#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
ABCA13	154664	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	48314043	48314043	+	Missense_Mutation	SNP	G	G	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr7:48314043G>A	ENST00000435803.1	+	17	4804	c.4780G>A	c.(4780-4782)Ggc>Agc	p.G1594S		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1594					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.G1539S(1)|p.G1594S(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						AAACAGTGTAGGCAATTCCAT	0.323																																																	2	Substitution - Missense(2)	kidney(2)											138.0	138.0	138.0					7																	48314043		1846	4086	5932	SO:0001583	missense	154664			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.4780G>A	7.37:g.48314043G>A	ENSP00000411096:p.Gly1594Ser		K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	10.46	1.356479	0.24598	.	.	ENSG00000179869	ENST00000435803	D	0.85258	-1.96	5.37	1.31	0.21738	.	0.147924	0.32015	N	0.006715	D	0.84924	0.5580	M	0.64997	1.995	0.09310	N	1	D	0.57257	0.979	P	0.55087	0.768	T	0.75010	-0.3468	9	.	.	.	.	4.4699	0.11706	0.2383:0.3404:0.4213:0.0	.	1594	Q86UQ4	ABCAD_HUMAN	S	1594	ENSP00000411096:G1594S	.	G	+	1	0	ABCA13	48284589	0.000000	0.05858	0.002000	0.10522	0.022000	0.10575	-0.032000	0.12266	0.285000	0.22329	0.563000	0.77884	GGC		0.323	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2		NM_152701	
ACOT9	23597	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	23754070	23754070	+	Silent	SNP	G	G	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chrX:23754070G>A	ENST00000336430.7	-	2	215	c.84C>T	c.(82-84)aaC>aaT	p.N28N	ACOT9_ENST00000379303.5_Silent_p.N28N|ACOT9_ENST00000492081.1_Intron|ACOT9_ENST00000379295.1_5'UTR	NM_001033583.2	NP_001028755.2	Q9Y305	ACOT9_HUMAN	acyl-CoA thioesterase 9	28					acyl-CoA metabolic process (GO:0006637)	mitochondrion (GO:0005739)	acetyl-CoA hydrolase activity (GO:0003986)|carboxylic ester hydrolase activity (GO:0052689)	p.N28N(1)		breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(4)|pancreas(1)|skin(1)	15						GTTTCTTGGGGTTCTGGGGTC	0.448																																																	1	Substitution - coding silent(1)	kidney(1)											285.0	238.0	254.0					X																	23754070		2203	4300	6503	SO:0001819	synonymous_variant	23597			AF132950	CCDS35216.1, CCDS43924.1	Xp22.11	2008-02-05			ENSG00000123130	ENSG00000123130		"""Acyl CoA thioesterases"""	17152	protein-coding gene	gene with protein product		300862				10383425, 10810093, 16103133, 16940157	Standard	XM_005274471		Approved	CGI-16, MT-ACT48, ACATE2	uc004dao.3	Q9Y305	OTTHUMG00000021257	ENST00000336430.7:c.84C>T	X.37:g.23754070G>A			B3KNC9|B7ZM94	Silent	SNP	ENST00000336430.7	37	CCDS35216.1																																																																																				0.448	ACOT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056065.1		NM_012332	
ADAM10	102	broad.mit.edu;ucsc.edu	37	15	58925453	58925453	+	Missense_Mutation	SNP	G	G	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr15:58925453G>T	ENST00000260408.3	-	9	1561	c.1118C>A	c.(1117-1119)cCt>cAt	p.P373H	ADAM10_ENST00000396140.2_Missense_Mutation_p.P72H|ADAM10_ENST00000561288.1_Intron|ADAM10_ENST00000402627.1_Intron	NM_001110.2	NP_001101.1	O14672	ADA10_HUMAN	ADAM metallopeptidase domain 10	373	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell death (GO:0008219)|cell-cell signaling (GO:0007267)|collagen catabolic process (GO:0030574)|constitutive protein ectodomain proteolysis (GO:0051089)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|negative regulation of cell adhesion (GO:0007162)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of T cell chemotaxis (GO:0010820)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|tetraspanin-enriched microdomain (GO:0097197)	endopeptidase activity (GO:0004175)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)	p.P373H(1)		breast(1)|endometrium(1)|kidney(5)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(3)	27				GBM - Glioblastoma multiforme(80;0.202)		GACTTTGGGAGGTACATGAGA	0.343																																																	1	Substitution - Missense(1)	kidney(1)											103.0	100.0	101.0					15																	58925453		2192	4292	6484	SO:0001583	missense	102			AF009615	CCDS10167.1	15q2	2006-09-25	2005-08-18		ENSG00000137845	ENSG00000137845		"""ADAM metallopeptidase domain containing"", ""CD molecules"""	188	protein-coding gene	gene with protein product		602192	"""a disintegrin and metalloproteinase domain 10"""			9344679, 9441766	Standard	XM_005254117		Approved	kuz, MADM, HsT18717, CD156c	uc002afd.1	O14672	OTTHUMG00000132633	ENST00000260408.3:c.1118C>A	15.37:g.58925453G>T	ENSP00000260408:p.Pro373His		B4DU28|Q10742|Q92650	Missense_Mutation	SNP	ENST00000260408.3	37	CCDS10167.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.774577	0.90108	.	.	ENSG00000137845	ENST00000260408;ENST00000396136;ENST00000396140	D;D	0.86694	-2.16;-2.16	5.82	5.82	0.92795	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.85682	D	0.000000	D	0.93294	0.7863	M	0.72353	2.195	0.80722	D	1	D;D	0.71674	0.998;0.992	D;D	0.73380	0.98;0.979	D	0.93106	0.6512	10	0.66056	D	0.02	-14.0967	20.099	0.97865	0.0:0.0:1.0:0.0	.	72;373	B4DU28;O14672	.;ADA10_HUMAN	H	373;192;72	ENSP00000260408:P373H;ENSP00000379444:P72H	ENSP00000260408:P373H	P	-	2	0	ADAM10	56712745	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.752000	0.94435	0.655000	0.94253	CCT		0.343	ADAM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255880.2		NM_001110	
ACSBG1	23205	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	78526760	78526760	+	Silent	SNP	G	G	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr15:78526760G>A	ENST00000258873.4	-	1	289	c.84C>T	c.(82-84)agC>agT	p.S28S	ACSBG1_ENST00000541759.1_5'UTR|ACSBG1_ENST00000558828.1_Intron|ACSBG1_ENST00000560817.1_Intron	NM_001199377.1|NM_015162.4	NP_001186306.1|NP_055977.3	Q96GR2	ACBG1_HUMAN	acyl-CoA synthetase bubblegum family member 1	28					long-chain fatty acid metabolic process (GO:0001676)|myelination (GO:0042552)|ovarian follicle atresia (GO:0001552)|response to glucocorticoid (GO:0051384)|very long-chain fatty acid metabolic process (GO:0000038)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)|very long-chain fatty acid-CoA ligase activity (GO:0031957)	p.S28S(1)		endometrium(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	37						TGTCCTGCCGGCTCTCCTGTG	0.572																																																	1	Substitution - coding silent(1)	kidney(1)											182.0	192.0	189.0					15																	78526760		2196	4293	6489	SO:0001819	synonymous_variant	23205			AB014531	CCDS10298.1	15q23-q24	2006-02-09			ENSG00000103740	ENSG00000103740		"""Acyl-CoA synthetase family"""	29567	protein-coding gene	gene with protein product	"""bubblegum"", ""very long-chain acyl-CoA synthetase"", ""lipidosin"""	614362				9734811, 10954726	Standard	NM_015162		Approved	BGM, FLJ30320, MGC14352, BG1, KIAA0631, hBG1, hsBG	uc002bdh.3	Q96GR2	OTTHUMG00000143734	ENST00000258873.4:c.84C>T	15.37:g.78526760G>A			B2RB61|O75126|Q76N27|Q9HC26	Silent	SNP	ENST00000258873.4	37	CCDS10298.1																																																																																				0.572	ACSBG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289802.2		NM_015162	
AFAP1	60312	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	7783208	7783208	+	Intron	SNP	C	C	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr4:7783208C>A	ENST00000360265.4	-	12	1765				AFAP1_ENST00000382543.3_Silent_p.L559L|AFAP1_ENST00000513842.1_5'UTR|AFAP1-AS1_ENST00000608442.1_RNA|AFAP1_ENST00000358461.2_Intron|AFAP1_ENST00000420658.1_Silent_p.L559L			Q8N556	AFAP1_HUMAN	actin filament associated protein 1							cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)		p.L559L(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(4)|stomach(2)	32						TGTCAGCAGACAGCCTAGAGG	0.537																																																	1	Substitution - coding silent(1)	kidney(1)											140.0	131.0	134.0					4																	7783208		692	1591	2283	SO:0001627	intron_variant	60312			AB209676	CCDS3397.1, CCDS47010.1	4p16	2014-02-12	2007-02-07		ENSG00000196526	ENSG00000196526		"""Pleckstrin homology (PH) domain containing"""	24017	protein-coding gene	gene with protein product		608252				14755689, 11641786, 11607843	Standard	NM_198595		Approved	AFAP-110, AFAP	uc011bwk.1	Q8N556	OTTHUMG00000125515	ENST00000360265.4:c.1531-2605G>T	4.37:g.7783208C>A			A8K442|B4DMU2|E9PDT7|Q59EY5|Q9HBY1	Silent	SNP	ENST00000360265.4	37	CCDS3397.1																																																																																				0.537	AFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246842.2		NM_021638	
AKNA	80709	broad.mit.edu;ucsc.edu	37	9	117139678	117139678	+	Missense_Mutation	SNP	C	C	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr9:117139678C>T	ENST00000307564.4	-	3	570	c.409G>A	c.(409-411)Gct>Act	p.A137T	AKNA_ENST00000223791.3_5'Flank|AKNA_ENST00000374088.3_Missense_Mutation_p.A137T|AKNA_ENST00000312033.3_Missense_Mutation_p.A137T|AKNA_ENST00000374075.5_Missense_Mutation_p.A56T	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	137					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.A137T(1)		breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						CTCTCTCCAGCCTCCTCAACC	0.617																																																	1	Substitution - Missense(1)	kidney(1)											41.0	38.0	39.0					9																	117139678		2203	4300	6503	SO:0001583	missense	80709			AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.409G>A	9.37:g.117139678C>T	ENSP00000303769:p.Ala137Thr		Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	37	CCDS6805.1	.	.	.	.	.	.	.	.	.	.	C	16.25	3.070016	0.55539	.	.	ENSG00000106948	ENST00000307564;ENST00000374088;ENST00000374075;ENST00000312033;ENST00000394574	T;T;T;T	0.48836	2.06;2.06;2.06;0.8	4.58	-1.11	0.09840	.	1.433560	0.04781	N	0.429837	T	0.48040	0.1478	L	0.32530	0.975	0.09310	N	1	B;B;D	0.67145	0.046;0.056;0.996	B;B;P	0.58928	0.023;0.02;0.848	T	0.41215	-0.9521	10	0.29301	T	0.29	0.038	4.7604	0.13104	0.0:0.4183:0.2968:0.2848	.	137;137;56	Q7Z591-6;Q7Z591;Q7Z591-2	.;AKNA_HUMAN;.	T	137;137;56;137;137	ENSP00000303769:A137T;ENSP00000363201:A137T;ENSP00000363188:A56T;ENSP00000309222:A137T	ENSP00000303769:A137T	A	-	1	0	AKNA	116179499	0.000000	0.05858	0.001000	0.08648	0.048000	0.14542	-1.359000	0.02602	-0.101000	0.12219	0.462000	0.41574	GCT		0.617	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2		NM_030767	
AMPH	273	broad.mit.edu;ucsc.edu	37	7	38431539	38431539	+	Missense_Mutation	SNP	G	G	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr7:38431539G>A	ENST00000356264.2	-	19	1903	c.1688C>T	c.(1687-1689)gCa>gTa	p.A563V	AMPH_ENST00000428293.2_Missense_Mutation_p.A521V|AMPH_ENST00000471913.1_5'Flank|AMPH_ENST00000325590.5_Missense_Mutation_p.A521V	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	563					endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)	p.A563V(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						CTTGGGCTCTGCACCTATAGT	0.592																																																	1	Substitution - Missense(1)	kidney(1)											70.0	67.0	68.0					7																	38431539		2203	4300	6503	SO:0001583	missense	273				CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"""amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)"", ""amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"""			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.1688C>T	7.37:g.38431539G>A	ENSP00000348602:p.Ala563Val		A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Missense_Mutation	SNP	ENST00000356264.2	37	CCDS5456.1	.	.	.	.	.	.	.	.	.	.	G	14.58	2.579178	0.46006	.	.	ENSG00000078053	ENST00000325590;ENST00000356264;ENST00000428293;ENST00000353242	T;T;T	0.61392	0.12;0.11;0.11	5.42	4.52	0.55395	.	0.641937	0.14536	N	0.313551	T	0.43100	0.1232	N	0.24115	0.695	0.18873	N	0.999988	B;B;B	0.27416	0.178;0.037;0.025	B;B;B	0.21708	0.036;0.016;0.02	T	0.25012	-1.0144	10	0.33940	T	0.23	-2.1666	13.3885	0.60809	0.0:0.1974:0.8026:0.0	.	521;563;451	P49418-2;P49418;Q8NFL4	.;AMPH_HUMAN;.	V	521;563;521;465	ENSP00000317441:A521V;ENSP00000348602:A563V;ENSP00000390734:A521V	ENSP00000317441:A521V	A	-	2	0	AMPH	38398064	0.005000	0.15991	0.142000	0.22268	0.127000	0.20565	1.298000	0.33412	2.545000	0.85829	0.591000	0.81541	GCA		0.592	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2		NM_001635	
ANKRD11	29123	hgsc.bcm.edu;ucsc.edu	37	16	89349043	89349043	+	Frame_Shift_Del	DEL	C	C	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr16:89349043delC	ENST00000301030.4	-	9	4367	c.3907delG	c.(3907-3909)gtcfs	p.V1303fs	ANKRD11_ENST00000378330.2_Frame_Shift_Del_p.V1303fs	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1303	Lys-rich.				bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		TCAGAGGAGACCTCGCTGATT	0.567																																																	0													47.0	48.0	48.0					16																	89349043		2198	4300	6498	SO:0001589	frameshift_variant	29123			AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"""Ankyrin repeat domain containing"""	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.3907delG	16.37:g.89349043delC	ENSP00000301030:p.Val1303fs		Q6NTG1|Q6QMF8	Frame_Shift_Del	DEL	ENST00000301030.4	37	CCDS32513.1																																																																																				0.567	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3		NM_013275	
ANKRD34B	340120	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	79855596	79855596	+	Missense_Mutation	SNP	G	G	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr5:79855596G>T	ENST00000338682.3	-	5	915	c.243C>A	c.(241-243)gaC>gaA	p.D81E		NM_001004441.2	NP_001004441.2	A5PLL1	AN34B_HUMAN	ankyrin repeat domain 34B	81						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.D81E(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	28		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-46)|Epithelial(54;5.64e-41)|all cancers(79;3.24e-36)		TCCCAGATTTGTCCTGTATGT	0.468																																																	1	Substitution - Missense(1)	kidney(1)											165.0	161.0	163.0					5																	79855596		2203	4300	6503	SO:0001583	missense	340120				CCDS34194.1	5q14.1	2014-08-12			ENSG00000189127	ENSG00000189127		"""Ankyrin repeat domain containing"""	33736	protein-coding gene	gene with protein product							Standard	NM_001004441		Approved	DP58	uc003kgw.3	A5PLL1	OTTHUMG00000162541	ENST00000338682.3:c.243C>A	5.37:g.79855596G>T	ENSP00000339802:p.Asp81Glu		B2RPH1|Q68D79	Missense_Mutation	SNP	ENST00000338682.3	37	CCDS34194.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.183813	0.78677	.	.	ENSG00000189127	ENST00000338682	T	0.44881	0.91	5.78	5.78	0.91487	Ankyrin repeat-containing domain (4);	0.000000	0.85682	U	0.000000	T	0.63343	0.2503	M	0.75777	2.31	0.52501	D	0.999958	D	0.89917	1.0	D	0.91635	0.999	T	0.66056	-0.6018	10	0.87932	D	0	-18.6062	11.9814	0.53121	0.0795:0.0:0.9205:0.0	.	81	A5PLL1	AN34B_HUMAN	E	81	ENSP00000339802:D81E	ENSP00000339802:D81E	D	-	3	2	ANKRD34B	79891352	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.812000	0.62613	2.726000	0.93360	0.561000	0.74099	GAC		0.468	ANKRD34B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369475.1		NM_001004441	
ANO1	55107	hgsc.bcm.edu;ucsc.edu	37	11	70017025	70017025	+	Missense_Mutation	SNP	G	G	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr11:70017025G>A	ENST00000355303.5	+	22	2535	c.2230G>A	c.(2230-2232)Gcc>Acc	p.A744T	ANO1_ENST00000531349.1_Missense_Mutation_p.A453T|ANO1_ENST00000525494.1_3'UTR|ANO1_ENST00000538023.1_Missense_Mutation_p.A744T|ANO1_ENST00000530676.1_Missense_Mutation_p.A598T|ANO1_ENST00000398543.2_Missense_Mutation_p.A598T	NM_018043.5	NP_060513.5	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	744					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of membrane potential (GO:0042391)|trachea development (GO:0060438)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(12)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)	29					Crofelemer(DB04941)	CCTGTTTGTCGCCTCCTTCCC	0.597																																																	0													66.0	74.0	71.0					11																	70017025		2122	4234	6356	SO:0001583	missense	55107			BC033036	CCDS44663.1	11q13.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000131620	ENSG00000131620		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	21625	protein-coding gene	gene with protein product		610108	"""oral cancer overexpressed 2"", ""transmembrane protein 16A"""	ORAOV2, TMEM16A		15067359, 18724360, 24692353	Standard	NM_018043		Approved	TAOS2, FLJ10261, DOG1	uc001opj.3	Q5XXA6	OTTHUMG00000167204	ENST00000355303.5:c.2230G>A	11.37:g.70017025G>A	ENSP00000347454:p.Ala744Thr		A8KAM3|Q8IYY8|Q8N7V3	Missense_Mutation	SNP	ENST00000355303.5	37	CCDS44663.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.704634	0.88924	.	.	ENSG00000131620	ENST00000355303;ENST00000538023;ENST00000398543;ENST00000546327;ENST00000530676;ENST00000531349;ENST00000539321	T;T;T;T;T	0.67698	-0.28;-0.28;-0.28;-0.28;-0.28	4.39	4.39	0.52855	.	0.113833	0.64402	D	0.000017	D	0.83959	0.5367	M	0.87456	2.885	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.987;0.999	D	0.86989	0.2109	9	.	.	.	.	17.3611	0.87350	0.0:0.0:1.0:0.0	.	453;744	E9PNA7;Q5XXA6	.;ANO1_HUMAN	T	744;744;598;502;598;453;71	ENSP00000347454:A744T;ENSP00000444689:A744T;ENSP00000381551:A598T;ENSP00000435797:A598T;ENSP00000432843:A453T	.	A	+	1	0	ANO1	69694673	1.000000	0.71417	0.714000	0.30535	0.749000	0.42624	9.553000	0.98118	2.185000	0.69588	0.462000	0.41574	GCC		0.597	ANO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393685.1		NM_018043	
ASCC3	10973	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	101110412	101110412	+	Splice_Site	SNP	C	C	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr6:101110412C>T	ENST00000369162.2	-	15	2631	c.2287G>A	c.(2287-2289)Gta>Ata	p.V763I		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	763	Helicase C-terminal 1. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)	p.V763I(1)		breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		GACCTTTGTACCTAGATACCA	0.323																																																	1	Substitution - Missense(1)	kidney(1)											64.0	63.0	63.0					6																	101110412		2203	4298	6501	SO:0001630	splice_region_variant	10973			AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"""RNA helicase family"""	614217	"""helicase, ATP binding 1"""	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.2287-1G>A	6.37:g.101110412C>T			E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	37	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	C	4.537	0.099757	0.08681	.	.	ENSG00000112249	ENST00000369162	T	0.42131	0.98	5.26	5.26	0.73747	Helicase, C-terminal (1);	0.323978	0.28307	N	0.015834	T	0.15132	0.0365	N	0.16130	0.375	0.80722	D	1	B	0.14012	0.009	B	0.16722	0.016	T	0.09079	-1.0691	10	0.13108	T	0.6	.	19.2367	0.93864	0.0:1.0:0.0:0.0	.	763	Q8N3C0	HELC1_HUMAN	I	763	ENSP00000358159:V763I	ENSP00000358159:V763I	V	-	1	0	ASCC3	101217133	1.000000	0.71417	0.861000	0.33841	0.087000	0.18053	2.337000	0.43947	2.616000	0.88540	0.650000	0.86243	GTA		0.323	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2		NM_006828	Missense_Mutation
BARD1	580	broad.mit.edu;hgsc.bcm.edu	37	2	215632207	215632207	+	Splice_Site	SNP	C	C	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr2:215632207C>T	ENST00000260947.4	-	6	1701	c.1567G>A	c.(1567-1569)Gtt>Att	p.V523I	BARD1_ENST00000449967.2_Splice_Site_p.V379I	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	523					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)	p.V523I(2)		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)		ACTACTTACACAGCATTTCTG	0.383									Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																																								2	Substitution - Missense(2)	kidney(2)											93.0	85.0	88.0					2																	215632207		2203	4300	6503	SO:0001630	splice_region_variant	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.1568+1G>A	2.37:g.215632207C>T			F6MDH7|F6MDH8|F6MDH9|O43574|Q53SS5	Missense_Mutation	SNP	ENST00000260947.4	37	CCDS2397.1	.	.	.	.	.	.	.	.	.	.	C	17.57	3.421994	0.62622	.	.	ENSG00000138376	ENST00000260947;ENST00000449967	T;T	0.65916	-0.18;-0.18	5.64	5.64	0.86602	Ankyrin repeat-containing domain (3);	0.064498	0.64402	D	0.000006	T	0.63510	0.2517	L	0.37750	1.13	0.48288	D	0.999627	B;P	0.41546	0.172;0.754	B;P	0.46362	0.082;0.514	T	0.62586	-0.6823	10	0.48119	T	0.1	-6.1283	20.0627	0.97684	0.0:1.0:0.0:0.0	.	379;523	E7EUI3;Q99728	.;BARD1_HUMAN	I	523;379	ENSP00000260947:V523I;ENSP00000406752:V379I	ENSP00000260947:V523I	V	-	1	0	BARD1	215340452	0.991000	0.36638	0.983000	0.44433	0.991000	0.79684	2.637000	0.46553	2.807000	0.96579	0.591000	0.81541	GTT		0.383	BARD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256602.1		NM_000465	Missense_Mutation
BCL9	607	broad.mit.edu;ucsc.edu	37	1	147091598	147091598	+	Missense_Mutation	SNP	C	C	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr1:147091598C>G	ENST00000234739.3	+	8	2377	c.1637C>G	c.(1636-1638)cCg>cGg	p.P546R		NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	546	Pro-rich.				canonical Wnt signaling pathway (GO:0060070)|myotube differentiation involved in skeletal muscle regeneration (GO:0014908)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)		p.P546R(1)		breast(1)|large_intestine(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	7	all_hematologic(923;0.115)					TCTCTGCCCCCGAGGGGCATG	0.592			T	"""IGH@, IGL@"""	B-ALL																																			Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	1	Substitution - Missense(1)	kidney(1)											54.0	60.0	58.0					1																	147091598		2203	4300	6503	SO:0001583	missense	607			Y13620	CCDS30833.1	1q21	2008-02-05			ENSG00000116128	ENSG00000116128			1008	protein-coding gene	gene with protein product		602597				9490669	Standard	NM_004326		Approved		uc001epq.3	O00512	OTTHUMG00000014031	ENST00000234739.3:c.1637C>G	1.37:g.147091598C>G	ENSP00000234739:p.Pro546Arg		Q5T489	Missense_Mutation	SNP	ENST00000234739.3	37	CCDS30833.1	.	.	.	.	.	.	.	.	.	.	C	15.80	2.941618	0.53079	.	.	ENSG00000116128	ENST00000234739	T	0.56444	0.46	5.51	4.61	0.57282	.	0.000000	0.85682	D	0.000000	T	0.53594	0.1806	L	0.51422	1.61	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.63597	0.916;0.916	T	0.53429	-0.8440	10	0.34782	T	0.22	-6.2061	14.5299	0.67917	0.0:0.9303:0.0:0.0697	.	546;546	Q1JQ81;O00512	.;BCL9_HUMAN	R	546	ENSP00000234739:P546R	ENSP00000234739:P546R	P	+	2	0	BCL9	145558222	0.976000	0.34144	0.909000	0.35828	0.988000	0.76386	2.470000	0.45119	1.577000	0.49804	0.561000	0.74099	CCG		0.592	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1		NM_004326	
KIAA1549L	25758	hgsc.bcm.edu;ucsc.edu	37	11	33565134	33565134	+	Silent	SNP	C	C	T	rs78046896	byFrequency	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr11:33565134C>T	ENST00000321505.4	+	1	1314	c.1134C>T	c.(1132-1134)tcC>tcT	p.S378S	KIAA1549L_ENST00000389726.3_Silent_p.S378S|KIAA1549L_ENST00000265654.5_Silent_p.S378S			Q6ZVL6	K154L_HUMAN	KIAA1549-like	378						integral component of membrane (GO:0016021)											CGCCCTCCTCCATGGATGTAT	0.478											OREG0020868	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	32	0.00638978	0.0234	0.0014	5008	,	,		20755	0.0		0.0	False		,,,				2504	0.0																0								C		72,3788		0,72,1858	41.0	40.0	41.0		1134	1.0	0.7	11	dbSNP_131	41	1,8263		0,1,4131	no	coding-synonymous	C11orf41	NM_012194.2		0,73,5989	TT,TC,CC		0.0121,1.8653,0.6021		378/1850	33565134	73,12051	1930	4132	6062	SO:0001819	synonymous_variant	0			U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"""chromosome 11 open reading frame 69"", ""chromosome 11 open reading frame 41"""	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.1134C>T	11.37:g.33565134C>T		841	B0QYU0	Silent	SNP	ENST00000321505.4	37	CCDS44565.2																																																																																				0.478	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1		NM_012194	
BIRC2	329	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	102221673	102221673	+	Splice_Site	SNP	A	A	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr11:102221673A>G	ENST00000227758.2	+	3	2393	c.994A>G	c.(994-996)Agg>Ggg	p.R332G	BIRC2_ENST00000532672.1_Splice_Site_p.R311G|BIRC2_ENST00000527910.1_3'UTR|BIRC2_ENST00000530675.1_Splice_Site_p.R283G	NM_001166.4|NM_001256163.1	NP_001157.1|NP_001243092.1	Q13490	BIRC2_HUMAN	baculoviral IAP repeat containing 2	332					apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein K48-linked ubiquitination (GO:1902524)|positive regulation of protein K63-linked ubiquitination (GO:1902523)|positive regulation of protein monoubiquitination (GO:1902527)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cell cycle (GO:0051726)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|regulation of transcription, DNA-templated (GO:0006355)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|protein N-terminus binding (GO:0047485)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R332G(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|Epithelial(9;0.11)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0144)		GTGGTTTCCAAGGTAATTGTT	0.378																																																	1	Substitution - Missense(1)	kidney(1)											261.0	248.0	252.0					11																	102221673		2203	4299	6502	SO:0001630	splice_region_variant	329			L49431	CCDS8316.1, CCDS58169.1	11q22	2011-01-25	2011-01-25		ENSG00000110330	ENSG00000110330		"""Baculoviral IAP repeat containing"", ""RING-type (C3HC4) zinc fingers"""	590	protein-coding gene	gene with protein product	"""NFR2-TRAF signalling complex protein"", ""apoptosis inhibitor 1"""	601712	"""baculoviral IAP repeat-containing 2"""	API1		8552191, 8548810	Standard	NM_001166		Approved	cIAP1, hiap-2, MIHB, RNF48, c-IAP1	uc010ruq.3	Q13490	OTTHUMG00000167325	ENST00000227758.2:c.995+1A>G	11.37:g.102221673A>G			B4E026|Q16516|Q4TTG0	Missense_Mutation	SNP	ENST00000227758.2	37	CCDS8316.1	.	.	.	.	.	.	.	.	.	.	A	13.10	2.136312	0.37728	.	.	ENSG00000110330	ENST00000530675;ENST00000227758;ENST00000541741;ENST00000532672	T;T;T	0.72167	-0.63;-0.63;-0.63	5.86	5.86	0.93980	Baculoviral inhibition of apoptosis protein repeat (5);	0.000000	0.85682	D	0.000000	T	0.80763	0.4685	L	0.54863	1.705	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.78795	-0.2064	10	0.33940	T	0.23	-21.8413	16.2668	0.82588	1.0:0.0:0.0:0.0	.	332	Q13490	BIRC2_HUMAN	G	283;332;332;311	ENSP00000431723:R283G;ENSP00000227758:R332G;ENSP00000434979:R311G	ENSP00000227758:R332G	R	+	1	2	BIRC2	101726883	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.570000	0.67398	2.240000	0.73641	0.533000	0.62120	AGG		0.378	BIRC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394170.1		NM_001166	Missense_Mutation
BPIFB1	92747	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	31873889	31873889	+	Missense_Mutation	SNP	C	C	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr20:31873889C>A	ENST00000253354.1	+	2	171	c.10C>A	c.(10-12)Ccg>Acg	p.P4T		NM_033197.2	NP_149974.2	Q8TDL5	BPIB1_HUMAN	BPI fold containing family B, member 1	4					innate immune response in mucosa (GO:0002227)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)	p.P4T(1)									GATGGCCGGCCCGTGGACCTT	0.617																																																	1	Substitution - Missense(1)	kidney(1)											110.0	94.0	99.0					20																	31873889		2203	4300	6503	SO:0001583	missense	0			BC008429	CCDS13218.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000125999	ENSG00000125999		"""BPI fold containing"""	16108	protein-coding gene	gene with protein product	"""von Ebner minor salivary gland protein"""		"""chromosome 20 open reading frame 114"""	C20orf114		11971875, 21787333	Standard	NM_033197		Approved	dJ1187J4.1, MGC14597, bA49G10.6, LPLUNC1, VEMSGP	uc002wyw.1	Q8TDL5	OTTHUMG00000032252	ENST00000253354.1:c.10C>A	20.37:g.31873889C>A	ENSP00000253354:p.Pro4Thr		A8K2H8|Q5QP43|Q6UWY1|Q6ZRU7|Q96HK6|Q9BQP8|Q9BWZ6|Q9H4V6	Missense_Mutation	SNP	ENST00000253354.1	37	CCDS13218.1	.	.	.	.	.	.	.	.	.	.	C	9.775	1.173749	0.21704	.	.	ENSG00000125999	ENST00000423645;ENST00000253354	T;T	0.53423	0.62;3.78	4.92	2.84	0.33178	.	0.623834	0.15959	N	0.236351	T	0.38348	0.1037	L	0.50333	1.59	0.09310	N	1	P;B	0.47106	0.89;0.451	B;B	0.40702	0.338;0.134	T	0.17137	-1.0379	10	0.39692	T	0.17	-4.2767	6.8705	0.24119	0.0:0.7714:0.0:0.2286	.	4;4	B2R7Z6;Q8TDL5	.;BPIB1_HUMAN	T	4	ENSP00000390471:P4T;ENSP00000253354:P4T	ENSP00000253354:P4T	P	+	1	0	BPIFB1	31337550	0.000000	0.05858	0.001000	0.08648	0.078000	0.17371	0.634000	0.24614	0.678000	0.31325	0.655000	0.94253	CCG		0.617	BPIFB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106499.2		NM_033197	
FAM205B	389715	broad.mit.edu	37	9	34834304	34834304	+	RNA	SNP	C	C	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr9:34834304C>T	ENST00000455647.2	-	0	2089							Q63HN1	F205B_HUMAN	family with sequence similarity 205, member B									p.R395R(1)									ACAAGTGTGGCCTGGGGATGG	0.587																																																	1	Substitution - coding silent(1)	kidney(1)																																										0					9p13.3	2013-05-22	2011-08-15	2011-08-15	ENSG00000257198	ENSG00000257198			24504	other	unknown			"""chromosome 9 open reading frame 144"""	C9orf144			Standard	NR_024481		Approved	DKFZp434J193, C9orf144A	uc003zvp.4	Q63HN1	OTTHUMG00000019839		9.37:g.34834304C>T			Q6ZRJ7	Silent	SNP	ENST00000455647.2	37																																																																																					0.587	FAM205B-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000052246.5		NR_024481	
CA10	56934	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	50149723	50149723	+	Missense_Mutation	SNP	C	C	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr17:50149723C>T	ENST00000285273.4	-	3	1203	c.92G>A	c.(91-93)gGc>gAc	p.G31D	CA10_ENST00000442502.2_Missense_Mutation_p.G31D|CA10_ENST00000340813.6_Missense_Mutation_p.G37D|CA10_ENST00000451037.2_Missense_Mutation_p.G31D|CA10_ENST00000570565.1_5'UTR	NM_001082533.1	NP_001076002.1	Q9NS85	CAH10_HUMAN	carbonic anhydrase X	31					brain development (GO:0007420)			p.G31D(1)		cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|skin(3)|stomach(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)		Zonisamide(DB00909)	TGCCCACCAGCCTTCATGGAT	0.393																																																	1	Substitution - Missense(1)	kidney(1)											122.0	118.0	119.0					17																	50149723		2203	4300	6503	SO:0001583	missense	56934			AF288385	CCDS32684.1	17q21	2012-08-21			ENSG00000154975	ENSG00000154975		"""Carbonic anhydrases"""	1369	protein-coding gene	gene with protein product		604642				8673298, 9921901	Standard	NM_020178		Approved	CARPX, CA-RPX, HUCEP-15	uc002itx.4	Q9NS85	OTTHUMG00000177544	ENST00000285273.4:c.92G>A	17.37:g.50149723C>T	ENSP00000285273:p.Gly31Asp		B2R7J0|B4DGL6	Missense_Mutation	SNP	ENST00000285273.4	37	CCDS32684.1	.	.	.	.	.	.	.	.	.	.	C	14.74	2.624702	0.46840	.	.	ENSG00000154975	ENST00000442502;ENST00000285273;ENST00000451037;ENST00000340813	T;T;T;T	0.68331	1.8;1.8;1.8;-0.32	6.17	6.17	0.99709	Carbonic anhydrase, alpha-class, catalytic domain (2);	0.000000	0.64402	D	0.000003	T	0.53594	0.1806	N	0.19112	0.55	0.58432	D	0.999992	B;B	0.18166	0.026;0.026	B;B	0.17433	0.018;0.018	T	0.45977	-0.9224	9	.	.	.	.	18.3732	0.90420	0.0:1.0:0.0:0.0	.	31;37	Q9NS85;Q68D28	CAH10_HUMAN;.	D	31;31;31;37	ENSP00000390666:G31D;ENSP00000285273:G31D;ENSP00000405388:G31D;ENSP00000340363:G37D	.	G	-	2	0	CA10	47504722	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.020000	0.64066	2.941000	0.99782	0.655000	0.94253	GGC		0.393	CA10-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000437480.1		NM_020178	
CABIN1	23523	hgsc.bcm.edu	37	22	24483439	24483440	+	Frame_Shift_Ins	INS	-	-	C			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr22:24483439_24483440insC	ENST00000398319.2	+	23	3683_3684	c.3298_3299insC	c.(3298-3300)gccfs	p.A1100fs	CABIN1_ENST00000405822.2_Frame_Shift_Ins_p.A1050fs|CABIN1_ENST00000263119.5_Frame_Shift_Ins_p.A1100fs	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	1100					cell surface receptor signaling pathway (GO:0007166)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of catalytic activity (GO:0043086)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						TCTGGCCCGGGCCAGCCGCATT	0.535																																																	0																																										SO:0001589	frameshift_variant	23523			AF072441	CCDS13823.1, CCDS74830.1	22q11.23	2008-09-16			ENSG00000099991	ENSG00000099991			24187	protein-coding gene	gene with protein product		604251				9655484, 9205841	Standard	NM_001199281		Approved	KIAA0330, PPP3IN	uc002zzi.1	Q9Y6J0	OTTHUMG00000150797	ENST00000398319.2:c.3300dupC	22.37:g.24483441_24483441dupC	ENSP00000381364:p.Ala1100fs		G5E9F3|Q6PHY0|Q9Y460	Frame_Shift_Ins	INS	ENST00000398319.2	37	CCDS13823.1																																																																																				0.535	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2		NM_012295	
CHD7	55636	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	61732614	61732614	+	Missense_Mutation	SNP	A	A	T	rs372474695		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr8:61732614A>T	ENST00000423902.2	+	9	3141	c.2662A>T	c.(2662-2664)Atg>Ttg	p.M888L	CHD7_ENST00000524602.1_Intron|CHD7_ENST00000525508.1_Missense_Mutation_p.M888L	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	888	Chromo 2. {ECO:0000255|PROSITE- ProRule:PRU00053}.				adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.M888L(2)		NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			TGACCGGATAATGGACTTTGC	0.388																																																	2	Substitution - Missense(2)	kidney(2)											119.0	116.0	117.0					8																	61732614		1887	4105	5992	SO:0001583	missense	55636			AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"""CHARGE association"""	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.2662A>T	8.37:g.61732614A>T	ENSP00000392028:p.Met888Leu		D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Missense_Mutation	SNP	ENST00000423902.2	37	CCDS47865.1	.	.	.	.	.	.	.	.	.	.	A	4.985	0.182992	0.09495	.	.	ENSG00000171316	ENST00000307121;ENST00000423902;ENST00000525508	T;T	0.61392	0.11;0.11	5.91	4.71	0.59529	Chromo domain (1);Chromo domain/shadow (2);	0.128928	0.52532	D	0.000061	T	0.10852	0.0265	N	0.00012	-2.96	0.36597	D	0.87443	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.47249	-0.9132	10	0.02654	T	1	-10.7461	9.801	0.40764	0.7119:0.1898:0.0:0.0984	.	888;888	Q9P2D1-2;Q9P2D1	.;CHD7_HUMAN	L	888	ENSP00000392028:M888L;ENSP00000436027:M888L	ENSP00000307304:M888L	M	+	1	0	CHD7	61895168	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.996000	0.49449	2.252000	0.74401	0.533000	0.62120	ATG		0.388	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2		XM_098762	
COL5A3	50509	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	10116391	10116391	+	Splice_Site	SNP	C	C	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr19:10116391C>T	ENST00000264828.3	-	4	523		c.e4-1			NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3						axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)	p.?(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			ACGGTGCCACCTGCAAGGGGA	0.632																																																	1	Unknown(1)	kidney(1)											53.0	47.0	49.0					19																	10116391		2203	4300	6503	SO:0001630	splice_region_variant	50509			AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"""Collagens"""	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.438-1G>A	19.37:g.10116391C>T			Q9NZQ6	Splice_Site	SNP	ENST00000264828.3	37	CCDS12222.1	.	.	.	.	.	.	.	.	.	.	C	13.61	2.288909	0.40494	.	.	ENSG00000080573	ENST00000264828	.	.	.	4.06	4.06	0.47325	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.5978	0.50984	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	COL5A3	9977391	1.000000	0.71417	1.000000	0.80357	0.442000	0.32017	5.975000	0.70475	2.128000	0.65567	0.313000	0.20887	.		0.632	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1		NM_015719	Intron
CPXM2	119587	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	125526488	125526488	+	Splice_Site	SNP	C	C	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr10:125526488C>T	ENST00000241305.3	-	10	1634		c.e10+1		CPXM2_ENST00000368854.3_Splice_Site	NM_198148.2	NP_937791.2	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.?(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)	47		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)		TTTTGACTCACCGTGGCATTT	0.468																																																	1	Unknown(1)	kidney(1)											89.0	82.0	85.0					10																	125526488		2203	4300	6503	SO:0001630	splice_region_variant	119587			AY358565	CCDS7637.1	10q26	2012-02-10			ENSG00000121898	ENSG00000121898			26977	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase"""					12975309	Standard	NM_198148		Approved	UNQ676, CPX2	uc001lhk.1	Q8N436	OTTHUMG00000019206	ENST00000241305.3:c.1479+1G>A	10.37:g.125526488C>T			B4E3Q2	Splice_Site	SNP	ENST00000241305.3	37	CCDS7637.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.479822	0.84747	.	.	ENSG00000121898	ENST00000241305;ENST00000540123;ENST00000418782	.	.	.	4.69	4.69	0.59074	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.8309	0.88682	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CPXM2	125516478	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	7.624000	0.83124	2.420000	0.82092	0.650000	0.86243	.		0.468	CPXM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050853.1		NM_198148	Intron
CTNS	1497	broad.mit.edu;ucsc.edu	37	17	3563239	3563239	+	Missense_Mutation	SNP	C	C	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr17:3563239C>A	ENST00000046640.3	+	11	1533	c.940C>A	c.(940-942)Ctg>Atg	p.L314M	CTNS_ENST00000414524.2_Missense_Mutation_p.L167M|CTNS_ENST00000441220.2_Missense_Mutation_p.L206M|CTNS_ENST00000381870.3_Missense_Mutation_p.L314M|RP11-235E17.6_ENST00000575741.1_RNA	NM_004937.2	NP_004928.2	O60931	CTNS_HUMAN	cystinosin, lysosomal cystine transporter	314	PQ-loop 2.				adult walking behavior (GO:0007628)|ATP metabolic process (GO:0046034)|brain development (GO:0007420)|cellular amino acid metabolic process (GO:0006520)|cognition (GO:0050890)|glutathione metabolic process (GO:0006749)|grooming behavior (GO:0007625)|L-cystine transport (GO:0015811)|lens development in camera-type eye (GO:0002088)|long-term memory (GO:0007616)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	L-cystine transmembrane transporter activity (GO:0015184)	p.L314M(2)		NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)	10				COAD - Colon adenocarcinoma(5;0.0829)	L-Cystine(DB00138)	CTTCAGCCTCCTGCAGATGTT	0.632																																																	2	Substitution - Missense(2)	kidney(2)											56.0	54.0	55.0					17																	3563239		2203	4300	6503	SO:0001583	missense	1497			AJ222967	CCDS11031.1, CCDS32530.1	17p13	2011-06-07	2011-06-07		ENSG00000040531	ENSG00000040531			2518	protein-coding gene	gene with protein product		606272	"""cystinosis, nephropathic"""			9537412, 15128704	Standard	NM_004937		Approved	CTNS-LSB, PQLC4	uc002fwa.3	O60931	OTTHUMG00000090693	ENST00000046640.3:c.940C>A	17.37:g.3563239C>A	ENSP00000046640:p.Leu314Met		D3DTJ5|Q8IZ01|Q9UNK6	Missense_Mutation	SNP	ENST00000046640.3	37	CCDS11031.1	.	.	.	.	.	.	.	.	.	.	c	20.4	3.981285	0.74474	.	.	ENSG00000040531	ENST00000046640;ENST00000381870;ENST00000441220;ENST00000414524	D;D;D;D	0.98602	-5.02;-5.02;-5.02;-5.02	5.33	5.33	0.75918	.	0.134081	0.51477	D	0.000081	D	0.98642	0.9545	M	0.73962	2.25	0.48040	D	0.999572	D;D;D	0.89917	0.999;0.975;1.0	D;P;D	0.74674	0.984;0.792;0.984	D	0.98730	1.0712	10	0.54805	T	0.06	-29.9382	14.0486	0.64719	0.0:0.8491:0.1509:0.0	.	206;314;314	F8W6Z1;O60931;O60931-2	.;CTNS_HUMAN;.	M	314;314;206;167	ENSP00000046640:L314M;ENSP00000371294:L314M;ENSP00000411465:L206M;ENSP00000395471:L167M	ENSP00000046640:L314M	L	+	1	2	CTNS	3509988	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	3.416000	0.52707	2.667000	0.90743	0.561000	0.74099	CTG		0.632	CTNS-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317696.1		NM_004937	
CXCR6	10663	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	45988547	45988547	+	Missense_Mutation	SNP	C	C	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr3:45988547C>T	ENST00000458629.1	+	1	2037	c.574C>T	c.(574-576)Ctt>Ttt	p.L192F	FYCO1_ENST00000296137.2_Intron|CXCR6_ENST00000457814.1_Missense_Mutation_p.L192F|CXCR6_ENST00000304552.4_Missense_Mutation_p.L192F|CXCR6_ENST00000438735.1_Missense_Mutation_p.L192F|FYCO1_ENST00000438446.1_Intron|FYCO1_ENST00000535325.1_Intron			O00574	CXCR6_HUMAN	chemokine (C-X-C motif) receptor 6	192					chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|viral genome replication (GO:0019079)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|G-protein coupled receptor activity (GO:0004930)	p.L192F(1)		central_nervous_system(1)|endometrium(1)|kidney(3)|lung(1)|prostate(1)|skin(1)	8				BRCA - Breast invasive adenocarcinoma(193;0.00113)|KIRC - Kidney renal clear cell carcinoma(197;0.0172)|Kidney(197;0.0203)		CACTGTGGTTCTTGCCACCCA	0.463																																					Esophageal Squamous(63;1005 1117 15521 45762 47089)												1	Substitution - Missense(1)	kidney(1)											130.0	130.0	130.0					3																	45988547		2203	4300	6503	SO:0001583	missense	10663			AF007545	CCDS2735.1	3p21	2012-08-08			ENSG00000172215	ENSG00000172215		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : C-X-C motif"""	16647	protein-coding gene	gene with protein product		605163				9166430, 9230441	Standard	XM_005264809		Approved	TYMSTR, STRL33, BONZO, CD186	uc003cpc.1	O00574	OTTHUMG00000133448	ENST00000458629.1:c.574C>T	3.37:g.45988547C>T	ENSP00000395704:p.Leu192Phe		O00575|Q9HCA5	Missense_Mutation	SNP	ENST00000458629.1	37	CCDS2735.1	.	.	.	.	.	.	.	.	.	.	C	18.74	3.689298	0.68271	.	.	ENSG00000172215	ENST00000438735;ENST00000304552;ENST00000458629;ENST00000457814	T;T;T;T	0.38077	1.16;1.16;1.16;1.16	5.57	5.57	0.84162	GPCR, rhodopsin-like superfamily (1);	0.937000	0.09002	N	0.862892	T	0.58264	0.2110	M	0.67517	2.055	0.25673	N	0.98587	D	0.89917	1.0	D	0.79784	0.993	T	0.49224	-0.8962	10	0.56958	D	0.05	.	9.9843	0.41832	0.153:0.6991:0.1479:0.0	.	192	O00574	CXCR6_HUMAN	F	192	ENSP00000396218:L192F;ENSP00000304414:L192F;ENSP00000395704:L192F;ENSP00000396886:L192F	ENSP00000304414:L192F	L	+	1	0	CXCR6	45963551	0.128000	0.22383	0.736000	0.30914	0.953000	0.61014	1.690000	0.37711	2.785000	0.95823	0.655000	0.94253	CTT		0.463	CXCR6-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344395.1			
DDB1	1642	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	61081631	61081632	+	Missense_Mutation	DNP	TC	TC	AT			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr11:61081631_61081632TC>AT	ENST00000301764.7	-	14	2037_2038	c.1640_1641GA>AT	c.(1639-1641)gGA>gAT	p.G547D	DDB1_ENST00000545930.1_5'Flank|DDB1_ENST00000450997.2_Intron	NM_001923.4	NP_001914.3	Q16531	DDB1_HUMAN	damage-specific DNA binding protein 1, 127kDa	547	Interaction with CDT1.|WD repeat beta-propeller B; Interaction with CUL4A.				DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of mitotic cell cycle phase transition (GO:1901990)|UV-damage excision repair (GO:0070914)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)	p.G547E(1)|p.G547G(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	48						CATTGCTGTCTCCTAATGGGGT	0.49								Nucleotide excision repair (NER)																																									2	Substitution - Missense(1)|Substitution - coding silent(1)	kidney(2)																																								SO:0001583	missense	1642			AJ002955	CCDS31576.1	11q12-q13	2014-09-17	2002-08-29		ENSG00000167986	ENSG00000167986			2717	protein-coding gene	gene with protein product		600045	"""damage-specific DNA binding protein 1 (127kD)"""			8530102, 10574459	Standard	NM_001923		Approved	XPE	uc001nrc.5	Q16531	OTTHUMG00000168209	ENST00000301764.7:c.1640_1641delinsAT	11.37:g.61081631_61081632delinsAT	ENSP00000301764:p.Gly547Asp		A6NG77|B2R648|B4DG00|O15176|Q13289|Q58F96	Silent|Missense_Mutation	SNP	ENST00000301764.7	37	CCDS31576.1																																																																																				0.490	DDB1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398816.1		NM_001923	
DISP1	84976	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	223179160	223179160	+	Missense_Mutation	SNP	G	G	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr1:223179160G>T	ENST00000284476.6	+	8	4585	c.4421G>T	c.(4420-4422)aGg>aTg	p.R1474M		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	1474					determination of left/right symmetry (GO:0007368)|diaphragm development (GO:0060539)|dorsal/ventral pattern formation (GO:0009953)|embryonic pattern specification (GO:0009880)|patched ligand maturation (GO:0007225)|peptide transport (GO:0015833)|protein homotrimerization (GO:0070207)|regulation of protein secretion (GO:0050708)|smoothened signaling pathway (GO:0007224)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)|peptide transporter activity (GO:0015197)	p.R1474M(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(20)|lung(25)|prostate(4)|skin(1)|stomach(1)|urinary_tract(5)	69				GBM - Glioblastoma multiforme(131;0.102)		GCTGGTTGTAGGTCTTGCCCA	0.428																																																	1	Substitution - Missense(1)	kidney(1)											75.0	74.0	74.0					1																	223179160		2203	4300	6503	SO:0001583	missense	84976			AK056569	CCDS1536.1	1q42.12	2008-02-05			ENSG00000154309	ENSG00000154309			19711	protein-coding gene	gene with protein product		607502				10619433	Standard	NM_032890		Approved	DISPA, MGC13130, DKFZP434I0428, MGC16796	uc001hnu.2	Q96F81	OTTHUMG00000037893	ENST00000284476.6:c.4421G>T	1.37:g.223179160G>T	ENSP00000284476:p.Arg1474Met		Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Missense_Mutation	SNP	ENST00000284476.6	37	CCDS1536.1	.	.	.	.	.	.	.	.	.	.	G	12.85	2.061137	0.36373	.	.	ENSG00000154309	ENST00000284476	D	0.91686	-2.89	5.29	4.3	0.51218	.	1.233450	0.05373	N	0.535729	D	0.84570	0.5501	N	0.14661	0.345	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.72849	-0.4168	10	0.72032	D	0.01	-1.4628	3.4084	0.07350	0.223:0.0:0.3174:0.4595	.	1474	Q96F81	DISP1_HUMAN	M	1474	ENSP00000284476:R1474M	ENSP00000284476:R1474M	R	+	2	0	DISP1	221245783	0.879000	0.30193	0.012000	0.15200	0.709000	0.40893	1.506000	0.35747	1.151000	0.42436	0.655000	0.94253	AGG		0.428	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1		NM_032890	
DMP1	1758	broad.mit.edu	37	4	88583134	88583134	+	Silent	SNP	C	C	T	rs375708823		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr4:88583134C>T	ENST00000339673.6	+	6	303	c.204C>T	c.(202-204)gaC>gaT	p.D68D	DMP1_ENST00000282479.7_Silent_p.D52D|RP11-742B18.1_ENST00000506814.1_RNA|RP11-742B18.1_ENST00000507894.1_RNA|RP11-742B18.1_ENST00000506480.1_RNA	NM_004407.3	NP_004398.1	Q13316	DMP1_HUMAN	dentin matrix acidic phosphoprotein 1	68					biomineral tissue development (GO:0031214)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|positive regulation of cell-substrate adhesion (GO:0010811)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)	p.D68D(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(1)|stomach(1)	32		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.227)		OV - Ovarian serous cystadenocarcinoma(123;0.000516)		ACCCCAGTGACAGCACTCAGT	0.463																																																	1	Substitution - coding silent(1)	kidney(1)						C	,	0,4406		0,0,2203	54.0	57.0	56.0		156,204	2.5	1.0	4		56	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	DMP1	NM_001079911.2,NM_004407.3	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	52/498,68/514	88583134	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1758			U34037	CCDS3623.1, CCDS43249.1	4q21	2008-08-29	2008-08-29		ENSG00000152592	ENSG00000152592			2932	protein-coding gene	gene with protein product		600980	"""dentin matrix acidic phosphoprotein"""			8586437, 9177774	Standard	NM_001079911		Approved		uc003hqv.3	Q13316	OTTHUMG00000130598	ENST00000339673.6:c.204C>T	4.37:g.88583134C>T			A1L4L3|O43265	Silent	SNP	ENST00000339673.6	37	CCDS3623.1																																																																																				0.463	DMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253047.1			
DMRT3	58524	hgsc.bcm.edu;ucsc.edu	37	9	990589	990589	+	Nonsense_Mutation	SNP	C	C	T	rs374319022		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr9:990589C>T	ENST00000190165.2	+	2	1041	c.1003C>T	c.(1003-1005)Cga>Tga	p.R335*		NM_021240.2	NP_067063.1	Q9NQL9	DMRT3_HUMAN	doublesex and mab-3 related transcription factor 3	335					adult walking behavior (GO:0007628)|male sex differentiation (GO:0046661)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|sex differentiation (GO:0007548)|transcription, DNA-templated (GO:0006351)|transmission of nerve impulse (GO:0019226)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(10;1.39e-08)|Lung NSC(10;1.42e-08)		Lung(218;0.0196)		ATCAGCCTTTCGAGTCCCAGA	0.577																																																	0								C	stop/ARG	1,4405	2.1+/-5.4	0,1,2202	112.0	102.0	106.0		1003	0.2	0.3	9		106	0,8600		0,0,4300	no	stop-gained	DMRT3	NM_021240.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		335/473	990589	1,13005	2203	4300	6503	SO:0001587	stop_gained	58524			AJ301581	CCDS6443.1	9p24.3	2008-07-21	2001-12-17	2001-12-07	ENSG00000064218	ENSG00000064218			13909	protein-coding gene	gene with protein product	"""testis-specific protein"""	614754	"""DMRT-like family A3"""	DMRTA3		11543627, 10729223	Standard	NM_021240		Approved		uc003zgw.2	Q9NQL9	OTTHUMG00000019436	ENST00000190165.2:c.1003C>T	9.37:g.990589C>T	ENSP00000190165:p.Arg335*		Q7LA03|Q7LCH8|Q96SC7|Q9NRQ9	Nonsense_Mutation	SNP	ENST00000190165.2	37	CCDS6443.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.717208	0.89205	2.27E-4	0.0	ENSG00000064218	ENST00000190165	.	.	.	4.95	0.169	0.15017	.	0.206172	0.38720	N	0.001592	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.6464	11.4219	0.49987	0.2857:0.6374:0.0768:0.0	.	.	.	.	X	335	.	ENSP00000190165:R335X	R	+	1	2	DMRT3	980589	0.951000	0.32395	0.282000	0.24776	0.978000	0.69477	0.261000	0.18442	-0.223000	0.09943	0.561000	0.74099	CGA		0.577	DMRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051490.1		NM_021240	
ECHDC3	79746	broad.mit.edu;ucsc.edu	37	10	11797428	11797428	+	Missense_Mutation	SNP	C	C	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr10:11797428C>G	ENST00000379215.4	+	4	623	c.412C>G	c.(412-414)Cac>Gac	p.H138D	ECHDC3_ENST00000496136.1_3'UTR	NM_024693.4	NP_078969	Q96DC8	ECHD3_HUMAN	enoyl CoA hydratase domain containing 3	138						mitochondrion (GO:0005739)	catalytic activity (GO:0003824)	p.H138D(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)	4						CATCCGGAACCACCCCGTTCC	0.552																																																	1	Substitution - Missense(1)	kidney(1)											73.0	52.0	59.0					10																	11797428		2203	4300	6503	SO:0001583	missense	79746			AF275677	CCDS7084.1	10p14	2010-04-30	2010-04-30		ENSG00000134463	ENSG00000134463			23489	protein-coding gene	gene with protein product			"""enoyl Coenzyme A hydratase domain containing 3"""			12477932	Standard	NM_024693		Approved	FLJ20909	uc001ikw.4	Q96DC8	OTTHUMG00000017675	ENST00000379215.4:c.412C>G	10.37:g.11797428C>G	ENSP00000368517:p.His138Asp		Q53HR9|Q5W0J7|Q8WYY8|Q9BVL8|Q9H7G4	Missense_Mutation	SNP	ENST00000379215.4	37	CCDS7084.1	.	.	.	.	.	.	.	.	.	.	C	14.15	2.449509	0.43531	.	.	ENSG00000134463	ENST00000379215;ENST00000420401;ENST00000422887	T;T;T	0.66995	1.99;0.98;-0.24	5.31	5.31	0.75309	Crotonase, core (1);	0.233546	0.43260	D	0.000594	T	0.79805	0.4509	L	0.54323	1.7	0.31527	N	0.661628	P	0.44195	0.828	D	0.72982	0.979	T	0.79797	-0.1652	10	0.45353	T	0.12	.	17.9543	0.89063	0.0:1.0:0.0:0.0	.	138	Q96DC8	ECHD3_HUMAN	D	138;191;65	ENSP00000368517:H138D;ENSP00000405584:H191D;ENSP00000398429:H65D	ENSP00000368517:H138D	H	+	1	0	ECHDC3	11837434	0.758000	0.28405	0.851000	0.33527	0.454000	0.32378	2.037000	0.41174	2.478000	0.83669	0.591000	0.81541	CAC		0.552	ECHDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046771.1		NM_024693	
EPHA5	2044	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	66197808	66197808	+	Missense_Mutation	SNP	G	G	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr4:66197808G>T	ENST00000273854.3	-	17	3491	c.2891C>A	c.(2890-2892)tCt>tAt	p.S964Y	EPHA5_ENST00000432638.2_Missense_Mutation_p.S801Y|EPHA5_ENST00000511294.1_Missense_Mutation_p.S965Y|EPHA5_ENST00000354839.4_Missense_Mutation_p.S942Y	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	964					axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)	p.S964Y(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						GTAGGCCCCAGATCCTAGTGG	0.358										TSP Lung(17;0.13)																																							1	Substitution - Missense(1)	kidney(1)											72.0	66.0	68.0					4																	66197808		2203	4300	6503	SO:0001583	missense	2044			L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3389	protein-coding gene	gene with protein product		600004	"""EphA5"""			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.2891C>A	4.37:g.66197808G>T	ENSP00000273854:p.Ser964Tyr		Q7Z3F2	Missense_Mutation	SNP	ENST00000273854.3	37	CCDS3513.1	.	.	.	.	.	.	.	.	.	.	G	1.214	-0.628714	0.03610	.	.	ENSG00000145242	ENST00000273854;ENST00000432638;ENST00000354839;ENST00000511294	T;T;T;D	0.82619	-0.7;-0.76;-0.65;-1.63	5.38	3.58	0.41010	Sterile alpha motif domain (1);Sterile alpha motif/pointed domain (2);	0.458728	0.19924	N	0.103035	T	0.58637	0.2136	N	0.01188	-0.97	0.31377	N	0.679478	B;B;B;P	0.34800	0.119;0.001;0.098;0.469	B;B;B;B	0.39419	0.102;0.006;0.047;0.299	T	0.61917	-0.6964	10	0.02654	T	1	.	12.2665	0.54681	0.0:0.391:0.4974:0.1116	.	943;965;942;964	B7ZKW7;B7ZKJ3;P54756-2;P54756	.;.;.;EPHA5_HUMAN	Y	964;801;942;965	ENSP00000273854:S964Y;ENSP00000389208:S801Y;ENSP00000346899:S942Y;ENSP00000427638:S965Y	ENSP00000273854:S964Y	S	-	2	0	EPHA5	65880403	0.994000	0.37717	0.975000	0.42487	0.978000	0.69477	0.943000	0.29030	0.680000	0.31366	0.491000	0.48974	TCT		0.358	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2		NM_004439	
ETV1	2115	broad.mit.edu;ucsc.edu	37	7	13975450	13975450	+	Missense_Mutation	SNP	G	G	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr7:13975450G>A	ENST00000430479.1	-	8	1104	c.437C>T	c.(436-438)tCc>tTc	p.S146F	ETV1_ENST00000242066.5_Missense_Mutation_p.S128F|ETV1_ENST00000405192.2_Missense_Mutation_p.S146F|ETV1_ENST00000343495.5_Missense_Mutation_p.S128F|ETV1_ENST00000405218.2_Missense_Mutation_p.S146F|ETV1_ENST00000476720.2_5'UTR|ETV1_ENST00000420159.2_Missense_Mutation_p.S88F|ETV1_ENST00000405358.4_Missense_Mutation_p.S160F|ETV1_ENST00000403685.1_Missense_Mutation_p.S128F|ETV1_ENST00000399357.3_Intron|ETV1_ENST00000403527.1_Missense_Mutation_p.S106F	NM_004956.4	NP_004947.2	P50549	ETV1_HUMAN	ets variant 1	146					axon guidance (GO:0007411)|cell differentiation (GO:0030154)|mechanosensory behavior (GO:0007638)|muscle organ development (GO:0007517)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S146F(1)|p.S106F(1)	TMPRSS2/ETV1(34)|ACSL3_ENST00000357430/ETV1(2)|EWSR1/ETV1(7)|KLK2/ETV1(3)|SLC45A3/ETV1(3)|HNRNPA2B1/ETV1(8)	breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31						ATGCAGTGGGGACACTGGCGT	0.562			T	"""EWSR1, TMPRSS2, SLC45A3, C15orf21, HNRNPA2B1. ACSL3"""	"""Ewing sarcoma, prostate"""																																			Dom	yes		7	7p22	2115	ets variant gene 1		"""M, E"""	2	Substitution - Missense(2)	kidney(2)											152.0	156.0	154.0					7																	13975450		2121	4256	6377	SO:0001583	missense	2115				CCDS55083.1, CCDS55084.1, CCDS55085.1, CCDS55086.1, CCDS55087.1, CCDS55088.1	7p22	2008-09-12	2008-09-12		ENSG00000006468	ENSG00000006468			3490	protein-coding gene	gene with protein product		600541	"""ets variant gene 1"""			1340465	Standard	NM_004956		Approved	ER81	uc003ssw.4	P50549	OTTHUMG00000152403	ENST00000430479.1:c.437C>T	7.37:g.13975450G>A	ENSP00000405327:p.Ser146Phe		A4D118|B2R768|B7Z2I4|B7Z618|B7Z9P2|C9JT37|E9PHB1|F5GXR2|O75849|Q4KMQ6|Q59GA7|Q6AI30|Q9UQ71|Q9Y636	Missense_Mutation	SNP	ENST00000430479.1	37	CCDS55088.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.838353	0.91117	.	.	ENSG00000006468	ENST00000430479;ENST00000242066;ENST00000343495;ENST00000420159;ENST00000405192;ENST00000405358;ENST00000403527;ENST00000405218;ENST00000403685;ENST00000438956	T;T;T;T;T;T;T;T;T;T	0.23552	1.9;1.9;1.9;1.9;1.9;1.9;1.9;1.9;1.9;1.9	5.83	5.83	0.93111	PEA3-type ETS-domain transcription factor, N-terminal (1);	0.241030	0.43260	D	0.000598	T	0.52996	0.1769	M	0.68593	2.085	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;0.961;0.999;0.994;0.998;0.989;1.0	D;P;D;D;D;P;D	0.91635	0.999;0.81;0.998;0.989;0.996;0.88;0.997	T	0.49418	-0.8942	10	0.62326	D	0.03	.	20.189	0.98225	0.0:0.0:1.0:0.0	.	157;128;160;88;106;88;146	Q59GA7;P50549-2;B5MCT2;F5GXR2;E9PHB1;B7Z618;P50549	.;.;.;.;.;.;ETV1_HUMAN	F	146;128;128;88;146;160;106;146;128;88	ENSP00000405327:S146F;ENSP00000242066:S128F;ENSP00000340853:S128F;ENSP00000411626:S88F;ENSP00000385381:S146F;ENSP00000384085:S160F;ENSP00000384138:S106F;ENSP00000385551:S146F;ENSP00000385686:S128F;ENSP00000393078:S88F	ENSP00000242066:S128F	S	-	2	0	ETV1	13941975	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	9.417000	0.97391	2.787000	0.95880	0.650000	0.86243	TCC		0.562	ETV1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326111.1		NM_004956	
TMEM255B	348013	broad.mit.edu;hgsc.bcm.edu	37	13	114514719	114514719	+	Missense_Mutation	SNP	G	G	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr13:114514719G>A	ENST00000375353.3	+	9	851	c.824G>A	c.(823-825)cGc>cAc	p.R275H	TMEM255B_ENST00000467169.1_3'UTR	NM_182614.2	NP_872420.1	Q8WV15	T255B_HUMAN	transmembrane protein 255B	275	Pro-rich.					integral component of membrane (GO:0016021)		p.R275H(1)									CCCTGCAGCCGCTTCCCAGTT	0.652																																																	1	Substitution - Missense(1)	kidney(1)											41.0	46.0	45.0					13																	114514719		2203	4300	6503	SO:0001583	missense	0			BC018995	CCDS45071.1	13q34	2012-11-30	2012-11-30	2012-11-30	ENSG00000184497	ENSG00000184497			28297	protein-coding gene	gene with protein product			"""family with sequence similarity 70, member B"""	FAM70B		12477932	Standard	NM_182614		Approved	MGC20579	uc001vuh.3	Q8WV15	OTTHUMG00000017398	ENST00000375353.3:c.824G>A	13.37:g.114514719G>A	ENSP00000364502:p.Arg275His			Missense_Mutation	SNP	ENST00000375353.3	37	CCDS45071.1	.	.	.	.	.	.	.	.	.	.	G	6.602	0.479534	0.12581	.	.	ENSG00000184497	ENST00000375353	T	0.43294	0.95	4.13	-4.37	0.03633	.	.	.	.	.	T	0.21962	0.0529	N	0.22421	0.69	0.09310	N	1	D	0.56746	0.977	B	0.41619	0.361	T	0.31166	-0.9953	9	0.15066	T	0.55	1.2582	8.4507	0.32869	0.3359:0.5458:0.1183:0.0	.	275	Q8WV15	FA70B_HUMAN	H	275	ENSP00000364502:R275H	ENSP00000364502:R275H	R	+	2	0	FAM70B	113599224	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.159000	0.03150	-0.548000	0.06199	0.585000	0.79938	CGC		0.652	TMEM255B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045953.4		NM_182614	
FAM92A1P2	403315	broad.mit.edu	37	4	183960484	183960484	+	RNA	DEL	A	A	-	rs542231248		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr4:183960484delA	ENST00000502308.1	+	0	1667					NR_003612.1				family with sequence similarity 92, member A1 pseudogene 2																		TTCAACATCCAAAAAAAAAAA	0.308																																																	0																																												0			BC022019		4q35.1	2012-04-19	2012-04-19	2012-04-19	ENSG00000230219	ENSG00000230219			32287	pseudogene	pseudogene			"""family with sequence similarity 92, member A3"""	FAM92A3		12477932	Standard	NR_003612		Approved	MGC71735, MGC102964	uc003ivi.4		OTTHUMG00000160675		4.37:g.183960484delA				RNA	DEL	ENST00000502308.1	37																																																																																					0.308	FAM92A1P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000361814.1			
GREB1L	80000	broad.mit.edu	37	18	19076571	19076571	+	Silent	SNP	A	A	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr18:19076571A>G	ENST00000580732.2	+	21	3684	c.3303A>G	c.(3301-3303)agA>agG	p.R1101R	GREB1L_ENST00000269218.6_Silent_p.R992R|GREB1L_ENST00000424526.1_Silent_p.R1101R|GREB1L_ENST00000400483.4_3'UTR			Q9C091	GRB1L_HUMAN	growth regulation by estrogen in breast cancer-like	1101						integral component of membrane (GO:0016021)		p.R1101R(1)		breast(5)|endometrium(4)|kidney(6)|lung(1)|skin(1)	17						AGCAGGAGAGAGCTGCTGTCA	0.602																																																	1	Substitution - coding silent(1)	kidney(1)											81.0	82.0	82.0					18																	19076571		692	1591	2283	SO:0001819	synonymous_variant	80000			AK023749	CCDS45836.1	18q11.2	2009-09-08	2009-09-08	2009-09-08					31042	protein-coding gene	gene with protein product			"""KIAA1772"""	KIAA1772		11214970	Standard	NM_001142966		Approved	FLJ13687, C18orf6	uc010xam.2	Q9C091		ENST00000580732.2:c.3303A>G	18.37:g.19076571A>G			A4QN17|Q9H8F1	Silent	SNP	ENST00000580732.2	37	CCDS45836.1																																																																																				0.602	GREB1L-003	KNOWN	not_organism_supported|upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443782.2		NM_024935	
GTF2I	2969	broad.mit.edu	37	7	74167453	74167453	+	Missense_Mutation	SNP	T	T	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr7:74167453T>A	ENST00000324896.4	+	29	2974	c.2585T>A	c.(2584-2586)gTt>gAt	p.V862D	GTF2I_ENST00000346152.4_Missense_Mutation_p.V841D|GTF2I_ENST00000416070.1_Missense_Mutation_p.V821D|GTF2I_ENST00000353920.4_Missense_Mutation_p.V842D	NM_032999.2	NP_127492.1	P78347	GTF2I_HUMAN	general transcription factor IIi	862					negative regulation of angiogenesis (GO:0016525)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V862D(1)		NS(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19						CTCTCGAAAGTTGAAAAAGCT	0.328																																																	1	Substitution - Missense(1)	kidney(1)											10.0	10.0	10.0					7																	74167453		2115	4208	6323	SO:0001583	missense	2969			U77948	CCDS5573.1, CCDS5574.1, CCDS5575.1, CCDS47614.1, CCDS64680.1	7q11.23	2011-05-25	2009-07-23			ENSG00000263001		"""General transcription factors"""	4659	protein-coding gene	gene with protein product		601679	"""general transcription factor II, i"""	WBSCR6		9334314, 9012831	Standard	NM_032999		Approved	TFII-I, BAP-135, SPIN, BTKAP1, DIWS, IB291	uc003uau.3	P78347		ENST00000324896.4:c.2585T>A	7.37:g.74167453T>A	ENSP00000322542:p.Val862Asp		O14743|O15359|O43546|O43588|O43589|Q75M85|Q75M86|Q75M87|Q75M88|Q86U51|Q9BSZ4	Missense_Mutation	SNP	ENST00000324896.4	37	CCDS5573.1	.	.	.	.	.	.	.	.	.	.	T	17.33	3.362304	0.61403	.	.	ENSG00000077809	ENST00000324896;ENST00000539339;ENST00000353920;ENST00000346152;ENST00000416070	T;T;T;T	0.39592	1.08;1.07;1.07;1.07	4.99	4.99	0.66335	.	0.186863	0.36167	N	0.002742	T	0.46814	0.1412	L	0.27053	0.805	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.987;0.996;0.999;0.992	D;P;D;D;D	0.85130	0.993;0.908;0.988;0.997;0.963	T	0.50742	-0.8792	10	0.87932	D	0	-12.1141	6.3424	0.21330	0.0:0.0838:0.1597:0.7564	.	840;821;842;841;862	Q499G6;P78347-2;P78347-3;P78347-4;P78347	.;.;.;.;GTF2I_HUMAN	D	862;857;842;841;821	ENSP00000322542:V862D;ENSP00000322671:V842D;ENSP00000322599:V841D;ENSP00000387651:V821D	ENSP00000322542:V862D	V	+	2	0	GTF2I	73805389	0.998000	0.40836	0.995000	0.50966	0.986000	0.74619	3.368000	0.52357	1.913000	0.55393	0.369000	0.22263	GTT		0.328	GTF2I-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252708.1		NM_032999	
HACE1	57531	broad.mit.edu;ucsc.edu	37	6	105233140	105233140	+	Nonsense_Mutation	SNP	C	C	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr6:105233140C>A	ENST00000262903.4	-	12	1405	c.1129G>T	c.(1129-1131)Gaa>Taa	p.E377*	HACE1_ENST00000369125.2_Nonsense_Mutation_p.E377*|HACE1_ENST00000517995.1_5'Flank	NM_020771.3	NP_065822.2	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1	377					cell cycle (GO:0007049)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|Rac protein signal transduction (GO:0016601)|regulation of cell migration (GO:0030334)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Rab GTPase binding (GO:0017137)|Rac GTPase binding (GO:0048365)|ubiquitin-protein transferase activity (GO:0004842)	p.E377*(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	44		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)		TTCATCAATTCTGTGGCTATT	0.363																																																	1	Substitution - Nonsense(1)	kidney(1)											72.0	73.0	73.0					6																	105233140		2203	4300	6503	SO:0001587	stop_gained	57531			BC034982	CCDS5050.1	6q21	2013-01-10	2012-02-23		ENSG00000085382	ENSG00000085382		"""Ankyrin repeat domain containing"""	21033	protein-coding gene	gene with protein product		610876				10718198	Standard	NM_020771		Approved	KIAA1320	uc003pqu.1	Q8IYU2	OTTHUMG00000015287	ENST00000262903.4:c.1129G>T	6.37:g.105233140C>A	ENSP00000262903:p.Glu377*		A8K6U5|B3KY89|B4DFM6|B4DTQ4|B7Z9X6|E9PGP0|Q5VU99|Q5VUA0|Q8ND12|Q9P2M6	Nonsense_Mutation	SNP	ENST00000262903.4	37	CCDS5050.1	.	.	.	.	.	.	.	.	.	.	C	42	9.493538	0.99186	.	.	ENSG00000085382	ENST00000262903;ENST00000369125	.	.	.	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.17832	T	0.49	.	18.5104	0.90914	0.0:1.0:0.0:0.0	.	.	.	.	X	377	.	ENSP00000262903:E377X	E	-	1	0	HACE1	105339833	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.151000	0.77411	2.375000	0.81037	0.460000	0.39030	GAA		0.363	HACE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041643.2		XM_045095	
HMCN1	83872	broad.mit.edu;ucsc.edu	37	1	185953431	185953431	+	Missense_Mutation	SNP	C	C	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr1:185953431C>T	ENST00000271588.4	+	19	3150	c.2921C>T	c.(2920-2922)tCt>tTt	p.S974F	HMCN1_ENST00000485744.1_3'UTR|HMCN1_ENST00000367492.2_Missense_Mutation_p.S974F	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	974	Ig-like C2-type 6.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.S974F(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						AAAACTACCTCTGTGGTTGTG	0.398																																																	1	Substitution - Missense(1)	kidney(1)											208.0	198.0	201.0					1																	185953431		2203	4300	6503	SO:0001583	missense	83872			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.2921C>T	1.37:g.185953431C>T	ENSP00000271588:p.Ser974Phe		A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	16.41	3.116064	0.56505	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.69040	-0.37;-0.37	5.81	2.66	0.31614	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.299822	0.37955	N	0.001875	T	0.50531	0.1621	N	0.21097	0.63	0.29837	N	0.82954	B;P	0.40107	0.338;0.703	B;B	0.43990	0.301;0.438	T	0.45469	-0.9259	10	0.17832	T	0.49	.	7.4112	0.27019	0.1094:0.5639:0.2601:0.0665	.	358;974	Q96RW7-3;Q96RW7	.;HMCN1_HUMAN	F	974	ENSP00000271588:S974F;ENSP00000356462:S974F	ENSP00000271588:S974F	S	+	2	0	HMCN1	184220054	0.329000	0.24696	0.999000	0.59377	0.994000	0.84299	0.852000	0.27764	1.354000	0.45846	0.655000	0.94253	TCT		0.398	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1		NM_031935	
IL20RB	53833	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	136710849	136710849	+	Missense_Mutation	SNP	T	T	C			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr3:136710849T>C	ENST00000329582.4	+	5	850	c.601T>C	c.(601-603)Tac>Cac	p.Y201H	IL20RB_ENST00000309741.5_Intron	NM_144717.3	NP_653318.2	Q6UXL0	I20RB_HUMAN	interleukin 20 receptor beta	201	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				homeostasis of number of cells within a tissue (GO:0048873)|immune response-inhibiting signal transduction (GO:0002765)|inflammatory response to antigenic stimulus (GO:0002437)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of type IV hypersensitivity (GO:0001808)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-4 production (GO:0032753)	integral component of membrane (GO:0016021)		p.Y201H(2)		kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14						AGGGGCTGCATACTGTGTGAA	0.517																																																	2	Substitution - Missense(2)	kidney(2)											155.0	142.0	147.0					3																	136710849		2203	4300	6503	SO:0001583	missense	53833			BC033292	CCDS3093.1	3q22.3	2013-02-11			ENSG00000174564	ENSG00000174564		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	6004	protein-coding gene	gene with protein product		605621	"""fibronectin type III domain containing 6"""	FNDC6		11163236, 16703417	Standard	NM_144717		Approved	DIRS1, IL-20R2, MGC34923	uc003eri.2	Q6UXL0	OTTHUMG00000159779	ENST00000329582.4:c.601T>C	3.37:g.136710849T>C	ENSP00000328133:p.Tyr201His		B4DL40|Q6P438|Q8IYY5|Q8TAJ7	Missense_Mutation	SNP	ENST00000329582.4	37	CCDS3093.1	.	.	.	.	.	.	.	.	.	.	T	17.94	3.510733	0.64522	.	.	ENSG00000174564	ENST00000329582	D	0.87103	-2.21	4.95	3.77	0.43336	Fibronectin, type III (1);Interferon alpha/beta receptor, beta chain (1);Immunoglobulin-like fold (1);	0.000000	0.56097	D	0.000027	D	0.87924	0.6300	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.85864	0.1412	10	0.51188	T	0.08	-3.9518	7.6902	0.28563	0.0:0.0979:0.0:0.9021	.	201	Q6UXL0	I20RB_HUMAN	H	201	ENSP00000328133:Y201H	ENSP00000328133:Y201H	Y	+	1	0	IL20RB	138193539	0.995000	0.38212	0.645000	0.29479	0.961000	0.63080	2.992000	0.49417	0.720000	0.32209	0.379000	0.24179	TAC		0.517	IL20RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357277.2		NM_144717	
INSRR	3645	broad.mit.edu;ucsc.edu	37	1	156812296	156812296	+	Missense_Mutation	SNP	C	C	T	rs138327752	byFrequency	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr1:156812296C>T	ENST00000368195.3	-	18	3527	c.3131G>A	c.(3130-3132)cGt>cAt	p.R1044H	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	1044	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.R1044H(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					ACCCAGGAGACGCACCTGGGA	0.552													C|||	2	0.000399361	0.0008	0.0	5008	,	,		19760	0.0		0.001	False		,,,				2504	0.0																1	Substitution - Missense(1)	kidney(1)						C	,HIS/ARG	0,4406		0,0,2203	68.0	70.0	69.0		,3131	4.4	1.0	1	dbSNP_134	69	6,8594	5.0+/-18.6	0,6,4294	yes	intron,missense	INSRR,NTRK1	NM_001007792.1,NM_014215.2	,29	0,6,6497	TT,TC,CC		0.0698,0.0,0.0461	,probably-damaging	,1044/1298	156812296	6,13000	2203	4300	6503	SO:0001583	missense	3645			J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"""Fibronectin type III domain containing"""	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.3131G>A	1.37:g.156812296C>T	ENSP00000357178:p.Arg1044His		O60724|Q5VZS3	Missense_Mutation	SNP	ENST00000368195.3	37	CCDS1160.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	23.7	4.448305	0.84101	0.0	6.98E-4	ENSG00000027644	ENST00000368195	D	0.90197	-2.63	4.38	4.38	0.52667	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.46758	D	0.000270	D	0.94571	0.8251	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.95258	0.8366	9	0.87932	D	0	.	15.6643	0.77213	0.0:1.0:0.0:0.0	.	1044	P14616	INSRR_HUMAN	H	1044	ENSP00000357178:R1044H	ENSP00000357178:R1044H	R	-	2	0	INSRR	155078920	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.627000	0.83176	2.288000	0.76882	0.561000	0.74099	CGT		0.552	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1		NM_014215	
INTU	27152	broad.mit.edu;ucsc.edu	37	4	128632123	128632123	+	Missense_Mutation	SNP	C	C	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr4:128632123C>A	ENST00000335251.6	+	14	2528	c.2425C>A	c.(2425-2427)Caa>Aaa	p.Q809K		NM_015693.3	NP_056508.2	Q9ULD6	INTU_HUMAN	inturned planar cell polarity protein	809					cilium assembly (GO:0042384)|hair follicle morphogenesis (GO:0031069)|keratinocyte differentiation (GO:0030216)|limb development (GO:0060173)|negative regulation of cell division (GO:0051782)|negative regulation of keratinocyte proliferation (GO:0010839)|nervous system development (GO:0007399)|positive regulation of smoothened signaling pathway (GO:0045880)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord dorsal/ventral patterning (GO:0021513)	cytoplasm (GO:0005737)		p.Q809K(1)		breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	43						AGAAACAGTGCAAGGAATCTT	0.378																																																	1	Substitution - Missense(1)	kidney(1)											116.0	108.0	111.0					4																	128632123		2203	4300	6503	SO:0001583	missense	27152			BC051698	CCDS34061.1	4q28.2	2013-03-05	2013-03-05	2006-10-24	ENSG00000164066	ENSG00000164066			29239	protein-coding gene	gene with protein product		610621	"""PDZ domain containing 6"", ""inturned planar cell polarity effector homolog (Drosophila)"""	PDZK6, PDZD6		10574462, 21761479	Standard	NM_015693		Approved	KIAA1284	uc003ifk.2	Q9ULD6	OTTHUMG00000161202	ENST00000335251.6:c.2425C>A	4.37:g.128632123C>A	ENSP00000334003:p.Gln809Lys		A1L4N5|D6RAE6|D6RBT4|Q4W5I8|Q86V55	Missense_Mutation	SNP	ENST00000335251.6	37	CCDS34061.1	.	.	.	.	.	.	.	.	.	.	C	18.08	3.544587	0.65198	.	.	ENSG00000164066	ENST00000335251	.	.	.	5.54	5.54	0.83059	.	0.060101	0.64402	D	0.000002	T	0.59715	0.2214	L	0.50919	1.6	0.80722	D	1	B	0.29988	0.264	B	0.28465	0.09	T	0.55982	-0.8054	9	0.37606	T	0.19	-13.3719	19.6745	0.95926	0.0:1.0:0.0:0.0	.	809	Q9ULD6	PDZD6_HUMAN	K	809	.	ENSP00000334003:Q809K	Q	+	1	0	INTU	128851573	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.547000	0.67249	2.880000	0.98712	0.650000	0.86243	CAA		0.378	INTU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364147.2		XM_371707	
KAT2B	8850	hgsc.bcm.edu	37	3	20113852	20113853	+	Frame_Shift_Ins	INS	-	-	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr3:20113852_20113853insG	ENST00000263754.4	+	2	786_787	c.331_332insG	c.(331-333)tggfs	p.W111fs	KAT2B_ENST00000426228.1_3'UTR	NM_003884.4	NP_003875.3	Q92831	KAT2B_HUMAN	K(lysine) acetyltransferase 2B	111					cell cycle arrest (GO:0007050)|cellular response to insulin stimulus (GO:0032869)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|histone H3-K9 acetylation (GO:0043970)|internal peptidyl-lysine acetylation (GO:0018393)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|Notch signaling pathway (GO:0007219)|peptidyl-lysine acetylation (GO:0018394)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein acetylation (GO:0006473)|regulation of protein ADP-ribosylation (GO:0010835)|rhythmic process (GO:0048511)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	A band (GO:0031672)|actomyosin (GO:0042641)|Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|I band (GO:0031674)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)	acetyltransferase activity (GO:0016407)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|histone acetyltransferase activity (GO:0004402)|histone deacetylase binding (GO:0042826)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	40						ATGTAATGGCTGGAAAAACCCT	0.455																																																	0																																										SO:0001589	frameshift_variant	8850			U57316	CCDS2634.1	3p24	2011-07-01	2008-07-04	2008-07-04	ENSG00000114166	ENSG00000114166		"""Chromatin-modifying enzymes / K-acetyltransferases"""	8638	protein-coding gene	gene with protein product		602303	"""p300/CBP-associated factor"""	PCAF		8684459, 9722949	Standard	NM_003884		Approved	P/CAF, GCN5, GCN5L	uc003cbq.3	Q92831	OTTHUMG00000130481	ENST00000263754.4:c.333dupG	3.37:g.20113854_20113854dupG	ENSP00000263754:p.Trp111fs		Q6NSK1	Frame_Shift_Ins	INS	ENST00000263754.4	37	CCDS2634.1																																																																																				0.455	KAT2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252880.1		NM_003884	
KIF4B	285643	broad.mit.edu;hgsc.bcm.edu	37	5	154394373	154394373	+	Silent	SNP	C	C	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr5:154394373C>T	ENST00000435029.4	+	1	1114	c.954C>T	c.(952-954)tcC>tcT	p.S318S		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	318	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|plus-end-directed microtubule motor activity (GO:0008574)	p.S318S(2)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(27)|ovary(2)|upper_aerodigestive_tract(1)	58	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CTGCTGACTCCAATCTAGAGG	0.428																																																	2	Substitution - coding silent(2)	kidney(2)											207.0	207.0	207.0					5																	154394373		2203	4300	6503	SO:0001819	synonymous_variant	285643			AF241316	CCDS47324.1	5q33.2	2010-06-22			ENSG00000226650	ENSG00000226650		"""Kinesins"""	6322	protein-coding gene	gene with protein product		609184					Standard	NM_001099293		Approved		uc010jih.1	Q2VIQ3	OTTHUMG00000164143	ENST00000435029.4:c.954C>T	5.37:g.154394373C>T				Silent	SNP	ENST00000435029.4	37	CCDS47324.1																																																																																				0.428	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1			
KLF8	11279	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	56292017	56292017	+	Silent	SNP	T	T	C			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chrX:56292017T>C	ENST00000468660.1	+	3	774	c.486T>C	c.(484-486)acT>acC	p.T162T	KLF8_ENST00000374928.3_Silent_p.T162T	NM_007250.4	NP_009181.2	O95600	KLF8_HUMAN	Kruppel-like factor 8	162					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T162T(1)		kidney(4)|large_intestine(6)|lung(5)|ovary(1)	16						TCATTCACACTATCCCCTCAG	0.512																																																	1	Substitution - coding silent(1)	kidney(1)											110.0	89.0	96.0					X																	56292017		2203	4300	6503	SO:0001819	synonymous_variant	11279			U28282	CCDS14373.1, CCDS55428.1	Xp11.21	2013-01-08			ENSG00000102349	ENSG00000102349		"""Zinc fingers, C2H2-type"", ""Kruppel-like transcription factors"""	6351	protein-coding gene	gene with protein product		300286					Standard	NM_007250		Approved	BKLF3, ZNF741, DXS741	uc004dur.3	O95600	OTTHUMG00000021666	ENST00000468660.1:c.486T>C	X.37:g.56292017T>C			B4DJN3|E7EQQ8|L0R3U8|L0R4U2|Q2M246|Q59GV5|Q5HYQ5|Q5JXP7|Q6MZJ7|Q9UGC4	Silent	SNP	ENST00000468660.1	37	CCDS14373.1																																																																																				0.512	KLF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056887.2		NM_007250	
LAMA2	3908	hgsc.bcm.edu;ucsc.edu	37	6	129419358	129419358	+	Frame_Shift_Del	DEL	C	C	-	rs143680577	byFrequency	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr6:129419358delC	ENST00000421865.2	+	4	486	c.437delC	c.(436-438)tccfs	p.S146fs		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	146	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		GCAGCTAACTCCCCCCGGCCT	0.443																																																	0													109.0	101.0	104.0					6																	129419358		2203	4300	6503	SO:0001589	frameshift_variant	3908			Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.437delC	6.37:g.129419358delC	ENSP00000400365:p.Ser146fs		Q14736|Q5VUM2|Q93022	Frame_Shift_Del	DEL	ENST00000421865.2	37	CCDS5138.1																																																																																				0.443	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			
LOXHD1	125336	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	44114312	44114312	+	Missense_Mutation	SNP	G	G	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr18:44114312G>T	ENST00000398722.4	-	20	3363	c.3364C>A	c.(3364-3366)Ctc>Atc	p.L1122I	LOXHD1_ENST00000582408.1_Missense_Mutation_p.L289I|LOXHD1_ENST00000441551.2_Missense_Mutation_p.L1194I|LOXHD1_ENST00000441893.2_Missense_Mutation_p.L333I|LOXHD1_ENST00000300591.6_Missense_Mutation_p.L289I|LOXHD1_ENST00000536736.1_Missense_Mutation_p.L1400I|LOXHD1_ENST00000579038.1_Missense_Mutation_p.L193I			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	1122	PLAT 8. {ECO:0000255|PROSITE- ProRule:PRU00152}.				calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|sensory perception of sound (GO:0007605)	membrane (GO:0016020)|stereocilium (GO:0032420)	calcium channel activity (GO:0005262)	p.L1122I(1)|p.L1400I(1)		NS(3)|autonomic_ganglia(1)|breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|pancreas(1)|prostate(4)|skin(4)|stomach(1)	36						TTATCCGGGAGGAGCCTGCGG	0.498																																																	2	Substitution - Missense(2)	kidney(2)											135.0	123.0	127.0					18																	44114312		692	1591	2283	SO:0001583	missense	125336			AK057232	CCDS45861.1, CCDS45862.1, CCDS54184.1	18q21.1	2009-09-11			ENSG00000167210	ENSG00000167210			26521	protein-coding gene	gene with protein product		613072	"""deafness, autosomal recessive 77"""	DFNB77		19732867	Standard	NM_144612		Approved	FLJ32670, LH2D1	uc010xcw.1	Q8IVV2	OTTHUMG00000132644	ENST00000398722.4:c.3364C>A	18.37:g.44114312G>T	ENSP00000381707:p.Leu1122Ile		B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Missense_Mutation	SNP	ENST00000398722.4	37		.	.	.	.	.	.	.	.	.	.	G	13.75	2.329979	0.41297	.	.	ENSG00000167210	ENST00000300591;ENST00000398722;ENST00000536736;ENST00000441893;ENST00000335730;ENST00000536111	T;T;T;T;T	0.65549	1.54;1.54;1.54;1.54;-0.16	5.27	4.39	0.52855	Lipoxygenase, LH2 (3);Lipase/lipooxygenase, PLAT/LH2 (1);	0.000000	0.64402	D	0.000001	T	0.75004	0.3791	M	0.62209	1.925	0.43321	D	0.995342	P;D;D;D	0.65815	0.93;0.992;0.988;0.995	D;D;D;D	0.83275	0.939;0.986;0.992;0.996	T	0.75741	-0.3211	10	0.51188	T	0.08	.	13.262	0.60111	0.0768:0.0:0.9232:0.0	.	1400;333;1122;1122	F5GZB4;F8WA52;Q8IVV2-2;Q8IVV2	.;.;.;LOXH1_HUMAN	I	289;1122;1400;333;1122;302	ENSP00000300591:L289I;ENSP00000381707:L1122I;ENSP00000444586:L1400I;ENSP00000409062:L333I;ENSP00000440060:L302I	ENSP00000300591:L289I	L	-	1	0	LOXHD1	42368310	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	3.448000	0.52943	2.446000	0.82766	0.561000	0.74099	CTC		0.498	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding			NM_144612	
LTBP4	8425	hgsc.bcm.edu;ucsc.edu	37	19	41129556	41129556	+	Frame_Shift_Del	DEL	G	G	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr19:41129556delG	ENST00000308370.7	+	29	3802	c.3802delG	c.(3802-3804)gtgfs	p.V1268fs	LTBP4_ENST00000545697.1_Frame_Shift_Del_p.V636fs|LTBP4_ENST00000396819.3_Frame_Shift_Del_p.V1201fs|LTBP4_ENST00000204005.9_Frame_Shift_Del_p.V1231fs|LTBP4_ENST00000243562.9_3'UTR|LTBP4_ENST00000602240.1_3'UTR	NM_001042544.1	NP_001036009.1	Q8N2S1	LTBP4_HUMAN	latent transforming growth factor beta binding protein 4	1269	EGF-like 13; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|growth hormone secretion (GO:0030252)|multicellular organismal development (GO:0007275)|protein folding (GO:0006457)|regulation of cell differentiation (GO:0045595)|regulation of cell growth (GO:0001558)|regulation of proteolysis (GO:0030162)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|integrin binding (GO:0005178)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			central_nervous_system(1)	1			Lung(22;0.000158)|LUSC - Lung squamous cell carcinoma(20;0.000384)			CAAGAGTGGCGTGTGTGTGAA	0.597																																																	0													85.0	91.0	89.0					19																	41129556		2106	4230	6336	SO:0001589	frameshift_variant	8425			Y13622	CCDS74368.1, CCDS74369.1, CCDS74370.1	19q13.1-q13.2	2011-10-20				ENSG00000090006		"""Latent transforming growth factor, beta binding proteins"""	6717	protein-coding gene	gene with protein product		604710				9660815, 9271198	Standard	NM_003573		Approved	LTBP-4, LTBP-4L, FLJ46318, FLJ90018	uc002ooh.1	Q8N2S1		ENST00000308370.7:c.3802delG	19.37:g.41129556delG	ENSP00000311905:p.Val1268fs		O00508|O75412|O75413	Frame_Shift_Del	DEL	ENST00000308370.7	37																																																																																					0.597	LTBP4-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding			NM_003573	
MUC4	4585	broad.mit.edu	37	3	195505839	195505839	+	Silent	SNP	A	A	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr3:195505839A>T	ENST00000463781.3	-	2	13071	c.12612T>A	c.(12610-12612)ggT>ggA	p.G4204G	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.G4204G	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.G4204G(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)		GGGTGGCGTGACCTGTGGATG	0.597																																																	2	Substitution - coding silent(2)	kidney(2)											16.0	14.0	14.0					3																	195505839		689	1580	2269	SO:0001819	synonymous_variant	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12612T>A	3.37:g.195505839A>T			O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																				0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MUC4	4585	broad.mit.edu	37	3	195506839	195506839	+	Missense_Mutation	SNP	G	G	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr3:195506839G>T	ENST00000463781.3	-	2	12071	c.11612C>A	c.(11611-11613)aCc>aAc	p.T3871N	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T3871N	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.T3871N(1)		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)		AGGAAGAGGGGTGGCGTGACC	0.592																																																	1	Substitution - Missense(1)	kidney(1)											12.0	11.0	11.0					3																	195506839		580	1535	2115	SO:0001583	missense	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.11612C>A	3.37:g.195506839G>T	ENSP00000417498:p.Thr3871Asn		O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	4.087	0.014141	0.07959	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33216	1.43;1.42	.	.	.	.	.	.	.	.	T	0.17916	0.0430	N	0.19112	0.55	0.09310	N	0.999995	P	0.47604	0.898	B	0.42959	0.403	T	0.13629	-1.0502	7	.	.	.	.	5.844	0.18652	9.0E-4:0.0:0.9991:0.0	.	3743	E7ESK3	.	N	3871	ENSP00000417498:T3871N;ENSP00000420243:T3871N	.	T	-	2	0	MUC4	196991618	0.013000	0.17824	0.058000	0.19502	0.059000	0.15707	0.788000	0.26872	0.064000	0.16427	0.064000	0.15345	ACC		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MUC4	4585	broad.mit.edu	37	3	195515290	195515290	+	Missense_Mutation	SNP	C	C	G	rs78535324		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr3:195515290C>G	ENST00000463781.3	-	2	3620	c.3161G>C	c.(3160-3162)aGc>aCc	p.S1054T	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S1054T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	484					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.S1054T(4)		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)		AAGAGGGGTGCTGTCACCTGT	0.572																																																	4	Substitution - Missense(4)	NS(2)|kidney(1)|endometrium(1)											16.0	11.0	13.0					3																	195515290		689	1583	2272	SO:0001583	missense	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.3161G>C	3.37:g.195515290C>G	ENSP00000417498:p.Ser1054Thr		O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	1.980	-0.434268	0.04669	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30714	1.53;1.52	1.0	-2.01	0.07410	.	.	.	.	.	T	0.12433	0.0302	N	0.08118	0	0.09310	N	1	B	0.13594	0.008	B	0.08055	0.003	T	0.20706	-1.0267	8	.	.	.	.	5.9202	0.19078	0.1903:0.2487:0.561:0.0	.	1054	E7ESK3	.	T	1054	ENSP00000417498:S1054T;ENSP00000420243:S1054T	.	S	-	2	0	MUC4	196999685	.	.	0.001000	0.08648	0.010000	0.07245	.	.	-2.658000	0.00420	-2.332000	0.00249	AGC		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MYCBP2	23077	hgsc.bcm.edu	37	13	77714290	77714290	+	Frame_Shift_Del	DEL	T	T	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr13:77714290delT	ENST00000544440.2	-	51	7313	c.7296delA	c.(7294-7296)aaafs	p.K2432fs	MYCBP2_ENST00000360084.5_5'UTR|MYCBP2_ENST00000407578.2_Frame_Shift_Del_p.K2470fs|MYCBP2_ENST00000357337.6_Frame_Shift_Del_p.K2432fs					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TGGCCACAAATTTTCGAACCT	0.423																																																	0													62.0	60.0	61.0					13																	77714290		2203	4300	6503	SO:0001589	frameshift_variant	23077			AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"""MYC binding protein 2"""			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.7296delA	13.37:g.77714290delT	ENSP00000444596:p.Lys2432fs			Frame_Shift_Del	DEL	ENST00000544440.2	37																																																																																					0.423	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1		NM_015057	
NCKAP5	344148	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	133540313	133540313	+	Silent	SNP	G	G	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr2:133540313G>A	ENST00000409261.1	-	14	4444	c.4071C>T	c.(4069-4071)agC>agT	p.S1357S	NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000473859.1_5'Flank|NCKAP5_ENST00000317721.6_Silent_p.S1357S	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1357								p.S1357S(1)		NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						GACTGCTGAAGCTGCCTGAGC	0.617																																																	1	Substitution - coding silent(1)	kidney(1)											40.0	40.0	40.0					2																	133540313		1908	4123	6031	SO:0001819	synonymous_variant	344148			AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"""Nck associated protein 5"", ""peripheral clock protein"""	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.4071C>T	2.37:g.133540313G>A			B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Silent	SNP	ENST00000409261.1	37	CCDS46418.1																																																																																				0.617	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1		NM_207481	
NOV	4856	broad.mit.edu;ucsc.edu	37	8	120435157	120435157	+	Missense_Mutation	SNP	T	T	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr8:120435157T>A	ENST00000259526.3	+	5	1086	c.859T>A	c.(859-861)Tac>Aac	p.Y287N	RP11-775B15.2_ENST00000519786.1_RNA	NM_002514.3	NP_002505.1	Q9UIW2	PLXA1_HUMAN	nephroblastoma overexpressed	0	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)	p.Y287N(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|skin(3)	21	all_cancers(13;3.84e-26)|Lung NSC(37;1.19e-08)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000507)			CCTGCACACCTACAAGCCCAG	0.512																																																	1	Substitution - Missense(1)	kidney(1)											86.0	86.0	86.0					8																	120435157		2203	4300	6503	SO:0001583	missense	4856			X96584	CCDS6328.1	8q24.12	2012-02-27	2012-02-27		ENSG00000136999	ENSG00000136999			7885	protein-coding gene	gene with protein product		164958	"""nephroblastoma overexpressed gene"""			1334251	Standard	NM_002514		Approved	IGFBP9, CCN3	uc003yoq.2	P48745	OTTHUMG00000164984	ENST00000259526.3:c.859T>A	8.37:g.120435157T>A	ENSP00000259526:p.Tyr287Asn			Missense_Mutation	SNP	ENST00000259526.3	37	CCDS6328.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.268550	0.80469	.	.	ENSG00000136999	ENST00000259526	T	0.51325	0.71	5.85	5.85	0.93711	Cystine knot (1);Cystine knot, C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.74291	0.3697	M	0.88979	2.995	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	T	0.79895	-0.1610	10	0.87932	D	0	-34.3665	16.2268	0.82300	0.0:0.0:0.0:1.0	.	287	P48745	NOV_HUMAN	N	287	ENSP00000259526:Y287N	ENSP00000259526:Y287N	Y	+	1	0	NOV	120504338	1.000000	0.71417	0.995000	0.50966	0.482000	0.33219	8.040000	0.89188	2.235000	0.73313	0.528000	0.53228	TAC		0.512	NOV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381301.1		NM_002514	
PCDH7	5099	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	30724917	30724917	+	Missense_Mutation	SNP	G	G	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr4:30724917G>T	ENST00000361762.2	+	1	2881	c.1873G>T	c.(1873-1875)Gtg>Ttg	p.V625L	PCDH7_ENST00000543491.1_Missense_Mutation_p.V625L	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	625	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V625L(1)|p.V578L(1)		NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						CAGCACTACGGTGATTGTGCA	0.493																																																	2	Substitution - Missense(2)	kidney(2)											96.0	101.0	99.0					4																	30724917		2203	4300	6503	SO:0001583	missense	5099			AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"""Cadherins / Protocadherins : Non-clustered"""	8659	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 120"""	602988	"""BH-protocadherin (brain-heart)"""			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000361762.2:c.1873G>T	4.37:g.30724917G>T	ENSP00000355243:p.Val625Leu		O60246|O60247|Q4W5C4	Missense_Mutation	SNP	ENST00000361762.2	37	CCDS33971.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.1|20.1	3.939966|3.939966	0.73557|0.73557	.|.	.|.	ENSG00000169851|ENSG00000169851	ENST00000511884|ENST00000361762;ENST00000543491;ENST00000333135	.|T;T	.|0.25250	.|1.81;1.81	5.37|5.37	5.37|5.37	0.77165|0.77165	.|Cadherin (5);Cadherin-like (1);	.|.	.|.	.|.	.|.	T|T	0.43678|0.43678	0.1258|0.1258	L|L	0.36672|0.36672	1.1|1.1	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.63046	.|0.992;0.992;0.988	.|D;D;D	.|0.69824	.|0.943;0.943;0.966	T|T	0.29488|0.29488	-1.0010|-1.0010	5|9	.|0.87932	.|D	.|0	.|.	19.2965|19.2965	0.94124|0.94124	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|625;578;625	.|F5GWJ1;O60245-3;O60245	.|.;.;PCDH7_HUMAN	V|L	314|625;625;578	.|ENSP00000355243:V625L;ENSP00000441802:V625L	.|ENSP00000330302:V578L	G|V	+|+	2|1	0|0	PCDH7|PCDH7	30334015|30334015	1.000000|1.000000	0.71417|0.71417	0.976000|0.976000	0.42696|0.42696	0.958000|0.958000	0.62258|0.62258	9.657000|9.657000	0.98554|0.98554	2.793000|2.793000	0.96121|0.96121	0.655000|0.655000	0.94253|0.94253	GGT|GTG		0.493	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1		NM_032457, NM_002589	
PCNX	22990	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	71514655	71514655	+	Missense_Mutation	SNP	A	A	C			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr14:71514655A>C	ENST00000304743.2	+	22	4738	c.4292A>C	c.(4291-4293)gAg>gCg	p.E1431A	PCNX_ENST00000238570.5_Missense_Mutation_p.E1431A|PCNX_ENST00000439984.3_Missense_Mutation_p.E1320A	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1431						integral component of membrane (GO:0016021)		p.E1431A(1)		NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		GCTTTTTCAGAGACCATGCTG	0.358																																																	1	Substitution - Missense(1)	kidney(1)											149.0	136.0	141.0					14																	71514655		2202	4299	6501	SO:0001583	missense	22990			AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"""pecanex-like 1 (Drosophila)"""	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.4292A>C	14.37:g.71514655A>C	ENSP00000304192:p.Glu1431Ala		B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	37	CCDS9806.1	.	.	.	.	.	.	.	.	.	.	A	19.79	3.892657	0.72524	.	.	ENSG00000100731	ENST00000304743;ENST00000238570;ENST00000439984	T;T;T	0.13420	2.99;2.94;2.59	5.41	5.41	0.78517	.	0.098661	0.64402	D	0.000002	T	0.43211	0.1237	M	0.86343	2.81	0.80722	D	1	D;D;D	0.71674	0.998;0.987;0.997	D;P;D	0.78314	0.991;0.798;0.98	T	0.46275	-0.9203	10	0.48119	T	0.1	.	15.7411	0.77899	1.0:0.0:0.0:0.0	.	1431;1320;1431	Q96RV3-3;B2RTR6;Q96RV3	.;.;PCX1_HUMAN	A	1431;1431;1320	ENSP00000304192:E1431A;ENSP00000238570:E1431A;ENSP00000396617:E1320A	ENSP00000238570:E1431A	E	+	2	0	PCNX	70584408	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.287000	0.95975	2.171000	0.68590	0.533000	0.62120	GAG		0.358	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1		NM_014982	
PIK3CG	5294	broad.mit.edu;ucsc.edu	37	7	106509653	106509653	+	Missense_Mutation	SNP	C	C	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr7:106509653C>A	ENST00000359195.3	+	2	1957	c.1647C>A	c.(1645-1647)aaC>aaA	p.N549K	PIK3CG_ENST00000440650.2_Missense_Mutation_p.N549K|PIK3CG_ENST00000496166.1_Missense_Mutation_p.N549K	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	549	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.N549K(1)		breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						AAATGCCCAACCAGCTTCGCA	0.532																																																	1	Substitution - Missense(1)	kidney(1)											78.0	73.0	75.0					7																	106509653		2203	4300	6503	SO:0001583	missense	5294				CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"""phosphoinositide-3-kinase, catalytic, gamma polypeptide"""				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.1647C>A	7.37:g.106509653C>A	ENSP00000352121:p.Asn549Lys		A4D0Q6|Q8IV23|Q9BZC8	Missense_Mutation	SNP	ENST00000359195.3	37	CCDS5739.1	.	.	.	.	.	.	.	.	.	.	C	12.23	1.876281	0.33162	.	.	ENSG00000105851	ENST00000440650;ENST00000496166;ENST00000359195	T;T;T	0.62639	0.01;0.01;0.01	5.81	0.319	0.15873	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.082018	0.85682	D	0.000000	T	0.43656	0.1257	L	0.27053	0.805	0.58432	D	0.999998	B	0.30236	0.274	B	0.34346	0.18	T	0.23726	-1.0180	10	0.06625	T	0.88	-38.894	12.164	0.54119	0.0:0.6852:0.0:0.3148	.	549	P48736	PK3CG_HUMAN	K	549	ENSP00000392258:N549K;ENSP00000419260:N549K;ENSP00000352121:N549K	ENSP00000352121:N549K	N	+	3	2	PIK3CG	106296889	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	1.308000	0.33528	0.106000	0.17784	-0.136000	0.14681	AAC		0.532	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1			
PITPNB	23760	hgsc.bcm.edu;ucsc.edu	37	22	28256199	28256199	+	Frame_Shift_Del	DEL	G	G	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr22:28256199delG	ENST00000335272.5	-	9	641	c.565delC	c.(565-567)cagfs	p.Q189fs	PITPNB_ENST00000455418.3_Frame_Shift_Del_p.Q191fs|PITPNB_ENST00000320996.10_Frame_Shift_Del_p.Q189fs	NM_012399.3	NP_036531.1	P48739	PIPNB_HUMAN	phosphatidylinositol transfer protein, beta	189					glycerophospholipid biosynthetic process (GO:0046474)|in utero embryonic development (GO:0001701)|lipid metabolic process (GO:0006629)|phospholipid metabolic process (GO:0006644)|phospholipid transport (GO:0015914)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)	lipid binding (GO:0008289)			large_intestine(4)|lung(3)|skin(1)	8						GCACACATCTGGGGACAGTCA	0.368																																																	0													75.0	74.0	74.0					22																	28256199		2203	4300	6503	SO:0001589	frameshift_variant	23760			D30037	CCDS13842.1, CCDS63433.1	22q12.1	2006-12-15			ENSG00000180957	ENSG00000180957			9002	protein-coding gene	gene with protein product		606876				10591208	Standard	NM_012399		Approved	VIB1B	uc003adk.3	P48739	OTTHUMG00000150976	ENST00000335272.5:c.565delC	22.37:g.28256199delG	ENSP00000334738:p.Gln189fs		B3KYB8|B7Z7Q0|Q8N5W1	Frame_Shift_Del	DEL	ENST00000335272.5	37	CCDS13842.1																																																																																				0.368	PITPNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320740.1			
PLXNA4	91584	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	131982903	131982903	+	Missense_Mutation	SNP	C	C	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr7:131982903C>A	ENST00000359827.3	-	4	2412	c.1450G>T	c.(1450-1452)Gat>Tat	p.D484Y	PLXNA4_ENST00000321063.4_Missense_Mutation_p.D484Y			Q9HCM2	PLXA4_HUMAN	plexin A4	484	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.D484Y(2)		NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						AAGGCCATATCCCGGAGGACT	0.577																																																	2	Substitution - Missense(2)	kidney(2)											73.0	79.0	77.0					7																	131982903		1956	4141	6097	SO:0001583	missense	91584			AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.1450G>T	7.37:g.131982903C>A	ENSP00000352882:p.Asp484Tyr		A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.901007	0.92035	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.11495	2.77;2.77	6.04	6.04	0.98038	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.42381	0.1200	M	0.87617	2.895	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.31613	-0.9937	10	0.62326	D	0.03	.	20.5792	0.99380	0.0:1.0:0.0:0.0	.	484	Q9HCM2	PLXA4_HUMAN	Y	484	ENSP00000323194:D484Y;ENSP00000352882:D484Y	ENSP00000323194:D484Y	D	-	1	0	PLXNA4	131633443	1.000000	0.71417	0.996000	0.52242	0.978000	0.69477	7.222000	0.78025	2.873000	0.98535	0.561000	0.74099	GAT		0.577	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2		NM_181775	
PRPF19	27339	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	60671329	60671329	+	Silent	SNP	A	A	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr11:60671329A>T	ENST00000227524.4	-	2	229	c.24T>A	c.(22-24)tcT>tcA	p.S8S	RP11-881M11.2_ENST00000544421.1_RNA	NM_014502.4	NP_055317.1			pre-mRNA processing factor 19									p.S8S(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	22						GCACTTCGTTAGAGACTGTAG	0.512																																																	1	Substitution - coding silent(1)	kidney(1)											76.0	73.0	74.0					11																	60671329		2203	4299	6502	SO:0001819	synonymous_variant	27339			BC018698	CCDS7995.1	11q12.2	2014-05-20	2013-06-10	2005-04-01	ENSG00000110107	ENSG00000110107		"""WD repeat domain containing"", ""U-box domain containing"""	17896	protein-coding gene	gene with protein product	"""nuclear matrix protein NMP200 related to splicing factor PRP19"", ""psoralen 4"""	608330	"""PRP19/PSO4 homolog (S. cerevisiae)"", ""PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae)"""	PRP19		12960389	Standard	NM_014502		Approved	UBOX4, NMP200, PSO4, hPSO4	uc001nqf.3	Q9UMS4	OTTHUMG00000167798	ENST00000227524.4:c.24T>A	11.37:g.60671329A>T				Silent	SNP	ENST00000227524.4	37	CCDS7995.1																																																																																				0.512	PRPF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396334.1		NM_014502	
PTPRT	11122	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	40713330	40713330	+	Silent	SNP	G	G	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr20:40713330G>T	ENST00000373187.1	-	29	4127	c.4128C>A	c.(4126-4128)gtC>gtA	p.V1376V	PTPRT_ENST00000373193.3_Silent_p.V1379V|PTPRT_ENST00000356100.2_Silent_p.V1385V|PTPRT_ENST00000373184.1_Silent_p.V1386V|PTPRT_ENST00000373201.1_Silent_p.V1366V|PTPRT_ENST00000373198.4_Silent_p.V1395V|PTPRT_ENST00000373190.1_Silent_p.V1375V			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	1376	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)	p.V1398V(1)		NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				ACAGGCAGTGGACCACAGTAC	0.607																																																	1	Substitution - coding silent(1)	kidney(1)											59.0	63.0	62.0					20																	40713330		2090	4199	6289	SO:0001819	synonymous_variant	11122			AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.4128C>A	20.37:g.40713330G>T			A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Silent	SNP	ENST00000373187.1	37	CCDS42874.1																																																																																				0.607	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			
RAPGEF3	10411	broad.mit.edu;ucsc.edu	37	12	48137448	48137448	+	Missense_Mutation	SNP	T	T	C	rs368286046	byFrequency	TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr12:48137448T>C	ENST00000449771.2	-	18	1778	c.1690A>G	c.(1690-1692)Atc>Gtc	p.I564V	RAPGEF3_ENST00000405493.2_Missense_Mutation_p.I522V|RAPGEF3_ENST00000549151.1_Missense_Mutation_p.I522V|RAPGEF3_ENST00000389212.3_Missense_Mutation_p.I564V|RP1-197B17.3_ENST00000547799.1_lincRNA|RAPGEF3_ENST00000548919.1_Intron|RAPGEF3_ENST00000171000.4_Missense_Mutation_p.I522V			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	564					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|cell proliferation (GO:0008283)|cellular response to cAMP (GO:0071320)|energy reserve metabolic process (GO:0006112)|establishment of endothelial barrier (GO:0061028)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of stress fiber assembly (GO:0051496)|Rap protein signal transduction (GO:0032486)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)	p.I522V(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|skin(7)	25	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)		GGCCGGCAGATGTCATAGGGG	0.612													T|||	2	0.000399361	0.0015	0.0	5008	,	,		20152	0.0		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	kidney(1)						T	VAL/ILE,VAL/ILE,VAL/ILE	1,4405	2.1+/-5.4	0,1,2202	56.0	48.0	51.0		1690,1564,1564	4.1	1.0	12		51	0,8600		0,0,4300	no	missense,missense,missense	RAPGEF3	NM_001098531.2,NM_001098532.2,NM_006105.5	29,29,29	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign,benign,benign	564/924,522/882,522/882	48137448	1,13005	2203	4300	6503	SO:0001583	missense	10411			AK092448	CCDS31784.1, CCDS41775.1	12q13.1	2006-04-12	2004-03-26		ENSG00000079337	ENSG00000079337			16629	protein-coding gene	gene with protein product	"""exchange protein directly activated by cAMP 1"""	606057	"""RAP guanine-nucleotide-exchange factor (GEF) 3"""			10777494, 9856955	Standard	NM_001098531		Approved	cAMP-GEFI, EPAC, bcm910	uc001rpz.4	O95398	OTTHUMG00000133667	ENST00000449771.2:c.1690A>G	12.37:g.48137448T>C	ENSP00000395708:p.Ile564Val		A8K2G5|E7EQC8|O95634|Q8WVN0	Missense_Mutation	SNP	ENST00000449771.2	37	CCDS41775.1	.	.	.	.	.	.	.	.	.	.	T	1.034	-0.681057	0.03353	2.27E-4	0.0	ENSG00000079337	ENST00000405493;ENST00000449771;ENST00000541821;ENST00000549151;ENST00000171000;ENST00000389211;ENST00000389212	T;T;T;T;T	0.61627	0.12;0.09;0.12;0.12;0.09	5.27	4.12	0.48240	Ras guanine nucleotide exchange factor, domain (1);	0.054462	0.64402	D	0.000001	T	0.34978	0.0916	N	0.16656	0.425	0.42039	D	0.991064	P	0.45044	0.849	B	0.42386	0.386	T	0.41142	-0.9525	10	0.02654	T	1	.	8.833	0.35096	0.0:0.0892:0.0:0.9108	.	564	O95398	RPGF3_HUMAN	V	522;564;211;522;522;522;564	ENSP00000384521:I522V;ENSP00000395708:I564V;ENSP00000448619:I522V;ENSP00000171000:I522V;ENSP00000373864:I564V	ENSP00000171000:I522V	I	-	1	0	RAPGEF3	46423715	1.000000	0.71417	1.000000	0.80357	0.589000	0.36550	1.900000	0.39828	2.136000	0.66102	0.533000	0.62120	ATC		0.612	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257848.1		NM_006105	
RASA1	5921	broad.mit.edu;hgsc.bcm.edu	37	5	86564707	86564707	+	Missense_Mutation	SNP	G	G	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr5:86564707G>A	ENST00000274376.6	+	1	1003	c.439G>A	c.(439-441)Ggg>Agg	p.G147R	RASA1_ENST00000456692.2_5'Flank|RASA1_ENST00000506290.1_5'Flank|RASA1_ENST00000512763.1_5'Flank	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	147					blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)	p.G147R(1)		NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		GCCCCCTTTGGGGGCGGGCCT	0.622																																																	1	Substitution - Missense(1)	kidney(1)											26.0	34.0	32.0					5																	86564707		2185	4272	6457	SO:0001583	missense	5921				CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	9871	protein-coding gene	gene with protein product	"""capillary malformation-arteriovenous malformation"""	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.439G>A	5.37:g.86564707G>A	ENSP00000274376:p.Gly147Arg		B2R6W3|Q9UDI1	Missense_Mutation	SNP	ENST00000274376.6	37	CCDS34200.1	.	.	.	.	.	.	.	.	.	.	G	13.77	2.336601	0.41398	.	.	ENSG00000145715	ENST00000274376;ENST00000534133	T	0.72394	-0.65	4.07	3.2	0.36748	.	1.434360	0.04345	N	0.354667	T	0.51924	0.1703	N	0.08118	0	0.80722	D	1	B;B	0.34015	0.435;0.069	B;B	0.27170	0.077;0.023	T	0.30707	-0.9969	10	0.59425	D	0.04	.	9.0188	0.36186	0.1061:0.0:0.8939:0.0	.	180;147	Q59GK3;P20936	.;RASA1_HUMAN	R	147;180	ENSP00000274376:G147R	ENSP00000274376:G147R	G	+	1	0	RASA1	86600463	1.000000	0.71417	0.992000	0.48379	0.782000	0.44232	2.977000	0.49297	0.828000	0.34709	0.561000	0.74099	GGG		0.622	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1		NM_002890	
RGL1	23179	broad.mit.edu;ucsc.edu	37	1	183891372	183891372	+	Missense_Mutation	SNP	A	A	G			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr1:183891372A>G	ENST00000360851.3	+	17	2199	c.2021A>G	c.(2020-2022)aAa>aGa	p.K674R	RGL1_ENST00000304685.4_Missense_Mutation_p.K709R|RGL1_ENST00000539189.1_Missense_Mutation_p.K645R|RGL1_ENST00000536277.1_Missense_Mutation_p.K672R			Q9NZL6	RGL1_HUMAN	ral guanine nucleotide dissociation stimulator-like 1	674	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				cellular lipid metabolic process (GO:0044255)|positive regulation of Ral GTPase activity (GO:0032852)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)	p.K709R(1)		breast(5)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(17)|ovary(4)|prostate(3)|stomach(1)	51						AGCCAGGATAAAACCCCCGCT	0.522											OREG0014047	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - Missense(1)	kidney(1)											73.0	66.0	68.0					1																	183891372		2203	4300	6503	SO:0001583	missense	23179			AF186780	CCDS1359.1, CCDS72992.1	1q25.2	2008-02-05			ENSG00000143344	ENSG00000143344			30281	protein-coding gene	gene with protein product		605667				10760592, 10231032	Standard	XM_005245010		Approved	RGL	uc001gqm.3	Q9NZL6	OTTHUMG00000035328	ENST00000360851.3:c.2021A>G	1.37:g.183891372A>G	ENSP00000354097:p.Lys674Arg	1987	Q5SXQ2|Q5SXQ6|Q9HBY3|Q9HBY4|Q9NZL5|Q9UG43|Q9Y2G6	Missense_Mutation	SNP	ENST00000360851.3	37		.	.	.	.	.	.	.	.	.	.	A	15.12	2.738820	0.49045	.	.	ENSG00000143344	ENST00000304685;ENST00000367531;ENST00000536277;ENST00000360851;ENST00000539189	T;T;T;T;T	0.16897	2.31;2.31;2.31;2.31;2.31	5.29	5.29	0.74685	Ras-association (3);	0.000000	0.85682	D	0.000000	T	0.33265	0.0857	L	0.45698	1.435	0.58432	D	0.999997	B;D;D;D	0.69078	0.05;0.997;0.997;0.997	B;D;D;D	0.80764	0.047;0.994;0.994;0.994	T	0.02385	-1.1167	10	0.22706	T	0.39	.	15.1668	0.72833	1.0:0.0:0.0:0.0	.	645;672;674;709	F5H6U6;B7Z2W5;Q9NZL6;Q5SXQ6	.;.;RGL1_HUMAN;.	R	709;709;672;674;645	ENSP00000303192:K709R;ENSP00000356501:K709R;ENSP00000438662:K672R;ENSP00000354097:K674R;ENSP00000437355:K645R	ENSP00000303192:K709R	K	+	2	0	RGL1	182157995	1.000000	0.71417	0.993000	0.49108	0.238000	0.25445	5.882000	0.69714	2.112000	0.64535	0.533000	0.62120	AAA		0.522	RGL1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000085742.1		NM_015149	
SEC23A	10484	hgsc.bcm.edu;ucsc.edu	37	14	39502467	39502467	+	Frame_Shift_Del	DEL	T	T	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr14:39502467delT	ENST00000307712.6	-	20	2791	c.2274delA	c.(2272-2274)aaafs	p.K758fs	SEC23A_ENST00000536508.1_Frame_Shift_Del_p.K656fs|SEC23A_ENST00000537403.1_Frame_Shift_Del_p.K556fs|SEC23A_ENST00000545328.2_Frame_Shift_Del_p.K729fs	NM_006364.2	NP_006355.2	Q15436	SC23A_HUMAN	Sec23 homolog A (S. cerevisiae)	758					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			kidney(2)|large_intestine(3)|liver(1)|lung(11)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(1)	23	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)		ACACAGCAAGTTTCTTCAAGT	0.313																																																	0													103.0	108.0	106.0					14																	39502467		2203	4299	6502	SO:0001589	frameshift_variant	10484			X97064	CCDS9668.1	14q21.1	2008-05-14	2001-11-28		ENSG00000100934	ENSG00000100934			10701	protein-coding gene	gene with protein product		610511	"""Sec23 (S. cerevisiae) homolog A"""			8898360, 10329445	Standard	NM_006364		Approved		uc001wup.1	Q15436	OTTHUMG00000028812	ENST00000307712.6:c.2274delA	14.37:g.39502467delT	ENSP00000306881:p.Lys758fs		B2R5P4|B3KXI2|Q8NE16	Frame_Shift_Del	DEL	ENST00000307712.6	37	CCDS9668.1																																																																																				0.313	SEC23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276728.2			
SFTPD	6441	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	81702178	81702178	+	Silent	SNP	G	G	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr10:81702178G>A	ENST00000372292.3	-	4	439	c.399C>T	c.(397-399)ggC>ggT	p.G133G		NM_003019.4	NP_003010.4	P35247	SFTPD_HUMAN	surfactant protein D	133	Collagen-like.				defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|lung alveolus development (GO:0048286)|macrophage chemotaxis (GO:0048246)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of phagocytosis (GO:0050766)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|regulation of cytokine production (GO:0001817)|respiratory gaseous exchange (GO:0007585)|surfactant homeostasis (GO:0043129)	collagen trimer (GO:0005581)|endocytic vesicle (GO:0030139)|extracellular region (GO:0005576)|lysosome (GO:0005764)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)	p.G133G(1)		endometrium(1)|kidney(3)|large_intestine(5)|lung(3)|skin(4)|urinary_tract(1)	17	Breast(12;0.000615)|Prostate(51;0.0095)|all_epithelial(25;0.027)		Epithelial(14;0.0244)|all cancers(16;0.0558)|Colorectal(32;0.109)			GGCCTGGCTTGCCCTGAGGTC	0.597																																																	1	Substitution - coding silent(1)	kidney(1)											93.0	84.0	87.0					10																	81702178		2203	4300	6503	SO:0001819	synonymous_variant	6441			L05485	CCDS7362.1	10q22.2-q23.1	2012-11-02	2008-08-26		ENSG00000133661	ENSG00000133661		"""Collectins"""	10803	protein-coding gene	gene with protein product		178635	"""surfactant, pulmonary-associated protein D"""	SFTP4		1898081, 1339284	Standard	NM_003019		Approved	SP-D, COLEC7	uc001kbh.3	P35247	OTTHUMG00000018590	ENST00000372292.3:c.399C>T	10.37:g.81702178G>A			Q5T0M3|Q6FH08|Q86YK9|Q8TCD8|Q9UCJ2|Q9UCJ3	Silent	SNP	ENST00000372292.3	37	CCDS7362.1																																																																																				0.597	SFTPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049011.1			
SLC9A4	389015	broad.mit.edu;ucsc.edu	37	2	103120043	103120043	+	Missense_Mutation	SNP	T	T	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr2:103120043T>A	ENST00000295269.4	+	3	1314	c.857T>A	c.(856-858)tTt>tAt	p.F286Y		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	286					epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)	p.F286Y(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						GTTTTTGGATTTATTTCTGCA	0.413																																																	1	Substitution - Missense(1)	kidney(1)											324.0	303.0	310.0					2																	103120043		2203	4300	6503	SO:0001583	missense	389015				CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"""Solute carriers"""	11077	protein-coding gene	gene with protein product		600531	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 4"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 4"""			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.857T>A	2.37:g.103120043T>A	ENSP00000295269:p.Phe286Tyr		Q69YK0	Missense_Mutation	SNP	ENST00000295269.4	37	CCDS33264.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.089207	0.76756	.	.	ENSG00000180251	ENST00000295269	T	0.14893	2.47	5.61	5.61	0.85477	Cation/H+ exchanger (1);	0.047345	0.85682	D	0.000000	T	0.31389	0.0795	M	0.62088	1.915	0.58432	D	0.999997	P	0.52577	0.954	P	0.52031	0.688	T	0.01739	-1.1284	10	0.49607	T	0.09	.	16.1025	0.81194	0.0:0.0:0.0:1.0	.	286	Q6AI14	SL9A4_HUMAN	Y	286	ENSP00000295269:F286Y	ENSP00000295269:F286Y	F	+	2	0	SLC9A4	102486475	1.000000	0.71417	0.998000	0.56505	0.112000	0.19704	7.997000	0.88414	2.254000	0.74563	0.533000	0.62120	TTT		0.413	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1		NM_001011552.3	
SPTA1	6708	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	158618345	158618345	+	Missense_Mutation	SNP	C	C	T	rs148714399		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr1:158618345C>T	ENST00000368147.4	-	26	3848	c.3668G>A	c.(3667-3669)cGa>cAa	p.R1223Q		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1223					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.R1223Q(1)		NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CTCATGCCGTCGCTGAAGAGC	0.507													C|||	1	0.000199681	0.0	0.0	5008	,	,		13940	0.001		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	kidney(1)						C	GLN/ARG	1,3899		0,1,1949	121.0	120.0	121.0		3668	5.5	1.0	1	dbSNP_134	121	0,8280		0,0,4140	no	missense	SPTA1	NM_003126.2	43	0,1,6089	TT,TC,CC		0.0,0.0256,0.0082	probably-damaging	1223/2420	158618345	1,12179	1950	4140	6090	SO:0001583	missense	6708			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.3668G>A	1.37:g.158618345C>T	ENSP00000357129:p.Arg1223Gln		Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	36	5.794612	0.96952	2.56E-4	0.0	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.48201	0.82;0.82	5.5	5.5	0.81552	.	0.000000	0.28560	N	0.014914	T	0.68044	0.2958	M	0.84082	2.675	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	T	0.70193	-0.4939	10	0.62326	D	0.03	.	18.1469	0.89661	0.0:1.0:0.0:0.0	.	1223	P02549	SPTA1_HUMAN	Q	1223	ENSP00000357130:R1223Q;ENSP00000357129:R1223Q	ENSP00000357129:R1223Q	R	-	2	0	SPTA1	156884969	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	7.130000	0.77235	2.861000	0.98227	0.655000	0.94253	CGA		0.507	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3		NM_003126	
SYK	6850	broad.mit.edu;ucsc.edu	37	9	93636536	93636536	+	Silent	SNP	G	G	A	rs200697355		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr9:93636536G>A	ENST00000375754.4	+	8	1114	c.966G>A	c.(964-966)ccG>ccA	p.P322P	SYK_ENST00000375746.1_Silent_p.P322P|SYK_ENST00000375747.1_Silent_p.P299P|SYK_ENST00000375751.4_Silent_p.P299P	NM_003177.5	NP_003168.2	P43405	KSYK_HUMAN	spleen tyrosine kinase	322	Interdomain B.				activation of JUN kinase activity (GO:0007257)|adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|B cell receptor signaling pathway (GO:0050853)|beta selection (GO:0043366)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|cell proliferation (GO:0008283)|cellular response to molecule of fungal origin (GO:0071226)|defense response to bacterium (GO:0042742)|enzyme linked receptor protein signaling pathway (GO:0007167)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte activation involved in immune response (GO:0002366)|leukocyte cell-cell adhesion (GO:0007159)|leukotriene biosynthetic process (GO:0019370)|lymph vessel development (GO:0001945)|macrophage activation involved in immune response (GO:0002281)|neutrophil activation involved in immune response (GO:0002283)|neutrophil chemotaxis (GO:0030593)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of bone resorption (GO:0045780)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-3 biosynthetic process (GO:0045401)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of arachidonic acid secretion (GO:0090237)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of neutrophil degranulation (GO:0043313)|regulation of phagocytosis (GO:0050764)|regulation of platelet activation (GO:0010543)|regulation of platelet aggregation (GO:0090330)|regulation of superoxide anion generation (GO:0032928)|serotonin secretion by platelet (GO:0002554)|viral process (GO:0016032)	B cell receptor complex (GO:0019815)|cytosol (GO:0005829)|early phagosome (GO:0032009)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|integrin binding (GO:0005178)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)	p.P322P(1)|p.P299P(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(3)|skin(2)|stomach(2)	26						CATTCAATCCGTATGAGCCAG	0.468			T	"""ETV6, ITK"""	"""MDS, peripheral T-cell lymphoma"""																																			Dom	yes		9	9q22	6850	spleen tyrosine kinase		L	2	Substitution - coding silent(2)	kidney(2)											96.0	90.0	92.0					9																	93636536		2203	4300	6503	SO:0001819	synonymous_variant	6850			L28824	CCDS6688.1, CCDS47992.1	9q22	2013-02-14			ENSG00000165025	ENSG00000165025		"""SH2 domain containing"""	11491	protein-coding gene	gene with protein product		600085				8082894, 1423621	Standard	XM_005252147		Approved		uc004aqz.3	P43405	OTTHUMG00000020200	ENST00000375754.4:c.966G>A	9.37:g.93636536G>A				Silent	SNP	ENST00000375754.4	37	CCDS6688.1																																																																																				0.468	SYK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053018.1			
TMEM71	137835	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	133764200	133764200	+	Missense_Mutation	SNP	C	C	T	rs200344505		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr8:133764200C>T	ENST00000356838.3	-	4	287	c.145G>A	c.(145-147)Ggc>Agc	p.G49S	TMEM71_ENST00000377901.4_Missense_Mutation_p.G49S|TMEM71_ENST00000523829.1_Missense_Mutation_p.G49S|TMEM71_ENST00000517538.1_5'UTR	NM_144649.2	NP_653250.2	Q6P5X7	TMM71_HUMAN	transmembrane protein 71	49						integral component of membrane (GO:0016021)		p.G49S(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|skin(2)	16	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			TCTATGGAGCCGCATTCAAAA	0.458													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18569	0.0		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	kidney(1)											82.0	81.0	81.0					8																	133764200		2203	4300	6503	SO:0001583	missense	137835			AK057631	CCDS6366.1, CCDS47921.1	8q24.22	2005-09-02				ENSG00000165071			26572	protein-coding gene	gene with protein product						12477932	Standard	NM_144649		Approved	FLJ33069	uc003ytn.3	Q6P5X7		ENST00000356838.3:c.145G>A	8.37:g.133764200C>T	ENSP00000349296:p.Gly49Ser		Q3KRC2|Q8WVZ4|Q96LX9	Missense_Mutation	SNP	ENST00000356838.3	37	CCDS6366.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	6.760	0.509168	0.12883	.	.	ENSG00000165071	ENST00000523829;ENST00000356838;ENST00000377901;ENST00000519187;ENST00000519304	.	.	.	5.8	-1.01	0.10169	.	0.449134	0.26553	N	0.023721	T	0.16041	0.0386	N	0.22421	0.69	0.22156	N	0.999321	B;B;B	0.18968	0.032;0.003;0.001	B;B;B	0.08055	0.003;0.003;0.002	T	0.10200	-1.0640	9	0.22706	T	0.39	-1.0508	1.9464	0.03358	0.4925:0.2525:0.1338:0.1212	.	49;49;49	Q6P5X7;Q6P5X7-3;Q6P5X7-2	TMM71_HUMAN;.;.	S	49	.	ENSP00000349296:G49S	G	-	1	0	TMEM71	133833382	1.000000	0.71417	0.694000	0.30210	0.012000	0.07955	0.868000	0.27982	-0.374000	0.07967	-2.922000	0.00089	GGC		0.458	TMEM71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379591.1		NM_144649	
TMPRSS11D	9407	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	68725379	68725379	+	Missense_Mutation	SNP	G	G	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr4:68725379G>A	ENST00000283916.6	-	2	124	c.26C>T	c.(25-27)tCg>tTg	p.S9L	TMPRSS11D_ENST00000545541.1_Intron|TMPRSS11D_ENST00000509584.1_Intron|UBA6-AS1_ENST00000500538.2_RNA	NM_004262.2	NP_004253.1	O60235	TM11D_HUMAN	transmembrane protease, serine 11D	9					proteolysis (GO:0006508)|respiratory gaseous exchange (GO:0007585)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)	p.S9L(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						TCTTGAAGTCGAAGTTACACG	0.393																																																	1	Substitution - Missense(1)	kidney(1)											94.0	83.0	87.0					4																	68725379		2203	4300	6503	SO:0001583	missense	9407			AB002134	CCDS3518.1	4q13.2	2010-04-13			ENSG00000153802	ENSG00000153802		"""Serine peptidases / Transmembrane"""	24059	protein-coding gene	gene with protein product	"""airway trypsin like protease"""	605369				9565616, 9070615	Standard	XM_005265710		Approved		uc003hdq.3	O60235	OTTHUMG00000129300	ENST00000283916.6:c.26C>T	4.37:g.68725379G>A	ENSP00000283916:p.Ser9Leu		Q08AF6	Missense_Mutation	SNP	ENST00000283916.6	37	CCDS3518.1	.	.	.	.	.	.	.	.	.	.	G	12.82	2.052437	0.36181	.	.	ENSG00000153802	ENST00000283916	D	0.87809	-2.3	5.19	4.33	0.51752	.	0.309933	0.23492	N	0.047585	D	0.82462	0.5042	M	0.63843	1.955	0.21184	N	0.999769	B	0.31503	0.326	B	0.22601	0.04	T	0.75950	-0.3137	10	0.52906	T	0.07	.	9.9045	0.41368	0.0947:0.0:0.9053:0.0	.	9	O60235	TM11D_HUMAN	L	9	ENSP00000283916:S9L	ENSP00000283916:S9L	S	-	2	0	TMPRSS11D	68407974	0.060000	0.20803	0.012000	0.15200	0.069000	0.16628	2.755000	0.47540	2.704000	0.92352	0.563000	0.77884	TCG		0.393	TMPRSS11D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251430.3		NM_004262	
TRAPPC10	7109	broad.mit.edu;ucsc.edu	37	21	45513966	45513966	+	Missense_Mutation	SNP	T	T	C			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr21:45513966T>C	ENST00000291574.4	+	20	3195	c.3020T>C	c.(3019-3021)gTg>gCg	p.V1007A	TRAPPC10_ENST00000483973.1_3'UTR	NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	1007					sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sodium ion transmembrane transporter activity (GO:0015081)	p.V1007A(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						AAGCAGTCGGTGTTCTTCGTC	0.537																																																	1	Substitution - Missense(1)	kidney(1)											147.0	130.0	136.0					21																	45513966		2203	4300	6503	SO:0001583	missense	7109			U19252	CCDS13704.1	21q22.3	2008-05-07	2008-05-07	2008-05-07	ENSG00000160218	ENSG00000160218		"""Trafficking protein particle complex"""	11868	protein-coding gene	gene with protein product	"""trafficking protein particle complex subunit 130"", ""TRAPP 130 kDa subunit"""	602103	"""transmembrane protein 1"""	TMEM1		7633421	Standard	NM_003274		Approved	EHOC-1, TRS130	uc002zea.3	P48553	OTTHUMG00000086894	ENST00000291574.4:c.3020T>C	21.37:g.45513966T>C	ENSP00000291574:p.Val1007Ala		Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Missense_Mutation	SNP	ENST00000291574.4	37	CCDS13704.1	.	.	.	.	.	.	.	.	.	.	T	16.88	3.245994	0.59103	.	.	ENSG00000160218	ENST00000291574;ENST00000542855	T	0.28895	1.59	5.11	5.11	0.69529	.	0.148349	0.46442	D	0.000294	T	0.38241	0.1033	L	0.43923	1.385	0.53688	D	0.999971	D;P;P	0.54601	0.967;0.835;0.732	P;B;B	0.51806	0.68;0.251;0.254	T	0.12116	-1.0560	10	0.45353	T	0.12	.	15.2088	0.73202	0.0:0.0:0.0:1.0	.	112;266;1007	B4DV34;B4DI17;P48553	.;.;TPC10_HUMAN	A	1007;138	ENSP00000291574:V1007A	ENSP00000291574:V1007A	V	+	2	0	TRAPPC10	44338394	1.000000	0.71417	0.994000	0.49952	0.924000	0.55760	4.868000	0.63021	2.047000	0.60756	0.533000	0.62120	GTG		0.537	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1		NM_003274	
TTN	7273	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	179406075	179406075	+	Missense_Mutation	SNP	T	T	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr2:179406075T>A	ENST00000591111.1	-	300	93030	c.92806A>T	c.(92806-92808)Att>Ttt	p.I30936F	TTN-AS1_ENST00000450692.2_RNA|RP11-65L3.4_ENST00000604692.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I23704F|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.I23637F|TTN-AS1_ENST00000585487.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.I23512F|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.I32577F|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.I30009F|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA			Q8WZ42	TITIN_HUMAN	titin	30936	Fibronectin type-III 125. {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)	p.I23704F(1)|p.I23512F(1)|p.I30007F(1)|p.I30009F(1)|p.I23637F(1)		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)			CTTGCATTAATGGCTGTGACA	0.458																																																	5	Substitution - Missense(5)	kidney(5)											72.0	73.0	72.0					2																	179406075		1943	4138	6081	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.92806A>T	2.37:g.179406075T>A	ENSP00000465570:p.Ile30936Phe		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		.	.	.	.	.	.	.	.	.	.	T	19.85	3.904292	0.72868	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57595	0.39;0.39;0.39;0.39	5.72	4.56	0.56223	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.52789	0.1756	L	0.39245	1.2	0.47698	D	0.99949	P;P;P;P	0.38582	0.638;0.638;0.638;0.638	P;P;P;P	0.47015	0.534;0.534;0.534;0.534	T	0.55276	-0.8166	9	0.87932	D	0	.	11.6361	0.51204	0.0:0.0693:0.0:0.9307	.	23512;23637;23704;30936	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	F	30009;23512;23704;23637;23509	ENSP00000343764:I30009F;ENSP00000434586:I23512F;ENSP00000340554:I23704F;ENSP00000352154:I23637F	ENSP00000340554:I23704F	I	-	1	0	TTN	179114321	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.267000	0.58877	0.996000	0.38943	0.459000	0.35465	ATT		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1		NM_133378	
TTN	7273	broad.mit.edu;ucsc.edu	37	2	179516238	179516238	+	Silent	SNP	A	A	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr2:179516238A>T	ENST00000591111.1	-	162	35192	c.34968T>A	c.(34966-34968)gtT>gtA	p.V11656V	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Silent_p.V13163V|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Silent_p.V10729V|TTN-AS1_ENST00000589487.1_RNA			Q8WZ42	TITIN_HUMAN	titin	11656	Glu-rich.|Pro-rich.				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)	p.V10729V(1)		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)			TCTTTTCAGGAACAACCTCCT	0.463																																																	1	Substitution - coding silent(1)	kidney(1)											66.0	63.0	64.0					2																	179516238		1838	4082	5920	SO:0001819	synonymous_variant	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.34968T>A	2.37:g.179516238A>T			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	Silent	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	A	9.666	1.145475	0.21288	.	.	ENSG00000155657	ENST00000426232	.	.	.	5.22	-2.64	0.06114	.	.	.	.	.	T	0.52273	0.1724	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48570	-0.9024	4	.	.	.	.	8.5876	0.33668	0.3447:0.0:0.5337:0.1216	.	.	.	.	T	4	.	.	S	-	1	0	TTN	179224483	0.000000	0.05858	0.980000	0.43619	0.978000	0.69477	-1.388000	0.02533	-0.388000	0.07797	0.528000	0.53228	TCC		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1		NM_133378	
UBR2	23304	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	42637945	42637945	+	Missense_Mutation	SNP	T	T	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr6:42637945T>A	ENST00000372899.1	+	35	4255	c.3997T>A	c.(3997-3999)Tgg>Agg	p.W1333R	UBR2_ENST00000372901.1_Missense_Mutation_p.W1333R|UBR2_ENST00000372883.3_3'UTR	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	1333					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.W1333R(1)		breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			CATAATGTGTTGGGGTAGCTG	0.418																																																	1	Substitution - Missense(1)	kidney(1)											143.0	122.0	129.0					6																	42637945		2203	4300	6503	SO:0001583	missense	23304			BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"""Ubiquitin protein ligase E3 component n-recognins"""	21289	protein-coding gene	gene with protein product		609134	"""chromosome 6 open reading frame 133"""	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.3997T>A	6.37:g.42637945T>A	ENSP00000361990:p.Trp1333Arg		O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	37	CCDS4870.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.652157	0.88056	.	.	ENSG00000024048	ENST00000372899;ENST00000372901	T;T	0.61040	0.14;0.14	5.36	5.36	0.76844	.	0.114965	0.64402	D	0.000005	T	0.70237	0.3201	M	0.80422	2.495	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.996	T	0.70941	-0.4735	10	0.33141	T	0.24	-0.0571	15.3602	0.74469	0.0:0.0:0.0:1.0	.	1333;1333	Q8IWV8-4;Q8IWV8	.;UBR2_HUMAN	R	1333	ENSP00000361990:W1333R;ENSP00000361992:W1333R	ENSP00000361990:W1333R	W	+	1	0	UBR2	42745923	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.698000	0.84413	2.027000	0.59764	0.533000	0.62120	TGG		0.418	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2		NM_015255	
CFAP57	149465	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	43647495	43647495	+	Missense_Mutation	SNP	G	G	T			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr1:43647495G>T	ENST00000372492.4	+	3	772	c.448G>T	c.(448-450)Gac>Tac	p.D150Y	WDR65_ENST00000528956.1_Missense_Mutation_p.D150Y	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		150								p.D150Y(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TGTTAGAATCGACACTCAGAA	0.388																																																	1	Substitution - Missense(1)	kidney(1)											56.0	60.0	59.0					1																	43647495		2203	4300	6503	SO:0001583	missense	149465																														ENST00000372492.4:c.448G>T	1.37:g.43647495G>T	ENSP00000361570:p.Asp150Tyr		A6NKQ3|Q17RI9|Q5TAI0	Missense_Mutation	SNP	ENST00000372492.4	37		.	.	.	.	.	.	.	.	.	.	G	16.59	3.165507	0.57476	.	.	ENSG00000243710	ENST00000372492;ENST00000528956;ENST00000529956	T;T;T	0.45276	1.13;1.18;0.9	5.57	5.57	0.84162	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.371984	0.33515	N	0.004830	T	0.59473	0.2196	L	0.51422	1.61	0.19575	N	0.999969	P;D	0.67145	0.942;0.996	B;D	0.65010	0.181;0.931	T	0.54516	-0.8282	10	0.62326	D	0.03	.	19.1541	0.93503	0.0:0.0:1.0:0.0	.	150;150	Q96MR6;Q96MR6-2	WDR65_HUMAN;.	Y	150	ENSP00000361570:D150Y;ENSP00000435310:D150Y;ENSP00000434133:D150Y	ENSP00000361570:D150Y	D	+	1	0	WDR65	43420082	0.920000	0.31207	0.078000	0.20375	0.958000	0.62258	2.992000	0.49417	2.626000	0.88956	0.557000	0.71058	GAC		0.388	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1			
ZAN	7455	hgsc.bcm.edu;ucsc.edu	37	7	100386875	100386875	+	RNA	DEL	A	A	-			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr7:100386875delA	ENST00000348028.3	+	0	7427				ZAN_ENST00000546213.1_RNA|ZAN_ENST00000542585.1_RNA|ZAN_ENST00000546292.1_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000443370.1_RNA|ZAN_ENST00000449052.1_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			CCTACAGGCCAAATGAACACC	0.562																																																	0													64.0	67.0	66.0					7																	100386875		1905	4127	6032			7455			U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"""zonadhesin"""			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100386875delA			A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Frame_Shift_Del	DEL	ENST00000348028.3	37																																																																																					0.562	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1		NM_003386	
ZFAT	57623	broad.mit.edu	37	8	135521987	135521987	+	Nonsense_Mutation	SNP	G	G	A	rs200421725		TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr8:135521987G>A	ENST00000377838.3	-	15	3541	c.3367C>T	c.(3367-3369)Cga>Tga	p.R1123*	ZFAT_ENST00000517307.1_5'Flank|ZFAT_ENST00000520214.1_Nonsense_Mutation_p.R1111*|ZFAT_ENST00000520356.1_Intron|ZFAT_ENST00000429442.2_Nonsense_Mutation_p.R1111*|ZFAT_ENST00000523399.1_Nonsense_Mutation_p.R1061*|ZFAT_ENST00000520727.1_Nonsense_Mutation_p.R1111*	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	1123					hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.R1123*(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			GGGTCCAGTCGGTCGCCTTAA	0.597													G|||	1	0.000199681	0.0	0.0014	5008	,	,		14795	0.0		0.0	False		,,,				2504	0.0																1	Substitution - Nonsense(1)	kidney(1)											98.0	102.0	101.0					8																	135521987		2085	4205	6290	SO:0001587	stop_gained	57623			BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827		"""Zinc fingers, C2H2-type"""	19899	protein-coding gene	gene with protein product		610931	"""zinc finger protein 406"""	ZNF406, ZFAT1		10819331, 18329245	Standard	NM_020863		Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.3367C>T	8.37:g.135521987G>A	ENSP00000367069:p.Arg1123*		B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Nonsense_Mutation	SNP	ENST00000377838.3	37	CCDS47924.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	16.89	3.248084	0.59103	.	.	ENSG00000066827	ENST00000520727;ENST00000429442;ENST00000377838;ENST00000520214;ENST00000521673;ENST00000318135;ENST00000523399	.	.	.	5.67	3.66	0.41972	.	0.294097	0.33477	N	0.004878	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.9944	9.0481	0.36358	0.0:0.0981:0.5162:0.3856	.	.	.	.	X	1111;1111;1123;1111;43;1010;1061	.	ENSP00000326997:R1010X	R	-	1	2	ZFAT	135591169	1.000000	0.71417	0.988000	0.46212	0.373000	0.29922	2.283000	0.43470	0.677000	0.31305	0.557000	0.71058	CGA		0.597	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1		NM_001029939	
ZNF24	7572	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	32919802	32919802	+	Missense_Mutation	SNP	T	T	A			TCGA-CZ-5462-01A-01D-1501-10	TCGA-CZ-5462-11A-01D-1501-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	74eed0c6-b3cc-4666-8ef0-194e1bbe1048	58ebedb1-02e5-437b-b5ec-c463a50b1f10	g.chr18:32919802T>A	ENST00000261332.6	-	3	738	c.559A>T	c.(559-561)Agg>Tgg	p.R187W	ZNF24_ENST00000399061.3_Missense_Mutation_p.R187W|ZNF24_ENST00000589881.1_Missense_Mutation_p.R187W	NM_006965.2	NP_008896.2	P17028	ZNF24_HUMAN	zinc finger protein 24	187					myelination (GO:0042552)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.R187W(1)		endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	15						CCACAGTGCCTTAGGGAATGG	0.507																																					Colon(42;769 913 8916 19469 46270)												1	Substitution - Missense(1)	kidney(1)											113.0	110.0	111.0					18																	32919802		2203	4300	6503	SO:0001583	missense	7572			AF016052	CCDS11912.1	18q12	2013-01-09	2006-05-10		ENSG00000172466	ENSG00000172466		"""-"", ""Zinc fingers, C2H2-type"""	13032	protein-coding gene	gene with protein product		194534	"""zinc finger protein 24 (KOX 17)"""	ZNF191			Standard	NM_006965		Approved	ZSCAN3, Zfp191, KOX17	uc002kys.2	P17028	OTTHUMG00000132565	ENST00000261332.6:c.559A>T	18.37:g.32919802T>A	ENSP00000261332:p.Arg187Trp		O14754|Q53YE4|Q6ICR5|Q8IZN4	Missense_Mutation	SNP	ENST00000261332.6	37	CCDS11912.1	.	.	.	.	.	.	.	.	.	.	T	17.71	3.457319	0.63401	.	.	ENSG00000172466	ENST00000261332;ENST00000399061	T;T	0.05319	3.46;3.46	5.22	-0.475	0.12104	.	0.000000	0.64402	D	0.000010	T	0.13543	0.0328	L	0.39898	1.24	0.29462	N	0.857652	D;D	0.67145	0.996;0.992	D;D	0.76071	0.987;0.971	T	0.02574	-1.1139	10	0.34782	T	0.22	.	12.5602	0.56277	0.0:0.0:0.5946:0.4054	.	187;187	P17028-2;P17028	.;ZNF24_HUMAN	W	187	ENSP00000261332:R187W;ENSP00000382015:R187W	ENSP00000261332:R187W	R	-	1	2	ZNF24	31173800	0.576000	0.26700	0.257000	0.24404	0.981000	0.71138	0.236000	0.17967	-0.115000	0.11915	-0.313000	0.08912	AGG		0.507	ZNF24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255769.1		NM_006965	
