#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_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_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
ACSF2	80221	hgsc.bcm.edu;ucsc.edu	37	17	48551039	48551039	+	Missense_Mutation	SNP	A	A	G			TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr17:48551039A>G	ENST00000300441.4	+	13	1593	c.1489A>G	c.(1489-1491)Atg>Gtg	p.M497V	ACSF2_ENST00000427954.2_Missense_Mutation_p.M522V|ACSF2_ENST00000502667.1_Missense_Mutation_p.M484V|ACSF2_ENST00000541920.1_Missense_Mutation_p.M337V|ACSF2_ENST00000506085.1_3'UTR|ACSF2_ENST00000504392.1_Missense_Mutation_p.M454V	NM_025149.4	NP_079425.3	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2	497					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ligase activity (GO:0016874)			endometrium(7)|kidney(3)|large_intestine(1)|lung(1)|stomach(1)	13	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			TGTCGCCACAATGAATGAGCA	0.512																																																	0													90.0	83.0	85.0					17																	48551039		2203	4300	6503	SO:0001583	missense	80221			AK024573, BC012053	CCDS11567.1, CCDS74103.1, CCDS74104.1, CCDS74105.1	17q21.33	2007-10-17			ENSG00000167107	ENSG00000167107		"""Acyl-CoA synthetase family"""	26101	protein-coding gene	gene with protein product		610465				17762044	Standard	NM_001288968		Approved	FLJ20920, ACSMW	uc002iqu.2	Q96CM8	OTTHUMG00000162128	ENST00000300441.4:c.1489A>G	17.37:g.48551039A>G	ENSP00000300441:p.Met497Val		B4DFQ6|B4DHT5|B4DUF5|Q9H7G2	Missense_Mutation	SNP	ENST00000300441.4	37	CCDS11567.1	.	.	.	.	.	.	.	.	.	.	A	10.86	1.471105	0.26423	.	.	ENSG00000167107	ENST00000300441;ENST00000541920;ENST00000504392;ENST00000427954;ENST00000502667	T;T;T;T;T	0.38560	1.13;1.13;1.13;1.13;1.13	4.94	3.79	0.43588	AMP-dependent synthetase/ligase (1);	0.324703	0.37809	N	0.001921	T	0.34019	0.0883	L	0.42529	1.33	0.38233	D	0.941096	B;B;B;B	0.20368	0.024;0.044;0.024;0.024	B;B;B;B	0.27887	0.084;0.084;0.084;0.084	T	0.36841	-0.9731	10	0.62326	D	0.03	-12.956	6.9474	0.24526	0.6788:0.1949:0.0:0.1263	.	484;522;454;497	B4DHT5;B4DFQ6;E9PF16;Q96CM8	.;.;.;ACSF2_HUMAN	V	497;337;454;522;484	ENSP00000300441:M497V;ENSP00000437987:M337V;ENSP00000425964:M454V;ENSP00000401831:M522V;ENSP00000421884:M484V	ENSP00000300441:M497V	M	+	1	0	ACSF2	45906038	0.285000	0.24296	0.245000	0.24217	0.049000	0.14656	0.919000	0.28692	1.856000	0.53863	0.402000	0.26972	ATG		0.512	ACSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367423.3		NM_025149	
ADAM21	8747	hgsc.bcm.edu	37	14	70924697	70924697	+	Missense_Mutation	SNP	A	A	G	rs386778613|rs45545935	byFrequency	TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr14:70924697A>G	ENST00000603540.1	+	2	739	c.481A>G	c.(481-483)Ata>Gta	p.I161V	RP11-486O13.4_ENST00000556646.1_lincRNA|ADAM21_ENST00000267499.3_Missense_Mutation_p.I161V	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	161				I -> V (in Ref. 1; AAD55255 and 3; AAI09025/AAI09026). {ECO:0000305}.	binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.I161V(1)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	31				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		GGTTTATAAGATAAACAGTAA	0.423													A|||	1254	0.250399	0.3026	0.1297	5008	,	,		19080	0.496		0.1173	False		,,,				2504	0.1493																1	Substitution - Missense(1)	stomach(1)											39.0	48.0	45.0					14																	70924697		2156	4294	6450	SO:0001583	missense	8747			AF029900	CCDS9804.1	14q24.1	2008-09-05	2005-08-18		ENSG00000139985	ENSG00000139985		"""ADAM metallopeptidase domain containing"""	200	protein-coding gene	gene with protein product		603713	"""a disintegrin and metalloproteinase domain 21"""			9469942	Standard	NM_003813		Approved	ADAM31	uc001xmd.3	Q9UKJ8		ENST00000603540.1:c.481A>G	14.37:g.70924697A>G	ENSP00000474385:p.Ile161Val		O43507|Q2VPC6|Q32MR0	Missense_Mutation	SNP	ENST00000603540.1	37	CCDS9804.1	.	.	.	.	.	.	.	.	.	.	A	0.700	-0.791263	0.02884	.	.	ENSG00000139985	ENST00000267499	T	0.01119	5.31	3.76	-5.66	0.02451	.	0.559418	0.13492	U	0.383910	T	0.00815	0.0027	L	0.41236	1.265	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.48210	-0.9055	10	0.28530	T	0.3	.	0.3958	0.00418	0.2927:0.2858:0.1722:0.2492	rs45545935	161	Q9UKJ8	ADA21_HUMAN	V	161	ENSP00000267499:I161V	ENSP00000267499:I161V	I	+	1	0	ADAM21	69994450	0.000000	0.05858	0.025000	0.17156	0.459000	0.32528	-1.436000	0.02421	-0.597000	0.05813	0.455000	0.32223	ATA		0.423	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3			
ADAMTS17	170691	hgsc.bcm.edu;ucsc.edu	37	15	100649280	100649281	+	In_Frame_Ins	INS	-	-	CTCCTT	rs533437573	byFrequency	TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr15:100649280_100649281insCTCCTT	ENST00000268070.4	-	14	2034_2035	c.1929_1930insAAGGAG	c.(1927-1932)gagtcc>gagAAGGAGtcc	p.642_643insEK		NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	642	Cys-rich.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)	50	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		AGCAGTGGGGACTCCTTCCCGA	0.624														6	0.00119808	0.0045	0.0	5008	,	,		21128	0.0		0.0	False		,,,				2504	0.0																0										20,4244		0,20,2112						4.0	1.0			53	2,8252		0,2,4125	no	coding	ADAMTS17	NM_139057.2		0,22,6237	A1A1,A1R,RR		0.0242,0.469,0.1757				22,12496				SO:0001652	inframe_insertion	170691			AJ315735	CCDS10383.1	15q24	2014-01-28	2005-08-19		ENSG00000140470	ENSG00000140470		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17109	protein-coding gene	gene with protein product		607511	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 17"""			11867212	Standard	NM_139057		Approved	FLJ32769, FLJ16363	uc002bvv.1	Q8TE56	OTTHUMG00000149867	ENST00000268070.4:c.1924_1929dupAAGGAG	15.37:g.100649281_100649286dupCTCCTT	ENSP00000268070:p.Lys642_Glu643insGluLys		Q2I7G4|Q6ZN75	In_Frame_Ins	INS	ENST00000268070.4	37	CCDS10383.1																																																																																				0.624	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313595.1		NM_139057	
AGK	55750	hgsc.bcm.edu;ucsc.edu	37	7	141336815	141336815	+	Nonsense_Mutation	SNP	A	A	T			TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr7:141336815A>T	ENST00000355413.4	+	11	984	c.724A>T	c.(724-726)Aag>Tag	p.K242*	AGK_ENST00000535825.1_Nonsense_Mutation_p.K239*|AGK_ENST00000473247.1_Nonsense_Mutation_p.K214*	NM_018238.3	NP_060708.1	Q53H12	AGK_HUMAN	acylglycerol kinase	242					ceramide biosynthetic process (GO:0046513)|glycerolipid metabolic process (GO:0046486)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acylglycerol kinase activity (GO:0047620)|ATP binding (GO:0005524)|ceramide kinase activity (GO:0001729)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(1)|endometrium(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(3)	17	Melanoma(164;0.0171)					CAGCACTCTTAAGGTAAATGT	0.318																																																	0													116.0	108.0	111.0					7																	141336815		2203	4300	6503	SO:0001587	stop_gained	55750			BC022777	CCDS5865.1	7q34	2010-05-04	2007-01-11	2007-01-11	ENSG00000006530	ENSG00000006530	2.7.1.94		21869	protein-coding gene	gene with protein product		610345	"""multiple substrate lipid kinase"""	MULK		15252046, 15939762, 17135245	Standard	NM_018238		Approved	FLJ10842	uc003vwi.2	Q53H12	OTTHUMG00000157499	ENST00000355413.4:c.724A>T	7.37:g.141336815A>T	ENSP00000347581:p.Lys242*		Q75KN1|Q96GC3|Q9NP48	Nonsense_Mutation	SNP	ENST00000355413.4	37	CCDS5865.1	.	.	.	.	.	.	.	.	.	.	A	36	5.721853	0.96839	.	.	ENSG00000006530	ENST00000355413;ENST00000473247;ENST00000535825	.	.	.	5.04	2.7	0.31948	.	0.169545	0.49305	D	0.000144	.	.	.	.	.	.	0.58432	A	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.3105	0.43706	0.5934:0.4066:0.0:0.0	.	.	.	.	X	242;214;239	.	ENSP00000347581:K242X	K	+	1	0	AGK	140983284	0.994000	0.37717	1.000000	0.80357	0.957000	0.61999	1.229000	0.32600	0.363000	0.24346	0.528000	0.53228	AAG		0.318	AGK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348969.1		NM_018238	
ANKRD55	79722	hgsc.bcm.edu	37	5	55466560	55466574	+	In_Frame_Del	DEL	CGGCCATTTTTATCT	CGGCCATTTTTATCT	-	rs142389026|rs370043337|rs78025637	byFrequency	TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	CGGCCATTTTTATCT	CGGCCATTTTTATCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr5:55466560_55466574delCGGCCATTTTTATCT	ENST00000341048.4	-	5	520_534	c.369_383delAGATAAAAATGGCCG	c.(367-384)ccagataaaaatggccgc>ccc	p.DKNGR124del	ANKRD55_ENST00000504958.2_In_Frame_Del_p.DKNGR124del|ANKRD55_ENST00000513241.2_In_Frame_Del_p.DKNGR95del	NM_024669.2	NP_078945.2	Q3KP44	ANR55_HUMAN	ankyrin repeat domain 55	124								p.D124E(1)|p.R128H(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(1)	34		Lung NSC(810;8.69e-05)|Prostate(74;0.00634)|Breast(144;0.0334)|Ovarian(174;0.223)				CAGTGGCAGGCGGCCATTTTTATCTGGGATATTGT	0.484																																																	2	Substitution - Missense(2)	large_intestine(1)|skin(1)																																								SO:0001651	inframe_deletion	79722			AK021857	CCDS34161.1	5q11.2	2013-01-10			ENSG00000164512	ENSG00000164512		"""Ankyrin repeat domain containing"""	25681	protein-coding gene	gene with protein product		615189					Standard	XM_005248599		Approved	FLJ11795	uc003jqu.3	Q3KP44	OTTHUMG00000162305	ENST00000341048.4:c.369_383delAGATAAAAATGGCCG	5.37:g.55466560_55466574delCGGCCATTTTTATCT	ENSP00000342295:p.Asp124_Arg128del		B3KVT8|Q3KP45|Q9HAD3	In_Frame_Del	DEL	ENST00000341048.4	37	CCDS34161.1																																																																																				0.484	ANKRD55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368510.4		NM_024669	
ATRX	546	hgsc.bcm.edu;ucsc.edu	37	X	76938884	76938884	+	Missense_Mutation	SNP	G	G	T			TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chrX:76938884G>T	ENST00000373344.5	-	9	2078	c.1864C>A	c.(1864-1866)Ccc>Acc	p.P622T	ATRX_ENST00000395603.3_Missense_Mutation_p.P584T|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	622					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						TCTAACTTGGGGTTCAGACCA	0.378			"""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)											181.0	202.0	195.0					X																	76938884		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.1864C>A	X.37:g.76938884G>T	ENSP00000362441:p.Pro622Thr		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Missense_Mutation	SNP	ENST00000373344.5	37	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	g	0.006	-2.104152	0.00356	.	.	ENSG00000085224	ENST00000373344;ENST00000395603;ENST00000400862	D;D	0.91894	-2.93;-2.91	5.22	-2.59	0.06209	.	1.109790	0.06910	N	0.807471	D	0.84183	0.5416	L	0.43152	1.355	0.09310	N	0.999998	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.08055	0.001;0.003;0.002;0.001	T	0.65212	-0.6223	10	0.22706	T	0.39	2.7578	0.2769	0.00239	0.2832:0.216:0.2775:0.2232	.	622;554;584;622	A4LAA3;P46100-6;P46100-4;P46100	.;.;.;ATRX_HUMAN	T	622;584;549	ENSP00000362441:P622T;ENSP00000378967:P584T	ENSP00000362441:P622T	P	-	1	0	ATRX	76825540	0.000000	0.05858	0.000000	0.03702	0.251000	0.25915	-0.410000	0.07151	-0.835000	0.04234	-0.318000	0.08688	CCC		0.378	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2		NM_000489	
AVIL	10677	hgsc.bcm.edu	37	12	58203422	58203423	+	Frame_Shift_Ins	INS	-	-	C			TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr12:58203422_58203423insC	ENST00000257861.3	-	8	1326_1327	c.896_897insG	c.(895-897)ggafs	p.G299fs	AVIL_ENST00000537081.1_Frame_Shift_Ins_p.G292fs	NM_006576.3	NP_006567.3	O75366	AVIL_HUMAN	advillin	299	Core. {ECO:0000250}.				actin filament capping (GO:0051693)|cilium morphogenesis (GO:0060271)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|positive regulation of neuron projection development (GO:0010976)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)	actin binding (GO:0003779)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(9)|ovary(1)|prostate(6)	32	Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)					CCTTTGTGGCTCCTTTTCCTTT	0.46																																																	0																																										SO:0001589	frameshift_variant	10677			AF041449	CCDS8959.1	12q13.11	2006-03-30				ENSG00000135407			14188	protein-coding gene	gene with protein product		613397				9664034, 12034507	Standard	NM_006576		Approved	p92, FLJ12386, ADVIL, DOC6	uc001sqj.2	O75366	OTTHUMG00000170461	ENST00000257861.3:c.897dupG	12.37:g.58203424_58203424dupC	ENSP00000257861:p.Gly299fs		B2RAU7|Q2NKM9	Frame_Shift_Ins	INS	ENST00000257861.3	37	CCDS8959.1																																																																																				0.460	AVIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409276.1		NM_006576	
BARD1	580	hgsc.bcm.edu;ucsc.edu	37	2	215645503	215645523	+	In_Frame_Del	DEL	TGGTGAAGAACATTCAGGCAA	TGGTGAAGAACATTCAGGCAA	-	rs201292946|rs200168806|rs141351035|rs28997575	byFrequency	TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	TGGTGAAGAACATTCAGGCAA	TGGTGAAGAACATTCAGGCAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr2:215645503_215645523delTGGTGAAGAACATTCAGGCAA	ENST00000260947.4	-	4	1209_1229	c.1075_1095delTTGCCTGAATGTTCTTCACCA	c.(1075-1095)ttgcctgaatgttcttcaccadel	p.LPECSSP359del	BARD1_ENST00000471787.1_5'Flank|BARD1_ENST00000449967.2_In_Frame_Del_p.LPECSSP215del	NM_000465.2|NM_001282543.1|NM_001282545.1|NM_001282548.1	NP_000456.2|NP_001269472.1|NP_001269474.1|NP_001269477.1	Q99728	BARD1_HUMAN	BRCA1 associated RING domain 1	359					cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA 3'-end processing (GO:0031441)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein catabolic process (GO:0045732)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of phosphorylation (GO:0042325)|tissue homeostasis (GO:0001894)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	kinase binding (GO:0019900)|ligase activity (GO:0016874)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|prostate(4)|upper_aerodigestive_tract(1)	35		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		TGCATGAAGGTGGTGAAGAACATTCAGGCAATGGTATATTT	0.421									Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome					224	0.0447284	0.0416	0.0346	5008	,	,		25266	0.0466		0.0149	False		,,,				2504	0.0849																0																																										SO:0001651	inframe_deletion	580	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease		CCDS2397.1, CCDS74645.1, CCDS74646.1, CCDS74647.1, CCDS74648.1	2q34-q35	2013-01-10			ENSG00000138376	ENSG00000138376		"""Ankyrin repeat domain containing"""	952	protein-coding gene	gene with protein product		601593				8944023, 9425226, 15159397	Standard	NM_001282548		Approved		uc002veu.2	Q99728	OTTHUMG00000133016	ENST00000260947.4:c.1075_1095delTTGCCTGAATGTTCTTCACCA	2.37:g.215645503_215645523delTGGTGAAGAACATTCAGGCAA	ENSP00000260947:p.Leu359_Pro365del		F6MDH7|F6MDH8|F6MDH9|O43574|Q53SS5	In_Frame_Del	DEL	ENST00000260947.4	37	CCDS2397.1																																																																																				0.421	BARD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256602.1		NM_000465	
ATG101	60673	hgsc.bcm.edu;ucsc.edu	37	12	52467675	52467697	+	Splice_Site	DEL	GGGGAGTTCAAGGTAAGGGTGTC	GGGGAGTTCAAGGTAAGGGTGTC	-	rs143921343|rs372834432|rs201392245|rs77525659	byFrequency	TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	GGGGAGTTCAAGGTAAGGGTGTC	GGGGAGTTCAAGGTAAGGGTGTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr12:52467675_52467697delGGGGAGTTCAAGGTAAGGGTGTC	ENST00000336854.4	+	3	719_730	c.241_252delGGGGAGTTCAAGGTAAGGGTGTC	c.(241-252)ggggagttcaagdel	p.GEFK81fs	RP11-1100L3.7_ENST00000550301.1_RNA	NM_001098673.1|NM_021934.4	NP_001092143.1|NP_068753.2	Q9BSB4	ATGA1_HUMAN		81					autophagic vacuole assembly (GO:0000045)	pre-autophagosomal structure (GO:0000407)	identical protein binding (GO:0042802)|protein complex binding (GO:0032403)			endometrium(1)|lung(2)|ovary(1)	4				BRCA - Breast invasive adenocarcinoma(357;0.0978)		CAAGGTTGTTGGGGAGTTCAAGGTAAGGGTGTCGGGGAGTTCA	0.565														310	0.061901	0.1263	0.0836	5008	,	,		24693	0.0		0.0467	False		,,,				2504	0.0389																0									,	399,3857		31,337,1760					,	-5.5	0.9		dbSNP_134	131	327,7927		15,297,3815	no	frameshift-near-splice,frameshift-near-splice	C12orf44	NM_021934.4,NM_001098673.1	,	46,634,5575	A1A1,A1R,RR		3.9617,9.375,5.8034	,	,		726,11784				SO:0001630	splice_region_variant	60673																														ENST00000336854.4:c.252+1GGGGAGTTCAAGGTAAGGGTGTC>-	12.37:g.52467675_52467697delGGGGAGTTCAAGGTAAGGGTGTC			Q9HAE2|Q9HBN1	Frame_Shift_Del	DEL	ENST00000336854.4	37	CCDS8820.1																																																																																				0.565	C12orf44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405063.1			Frame_Shift_Del
NCOR1P1	149934	hgsc.bcm.edu	37	20	26084251	26084251	+	RNA	SNP	C	C	T	rs61752036	byFrequency	TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr20:26084251C>T	ENST00000478176.1	-	0	206					NR_003678.1		Q9H4R4	CT191_HUMAN	nuclear receptor corepressor 1 pseudogene 1																		CATCTCCACACGGTTGCCCCA	0.388																																																	0													34.0	26.0	28.0					20																	26084251		692	1590	2282			0			AL391119		20p11.1	2011-09-16	2011-09-16	2011-09-16	ENSG00000240108	ENSG00000240108			16724	pseudogene	pseudogene			"""chromosome 20 open reading frame 191"""	C20orf191			Standard	NR_003678		Approved	bB329D4.2	uc002wvj.5	Q9H4R4	OTTHUMG00000032145		20.37:g.26084251C>T			A2RUA0	RNA	SNP	ENST00000478176.1	37																																																																																					0.388	NCOR1P1-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000078478.2			
CACNA1E	777	hgsc.bcm.edu;ucsc.edu	37	1	181705481	181705481	+	Silent	SNP	G	G	A	rs569675496		TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr1:181705481G>A	ENST00000367573.2	+	22	3333	c.3333G>A	c.(3331-3333)gtG>gtA	p.V1111V	CACNA1E_ENST00000367570.1_Silent_p.V1111V|CACNA1E_ENST00000526775.1_Silent_p.V1092V|CACNA1E_ENST00000358338.5_Silent_p.V1043V|CACNA1E_ENST00000357570.5_Silent_p.V1062V|CACNA1E_ENST00000367567.4_Silent_p.V718V|CACNA1E_ENST00000360108.3_Silent_p.V1092V	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1111					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						aggaggaggtggagaagaaga	0.527													G|||	1	0.000199681	0.0008	0.0	5008	,	,		20999	0.0		0.0	False		,,,				2504	0.0																0													92.0	116.0	108.0					1																	181705481		2158	4255	6413	SO:0001819	synonymous_variant	777			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.3333G>A	1.37:g.181705481G>A			B1AM12|B1AM13|B1AM14|Q14580|Q14581	Silent	SNP	ENST00000367573.2	37	CCDS55664.1																																																																																				0.527	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2		NM_000721	
CCDC144NL	339184	hgsc.bcm.edu	37	17	20768763	20768763	+	Missense_Mutation	SNP	T	T	C	rs201148033		TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr17:20768763T>C	ENST00000327925.5	-	4	750	c.631A>G	c.(631-633)Aag>Gag	p.K211E	CCDC144NL_ENST00000539484.1_5'UTR|RP11-344E13.3_ENST00000577537.1_RNA	NM_001004306.1	NP_001004306.1	Q6NUI1	C144L_HUMAN	coiled-coil domain containing 144 family, N-terminal like	211										large_intestine(3)|lung(3)|skin(1)	7						TTCTTCCCCTTTCTTTTTCCT	0.368																																																	0													103.0	95.0	98.0					17																	20768763		2203	4300	6503	SO:0001583	missense	339184				CCDS32591.1	17p11.2	2009-01-15			ENSG00000205212	ENSG00000205212			33735	protein-coding gene	gene with protein product							Standard	NM_001004306		Approved	MGC87631	uc002gyf.3	Q6NUI1	OTTHUMG00000132271	ENST00000327925.5:c.631A>G	17.37:g.20768763T>C	ENSP00000328054:p.Lys211Glu			Missense_Mutation	SNP	ENST00000327925.5	37	CCDS32591.1	.	.	.	.	.	.	.	.	.	.	t	0.914	-0.718026	0.03182	.	.	ENSG00000205212	ENST00000327925	T	0.17854	2.25	.	.	.	.	.	.	.	.	T	0.07098	0.0180	N	0.08118	0	0.09310	N	1	B	0.29162	0.235	B	0.16289	0.015	T	0.29458	-1.0011	7	0.72032	D	0.01	.	.	.	.	.	211	Q6NUI1	C144L_HUMAN	E	211	ENSP00000328054:K211E	ENSP00000328054:K211E	K	-	1	0	CCDC144NL	20709355	0.087000	0.21565	0.028000	0.17463	0.028000	0.11728	0.077000	0.14738	0.077000	0.16863	0.076000	0.15429	AAG		0.368	CCDC144NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255361.2		NM_001004306	
CDCA7	83879	hgsc.bcm.edu;ucsc.edu	37	2	174224187	174224187	+	Intron	SNP	G	G	A			TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr2:174224187G>A	ENST00000347703.3	+	2	291				CDCA7_ENST00000410019.3_Intron|CDCA7_ENST00000410101.3_Missense_Mutation_p.G74S|CDCA7_ENST00000392567.2_Intron|CDCA7_ENST00000306721.3_Missense_Mutation_p.G118S	NM_145810.2	NP_665809.1	Q9BWT1	CDCA7_HUMAN	cell division cycle associated 7						apoptotic process (GO:0006915)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.116)			ATCATTTTGCGGTTTCTCAGA	0.388																																																	0													98.0	96.0	97.0					2																	174224187		2203	4300	6503	SO:0001627	intron_variant	83879			BG354580	CCDS2252.1, CCDS2253.1	2q31.1	2008-02-05			ENSG00000144354	ENSG00000144354			14628	protein-coding gene	gene with protein product		609937				11598121, 12188893	Standard	NM_145810		Approved	FLJ14736, JPO1	uc002uic.1	Q9BWT1	OTTHUMG00000132296	ENST00000347703.3:c.147+622G>A	2.37:g.174224187G>A			B4DLP8|B4DV66|Q53EW5|Q580W9|Q658K4|Q658N4|Q8NBY9|Q96BV8|Q96SP5	Missense_Mutation	SNP	ENST00000347703.3	37	CCDS2253.1	.	.	.	.	.	.	.	.	.	.	G	17.65	3.441964	0.63067	.	.	ENSG00000144354	ENST00000306721;ENST00000410101	T;T	0.51817	0.89;0.69	5.87	4.99	0.66335	.	0.198263	0.42294	D	0.000728	T	0.56615	0.1997	M	0.69358	2.11	0.80722	D	1	D;D	0.69078	0.992;0.997	P;P	0.59171	0.518;0.853	T	0.58086	-0.7698	10	0.06757	T	0.87	-11.6028	12.8376	0.57782	0.0759:0.0:0.9241:0.0	.	74;118	B4DV66;Q9BWT1-2	.;.	S	118;74	ENSP00000306968:G118S;ENSP00000386656:G74S	ENSP00000306968:G118S	G	+	1	0	CDCA7	173932433	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.122000	0.57910	1.484000	0.48361	0.650000	0.86243	GGT		0.388	CDCA7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255400.1		NM_031942	
CEACAM3	1084	hgsc.bcm.edu	37	19	42301733	42301733	+	Missense_Mutation	SNP	G	G	C	rs61737016	byFrequency	TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr19:42301733G>C	ENST00000357396.3	+	2	518	c.277G>C	c.(277-279)Gcc>Ccc	p.A93P	CEACAM3_ENST00000344550.4_Missense_Mutation_p.A93P|CEACAM3_ENST00000595255.1_3'UTR|CEACAM3_ENST00000221999.4_Missense_Mutation_p.A93P	NM_001815.2	NP_001806.2	P40198	CEAM3_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 3	93	Ig-like V-type.					integral component of membrane (GO:0016021)		p.A93P(1)		endometrium(2)|kidney(4)|large_intestine(1)|lung(4)|prostate(3)|skin(4)|stomach(1)	19						TACCCCAGGGGCCGCATACAG	0.463																																																	1	Substitution - Missense(1)	large_intestine(1)						G	PRO/ALA	41,4317		16,9,2154	182.0	204.0	197.0		277	-0.6	0.0	19	dbSNP_129	197	0,8600		0,0,4300	no	missense	CEACAM3	NM_001815.2	27	16,9,6454	CC,CG,GG		0.0,0.9408,0.3164	benign	93/253	42301733	41,12917	2179	4300	6479	SO:0001583	missense	1084			E03349	CCDS12586.2, CCDS62685.1	19q13.2	2013-01-11			ENSG00000170956	ENSG00000170956		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1815	protein-coding gene	gene with protein product		609142		CGM1			Standard	NM_001815		Approved	CD66d	uc002orn.2	P40198	OTTHUMG00000150142	ENST00000357396.3:c.277G>C	19.37:g.42301733G>C	ENSP00000349971:p.Ala93Pro		G5E978|Q3KPH9	Missense_Mutation	SNP	ENST00000357396.3	37	CCDS12586.2	73	0.033424908424908424	61	0.12398373983739837	11	0.03038674033149171	1	0.0017482517482517483	0	0.0	G	0.017	-1.506343	0.00992	0.009408	0.0	ENSG00000170956	ENST00000357396;ENST00000389667;ENST00000221999;ENST00000344550	T;T;T	0.01388	4.95;4.95;4.95	3.44	-0.646	0.11472	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.00012	-2.96	0.09310	N	1	B;B	0.09022	0.002;0.0	B;B	0.09377	0.004;0.0	T	0.44667	-0.9313	9	0.02654	T	1	.	6.885	0.24195	0.1778:0.4701:0.3521:0.0	rs61737016	93;93	G5E978;P40198	.;CEAM3_HUMAN	P	93	ENSP00000349971:A93P;ENSP00000221999:A93P;ENSP00000341725:A93P	ENSP00000221999:A93P	A	+	1	0	CEACAM3	46993573	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.640000	0.05440	0.106000	0.17784	-0.286000	0.09958	GCC		0.463	CEACAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316509.2		NM_001815	
CEACAM3	1084	hgsc.bcm.edu;ucsc.edu	37	19	42301763	42301763	+	Missense_Mutation	SNP	A	A	C	rs61737014	byFrequency	TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr19:42301763A>C	ENST00000357396.3	+	2	548	c.307A>C	c.(307-309)Acc>Ccc	p.T103P	CEACAM3_ENST00000344550.4_Missense_Mutation_p.T103P|CEACAM3_ENST00000595255.1_3'UTR|CEACAM3_ENST00000221999.4_Missense_Mutation_p.T103P	NM_001815.2	NP_001806.2	P40198	CEAM3_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 3	103	Ig-like V-type.					integral component of membrane (GO:0016021)		p.R98_S106delRETIYTNAS(1)		endometrium(2)|kidney(4)|large_intestine(1)|lung(4)|prostate(3)|skin(4)|stomach(1)	19						GACAATATACACCAATGCATC	0.458													N|||	303	0.0605032	0.2126	0.0274	5008	,	,		21051	0.001		0.002	False		,,,				2504	0.0																1	Deletion - In frame(1)	stomach(1)						C	PRO/THR	274,4132		73,128,2002	230.0	251.0	244.0		307	-0.4	0.0	19	dbSNP_129	244	5,8595		0,5,4295	no	missense	CEACAM3	NM_001815.2	38	73,133,6297	CC,CA,AA		0.0581,6.2188,2.1452	benign	103/253	42301763	279,12727	2203	4300	6503	SO:0001583	missense	1084			E03349	CCDS12586.2, CCDS62685.1	19q13.2	2013-01-11			ENSG00000170956	ENSG00000170956		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1815	protein-coding gene	gene with protein product		609142		CGM1			Standard	NM_001815		Approved	CD66d	uc002orn.2	P40198	OTTHUMG00000150142	ENST00000357396.3:c.307A>C	19.37:g.42301763A>C	ENSP00000349971:p.Thr103Pro		G5E978|Q3KPH9	Missense_Mutation	SNP	ENST00000357396.3	37	CCDS12586.2	78	0.03571428571428571	63	0.12804878048780488	13	0.03591160220994475	1	0.0017482517482517483	1	0.0013192612137203166	C	0.007	-1.955855	0.00470	0.062188	5.81E-4	ENSG00000170956	ENST00000357396;ENST00000389667;ENST00000221999;ENST00000344550	T;T;T	0.01464	4.86;4.86;4.86	3.44	-0.421	0.12332	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.00076	-2.245	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39313	-0.9620	8	0.02654	T	1	.	4.92	0.13865	0.2929:0.5004:0.0:0.2066	rs61737014	103;103	G5E978;P40198	.;CEAM3_HUMAN	P	103	ENSP00000349971:T103P;ENSP00000221999:T103P;ENSP00000341725:T103P	ENSP00000221999:T103P	T	+	1	0	CEACAM3	46993603	0.000000	0.05858	0.014000	0.15608	0.002000	0.02628	-0.938000	0.03938	-0.569000	0.06030	-2.519000	0.00185	ACC		0.458	CEACAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316509.2		NM_001815	
DPCR1	135656	hgsc.bcm.edu	37	6	30917574	30917574	+	Missense_Mutation	SNP	A	A	G			TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr6:30917574A>G	ENST00000462446.1	+	2	1361	c.1333A>G	c.(1333-1335)Aga>Gga	p.R445G	HCG21_ENST00000419481.1_RNA|DPCR1_ENST00000304311.2_5'UTR			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	336						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						TACAGAAAATAGAGAAAGGAC	0.512																																																	0													178.0	220.0	207.0					6																	30917574		692	1591	2283	SO:0001583	missense	135656			AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.1333A>G	6.37:g.30917574A>G	ENSP00000417182:p.Arg445Gly		C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	37	CCDS4692.2	.	.	.	.	.	.	.	.	.	.	-	2.003	-0.429049	0.04701	.	.	ENSG00000168631	ENST00000462446	T	0.35421	1.31	1.56	-2.11	0.07187	.	.	.	.	.	T	0.01835	0.0058	N	0.00289	-1.7	0.09310	N	0.999998	B	0.02656	0.0	B	0.01281	0.0	T	0.41805	-0.9488	9	0.22109	T	0.4	.	4.2407	0.10647	0.3781:0.1779:0.444:0.0	.	445	E9PEI6	.	G	445	ENSP00000417182:R445G	ENSP00000417182:R445G	R	+	1	2	DPCR1	31025553	0.000000	0.05858	0.000000	0.03702	0.504000	0.33889	-1.010000	0.03656	-1.070000	0.03149	0.000000	0.15137	AGA		0.512	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3		NM_080870	
GPR50	9248	hgsc.bcm.edu;ucsc.edu	37	X	150349558	150349569	+	In_Frame_Del	DEL	CACCACTGGCCA	CACCACTGGCCA	-	rs377556761|rs199797606|rs68058591|rs200787393		TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	CACCACTGGCCA	CACCACTGGCCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chrX:150349558_150349569delCACCACTGGCCA	ENST00000218316.3	+	2	1572_1583	c.1503_1514delCACCACTGGCCA	c.(1501-1515)cccaccactggccac>ccc	p.TTGH502del	AF003625.3_ENST00000602313.1_lincRNA	NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	502	Pro-rich.		Missing (lower fasting circulating triglyceride levels). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8647286, ECO:0000269|Ref.2}.		cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|identical protein binding (GO:0042802)|melatonin receptor activity (GO:0008502)	p.T502_H505delTTGH(1)		breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	38	Acute lymphoblastic leukemia(192;6.56e-05)					ACCCTAAACCCACCACTGGCCACATCAAGCCA	0.608																																																	1	Deletion - In frame(1)	ovary(1)								1488,2015		315,617,241,554,290						2.6	0.0		dbSNP_130	100	2487,3842		404,1011,668,899,1033	no	coding	GPR50	NM_004224.3		719,1628,909,1453,1323	A1A1,A1R,A1,RR,R		39.2953,42.4779,40.4292				3975,5857				SO:0001651	inframe_deletion	9248			U52219	CCDS44012.1	Xq28	2012-08-21			ENSG00000102195	ENSG00000102195		"""GPCR / Class A : Orphans"""	4506	protein-coding gene	gene with protein product		300207				9933574, 18400093	Standard	NM_004224		Approved	H9, Mel1c	uc010ntg.2	Q13585	OTTHUMG00000024166	ENST00000218316.3:c.1503_1514delCACCACTGGCCA	X.37:g.150349558_150349569delCACCACTGGCCA	ENSP00000218316:p.Thr502_His505del		Q0VGG3|Q3ZAR0	In_Frame_Del	DEL	ENST00000218316.3	37	CCDS44012.1																																																																																				0.608	GPR50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060874.1		NM_004224	
GPRC6A	222545	hgsc.bcm.edu	37	6	117113761	117113762	+	Frame_Shift_Ins	INS	-	-	GG	rs386705086|rs371464745|rs550458778	byFrequency	TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr6:117113761_117113762insGG	ENST00000310357.3	-	6	2345_2346	c.2324_2325insCC	c.(2323-2325)tatfs	p.Y775fs	GPRC6A_ENST00000368549.3_Frame_Shift_Ins_p.Y704fs|GPRC6A_ENST00000530250.1_Frame_Shift_Ins_p.Y600fs	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	775					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		TGTAATTCTCATATTTGCCTTT	0.411														798	0.159345	0.4009	0.1657	5008	,	,		24205	0.006		0.0815	False		,,,				2504	0.0665																0																																										SO:0001589	frameshift_variant	222545			AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"""GPCR / Class C : Calcium-sensing receptors"""	18510	protein-coding gene	gene with protein product			"""G protein-coupled receptor, family C, group 6, member A"""				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.2324_2325insCC	6.37:g.117113761_117113762insGG	ENSP00000309493:p.Tyr775fs		Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Frame_Shift_Ins	INS	ENST00000310357.3	37	CCDS5112.1																																																																																				0.411	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2			
GPRC6A	222545	hgsc.bcm.edu	37	6	117113762	117113763	+	Frame_Shift_Ins	INS	-	-	A	rs386705086|rs371464745		TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr6:117113762_117113763insA	ENST00000310357.3	-	6	2344_2345	c.2323_2324insT	c.(2323-2325)tatfs	p.Y775fs	GPRC6A_ENST00000368549.3_Frame_Shift_Ins_p.Y704fs|GPRC6A_ENST00000530250.1_Frame_Shift_Ins_p.Y600fs	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	775					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		GTAATTCTCATATTTGCCTTTG	0.416																																																	0																																										SO:0001589	frameshift_variant	222545			AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"""GPCR / Class C : Calcium-sensing receptors"""	18510	protein-coding gene	gene with protein product			"""G protein-coupled receptor, family C, group 6, member A"""				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.2324dupT	6.37:g.117113763_117113763dupA	ENSP00000309493:p.Tyr775fs		Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Frame_Shift_Ins	INS	ENST00000310357.3	37	CCDS5112.1																																																																																				0.416	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2			
GPRC6A	222545	hgsc.bcm.edu;ucsc.edu	37	6	117113765	117113766	+	In_Frame_Ins	INS	-	-	TCC	rs386705086|rs111974433|rs368671066	byFrequency	TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr6:117113765_117113766insTCC	ENST00000310357.3	-	6	2341_2342	c.2320_2321insGGA	c.(2320-2322)aaa>aGGAaa	p.773_774insR	GPRC6A_ENST00000368549.3_In_Frame_Ins_p.702_703insR|GPRC6A_ENST00000530250.1_In_Frame_Ins_p.598_599insR	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	773					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		ATTCTCATATTTGCCTTTGAAA	0.421														798	0.159345	0.4009	0.1657	5008	,	,		22554	0.006		0.0815	False		,,,				2504	0.0665																0																																										SO:0001652	inframe_insertion	222545			AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"""GPCR / Class C : Calcium-sensing receptors"""	18510	protein-coding gene	gene with protein product			"""G protein-coupled receptor, family C, group 6, member A"""				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.2320_2321insGGA	6.37:g.117113765_117113766insTCC	ENSP00000309493:p.Gly773_Lys774insArg		Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	In_Frame_Ins	INS	ENST00000310357.3	37	CCDS5112.1																																																																																				0.421	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2			
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168377092	168377092	+	lincRNA	SNP	G	G	T	rs199609073|rs75642682	byFrequency	TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr6:168377092G>T	ENST00000538528.1	-	0	527																											CCTGCAGTGTGGGGGGAGGAG	0.622																																																	0													4.0	6.0	5.0					6																	168377092		630	1507	2137			100128124																															6.37:g.168377092G>T				Missense_Mutation	SNP	ENST00000538528.1	37																																																																																					0.622	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA				
HHLA2	11148	hgsc.bcm.edu	37	3	108081191	108081195	+	Frame_Shift_Del	DEL	CCGAG	CCGAG	-	rs267599526	byFrequency	TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	CCGAG	CCGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr3:108081191_108081195delCCGAG	ENST00000357759.5	+	7	1420_1424	c.1006_1010delCCGAG	c.(1006-1011)ccgagcfs	p.PS336fs	HHLA2_ENST00000489514.2_Frame_Shift_Del_p.PS336fs|HHLA2_ENST00000467562.1_Frame_Shift_Del_p.PS272fs|HHLA2_ENST00000491820.1_Frame_Shift_Del_p.PS336fs|HHLA2_ENST00000467761.1_Frame_Shift_Del_p.PS336fs	NM_007072.2	NP_009003.1	Q9UM44	HHLA2_HUMAN	HERV-H LTR-associating 2	336					positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(14)|ovary(1)	18						TTTTTTAGAACCGAGCCAAGAAACA	0.4																																																	0										13,3495		1,11,1742						0.2	0.1			65	8,7802		4,0,3901	no	frameshift	HHLA2	NM_007072.2		5,11,5643	A1A1,A1R,RR		0.1024,0.3706,0.1855				21,11297				SO:0001589	frameshift_variant	11148			AF126162	CCDS46883.1, CCDS63713.1, CCDS74975.1	3q13.13	2013-01-11			ENSG00000114455	ENSG00000114455		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	4905	protein-coding gene	gene with protein product		604371				10444326	Standard	NM_007072		Approved	B7H7	uc003dwz.3	Q9UM44	OTTHUMG00000159224	ENST00000357759.5:c.1006_1010delCCGAG	3.37:g.108081191_108081195delCCGAG	ENSP00000350402:p.Pro336fs		B4DKN2|D3DN60|Q9NWQ6	Frame_Shift_Del	DEL	ENST00000357759.5	37	CCDS46883.1																																																																																				0.400	HHLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353924.1		NM_007072	
HIST1H2BM	8342	hgsc.bcm.edu;ucsc.edu	37	6	27782814	27782832	+	Start_Codon_Del	DEL	TTTCCACCATGCCTGAACC	TTTCCACCATGCCTGAACC	-	rs143108953|rs149507584|rs200137511|rs374803189	byFrequency	TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	TTTCCACCATGCCTGAACC	TTTCCACCATGCCTGAACC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr6:27782814_27782832delTTTCCACCATGCCTGAACC	ENST00000359465.4	+	0	0_11				HIST1H2AJ_ENST00000333151.3_5'Flank	NM_003521.2	NP_003512.1	Q99879	H2B1M_HUMAN	histone cluster 1, H2bm						chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E3Q(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)	12						TTTATTTTGTTTTCCACCATGCCTGAACCAGTCAAATCT	0.429														12	0.00239617	0.0083	0.0014	5008	,	,		23920	0.0		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)																																								SO:0001582	initiator_codon_variant	8342			Z83738	CCDS4629.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000196374	ENSG00000273703		"""Histones / Replication-dependent"""	4750	protein-coding gene	gene with protein product		602802	"""H2B histone family, member E"", ""histone 1, H2bm"""	H2BFE		9439656, 12408966	Standard	NM_003521		Approved	H2B/e, dJ160A22.3	uc003njo.3	Q99879	OTTHUMG00000014489		6.37:g.27782814_27782832delTTTCCACCATGCCTGAACC			Q6NWQ3	Frame_Shift_Del	DEL	ENST00000359465.4	37	CCDS4629.1																																																																																				0.429	HIST1H2BM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040157.1		NM_003521	
ICMT	23463	hgsc.bcm.edu;ucsc.edu	37	1	6295024	6295024	+	Missense_Mutation	SNP	C	C	T			TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr1:6295024C>T	ENST00000343813.5	-	2	234	c.206G>A	c.(205-207)cGa>cAa	p.R69Q	LINC00337_ENST00000441724.1_RNA|LINC00337_ENST00000429480.2_RNA|ICMT_ENST00000362035.3_Missense_Mutation_p.R69Q	NM_012405.3	NP_036537.1	O60725	ICMT_HUMAN	isoprenylcysteine carboxyl methyltransferase	69					C-terminal protein methylation (GO:0006481)|cellular protein modification process (GO:0006464)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|multicellular organism growth (GO:0035264)|positive regulation of cell proliferation (GO:0008284)|protein targeting to membrane (GO:0006612)|regulation of Ras protein signal transduction (GO:0046578)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cAMP response element binding protein binding (GO:0008140)|protein C-terminal carboxyl O-methyltransferase activity (GO:0003880)|protein C-terminal S-isoprenylcysteine carboxyl O-methyltransferase activity (GO:0004671)			NS(1)|endometrium(2)	3	Ovarian(185;0.0634)	all_cancers(23;5.85e-39)|all_epithelial(116;2.4e-22)|all_lung(118;2.65e-08)|Lung NSC(185;6.45e-07)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000688)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;5.52e-38)|GBM - Glioblastoma multiforme(13;6.51e-32)|OV - Ovarian serous cystadenocarcinoma(86;3.03e-19)|Colorectal(212;7.08e-08)|COAD - Colon adenocarcinoma(227;8.35e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(365;0.00109)|STAD - Stomach adenocarcinoma(132;0.00313)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		GAAACAAGCTCGGATGGCTAT	0.512																																																	0													82.0	83.0	83.0					1																	6295024		2203	4300	6503	SO:0001583	missense	23463			AF064084	CCDS61.1	1p36	2010-04-29			ENSG00000116237	ENSG00000116237	2.1.1.100		5350	protein-coding gene	gene with protein product	"""protein-S-isoprenylcysteine O-methyltransferase"""	605851				9614111, 10441503	Standard	XM_005263437		Approved	PCCMT, HSTE14, PPMT	uc001amk.3	O60725	OTTHUMG00000001254	ENST00000343813.5:c.206G>A	1.37:g.6295024C>T	ENSP00000343552:p.Arg69Gln		Q6FHT0	Missense_Mutation	SNP	ENST00000343813.5	37	CCDS61.1	.	.	.	.	.	.	.	.	.	.	C	36	5.698244	0.96802	.	.	ENSG00000116237	ENST00000343813;ENST00000362035	.	.	.	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.62998	0.2474	M	0.76170	2.325	0.80722	D	1	D	0.65815	0.995	P	0.46320	0.512	T	0.66830	-0.5824	9	0.39692	T	0.17	.	15.8873	0.79261	0.0:1.0:0.0:0.0	.	69	O60725	ICMT_HUMAN	Q	69	.	ENSP00000343552:R69Q	R	-	2	0	ICMT	6217611	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	7.110000	0.77069	2.338000	0.79540	0.563000	0.77884	CGA		0.512	ICMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003681.1		NM_012405	
IFNK	56832	hgsc.bcm.edu	37	9	27524364	27524365	+	Frame_Shift_Ins	INS	-	-	TGTT	rs375249919|rs376708678|rs144060127	byFrequency	TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr9:27524364_27524365insTGTT	ENST00000276943.2	+	1	53_54	c.30_31insTGTT	c.(31-33)tgtfs	p.-12fs	MOB3B_ENST00000262244.5_Intron	NM_020124.2	NP_064509.2	Q9P0W0	IFNK_HUMAN	interferon, kappa						adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation (GO:0030101)|natural killer cell activation involved in immune response (GO:0002323)|negative regulation of cell proliferation (GO:0008285)|positive regulation of innate immune response (GO:0045089)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of transcription, DNA-templated (GO:0006355)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|T cell activation involved in immune response (GO:0002286)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			large_intestine(1)	1		all_neural(11;7.9e-11)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.000158)		TGATTCAAAAGTGTTTGTGGCT	0.396														165	0.0329473	0.0567	0.0187	5008	,	,		18599	0.003		0.0298	False		,,,				2504	0.045																0									,	180,4084		2,176,1954					,	0.1	0.0		dbSNP_134	73	255,7999		4,247,3876	no	intron,frameshift	IFNK,MOB3B	NM_024761.4,NM_020124.2	,	6,423,5830	A1A1,A1R,RR		3.0894,4.2214,3.475	,	,		435,12083				SO:0001589	frameshift_variant	56832			AF384048	CCDS6521.1	9p21.2	2008-02-05			ENSG00000147896	ENSG00000147896		"""Interferons"""	21714	protein-coding gene	gene with protein product		615326				12391192, 11514542	Standard	NM_020124		Approved		uc003zqp.3	Q9P0W0	OTTHUMG00000019715	ENST00000276943.2:c.31_34dupTGTT	9.37:g.27524365_27524368dupTGTT	ENSP00000276943:p.Leu12fs		Q5T166	Frame_Shift_Ins	INS	ENST00000276943.2	37	CCDS6521.1																																																																																				0.396	IFNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051968.1		NM_020124	
KRTAP4-1	85285	hgsc.bcm.edu;ucsc.edu	37	17	39341039	39341039	+	Missense_Mutation	SNP	G	G	A			TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr17:39341039G>A	ENST00000398472.1	-	1	555	c.68C>T	c.(67-69)aCc>aTc	p.T23I				Q9BYQ7	KRA41_HUMAN	keratin associated protein 4-1	23	18 X 5 AA repeats of C-C-[GRQC]-[SPT]- [VSTL].					keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	5		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			GCGGCAGCAGGTCTCTTGGCA	0.592																																																	0													27.0	31.0	30.0					17																	39341039		2194	4297	6491	SO:0001583	missense	85285			AC006070		17q21.2	2013-06-25			ENSG00000198443	ENSG00000198443		"""Keratin associated proteins"""	18907	protein-coding gene	gene with protein product			"""keratin associated protein 4-10"""	KRTAP4-10		11279113	Standard	NM_033060		Approved	KAP4.1, KAP4.10	uc002hwe.4	Q9BYQ7	OTTHUMG00000132081	ENST00000398472.1:c.68C>T	17.37:g.39341039G>A	ENSP00000381489:p.Thr23Ile		A8MWS7|Q3SYF2	Missense_Mutation	SNP	ENST00000398472.1	37		.	.	.	.	.	.	.	.	.	.	G	10.50	1.367282	0.24771	.	.	ENSG00000198443	ENST00000398472;ENST00000334190	T	0.01422	4.91	3.67	0.133	0.14766	.	.	.	.	.	T	0.01558	0.0050	.	.	.	0.09310	N	0.99999	P	0.40731	0.728	B	0.40444	0.329	T	0.49476	-0.8936	8	0.59425	D	0.04	.	5.9257	0.19110	0.0:0.4376:0.2954:0.267	.	23	Q9BYQ7	KRA41_HUMAN	I	23	ENSP00000381489:T23I	ENSP00000335483:T23I	T	-	2	0	KRTAP4-1	36594565	0.973000	0.33851	0.198000	0.23420	0.091000	0.18340	2.690000	0.47001	0.208000	0.20626	0.655000	0.94253	ACC		0.592	KRTAP4-1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255108.1		NM_033060	
LAD1	3898	hgsc.bcm.edu	37	1	201356002	201356004	+	In_Frame_Del	DEL	CCA	CCA	-	rs78190062|rs552300739|rs35119736|rs398053706|rs386638482	byFrequency	TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	CCA	CCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr1:201356002_201356004delCCA	ENST00000391967.2	-	3	786_788	c.485_487delTGG	c.(484-489)gtgggc>ggc	p.V162del	LAD1_ENST00000367313.3_In_Frame_Del_p.V176del	NM_005558.3	NP_005549.2	O00515	LAD1_HUMAN	ladinin 1	162						basement membrane (GO:0005604)	structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(6)|prostate(2)|skin(2)	19						GGCTCCCTGCCCACCAAGCTCTC	0.586														301	0.0601038	0.0666	0.0504	5008	,	,		15375	0.0575		0.0686	False		,,,				2504	0.0521																0										826,3440		92,642,1399						-0.4	0.0		dbSNP_131	54	717,7533		40,637,3448	no	coding	LAD1	NM_005558.3		132,1279,4847	A1A1,A1R,RR		8.6909,19.3624,12.3282				1543,10973				SO:0001651	inframe_deletion	3898			U42408	CCDS1410.1	1q25.1-q32.3	2008-02-05			ENSG00000159166	ENSG00000159166			6472	protein-coding gene	gene with protein product		602314				8618013, 9119369	Standard	NM_005558		Approved		uc001gwm.3	O00515	OTTHUMG00000035737	ENST00000391967.2:c.485_487delTGG	1.37:g.201356005_201356007delCCA	ENSP00000375829:p.Val162del		O95614|Q96GD8	In_Frame_Del	DEL	ENST00000391967.2	37	CCDS1410.1																																																																																				0.586	LAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086946.1		NM_005558	
LNP1	348801	hgsc.bcm.edu	37	3	100170598	100170598	+	Silent	SNP	C	C	T	rs78633312|rs386663873	byFrequency	TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr3:100170598C>T	ENST00000383693.3	+	3	1472	c.192C>T	c.(190-192)tgC>tgT	p.C64C	LNP1_ENST00000489752.1_Silent_p.C77C	NM_001085451.1	NP_001078920.1	A1A4G5	LNP1_HUMAN	leukemia NUP98 fusion partner 1	64										cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	6						CATCTGACTGCCATCCTAGAA	0.443																																																	0													78.0	71.0	73.0					3																	100170598		1873	4103	5976	SO:0001819	synonymous_variant	348801				CCDS43120.1	3q12.2	2014-05-12			ENSG00000206535	ENSG00000206535			28014	protein-coding gene	gene with protein product						16467868	Standard	NM_001085451		Approved	NP3	uc003dtx.4	A1A4G5	OTTHUMG00000159082	ENST00000383693.3:c.192C>T	3.37:g.100170598C>T			B7ZLT3	Silent	SNP	ENST00000383693.3	37	CCDS43120.1																																																																																				0.443	LNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353232.1			
MUC4	4585	hgsc.bcm.edu	37	3	195506271	195506318	+	In_Frame_Del	DEL	ACCTGTGGATAATGAGGAAGCATTGGTGACAGGAAGAGGGGTGGTGTC	ACCTGTGGATAATGAGGAAGCATTGGTGACAGGAAGAGGGGTGGTGTC	-	rs199896027|rs201839412|rs192584273|rs62282465|rs199596856|rs62282466|rs77023345|rs551098007|rs563580319|rs201564403|rs201191776|rs200161977|rs377584277|rs202208985|rs200602926|rs201679145	byFrequency	TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	ACCTGTGGATAATGAGGAAGCATTGGTGACAGGAAGAGGGGTGGTGTC	ACCTGTGGATAATGAGGAAGCATTGGTGACAGGAAGAGGGGTGGTGTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr3:195506271_195506318delACCTGTGGATAATGAGGAAGCATTGGTGACAGGAAGAGGGGTGGTGTC	ENST00000463781.3	-	2	12592_12639	c.12133_12180delGACACCACCCCTCTTCCTGTCACCAATGCTTCCTCATTATCCACAGGT	c.(12133-12180)gacaccacccctcttcctgtcaccaatgcttcctcattatccacaggtdel	p.DTTPLPVTNASSLSTG4045del	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_In_Frame_Del_p.DTTPLPVTNASSLSTG4045del	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.P4050T(3)|p.T4046A(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGGTGGCGTGACCTGTGGATAATGAGGAAGCATTGGTGACAGGAAGAGGGGTGGTGTCACCTGTGGAT	0.589																																																	5	Substitution - Missense(5)	kidney(3)|haematopoietic_and_lymphoid_tissue(2)							,,	213,2197		69,75,1061					,,		0.0			23	808,3672		295,218,1727	no	intron,coding,intron	MUC4	NM_138297.4,NM_018406.6,NM_004532.5	,,	364,293,2788	A1A1,A1R,RR		18.0357,8.8382,14.8186	,,	,,		1021,5869				SO:0001651	inframe_deletion	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12133_12180delGACACCACCCCTCTTCCTGTCACCAATGCTTCCTCATTATCCACAGGT	3.37:g.195506271_195506318delACCTGTGGATAATGAGGAAGCATTGGTGACAGGAAGAGGGGTGGTGTC	ENSP00000417498:p.Asp4045_Gly4060del		O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																				0.589	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
NTRK1	4914	hgsc.bcm.edu;ucsc.edu	37	1	156845424	156845424	+	Missense_Mutation	SNP	C	C	A			TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr1:156845424C>A	ENST00000524377.1	+	12	1508	c.1467C>A	c.(1465-1467)caC>caA	p.H489Q	NTRK1_ENST00000392302.2_Missense_Mutation_p.H453Q|NTRK1_ENST00000368196.3_Missense_Mutation_p.H483Q|NTRK1_ENST00000358660.3_Missense_Mutation_p.H483Q	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	489	Interaction with SQSTM1. {ECO:0000250}.				activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|axon guidance (GO:0007411)|axonogenesis involved in innervation (GO:0060385)|B cell differentiation (GO:0030183)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to nicotine (GO:0071316)|circadian rhythm (GO:0007623)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|developmental programmed cell death (GO:0010623)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory nerve development (GO:0021553)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to hydrostatic pressure (GO:0051599)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|Sertoli cell development (GO:0060009)|small GTPase mediated signal transduction (GO:0007264)|sympathetic nervous system development (GO:0048485)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	74	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Amitriptyline(DB00321)|Imatinib(DB00619)|Regorafenib(DB08896)	TCCAAGGCCACATCATCGAGA	0.582			T	"""TPM3, TPR, TFG"""	papillary thyroid					TSP Lung(10;0.080)																														Dom	yes		1	1q21-q22	4914	"""neurotrophic tyrosine kinase, receptor, type 1"""		E	0													99.0	81.0	87.0					1																	156845424		2203	4300	6503	SO:0001583	missense	4914			Y09028	CCDS1161.1, CCDS30890.1, CCDS30891.1	1q21-q22	2014-09-17			ENSG00000198400	ENSG00000198400	2.7.10.1	"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8031	protein-coding gene	gene with protein product	"""high affinity nerve growth factor receptor"""	191315				2869410	Standard	NM_001007792		Approved	TRK, TRKA, MTC	uc001fqh.1	P04629	OTTHUMG00000041304	ENST00000524377.1:c.1467C>A	1.37:g.156845424C>A	ENSP00000431418:p.His489Gln		B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Missense_Mutation	SNP	ENST00000524377.1	37	CCDS1161.1	.	.	.	.	.	.	.	.	.	.	C	10.68	1.417524	0.25552	.	.	ENSG00000198400	ENST00000392302;ENST00000368196;ENST00000524377;ENST00000358660	T;T;T;T	0.75260	-0.91;-0.9;-0.92;-0.91	4.64	3.73	0.42828	.	0.116103	0.38720	N	0.001583	T	0.41442	0.1159	L	0.29908	0.895	0.31269	N	0.69194	B;B;B;B	0.10296	0.001;0.0;0.001;0.003	B;B;B;B	0.08055	0.001;0.002;0.001;0.003	T	0.16867	-1.0388	10	0.21014	T	0.42	.	11.3417	0.49537	0.0:0.9102:0.0:0.0898	.	483;483;489;453	A8K3Z4;P04629-2;P04629;A6NF12	.;.;NTRK1_HUMAN;.	Q	453;483;489;483	ENSP00000376120:H453Q;ENSP00000357179:H483Q;ENSP00000431418:H489Q;ENSP00000351486:H483Q	ENSP00000351486:H483Q	H	+	3	2	NTRK1	155112048	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	3.861000	0.56002	1.167000	0.42706	0.462000	0.41574	CAC		0.582	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392279.1		NM_002529	
OR2L3	391192	hgsc.bcm.edu	37	1	248224587	248224587	+	Missense_Mutation	SNP	A	A	G	rs61525219	byFrequency	TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr1:248224587A>G	ENST00000359959.3	+	1	604	c.604A>G	c.(604-606)Acc>Gcc	p.T202A	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, member 3	202						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(7)|lung(28)|prostate(1)|skin(1)|urinary_tract(1)	41	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			GTTTTTGAGCACCACCATCTT	0.493													a|||	288	0.057508	0.1218	0.0216	5008	,	,		24287	0.0704		0.0298	False		,,,				2504	0.0112																0													194.0	212.0	206.0					1																	248224587		2187	4300	6487	SO:0001583	missense	391192			AB065950	CCDS31104.1	1q44	2012-08-09			ENSG00000198128	ENSG00000198128		"""GPCR / Class A : Olfactory receptors"""	15009	protein-coding gene	gene with protein product							Standard	NM_001004687		Approved		uc001idx.1	Q8NG85	OTTHUMG00000040195	ENST00000359959.3:c.604A>G	1.37:g.248224587A>G	ENSP00000353044:p.Thr202Ala		B9EH44	Missense_Mutation	SNP	ENST00000359959.3	37	CCDS31104.1	.	.	.	.	.	.	.	.	.	.	A	0.713	-0.786430	0.02907	.	.	ENSG00000198128	ENST00000359959	T	0.36157	1.27	2.05	-0.724	0.11177	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34002	U	0.004342	T	0.19967	0.0480	N	0.11756	0.17	0.09310	N	1	B	0.18013	0.025	B	0.30646	0.118	T	0.21109	-1.0255	10	0.56958	D	0.05	.	7.7621	0.28959	0.3671:0.0:0.6329:0.0	rs61525219	202	Q8NG85	OR2L3_HUMAN	A	202	ENSP00000353044:T202A	ENSP00000353044:T202A	T	+	1	0	OR2L3	246291210	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.037000	0.01420	-0.358000	0.08162	-1.678000	0.00738	ACC		0.493	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1		NM_001004687	
OR4C15	81309	hgsc.bcm.edu	37	11	55322611	55322635	+	Frame_Shift_Del	DEL	TCTCTGAGAACACACAGTTCTGAAG	TCTCTGAGAACACACAGTTCTGAAG	-	rs374784954|rs564856673|rs144837445|rs72140406|rs149441744|rs368978918	byFrequency	TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	TCTCTGAGAACACACAGTTCTGAAG	TCTCTGAGAACACACAGTTCTGAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr11:55322611_55322635delTCTCTGAGAACACACAGTTCTGAAG	ENST00000314644.2	+	1	829_853	c.829_853delTCTCTGAGAACACACAGTTCTGAAG	c.(829-855)tctctgagaacacacagttctgaagggfs	p.SLRTHSSEG277fs		NM_001001920.1	NP_001001920.1	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C, member 15	223						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L278P(1)|p.S283Y(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(31)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(5)	56						CATCTTGCTCTCTCTGAGAACACACAGTTCTGAAGGGCGCTGGAA	0.444										HNSCC(20;0.049)				87	0.0173722	0.0628	0.0058	5008	,	,		22046	0.0		0.0	False		,,,				2504	0.0																2	Substitution - Missense(2)	large_intestine(1)|prostate(1)																																								SO:0001589	frameshift_variant	81309			BK004319	CCDS31501.1	11q11	2012-08-09			ENSG00000181939	ENSG00000181939		"""GPCR / Class A : Olfactory receptors"""	15171	protein-coding gene	gene with protein product							Standard	NM_001001920		Approved		uc010rig.2	Q8NGM1	OTTHUMG00000166714	ENST00000314644.2:c.829_853delTCTCTGAGAACACACAGTTCTGAAG	11.37:g.55322611_55322635delTCTCTGAGAACACACAGTTCTGAAG	ENSP00000324958:p.Ser277fs		Q6IFE2	Frame_Shift_Del	DEL	ENST00000314644.2	37	CCDS31501.1																																																																																				0.444	OR4C15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391164.1		NM_001001920	
OR51B5	282763	hgsc.bcm.edu;ucsc.edu	37	11	5364542	5364558	+	Frame_Shift_Del	DEL	CAGCCCCAGGTCTGTGG	CAGCCCCAGGTCTGTGG	-	rs546965603|rs372207902|rs147062602	byFrequency	TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	CAGCCCCAGGTCTGTGG	CAGCCCCAGGTCTGTGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr11:5364542_5364558delCAGCCCCAGGTCTGTGG	ENST00000300773.2	-	1	251_267	c.197_213delCCACAGACCTGGGGCTG	c.(196-213)gccacagacctggggctgfs	p.ATDLGL66fs	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	66					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A66fs*48(1)		NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGGTCAGGGCCAGCCCCAGGTCTGTGGCAGCCAGCAT	0.525														252	0.0503195	0.1377	0.0274	5008	,	,		22155	0.0		0.0457	False		,,,				2504	0.0051																1	Deletion - Frameshift(1)	upper_aerodigestive_tract(1)								487,3771		28,431,1670						3.6	0.1		dbSNP_134	48	401,7853		15,371,3741	no	frameshift	OR51B5	NM_001005567.2		43,802,5411	A1A1,A1R,RR		4.8583,11.4373,7.0972				888,11624				SO:0001589	frameshift_variant	282763			BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"""GPCR / Class A : Olfactory receptors"""	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.197_213delCCACAGACCTGGGGCTG	11.37:g.5364542_5364558delCAGCCCCAGGTCTGTGG	ENSP00000300773:p.Ala66fs		B2RN59	Frame_Shift_Del	DEL	ENST00000300773.2	37	CCDS31378.1																																																																																				0.525	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1		NM_001005567	
PER3	8863	hgsc.bcm.edu	37	1	7890053	7890053	+	Missense_Mutation	SNP	G	G	A	rs1776342	byFrequency	TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr1:7890053G>A	ENST00000361923.2	+	18	3194	c.3019G>A	c.(3019-3021)Gct>Act	p.A1007T	RP3-467L1.4_ENST00000451646.1_RNA|PER3_ENST00000377532.3_Missense_Mutation_p.A1016T	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	1007	5 X 18 AA tandem repeats of S-[HP]-[AP]- T-[AT]-[GST]-[ATV]-L-S-[MT]-G-[LS]-P-P- [MRS]-[EKR]-[NST]-P.|Ser-rich.		A -> T (in dbSNP:rs1776342).|Missing (associated with eveningness and better cognitive performance during sleep deprivation exepriments; dbSNP:rs57875989).		circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)	p.A1007T(1)		breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		TACTGCCAGCGCTCTGTCCAC	0.587																																																	1	Substitution - Missense(1)	kidney(1)											87.0	69.0	75.0					1																	7890053		1995	3902	5897	SO:0001583	missense	8863			BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.3019G>A	1.37:g.7890053G>A	ENSP00000355031:p.Ala1007Thr		Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	.	.	.	.	.	.	.	.	.	.	g	0.668	-0.803078	0.02841	.	.	ENSG00000049246	ENST00000377532;ENST00000361923	T;T	0.14391	2.51;2.51	0.119	0.119	0.14685	Period circadian-like, C-terminal (1);	9.368370	0.00166	N	0.000019	T	0.09158	0.0226	N	0.20685	0.6	0.09310	N	1	B;B;B;B;B	0.25048	0.025;0.007;0.066;0.117;0.007	B;B;B;B;B	0.23018	0.002;0.004;0.004;0.043;0.004	T	0.25676	-1.0125	9	0.18710	T	0.47	.	.	.	.	rs1776342	56;1007;1016;1016;1007	B4DR65;A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;.;PER3_HUMAN	T	1016;1007	ENSP00000366755:A1016T;ENSP00000355031:A1007T	ENSP00000355031:A1007T	A	+	1	0	PER3	7812640	0.000000	0.05858	0.068000	0.19968	0.074000	0.17049	-0.849000	0.04322	0.275000	0.22094	0.280000	0.19369	GCT		0.587	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1		NM_016831	
RPGR	6103	hgsc.bcm.edu	37	X	38145700	38145700	+	Intron	SNP	T	T	C			TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chrX:38145700T>C	ENST00000339363.3	-	14	2688				RPGR_ENST00000318842.7_Intron|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000338898.3_Intron|RPGR_ENST00000378505.2_Missense_Mutation_p.E851G|RPGR_ENST00000342811.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						tccttcctcctcttccccctc	0.597													t|||	8	0.00211921	0.0038	0.0014	3775	,	,		4975	0.0		0.001	False		,,,				2504	0.001																0													34.0	21.0	26.0					X																	38145700		1743	3348	5091	SO:0001627	intron_variant	6103			U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+646A>G	X.37:g.38145700T>C			B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Missense_Mutation	SNP	ENST00000339363.3	37		.	.	.	.	.	.	.	.	.	.	t	7.071	0.568249	0.13560	.	.	ENSG00000156313	ENST00000378505	T	0.02446	4.29	1.54	1.54	0.23209	.	5.599050	0.00797	U	0.001382	T	0.01592	0.0051	N	0.04508	-0.205	0.80722	D	1	P	0.45531	0.86	B	0.31390	0.129	T	0.52366	-0.8585	10	0.27082	T	0.32	.	8.3427	0.32254	0.0:0.0:0.0:1.0	.	851	E9PE28	.	G	851	ENSP00000367766:E851G	ENSP00000367766:E851G	E	-	2	0	RPGR	38030644	0.000000	0.05858	0.045000	0.18777	0.000000	0.00434	0.029000	0.13666	0.671000	0.31185	0.000000	0.15137	GAG		0.597	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding			NM_000328	
RPGR	6103	hgsc.bcm.edu	37	X	38145704	38145704	+	Intron	SNP	C	C	T			TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chrX:38145704C>T	ENST00000339363.3	-	14	2688				RPGR_ENST00000318842.7_Intron|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000338898.3_Intron|RPGR_ENST00000378505.2_Missense_Mutation_p.E850K|RPGR_ENST00000342811.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						tcctcctcttccccctcccct	0.607																																																	0			GRCh37	CD077431	orf15	D							36.0	22.0	27.0					X																	38145704		1739	3343	5082	SO:0001627	intron_variant	6103			U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+642G>A	X.37:g.38145704C>T			B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Missense_Mutation	SNP	ENST00000339363.3	37		.	.	.	.	.	.	.	.	.	.	c	5.746	0.322013	0.10900	.	.	ENSG00000156313	ENST00000378505	T	0.02446	4.29	1.54	0.206	0.15208	.	2.503780	0.02039	U	0.049173	T	0.02193	0.0068	L	0.43152	1.355	0.09310	N	1	P	0.45531	0.86	B	0.28991	0.097	T	0.47886	-0.9082	10	0.06236	T	0.91	.	6.5691	0.22529	0.4445:0.5555:0.0:0.0	.	850	E9PE28	.	K	850	ENSP00000367766:E850K	ENSP00000367766:E850K	E	-	1	0	RPGR	38030648	0.000000	0.05858	0.073000	0.20177	0.000000	0.00434	0.538000	0.23160	0.816000	0.34421	-0.000000	0.15137	GAA		0.607	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding			NM_000328	
SAMD9L	219285	hgsc.bcm.edu	37	7	92761054	92761054	+	Missense_Mutation	SNP	G	G	C	rs4729075		TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr7:92761054G>C	ENST00000318238.4	-	5	5447	c.4231C>G	c.(4231-4233)Cga>Gga	p.R1411G	SAMD9L_ENST00000411955.1_Missense_Mutation_p.R1411G|SAMD9L_ENST00000437805.1_Missense_Mutation_p.R1411G	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	1411					common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)		p.R1411*(1)		central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			AAGACCTCTCGGAGTTGTTTT	0.398																																																	1	Substitution - Nonsense(1)	large_intestine(1)											151.0	152.0	151.0					7																	92761054		2203	4300	6503	SO:0001583	missense	219285			AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"""Sterile alpha motif (SAM) domain containing"""	1349	protein-coding gene	gene with protein product		611170	"""chromosome 7 open reading frame 6"""	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.4231C>G	7.37:g.92761054G>C	ENSP00000326247:p.Arg1411Gly		A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Missense_Mutation	SNP	ENST00000318238.4	37	CCDS34681.1	.	.	.	.	.	.	.	.	.	.	G	5.774	0.327260	0.10900	.	.	ENSG00000177409	ENST00000318238;ENST00000411955;ENST00000437805;ENST00000394472	T;T;T	0.23348	1.91;1.91;1.91	5.22	2.25	0.28309	.	0.369870	0.24063	N	0.041899	T	0.34308	0.0893	L	0.53249	1.67	0.25083	N	0.990916	D	0.55385	0.971	P	0.50590	0.645	T	0.23655	-1.0182	10	0.62326	D	0.03	-5.8818	14.3967	0.67015	0.0:0.0:0.3555:0.6445	.	1411	Q8IVG5	SAM9L_HUMAN	G	1411;1411;1411;233	ENSP00000326247:R1411G;ENSP00000405760:R1411G;ENSP00000408796:R1411G	ENSP00000326247:R1411G	R	-	1	2	SAMD9L	92598990	0.000000	0.05858	0.999000	0.59377	0.095000	0.18619	-0.027000	0.12371	0.271000	0.22005	0.467000	0.42956	CGA		0.398	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1		NM_152703	
SLC3A2	6520	hgsc.bcm.edu;ucsc.edu	37	11	62650410	62650410	+	Missense_Mutation	SNP	A	A	G			TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr11:62650410A>G	ENST00000377890.2	+	6	1100	c.932A>G	c.(931-933)aAc>aGc	p.N311S	SLC3A2_ENST00000535296.1_Missense_Mutation_p.N280S|SLC3A2_ENST00000377891.2_Missense_Mutation_p.N312S|SLC3A2_ENST00000377892.1_Missense_Mutation_p.N342S|SLC3A2_ENST00000377889.2_Missense_Mutation_p.N249S|SLC3A2_ENST00000536981.1_5'UTR|SLC3A2_ENST00000538682.1_3'UTR|SLC3A2_ENST00000338663.7_Missense_Mutation_p.N210S	NM_002394.5	NP_002385.3	P08195	4F2_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 2	311					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|carbohydrate metabolic process (GO:0005975)|cell growth (GO:0016049)|ion transport (GO:0006811)|leucine import (GO:0060356)|leukocyte migration (GO:0050900)|response to exogenous dsRNA (GO:0043330)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|tryptophan transport (GO:0015827)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|double-stranded RNA binding (GO:0003725)|neutral amino acid transmembrane transporter activity (GO:0015175)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)	22						CTTACTCCCAACTACCGGGGT	0.488																																																	0													156.0	126.0	136.0					11																	62650410		2201	4298	6499	SO:0001583	missense	6520				CCDS8039.2, CCDS31588.1, CCDS31589.1, CCDS31590.1	11q12-q22	2013-07-19	2013-07-19		ENSG00000168003	ENSG00000168003		"""Solute carriers"""	11026	protein-coding gene	gene with protein product	"""antigen identified by monoclonal antibodies 4F2, TRA1.10, TROP4, and T43"", ""antigen defined by monoclonal antibody 4F2"", ""heavy chain"", ""4F2 heavy chain"", ""CD98 heavy chain"", ""monoclonal antibody 44D7"", ""4F2 cell-surface antigen heavy chain"", ""lymphocyte activation antigen 4F2 large subunit"""	158070	"""solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2"""	MDU1		3036867	Standard	NM_001012662		Approved	4T2HC, 4F2, NACAE, CD98, CD98HC, 4F2HC	uc001nwd.3	P08195	OTTHUMG00000074091	ENST00000377890.2:c.932A>G	11.37:g.62650410A>G	ENSP00000367122:p.Asn311Ser		Q13543	Missense_Mutation	SNP	ENST00000377890.2	37	CCDS8039.2	.	.	.	.	.	.	.	.	.	.	A	17.06	3.293194	0.60086	.	.	ENSG00000168003	ENST00000377892;ENST00000377891;ENST00000377890;ENST00000542007;ENST00000377889;ENST00000535296;ENST00000338663;ENST00000422606	D;D;D;D;D;D	0.99846	-7.13;-7.13;-7.13;-7.13;-7.13;-7.13	5.05	5.05	0.67936	Glycoside hydrolase, subgroup, catalytic domain (1);Glycosyl hydrolase, family 13, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.99684	0.9881	M	0.65498	2.005	0.80722	D	1	D;D;D;D;D	0.89917	0.999;0.998;1.0;0.999;0.995	D;P;D;P;D	0.83275	0.943;0.895;0.996;0.898;0.909	D	0.97891	1.0297	10	0.35671	T	0.21	-17.3975	12.7763	0.57451	1.0:0.0:0.0:0.0	.	249;280;311;210;342	P08195-3;F5GZS6;P08195;P08195-2;P08195-4	.;.;4F2_HUMAN;.;.	S	342;312;311;312;249;280;210;192	ENSP00000367124:N342S;ENSP00000367123:N312S;ENSP00000367122:N311S;ENSP00000367121:N249S;ENSP00000444236:N280S;ENSP00000340815:N210S	ENSP00000340815:N210S	N	+	2	0	SLC3A2	62406986	1.000000	0.71417	0.997000	0.53966	0.042000	0.13812	7.348000	0.79366	1.915000	0.55452	0.459000	0.35465	AAC		0.488	SLC3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157306.1		NM_001012661	
STK35	140901	hgsc.bcm.edu;ucsc.edu	37	20	2097952	2097952	+	Silent	SNP	T	T	A			TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr20:2097952T>A	ENST00000381482.3	+	3	1804	c.1533T>A	c.(1531-1533)gcT>gcA	p.A511A	STK35_ENST00000246032.3_Silent_p.A378A|STK35_ENST00000400064.3_Intron			Q8TDR2	STK35_HUMAN	serine/threonine kinase 35	511	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(2)|liver(2)|lung(6)|ovary(1)|prostate(2)	13						ATATGTTAGCTGCTAACCCAC	0.483																																																	0													85.0	80.0	82.0					20																	2097952		2203	4300	6503	SO:0001819	synonymous_variant	140901			AL359916	CCDS13024.1, CCDS13024.2	20p13	2008-07-02			ENSG00000125834	ENSG00000125834			16254	protein-coding gene	gene with protein product	"""CLP-36 interacting kinase"""	609370				11973348	Standard	NM_080836		Approved	bA550O8.2, CLIK1	uc002wfw.4	Q8TDR2	OTTHUMG00000031688	ENST00000381482.3:c.1533T>A	20.37:g.2097952T>A			B2RBM3|C7ENV8|Q2NKW6|Q5T3R1|Q5T3R2|Q96AB4|Q9BZ06	Silent	SNP	ENST00000381482.3	37	CCDS13024.2																																																																																				0.483	STK35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077574.3		NM_080836	
SYNPO2	171024	hgsc.bcm.edu	37	4	119947962	119947964	+	In_Frame_Del	DEL	AAG	AAG	-	rs70944826	byFrequency	TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr4:119947962_119947964delAAG	ENST00000429713.2	+	3	620_622	c.438_440delAAG	c.(436-441)caaaga>caa	p.R147del	SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000307142.4_In_Frame_Del_p.R147del|SYNPO2_ENST00000434046.2_In_Frame_Del_p.R147del	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	147				Missing (in Ref. 3; AL832031). {ECO:0000305}.		actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						CTGAGAACCAAAGAAGTGGTCCC	0.552														1780	0.355431	0.2375	0.4654	5008	,	,		17830	0.496		0.3489	False		,,,				2504	0.2986																0									,,	1140,3126		155,830,1148					,,	2.9	0.4		dbSNP_130	44	3087,5167		549,1989,1589	no	coding,coding,coding	SYNPO2	NM_133477.2,NM_001128934.1,NM_001128933.1	,,	704,2819,2737	A1A1,A1R,RR		37.4,26.7229,33.762	,,	,,		4227,8293				SO:0001651	inframe_deletion	171024			AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.438_440delAAG	4.37:g.119947965_119947967delAAG	ENSP00000395143:p.Arg147del		B2RWP6|B2Y8J9|Q9UK89|S5XAM4	In_Frame_Del	DEL	ENST00000429713.2	37	CCDS47129.1																																																																																				0.552	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1			
TM6SF2	53345	hgsc.bcm.edu	37	19	19381023	19381023	+	Silent	SNP	G	G	A			TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr19:19381023G>A	ENST00000389363.4	-	4	432	c.360C>T	c.(358-360)caC>caT	p.H120H	TM6SF2_ENST00000586107.1_5'UTR|AC138430.4_ENST00000586064.2_RNA	NM_001001524.2	NP_001001524.2	Q9BZW4	TM6S2_HUMAN	transmembrane 6 superfamily member 2	120						integral component of membrane (GO:0016021)				breast(2)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	14			Epithelial(12;0.0151)			AGAGGAGGTAGTGAACAGTGC	0.632																																																	0													50.0	54.0	53.0					19																	19381023		2084	4220	6304	SO:0001819	synonymous_variant	53345			AF255923	CCDS42528.1	19p13.3-p12	2008-02-05							11861	protein-coding gene	gene with protein product		606563				11124529	Standard	NM_001001524		Approved	Lpr4	uc002nmd.1	Q9BZW4		ENST00000389363.4:c.360C>T	19.37:g.19381023G>A			Q0IJ64	Silent	SNP	ENST00000389363.4	37	CCDS42528.1	.	.	.	.	.	.	.	.	.	.	G	10.98	1.505660	0.26949	.	.	ENSG00000213996	ENST00000431465	.	.	.	4.74	2.57	0.30868	.	.	.	.	.	T	0.62865	0.2463	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.64232	-0.6456	5	0.87932	D	0	-25.3371	7.2682	0.26242	0.2849:0.0:0.7151:0.0	.	.	.	.	I	143	.	ENSP00000391180:T143I	T	-	2	0	TM6SF2	19242023	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	3.621000	0.54210	1.005000	0.39183	0.505000	0.49811	ACT		0.632	TM6SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460122.2		NM_203510	
TOP2A	7153	hgsc.bcm.edu;ucsc.edu	37	17	38557157	38557157	+	Missense_Mutation	SNP	C	C	T	rs192926120		TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr17:38557157C>T	ENST00000423485.1	-	21	2767	c.2609G>A	c.(2608-2610)cGt>cAt	p.R870H		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	870					apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	TACAATTTCACGCACATCAAA	0.428													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19230	0.0		0.0	False		,,,				2504	0.0																0								C	HIS/ARG	0,3854		0,0,1927	288.0	275.0	279.0		2609	5.2	1.0	17		279	1,8271		0,1,4135	no	missense	TOP2A	NM_001067.3	29	0,1,6062	TT,TC,CC		0.0121,0.0,0.0082	probably-damaging	870/1532	38557157	1,12125	1927	4136	6063	SO:0001583	missense	7153				CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"""topoisomerase (DNA) II alpha (170kD)"""	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.2609G>A	17.37:g.38557157C>T	ENSP00000411532:p.Arg870His		B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Missense_Mutation	SNP	ENST00000423485.1	37	CCDS45672.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	29.8	5.038065	0.93630	0.0	1.21E-4	ENSG00000131747	ENST00000423485;ENST00000269577;ENST00000348049;ENST00000357601	T	0.26373	1.74	5.21	5.21	0.72293	DNA topoisomerase, type IIA, subunit A/C-terminal (2);DNA topoisomerase, type IIA, subunit A/ C-terminal, alpha-beta (1);DNA topoisomerase, type IIA, central (1);	0.000000	0.85682	D	0.000000	T	0.52240	0.1722	M	0.86740	2.835	0.80722	D	1	P	0.51449	0.945	P	0.54889	0.763	T	0.59762	-0.7393	10	0.56958	D	0.05	.	19.1085	0.93307	0.0:1.0:0.0:0.0	.	870	P11388	TOP2A_HUMAN	H	870;950;893;906	ENSP00000411532:R870H	ENSP00000269577:R950H	R	-	2	0	TOP2A	35810683	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	7.750000	0.85110	2.586000	0.87340	0.467000	0.42956	CGT		0.428	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1			
TTN	7273	hgsc.bcm.edu;ucsc.edu	37	2	179422465	179422465	+	Missense_Mutation	SNP	C	C	T			TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr2:179422465C>T	ENST00000591111.1	-	278	82917	c.82693G>A	c.(82693-82695)Gaa>Aaa	p.E27565K	TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.E20266K|TTN_ENST00000460472.2_Missense_Mutation_p.E20141K|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.E20333K|TTN_ENST00000589042.1_Missense_Mutation_p.E29206K|TTN_ENST00000342992.6_Missense_Mutation_p.E26638K|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	27565	Fibronectin type-III 100. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGGTATTCTTCTCCTGTGGTC	0.418																																																	0													338.0	332.0	334.0					2																	179422465		1951	4144	6095	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.82693G>A	2.37:g.179422465C>T	ENSP00000465570:p.Glu27565Lys		A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	17.13	3.311042	0.60414	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56611	0.45;0.45;0.45;0.45	5.66	5.66	0.87406	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.38878	0.1057	N	0.04355	-0.22	0.51233	D	0.999919	P;P;P;P	0.35226	0.491;0.491;0.491;0.491	B;B;B;B	0.37780	0.258;0.258;0.258;0.258	T	0.49437	-0.8940	9	0.87932	D	0	.	20.1041	0.97884	0.0:1.0:0.0:0.0	.	20141;20266;20333;27565	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	K	26638;20141;20333;20266;20138	ENSP00000343764:E26638K;ENSP00000434586:E20141K;ENSP00000340554:E20333K;ENSP00000352154:E20266K	ENSP00000340554:E20333K	E	-	1	0	TTN	179130711	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.121000	0.57904	2.826000	0.97356	0.655000	0.94253	GAA		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1		NM_133378	
ZNF208	7757	hgsc.bcm.edu	37	19	22156286	22156286	+	Missense_Mutation	SNP	C	C	T			TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr19:22156286C>T	ENST00000397126.4	-	4	1698	c.1550G>A	c.(1549-1551)aGa>aAa	p.R517K	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	517					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				AGTATGAATTCTCTTATGTTC	0.388																																																	0													14.0	14.0	14.0					19																	22156286		692	1589	2281	SO:0001583	missense	7757			BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"""Zinc fingers, C2H2-type"", ""-"""	12999	protein-coding gene	gene with protein product	"""zinc finger protein 95"""	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.1550G>A	19.37:g.22156286C>T	ENSP00000380315:p.Arg517Lys			Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	C	8.397	0.841009	0.16891	.	.	ENSG00000160321	ENST00000397126	T	0.18338	2.22	2.98	-5.96	0.02234	.	.	.	.	.	T	0.10809	0.0264	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.34601	-0.9822	6	0.34782	T	0.22	.	5.0173	0.14343	0.5497:0.2714:0.0:0.179	.	.	.	.	K	517	ENSP00000380315:R517K	ENSP00000380315:R517K	R	-	2	0	ZNF208	21948126	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.497000	0.06428	-1.149000	0.02843	-3.138000	0.00060	AGA		0.388	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1		NM_007153	
ZNF676	163223	hgsc.bcm.edu	37	19	22363631	22363631	+	Silent	SNP	G	G	A	rs75683199	byFrequency	TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr19:22363631G>A	ENST00000397121.2	-	3	1205	c.888C>T	c.(886-888)ctC>ctT	p.L296L		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	296					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				TATGTTCCATGAGCTTTGAGG	0.438																																																	0													96.0	100.0	98.0					19																	22363631		2141	4270	6411	SO:0001819	synonymous_variant	163223			AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"""Zinc fingers, C2H2-type"""	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.888C>T	19.37:g.22363631G>A			A8MVX5	Silent	SNP	ENST00000397121.2	37	CCDS42539.1																																																																																				0.438	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1		NM_001001411	
ZNF676	163223	hgsc.bcm.edu	37	19	22363634	22363634	+	Missense_Mutation	SNP	C	C	A	rs76456473	byFrequency	TCGA-DV-5576-01A-01D-1534-10	TCGA-DV-5576-10A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	dc677d8e-ec39-4038-a86c-8290dacd377b	827b7591-b763-4d3f-beb3-c8c53b03bc21	g.chr19:22363634C>A	ENST00000397121.2	-	3	1202	c.885G>T	c.(883-885)aaG>aaT	p.K295N		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	295					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				GTTCCATGAGCTTTGAGGACG	0.433																																																	0													98.0	102.0	100.0					19																	22363634		2149	4273	6422	SO:0001583	missense	163223			AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"""Zinc fingers, C2H2-type"""	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.885G>T	19.37:g.22363634C>A	ENSP00000380310:p.Lys295Asn		A8MVX5	Missense_Mutation	SNP	ENST00000397121.2	37	CCDS42539.1	.	.	.	.	.	.	.	.	.	.	.	0.001	-3.874663	0.00003	.	.	ENSG00000196109	ENST00000397121	T	0.07908	3.15	0.85	-1.7	0.08159	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02156	0.0067	N	0.02775	-0.495	0.09310	N	1	P	0.40731	0.728	B	0.37833	0.259	T	0.20940	-1.0260	9	0.08381	T	0.77	.	0.8725	0.01217	0.1932:0.2181:0.3753:0.2135	.	295	Q8N7Q3	ZN676_HUMAN	N	295	ENSP00000380310:K295N	ENSP00000380310:K295N	K	-	3	2	ZNF676	22155474	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.885000	0.01620	-1.157000	0.02815	-1.151000	0.01829	AAG		0.433	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1		NM_001001411	
