSP00000351631:K217N	K	-	3	2	FAM76B	95152460	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.710000	0.84655	2.683000	0.91414	0.650000	0.86243	AAG		0.308	FAM76B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395969.1	NM_144664		20	172	20	172
MGAT4C	25834	hgsc.bcm.edu;broad.mit.edu	37	12	86373270	86373270	+	Missense_Mutation	SNP	C	C	G			TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chr12:86373270C>G	ENST00000604798.1	-	8	2438	c.1234G>C	c.(1234-1236)Gat>Cat	p.D412H	MGAT4C_ENST00000393205.2_Missense_Mutation_p.D441H|MGAT4C_ENST00000548651.1_Missense_Mutation_p.D412H|MGAT4C_ENST00000552808.2_Missense_Mutation_p.D412H|MGAT4C_ENST00000549405.2_Missense_Mutation_p.D412H|MGAT4C_ENST00000332156.1_Missense_Mutation_p.D412H			Q9UBM8	MGT4C_HUMAN	MGAT4 family, member C	412					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						TCCCCAACATCTAGGGCTCCA	0.318																																																0													88.0	88.0	88.0					12																	86373270		2203	4300	6503	SO:0001583	missense	25834				CCDS9030.1	12q21	2014-07-14	2014-07-14		ENSG00000182050	ENSG00000182050		"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	30871	protein-coding gene	gene with protein product		607385	"""mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"""			10570912	Standard	NM_013244		Approved	HGNT-IV-H	uc001tal.4	Q9UBM8	OTTHUMG00000169846	ENST00000604798.1:c.1234G>C	12.37:g.86373270C>G	ENSP00000474896:p.Asp412His		B4DRH2|Q4G199|Q9UIU5	Missense_Mutation	SNP	ENST00000604798.1	37	CCDS9030.1	.	.	.	.	.	.	.	.	.	.	C	12.23	1.875886	0.33162	.	.	ENSG00000182050	ENST00000332156;ENST00000393205;ENST00000549405;ENST00000550460;ENST00000552808;ENST00000548651	T;T;T;T;T	0.30981	1.52;1.51;1.52;1.52;1.52	5.76	5.76	0.90799	.	0.168546	0.49916	D	0.000121	T	0.36496	0.0969	L	0.40543	1.245	0.58432	D	0.999993	P;P	0.43287	0.802;0.694	P;B	0.45037	0.467;0.444	T	0.07673	-1.0760	10	0.62326	D	0.03	-7.2935	19.9607	0.97248	0.0:1.0:0.0:0.0	.	441;412	B4DRH2;Q9UBM8	.;MGT4C_HUMAN	H	412;441;412;412;412;412	ENSP00000331664:D412H;ENSP00000376900:D441H;ENSP00000449022:D412H;ENSP00000446647:D412H;ENSP00000447253:D412H	ENSP00000331664:D412H	D	-	1	0	MGAT4C	84897401	1.000000	0.71417	0.999000	0.59377	0.040000	0.13550	7.814000	0.86154	2.713000	0.92767	0.585000	0.79938	GAT		0.318	MGAT4C-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406212.2	NM_013244		5	65	5	65
HECTD1	25831	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	31590686	31590686	+	Missense_Mutation	SNP	C	C	T	rs370774239		TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chr14:31590686C>T	ENST00000399332.1	-	28	5629	c.5141G>A	c.(5140-5142)cGt>cAt	p.R1714H	HECTD1_ENST00000553700.1_Missense_Mutation_p.R1714H	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	1714					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		GCCAGCTCGACGTTGCAGGGA	0.507																																																0								C	HIS/ARG	1,3875		0,1,1937	63.0	68.0	66.0		5141	4.6	1.0	14		66	0,8262		0,0,4131	no	missense	HECTD1	NM_015382.2	29	0,1,6068	TT,TC,CC		0.0,0.0258,0.0082	benign	1714/2611	31590686	1,12137	1938	4131	6069	SO:0001583	missense	25831			AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"""Ankyrin repeat domain containing"""	20157	protein-coding gene	gene with protein product			"""HECT domain containing 1"""			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.5141G>A	14.37:g.31590686C>T	ENSP00000382269:p.Arg1714His		D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	37	CCDS41939.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.17|10.17	1.276533|1.276533	0.23307|0.23307	2.58E-4|2.58E-4	0.0|0.0	ENSG00000092148|ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332;ENST00000553957|ENST00000554882	T;T;T|.	0.08102|.	3.13;3.13;3.13|.	5.5|5.5	4.61|4.61	0.57282|0.57282	.|.	0.373597|.	0.17807|.	U|.	0.161334|.	T|T	0.20659|0.20659	0.0497|0.0497	N|N	0.08118|0.08118	0|0	0.27686|0.27686	N|N	0.946275|0.946275	B;B|.	0.06786|.	0.0;0.001|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.18272|0.18272	-1.0342|-1.0342	10|5	0.21014|.	T|.	0.42|.	-8.564|-8.564	10.4469|10.4469	0.44499|0.44499	0.0:0.9099:0.0:0.0901|0.0:0.9099:0.0:0.0901	.|.	1714;1714|.	D3DS86;Q9ULT8|.	.;HECD1_HUMAN|.	H|I	1714;1716;1714;1141|80	ENSP00000450697:R1714H;ENSP00000382269:R1714H;ENSP00000451860:R1141H|.	ENSP00000261312:R1716H|.	R|V	-|-	2|1	0|0	HECTD1|HECTD1	30660437|30660437	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.016000|0.016000	0.09150|0.09150	3.549000|3.549000	0.53681|0.53681	1.317000|1.317000	0.45149|0.45149	-0.150000|-0.150000	0.13652|0.13652	CGT|GTC		0.507	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			18	38	18	38
PNN	5411	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	39648579	39648579	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chr14:39648579A>G	ENST00000216832.4	+	8	773	c.706A>G	c.(706-708)Aag>Gag	p.K236E	PNN_ENST00000557680.1_3'UTR	NM_002687.3	NP_002678	Q9H307	PININ_HUMAN	pinin, desmosome associated protein	236	Glu-rich.|Necessary for interaction with RNPS1.|Sufficient for PSAP complex assembly.				cell adhesion (GO:0007155)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			breast(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(2)|stomach(1)	27	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0119)		TATAAGAACTAAGACAAAGCC	0.338																																																0													60.0	63.0	62.0					14																	39648579		2202	4299	6501	SO:0001583	missense	5411			U77718	CCDS9671.1	14q21.1	2010-07-02			ENSG00000100941	ENSG00000100941			9162	protein-coding gene	gene with protein product		603154				8922384	Standard	NM_002687		Approved	memA	uc001wuw.4	Q9H307	OTTHUMG00000028821	ENST00000216832.4:c.706A>G	14.37:g.39648579A>G	ENSP00000216832:p.Lys236Glu		B4DZX8|O60899|Q53EM7|Q6P5X4|Q7KYL1|Q99738|Q9UHZ9|Q9UQR9	Missense_Mutation	SNP	ENST00000216832.4	37	CCDS9671.1	.	.	.	.	.	.	.	.	.	.	A	26.5	4.746867	0.89663	.	.	ENSG00000100941	ENST00000216832	T	0.39406	1.08	5.96	5.96	0.96718	Pinin/SDK/MemA protein (1);	0.000000	0.85682	D	0.000000	T	0.60457	0.2270	M	0.76433	2.335	0.80722	D	1	D	0.57571	0.98	P	0.56474	0.799	T	0.63655	-0.6588	10	0.56958	D	0.05	-17.7915	16.4338	0.83864	1.0:0.0:0.0:0.0	.	236	Q9H307	PININ_HUMAN	E	236	ENSP00000216832:K236E	ENSP00000216832:K236E	K	+	1	0	PNN	38718330	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.058000	0.93896	2.270000	0.75569	0.533000	0.62120	AAG		0.338	PNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276776.2	NM_002687		4	25	4	25
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	7577121	7577121	+	Missense_Mutation	SNP	G	G	A	rs121913343		TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chr17:7577121G>A	ENST00000269305.4	-	8	1006	c.817C>T	c.(817-819)Cgt>Tgt	p.R273C	TP53_ENST00000413465.2_Intron|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.R273C|TP53_ENST00000455263.2_Missense_Mutation_p.R273C|TP53_ENST00000420246.2_Missense_Mutation_p.R273C|TP53_ENST00000445888.2_Missense_Mutation_p.R273C	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	273	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:7887414, ECO:0000269|PubMed:9450901}.|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; abolishes sequence-specific DNA binding; does not induce SNAI1 degradation; dbSNP:rs28934576). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:1565144, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1699228, ECO:0000269|PubMed:1868473, ECO:0000269|PubMed:7682763, ECO:0000269|Ref.14}.|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R273C(481)|p.R273S(16)|p.R273G(9)|p.0?(8)|p.?(2)|p.R273fs*72(2)|p.R273fs*33(2)|p.R273fs*32(2)|p.V272>?(2)|p.F270fs*72(1)|p.R273_C275delRVC(1)|p.L265_K305del41(1)|p.S269fs*21(1)|p.E258fs*71(1)|p.R273fs*71(1)|p.F270_D281del12(1)|p.E271_R273delEVR(1)|p.V272_K292del21(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCACAAACACGCACCTCAAAG	0.542	R273C(8MGBA_CENTRAL_NERVOUS_SYSTEM)|R273C(BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(EFO27_OVARY)|R273C(KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(MFE319_ENDOMETRIUM)|R273C(NCIH1048_LUNG)|R273C(PANC0213_PANCREAS)|R273C(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(RDES_BONE)|R273C(RH30_SOFT_TISSUE)|R273C(RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SH10TC_STOMACH)|R273C(SJRH30_SOFT_TISSUE)|R273C(SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SW1710_URINARY_TRACT)|R273C(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273C(TT2609C02_THYROID)	111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	533	Substitution - Missense(506)|Whole gene deletion(8)|Deletion - Frameshift(8)|Deletion - In frame(5)|Insertion - Frameshift(2)|Unknown(2)|Complex(2)	central_nervous_system(117)|large_intestine(108)|ovary(32)|haematopoietic_and_lymphoid_tissue(31)|upper_aerodigestive_tract(30)|stomach(25)|urinary_tract(23)|lung(21)|breast(21)|liver(20)|endometrium(17)|oesophagus(17)|bone(16)|pancreas(15)|prostate(8)|skin(7)|cervix(6)|biliary_tract(6)|kidney(3)|thyroid(3)|vulva(2)|genital_tract(1)|penis(1)|adrenal_gland(1)|salivary_gland(1)|small_intestine(1)	GRCh37	CM010471|CM010473|CM951233	TP53	M	rs121913343						65.0	56.0	59.0					17																	7577121		2203	4300	6503	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.817C>T	17.37:g.7577121G>A	ENSP00000269305:p.Arg273Cys		Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.400216	0.62177	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.92	3.95	0.45737	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99851	0.9931	M	0.90759	3.145	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.998;0.999;0.996	D	0.96877	0.9643	10	0.87932	D	0	-11.9995	11.2235	0.48869	0.0895:0.0:0.9105:0.0	.	273;273;273;273	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	C	273;273;273;273;273;262;141	ENSP00000352610:R273C;ENSP00000269305:R273C;ENSP00000398846:R273C;ENSP00000391127:R273C;ENSP00000391478:R273C;ENSP00000425104:R141C	ENSP00000269305:R273C	R	-	1	0	TP53	7517846	1.000000	0.71417	0.066000	0.19879	0.723000	0.41478	4.540000	0.60664	1.299000	0.44798	0.462000	0.41574	CGT		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		35	2	35	2
NLRP5	126206	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	56539141	56539141	+	Silent	SNP	C	C	T			TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chr19:56539141C>T	ENST00000390649.3	+	7	1542	c.1542C>T	c.(1540-1542)ggC>ggT	p.G514G		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	514	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		CCCCTCGAGGCGTGGTCCGGC	0.592																																																0													41.0	42.0	42.0					19																	56539141		2123	4230	6353	SO:0001819	synonymous_variant	126206			AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"""Nucleotide-binding domain and leucine rich repeat containing"""	21269	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"""	609658	"""NACHT, leucine rich repeat and PYD containing 5"""	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.1542C>T	19.37:g.56539141C>T			A8MTY4|Q86W29	Silent	SNP	ENST00000390649.3	37	CCDS12938.1																																																																																				0.592	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447		17	22	17	22
OR6N2	81442	hgsc.bcm.edu;broad.mit.edu	37	1	158747181	158747181	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chr1:158747181A>G	ENST00000339258.1	-	1	244	c.245T>C	c.(244-246)tTg>tCg	p.L82S		NM_001005278.1	NP_001005278.1	Q8NGY6	OR6N2_HUMAN	olfactory receptor, family 6, subfamily N, member 2	82						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(6)|lung(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_hematologic(112;0.0378)					AATATTAGACAACATCTTAGG	0.448																																																0													156.0	149.0	151.0					1																	158747181		2203	4300	6503	SO:0001583	missense	81442			BK004200	CCDS30906.1	1q23.1	2012-08-09			ENSG00000188340	ENSG00000188340		"""GPCR / Class A : Olfactory receptors"""	15035	protein-coding gene	gene with protein product							Standard	NM_001005278		Approved		uc010pir.2	Q8NGY6	OTTHUMG00000022775	ENST00000339258.1:c.245T>C	1.37:g.158747181A>G	ENSP00000344101:p.Leu82Ser		Q6IFR2	Missense_Mutation	SNP	ENST00000339258.1	37	CCDS30906.1	.	.	.	.	.	.	.	.	.	.	A	19.54	3.846918	0.71603	.	.	ENSG00000188340	ENST00000339258	T	0.00428	7.44	5.17	5.17	0.71159	GPCR, rhodopsin-like superfamily (1);	0.000000	0.30419	N	0.009661	T	0.01189	0.0039	H	0.96333	3.805	0.38858	D	0.956418	D	0.89917	1.0	D	0.87578	0.998	T	0.15549	-1.0433	10	0.87932	D	0	-6.0412	14.1215	0.65189	1.0:0.0:0.0:0.0	.	82	Q8NGY6	OR6N2_HUMAN	S	82	ENSP00000344101:L82S	ENSP00000344101:L82S	L	-	2	0	OR6N2	157013805	0.891000	0.30450	0.989000	0.46669	0.903000	0.53119	7.180000	0.77674	2.169000	0.68431	0.528000	0.53228	TTG		0.448	OR6N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059068.1			11	167	11	167
SOGA1	140710	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	20	35445842	35445842	+	Silent	SNP	G	G	A			TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chr20:35445842G>A	ENST00000357779.3	-	4	714	c.388C>T	c.(388-390)Ctg>Ttg	p.L130L	SOGA1_ENST00000456801.2_5'Flank|SOGA1_ENST00000279034.6_Silent_p.L130L|SOGA1_ENST00000237536.4_Silent_p.L368L			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	130					insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						GCCTTCCCCAGGGAGCGGGTT	0.453																																																0													38.0	36.0	37.0					20																	35445842		1815	4069	5884	SO:0001819	synonymous_variant	140710			AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639			16111	protein-coding gene	gene with protein product	"""suppressor of glucose by autophagy"", ""suppressor of glucose from autophagy"""		"""chromosome 20 open reading frame 117"", ""KIAA0889"""	C20orf117, KIAA0889		20813965	Standard	NM_080627		Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000357779.3:c.388C>T	20.37:g.35445842G>A			A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Silent	SNP	ENST00000357779.3	37																																																																																					0.453	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181		12	13	12	13
KRTAP13-3	337960	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	21	31798186	31798186	+	Silent	SNP	G	G	A			TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chr21:31798186G>A	ENST00000390690.2	-	1	100	c.45C>T	c.(43-45)caC>caT	p.H15H		NM_181622.1	NP_853653.1	Q3SY46	KR133_HUMAN	keratin associated protein 13-3	15						intermediate filament (GO:0005882)				endometrium(1)|large_intestine(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	14						AGTAACCCCCGTGGGAGCAGG	0.542																																																0													83.0	86.0	85.0					21																	31798186		2203	4300	6503	SO:0001819	synonymous_variant	337960			AP001708	CCDS13591.1	21q22.1	2006-03-13			ENSG00000240432	ENSG00000240432		"""Keratin associated proteins"""	18925	protein-coding gene	gene with protein product						12359730	Standard	NM_181622		Approved	KAP13.3	uc002yob.1	Q3SY46	OTTHUMG00000057776	ENST00000390690.2:c.45C>T	21.37:g.31798186G>A			Q3LI78	Silent	SNP	ENST00000390690.2	37	CCDS13591.1																																																																																				0.542	KRTAP13-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128228.2			79	102	79	102
COLEC11	78989	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	3691639	3691639	+	Silent	SNP	C	C	T			TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chr2:3691639C>T	ENST00000349077.4	+	7	850	c.747C>T	c.(745-747)ggC>ggT	p.G249G	COLEC11_ENST00000403096.3_Silent_p.G223G|COLEC11_ENST00000236693.7_Silent_p.G246G|COLEC11_ENST00000382062.2_Silent_p.G225G|COLEC11_ENST00000404205.1_Silent_p.G175G|COLEC11_ENST00000402922.1_Silent_p.G199G|COLEC11_ENST00000487365.1_3'UTR|COLEC11_ENST00000418971.2_Silent_p.G263G|COLEC11_ENST00000402794.1_Silent_p.G199G	NM_024027.4	NP_076932.1	Q9BWP8	COL11_HUMAN	collectin sub-family member 11	249	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				developmental process (GO:0032502)|multicellular organismal development (GO:0007275)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)	mannose binding (GO:0005537)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|soft_tissue(1)	22	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.127)		TGGCCTCGGGCGGCTGGAACG	0.617																																																0													58.0	61.0	60.0					2																	3691639		2203	4300	6503	SO:0001819	synonymous_variant	78989			BC000078	CCDS1649.1, CCDS1650.1, CCDS58689.1, CCDS58690.1, CCDS58691.1, CCDS58692.1, CCDS58693.1, CCDS58694.1	2p25.3	2014-09-17			ENSG00000118004	ENSG00000118004		"""Collectins"""	17213	protein-coding gene	gene with protein product	"""Collectin K1"""	612502					Standard	NM_024027		Approved	MGC3279, CL-K1	uc031rnn.1	Q9BWP8	OTTHUMG00000090304	ENST00000349077.4:c.747C>T	2.37:g.3691639C>T			A1IGE4|A1IGE5|A1IGE6|A7VJJ2|A7VJJ3|A7VJJ4|A7VJJ5|B2R9M5|B4E1G0|J3KQY9|Q5CZ85|Q7Z6N1	Silent	SNP	ENST00000349077.4	37	CCDS1649.1																																																																																				0.617	COLEC11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206666.1	NM_024027		52	71	52	71
XDH	7498	hgsc.bcm.edu;broad.mit.edu	37	2	31589846	31589846	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chr2:31589846C>T	ENST00000379416.3	-	21	2260	c.2212G>A	c.(2212-2214)Ggt>Agt	p.G738S		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	738					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	TCTTGGCCACCGATGTATATC	0.537																																					Colon(66;682 1445 30109 40147)											0													131.0	104.0	113.0					2																	31589846		2203	4300	6503	SO:0001583	missense	7498			D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"""xanthene dehydrogenase"""			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.2212G>A	2.37:g.31589846C>T	ENSP00000368727:p.Gly738Ser		Q16681|Q16712|Q4PJ16	Missense_Mutation	SNP	ENST00000379416.3	37	CCDS1775.1	.	.	.	.	.	.	.	.	.	.	C	35	5.472564	0.96274	.	.	ENSG00000158125	ENST00000379416	T	0.46451	0.87	5.84	5.84	0.93424	Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding (3);	0.000000	0.85682	D	0.000000	T	0.70771	0.3262	M	0.85945	2.785	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.73956	-0.3819	10	0.72032	D	0.01	.	19.745	0.96248	0.0:1.0:0.0:0.0	.	738	P47989	XDH_HUMAN	S	738	ENSP00000368727:G738S	ENSP00000368727:G738S	G	-	1	0	XDH	31443350	1.000000	0.71417	0.873000	0.34254	0.835000	0.47333	7.703000	0.84585	2.765000	0.95021	0.655000	0.94253	GGT		0.537	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379		8	136	8	136
LRP2	4036	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	170026253	170026253	+	Missense_Mutation	SNP	C	C	A			TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chr2:170026253C>A	ENST00000263816.3	-	60	11741	c.11456G>T	c.(11455-11457)gGa>gTa	p.G3819V		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3819	LDL-receptor class A 33. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	GTCAGCGGATCCATCGCATTT	0.428																																																0													221.0	173.0	189.0					2																	170026253		2203	4300	6503	SO:0001583	missense	4036				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.11456G>T	2.37:g.170026253C>A	ENSP00000263816:p.Gly3819Val		O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.969617	0.74246	.	.	ENSG00000081479	ENST00000263816	D	0.96913	-4.17	6.03	6.03	0.97812	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.98905	0.9629	H	0.96365	3.81	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98977	1.0803	10	0.72032	D	0.01	.	20.5568	0.99304	0.0:1.0:0.0:0.0	.	3819	P98164	LRP2_HUMAN	V	3819	ENSP00000263816:G3819V	ENSP00000263816:G3819V	G	-	2	0	LRP2	169734499	1.000000	0.71417	0.931000	0.37212	0.176000	0.22953	5.912000	0.69948	2.861000	0.98227	0.655000	0.94253	GGA		0.428	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		17	138	17	138
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113113	209113113	+	Missense_Mutation	SNP	G	G	A	rs121913499		TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chr2:209113113G>A	ENST00000415913.1	-	4	775	c.394C>T	c.(394-396)Cgt>Tgt	p.R132C	IDH1_ENST00000345146.2_Missense_Mutation_p.R132C|IDH1_ENST00000446179.1_Missense_Mutation_p.R132C	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.R132C(446)|p.R132G(125)|p.R132S(106)|p.G131_R132>VL(1)|p.R132V(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)		TAAGCATGACGACCTATGATG	0.398			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	679	Substitution - Missense(678)|Complex - compound substitution(1)	haematopoietic_and_lymphoid_tissue(280)|central_nervous_system(181)|bone(177)|biliary_tract(21)|soft_tissue(12)|large_intestine(2)|skin(2)|autonomic_ganglia(1)|endometrium(1)|NS(1)|prostate(1)											81.0	74.0	76.0					2																	209113113		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.394C>T	2.37:g.209113113G>A	ENSP00000390265:p.Arg132Cys		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.550898	0.86127	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.87029	-2.2;-2.2;-2.2;-2.2	5.57	5.57	0.84162	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.94049	0.8093	H	0.99379	4.54	0.80722	D	1	B	0.29862	0.259	B	0.31245	0.126	D	0.94048	0.7315	10	0.87932	D	0	-20.0399	19.5341	0.95242	0.0:0.0:1.0:0.0	.	132	O75874	IDHC_HUMAN	C	132	ENSP00000260985:R132C;ENSP00000410513:R132C;ENSP00000390265:R132C;ENSP00000391075:R132C	ENSP00000260985:R132C	R	-	1	0	IDH1	208821358	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.074000	0.76791	2.616000	0.88540	0.555000	0.69702	CGT		0.398	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			54	59	54	59
FYCO1	79443	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	46023170	46023170	+	Splice_Site	SNP	T	T	C			TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chr3:46023170T>C	ENST00000296137.2	-	3	261		c.e3-2		FYCO1_ENST00000535325.1_Splice_Site	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1						plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		TCACAGCATCTTTAAGACAAC	0.408																																																0													115.0	112.0	113.0					3																	46023170		2203	4300	6503	SO:0001630	splice_region_variant	79443			AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"""Zinc fingers, FYVE domain containing"""	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.56-2A>G	3.37:g.46023170T>C			B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Splice_Site	SNP	ENST00000296137.2	37	CCDS2734.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.405671	0.83230	.	.	ENSG00000163820	ENST00000296137;ENST00000535325	.	.	.	5.66	5.66	0.87406	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7731	0.69693	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	FYCO1	45998174	1.000000	0.71417	0.939000	0.37840	0.982000	0.71751	7.627000	0.83176	2.285000	0.76669	0.533000	0.62120	.		0.408	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	Intron	36	42	36	42
EPHA3	2042	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	89480429	89480429	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chr3:89480429A>G	ENST00000336596.2	+	13	2491	c.2266A>G	c.(2266-2268)Agt>Ggt	p.S756G	EPHA3_ENST00000494014.1_Missense_Mutation_p.S756G	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	756	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)		CTTGATCAACAGTAACTTGGT	0.478										TSP Lung(6;0.00050)																																						0													168.0	152.0	157.0					3																	89480429		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.2266A>G	3.37:g.89480429A>G	ENSP00000337451:p.Ser756Gly		Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	A	17.56	3.420760	0.62622	.	.	ENSG00000044524	ENST00000336596;ENST00000494014	D;D	0.83250	-1.7;-1.7	5.33	5.33	0.75918	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.83972	0.5370	N	0.17764	0.52	0.80722	D	1	D	0.69078	0.997	D	0.72625	0.978	D	0.83367	0.0005	9	.	.	.	.	15.5821	0.76452	1.0:0.0:0.0:0.0	.	756	P29320	EPHA3_HUMAN	G	756	ENSP00000337451:S756G;ENSP00000419190:S756G	.	S	+	1	0	EPHA3	89563119	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	9.287000	0.95975	2.139000	0.66308	0.477000	0.44152	AGT		0.478	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		21	44	21	44
SLCO4C1	353189	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	101631898	101631898	+	Missense_Mutation	SNP	C	C	G			TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chr5:101631898C>G	ENST00000310954.6	-	1	355	c.69G>C	c.(67-69)ttG>ttC	p.L23F		NM_180991.4	NP_851322.3			solute carrier organic anion transporter family, member 4C1											breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	50		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)		GCGACGCAGACAAGCGGCGCA	0.577																																																0													74.0	83.0	80.0					5																	101631898		2203	4300	6503	SO:0001583	missense	353189			AY273896	CCDS34205.1	5q21	2013-05-22	2003-11-25		ENSG00000173930	ENSG00000173930		"""Solute carriers"""	23612	protein-coding gene	gene with protein product		609013					Standard	NM_180991		Approved	SLC21A20, OATP4C1, OATPX, OATP-H	uc003knm.3	Q6ZQN7	OTTHUMG00000162757	ENST00000310954.6:c.69G>C	5.37:g.101631898C>G	ENSP00000309741:p.Leu23Phe			Missense_Mutation	SNP	ENST00000310954.6	37	CCDS34205.1	.	.	.	.	.	.	.	.	.	.	C	9.463	1.093572	0.20471	.	.	ENSG00000173930	ENST00000310954	T	0.40476	1.03	4.11	-0.0722	0.13740	.	4.406720	0.00531	N	0.000211	T	0.29491	0.0735	L	0.38175	1.15	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.05582	-1.0876	10	0.09843	T	0.71	.	3.6401	0.08163	0.1483:0.4116:0.3446:0.0955	.	23	Q6ZQN7	SO4C1_HUMAN	F	23	ENSP00000309741:L23F	ENSP00000309741:L23F	L	-	3	2	SLCO4C1	101659797	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-0.322000	0.08007	0.010000	0.14839	-0.282000	0.10007	TTG		0.577	SLCO4C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370332.1	NM_180991		24	39	24	39
MUC17	140453	hgsc.bcm.edu;ucsc.edu	37	7	100684864	100684864	+	Silent	SNP	A	A	T			TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chr7:100684864A>T	ENST00000306151.4	+	3	10231	c.10167A>T	c.(10165-10167)atA>atT	p.I3389I		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3389	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					GTACCAGCATACCAACCTCAA	0.502																																																0													291.0	302.0	298.0					7																	100684864		2203	4300	6503	SO:0001819	synonymous_variant	140453			AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.10167A>T	7.37:g.100684864A>T			O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																				0.502	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		573	511	573	511
ERICH5	203111	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	99101917	99101917	+	Missense_Mutation	SNP	G	G	C			TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chr8:99101917G>C	ENST00000318528.3	+	2	1031	c.672G>C	c.(670-672)gaG>gaC	p.E224D	C8orf47_ENST00000545282.1_Intron	NM_173549.2	NP_775820.2	Q6P6B1	ERIC5_HUMAN		224	Glu-rich.									kidney(1)|large_intestine(5)|lung(4)|prostate(1)|skin(2)	13	Breast(36;2.31e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.214)			TTTCCAAAGAGAATGAATCTC	0.483																																																0													30.0	30.0	30.0					8																	99101917		2203	4298	6501	SO:0001583	missense	0																														ENST00000318528.3:c.672G>C	8.37:g.99101917G>C	ENSP00000315614:p.Glu224Asp		G3V1K4|Q8N1L8	Missense_Mutation	SNP	ENST00000318528.3	37	CCDS34929.1	.	.	.	.	.	.	.	.	.	.	G	18.15	3.560750	0.65538	.	.	ENSG00000177459	ENST00000318528	T	0.50548	0.74	5.23	2.36	0.29203	.	0.242590	0.29246	N	0.012709	T	0.45377	0.1339	L	0.56769	1.78	0.09310	N	1	P	0.52316	0.952	P	0.49301	0.606	T	0.33574	-0.9863	10	0.51188	T	0.08	-2.6275	4.223	0.10567	0.1864:0.0:0.6313:0.1823	.	224	Q6P6B1	CH047_HUMAN	D	224	ENSP00000315614:E224D	ENSP00000315614:E224D	E	+	3	2	C8orf47	99171093	0.013000	0.17824	0.022000	0.16811	0.322000	0.28314	0.301000	0.19174	1.435000	0.47434	0.655000	0.94253	GAG		0.483	C8orf47-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380465.1			18	38	18	38
ZFAT	57623	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	135649705	135649705	+	Splice_Site	SNP	T	T	C			TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chr8:135649705T>C	ENST00000377838.3	-	3	621	c.447A>G	c.(445-447)gcA>gcG	p.A149A	ZFAT_ENST00000520356.1_Splice_Site_p.A137A|ZFAT_ENST00000520214.1_Splice_Site_p.A137A|ZFAT_ENST00000523399.1_Splice_Site_p.A149A|ZFAT_ENST00000520727.1_Splice_Site_p.A137A|ZFAT_ENST00000429442.2_Splice_Site_p.A137A	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	149					hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			AGCATTTACCTGCTTCTCCTT	0.468																																																0													99.0	104.0	102.0					8																	135649705		2035	4194	6229	SO:0001630	splice_region_variant	57623			BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827		"""Zinc fingers, C2H2-type"""	19899	protein-coding gene	gene with protein product		610931	"""zinc finger protein 406"""	ZNF406, ZFAT1		10819331, 18329245	Standard	NM_020863		Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.448+1A>G	8.37:g.135649705T>C			B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Splice_Site	SNP	ENST00000377838.3	37	CCDS47924.1																																																																																				0.468	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939	Silent	100	137	100	137
OR5C1	392391	hgsc.bcm.edu;broad.mit.edu	37	9	125551909	125551909	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chr9:125551909G>A	ENST00000373680.2	+	1	760	c.698G>A	c.(697-699)cGc>cAc	p.R233H		NM_001001923.1	NP_001001923.1	Q8NGR4	OR5C1_HUMAN	olfactory receptor, family 5, subfamily C, member 1	233						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|large_intestine(5)|lung(6)|pancreas(1)|prostate(5)|skin(1)	20						ATCCACATGCGCTCGGTCGAG	0.592																																																0													74.0	69.0	71.0					9																	125551909		2203	4300	6503	SO:0001583	missense	392391			AF399514	CCDS35131.1	9q34.2	2012-08-09			ENSG00000148215	ENSG00000148215		"""GPCR / Class A : Olfactory receptors"""	8331	protein-coding gene	gene with protein product				OR5C2P			Standard	NM_001001923		Approved	OR9-F, hRPK-465_F_21	uc011lzd.2	Q8NGR4	OTTHUMG00000020622	ENST00000373680.2:c.698G>A	9.37:g.125551909G>A	ENSP00000362784:p.Arg233His		B2RN54|B9EGT0|Q96RC4	Missense_Mutation	SNP	ENST00000373680.2	37	CCDS35131.1	.	.	.	.	.	.	.	.	.	.	G	0.414	-0.912010	0.02415	.	.	ENSG00000148215	ENST00000373680	T	0.39229	1.09	5.46	-2.97	0.05530	GPCR, rhodopsin-like superfamily (1);	1.106120	0.07134	N	0.846175	T	0.20007	0.0481	N	0.12443	0.215	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.29518	-1.0009	10	0.09590	T	0.72	.	7.9826	0.30192	0.5388:0.112:0.3492:0.0	.	233	Q8NGR4	OR5C1_HUMAN	H	233	ENSP00000362784:R233H	ENSP00000362784:R233H	R	+	2	0	OR5C1	124591730	0.000000	0.05858	0.553000	0.28255	0.039000	0.13416	-1.092000	0.03366	-0.391000	0.07763	-0.137000	0.14449	CGC		0.592	OR5C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053953.1			7	87	7	87
PAGE1	8712	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	49455852	49455852	+	Splice_Site	SNP	C	C	T			TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chrX:49455852C>T	ENST00000376150.3	-	4	424	c.292G>A	c.(292-294)Ggg>Agg	p.G98R		NM_003785.3	NP_003776.2	O75459	PAGE1_HUMAN	P antigen family, member 1 (prostate associated)	98					cellular defense response (GO:0006968)					endometrium(1)|large_intestine(2)|lung(2)|skin(1)|urinary_tract(1)	7	Ovarian(276;0.236)					GACTACCTACCTTCTGCGGGC	0.468																																																0													142.0	112.0	122.0					X																	49455852		2203	4300	6503	SO:0001630	splice_region_variant	8712			AF058989	CCDS14327.1	Xp11.23	2009-06-17	2005-01-26	2005-01-27	ENSG00000068985	ENSG00000068985			4107	protein-coding gene	gene with protein product		300288	"""G antigen, family B, 1 (prostate associated)"""	GAGEB1		9651357, 9724777	Standard	NM_003785		Approved	PAGE-1, GAGE-9, CT16.3	uc004dom.3	O75459	OTTHUMG00000033224	ENST00000376150.3:c.292+1G>A	X.37:g.49455852C>T			Q6FGM3|Q9BSS7	Splice_Site	SNP	ENST00000376150.3	37	CCDS14327.1	.	.	.	.	.	.	.	.	.	.	.	12.31	1.898741	0.33535	.	.	ENSG00000068985	ENST00000376150	T	0.16324	2.35	1.47	1.47	0.22746	.	.	.	.	.	T	0.38904	0.1058	M	0.82323	2.585	0.09310	N	1	D	0.76494	0.999	D	0.81914	0.995	T	0.06991	-1.0796	8	.	.	.	.	5.8786	0.18842	0.0:1.0:0.0:0.0	.	98	O75459	GAGB1_HUMAN	R	98	ENSP00000365320:G98R	.	G	-	1	0	PAGE1	49342556	0.483000	0.25956	0.040000	0.18447	0.049000	0.14656	0.723000	0.25939	1.027000	0.39758	0.462000	0.41574	GGG		0.468	PAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081210.1		Missense_Mutation	16	71	16	71
TAF1	6872	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	70618475	70618475	+	Missense_Mutation	SNP	G	G	A			TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chrX:70618475G>A	ENST00000373790.4	+	24	3722	c.3671G>A	c.(3670-3672)cGg>cAg	p.R1224Q	TAF1_ENST00000449580.1_Missense_Mutation_p.R1224Q|TAF1_ENST00000423759.1_Missense_Mutation_p.R1245Q|TAF1_ENST00000276072.3_Missense_Mutation_p.R1245Q	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	1224					cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				CGAAAAGAACGGCGGAGGATT	0.473																																																0													89.0	76.0	80.0					X																	70618475		2203	4300	6503	SO:0001583	missense	6872				CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"""Chromatin-modifying enzymes / K-acetyltransferases"""	11535	protein-coding gene	gene with protein product		313650	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD"", ""dystonia 3 (with Parkinsonism)"""	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.3671G>A	X.37:g.70618475G>A	ENSP00000362895:p.Arg1224Gln		A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	37	CCDS35325.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	36|36	5.661902|5.661902	0.96734|0.96734	.|.	.|.	ENSG00000147133|ENSG00000147133	ENST00000483985|ENST00000373790;ENST00000449580;ENST00000423759;ENST00000276072	.|T;T;T;T	.|0.63096	.|-0.02;-0.02;-0.02;-0.02	5.54|5.54	5.54|5.54	0.83059|0.83059	.|.	.|0.105596	.|0.64402	.|D	.|0.000005	T|T	0.69904|0.69904	0.3163|0.3163	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.71674	.|0.997;0.988;0.998	.|P;P;P	.|0.59948	.|0.809;0.57;0.866	T|T	0.72232|0.72232	-0.4353|-0.4353	5|10	.|0.59425	.|D	.|0.04	.|.	18.5393|18.5393	0.91022|0.91022	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1224;1224;1245	.|P21675-4;P21675;P21675-2	.|.;TAF1_HUMAN;.	S|Q	135|1224;1224;1245;1245	.|ENSP00000362895:R1224Q;ENSP00000389000:R1224Q;ENSP00000406549:R1245Q;ENSP00000276072:R1245Q	.|ENSP00000276072:R1245Q	G|R	+|+	1|2	0|0	TAF1|TAF1	70535200|70535200	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	9.473000|9.473000	0.97714|0.97714	2.321000|2.321000	0.78463|0.78463	0.468000|0.468000	0.43344|0.43344	GGC|CGG		0.473	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		29	44	29	44
ATRX	546	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	76813058	76813058	+	Missense_Mutation	SNP	C	C	T			TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chrX:76813058C>T	ENST00000373344.5	-	30	6777	c.6563G>A	c.(6562-6564)cGa>cAa	p.R2188Q	ATRX_ENST00000395603.3_Missense_Mutation_p.R2150Q|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	2188	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.|Interaction with MECP2.				ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						ATCAACAACTCGAAAAGACAG	0.343			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																																Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	1	Unknown(1)	bone(1)											143.0	130.0	135.0					X																	76813058		2203	4296	6499	SO:0001583	missense	546			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.6563G>A	X.37:g.76813058C>T	ENSP00000362441:p.Arg2188Gln		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Missense_Mutation	SNP	ENST00000373344.5	37	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.253862	0.80135	.	.	ENSG00000085224	ENST00000373344;ENST00000395603	D;D	0.91945	-2.94;-2.94	5.57	5.57	0.84162	Helicase, C-terminal (1);	0.000000	0.64402	D	0.000002	D	0.95004	0.8383	L	0.49571	1.57	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.994	D	0.95483	0.8562	10	0.87932	D	0	-4.7575	18.5479	0.91054	0.0:1.0:0.0:0.0	.	2150;2188	P46100-4;P46100	.;ATRX_HUMAN	Q	2188;2150	ENSP00000362441:R2188Q;ENSP00000378967:R2150Q	ENSP00000362441:R2188Q	R	-	2	0	ATRX	76699714	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.484000	0.81180	2.323000	0.78572	0.600000	0.82982	CGA		0.343	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		66	83	66	83
HDX	139324	hgsc.bcm.edu;broad.mit.edu	37	X	83723854	83723854	+	Missense_Mutation	SNP	A	A	G			TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chrX:83723854A>G	ENST00000297977.5	-	3	988	c.877T>C	c.(877-879)Tgt>Cgt	p.C293R	HDX_ENST00000506585.2_Missense_Mutation_p.C235R|HDX_ENST00000373177.2_Missense_Mutation_p.C293R	NM_001177479.1|NM_144657.4	NP_001170950.1|NP_653258.2	Q7Z353	HDX_HUMAN	highly divergent homeobox	293						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(6)|kidney(2)|large_intestine(12)|liver(1)|lung(19)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						ATGGACAAACAATTTCCTTCT	0.473																																					Pancreas(53;231 1169 36156 43751 51139)											0													117.0	103.0	108.0					X																	83723854		2203	4300	6503	SO:0001583	missense	139324			BX538112	CCDS35342.1, CCDS55456.1	Xq21.1	2012-03-09	2007-07-13	2007-07-13	ENSG00000165259	ENSG00000165259		"""Homeoboxes / POU class"""	26411	protein-coding gene	gene with protein product			"""chromosome X open reading frame 43"""	CXorf43			Standard	NM_144657		Approved	FLJ30678	uc004eek.2	Q7Z353	OTTHUMG00000021926	ENST00000297977.5:c.877T>C	X.37:g.83723854A>G	ENSP00000297977:p.Cys293Arg		A8K1Y5|B7ZL18|Q5JZB4|Q96NK7	Missense_Mutation	SNP	ENST00000297977.5	37	CCDS35342.1	.	.	.	.	.	.	.	.	.	.	A	10.06	1.246894	0.22796	.	.	ENSG00000165259	ENST00000297977;ENST00000373177;ENST00000506585	T;T;T	0.31769	1.5;1.48;1.5	4.94	4.94	0.65067	.	0.239138	0.43747	D	0.000532	T	0.27134	0.0665	L	0.43152	1.355	0.58432	D	0.999992	P	0.37015	0.578	B	0.33042	0.157	T	0.09684	-1.0663	10	0.72032	D	0.01	-19.276	13.9638	0.64196	1.0:0.0:0.0:0.0	.	293	Q7Z353	HDX_HUMAN	R	293;235;293	ENSP00000297977:C293R;ENSP00000362272:C235R;ENSP00000423670:C293R	ENSP00000297977:C293R	C	-	1	0	HDX	83610510	1.000000	0.71417	1.000000	0.80357	0.787000	0.44495	4.438000	0.59961	1.743000	0.51761	0.345000	0.21793	TGT		0.473	HDX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057379.2	NM_144657		9	147	9	147
ALG13	79868	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	110952273	110952273	+	Missense_Mutation	SNP	G	G	C			TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chrX:110952273G>C	ENST00000394780.3	+	5	843	c.831G>C	c.(829-831)gaG>gaC	p.E277D	ALG13-AS1_ENST00000430794.1_RNA|ALG13_ENST00000251943.4_Missense_Mutation_p.E173D	NM_001099922.2|NM_001257231.1	NP_001093392.1|NP_001244160.1	Q9NP73	ALG13_HUMAN	ALG13, UDP-N-acetylglucosaminyltransferase subunit	277	Deubiquitinase activity.|OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.				cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|lipid glycosylation (GO:0030259)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)	carbohydrate binding (GO:0030246)|cysteine-type peptidase activity (GO:0008234)|N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity (GO:0004577)|poly(A) RNA binding (GO:0044822)			endometrium(2)|lung(10)|skin(1)	13						AAACTTTTGAGTCTGTAAGTA	0.388																																																0													92.0	75.0	80.0					X																	110952273		1567	3577	5144	SO:0001583	missense	79868			AF220051	CCDS14559.1, CCDS55477.1, CCDS59173.1, CCDS76011.1, CCDS76012.1, CCDS76013.1	Xq23	2014-02-24	2013-02-21	2006-11-07	ENSG00000101901	ENSG00000101901	2.4.1.141	"""Tudor domain containing"", ""OTU domain containing"""	30881	protein-coding gene	gene with protein product	"""tudor domain containing 13"", ""N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase"""	300776	"""glycosyltransferase 28 domain containing 1"", ""chromosome X open reading frame 45"", ""asparagine-linked glycosylation 13 homolog (S. cerevisiae)"""	GLT28D1, CXorf45		12477932	Standard	NM_018466		Approved	MDS031, YGL047W, FLJ23018, TDRD13	uc011msy.2	Q9NP73	OTTHUMG00000022209	ENST00000394780.3:c.831G>C	X.37:g.110952273G>C	ENSP00000378260:p.Glu277Asp		B1AKD6|B1AKM1|B2R5L5|B7Z6J0|B7Z804|B7Z847|B7Z9A8|B7ZAJ1|B7ZB57|Q17RC3|Q5JXY9|Q9H5U8	Missense_Mutation	SNP	ENST00000394780.3	37	CCDS55477.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.086733	0.76642	.	.	ENSG00000101901	ENST00000251943;ENST00000394780;ENST00000495283	T;T;T	0.33654	1.4;1.4;1.4	5.41	1.66	0.24008	Ovarian tumour, otubain (2);	0.000000	0.64402	U	0.000020	T	0.57592	0.2064	M	0.87269	2.87	0.34799	D	0.73656	D;D;D	0.63046	0.99;0.992;0.99	P;D;P	0.63488	0.861;0.915;0.861	T	0.68322	-0.5439	10	0.72032	D	0.01	-9.3363	9.0041	0.36100	0.412:0.0:0.588:0.0	.	199;277;173	Q9NP73-3;Q9NP73;Q9NP73-4	.;ALG13_HUMAN;.	D	173;277;173	ENSP00000251943:E173D;ENSP00000378260:E277D;ENSP00000427093:E173D	ENSP00000251943:E173D	E	+	3	2	ALG13	110838929	0.999000	0.42202	1.000000	0.80357	0.994000	0.84299	0.402000	0.20965	0.222000	0.20900	0.600000	0.82982	GAG		0.388	ALG13-011	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272895.1	NM_018466		5	11	5	11
MMGT1	93380	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	135047268	135047268	+	Missense_Mutation	SNP	G	G	A	rs150859420		TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chrX:135047268G>A	ENST00000305963.2	-	4	698	c.311C>T	c.(310-312)tCg>tTg	p.S104L	MMGT1_ENST00000433339.2_Missense_Mutation_p.S169L	NM_173470.1	NP_775741.1	Q8N4V1	MMGT1_HUMAN	membrane magnesium transporter 1	104					magnesium ion transport (GO:0015693)	early endosome (GO:0005769)|ER membrane protein complex (GO:0072546)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	magnesium ion transmembrane transporter activity (GO:0015095)			cervix(1)|endometrium(1)|kidney(1)	3						TGCTGTATCCGAAGGCCGGAA	0.358																																																0								G	LEU/SER	1,3834		0,1,1631,571	190.0	176.0	181.0		311	4.8	1.0	X	dbSNP_134	181	1,6727		0,1,2427,1872	yes	missense	MMGT1	NM_173470.1	145	0,2,4058,2443	AA,AG,GG,G		0.0149,0.0261,0.0189	possibly-damaging	104/132	135047268	2,10561	2203	4300	6503	SO:0001583	missense	93380			AL157477	CCDS14653.1	Xq26.3	2012-05-23	2008-11-21	2008-11-21	ENSG00000169446	ENSG00000169446			28100	protein-coding gene	gene with protein product	"""ER membrane protein complex subunit 5"""		"""transmembrane protein 32"""	TMEM32		18057121, 22119785	Standard	NM_173470		Approved	EMC5	uc004ezi.1	Q8N4V1	OTTHUMG00000022499	ENST00000305963.2:c.311C>T	X.37:g.135047268G>A	ENSP00000306220:p.Ser104Leu		B2R625|B4DIY3|D3DWG7|Q5JPP7	Missense_Mutation	SNP	ENST00000305963.2	37	CCDS14653.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.176274	0.78564	2.61E-4	1.49E-4	ENSG00000169446	ENST00000305963;ENST00000433339	.	.	.	5.67	4.81	0.61882	.	0.113599	0.64402	D	0.000013	T	0.45518	0.1346	N	0.14661	0.345	0.34242	D	0.677799	D;P	0.76494	0.999;0.553	P;B	0.61940	0.896;0.043	T	0.49360	-0.8948	9	0.10111	T	0.7	.	14.9912	0.71390	0.0:0.139:0.861:0.0	.	169;104	Q8N4V1-2;Q8N4V1	.;MMGT1_HUMAN	L	104;169	.	ENSP00000306220:S104L	S	-	2	0	MMGT1	134874934	1.000000	0.71417	0.972000	0.41901	0.909000	0.53808	7.352000	0.79404	1.264000	0.44198	0.600000	0.82982	TCG		0.358	MMGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058453.3	NM_173470		40	283	40	283
TSR2	90121	broad.mit.edu;ucsc.edu	37	X	54470611	54470611	+	Missense_Mutation	SNP	G	G	C			TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chrX:54470611G>C	ENST00000375151.4	+	4	456	c.435G>C	c.(433-435)gaG>gaC	p.E145D		NM_058163.1	NP_477511.1	Q969E8	TSR2_HUMAN	TSR2, 20S rRNA accumulation, homolog (S. cerevisiae)	145					rRNA processing (GO:0006364)					breast(1)|endometrium(3)|lung(2)	6						GTGTGGAAGAGATGGAGGTGA	0.498																																																0													108.0	85.0	93.0					X																	54470611		2203	4300	6503	SO:0001583	missense	90121			BC007699	CCDS14358.1	Xp11.22	2008-10-01			ENSG00000158526	ENSG00000158526			25455	protein-coding gene	gene with protein product	"""WGG motif containing 1"""					9417904	Standard	NM_058163		Approved	DT1P1A10, RP1-112K5.2, WGG1	uc004dte.3	Q969E8	OTTHUMG00000021628	ENST00000375151.4:c.435G>C	X.37:g.54470611G>C	ENSP00000364293:p.Glu145Asp			Missense_Mutation	SNP	ENST00000375151.4	37	CCDS14358.1	.	.	.	.	.	.	.	.	.	.	g	11.56	1.674565	0.29693	.	.	ENSG00000158526	ENST00000375151	.	.	.	6.07	2.34	0.29019	.	0.371203	0.28140	N	0.016458	T	0.34483	0.0899	L	0.29908	0.895	0.36821	D	0.886386	D	0.56521	0.976	P	0.47603	0.551	T	0.28396	-1.0045	9	0.10111	T	0.7	-23.2551	8.6503	0.34031	0.3245:0.0:0.6755:0.0	.	145	Q969E8	TSR2_HUMAN	D	145	.	ENSP00000364293:E145D	E	+	3	2	TSR2	54487336	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	0.441000	0.21611	0.295000	0.22570	-0.196000	0.12772	GAG		0.498	TSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056802.1	NM_058163		73	98	73	98
AFF2	2334	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	148035253	148035253	+	Missense_Mutation	SNP	G	G	A	rs369100046		TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chrX:148035253G>A	ENST00000370460.2	+	10	2020	c.1541G>A	c.(1540-1542)cGt>cAt	p.R514H	AFF2_ENST00000370457.5_Missense_Mutation_p.R481H|AFF2_ENST00000286437.5_Missense_Mutation_p.R155H|AFF2_ENST00000342251.3_Missense_Mutation_p.R481H	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	514					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					GAGGCACCTCGTGTGGCAACT	0.567																																																0								G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,3834		0,0,1,1632,570	104.0	96.0	99.0		1442,1511,1436,1424,464,1541	4.2	0.9	X		99	0,6728		0,0,0,2428,1872	no	missense,missense,missense,missense,missense,missense	AFF2	NM_001169122.1,NM_001169123.1,NM_001169124.1,NM_001169125.1,NM_001170628.1,NM_002025.3	29,29,29,29,29,29	0,0,1,4060,2442	AA,AG,A,GG,G		0.0,0.0261,0.0095	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	481/1277,504/1302,479/1277,475/1273,155/953,514/1312	148035253	1,10562	2203	4300	6503	SO:0001583	missense	2334			U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"""fragile X mental retardation 2"""	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.1541G>A	X.37:g.148035253G>A	ENSP00000359489:p.Arg514His		A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	ENST00000370460.2	37	CCDS14684.1	.	.	.	.	.	.	.	.	.	.	G	16.42	3.118873	0.56505	2.61E-4	0.0	ENSG00000155966	ENST00000370460;ENST00000370457;ENST00000342251;ENST00000286437	T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14	5.12	4.24	0.50183	.	0.060464	0.64402	D	0.000005	T	0.69369	0.3103	L	0.41027	1.25	0.51767	D	0.999932	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.69824	0.966;0.942;0.942;0.942;0.942;0.966	T	0.65825	-0.6074	10	0.28530	T	0.3	.	14.3204	0.66482	0.0:0.0:0.8505:0.1495	.	155;479;481;475;504;514	B4DXD5;P51816-6;P51816-3;P51816-2;P51816-5;P51816	.;.;.;.;.;AFF2_HUMAN	H	514;481;481;155	ENSP00000359489:R514H;ENSP00000359486:R481H;ENSP00000345459:R481H;ENSP00000286437:R155H	ENSP00000286437:R155H	R	+	2	0	AFF2	147842953	0.997000	0.39634	0.851000	0.33527	0.893000	0.52053	3.371000	0.52379	1.020000	0.39573	0.600000	0.82982	CGT		0.567	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025		88	125	88	125
CD248	57124	broad.mit.edu;ucsc.edu	37	11	66084109	66084109	+	Silent	SNP	G	G	A	rs574387936		TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chr11:66084109G>A	ENST00000311330.3	-	1	406	c.390C>T	c.(388-390)cgC>cgT	p.R130R	RP11-867G23.13_ENST00000534065.1_RNA	NM_020404.2	NP_065137.1	Q9HCU0	CD248_HUMAN	CD248 molecule, endosialin	130	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				anatomical structure regression (GO:0060033)|cell migration (GO:0016477)|lymph node development (GO:0048535)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|extracellular matrix binding (GO:0050840)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	26						GGGCCACACAGCGCTGGGCCG	0.701													G|||	1	0.000199681	0.0	0.0	5008	,	,		15904	0.0		0.0	False		,,,				2504	0.001															0													19.0	19.0	19.0					11																	66084109		2161	4236	6397	SO:0001819	synonymous_variant	57124			AF279142	CCDS8134.1	11q13	2006-04-12	2006-03-28	2005-02-11	ENSG00000174807	ENSG00000174807		"""CD molecules"""	18219	protein-coding gene	gene with protein product	"""endosialin"", ""tumor endothelial marker 1"""	606064	"""CD164 sialomucin-like 1"", ""CD248 antigen, endosialin"""	CD164L1		10947988, 11084048	Standard	NM_020404		Approved	TEM1	uc001ohm.1	Q9HCU0	OTTHUMG00000167073	ENST00000311330.3:c.390C>T	11.37:g.66084109G>A			Q2M2V5|Q3SX55|Q96KB6	Silent	SNP	ENST00000311330.3	37	CCDS8134.1																																																																																				0.701	CD248-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392922.2	NM_020404		32	18	32	18
CELSR1	9620	broad.mit.edu;ucsc.edu	37	22	46793715	46793715	+	Missense_Mutation	SNP	C	C	T	rs370579193		TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chr22:46793715C>T	ENST00000262738.3	-	12	5556	c.5557G>A	c.(5557-5559)Gtc>Atc	p.V1853I		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1853	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		AGGGTGGCGACGTTGGTGGGC	0.602																																																0								C	ILE/VAL	0,4404		0,0,2202	117.0	71.0	87.0		5557	0.6	1.0	22		87	1,8599	1.2+/-3.3	0,1,4299	no	missense	CELSR1	NM_014246.1	29	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	benign	1853/3015	46793715	1,13003	2202	4300	6502	SO:0001583	missense	9620			AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.5557G>A	22.37:g.46793715C>T	ENSP00000262738:p.Val1853Ile		O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	C	4.544	0.100918	0.08731	0.0	1.16E-4	ENSG00000075275	ENST00000262738	T	0.68479	-0.33	3.98	0.547	0.17202	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.309767	0.25897	N	0.027588	T	0.29288	0.0729	N	0.01168	-0.975	0.80722	D	1	B;B	0.24618	0.107;0.006	B;B	0.14578	0.011;0.001	T	0.05468	-1.0883	10	0.12430	T	0.62	.	8.3492	0.32292	0.0:0.3457:0.0:0.6543	.	174;1853	B7Z7U7;Q9NYQ6	.;CELR1_HUMAN	I	1853	ENSP00000262738:V1853I	ENSP00000262738:V1853I	V	-	1	0	CELSR1	45172379	0.868000	0.29978	0.984000	0.44739	0.534000	0.34807	0.054000	0.14205	-0.162000	0.10964	-0.339000	0.08088	GTC		0.602	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		15	19	15	19
SULT1E1	6783	broad.mit.edu;ucsc.edu	37	4	70709895	70709895	+	Silent	SNP	C	C	T	rs376968582		TCGA-HT-7693-01A-11D-2253-08	TCGA-HT-7693-10A-01D-2253-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6f18cb1e-8576-4fd3-a7a1-eb549089bad2	eb46a1d3-0492-467e-9576-fd233bbff676	g.chr4:70709895C>T	ENST00000226444.3	-	7	868	c.756G>A	c.(754-756)tcG>tcA	p.S252S		NM_005420.2	NP_005411.1	P49888	ST1E1_HUMAN	sulfotransferase family 1E, estrogen-preferring, member 1	252					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|estrogen metabolic process (GO:0008210)|female pregnancy (GO:0007565)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	estrone sulfotransferase activity (GO:0004304)|flavonol 3-sulfotransferase activity (GO:0047894)|steroid binding (GO:0005496)|steroid sulfotransferase activity (GO:0050294)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	10					Acetaminophen(DB00316)|Cyclizine(DB01176)	TCATGAAGGGCGACAATTTCT	0.393													C|||	1	0.000199681	0.0	0.0	5008	,	,		18143	0.0		0.0	False		,,,				2504	0.001															0								C		0,4406		0,0,2203	265.0	233.0	244.0		756	-7.9	0.1	4		244	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SULT1E1	NM_005420.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		252/295	70709895	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	6783			BC027956	CCDS3531.1	4q13.1	2008-02-05	2004-02-06	2004-02-04	ENSG00000109193	ENSG00000109193	2.8.2.4	"""Sulfotransferases, cytosolic"""	11377	protein-coding gene	gene with protein product		600043	"""sulfotransferase, estrogen-preferring"""	STE		7961757	Standard	NM_005420		Approved	EST	uc003heo.3	P49888	OTTHUMG00000129403	ENST00000226444.3:c.756G>A	4.37:g.70709895C>T			Q8N6X5	Silent	SNP	ENST00000226444.3	37	CCDS3531.1																																																																																				0.393	SULT1E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251559.1	NM_005420		66	146	66	146
