#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_Chromosome_hg18	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_End_position_hg18	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_Start_position_hg18	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
ATP13A5	344905	hgsc.bcm.edu	37	3	193081108	193081108	+	Missense_Mutation	SNP	G	G	T	rs373214053		TCGA-24-1546-01A-01W-0615-10	TCGA-24-1546-10A-01W-0615-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_III	WXS	Sanger_PCR_WGA			SOLID	6bf554da-cc72-4daf-9287-a44792c87b8f	a70e1da0-e64d-472d-bdcf-dca6624e490f	g.chr3:193081108G>T	ENST00000342358.4	-	3	418	c.301C>A	c.(301-303)Cct>Act	p.P101T		NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	101						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)	p.P101T(1)		NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		TTGCTTACAGGAAACTTCAGT	0.408																																																1	Substitution - Missense(1)	ovary(1)	3											103.0	101.0	102.0					3																	193081108		2203	4300	6503	194563802	SO:0001583	missense	344905			AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"""ATPases / P-type"""	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.301C>A	3.37:g.193081108G>T	ENSP00000341942:p.Pro101Thr		194563802	Q6UWS4|Q6ZWL0	Missense_Mutation	SNP	ENST00000342358.4	37	CCDS33914.1	.	.	.	.	.	.	.	.	.	.	G	13.88	2.370367	0.42003	.	.	ENSG00000187527	ENST00000342358;ENST00000446087	T;T	0.17691	2.26;2.26	5.02	5.02	0.67125	.	0.091218	0.48767	D	0.000173	T	0.11836	0.0288	N	0.12182	0.205	0.43175	D	0.994989	B	0.17038	0.02	B	0.25405	0.06	T	0.17930	-1.0353	10	0.23891	T	0.37	-5.8421	16.7236	0.85416	0.0:0.0:1.0:0.0	.	101	Q4VNC0	AT135_HUMAN	T	101;123	ENSP00000341942:P101T;ENSP00000389416:P123T	ENSP00000341942:P101T	P	-	1	0	ATP13A5	194563802	0.078000	0.21339	0.981000	0.43875	0.723000	0.41478	1.494000	0.35616	2.742000	0.94016	0.650000	0.86243	CCT		0.408	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505	
ATP13A5	344905	hgsc.bcm.edu	37	3	193081122	193081122	+	Missense_Mutation	SNP	G	G	T	rs12637558	byFrequency	TCGA-24-1546-01A-01W-0615-10	TCGA-24-1546-10A-01W-0615-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_III	WXS	Sanger_PCR_WGA			SOLID	6bf554da-cc72-4daf-9287-a44792c87b8f	a70e1da0-e64d-472d-bdcf-dca6624e490f	g.chr3:193081122G>T	ENST00000342358.4	-	3	404	c.287C>A	c.(286-288)tCc>tAc	p.S96Y		NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	96			S -> Y (in dbSNP:rs12637558). {ECO:0000269|PubMed:14702039}.			integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)	p.S96F(1)|p.S96Y(1)		NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		CTTCAGTGTGGATAAGTAGAG	0.398													G|||	2083	0.415935	0.2133	0.4337	5008	,	,		18153	0.5764		0.4125	False		,,,				2504	0.5153															2	Substitution - Missense(2)	ovary(1)|NS(1)	3						G	TYR/SER	1146,3260	409.1+/-334.9	155,836,1212	98.0	96.0	97.0		287	4.2	1.0	3	dbSNP_120	97	3666,4934	527.1+/-381.1	807,2052,1441	yes	missense	ATP13A5	NM_198505.2	144	962,2888,2653	TT,TG,GG		42.6279,26.01,36.9983	probably-damaging	96/1219	193081122	4812,8194	2203	4300	6503	194563816	SO:0001583	missense	344905			AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"""ATPases / P-type"""	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.287C>A	3.37:g.193081122G>T	ENSP00000341942:p.Ser96Tyr		194563816	Q6UWS4|Q6ZWL0	Missense_Mutation	SNP	ENST00000342358.4	37	CCDS33914.1	893	0.4088827838827839	119	0.241869918699187	143	0.39502762430939226	323	0.5646853146853147	308	0.40633245382585753	G	16.92	3.255259	0.59321	0.2601	0.426279	ENSG00000187527	ENST00000342358;ENST00000446087	T;T	0.44881	0.91;0.91	5.06	4.17	0.49024	.	0.195010	0.36893	N	0.002353	T	0.00012	0.0000	M	0.73962	2.25	0.29320	P	0.867429	P	0.36733	0.567	B	0.41764	0.366	T	0.48980	-0.8986	9	0.59425	D	0.04	-6.0887	13.2983	0.60311	0.0:0.0:0.84:0.16	rs12637558;rs59613984	96	Q4VNC0	AT135_HUMAN	Y	96;118	ENSP00000341942:S96Y;ENSP00000389416:S118Y	ENSP00000341942:S96Y	S	-	2	0	ATP13A5	194563816	1.000000	0.71417	0.987000	0.45799	0.953000	0.61014	3.546000	0.53656	1.428000	0.47296	0.655000	0.94253	TCC		0.398	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505	
CSMD3	114788	hgsc.bcm.edu	37	8	113697844	113697844	+	Missense_Mutation	SNP	C	C	T			TCGA-24-1546-01A-01W-0615-10	TCGA-24-1546-10A-01W-0615-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_III	WXS	Sanger_PCR_WGA			SOLID	6bf554da-cc72-4daf-9287-a44792c87b8f	a70e1da0-e64d-472d-bdcf-dca6624e490f	g.chr8:113697844C>T	ENST00000297405.5	-	15	2517	c.2273G>A	c.(2272-2274)cGg>cAg	p.R758Q	CSMD3_ENST00000343508.3_Missense_Mutation_p.R718Q|CSMD3_ENST00000455883.2_Missense_Mutation_p.R654Q|CSMD3_ENST00000352409.3_Missense_Mutation_p.R758Q	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	758	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R758Q(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						AAGATGTATCCGGCTCCCTGG	0.413										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																																						1	Substitution - Missense(1)	ovary(1)	8											99.0	107.0	104.0					8																	113697844		2203	4299	6502	113767020	SO:0001583	missense	114788			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.2273G>A	8.37:g.113697844C>T	ENSP00000297405:p.Arg758Gln		113767020	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.606831	0.87157	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.17528	2.27;2.27;2.27;2.27;2.27	5.96	5.96	0.96718	CUB (5);	0.000000	0.64402	D	0.000002	T	0.40297	0.1111	L	0.56199	1.76	0.43145	D	0.994906	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.91635	0.994;0.998;0.999	T	0.00970	-1.1496	10	0.34782	T	0.22	.	20.4008	0.98991	0.0:1.0:0.0:0.0	.	654;758;718	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	Q	718;758;98;654;758	ENSP00000345799:R718Q;ENSP00000297405:R758Q;ENSP00000341558:R98Q;ENSP00000412263:R654Q;ENSP00000343124:R758Q	ENSP00000297405:R758Q	R	-	2	0	CSMD3	113767020	1.000000	0.71417	0.996000	0.52242	0.980000	0.70556	7.818000	0.86416	2.826000	0.97356	0.655000	0.94253	CGG		0.413	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
DCC	1630	hgsc.bcm.edu	37	18	50976947	50976947	+	Missense_Mutation	SNP	G	G	T			TCGA-24-1546-01A-01W-0615-10	TCGA-24-1546-10A-01W-0615-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_III	WXS	Sanger_PCR_WGA			SOLID	6bf554da-cc72-4daf-9287-a44792c87b8f	a70e1da0-e64d-472d-bdcf-dca6624e490f	g.chr18:50976947G>T	ENST00000442544.2	+	23	3923	c.3307G>T	c.(3307-3309)Gtg>Ttg	p.V1103L	DCC_ENST00000581580.1_Missense_Mutation_p.V738L	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	1103					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)	p.V1103L(1)		NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		TGTGATCATTGTGGTCACCGT	0.532																																																1	Substitution - Missense(1)	ovary(1)	18											140.0	112.0	122.0					18																	50976947		2203	4300	6503	49230945	SO:0001583	missense	1630			X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2701	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 1"""	120470	"""deleted in colorectal carcinoma"""			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.3307G>T	18.37:g.50976947G>T	ENSP00000389140:p.Val1103Leu		49230945		Missense_Mutation	SNP	ENST00000442544.2	37	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	G	16.40	3.113306	0.56398	.	.	ENSG00000187323	ENST00000442544	T	0.50001	0.76	5.67	5.67	0.87782	.	0.000000	0.64402	D	0.000003	T	0.45296	0.1335	L	0.47716	1.5	0.52099	D	0.999945	P	0.37276	0.589	B	0.36378	0.223	T	0.38373	-0.9664	10	0.41790	T	0.15	-7.8909	18.5478	0.91053	0.0:0.0:1.0:0.0	.	1103	P43146	DCC_HUMAN	L	1103	ENSP00000389140:V1103L	ENSP00000389140:V1103L	V	+	1	0	DCC	49230945	1.000000	0.71417	0.961000	0.40146	0.917000	0.54804	6.119000	0.71590	2.684000	0.91462	0.650000	0.86243	GTG		0.532	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215	
LRP1	4035	hgsc.bcm.edu	37	12	57567113	57567113	+	Missense_Mutation	SNP	A	A	G			TCGA-24-1546-01A-01W-0615-10	TCGA-24-1546-10A-01W-0615-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_III	WXS	Sanger_PCR_WGA			SOLID	6bf554da-cc72-4daf-9287-a44792c87b8f	a70e1da0-e64d-472d-bdcf-dca6624e490f	g.chr12:57567113A>G	ENST00000243077.3	+	21	3792	c.3326A>G	c.(3325-3327)aAg>aGg	p.K1109R		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	1109	LDL-receptor class A 9. {ECO:0000255|PROSITE-ProRule:PRU00124}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)	p.K1109R(1)		NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CCCAGTGTCAAGTTTGGCTGC	0.592											OREG0021936	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																				1	Substitution - Missense(1)	ovary(1)	12											77.0	64.0	68.0					12																	57567113		2203	4300	6503	55853380	SO:0001583	missense	4035			X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.3326A>G	12.37:g.57567113A>G	ENSP00000243077:p.Lys1109Arg	1024	55853380	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.878413	0.91740	.	.	ENSG00000123384	ENST00000243077	D	0.95518	-3.73	5.04	5.04	0.67666	.	0.000000	0.64402	D	0.000001	D	0.95364	0.8495	L	0.28115	0.83	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	D	0.95147	0.8269	10	0.42905	T	0.14	.	13.9015	0.63806	1.0:0.0:0.0:0.0	.	1109	Q07954	LRP1_HUMAN	R	1109	ENSP00000243077:K1109R	ENSP00000243077:K1109R	K	+	2	0	LRP1	55853380	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.097000	0.94193	2.117000	0.64856	0.459000	0.35465	AAG		0.592	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
NLRP4	147945	hgsc.bcm.edu	37	19	56369244	56369244	+	Missense_Mutation	SNP	C	C	T	rs117212164	byFrequency	TCGA-24-1546-01A-01W-0615-10	TCGA-24-1546-10A-01W-0615-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_III	WXS	Sanger_PCR_WGA			SOLID	6bf554da-cc72-4daf-9287-a44792c87b8f	a70e1da0-e64d-472d-bdcf-dca6624e490f	g.chr19:56369244C>T	ENST00000301295.6	+	3	907	c.485C>T	c.(484-486)aCg>aTg	p.T162M	NLRP4_ENST00000587891.1_Missense_Mutation_p.T87M|NLRP4_ENST00000346986.5_Missense_Mutation_p.T162M	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	162	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.T162M(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		ATTGGAAAAACGACACTCCTG	0.483													C|||	4	0.000798722	0.0	0.0	5008	,	,		20730	0.0		0.004	False		,,,				2504	0.0															1	Substitution - Missense(1)	ovary(1)	19						C	MET/THR	4,4402	9.9+/-24.2	0,4,2199	132.0	118.0	122.0		485	4.1	0.0	19	dbSNP_133	122	39,8561	26.3+/-74.7	0,39,4261	yes	missense	NLRP4	NM_134444.4	81	0,43,6460	TT,TC,CC		0.4535,0.0908,0.3306	probably-damaging	162/995	56369244	43,12963	2203	4300	6503	61061056	SO:0001583	missense	147945			AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22943	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4"", ""cancer/testis antigen 58"""	609645	"""NACHT, leucine rich repeat and PYD containing 4"""	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.485C>T	19.37:g.56369244C>T	ENSP00000301295:p.Thr162Met		61061056	Q86W87|Q96AY6	Missense_Mutation	SNP	ENST00000301295.6	37	CCDS12936.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	18.10	3.547856	0.65311	9.08E-4	0.004535	ENSG00000160505	ENST00000301295;ENST00000346986	D;D	0.92805	-3.11;-3.11	4.09	4.09	0.47781	NACHT nucleoside triphosphatase (1);	.	.	.	.	D	0.94450	0.8214	M	0.82517	2.595	0.37152	D	0.902209	D;D	0.89917	1.0;1.0	D;D	0.85130	0.996;0.997	D	0.95580	0.8645	9	0.87932	D	0	.	14.1967	0.65675	0.0:1.0:0.0:0.0	.	87;162	Q96MN2-3;Q96MN2	.;NALP4_HUMAN	M	162	ENSP00000301295:T162M;ENSP00000344787:T162M	ENSP00000301295:T162M	T	+	2	0	NLRP4	61061056	0.965000	0.33210	0.012000	0.15200	0.005000	0.04900	3.954000	0.56708	2.277000	0.76020	0.655000	0.94253	ACG		0.483	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
TAF1	6872	hgsc.bcm.edu	37	X	70601607	70601607	+	Missense_Mutation	SNP	C	C	G			TCGA-24-1546-01A-01W-0615-10	TCGA-24-1546-10A-01W-0615-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_III	WXS	Sanger_PCR_WGA			SOLID	6bf554da-cc72-4daf-9287-a44792c87b8f	a70e1da0-e64d-472d-bdcf-dca6624e490f	g.chrX:70601607C>G	ENST00000373790.4	+	9	1423	c.1372C>G	c.(1372-1374)Ctt>Gtt	p.L458V	TAF1_ENST00000276072.3_Missense_Mutation_p.L479V|TAF1_ENST00000423759.1_Missense_Mutation_p.L479V|TAF1_ENST00000449580.1_Missense_Mutation_p.L458V	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	458					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)	p.L458V(1)		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)				TGCAGCCACTCTTGATGATGA	0.408																																																1	Substitution - Missense(1)	ovary(1)	X											145.0	117.0	127.0					X																	70601607		2203	4300	6503	70518332	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.1372C>G	X.37:g.70601607C>G	ENSP00000362895:p.Leu458Val		70518332	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	37	CCDS35325.1	.	.	.	.	.	.	.	.	.	.	.	7.668	0.686372	0.14973	.	.	ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000276072	T;T;T;T	0.09445	2.98;3.04;3.04;2.98	5.3	2.53	0.30540	.	0.346876	0.28883	N	0.013836	T	0.07324	0.0185	L	0.39898	1.24	0.25800	N	0.984513	B;B	0.16166	0.016;0.012	B;B	0.20384	0.027;0.029	T	0.39313	-0.9620	10	0.14252	T	0.57	.	4.3224	0.11023	0.1597:0.5811:0.0:0.2592	.	458;479	P21675;P21675-2	TAF1_HUMAN;.	V	458;458;479;479	ENSP00000362895:L458V;ENSP00000389000:L458V;ENSP00000406549:L479V;ENSP00000276072:L479V	ENSP00000276072:L479V	L	+	1	0	TAF1	70518332	0.046000	0.20272	0.552000	0.28243	0.954000	0.61252	0.432000	0.21461	0.420000	0.25954	0.594000	0.82650	CTT		0.408	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606	
VAV1	7409	hgsc.bcm.edu	37	19	6829836	6829836	+	Missense_Mutation	SNP	G	G	T			TCGA-24-1546-01A-01W-0615-10	TCGA-24-1546-10A-01W-0615-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_III	WXS	Sanger_PCR_WGA			SOLID	6bf554da-cc72-4daf-9287-a44792c87b8f	a70e1da0-e64d-472d-bdcf-dca6624e490f	g.chr19:6829836G>T	ENST00000602142.1	+	14	1387	c.1305G>T	c.(1303-1305)aaG>aaT	p.K435N	VAV1_ENST00000304076.2_Missense_Mutation_p.K435N|VAV1_ENST00000596764.1_Missense_Mutation_p.K403N|VAV1_ENST00000539284.1_Missense_Mutation_p.K338N|VAV1_ENST00000599806.1_Missense_Mutation_p.K380N	NM_005428.3	NP_005419.2	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	435	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|reactive oxygen species metabolic process (GO:0072593)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K435N(1)		biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(16)|lung(18)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	62						TCATCTGTAAGCGCAGGGGAG	0.537																																																1	Substitution - Missense(1)	ovary(1)	19											151.0	123.0	132.0					19																	6829836		2203	4300	6503	6780836	SO:0001583	missense	7409				CCDS12174.1, CCDS59341.1, CCDS59342.1	19p13.2	2013-02-14	2007-07-25			ENSG00000141968		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12657	protein-coding gene	gene with protein product		164875	"""vav 1 oncogene"""	VAV		9438848	Standard	NM_005428		Approved		uc010xjh.2	P15498		ENST00000602142.1:c.1305G>T	19.37:g.6829836G>T	ENSP00000472929:p.Lys435Asn		6780836	B4DVK9|M0QXX6|Q15860	Missense_Mutation	SNP	ENST00000602142.1	37	CCDS12174.1	.	.	.	.	.	.	.	.	.	.	G	18.32	3.598222	0.66332	.	.	ENSG00000141968	ENST00000304076;ENST00000539284	D;D	0.91740	-2.9;-2.9	4.82	-3.4	0.04853	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	D	0.94152	0.8124	M	0.79123	2.44	0.54753	D	0.999989	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.999;0.998;1.0	D	0.92114	0.5698	10	0.87932	D	0	.	9.9883	0.41854	0.6873:0.0:0.3127:0.0	.	338;435;380;435	F5H5P4;B2R8B5;Q96D37;P15498	.;.;.;VAV_HUMAN	N	435;338	ENSP00000302269:K435N;ENSP00000443242:K338N	ENSP00000302269:K435N	K	+	3	2	VAV1	6780836	1.000000	0.71417	0.954000	0.39281	0.926000	0.56050	0.657000	0.24963	-0.288000	0.09051	-0.766000	0.03442	AAG		0.537	VAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458475.1		
SUGP1	57794	hgsc.bcm.edu	37	19	19427283	19427283	+	Nonsense_Mutation	SNP	G	G	A			TCGA-24-1546-01A-01W-0615-10	TCGA-24-1546-10A-01W-0615-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_III	WXS	Sanger_PCR_WGA			SOLID	6bf554da-cc72-4daf-9287-a44792c87b8f	a70e1da0-e64d-472d-bdcf-dca6624e490f	g.chr19:19427283G>A	ENST00000247001.5	-	2	501	c.154C>T	c.(154-156)Cag>Tag	p.Q52*	SUGP1_ENST00000334782.5_Nonsense_Mutation_p.Q52*|SUGP1_ENST00000585763.1_5'UTR	NM_172231.3	NP_757386.2	Q8IWZ8	SUGP1_HUMAN	SURP and G patch domain containing 1	52					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)	p.Q52*(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	22						TTGGCTTTCTGTTCCATTTTG	0.532																																																1	Substitution - Nonsense(1)	ovary(1)	19											179.0	126.0	144.0					19																	19427283		2203	4300	6503	19288283	SO:0001587	stop_gained	57794			AF521128	CCDS12399.1	19p13	2013-01-28	2010-08-10	2010-08-10		ENSG00000105705		"""G patch domain containing"""	18643	protein-coding gene	gene with protein product		607992	"""splicing factor 4"""	SF4		12594045	Standard	NM_172231		Approved	F23858, DKFZp434E2216, RBP	uc002nmh.3	Q8IWZ8		ENST00000247001.5:c.154C>T	19.37:g.19427283G>A	ENSP00000247001:p.Gln52*		19288283	O60378|Q6P3X9|Q8TCQ4|Q8WWT4|Q8WWT5|Q9NTG3	Nonsense_Mutation	SNP	ENST00000247001.5	37	CCDS12399.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.867529	0.91587	.	.	ENSG00000105705	ENST00000247001;ENST00000535070;ENST00000334782	.	.	.	4.87	4.87	0.63330	.	0.123330	0.56097	D	0.000031	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	16.9301	0.86188	0.0:0.0:1.0:0.0	.	.	.	.	X	52	.	ENSP00000247001:Q52X	Q	-	1	0	SUGP1	19288283	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.799000	0.62517	2.421000	0.82119	0.555000	0.69702	CAG		0.532	SUGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460128.4	NM_021164	
PCDHGC4	56098	hgsc.bcm.edu	37	5	140866165	140866165	+	Nonsense_Mutation	SNP	C	C	A			TCGA-24-1546-01A-01W-0615-10	TCGA-24-1546-10A-01W-0615-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_III	WXS	Sanger_PCR_WGA			SOLID	6bf554da-cc72-4daf-9287-a44792c87b8f	a70e1da0-e64d-472d-bdcf-dca6624e490f	g.chr5:140866165C>A	ENST00000306593.1	+	1	1425	c.1425C>A	c.(1423-1425)tgC>tgA	p.C475*	PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGC5_ENST00000252087.1_5'Flank|PCDHGB2_ENST00000522605.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_018928.2|NM_032406.1	NP_061751.1|NP_115782.1	Q9Y5F7	PCDGL_HUMAN	protocadherin gamma subfamily C, 4	475	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.C475*(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(13)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	42			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACCTGCTTTGCTCCCTTGCAG	0.488																																																1	Substitution - Nonsense(1)	ovary(1)	5											101.0	102.0	102.0					5																	140866165		2203	4300	6503	140846349	SO:0001587	stop_gained	56098			AF152525	CCDS4262.1, CCDS75349.1	5q31	2010-01-26			ENSG00000242419	ENSG00000242419		"""Cadherins / Protocadherins : Clustered"""	8717	other	protocadherin		606305				10380929	Standard	NM_018928		Approved	PCDH-GAMMA-C4		Q9Y5F7	OTTHUMG00000129625	ENST00000306593.1:c.1425C>A	5.37:g.140866165C>A	ENSP00000306918:p.Cys475*		140846349	Q495T2|Q9Y5C3	Nonsense_Mutation	SNP	ENST00000306593.1	37	CCDS4262.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.642920	0.87859	.	.	ENSG00000242419	ENST00000306593	.	.	.	5.41	2.55	0.30701	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	.	4.0751	0.09901	0.1534:0.5157:0.0:0.3309	.	.	.	.	X	475	.	ENSP00000306918:C475X	C	+	3	2	PCDHGC4	140846349	0.000000	0.05858	1.000000	0.80357	0.991000	0.79684	0.012000	0.13287	0.209000	0.20645	0.467000	0.42956	TGC		0.488	PCDHGC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251820.1	NM_018928	
ARSE	415	hgsc.bcm.edu	37	X	2861125	2861125	+	Silent	SNP	G	G	T			TCGA-24-1546-01A-01W-0615-10	TCGA-24-1546-10A-01W-0615-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_III	WXS	Sanger_PCR_WGA			SOLID	6bf554da-cc72-4daf-9287-a44792c87b8f	a70e1da0-e64d-472d-bdcf-dca6624e490f	g.chrX:2861125G>T	ENST00000381134.3	-	8	1173	c.1107C>A	c.(1105-1107)ggC>ggA	p.G369G	ARSE_ENST00000540563.1_Silent_p.G324G|ARSE_ENST00000545496.1_Silent_p.G394G	NM_000047.2	NP_000038.2	P51690	ARSE_HUMAN	arylsulfatase E (chondrodysplasia punctata 1)	369					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)	p.G369G(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TTCCATTCCAGCCACCATACT	0.468																																																1	Substitution - coding silent(1)	ovary(1)	X											104.0	100.0	101.0					X																	2861125		2203	4300	6503	2871125	SO:0001819	synonymous_variant	415			X83573	CCDS14122.1, CCDS75948.1, CCDS75949.1	Xp22.33	2013-02-14			ENSG00000157399	ENSG00000157399		"""Arylsulfatase family"""	719	protein-coding gene	gene with protein product		300180		CDPX, CDPX1		7720070	Standard	NM_000047		Approved		uc004crc.4	P51690	OTTHUMG00000137358	ENST00000381134.3:c.1107C>A	X.37:g.2861125G>T			2871125	Q53FT2|Q53FU8	Silent	SNP	ENST00000381134.3	37	CCDS14122.1																																																																																				0.468	ARSE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055643.1	NM_000047	
EDEM1	9695	hgsc.bcm.edu	37	3	5249831	5249831	+	Silent	SNP	C	C	T			TCGA-24-1546-01A-01W-0615-10	TCGA-24-1546-10A-01W-0615-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_III	WXS	Sanger_PCR_WGA			SOLID	6bf554da-cc72-4daf-9287-a44792c87b8f	a70e1da0-e64d-472d-bdcf-dca6624e490f	g.chr3:5249831C>T	ENST00000256497.4	+	8	1525	c.1392C>T	c.(1390-1392)gcC>gcT	p.A464A	EDEM1_ENST00000445686.1_Silent_p.A269A	NM_014674.2	NP_055489.1	Q92611	EDEM1_HUMAN	ER degradation enhancer, mannosidase alpha-like 1	464					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	calcium ion binding (GO:0005509)|misfolded protein binding (GO:0051787)	p.A464A(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22				Epithelial(13;0.0588)|OV - Ovarian serous cystadenocarcinoma(96;0.0682)		TCTACTATGCCATATGGAAAC	0.502																																																1	Substitution - coding silent(1)	ovary(1)	3											242.0	204.0	217.0					3																	5249831		2203	4300	6503	5224831	SO:0001819	synonymous_variant	9695			D86967	CCDS33686.1	3p26.1	2008-02-05			ENSG00000134109	ENSG00000134109			18967	protein-coding gene	gene with protein product		607673				12610306	Standard	NM_014674		Approved	KIAA0212, EDEM	uc003bqi.3	Q92611	OTTHUMG00000154896	ENST00000256497.4:c.1392C>T	3.37:g.5249831C>T			5224831	A8K9C8|B4DXP3	Silent	SNP	ENST00000256497.4	37	CCDS33686.1																																																																																				0.502	EDEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337566.2	NM_014674	
