#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_AAChange	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_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	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_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	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_Mutation_Status	i_NTotCov_SOL	i_NVarCov_SOL	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_TTotCov_SOL	i_TVarCov_SOL	i_Transcript_Id	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_dbSNPPopFreq	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
NBEAL1	65065	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	2	204022462	204022462	+	Frame_Shift_Del	DEL	G	G	-			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr2:204022462delG	ENST00000449802.1	+	35	5874	c.5541delG	c.(5539-5541)ttgfs	p.L1847fs		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	1847										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						CATTGCTTTTGGAAGTAGTGA	0.308																																					p.L1847fs		.											.	.	.	0			c.5540delT						.						122.0	117.0	119.0					2																	204022462		1821	4084	5905	SO:0001589	frameshift_variant	65065	exon35			GCTTTTGGAAGTA	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"""WD repeat domain containing"""	20681	protein-coding gene	gene with protein product		609816	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17"", ""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"""	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.5541delG	2.37:g.204022462delG	ENSP00000399903:p.Leu1847fs	Somatic	48	0		WXS	Illumina HiSeq	.	88	26	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Frame_Shift_Del	DEL	ENST00000449802.1	37	CCDS46495.1																																																																																			.		0.308	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4		
NAIP	4671	hgsc.bcm.edu	37	5	70299665	70299666	+	Frame_Shift_Ins	INS	-	-	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr5:70299665_70299666insA	ENST00000517649.1	-	6	977_978	c.687_688insT	c.(685-690)agtaagfs	p.K230fs	NAIP_ENST00000508426.2_Frame_Shift_Ins_p.K230fs|NAIP_ENST00000503719.2_Frame_Shift_Ins_p.K68fs|NAIP_ENST00000523981.1_Frame_Shift_Ins_p.K68fs|NAIP_ENST00000194097.4_Frame_Shift_Ins_p.K230fs	NM_004536.2	NP_004527.2	Q13075	BIRC1_HUMAN	NLR family, apoptosis inhibitory protein	230					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|metal ion binding (GO:0046872)			central_nervous_system(1)	1		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)		GAGGATTTCTTACTCCGAAGAA	0.312																																					p.K230_K231delinsX		.											.	.	.	0			c.688_689insT						.																																			SO:0001589	frameshift_variant	4671	exon6			ATTTCTTACTCCG	U19251	CCDS4009.1, CCDS43327.1	5q13.2	2010-06-16	2006-12-08	2006-12-08	ENSG00000249437	ENSG00000249437		"""Baculoviral IAP repeat containing"", ""Nucleotide-binding domain and leucine rich repeat containing"""	7634	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and BIR domain containing 1"", ""NLR family, BIR domain containing 1"""	600355	"""baculoviral IAP repeat-containing 1"""	BIRC1		7813013	Standard	NM_022892		Approved	NLRB1	uc003jyj.1	Q13075	OTTHUMG00000163318	ENST00000517649.1:c.688dupT	5.37:g.70299666_70299666dupA	ENSP00000428657:p.Lys230fs	Somatic	465	0		WXS	Illumina HiSeq	.	520	41	NM_004536	B9EG72|E9PHD1|O75857|Q13730|Q59GI6|Q8TDZ4|Q99796	Frame_Shift_Ins	INS	ENST00000517649.1	37	CCDS4009.1																																																																																			.		0.312	NAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372649.6	NM_004536	
CTCF	10664	hgsc.bcm.edu	37	16	67650656	67650657	+	Frame_Shift_Ins	INS	-	-	CT			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr16:67650656_67650657insCT	ENST00000264010.4	+	5	1405_1406	c.961_962insCT	c.(961-963)cctfs	p.P321fs	AC009095.4_ENST00000388909.4_RNA|CTCF_ENST00000401394.1_5'UTR	NM_006565.3	NP_006556.1	P49711	CTCF_HUMAN	CCCTC-binding factor (zinc finger protein)	321					chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|DNA methylation (GO:0006306)|maintenance of DNA methylation (GO:0010216)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome positioning (GO:0016584)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone acetylation (GO:0035065)|regulation of histone methylation (GO:0031060)|regulation of molecular function, epigenetic (GO:0040030)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin insulator sequence binding (GO:0043035)|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 negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(6)|central_nervous_system(2)|cervix(1)|endometrium(34)|haematopoietic_and_lymphoid_tissue(7)|kidney(3)|large_intestine(9)|liver(1)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	79		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0166)|Epithelial(162;0.0577)		AGGTACTCGTCCTCACAAGTGC	0.495																																					p.P321fs	Colon(175;1200 1966 6945 23069 27405)	.											.	.	.	0			c.961_962insCT						.																																			SO:0001589	frameshift_variant	10664	exon5			ACTCGTCCTCACA	U25435	CCDS10841.1, CCDS54029.1	16q21-q22.3	2013-01-08			ENSG00000102974	ENSG00000102974		"""Zinc fingers, C2H2-type"""	13723	protein-coding gene	gene with protein product	"""11 zinc finger transcriptional repressor"""	604167				8649389, 18550811	Standard	NM_006565		Approved		uc002etl.3	P49711	OTTHUMG00000137539	ENST00000264010.4:c.962_963dupCT	16.37:g.67650657_67650658dupCT	ENSP00000264010:p.Pro321fs	Somatic	64	0		WXS	Illumina HiSeq	.	48	13	NM_006565	B5MC38|Q53XI7|Q59EL8	Frame_Shift_Ins	INS	ENST00000264010.4	37	CCDS10841.1																																																																																			.		0.495	CTCF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268870.2	NM_006565	
Unknown	0	hgsc.bcm.edu	37	5	69424242	69424243	+	IGR	INS	-	-	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr5:69424242_69424243insA								SMN2 (50821 upstream) : GTF2H2B (287026 downstream)																							GAGGATTTCTTACTCCGAAGAA	0.312																																					.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	6606	.			ATTTCTTACTCCG																													5.37:g.69424243_69424243dupA		Somatic	509	0		WXS	Illumina HiSeq	.	503	36	.		RNA	INS		37																																																																																				.	0	0.312								
MLXIPL	51085	hgsc.bcm.edu	37	7	73030462	73030463	+	Frame_Shift_Ins	INS	-	-	T	rs149713253	byFrequency	TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr7:73030462_73030463insT	ENST00000313375.3	-	2	385_386	c.338_339insA	c.(337-339)aagfs	p.K113fs	MLXIPL_ENST00000429400.2_Frame_Shift_Ins_p.K113fs|MLXIPL_ENST00000395189.1_Frame_Shift_Ins_p.K113fs|MLXIPL_ENST00000414749.2_Frame_Shift_Ins_p.K113fs|MLXIPL_ENST00000434326.1_Frame_Shift_Ins_p.K113fs|MLXIPL_ENST00000354613.1_Frame_Shift_Ins_p.K113fs	NM_032951.2|NM_032953.2	NP_116569.1|NP_116571.1	Q9NP71	MLXPL_HUMAN	MLX interacting protein-like	113					anatomical structure morphogenesis (GO:0009653)|energy reserve metabolic process (GO:0006112)|fatty acid homeostasis (GO:0055089)|glucose homeostasis (GO:0042593)|glucose mediated signaling pathway (GO:0010255)|intracellular signal transduction (GO:0035556)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of oxidative phosphorylation (GO:0090324)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular metabolic process (GO:0031325)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of glycolytic process (GO:0045821)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of energy homeostasis (GO:2000505)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride homeostasis (GO:0070328)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	carbohydrate response element binding (GO:0035538)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			cervix(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	13		Lung NSC(55;0.0659)|all_lung(88;0.152)				TGCAGAGCAGCTTGAGGCCTTT	0.574																																					p.K113fs		.											.	.	.	0			c.339_340insA						.																																			SO:0001589	frameshift_variant	51085	exon2			GAGCAGCTTGAGG	AK055029	CCDS5553.1, CCDS5554.1, CCDS47605.1, CCDS47606.1	7q11.23	2013-05-21	2005-10-31	2005-10-31	ENSG00000009950	ENSG00000009950			12744	protein-coding gene	gene with protein product	"""carbohydrate response element binding protein"""	605678	"""Williams Beuren syndrome chromosome region 14"""	WBSCR14		9860302	Standard	XM_005250399		Approved	WS-bHLH, MIO, CHREBP, MONDOB, bHLHd14	uc003tyn.1	Q9NP71	OTTHUMG00000129995	ENST00000313375.3:c.339dupA	7.37:g.73030464_73030464dupT	ENSP00000320886:p.Lys113fs	Somatic	41	0		WXS	Illumina HiSeq	.	53	15	NM_032953	C5HU02|C5HU03|C5HU04|Q96E48|Q9BY03|Q9BY04|Q9BY05|Q9BY06|Q9Y2P3	Frame_Shift_Ins	INS	ENST00000313375.3	37	CCDS5553.1																																																																																			.		0.574	MLXIPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252262.1	NM_032951	
CACNG2	10369	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	22	37098604	37098604	+	Silent	SNP	T	T	G			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr22:37098604T>G	ENST00000300105.6	-	1	999	c.18A>C	c.(16-18)cgA>cgC	p.R6R	RP1-293L6.1_ENST00000430281.1_RNA	NM_006078.3	NP_006069.1	Q9Y698	CCG2_HUMAN	calcium channel, voltage-dependent, gamma subunit 2	6					membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|neuromuscular junction development (GO:0007528)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	18						TTTGAACACCTCGATCAAACA	0.468																																					p.R6R		.											.	.	.	0			c.A18C						.						113.0	106.0	109.0					22																	37098604		2203	4300	6503	SO:0001819	synonymous_variant	10369	exon1			AACACCTCGATCA	AF096322	CCDS13931.1	22q13.1	2006-08-01			ENSG00000166862	ENSG00000166862		"""Calcium channel subunits"""	1406	protein-coding gene	gene with protein product		602911					Standard	NM_006078		Approved	stargazin, MGC138502, MGC138504	uc003aps.2	Q9Y698	OTTHUMG00000030612	ENST00000300105.6:c.18A>C	22.37:g.37098604T>G		Somatic	84	0		WXS	Illumina HiSeq	.	71	5	NM_006078	Q2M1M1|Q5TGT3|Q9UGZ7	Silent	SNP	ENST00000300105.6	37	CCDS13931.1																																																																																			.		0.468	CACNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075500.2		
PCDHAC2	56134	hgsc.bcm.edu;broad.mit.edu	37	5	140347642	140347642	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr5:140347642C>T	ENST00000289269.5	+	1	1823	c.1291C>T	c.(1291-1293)Cgg>Tgg	p.R431W	PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA8_ENST00000531613.1_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	431	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGACCGAGAGCGGGTGGCTGT	0.562																																					p.R431W	Melanoma(190;638 2083 3390 11909 52360)	.											PCDHAC2,caecum,carcinoma,0,1	PCDHAC2	0	0			c.C1291T						.						86.0	90.0	88.0					5																	140347642		2203	4300	6503	SO:0001583	missense	56134	exon1			CGAGAGCGGGTGG	AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"""Cadherins / Protocadherins : Clustered"""	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.1291C>T	5.37:g.140347642C>T	ENSP00000289269:p.Arg431Trp	Somatic	22	0		WXS	Illumina HiSeq	.	23	3	NM_031883	Q2M3V1|Q9Y5F4	Missense_Mutation	SNP	ENST00000289269.5	37	CCDS4242.1	.	.	.	.	.	.	.	.	.	.	C	15.31	2.795443	0.50208	.	.	ENSG00000243232	ENST00000289269	T	0.52983	0.64	5.79	2.72	0.32119	Cadherin (4);Cadherin-like (1);	0.000000	0.38164	N	0.001788	T	0.65165	0.2665	M	0.75884	2.315	0.34555	D	0.711778	D;D	0.76494	0.999;0.999	D;D	0.67103	0.949;0.94	T	0.78360	-0.2234	10	0.72032	D	0.01	.	13.5873	0.61940	0.5084:0.4916:0.0:0.0	.	431;431	Q9Y5I4-2;Q9Y5I4	.;PCDC2_HUMAN	W	431	ENSP00000289269:R431W	ENSP00000289269:R431W	R	+	1	2	PCDHAC2	140327826	0.109000	0.22037	0.833000	0.33012	0.951000	0.60555	0.866000	0.27954	1.420000	0.47138	0.563000	0.77884	CGG	.		0.562	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899	
CSMD3	114788	hgsc.bcm.edu	37	8	113349922	113349922	+	Silent	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr8:113349922G>T	ENST00000297405.5	-	43	6935	c.6691C>A	c.(6691-6693)Cga>Aga	p.R2231R	CSMD3_ENST00000343508.3_Silent_p.R2191R|CSMD3_ENST00000455883.2_Silent_p.R2127R|CSMD3_ENST00000352409.3_Silent_p.R2161R	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2231	Sushi 12. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R2231*(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						AAACCATTTCGAAACGGGCGT	0.388										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.R2231R		.											CSMD3_ENST00000343508,caecum,carcinoma,+1,7	CSMD3_ENST00000343508	+1	1	Substitution - Nonsense(1)	large_intestine(1)	c.C6691A						.						92.0	94.0	93.0					8																	113349922		2203	4300	6503	SO:0001819	synonymous_variant	114788	exon43			CATTTCGAAACGG	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.6691C>A	8.37:g.113349922G>T		Somatic	118	0		WXS	Illumina HiSeq	.	55	3	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																			.		0.388	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
ULK4	54986	hgsc.bcm.edu	37	3	41860985	41860985	+	Missense_Mutation	SNP	T	T	C	rs76318575		TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr3:41860985T>C	ENST00000301831.4	-	19	2240	c.1778A>G	c.(1777-1779)aAg>aGg	p.K593R		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	593					cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.K593fs*17(1)		breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		TCTAGGGTTCTTTTTTTTTTC	0.448																																					p.K593R		.											.,10	.	150	1	Deletion - Frameshift(1)	ovary(1)	c.A1778G						.						62.0	63.0	63.0					3																	41860985		1844	4089	5933	SO:0001583	missense	54986	exon19			GGGTTCTTTTTTT	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.1778A>G	3.37:g.41860985T>C	ENSP00000301831:p.Lys593Arg	Somatic	59	1		WXS	Illumina HiSeq	.	32	3	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	.	.	.	.	.	.	.	.	.	.	T	11.25	1.582654	0.28180	.	.	ENSG00000168038	ENST00000301831	T	0.64618	-0.11	5.16	3.99	0.46301	Armadillo-like helical (1);Armadillo-type fold (2);	1.026200	0.07781	U	0.953336	T	0.45418	0.1341	N	0.14661	0.345	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.16335	-1.0406	10	0.23302	T	0.38	.	10.5744	0.45219	0.0:0.0761:0.0:0.9239	.	593;593	B4E2M4;Q96C45	.;ULK4_HUMAN	R	593	ENSP00000301831:K593R	ENSP00000301831:K593R	K	-	2	0	ULK4	41835989	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.530000	0.36007	2.070000	0.61991	0.528000	0.53228	AAG	.		0.448	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989	
SNX31	169166	hgsc.bcm.edu;bcgsc.ca	37	8	101596346	101596346	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr8:101596346G>A	ENST00000311812.2	-	12	1313	c.1163C>T	c.(1162-1164)aCa>aTa	p.T388I	SNX31_ENST00000519521.1_5'UTR|SNX31_ENST00000428383.2_Missense_Mutation_p.T289I	NM_152628.3	NP_689841.3	Q8N9S9	SNX31_HUMAN	sorting nexin 31	388					protein transport (GO:0015031)	protein complex (GO:0043234)	phosphatidylinositol binding (GO:0035091)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|prostate(1)|skin(3)|urinary_tract(1)	26	all_cancers(14;4.01e-05)|all_epithelial(15;1.26e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;1.21e-11)|all cancers(13;2.62e-09)|OV - Ovarian serous cystadenocarcinoma(57;3.22e-06)|STAD - Stomach adenocarcinoma(118;0.206)			CACCATTTCTGTATTCTCAGC	0.413																																					p.T388I		.											.	.	.	0			c.C1163T						.						158.0	132.0	141.0					8																	101596346		2203	4300	6503	SO:0001583	missense	169166	exon12			ATTTCTGTATTCT		CCDS6288.1	8q22.3	2011-05-03			ENSG00000174226	ENSG00000174226		"""Sorting nexins"""	28605	protein-coding gene	gene with protein product						16782399	Standard	NM_152628		Approved	MGC39715	uc003yjr.3	Q8N9S9	OTTHUMG00000164725	ENST00000311812.2:c.1163C>T	8.37:g.101596346G>A	ENSP00000312368:p.Thr388Ile	Somatic	75	0		WXS	Illumina HiSeq	.	72	4	NM_152628	C9J6L9|Q8N0U9	Missense_Mutation	SNP	ENST00000311812.2	37	CCDS6288.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.34|11.34	1.610474|1.610474	0.28712|0.28712	.|.	.|.	ENSG00000174226|ENSG00000174226	ENST00000518342|ENST00000311812;ENST00000428383	.|T;T	.|0.20463	.|2.38;2.07	6.03|6.03	6.03|6.03	0.97812|0.97812	.|.	.|0.194717	.|0.36066	.|N	.|0.002814	.|T	.|0.07863	.|0.0197	N|N	0.01576|0.01576	-0.805|-0.805	0.23882|0.23882	N|N	0.996577|0.996577	.|B;B	.|0.29766	.|0.256;0.167	.|B;B	.|0.23419	.|0.039;0.046	.|T	.|0.24941	.|-1.0146	.|10	.|0.10377	.|T	.|0.69	-4.9781|-4.9781	16.0667|16.0667	0.80887|0.80887	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|289;388	.|Q8N9S9-2;Q8N9S9	.|.;SNX31_HUMAN	X|I	15|388;289	.|ENSP00000312368:T388I;ENSP00000405024:T289I	.|ENSP00000312368:T388I	Q|T	-|-	1|2	0|0	SNX31|SNX31	101665522|101665522	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.895000|0.895000	0.52256|0.52256	3.219000|3.219000	0.51200|0.51200	2.854000|2.854000	0.98071|0.98071	0.655000|0.655000	0.94253|0.94253	CAG|ACA	.		0.413	SNX31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379910.1	NM_152628	
RTF1	23168	hgsc.bcm.edu	37	15	41749983	41749983	+	Nonsense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr15:41749983G>T	ENST00000389629.4	+	4	583	c.571G>T	c.(571-573)Gaa>Taa	p.E191*		NM_015138.4	NP_055953.3	Q92541	RTF1_HUMAN	Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	191	Glu-rich.				DNA-templated transcription, initiation (GO:0006352)|endodermal cell fate commitment (GO:0001711)|histone H3-K4 trimethylation (GO:0080182)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)	18		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)		GGGAGATGAGGAAGACAGGGC	0.478																																					p.E191X		.											.	.	.	0			c.G571T						.						164.0	158.0	160.0					15																	41749983		2203	4300	6503	SO:0001587	stop_gained	23168	exon4			GATGAGGAAGACA	D87440	CCDS32200.2	15q14	2004-03-03	2005-07-20	2005-07-20	ENSG00000137815	ENSG00000137815			28996	protein-coding gene	gene with protein product		611633	"""KIAA0252"""	KIAA0252		15632063	Standard	NM_015138		Approved		uc001zny.3	Q92541	OTTHUMG00000133744	ENST00000389629.4:c.571G>T	15.37:g.41749983G>T	ENSP00000374280:p.Glu191*	Somatic	86	0		WXS	Illumina HiSeq	.	76	4	NM_015138	Q96BX6	Nonsense_Mutation	SNP	ENST00000389629.4	37	CCDS32200.2	.	.	.	.	.	.	.	.	.	.	G	36	5.607040	0.96626	.	.	ENSG00000137815	ENST00000389629	.	.	.	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.35671	T	0.21	-20.8349	19.7706	0.96363	0.0:0.0:1.0:0.0	.	.	.	.	X	191	.	ENSP00000374280:E191X	E	+	1	0	RTF1	39537275	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.476000	0.97823	2.697000	0.92050	0.655000	0.94253	GAA	.		0.478	RTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258111.1	NM_015138	
SELPLG	6404	hgsc.bcm.edu;bcgsc.ca	37	12	109017495	109017495	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr12:109017495C>T	ENST00000550948.1	-	2	813	c.589G>A	c.(589-591)Gca>Aca	p.A197T	SELPLG_ENST00000228463.6_Missense_Mutation_p.A213T|SELPLG_ENST00000388962.3_Missense_Mutation_p.A187T			Q14242	SELPL_HUMAN	selectin P ligand	197	12 X 10 AA tandem repeats.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						TCCATGGCTGCTGGTGCAGTG	0.617																																					p.A213T		.											.	.	.	0			c.G637A						.						161.0	135.0	144.0					12																	109017495		2203	4300	6503	SO:0001583	missense	6404	exon2			TGGCTGCTGGTGC		CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"""CD molecules"", ""Endogenous ligands"""	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.589G>A	12.37:g.109017495C>T	ENSP00000447752:p.Ala197Thr	Somatic	88	0		WXS	Illumina HiSeq	.	67	4	NM_001206609	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	Missense_Mutation	SNP	ENST00000550948.1	37	CCDS31895.2	.	.	.	.	.	.	.	.	.	.	C	11.63	1.697410	0.30142	.	.	ENSG00000110876	ENST00000388962;ENST00000550948;ENST00000228463	T;T;T	0.12569	2.67;2.67;2.67	3.31	-4.57	0.03421	.	2.234190	0.02260	N	0.067461	T	0.12220	0.0297	L	0.43152	1.355	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.002;0.002	T	0.27123	-1.0083	10	0.31617	T	0.26	-0.2745	8.0007	0.30295	0.0:0.146:0.3819:0.4721	.	213;197;157	B7Z5C7;Q14242;B4DHR9	.;SELPL_HUMAN;.	T	187;197;213	ENSP00000373614:A187T;ENSP00000447752:A197T;ENSP00000228463:A213T	ENSP00000228463:A213T	A	-	1	0	SELPLG	107541624	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.448000	0.00232	-1.189000	0.02702	-1.169000	0.01745	GCA	.		0.617	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403904.1		
RTN4IP1	84816	hgsc.bcm.edu	37	6	107076815	107076815	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr6:107076815G>T	ENST00000369063.3	-	1	547	c.82C>A	c.(82-84)Cct>Act	p.P28T	QRSL1_ENST00000369046.4_5'Flank|RTN4IP1_ENST00000539449.1_Missense_Mutation_p.P28T|QRSL1_ENST00000369044.1_5'Flank	NM_032730.4	NP_116119.2	Q8WWV3	RT4I1_HUMAN	reticulon 4 interacting protein 1	28						mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			breast(1)|kidney(3)|large_intestine(2)|lung(6)|urinary_tract(1)	13	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;9.45e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0144)	Epithelial(6;0.000873)|all cancers(7;0.00363)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0394)	all cancers(137;0.113)|BRCA - Breast invasive adenocarcinoma(108;0.127)|Epithelial(106;0.144)		CTAACTGAAGGCTTTTGGACA	0.418																																					p.P28T		.											RTN4IP1,neck,malignant_melanoma,0,1	RTN4IP1	0	0			c.C82A						.						108.0	101.0	103.0					6																	107076815		2203	4300	6503	SO:0001583	missense	84816	exon1			CTGAAGGCTTTTG	AF336861	CCDS5056.1	6q21	2008-02-05			ENSG00000130347	ENSG00000130347			18647	protein-coding gene	gene with protein product		610502					Standard	NM_032730		Approved	NIMP	uc003prj.3	Q8WWV3	OTTHUMG00000015304	ENST00000369063.3:c.82C>A	6.37:g.107076815G>T	ENSP00000358059:p.Pro28Thr	Somatic	44	0		WXS	Illumina HiSeq	.	44	2	NM_032730	Q8N9B3|Q8WZ66|Q9BRA4	Missense_Mutation	SNP	ENST00000369063.3	37	CCDS5056.1	.	.	.	.	.	.	.	.	.	.	G	13.79	2.341450	0.41498	.	.	ENSG00000130347	ENST00000539449;ENST00000369063	T;T	0.43688	0.94;2.0	5.85	-0.671	0.11381	.	1.019650	0.07750	N	0.948347	T	0.10809	0.0264	L	0.48642	1.525	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.0	T	0.25779	-1.0122	10	0.21014	T	0.42	-0.3595	0.9739	0.01422	0.2341:0.1238:0.3886:0.2535	.	28;28	G3V1R2;Q8WWV3	.;RT4I1_HUMAN	T	28	ENSP00000444261:P28T;ENSP00000358059:P28T	ENSP00000358059:P28T	P	-	1	0	RTN4IP1	107183508	0.015000	0.18098	0.002000	0.10522	0.581000	0.36288	0.934000	0.28910	-0.136000	0.11475	0.655000	0.94253	CCT	.		0.418	RTN4IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041673.1		
C17orf78	284099	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	17	35746204	35746204	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr17:35746204G>T	ENST00000300618.4	+	6	707	c.657G>T	c.(655-657)aaG>aaT	p.K219N	C17orf78_ENST00000586700.1_Missense_Mutation_p.A139S|ACACA_ENST00000416895.1_Intron|RP11-378E13.3_ENST00000592238.1_RNA|ACACA_ENST00000353139.5_Intron|ACACA_ENST00000589665.1_Intron	NM_173625.3	NP_775896.3	Q8N4C9	CQ078_HUMAN	chromosome 17 open reading frame 78	219						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|large_intestine(1)|lung(2)|stomach(1)	6		Breast(25;0.00295)|Ovarian(249;0.15)				GAGCCAGGAAGCTGTGCCAAT	0.502																																					p.K219N		.											.	.	.	0			c.G657T						.						46.0	47.0	47.0					17																	35746204		1973	4164	6137	SO:0001583	missense	284099	exon6			CAGGAAGCTGTGC	BC034672	CCDS45655.1	17q12	2014-05-06			ENSG00000167230	ENSG00000278505			26831	protein-coding gene	gene with protein product						14702039	Standard	NM_173625		Approved	FLJ39647	uc002hns.3	Q8N4C9	OTTHUMG00000188467	ENST00000300618.4:c.657G>T	17.37:g.35746204G>T	ENSP00000300618:p.Lys219Asn	Somatic	33	0		WXS	Illumina HiSeq	.	29	4	NM_173625	Q8N8D2	Missense_Mutation	SNP	ENST00000300618.4	37	CCDS45655.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.03|14.03	2.413976|2.413976	0.42817|0.42817	.|.	.|.	ENSG00000167230|ENSG00000167230	ENST00000321564|ENST00000300618	.|T	.|0.49139	.|0.79	4.89|4.89	0.276|0.276	0.15663|0.15663	.|.	.|1.777860	.|0.02641	.|N	.|0.105352	T|T	0.26882|0.26882	0.0658|0.0658	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B|B	0.30937|0.06786	0.301|0.001	B|B	0.27715|0.04013	0.082|0.001	T|T	0.16364|0.16364	-1.0405|-1.0405	8|10	0.15499|0.38643	T|T	0.54|0.18	0.541|0.541	3.253|3.253	0.06822|0.06822	0.3119:0.0:0.5058:0.1822|0.3119:0.0:0.5058:0.1822	.|.	139|219	Q8N4C9-2|Q8N4C9	.|CQ078_HUMAN	S|N	139|219	.|ENSP00000300618:K219N	ENSP00000318689:A139S|ENSP00000300618:K219N	A|K	+|+	1|3	0|2	C17orf78|C17orf78	32820317|32820317	0.002000|0.002000	0.14202|0.14202	0.332000|0.332000	0.25469|0.25469	0.558000|0.558000	0.35554|0.35554	-0.069000|-0.069000	0.11542|0.11542	0.331000|0.331000	0.23511|0.23511	0.650000|0.650000	0.86243|0.86243	GCT|AAG	.		0.502	C17orf78-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451570.2	NM_173625	
NOL9	79707	hgsc.bcm.edu	37	1	6593398	6593398	+	Silent	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr1:6593398C>T	ENST00000377705.5	-	7	1211	c.1179G>A	c.(1177-1179)gtG>gtA	p.V393V		NM_024654.4	NP_078930	Q5SY16	NOL9_HUMAN	nucleolar protein 9	393					maturation of 5.8S rRNA (GO:0000460)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|polynucleotide 5'-hydroxyl-kinase activity (GO:0051731)|RNA binding (GO:0003723)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|skin(2)|urinary_tract(1)	19	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;2.46e-35)|all_epithelial(116;1.41e-22)|all_lung(118;7.59e-07)|Lung NSC(185;4.28e-06)|Colorectal(325;4.52e-05)|Breast(487;0.000353)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.47e-07)|COAD - Colon adenocarcinoma(227;1.47e-05)|Kidney(185;5.27e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|BRCA - Breast invasive adenocarcinoma(365;0.00113)|STAD - Stomach adenocarcinoma(132;0.0017)|READ - Rectum adenocarcinoma(331;0.0649)		AAGCGCTGAACACATATTTCA	0.438																																					p.V393V		.											NOL9,NS,carcinoma,0,1	NOL9	0	0			c.G1179A						.						126.0	118.0	120.0					1																	6593398		2203	4300	6503	SO:0001819	synonymous_variant	79707	exon7			GCTGAACACATAT	AK091284	CCDS80.1	1p36.31	2012-05-02			ENSG00000162408	ENSG00000162408			26265	protein-coding gene	gene with protein product	"""polynucleotide 5'-kinase"""					21063389	Standard	NM_024654		Approved	FLJ23323, NET6, Grc3	uc001ans.3	Q5SY16	OTTHUMG00000000904	ENST00000377705.5:c.1179G>A	1.37:g.6593398C>T		Somatic	43	0		WXS	Illumina HiSeq	.	41	2	NM_024654	Q2NL84|Q4VBY3|Q6P472|Q7L4D6|Q96EE0|Q9H5L4	Silent	SNP	ENST00000377705.5	37	CCDS80.1																																																																																			.		0.438	NOL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002625.1	NM_024654	
RLTPR	146206	hgsc.bcm.edu	37	16	67681421	67681421	+	Nonsense_Mutation	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr16:67681421C>T	ENST00000334583.6	+	11	1115	c.787C>T	c.(787-789)Cga>Tga	p.R263*	RLTPR_ENST00000545661.1_Nonsense_Mutation_p.R263*	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	263					cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		AGACTTTGTCCGACGACTGGC	0.652																																					p.R263X		.											.	.	.	0			c.C787T						.						17.0	23.0	21.0					16																	67681421		1948	4119	6067	SO:0001587	stop_gained	146206	exon11			TTTGTCCGACGAC	AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"""RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein"", ""leucine rich repeat containing 16C"""	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.787C>T	16.37:g.67681421C>T	ENSP00000334958:p.Arg263*	Somatic	79	0		WXS	Illumina HiSeq	.	80	4	NM_001013838	B8X2Z3	Nonsense_Mutation	SNP	ENST00000334583.6	37	CCDS45513.1	.	.	.	.	.	.	.	.	.	.	C	36	5.907449	0.97093	.	.	ENSG00000159753	ENST00000334583;ENST00000545661	.	.	.	5.22	3.2	0.36748	.	0.452267	0.21430	N	0.074676	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	-13.1802	6.1411	0.20261	0.3484:0.5634:0.0:0.0882	.	.	.	.	X	263	.	ENSP00000334958:R263X	R	+	1	2	RLTPR	66238922	0.039000	0.19947	1.000000	0.80357	0.970000	0.65996	1.120000	0.31271	0.526000	0.28541	0.563000	0.77884	CGA	.		0.652	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838	
LRP4	4038	hgsc.bcm.edu;bcgsc.ca	37	11	46897416	46897416	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr11:46897416G>T	ENST00000378623.1	-	26	3880	c.3638C>A	c.(3637-3639)cCc>cAc	p.P1213H	LRP4-AS1_ENST00000502049.2_RNA|LRP4-AS1_ENST00000531719.1_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	1213					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		CAGTCCATTGGGCCATCCTAG	0.592																																					p.P1213H		.											.	.	.	0			c.C3638A						.						127.0	95.0	106.0					11																	46897416		2201	4299	6500	SO:0001583	missense	4038	exon26			CCATTGGGCCATC	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"""Low density lipoprotein receptors"""	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.3638C>A	11.37:g.46897416G>T	ENSP00000367888:p.Pro1213His	Somatic	62	0		WXS	Illumina HiSeq	.	48	4	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	37	CCDS31478.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.763490	0.89932	.	.	ENSG00000134569	ENST00000378623	D	0.99571	-6.19	5.71	5.71	0.89125	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.99840	0.9927	H	0.98333	4.205	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.96757	0.9558	10	0.87932	D	0	.	19.8574	0.96764	0.0:0.0:1.0:0.0	.	1213	O75096	LRP4_HUMAN	H	1213	ENSP00000367888:P1213H	ENSP00000367888:P1213H	P	-	2	0	LRP4	46853992	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.667000	0.98616	2.704000	0.92352	0.555000	0.69702	CCC	.		0.592	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334	
PRKX	5613	hgsc.bcm.edu;bcgsc.ca	37	X	3573313	3573313	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chrX:3573313G>A	ENST00000262848.5	-	3	830	c.476C>T	c.(475-477)gCc>gTc	p.A159V	PRKX_ENST00000425240.1_5'UTR	NM_005044.4	NP_005035.1	P51817	PRKX_HUMAN	protein kinase, X-linked	159	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial tube morphogenesis (GO:0060562)|kidney morphogenesis (GO:0060993)|myeloid cell differentiation (GO:0030099)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of epithelial cell differentiation involved in kidney development (GO:2000696)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)			kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|skin(2)	12		all_lung(23;0.000396)|Lung NSC(23;0.00123)				GTACTCGATGGCACAGATGAT	0.577																																					p.A159V		.											.	.	.	0			c.C476T						.						123.0	104.0	110.0					X																	3573313		2203	4300	6503	SO:0001583	missense	5613	exon3			TCGATGGCACAGA		CCDS14125.1	Xp22.3	2008-08-01			ENSG00000183943	ENSG00000183943	2.7.11.1		9441	protein-coding gene	gene with protein product		300083				7633447	Standard	NM_005044		Approved	PKX1	uc010nde.3	P51817	OTTHUMG00000021087	ENST00000262848.5:c.476C>T	X.37:g.3573313G>A	ENSP00000262848:p.Ala159Val	Somatic	67	0		WXS	Illumina HiSeq	.	56	4	NM_005044		Missense_Mutation	SNP	ENST00000262848.5	37	CCDS14125.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.029967	0.75504	.	.	ENSG00000183943	ENST00000262848	T	0.14893	2.47	3.7	2.8	0.32819	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.31638	0.0803	M	0.84773	2.715	0.80722	D	1	P	0.47962	0.903	P	0.48552	0.581	T	0.19257	-1.0311	10	0.72032	D	0.01	-24.3364	11.2632	0.49095	0.0:0.1827:0.8173:0.0	.	159	P51817	PRKX_HUMAN	V	159	ENSP00000262848:A159V	ENSP00000262848:A159V	A	-	2	0	PRKX	3583313	1.000000	0.71417	0.015000	0.15790	0.874000	0.50279	7.990000	0.88215	0.429000	0.26202	0.529000	0.55759	GCC	.		0.577	PRKX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055659.1	NM_005044	
ZAK	51776	hgsc.bcm.edu	37	2	174123303	174123303	+	Intron	SNP	G	G	A	rs564710855|rs201302619		TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr2:174123303G>A	ENST00000375213.3	+	17	1437				MLTK_ENST00000409176.2_Intron|MLK7-AS1_ENST00000422703.1_RNA|MLK7-AS1_ENST00000423106.2_RNA	NM_016653.2	NP_057737.2	Q9NYL2	MLTK_HUMAN							activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell death (GO:0008219)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|DNA damage checkpoint (GO:0000077)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|response to radiation (GO:0009314)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)										TATTGAAAAAGGAAAAAAAAA	0.279																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	339751	.			GAAAAAGGAAAAA																												ENST00000375213.3:c.1360-124G>A	2.37:g.174123303G>A		Somatic	42	0		WXS	Illumina HiSeq	.	62	7	.	B3KPG2|Q53SX1|Q580W8|Q59GY5|Q86YW8|Q9HCC4|Q9HCC5|Q9HDD2|Q9NYE9	RNA	SNP	ENST00000375213.3	37	CCDS42777.1																																																																																			.		0.279	MLTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255401.1		
MT-CYB	4519	hgsc.bcm.edu	37	M	15744	15744	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chrM:15744T>C	ENST00000361789.2	+	1	998	c.998T>C	c.(997-999)cTc>cCc	p.L333P	MT-TT_ENST00000387460.2_RNA|MT-TP_ENST00000387461.2_RNA|MT-ND6_ENST00000361681.2_5'Flank|MT-TE_ENST00000387459.1_RNA			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	333					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						CGCAGACCTCCTCATTCTAAC	0.418																																					p.L333P		.											.	.	.	0			c.T998C						.																																			SO:0001583	missense	0	exon1			ACCTCCTCATTCT			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.998T>C	M.37:g.15744T>C	ENSP00000354554:p.Leu333Pro	Somatic	7	0		WXS	Illumina HiSeq	.	22	11	ENST00000361789	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Missense_Mutation	SNP	ENST00000361789.2	37																																																																																				.		0.418	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
CALD1	800	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	134632323	134632323	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr7:134632323G>A	ENST00000361675.2	+	8	1826	c.1597G>A	c.(1597-1599)Ggc>Agc	p.G533S	CALD1_ENST00000495522.1_Missense_Mutation_p.G298S|CALD1_ENST00000361901.2_Missense_Mutation_p.G278S|CALD1_ENST00000424922.1_Missense_Mutation_p.G272S|CALD1_ENST00000422748.1_Missense_Mutation_p.G304S|CALD1_ENST00000543443.1_Missense_Mutation_p.G283S|CALD1_ENST00000393118.2_Missense_Mutation_p.G298S|CALD1_ENST00000417172.1_Missense_Mutation_p.G278S|CALD1_ENST00000361388.2_Missense_Mutation_p.G304S			Q05682	CALD1_HUMAN	caldesmon 1	533					cellular component movement (GO:0006928)|muscle contraction (GO:0006936)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|calmodulin binding (GO:0005516)|tropomyosin binding (GO:0005523)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(15)|lung(10)	43						GGTGGAAGCCGGCAAAAGGCT	0.642																																					p.G533S		.											.	.	.	0			c.G1597A						.						17.0	17.0	17.0					7																	134632323		2170	4262	6432	SO:0001583	missense	800	exon8			GAAGCCGGCAAAA	M64110	CCDS5834.1, CCDS5835.1, CCDS5836.1, CCDS47716.1, CCDS47717.1, CCDS5836.2	7q33	2007-04-23			ENSG00000122786	ENSG00000122786			1441	protein-coding gene	gene with protein product		114213				1885618	Standard	NM_004342		Approved	CDM, H-CAD, L-CAD	uc003vrz.3	Q05682	OTTHUMG00000155407	ENST00000361675.2:c.1597G>A	7.37:g.134632323G>A	ENSP00000354826:p.Gly533Ser	Somatic	100	0		WXS	Illumina HiSeq	.	68	8	NM_033138	A8K0X1|Q13978|Q13979|Q14741|Q14742|Q9UD91	Missense_Mutation	SNP	ENST00000361675.2	37	CCDS5835.1	.	.	.	.	.	.	.	.	.	.	G	15.82	2.946812	0.53186	.	.	ENSG00000122786	ENST00000417172;ENST00000436461;ENST00000361388;ENST00000422748;ENST00000361675;ENST00000361901;ENST00000393118;ENST00000424922;ENST00000495522;ENST00000543443	T;T;T;T;T;T;T;T;T;T	0.52754	0.65;0.65;0.65;0.65;0.65;0.65;0.65;0.65;0.65;0.65	5.48	5.48	0.80851	.	0.000000	0.53938	D	0.000060	T	0.68026	0.2956	M	0.80028	2.48	0.45250	D	0.998251	D;D;D;D;D;D;D;D;D;D	0.76494	0.99;0.999;0.997;0.999;0.997;0.997;0.997;0.997;0.999;0.997	P;D;P;D;P;P;P;P;D;P	0.67725	0.778;0.922;0.867;0.953;0.79;0.839;0.79;0.79;0.953;0.9	T	0.64343	-0.6430	10	0.15952	T	0.53	-14.1336	18.1304	0.89599	0.0:0.0:1.0:0.0	.	227;283;304;298;272;298;278;304;533;278	B4DPW5;F5H1Z9;A8K0X1;E7EX44;Q05682-5;Q05682-3;Q05682-4;Q05682-2;Q05682;Q9NYG1	.;.;.;.;.;.;.;.;CALD1_HUMAN;.	S	278;278;304;304;533;278;298;272;298;283	ENSP00000398826:G278S;ENSP00000411476:G278S;ENSP00000355000:G304S;ENSP00000395710:G304S;ENSP00000354826:G533S;ENSP00000354513:G278S;ENSP00000376826:G298S;ENSP00000393621:G272S;ENSP00000419673:G298S;ENSP00000445641:G283S	ENSP00000355000:G304S	G	+	1	0	CALD1	134282863	1.000000	0.71417	0.823000	0.32752	0.003000	0.03518	5.972000	0.70448	2.569000	0.86673	0.563000	0.77884	GGC	.		0.642	CALD1-005	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339939.1	NM_033138	
SPTA1	6708	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	158605703	158605703	+	Splice_Site	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr1:158605703C>T	ENST00000368147.4	-	38	5612	c.5432G>A	c.(5431-5433)cGa>cAa	p.R1811Q		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1811					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)			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)					TCCCACTCACCGGGCCTTGGC	0.532																																					p.R1811Q		.											.	.	.	0			c.G5432A						.						74.0	77.0	76.0					1																	158605703		1926	4140	6066	SO:0001630	splice_region_variant	6708	exon38			ACTCACCGGGCCT	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.5432+1G>A	1.37:g.158605703C>T		Somatic	37	0		WXS	Illumina HiSeq	.	33	13	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	36	5.697918	0.96802	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.62639	0.01;0.14	5.65	5.65	0.86999	.	0.000000	0.27139	N	0.020757	D	0.84977	0.5592	H	0.96460	3.825	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88488	0.3073	9	.	.	.	.	18.4695	0.90767	0.0:1.0:0.0:0.0	.	1811	P02549	SPTA1_HUMAN	Q	1811	ENSP00000357130:R1811Q;ENSP00000357129:R1811Q	.	R	-	2	0	SPTA1	156872327	1.000000	0.71417	0.994000	0.49952	0.962000	0.63368	7.106000	0.77039	2.941000	0.99782	0.655000	0.94253	CGA	.		0.532	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	Missense_Mutation
LRRC1	55227	hgsc.bcm.edu	37	6	53764614	53764614	+	Nonsense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr6:53764614G>T	ENST00000370888.1	+	8	989	c.712G>T	c.(712-714)Gaa>Taa	p.E238*		NM_018214.4	NP_060684.4	Q9BTT6	LRRC1_HUMAN	leucine rich repeat containing 1	238						cytoplasm (GO:0005737)|membrane (GO:0016020)				cervix(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)		ACTTCCTGAAGAAATCAGTGG	0.388																																					p.E238X		.											LRRC1,NS,carcinoma,0,4	LRRC1	0	0			c.G712T						.						126.0	116.0	119.0					6																	53764614		1857	4086	5943	SO:0001587	stop_gained	55227	exon8			CCTGAAGAAATCA	AF332199	CCDS4953.2	6p12.2	2014-07-30	2003-11-19		ENSG00000137269	ENSG00000137269			14307	protein-coding gene	gene with protein product		608195	"""leucine-rich repeat-containing 1"""				Standard	NM_018214		Approved	dJ523E19.1, LANO, FLJ10775, FLJ11834	uc003pcd.1	Q9BTT6	OTTHUMG00000014885	ENST00000370888.1:c.712G>T	6.37:g.53764614G>T	ENSP00000359925:p.Glu238*	Somatic	136	0		WXS	Illumina HiSeq	.	109	4	NM_018214	Q5TGN3|Q9HAC0|Q9NVF1	Nonsense_Mutation	SNP	ENST00000370888.1	37	CCDS4953.2	.	.	.	.	.	.	.	.	.	.	G	39	7.555192	0.98355	.	.	ENSG00000137269	ENST00000370888	.	.	.	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.35671	T	0.21	.	18.693	0.91590	0.0:0.0:1.0:0.0	.	.	.	.	X	238	.	ENSP00000359925:E238X	E	+	1	0	LRRC1	53872573	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.429000	0.97481	2.654000	0.90174	0.650000	0.86243	GAA	.		0.388	LRRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040970.2	NM_025168	
COL9A1	1297	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	70964698	70964698	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr6:70964698G>A	ENST00000357250.6	-	24	1791	c.1633C>T	c.(1633-1635)Cgt>Tgt	p.R545C	COL9A1_ENST00000489611.1_5'UTR|COL9A1_ENST00000320755.7_Missense_Mutation_p.R302C|COL9A1_ENST00000370499.4_Missense_Mutation_p.R302C	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	545	Triple-helical region (COL2).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|organ morphogenesis (GO:0009887)|tissue homeostasis (GO:0001894)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(44)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)	80						ATCCCATCACGGCCATCCACA	0.458																																					p.R545C		.											.	.	.	0			c.C1633T						.						132.0	116.0	122.0					6																	70964698		2203	4300	6503	SO:0001583	missense	1297	exon24			CATCACGGCCATC		CCDS4971.1, CCDS47447.1	6q13	2013-05-07			ENSG00000112280	ENSG00000112280		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2217	protein-coding gene	gene with protein product		120210				1429648	Standard	NM_001851		Approved		uc003pfg.4	P20849	OTTHUMG00000014988	ENST00000357250.6:c.1633C>T	6.37:g.70964698G>A	ENSP00000349790:p.Arg545Cys	Somatic	78	0		WXS	Illumina HiSeq	.	72	17	NM_001851	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Missense_Mutation	SNP	ENST00000357250.6	37	CCDS4971.1	.	.	.	.	.	.	.	.	.	.	G	18.56	3.650358	0.67472	.	.	ENSG00000112280	ENST00000357250;ENST00000320755;ENST00000370499	D;D;D	0.93426	-3.22;-3.22;-3.22	5.38	5.38	0.77491	.	0.051053	0.85682	D	0.000000	D	0.95943	0.8679	M	0.74881	2.28	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;P	0.68765	0.935;0.96;0.861	D	0.95727	0.8771	10	0.59425	D	0.04	.	17.666	0.88203	0.0:0.0:1.0:0.0	.	545;302;118	P20849;P20849-2;B3KWS8	CO9A1_HUMAN;.;.	C	545;302;302	ENSP00000349790:R545C;ENSP00000315252:R302C;ENSP00000359530:R302C	ENSP00000315252:R302C	R	-	1	0	COL9A1	71021419	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.042000	0.89430	2.680000	0.91292	0.655000	0.94253	CGT	.		0.458	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2		
OR10H4	126541	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	16060302	16060302	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr19:16060302C>T	ENST00000322107.1	+	1	485	c.485C>T	c.(484-486)aCg>aTg	p.T162M		NM_001004465.1	NP_001004465.1	Q8NGA5	O10H4_HUMAN	olfactory receptor, family 10, subfamily H, member 4	162						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	17						ATGGTGACAACGATAGTTTTC	0.502																																					p.T162M		.											.	.	.	0			c.C485T						.						241.0	202.0	215.0					19																	16060302		2203	4300	6503	SO:0001583	missense	126541	exon1			TGACAACGATAGT	AC011517	CCDS32941.1	19p13.12	2013-09-24			ENSG00000176231	ENSG00000176231		"""GPCR / Class A : Olfactory receptors"""	15388	protein-coding gene	gene with protein product							Standard	NM_001004465		Approved		uc010xov.2	Q8NGA5	OTTHUMG00000182268	ENST00000322107.1:c.485C>T	19.37:g.16060302C>T	ENSP00000318834:p.Thr162Met	Somatic	68	0		WXS	Illumina HiSeq	.	37	10	NM_001004465	Q6IFJ2|Q96R57	Missense_Mutation	SNP	ENST00000322107.1	37	CCDS32941.1	.	.	.	.	.	.	.	.	.	.	N	2.045	-0.419112	0.04766	.	.	ENSG00000176231	ENST00000322107	T	0.00265	8.39	1.53	-1.37	0.09056	GPCR, rhodopsin-like superfamily (1);	1.568010	0.04672	N	0.410809	T	0.00210	0.0006	L	0.56199	1.76	0.09310	N	1	B	0.14805	0.011	B	0.14023	0.01	T	0.35748	-0.9776	10	0.40728	T	0.16	.	6.7009	0.23225	0.0:0.4541:0.0:0.5459	.	162	Q8NGA5	O10H4_HUMAN	M	162	ENSP00000318834:T162M	ENSP00000318834:T162M	T	+	2	0	OR10H4	15921302	0.000000	0.05858	0.008000	0.14137	0.007000	0.05969	-4.231000	0.00269	-1.400000	0.02061	-1.523000	0.00931	ACG	.		0.502	OR10H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460311.1		
PDGFD	80310	hgsc.bcm.edu	37	11	103870948	103870948	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr11:103870948C>T	ENST00000393158.2	-	2	339	c.160G>A	c.(160-162)Gag>Aag	p.E54K	PDGFD_ENST00000302251.5_Missense_Mutation_p.E48K			Q9GZP0	PDGFD_HUMAN	platelet derived growth factor D	54	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cellular response to amino acid stimulus (GO:0071230)|multicellular organismal development (GO:0007275)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)		p.E54K(2)		biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)|prostate(3)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Melanoma(852;0.0563)|all_neural(303;0.165)		BRCA - Breast invasive adenocarcinoma(274;0.00136)|Epithelial(105;0.111)		TGGATGGTCTCATCTCTTCGG	0.468																																					p.E54K		.											PDGFD_ENST00000393158,NS,carcinoma,0,2	PDGFD_ENST00000393158	0	2	Substitution - Missense(2)	lung(2)	c.G160A						.						191.0	159.0	170.0					11																	103870948		2202	4299	6501	SO:0001583	missense	80310	exon2			TGGTCTCATCTCT	AF113216	CCDS8326.1, CCDS41703.1	11q22.3	2008-02-05			ENSG00000170962	ENSG00000170962			30620	protein-coding gene	gene with protein product	"""spinal cord derived growth factor B"""	609673				11162582, 11980634	Standard	NM_033135		Approved	SCDGF-B, MSTP036, IEGF	uc001phq.3	Q9GZP0	OTTHUMG00000165953	ENST00000393158.2:c.160G>A	11.37:g.103870948C>T	ENSP00000376865:p.Glu54Lys	Somatic	82	0		WXS	Illumina HiSeq	.	45	2	NM_025208	A8K9T6|Q9BWV5	Missense_Mutation	SNP	ENST00000393158.2	37	CCDS41703.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.028096	0.75390	.	.	ENSG00000170962	ENST00000393158;ENST00000302251;ENST00000529268	T;T;T	0.26957	1.74;1.77;1.7	5.85	4.93	0.64822	CUB (2);	0.160644	0.53938	D	0.000051	T	0.15565	0.0375	N	0.11201	0.11	0.58432	D	0.999991	B;B	0.32409	0.37;0.319	B;B	0.34242	0.178;0.111	T	0.12268	-1.0554	10	0.22109	T	0.4	-23.4081	15.3594	0.74460	0.0:0.9318:0.0:0.0682	.	54;48	Q9GZP0;Q9GZP0-2	PDGFD_HUMAN;.	K	54;48;77	ENSP00000376865:E54K;ENSP00000302193:E48K;ENSP00000432909:E77K	ENSP00000302193:E48K	E	-	1	0	PDGFD	103376158	1.000000	0.71417	0.793000	0.32043	0.957000	0.61999	4.631000	0.61304	2.765000	0.95021	0.561000	0.74099	GAG	.		0.468	PDGFD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387231.2	NM_025208	
CNTN2	6900	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	205027755	205027755	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr1:205027755G>T	ENST00000331830.4	+	5	735	c.451G>T	c.(451-453)Gtg>Ttg	p.V151L		NM_005076.3	NP_005067.1	Q02246	CNTN2_HUMAN	contactin 2 (axonal)	151	Ig-like C2-type 2.				adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|central nervous system myelination (GO:0022010)|cerebral cortex GABAergic interneuron migration (GO:0021853)|clustering of voltage-gated potassium channels (GO:0045163)|establishment of protein localization to juxtaparanode region of axon (GO:0071206)|learning (GO:0007612)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|positive regulation of protein processing (GO:0010954)|presynaptic membrane organization (GO:0097090)|receptor internalization (GO:0031623)|regulation of astrocyte differentiation (GO:0048710)|regulation of axon diameter (GO:0031133)|regulation of neuronal synaptic plasticity (GO:0048168)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|juxtaparanode region of axon (GO:0044224)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated potassium channel complex (GO:0008076)	carbohydrate binding (GO:0030246)|identical protein binding (GO:0042802)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(11)|lung(23)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	54	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			AGGCTGGGGGGTGATGTTGCC	0.607																																					p.V151L	Melanoma(183;2548 2817 37099 41192)	.											.	.	.	0			c.G451T						.						48.0	47.0	48.0					1																	205027755		2203	4300	6503	SO:0001583	missense	6900	exon5			TGGGGGGTGATGT	X67734	CCDS1449.1	1q32.1	2013-02-11			ENSG00000184144	ENSG00000184144		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2172	protein-coding gene	gene with protein product		190197		TAX, AXT		8307567, 8586965	Standard	NM_005076		Approved	TAG-1, TAX1	uc001hbr.3	Q02246	OTTHUMG00000037105	ENST00000331830.4:c.451G>T	1.37:g.205027755G>T	ENSP00000330633:p.Val151Leu	Somatic	46	0		WXS	Illumina HiSeq	.	32	13	NM_005076	P78432|Q5T054	Missense_Mutation	SNP	ENST00000331830.4	37	CCDS1449.1	.	.	.	.	.	.	.	.	.	.	G	15.34	2.805218	0.50315	.	.	ENSG00000184144	ENST00000331830	T	0.03580	3.88	4.8	4.8	0.61643	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.47852	D	0.000202	T	0.04452	0.0122	L	0.33137	0.985	0.43608	D	0.995972	B;B;B	0.15719	0.014;0.014;0.007	B;B;B	0.17098	0.017;0.017;0.017	T	0.48927	-0.8991	10	0.20046	T	0.44	.	17.4492	0.87587	0.0:0.0:1.0:0.0	.	151;151;42	A1L3A3;Q02246;Q68DA2	.;CNTN2_HUMAN;.	L	151	ENSP00000330633:V151L	ENSP00000330633:V151L	V	+	1	0	CNTN2	203294378	0.992000	0.36948	0.990000	0.47175	0.938000	0.57974	2.143000	0.42187	2.223000	0.72356	0.555000	0.69702	GTG	.		0.607	CNTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090080.3	NM_005076	
BRCA1	672	hgsc.bcm.edu	37	17	41219699	41219699	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr17:41219699T>G	ENST00000357654.3	-	16	5118	c.5000A>C	c.(4999-5001)aAg>aCg	p.K1667T	BRCA1_ENST00000491747.2_Missense_Mutation_p.K563T|BRCA1_ENST00000493795.1_Missense_Mutation_p.K1620T|BRCA1_ENST00000352993.3_Missense_Mutation_p.K525T|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000471181.2_Missense_Mutation_p.K1688T|BRCA1_ENST00000468300.1_Missense_Mutation_p.K563T|BRCA1_ENST00000346315.3_Intron|BRCA1_ENST00000354071.3_Intron|BRCA1_ENST00000351666.3_Missense_Mutation_p.K484T|BRCA1_ENST00000591534.1_Missense_Mutation_p.K158T|BRCA1_ENST00000309486.4_Missense_Mutation_p.K1371T	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	1667	BRCT 1. {ECO:0000255|PROSITE- ProRule:PRU00033}.				androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		TCTGGCAAACTTGTACACGAG	0.343			"""D, Mis, N, F, S"""		ovarian	"""breast, ovarian"""		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.K1688T		.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	BRCA1,NS,carcinoma,0,1	BRCA1	0	0			c.A5063C						.						122.0	118.0	119.0					17																	41219699		2202	4300	6502	SO:0001583	missense	672	exon17	Familial Cancer Database		GCAAACTTGTACA	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1100	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 1"", ""protein phosphatase 1, regulatory subunit 53"""	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.5000A>C	17.37:g.41219699T>G	ENSP00000350283:p.Lys1667Thr	Somatic	47	0		WXS	Illumina HiSeq	.	42	2	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	37	CCDS11453.1	.	.	.	.	.	.	.	.	.	.	T	14.18	2.457817	0.43634	.	.	ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000352993;ENST00000351666;ENST00000309486;ENST00000468300;ENST00000393691;ENST00000471181;ENST00000493795;ENST00000491747;ENST00000478531;ENST00000484087;ENST00000493919	T;T;T;T;T;T;T;T;T;T	0.80393	-1.37;-1.37;-1.37;-1.37;-1.37;-1.37;-1.37;-1.37;-1.37;-1.37	5.24	4.16	0.48862	BRCT (4);	0.000000	0.53938	D	0.000051	D	0.87997	0.6319	M	0.79926	2.475	0.37050	D	0.897536	D;D;D;D;D;D;D;D	0.76494	0.997;0.958;0.994;0.997;0.974;0.997;0.988;0.999	D;P;D;D;D;D;P;D	0.79108	0.983;0.88;0.964;0.965;0.964;0.992;0.906;0.987	D	0.89266	0.3601	10	0.87932	D	0	-12.5409	8.0086	0.30340	0.0:0.0935:0.0:0.9065	.	563;516;562;564;563;1689;1667;1667	E7EUM2;B4DES0;E7ETR2;P38398-3;Q6IN79;E9PFC7;P38398;P38398-2	.;.;.;.;.;.;BRCA1_HUMAN;.	T	1667;1688;525;484;1371;563;516;1689;1620;562;563;438;517	ENSP00000350283:K1667T;ENSP00000312236:K525T;ENSP00000338007:K484T;ENSP00000310938:K1371T;ENSP00000417148:K563T;ENSP00000377294:K516T;ENSP00000418775:K1620T;ENSP00000420412:K563T;ENSP00000419481:K438T;ENSP00000418819:K517T	ENSP00000310938:K1371T	K	-	2	0	BRCA1	38473225	1.000000	0.71417	0.982000	0.44146	0.304000	0.27724	2.884000	0.48562	0.937000	0.37394	0.454000	0.30748	AAG	.		0.343	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294	
KAT6A	7994	hgsc.bcm.edu	37	8	41806877	41806877	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr8:41806877G>T	ENST00000396930.3	-	11	2146	c.1603C>A	c.(1603-1605)Ccc>Acc	p.P535T	KAT6A_ENST00000265713.2_Missense_Mutation_p.P535T|KAT6A_ENST00000406337.1_Missense_Mutation_p.P535T|KAT6A_ENST00000485568.1_Missense_Mutation_p.P535T	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	535	Catalytic.|Interaction with PML.|Interaction with RUNX1-1.|MYST-type HAT.|Mediates interaction with BRPF1, required for histone H3 acetyltransferase activity.				aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.P535S(1)									TACAATTTGGGCAGCCTGTAA	0.348																																					p.P535T		.											MYST3,NS,carcinoma,0,1	MYST3	0	1	Substitution - Missense(1)	lung(1)	c.C1603A						.						32.0	34.0	33.0					8																	41806877		2202	4299	6501	SO:0001583	missense	7994	exon11			ATTTGGGCAGCCT	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	13013	protein-coding gene	gene with protein product	"""Monocytic leukemia zinc finger protein"""	601408	"""runt-related transcription factor binding protein 2"", ""MYST histone acetyltransferase (monocytic leukemia) 3"""	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.1603C>A	8.37:g.41806877G>T	ENSP00000380136:p.Pro535Thr	Somatic	57	0		WXS	Illumina HiSeq	.	77	3	NM_001099412	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	37	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	G	11.07	1.529920	0.27387	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930;ENST00000418721;ENST00000485568	T;T;T;D	0.84516	0.17;0.17;0.17;-1.86	5.24	5.24	0.73138	.	0.000000	0.64402	D	0.000001	D	0.89458	0.6721	L	0.49126	1.545	0.80722	D	1	B;D	0.58268	0.382;0.982	B;P	0.59595	0.289;0.86	D	0.89920	0.4058	10	0.62326	D	0.03	-15.7132	19.2204	0.93795	0.0:0.0:1.0:0.0	.	535;535	A5PLL3;Q92794	.;KAT6A_HUMAN	T	535;535;535;115;535	ENSP00000265713:P535T;ENSP00000385888:P535T;ENSP00000380136:P535T;ENSP00000430606:P535T	ENSP00000265713:P535T	P	-	1	0	KAT6A	41926034	1.000000	0.71417	1.000000	0.80357	0.307000	0.27823	9.476000	0.97823	2.618000	0.88619	0.591000	0.81541	CCC	.		0.348	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766	
CD6	923	hgsc.bcm.edu	37	11	60780933	60780933	+	Silent	SNP	C	C	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr11:60780933C>A	ENST00000313421.7	+	7	1375	c.1189C>A	c.(1189-1191)Cgg>Agg	p.R397R	CD6_ENST00000545105.1_3'UTR|CD6_ENST00000352009.5_Silent_p.R397R|CD6_ENST00000452451.2_Silent_p.R397R|CD6_ENST00000346437.4_Silent_p.R397R|CD6_ENST00000344028.5_Silent_p.R397R	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	397					cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						CAAGGAATCTCGGGAGCTAAT	0.443																																					p.R397R	Pancreas(169;904 2017 4767 38890 42505)	.											CD6_ENST00000313421,caecum,carcinoma,0,2	CD6_ENST00000313421	0	0			c.C1189A						.						189.0	192.0	191.0					11																	60780933		2203	4299	6502	SO:0001819	synonymous_variant	923	exon7			GAATCTCGGGAGC		CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"""CD molecules"""	1691	protein-coding gene	gene with protein product		186720	"""CD6 antigen"""			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.1189C>A	11.37:g.60780933C>A		Somatic	40	0		WXS	Illumina HiSeq	.	45	2	NM_006725	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	Silent	SNP	ENST00000313421.7	37	CCDS7999.1																																																																																			.		0.443	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725	
GSDMA	284110	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	38128387	38128387	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr17:38128387C>A	ENST00000301659.4	+	6	779	c.661C>A	c.(661-663)Cca>Aca	p.P221T		NM_178171.4	NP_835465.2	Q96QA5	GSDMA_HUMAN	gasdermin A	221					apoptotic process (GO:0006915)	perinuclear region of cytoplasm (GO:0048471)				NS(1)|endometrium(2)|large_intestine(3)|lung(1)	7						CACAGATATTCCACATATCTG	0.517																																					p.P221T		.											.	.	.	0			c.C661A						.						40.0	37.0	38.0					17																	38128387		1831	4075	5906	SO:0001583	missense	284110	exon6			GATATTCCACATA	AB093591	CCDS45669.1	17q21.2	2008-07-31	2008-07-31	2008-07-31		ENSG00000167914			13311	protein-coding gene	gene with protein product		611218	"""gasdermin"", ""gasdermin 1"""	GSDM, GSDM1		12883658, 15010812, 17350798	Standard	NM_178171		Approved	FLJ39120	uc002htl.1	Q96QA5		ENST00000301659.4:c.661C>A	17.37:g.38128387C>A	ENSP00000301659:p.Pro221Thr	Somatic	58	0		WXS	Illumina HiSeq	.	42	12	NM_178171	Q32MC5|Q86VE7|Q8N1M6	Missense_Mutation	SNP	ENST00000301659.4	37	CCDS45669.1	.	.	.	.	.	.	.	.	.	.	C	15.73	2.918420	0.52546	.	.	ENSG00000167914	ENST00000301659	T	0.21543	2.0	5.72	5.72	0.89469	.	0.410869	0.23573	N	0.046724	T	0.44456	0.1294	M	0.68317	2.08	0.37531	D	0.917934	D	0.89917	1.0	D	0.75484	0.986	T	0.32877	-0.9890	10	0.35671	T	0.21	-19.718	15.3863	0.74703	0.0:1.0:0.0:0.0	.	221	Q96QA5	GSDMA_HUMAN	T	221	ENSP00000301659:P221T	ENSP00000301659:P221T	P	+	1	0	GSDMA	35381913	0.865000	0.29922	0.786000	0.31890	0.648000	0.38561	3.521000	0.53472	2.711000	0.92665	0.655000	0.94253	CCA	.		0.517	GSDMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446847.1	NM_178171	
GPBP1	65056	hgsc.bcm.edu;broad.mit.edu	37	5	56557038	56557038	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr5:56557038A>G	ENST00000506184.2	+	11	2297	c.1192A>G	c.(1192-1194)Agt>Ggt	p.S398G	GPBP1_ENST00000511209.1_Missense_Mutation_p.S390G|GPBP1_ENST00000264779.6_Missense_Mutation_p.S405G|GPBP1_ENST00000424459.3_Missense_Mutation_p.S418G|GPBP1_ENST00000514387.2_Missense_Mutation_p.S227G|GPBP1_ENST00000538707.1_Missense_Mutation_p.S405G|GPBP1_ENST00000454432.2_Missense_Mutation_p.S418G			Q86WP2	GPBP1_HUMAN	GC-rich promoter binding protein 1	398					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	19		Lung NSC(810;0.000861)|Prostate(74;0.0305)|Breast(144;0.222)		OV - Ovarian serous cystadenocarcinoma(10;7.64e-39)		GCAGGAAGACAGTGAAAATGA	0.363																																					p.S405G		.											.	.	.	0			c.A1213G						.						156.0	158.0	157.0					5																	56557038		2203	4299	6502	SO:0001583	missense	65056	exon10			GAAGACAGTGAAA		CCDS34162.1, CCDS47211.1, CCDS47212.1, CCDS47212.2, CCDS56368.1	5q11.2	2008-02-05				ENSG00000062194			29520	protein-coding gene	gene with protein product		608412				12842993	Standard	NM_022913		Approved	DKFZp761C169, vasculin	uc003jrk.4	Q86WP2		ENST00000506184.2:c.1192A>G	5.37:g.56557038A>G	ENSP00000421202:p.Ser398Gly	Somatic	87	0		WXS	Illumina HiSeq	.	94	4	NM_001127236	A6NKW3|Q6NSH6|Q9H0D4|Q9H785|Q9NSN4	Missense_Mutation	SNP	ENST00000506184.2	37	CCDS34162.1	.	.	.	.	.	.	.	.	.	.	A	15.13	2.741204	0.49151	.	.	ENSG00000062194	ENST00000424459;ENST00000514387;ENST00000506184;ENST00000454432;ENST00000511209;ENST00000264779;ENST00000538707	T;T;T;T;T;T;T	0.50277	0.75;0.75;0.75;0.75;0.75;0.75;0.75	5.81	3.45	0.39498	.	0.245382	0.48767	D	0.000169	T	0.29524	0.0736	N	0.21448	0.665	0.33001	D	0.526215	B;B;B;B	0.12013	0.005;0.001;0.0;0.0	B;B;B;B	0.14578	0.011;0.004;0.003;0.004	T	0.31194	-0.9952	10	0.15499	T	0.54	-19.6388	9.6177	0.39701	0.8592:0.0:0.1408:0.0	.	418;405;390;398	D4PHA4;Q86WP2-2;Q86WP2-3;Q86WP2	.;.;.;GPBP1_HUMAN	G	418;227;398;418;390;405;405	ENSP00000401596:S418G;ENSP00000421709:S227G;ENSP00000421202:S398G;ENSP00000403522:S418G;ENSP00000422337:S390G;ENSP00000264779:S405G;ENSP00000440090:S405G	ENSP00000264779:S405G	S	+	1	0	GPBP1	56592795	1.000000	0.71417	0.998000	0.56505	0.953000	0.61014	4.143000	0.58051	1.019000	0.39547	0.533000	0.62120	AGT	.		0.363	GPBP1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000374496.1	NM_022913	
CRB1	23418	hgsc.bcm.edu	37	1	197313409	197313409	+	Splice_Site	SNP	A	A	G			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr1:197313409A>G	ENST00000367400.3	+	3	787		c.e3-1		CRB1_ENST00000367399.2_Intron|CRB1_ENST00000535699.1_Splice_Site|CRB1_ENST00000543483.1_Splice_Site|CRB1_ENST00000538660.1_Splice_Site	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated						cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						CTTTTTTAAAAGGTGTAAACT	0.383																																					.		.											.	.	.	0			c.446-2A>G						.						136.0	141.0	139.0					1																	197313409		2203	4300	6503	SO:0001630	splice_region_variant	23418	exon5			TTTAAAAGGTGTA		CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"""crumbs (Drosophila) homolog 1"", ""crumbs homolog 1 (Drosophila)"""	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.653-1A>G	1.37:g.197313409A>G		Somatic	106	0		WXS	Illumina HiSeq	.	90	4	NM_001257965	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Splice_Site	SNP	ENST00000367400.3	37	CCDS1390.1	.	.	.	.	.	.	.	.	.	.	A	10.17	1.276795	0.23307	.	.	ENSG00000134376	ENST00000535699;ENST00000538660;ENST00000367400	.	.	.	4.55	4.55	0.56014	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5951	0.68400	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CRB1	195580032	1.000000	0.71417	0.748000	0.31131	0.064000	0.16182	8.328000	0.90014	1.979000	0.57680	0.455000	0.32223	.	.		0.383	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	NM_201253	Intron
EFNA5	1946	hgsc.bcm.edu	37	5	106762982	106762982	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr5:106762982G>T	ENST00000333274.6	-	2	635	c.354C>A	c.(352-354)ttC>ttA	p.F118L	EFNA5_ENST00000509503.1_Missense_Mutation_p.F118L	NM_001962.2	NP_001953.1	P52803	EFNA5_HUMAN	ephrin-A5	118	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.				axon guidance (GO:0007411)|ephrin receptor signaling pathway (GO:0048013)|nervous system development (GO:0007399)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell-cell adhesion (GO:0022407)|regulation of focal adhesion assembly (GO:0051893)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rho GTPase activity (GO:0032319)|retinal ganglion cell axon guidance (GO:0031290)	anchored component of external side of plasma membrane (GO:0031362)|plasma membrane (GO:0005886)	chemorepellent activity (GO:0045499)|ephrin receptor binding (GO:0046875)			large_intestine(6)	6		all_cancers(142;5.15e-06)|all_epithelial(76;4.39e-07)|Prostate(80;0.00726)|Lung NSC(167;0.0736)|Ovarian(225;0.0797)|all_lung(232;0.0854)|Colorectal(57;0.241)		Epithelial(69;1.25e-12)|OV - Ovarian serous cystadenocarcinoma(64;1.32e-11)|BRCA - Breast invasive adenocarcinoma(61;0.0376)|COAD - Colon adenocarcinoma(37;0.109)		TGAAGAGCTGGAATTTTTCAG	0.463																																					p.F118L		.											.	.	.	0			c.C354A						.						67.0	68.0	68.0					5																	106762982		2202	4300	6502	SO:0001583	missense	1946	exon2			GAGCTGGAATTTT	U26403	CCDS4097.1	5q21	2011-03-09			ENSG00000184349	ENSG00000184349		"""Ephrins"""	3225	protein-coding gene	gene with protein product		601535		EPLG7		8661153, 9245480	Standard	NM_001962		Approved	AF1, LERK7	uc003kol.3	P52803	OTTHUMG00000128741	ENST00000333274.6:c.354C>A	5.37:g.106762982G>T	ENSP00000328777:p.Phe118Leu	Somatic	80	0		WXS	Illumina HiSeq	.	67	3	NM_001962		Missense_Mutation	SNP	ENST00000333274.6	37	CCDS4097.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.213334	0.79352	.	.	ENSG00000184349	ENST00000333274;ENST00000509503	T;T	0.58940	0.3;0.3	6.17	6.17	0.99709	Ephrin, conserved site (1);Cupredoxin (2);	0.000000	0.85682	D	0.000000	T	0.80008	0.4545	M	0.90252	3.1	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.987	T	0.82460	-0.0446	10	0.62326	D	0.03	-15.634	13.9957	0.64397	0.0685:0.0:0.9315:0.0	.	118;118	D6RDV5;P52803	.;EFNA5_HUMAN	L	118	ENSP00000328777:F118L;ENSP00000426989:F118L	ENSP00000328777:F118L	F	-	3	2	EFNA5	106790881	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.795000	0.75140	2.941000	0.99782	0.655000	0.94253	TTC	.		0.463	EFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250652.1	NM_001962	
KIF9	64147	hgsc.bcm.edu	37	3	47284677	47284677	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr3:47284677C>T	ENST00000265529.3	-	17	2253	c.1573G>A	c.(1573-1575)Gtt>Att	p.V525I	KIF9_ENST00000444589.2_Intron|KIF9_ENST00000335044.2_Missense_Mutation_p.V525I|KIF9-AS1_ENST00000429315.3_RNA|KIF9_ENST00000452770.2_Missense_Mutation_p.V525I|KIF9_ENST00000487440.1_5'UTR|KIF9_ENST00000352910.4_Intron			Q9HAQ2	KIF9_HUMAN	kinesin family member 9	525					ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|extracellular matrix disassembly (GO:0022617)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle disassembly (GO:1903008)|regulation of podosome assembly (GO:0071801)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|podosome (GO:0002102)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|protein dimerization activity (GO:0046983)	p.V525I(1)		central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(15)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)	34		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000284)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		GAGGTGGAAACGTAATCCAAG	0.562																																					p.V525I	Colon(44;962 1147 15977 24541)	.											KIF9,colon,carcinoma,0,1	KIF9	0	1	Substitution - Missense(1)	large_intestine(1)	c.G1573A						.						102.0	82.0	88.0					3																	47284677		2203	4300	6503	SO:0001583	missense	64147	exon16			TGGAAACGTAATC	AF311212	CCDS2751.1, CCDS2752.1	3p21.31	2008-03-03			ENSG00000088727	ENSG00000088727		"""Kinesins"""	16666	protein-coding gene	gene with protein product		607910				11483511	Standard	NM_022342		Approved	MGC104186	uc003cqx.3	Q9HAQ2	OTTHUMG00000133512	ENST00000265529.3:c.1573G>A	3.37:g.47284677C>T	ENSP00000265529:p.Val525Ile	Somatic	54	0		WXS	Illumina HiSeq	.	29	2	NM_182902	Q86Z28|Q9H8A4	Missense_Mutation	SNP	ENST00000265529.3	37	CCDS2752.1	.	.	.	.	.	.	.	.	.	.	C	2.411	-0.335321	0.05278	.	.	ENSG00000088727	ENST00000335044;ENST00000265529;ENST00000452770	T;T;T	0.43294	0.95;0.95;0.95	5.49	-11.0	0.00169	.	1.478100	0.03515	N	0.220081	T	0.20740	0.0499	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.05750	-1.0866	10	0.22706	T	0.39	.	4.4683	0.11700	0.2179:0.1431:0.0733:0.5657	.	525	Q9HAQ2	KIF9_HUMAN	I	525	ENSP00000333942:V525I;ENSP00000265529:V525I;ENSP00000391100:V525I	ENSP00000265529:V525I	V	-	1	0	KIF9	47259681	0.000000	0.05858	0.000000	0.03702	0.073000	0.16967	-4.108000	0.00293	-2.799000	0.00353	-0.291000	0.09656	GTT	.		0.562	KIF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257475.2		
EPHA2	1969	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	16462176	16462176	+	Nonsense_Mutation	SNP	T	T	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr1:16462176T>A	ENST00000358432.5	-	6	1556	c.1402A>T	c.(1402-1404)Aag>Tag	p.K468*		NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2	468	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|axial mesoderm formation (GO:0048320)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|ephrin receptor signaling pathway (GO:0048013)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinocyte differentiation (GO:0030216)|lens fiber cell morphogenesis (GO:0070309)|mammary gland epithelial cell proliferation (GO:0033598)|multicellular organismal development (GO:0007275)|negative regulation of protein kinase B signaling (GO:0051898)|neural tube development (GO:0021915)|neuron differentiation (GO:0030182)|notochord cell development (GO:0060035)|notochord formation (GO:0014028)|osteoblast differentiation (GO:0001649)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|post-anal tail morphogenesis (GO:0036342)|protein kinase B signaling (GO:0043491)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of lamellipodium assembly (GO:0010591)|response to growth factor (GO:0070848)|skeletal system development (GO:0001501)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell projection (GO:0042995)|cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)|Regorafenib(DB08896)	ACCTCGTACTTCCACACTCGG	0.652																																					p.K468X		.											.	.	.	0			c.A1402T						.						64.0	61.0	62.0					1																	16462176		2203	4300	6503	SO:0001587	stop_gained	1969	exon6			CGTACTTCCACAC	BC037166	CCDS169.1	1p36	2013-02-11	2004-10-28		ENSG00000142627	ENSG00000142627	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3386	protein-coding gene	gene with protein product		176946	"""EphA2"""	ECK		9119409	Standard	NM_004431		Approved		uc001aya.2	P29317	OTTHUMG00000009527	ENST00000358432.5:c.1402A>T	1.37:g.16462176T>A	ENSP00000351209:p.Lys468*	Somatic	75	0		WXS	Illumina HiSeq	.	45	9	NM_004431	B5A968|Q8N3Z2	Nonsense_Mutation	SNP	ENST00000358432.5	37	CCDS169.1	.	.	.	.	.	.	.	.	.	.	T	39	7.868116	0.98534	.	.	ENSG00000142627	ENST00000358432	.	.	.	5.26	5.26	0.73747	.	0.000000	0.56097	D	0.000039	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.23891	T	0.37	.	13.1243	0.59344	0.0:0.0:0.0:1.0	.	.	.	.	X	468	.	ENSP00000351209:K468X	K	-	1	0	EPHA2	16334763	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.069000	0.41481	1.996000	0.58369	0.454000	0.30748	AAG	.		0.652	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	NM_004431	
SLAIN2	57606	hgsc.bcm.edu;bcgsc.ca	37	4	48385777	48385777	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr4:48385777C>A	ENST00000264313.6	+	6	1754	c.1336C>A	c.(1336-1338)Cgt>Agt	p.R446S	SLAIN2_ENST00000512093.1_Missense_Mutation_p.R253S	NM_020846.1	NP_065897.1	Q9P270	SLAI2_HUMAN	SLAIN motif family, member 2	446					cytoplasmic microtubule organization (GO:0031122)|microtubule nucleation (GO:0007020)|positive regulation of microtubule polymerization (GO:0031116)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(1)	13						AGGAATACCTCGTATGCAACC	0.383																																					p.R446S		.											.	.	.	0			c.C1336A						.						67.0	66.0	66.0					4																	48385777		1880	4107	5987	SO:0001583	missense	57606	exon6			ATACCTCGTATGC	BC006139	CCDS47051.1	4p12	2008-02-05	2006-09-12	2006-09-12	ENSG00000109171	ENSG00000109171			29282	protein-coding gene	gene with protein product		610492	"""KIAA1458"""	KIAA1458		16546155	Standard	NM_020846		Approved	FLJ21611	uc003gya.4	Q9P270	OTTHUMG00000161701	ENST00000264313.6:c.1336C>A	4.37:g.48385777C>A	ENSP00000264313:p.Arg446Ser	Somatic	60	0		WXS	Illumina HiSeq	.	59	4	NM_020846	A8K4P1|Q8N5R3	Missense_Mutation	SNP	ENST00000264313.6	37	CCDS47051.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.6|29.6	5.022783|5.022783	0.93462|0.93462	.|.	.|.	ENSG00000109171|ENSG00000109171	ENST00000264313;ENST00000512093|ENST00000510595	.|.	.|.	.|.	5.68|5.68	5.68|5.68	0.88126|0.88126	.|.	0.113705|.	0.64402|.	D|.	0.000008|.	T|.	0.78748|.	0.4332|.	M|M	0.79475|0.79475	2.455|2.455	0.80722|0.80722	D|D	1|1	P;D|.	0.57571|.	0.632;0.98|.	B;P|.	0.53861|.	0.278;0.736|.	T|.	0.78163|.	-0.2311|.	9|.	0.37606|.	T|.	0.19|.	-6.9554|-6.9554	19.7895|19.7895	0.96452|0.96452	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	116;446|.	Q9H705;Q9P270|.	.;SLAI2_HUMAN|.	S|X	446;253|28	.|.	ENSP00000264313:R446S|.	R|S	+|+	1|2	0|0	SLAIN2|SLAIN2	48080534|48080534	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	6.966000|6.966000	0.76073|0.76073	2.675000|2.675000	0.91044|0.91044	0.561000|0.561000	0.74099|0.74099	CGT|TCG	.		0.383	SLAIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365807.4	NM_020846	
FBXO42	54455	hgsc.bcm.edu	37	1	16632409	16632409	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr1:16632409C>T	ENST00000375592.3	-	3	472	c.256G>A	c.(256-258)Gcc>Acc	p.A86T	FBXO42_ENST00000478089.1_5'UTR	NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	86	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.									autonomic_ganglia(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	26		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)		CACTGATGGGCTACACCTAAG	0.408																																					p.A86T		.											FBXO42,NS,carcinoma,0,1	FBXO42	0	0			c.G256A						.						156.0	135.0	143.0					1																	16632409		2203	4300	6503	SO:0001583	missense	54455	exon3			GATGGGCTACACC	BC063864	CCDS30613.1	1p36.23-p36.11	2008-02-05			ENSG00000037637	ENSG00000037637		"""F-boxes /  ""other"""""	29249	protein-coding gene	gene with protein product		609109				10718198	Standard	XM_006710698		Approved	KIAA1332, Fbx42	uc001ayg.3	Q6P3S6	OTTHUMG00000002218	ENST00000375592.3:c.256G>A	1.37:g.16632409C>T	ENSP00000364742:p.Ala86Thr	Somatic	26	0		WXS	Illumina HiSeq	.	20	2	NM_018994	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	Missense_Mutation	SNP	ENST00000375592.3	37	CCDS30613.1	.	.	.	.	.	.	.	.	.	.	C	36	5.640899	0.96693	.	.	ENSG00000037637	ENST00000375592	T	0.03982	3.74	5.72	5.72	0.89469	F-box domain, cyclin-like (2);	0.000000	0.85682	D	0.000000	T	0.09598	0.0236	N	0.21583	0.68	0.80722	D	1	D	0.60160	0.987	P	0.60012	0.867	T	0.47086	-0.9144	10	0.10636	T	0.68	-16.5927	18.8634	0.92281	0.0:1.0:0.0:0.0	.	86	Q6P3S6	FBX42_HUMAN	T	86	ENSP00000364742:A86T	ENSP00000364742:A86T	A	-	1	0	FBXO42	16504996	1.000000	0.71417	0.998000	0.56505	0.870000	0.49936	7.376000	0.79658	2.711000	0.92665	0.655000	0.94253	GCC	.		0.408	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006285.1		
TP53BP1	7158	hgsc.bcm.edu	37	15	43748037	43748037	+	Intron	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr15:43748037C>T	ENST00000263801.3	-	12	2954				TP53BP1_ENST00000450115.2_Intron|TP53BP1_ENST00000382039.3_Intron|TP53BP1_ENST00000605155.1_Intron|TP53BP1_ENST00000382044.4_Intron	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1						cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		GCCAACTTTCCATTCCAGATT	0.378								Other conserved DNA damage response genes																													.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	100873756	.			ACTTTCCATTCCA	U09477	CCDS10096.1, CCDS45250.1, CCDS45251.1	15q15-q21	2007-08-02	2007-08-02		ENSG00000067369	ENSG00000067369			11999	protein-coding gene	gene with protein product		605230	"""tumor protein p53-binding protein, 1"""			8016121, 9748285	Standard	NM_005657		Approved	53BP1, p202	uc001zrr.4	Q12888	OTTHUMG00000059757	ENST00000263801.3:c.2701+52G>A	15.37:g.43748037C>T		Somatic	80	0		WXS	Illumina HiSeq	.	51	4	.	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	RNA	SNP	ENST00000263801.3	37	CCDS10096.1																																																																																			.		0.378	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3		
HSP90AB1	3326	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	6	44221323	44221323	+	Silent	SNP	A	A	G			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr6:44221323A>G	ENST00000371554.1	+	12	2377	c.2163A>G	c.(2161-2163)gaA>gaG	p.E721E	SLC35B2_ENST00000495706.1_5'Flank|HSP90AB1_ENST00000371646.5_Silent_p.E721E|MIR4647_ENST00000583964.1_RNA|HSP90AB1_ENST00000353801.3_Silent_p.E721E			P08238	HS90B_HUMAN	heat shock protein 90kDa alpha (cytosolic), class B member 1	721					axon guidance (GO:0007411)|cellular response to interleukin-4 (GO:0071353)|cellular response to organic cyclic compound (GO:0071407)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|placenta development (GO:0001890)|positive regulation of cell size (GO:0045793)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein folding (GO:0006457)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to salt stress (GO:0009651)|response to unfolded protein (GO:0006986)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|CTP binding (GO:0002135)|dATP binding (GO:0032564)|double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|poly(A) RNA binding (GO:0044822)|TPR domain binding (GO:0030911)|UTP binding (GO:0002134)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(12)|prostate(2)|skin(2)|urinary_tract(2)	33	all_cancers(18;1.7e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CTCGCATGGAAGAAGTCGATT	0.542											OREG0017471	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E721E		.											.	.	.	0			c.A2163G						.						70.0	73.0	72.0					6																	44221323		2203	4300	6503	SO:0001819	synonymous_variant	3326	exon12			CATGGAAGAAGTC	AF275719	CCDS4909.1	6p12	2011-09-02	2006-02-24	2006-02-24	ENSG00000096384	ENSG00000096384		"""Heat shock proteins / HSPC"""	5258	protein-coding gene	gene with protein product		140572	"""heat shock 90kD protein 1, beta"", ""heat shock 90kDa protein 1, beta"""	HSPC2, HSPCB		2768249, 16269234	Standard	NM_001271969		Approved		uc031sor.1	P08238	OTTHUMG00000014761	ENST00000371554.1:c.2163A>G	6.37:g.44221323A>G		Somatic	73	0	922	WXS	Illumina HiSeq	.	43	4	NM_007355	B2R5P0|Q5T9W7|Q9NQW0|Q9NTK6	Silent	SNP	ENST00000371554.1	37	CCDS4909.1																																																																																			.		0.542	HSP90AB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040730.1	NM_007355	
ALDH3A1	218	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	19645434	19645434	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr17:19645434C>G	ENST00000457500.2	-	4	901	c.572G>C	c.(571-573)gGg>gCg	p.G191A	ALDH3A1_ENST00000444455.1_Missense_Mutation_p.G191A|ALDH3A1_ENST00000225740.6_Missense_Mutation_p.G191A|ALDH3A1_ENST00000485231.1_5'Flank|ALDH3A1_ENST00000395555.3_Missense_Mutation_p.G191A|ALDH3A1_ENST00000494157.2_Missense_Mutation_p.G118A	NM_001135168.1	NP_001128640.1	P30838	AL3A1_HUMAN	aldehyde dehydrogenase 3 family, member A1	191					aging (GO:0007568)|cellular aldehyde metabolic process (GO:0006081)|oxidation-reduction process (GO:0055114)|positive regulation of cell proliferation (GO:0008284)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|alcohol dehydrogenase (NADP+) activity (GO:0008106)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|urinary_tract(1)	13	all_cancers(12;4.01e-05)|all_epithelial(12;0.00301)|Breast(13;0.186)			Colorectal(15;0.0829)		CTTCCCCACCCCCGTGCTGCC	0.587																																					p.G191A		.											.	.	.	0			c.G572C						.						162.0	110.0	128.0					17																	19645434		2203	4300	6503	SO:0001583	missense	218	exon4			CCCACCCCCGTGC	M74542	CCDS11212.1	17p11.2	2010-05-07	2010-05-07		ENSG00000108602	ENSG00000108602	1.2.1.5	"""Aldehyde dehydrogenases"""	405	protein-coding gene	gene with protein product	"""aldehyde dehydrogenase, dimeric NADP-preferring"""	100660		ALDH3		7774944, 1737758	Standard	NM_000691		Approved		uc010cqu.3	P30838	OTTHUMG00000059469	ENST00000457500.2:c.572G>C	17.37:g.19645434C>G	ENSP00000411821:p.Gly191Ala	Somatic	16	0		WXS	Illumina HiSeq	.	14	6	NM_001135168	A8K828|Q9BT37	Missense_Mutation	SNP	ENST00000457500.2	37	CCDS11212.1	.	.	.	.	.	.	.	.	.	.	C	0.489	-0.876164	0.02550	.	.	ENSG00000108602	ENST00000225740;ENST00000395555;ENST00000379258;ENST00000444455;ENST00000457500;ENST00000457844;ENST00000439102;ENST00000426645	D;D;D;D;D	0.83755	-1.76;-1.76;-1.76;-1.76;-1.76	4.49	-1.38	0.09027	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.502887	0.21704	N	0.070364	T	0.49423	0.1556	N	0.00750	-1.22	0.09310	N	1	B;B;B	0.19200	0.0;0.034;0.0	B;B;B	0.17722	0.001;0.019;0.001	T	0.52245	-0.8601	10	0.02654	T	1	.	12.0321	0.53403	0.0:0.3236:0.5938:0.0826	.	191;308;191	A8K828;Q8N9T9;P30838	.;.;AL3A1_HUMAN	A	191;191;249;191;191;118;191;191	ENSP00000225740:G191A;ENSP00000378923:G191A;ENSP00000388469:G191A;ENSP00000411821:G191A;ENSP00000389766:G191A	ENSP00000225740:G191A	G	-	2	0	ALDH3A1	19586026	0.000000	0.05858	0.000000	0.03702	0.775000	0.43874	0.492000	0.22435	-0.122000	0.11766	0.462000	0.41574	GGG	.		0.587	ALDH3A1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132265.4	NM_000691	
TSSC4	10078	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	2424013	2424013	+	Silent	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr11:2424013C>T	ENST00000333256.6	+	3	593	c.150C>T	c.(148-150)tcC>tcT	p.S50S	TSSC4_ENST00000451491.2_Silent_p.S50S|AC124057.5_ENST00000433035.1_RNA|TSSC4_ENST00000380992.1_Intron|TSSC4_ENST00000380996.5_Intron			Q9Y5U2	TSSC4_HUMAN	tumor suppressing subtransferable candidate 4	50										endometrium(3)|large_intestine(1)|lung(4)	8		all_epithelial(84;0.000161)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.0137)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.00145)|LUSC - Lung squamous cell carcinoma(625;0.19)		AAGCACTGTCCCCGATGGGGC	0.637																																					p.S50S		.											.	.	.	0			c.C150T						.						58.0	38.0	45.0					11																	2424013		2186	4281	6467	SO:0001819	synonymous_variant	10078	exon2			ACTGTCCCCGATG	AF125568	CCDS7735.1, CCDS73241.1	11p15.5	2008-02-05			ENSG00000184281	ENSG00000184281			12386	protein-coding gene	gene with protein product		603852				10072438	Standard	XM_005252722		Approved		uc001lwl.3	Q9Y5U2	OTTHUMG00000009895	ENST00000333256.6:c.150C>T	11.37:g.2424013C>T		Somatic	76	0		WXS	Illumina HiSeq	.	54	19	NM_005706	C9JS66|Q86VL2|Q9BRS6	Silent	SNP	ENST00000333256.6	37	CCDS7735.1																																																																																			.		0.637	TSSC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027369.3	NM_005706	
HPS5	11234	hgsc.bcm.edu	37	11	18313248	18313248	+	Silent	SNP	G	G	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr11:18313248G>A	ENST00000349215.3	-	16	2458	c.2181C>T	c.(2179-2181)tgC>tgT	p.C727C	HPS5_ENST00000352460.3_5'UTR|HPS5_ENST00000396253.3_Silent_p.C613C|HPS5_ENST00000438420.2_Silent_p.C613C	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	727					blood coagulation (GO:0007596)|organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)		p.C727C(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						TTGCAATGGCGCATGGAGAAC	0.408									Hermansky-Pudlak syndrome																												p.C727C		.											HPS5,NS,carcinoma,0,1	HPS5	0	1	Substitution - coding silent(1)	lung(1)	c.C2181T						.						170.0	159.0	163.0					11																	18313248		2199	4293	6492	SO:0001819	synonymous_variant	11234	exon16	Familial Cancer Database	HPS, HPS1-8	AATGGCGCATGGA	AB023234	CCDS7836.1, CCDS7837.1	11p14	2014-06-18			ENSG00000110756	ENSG00000110756			17022	protein-coding gene	gene with protein product		607521				10231032, 10094488	Standard	NM_181507		Approved		uc001mod.1	Q9UPZ3	OTTHUMG00000166612	ENST00000349215.3:c.2181C>T	11.37:g.18313248G>A		Somatic	54	0		WXS	Illumina HiSeq	.	37	2	NM_181507	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Silent	SNP	ENST00000349215.3	37	CCDS7836.1																																																																																			.		0.408	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1	NM_181507	
MT-ND2	4536	hgsc.bcm.edu	37	M	5196	5196	+	Silent	SNP	T	T	C			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chrM:5196T>C	ENST00000361453.3	+	1	727	c.727T>C	c.(727-729)Tta>Cta	p.L243L	MT-TY_ENST00000387409.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-CO2_ENST00000361739.1_5'Flank|MT-TM_ENST00000387377.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-CO1_ENST00000361624.2_5'Flank|MT-RNR2_ENST00000387347.2_RNA|MT-TL1_ENST00000386347.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-TI_ENST00000387365.1_RNA			P03891	NU2M_HUMAN	mitochondrially encoded NADH dehydrogenase 2	243					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|lung(1)	3						GACTAACACCCTTAATTCCAT	0.473																																					p.L243L		.											.	.	.	0			c.T727C						.																																			SO:0001819	synonymous_variant	0	exon1			ACACCCTTAATTC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198763	ENSG00000198763	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7456	protein-coding gene	gene with protein product	"""complex I ND2 subunit"", ""NADH-ubiquinone oxidoreductase chain 2"""	516001	"""NADH dehydrogenase 2"""	MTND2			Standard			Approved	ND2, NAD2		P03891		ENST00000361453.3:c.727T>C	M.37:g.5196T>C		Somatic	13	0		WXS	Illumina HiSeq	.	39	19	ENST00000361453	Q34769|Q9TGI0|Q9TGI1|Q9TGI2|Q9TGI3|Q9TGI4	Silent	SNP	ENST00000361453.3	37																																																																																				.		0.473	MT-ND2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024027	
DOK3	79930	hgsc.bcm.edu	37	5	176930174	176930174	+	IGR	SNP	G	G	A	rs79945738|rs370427653|rs138153794	byFrequency	TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr5:176930174G>A	ENST00000357198.4	-	0	1729				RP11-1334A24.6_ENST00000506025.1_RNA|DOK3_ENST00000312943.6_Missense_Mutation_p.L289F|DOK3_ENST00000377112.4_Missense_Mutation_p.L187F	NM_024872.2	NP_079148.2	Q7L591	DOK3_HUMAN	docking protein 3						Ras protein signal transduction (GO:0007265)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|lung(7)	13	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.191)			CAGGAGCAGAGGAGGGAACGC	0.632																																					p.L289F		.											DOK3_ENST00000312943,colon,carcinoma,0,5	DOK3_ENST00000312943	0	0			c.C865T						.						29.0	27.0	27.0					5																	176930174		688	1541	2229	SO:0001628	intergenic_variant	79930	exon6			AGCAGAGGAGGGA	AK026223	CCDS4426.1, CCDS47349.1, CCDS47350.1	5q35	2008-02-05			ENSG00000146094	ENSG00000146094			24583	protein-coding gene	gene with protein product		611435				10733577, 12595900	Standard	NM_024872		Approved	FLJ22570	uc003mhk.3	Q7L591	OTTHUMG00000130850		5.37:g.176930174G>A		Somatic	28	0		WXS	Illumina HiSeq	.	28	3	NM_001144875	E9PAT0|H7BXS0|Q8N864|Q9BQB3|Q9H666	Missense_Mutation	SNP	ENST00000357198.4	37	CCDS4426.1	.	.	.	.	.	.	.	.	.	.	G	14.78	2.637846	0.47049	.	.	ENSG00000146094	ENST00000312943;ENST00000377112	T;T	0.56611	0.52;0.45	2.12	0.0934	0.14477	.	.	.	.	.	T	0.23649	0.0572	N	0.08118	0	0.09310	N	1	P;P;P	0.49253	0.872;0.804;0.921	B;B;B	0.36534	0.114;0.144;0.227	T	0.11446	-1.0587	9	0.39692	T	0.17	.	4.2422	0.10654	0.4197:0.0:0.5803:0.0	.	187;289;175	E9PAT0;Q7L591-3;Q7L591-2	.;.;.	F	289;187	ENSP00000325174:L289F;ENSP00000366316:L187F	ENSP00000325174:L289F	L	-	1	0	DOK3	176862780	0.000000	0.05858	0.000000	0.03702	0.315000	0.28087	-0.417000	0.07088	0.001000	0.14605	0.297000	0.19635	CTC	.		0.632	DOK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253420.4	NM_024872	
SMPD3	55512	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	16	68395639	68395639	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr16:68395639C>T	ENST00000219334.5	-	8	2336	c.1733G>A	c.(1732-1734)cGc>cAc	p.R578H	SMPD3_ENST00000566009.1_5'Flank|SMPD3_ENST00000563226.1_Missense_Mutation_p.R570H|SMPD3_ENST00000568373.1_Intron	NM_018667.3	NP_061137.1	Q9NY59	NSMA2_HUMAN	sphingomyelin phosphodiesterase 3, neutral membrane (neutral sphingomyelinase II)	578					cell cycle (GO:0007049)|glycosphingolipid metabolic process (GO:0006687)|hematopoietic progenitor cell differentiation (GO:0002244)|peptide hormone secretion (GO:0030072)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)	Golgi cis cisterna (GO:0000137)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0184)|Epithelial(162;0.0785)	Phosphatidylserine(DB00144)	GTACTCCCTGCGGCCCTCCTC	0.672																																					p.R578H		.											.	.	.	0			c.G1733A						.						45.0	34.0	38.0					16																	68395639		2198	4300	6498	SO:0001583	missense	55512	exon8			TCCCTGCGGCCCT	AJ250460	CCDS10867.1	16q22.1	2008-02-05			ENSG00000103056	ENSG00000103056			14240	protein-coding gene	gene with protein product		605777				10823942	Standard	NM_018667		Approved	NSMASE2	uc002ewa.3	Q9NY59	OTTHUMG00000137559	ENST00000219334.5:c.1733G>A	16.37:g.68395639C>T	ENSP00000219334:p.Arg578His	Somatic	67	0		WXS	Illumina HiSeq	.	66	4	NM_018667	B7ZL82|Q2M1S8	Missense_Mutation	SNP	ENST00000219334.5	37	CCDS10867.1	.	.	.	.	.	.	.	.	.	.	C	18.89	3.719307	0.68844	.	.	ENSG00000103056	ENST00000219334	.	.	.	5.6	5.6	0.85130	Endonuclease/exonuclease/phosphatase (2);	0.000000	0.85682	D	0.000000	T	0.77611	0.4156	M	0.64997	1.995	0.80722	D	1	D;D	0.89917	0.983;1.0	P;D	0.91635	0.721;0.999	T	0.79125	-0.1932	9	0.87932	D	0	-27.0255	17.0961	0.86635	0.0:1.0:0.0:0.0	.	570;578	B7ZL82;Q9NY59	.;NSMA2_HUMAN	H	578	.	ENSP00000219334:R578H	R	-	2	0	SMPD3	66953140	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	7.295000	0.78780	2.653000	0.90120	0.561000	0.74099	CGC	.		0.672	SMPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268895.3	NM_018667	
ATXN1L	342371	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	71884890	71884890	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr16:71884890C>A	ENST00000427980.2	+	3	1540	c.1247C>A	c.(1246-1248)gCc>gAc	p.A416D	ATXN1L_ENST00000569119.1_Intron	NM_001137675.3	NP_001131147.1	P0C7T5	ATX1L_HUMAN	ataxin 1-like	416					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell projection (GO:0042995)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)	4						ATGGTTGTAGCCAATGGCAAC	0.567																																					p.A416D		.											.	.	.	0			c.C1247A						.						78.0	81.0	80.0					16																	71884890		692	1591	2283	SO:0001583	missense	342371	exon3			TTGTAGCCAATGG		CCDS45523.1	16q22.2	2014-09-04			ENSG00000224470	ENSG00000224470			33279	protein-coding gene	gene with protein product	"""brother of ataxin 1"""	614301				16121196, 17322884, 21475249	Standard	NM_001137675		Approved	BOAT1	uc002fbd.3	P0C7T5	OTTHUMG00000176872	ENST00000427980.2:c.1247C>A	16.37:g.71884890C>A	ENSP00000415822:p.Ala416Asp	Somatic	57	0		WXS	Illumina HiSeq	.	49	12	NM_001137675		Missense_Mutation	SNP	ENST00000427980.2	37	CCDS45523.1	.	.	.	.	.	.	.	.	.	.	C	17.54	3.414012	0.62511	.	.	ENSG00000224470	ENST00000427980	T	0.35789	1.29	5.37	5.37	0.77165	.	.	.	.	.	T	0.41396	0.1157	N	0.08118	0	0.58432	D	0.999994	D	0.76494	0.999	D	0.66084	0.941	T	0.52094	-0.8621	9	0.56958	D	0.05	.	19.4859	0.95028	0.0:1.0:0.0:0.0	.	416	P0C7T5	ATX1L_HUMAN	D	416	ENSP00000415822:A416D	ENSP00000415822:A416D	A	+	2	0	ATXN1L	70442391	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.346000	0.72999	2.706000	0.92434	0.555000	0.69702	GCC	.		0.567	ATXN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434171.1	NM_001137675.2	
PEX16	9409	hgsc.bcm.edu	37	11	45939028	45939028	+	Silent	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr11:45939028C>T	ENST00000378750.5	-	2	372	c.129G>A	c.(127-129)tcG>tcA	p.S43S	PEX16_ENST00000532681.1_5'UTR|PEX16_ENST00000241041.3_Silent_p.S43S|PEX16_ENST00000532554.1_5'UTR			Q9Y5Y5	PEX16_HUMAN	peroxisomal biogenesis factor 16	43					ER-dependent peroxisome organization (GO:0032581)|peroxisome membrane biogenesis (GO:0016557)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome membrane (GO:0045046)|protein localization to endoplasmic reticulum (GO:0070972)|protein targeting to peroxisome (GO:0006625)|protein to membrane docking (GO:0022615)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	protein C-terminus binding (GO:0008022)			large_intestine(2)|lung(2)|ovary(2)|skin(1)	7				GBM - Glioblastoma multiforme(35;0.223)		ACAGCTCGTGCGAATCGGCGA	0.647																																					p.S43S		.											.	.	.	0			c.G129A						.						52.0	54.0	53.0					11																	45939028		2203	4299	6502	SO:0001819	synonymous_variant	9409	exon2			CTCGTGCGAATCG	AF118240	CCDS7917.1, CCDS31472.1	11p	2007-12-14			ENSG00000121680	ENSG00000121680			8857	protein-coding gene	gene with protein product		603360				9922452	Standard	NM_057174		Approved		uc001nbt.3	Q9Y5Y5	OTTHUMG00000167005	ENST00000378750.5:c.129G>A	11.37:g.45939028C>T		Somatic	93	0		WXS	Illumina HiSeq	.	68	3	NM_004813	Q9BWB9	Silent	SNP	ENST00000378750.5	37	CCDS31472.1																																																																																			.		0.647	PEX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392398.1	NM_057174	
CD96	10225	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	3	111261150	111261150	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr3:111261150G>T	ENST00000283285.5	+	1	186	c.55G>T	c.(55-57)Gtc>Ttc	p.V19F	CD96_ENST00000438817.2_Missense_Mutation_p.V19F|CD96_ENST00000352690.4_Missense_Mutation_p.V19F	NM_198196.2	NP_937839.1	P40200	TACT_HUMAN	CD96 molecule	19					cell adhesion (GO:0007155)|immune response (GO:0006955)|regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(4)|liver(2)|lung(14)|skin(5)	35						GATACATTTTGTCAAGGGTAA	0.438									Opitz Trigonocephaly syndrome																												p.V19F		.											.	.	.	0			c.G55T						.						128.0	119.0	122.0					3																	111261150		2203	4300	6503	SO:0001583	missense	10225	exon1	Familial Cancer Database	C syndrome, Trigonocephaly syndrome	CATTTTGTCAAGG	M88282	CCDS2958.1, CCDS2959.1	3p13-q13.2	2013-01-11	2006-03-28		ENSG00000153283	ENSG00000153283		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	16892	protein-coding gene	gene with protein product		606037	"""CD96 antigen"""			1313846	Standard	XR_241462		Approved	TACTILE	uc003dxx.3	P40200	OTTHUMG00000159275	ENST00000283285.5:c.55G>T	3.37:g.111261150G>T	ENSP00000283285:p.Val19Phe	Somatic	53	0		WXS	Illumina HiSeq	.	49	4	NM_005816	Q5JPB3	Missense_Mutation	SNP	ENST00000283285.5	37	CCDS2959.1	.	.	.	.	.	.	.	.	.	.	G	3.674	-0.066924	0.07273	.	.	ENSG00000153283	ENST00000352690;ENST00000283285;ENST00000438817	T;T;T	0.66995	-0.2;-0.22;-0.24	5.59	-1.98	0.07480	.	0.566504	0.16296	N	0.220674	T	0.36026	0.0952	N	0.11560	0.145	0.09310	N	0.999997	B;B;B;B	0.20261	0.025;0.043;0.025;0.025	B;B;B;B	0.21546	0.016;0.035;0.016;0.016	T	0.11916	-1.0568	10	0.25106	T	0.35	-0.9839	1.4935	0.02461	0.3553:0.1299:0.3742:0.1407	.	19;19;19;19	E9PEJ1;P40200-2;P40200;Q8WUE2	.;.;TACT_HUMAN;.	F	19	ENSP00000342040:V19F;ENSP00000283285:V19F;ENSP00000389801:V19F	ENSP00000283285:V19F	V	+	1	0	CD96	112743840	0.461000	0.25783	0.260000	0.24451	0.165000	0.22458	-0.254000	0.08781	-0.419000	0.07439	-0.423000	0.05987	GTC	.		0.438	CD96-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354312.2		
NR2C1	7181	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	95416118	95416118	+	Nonsense_Mutation	SNP	C	C	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr12:95416118C>A	ENST00000333003.5	-	14	2029	c.1699G>T	c.(1699-1701)Gaa>Taa	p.E567*		NM_003297.3	NP_003288.2	P13056	NR2C1_HUMAN	nuclear receptor subfamily 2, group C, member 1	567					gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	DNA binding (GO:0003677)|receptor activity (GO:0004872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)	13						AAAAACAATTCTTCAGTGATG	0.358																																					p.E567X		.											NR2C1,NS,carcinoma,0,1	NR2C1	0	0			c.G1699T						.						204.0	218.0	213.0					12																	95416118		2203	4300	6503	SO:0001587	stop_gained	7181	exon14			ACAATTCTTCAGT	M29960	CCDS9051.1, CCDS41821.1, CCDS44953.1	12q22	2013-01-16				ENSG00000120798		"""Nuclear hormone receptors"""	7971	protein-coding gene	gene with protein product		601529		TR2		2597158	Standard	NM_001032287		Approved	TR2-11	uc001tdm.5	P13056	OTTHUMG00000170131	ENST00000333003.5:c.1699G>T	12.37:g.95416118C>A	ENSP00000333275:p.Glu567*	Somatic	89	0		WXS	Illumina HiSeq	.	51	7	NM_003297	A8K5K4|Q15625|Q15626	Nonsense_Mutation	SNP	ENST00000333003.5	37	CCDS9051.1	.	.	.	.	.	.	.	.	.	.	C	33	5.218925	0.95104	.	.	ENSG00000120798	ENST00000333003	.	.	.	5.74	4.85	0.62838	.	0.139297	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	.	14.9123	0.70767	0.0:0.9312:0.0:0.0688	.	.	.	.	X	567	.	ENSP00000333275:E567X	E	-	1	0	NR2C1	93940249	1.000000	0.71417	0.998000	0.56505	0.087000	0.18053	7.818000	0.86416	1.444000	0.47605	0.650000	0.86243	GAA	.		0.358	NR2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407565.2	NM_003297	
ZNF43	7594	hgsc.bcm.edu	37	19	21991811	21991811	+	Missense_Mutation	SNP	G	G	T	rs149679417		TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr19:21991811G>T	ENST00000354959.4	-	4	1197	c.1028C>A	c.(1027-1029)aCa>aAa	p.T343K	ZNF43_ENST00000594012.1_Missense_Mutation_p.T337K|ZNF43_ENST00000595461.1_Missense_Mutation_p.T337K|ZNF43_ENST00000598381.1_Missense_Mutation_p.T337K	NM_003423.3	NP_003414.2	P17038	ZNF43_HUMAN	zinc finger protein 43	343					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	51		Renal(1328;0.000219)|Hepatocellular(1079;0.121)		GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127)		TTCTTCACATGTGTAGGGTTT	0.383																																					p.T352K		.											ZNF43,NS,carcinoma,0,2	ZNF43	0	0			c.C1055A						.																																			SO:0001583	missense	7594	exon4			TCACATGTGTAGG	X59244	CCDS12413.2, CCDS59367.1, CCDS74321.1	19p13.1-p12	2013-01-08	2006-05-11		ENSG00000198521	ENSG00000198521		"""Zinc fingers, C2H2-type"", ""-"""	13109	protein-coding gene	gene with protein product		603972	"""zinc finger protein 39-like 1 (KOX 27)"", ""zinc finger protein 43 (HTF6)"""	ZNF39L1		1711675	Standard	NM_001256649		Approved	HTF6, KOX27	uc031rka.1	P17038	OTTHUMG00000128543	ENST00000354959.4:c.1028C>A	19.37:g.21991811G>T	ENSP00000347045:p.Thr343Lys	Somatic	51	1		WXS	Illumina HiSeq	.	43	3	NM_001256653	A8K5N8|P28160|Q53XQ2|Q5H9T3|Q96DG1	Missense_Mutation	SNP	ENST00000354959.4	37	CCDS12413.2	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.412760	0.00191	.	.	ENSG00000198521	ENST00000397148;ENST00000354959	T	0.35973	1.28	1.76	-2.18	0.07037	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09423	0.0232	N	0.01122	-1.005	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.34625	-0.9821	9	0.02654	T	1	.	8.658	0.34075	0.0:0.0:0.6228:0.3772	.	343	P17038	ZNF43_HUMAN	K	342;343	ENSP00000347045:T343K	ENSP00000347045:T343K	T	-	2	0	ZNF43	21783651	0.000000	0.05858	0.000000	0.03702	0.079000	0.17450	-2.438000	0.01017	-0.689000	0.05149	-0.856000	0.03024	ACA	.		0.383	ZNF43-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250380.2	NM_003423	
RALGAPB	57148	hgsc.bcm.edu;broad.mit.edu	37	20	37191223	37191223	+	Nonsense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr20:37191223G>T	ENST00000262879.6	+	24	3864	c.3580G>T	c.(3580-3582)Gaa>Taa	p.E1194*	RALGAPB_ENST00000397040.1_Nonsense_Mutation_p.E1194*|RALGAPB_ENST00000397038.1_Nonsense_Mutation_p.E972*|RALGAPB_ENST00000397042.3_Nonsense_Mutation_p.E1190*			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	1194	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)|Ral protein signal transduction (GO:0032484)|regulation of exocyst localization (GO:0060178)		protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(29)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						ACATTTCCTAGAATTTTTGCT	0.393																																					p.E1194X		.											.	.	.	0			c.G3580T						.						139.0	128.0	132.0					20																	37191223		2203	4300	6503	SO:0001587	stop_gained	57148	exon24			TTCCTAGAATTTT	AB033045	CCDS13305.1, CCDS63272.1	20q11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000170471	ENSG00000170471			29221	protein-coding gene	gene with protein product			"""KIAA1219"""	KIAA1219		19520869	Standard	XM_005260462		Approved	DKFZp781M2411, RalGAPbeta	uc002xiw.3	Q86X10	OTTHUMG00000140270	ENST00000262879.6:c.3580G>T	20.37:g.37191223G>T	ENSP00000262879:p.Glu1194*	Somatic	106	0		WXS	Illumina HiSeq	.	67	4	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Nonsense_Mutation	SNP	ENST00000262879.6	37	CCDS13305.1	.	.	.	.	.	.	.	.	.	.	G	49	15.150759	0.99824	.	.	ENSG00000170471	ENST00000262879;ENST00000397042;ENST00000397038;ENST00000397040;ENST00000438490	.	.	.	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	.	20.0498	0.97621	0.0:0.0:1.0:0.0	.	.	.	.	X	1194;1190;972;1194;1022	.	ENSP00000262879:E1194X	E	+	1	0	RALGAPB	36624637	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.454000	0.97621	2.753000	0.94483	0.557000	0.71058	GAA	.		0.393	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336	
FAM60A	58516	hgsc.bcm.edu	37	12	31477808	31477808	+	Intron	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr12:31477808C>T	ENST00000337682.4	-	1	349				FAM60A_ENST00000539409.1_Intron|AC024940.1_ENST00000313737.4_Missense_Mutation_p.R11W|FAM60A_ENST00000395766.1_Intron|FAM60A_ENST00000536836.1_Intron|FAM60A_ENST00000454658.2_5'Flank|FAM60A_ENST00000542983.1_Intron	NM_001135812.1	NP_001129284.1	Q9NP50	FA60A_HUMAN	family with sequence similarity 60, member A						negative regulation of cell migration (GO:0030336)	Sin3 complex (GO:0016580)				large_intestine(1)|lung(2)	3	all_cancers(9;5.22e-13)|all_epithelial(9;4e-13)|all_lung(12;1.2e-11)|Lung NSC(12;2.17e-09)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0207)|Lung SC(12;0.0592)|Esophageal squamous(101;0.162)					CCGCCCCGCACGGGCGGAGAG	0.612																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	0	.			CCCGCACGGGCGG	AF212220	CCDS8723.1	12p11.21	2012-11-30	2005-04-07	2005-04-07	ENSG00000139146	ENSG00000139146			30702	protein-coding gene	gene with protein product		615027	"""chromosome 12 open reading frame 14"""	C12orf14		11042152, 22984288, 22865885	Standard	NM_021238		Approved	TERA	uc001rke.3	Q9NP50	OTTHUMG00000168586	ENST00000337682.4:c.19+1149G>A	12.37:g.31477808C>T		Somatic	111	0		WXS	Illumina HiSeq	.	93	4	.	D3DUV8|Q9BSZ8	RNA	SNP	ENST00000337682.4	37	CCDS8723.1	.	.	.	.	.	.	.	.	.	.	C	10.40	1.339469	0.24339	.	.	ENSG00000177340	ENST00000313737	.	.	.	2.7	0.68	0.17980	.	.	.	.	.	T	0.35422	0.0931	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.36792	-0.9733	5	0.87932	D	0	.	2.959	0.05886	0.27:0.5701:0.0:0.1599	.	.	.	.	W	11	.	ENSP00000324000:R11W	R	+	1	2	AC024940.1	31369075	0.011000	0.17503	0.001000	0.08648	0.493000	0.33554	0.017000	0.13399	0.018000	0.15052	0.491000	0.48974	CGG	.		0.612	FAM60A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400347.1	NM_021238	
SLA	6503	hgsc.bcm.edu;bcgsc.ca	37	8	134062164	134062164	+	Silent	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr8:134062164C>T	ENST00000338087.5	-	5	1050	c.231G>A	c.(229-231)gtG>gtA	p.V77V	SLA_ENST00000524345.1_5'UTR|SLA_ENST00000517648.1_Silent_p.V94V|SLA_ENST00000427060.2_Silent_p.V117V|SLA_ENST00000518565.1_5'UTR|TG_ENST00000542445.1_Intron|SLA_ENST00000395352.3_Silent_p.V94V|TG_ENST00000377869.1_Intron|TG_ENST00000519543.1_Intron|TG_ENST00000220616.4_Intron	NM_001045556.2	NP_001039021.1	Q13239	SLAP1_HUMAN	Src-like-adaptor	77	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				positive regulation of signal transduction (GO:0009967)	endosome (GO:0005768)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(1)|lung(6)|prostate(1)|skin(1)	17	all_epithelial(106;3.51e-21)|Lung NSC(106;4.24e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0279)|Breast(495;0.037)	BRCA - Breast invasive adenocarcinoma(115;0.000701)			AAACTCTGGCCACACATATTC	0.448																																					p.V117V		.											.	.	.	0			c.G351A						.						141.0	118.0	126.0					8																	134062164		2203	4300	6503	SO:0001819	synonymous_variant	6503	exon3			TCTGGCCACACAT		CCDS6370.1, CCDS47922.1, CCDS47923.1, CCDS64977.1, CCDS64978.1	8q24.22	2013-09-19	2001-11-28		ENSG00000155926	ENSG00000155926		"""SH2 domain containing"""	10902	protein-coding gene	gene with protein product		601099	"""Src-like-adapter"""			8825655, 11179692	Standard	NM_001045556		Approved	SLA1	uc011ljd.2	Q13239	OTTHUMG00000164439	ENST00000338087.5:c.231G>A	8.37:g.134062164C>T		Somatic	64	0		WXS	Illumina HiSeq	.	76	4	NM_006748	B7Z4J2|B7Z4L6|Q6FI01|Q9UMQ8	Silent	SNP	ENST00000338087.5	37	CCDS6370.1																																																																																			.		0.448	SLA-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378771.1		
CRKL	1399	hgsc.bcm.edu	37	22	21304043	21304043	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr22:21304043G>T	ENST00000354336.3	+	3	1331	c.822G>T	c.(820-822)caG>caT	p.Q274H		NM_005207.3	NP_005198.1	P46109	CRKL_HUMAN	v-crk avian sarcoma virus CT10 oncogene homolog-like	274	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.				activation of MAPKK activity (GO:0000186)|anterior/posterior pattern specification (GO:0009952)|blood vessel development (GO:0001568)|heart development (GO:0007507)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|parathyroid gland development (GO:0060017)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|thymus development (GO:0048538)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)	poly(A) RNA binding (GO:0044822)|SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)	14	all_cancers(11;1.16e-25)|all_epithelial(7;3.37e-24)|Lung NSC(8;7.25e-16)|all_lung(8;1.37e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.176)			TAAATGGCCAGTGGGAAGGCG	0.443																																					p.Q274H	Pancreas(85;3 1441 23889 42519 42763)	.											CRKL,NS,carcinoma,0,1	CRKL	0	0			c.G822T						.						184.0	176.0	179.0					22																	21304043		2203	4300	6503	SO:0001583	missense	1399	exon3			TGGCCAGTGGGAA		CCDS13785.1	22q11.21	2013-07-09	2013-07-09		ENSG00000099942	ENSG00000099942		"""SH2 domain containing"""	2363	protein-coding gene	gene with protein product		602007				8361759, 8798523	Standard	NM_005207		Approved		uc002ztf.2	P46109	OTTHUMG00000150807	ENST00000354336.3:c.822G>T	22.37:g.21304043G>T	ENSP00000346300:p.Gln274His	Somatic	85	0		WXS	Illumina HiSeq	.	52	3	NM_005207	A8KA44|D3DX35	Missense_Mutation	SNP	ENST00000354336.3	37	CCDS13785.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.105535	0.77096	.	.	ENSG00000099942	ENST00000354336	T	0.29397	1.57	5.31	0.675	0.17952	Src homology-3 domain (2);Variant SH3 (1);	0.000000	0.85682	D	0.000000	T	0.48677	0.1513	M	0.70595	2.14	0.80722	D	1	D	0.67145	0.996	D	0.79108	0.992	T	0.46289	-0.9202	10	0.72032	D	0.01	.	9.3827	0.38325	0.3163:0.0:0.6837:0.0	.	274	P46109	CRKL_HUMAN	H	274	ENSP00000346300:Q274H	ENSP00000346300:Q274H	Q	+	3	2	CRKL	19634043	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.322000	0.33689	0.220000	0.20860	0.591000	0.81541	CAG	.		0.443	CRKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320158.1	NM_005207	
TSC2	7249	hgsc.bcm.edu	37	16	2100432	2100432	+	Missense_Mutation	SNP	G	G	A	rs397515042|rs397514949		TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr16:2100432G>A	ENST00000219476.3	+	3	800	c.170G>A	c.(169-171)cGc>cAc	p.R57H	TSC2_ENST00000353929.4_Missense_Mutation_p.R57H|TSC2_ENST00000350773.4_Missense_Mutation_p.R57H|TSC2_ENST00000568454.1_Missense_Mutation_p.R68H|TSC2_ENST00000439673.2_Missense_Mutation_p.R57H|NTHL1_ENST00000219066.1_5'Flank|TSC2_ENST00000401874.2_Missense_Mutation_p.R57H|TSC2_ENST00000382538.6_Missense_Mutation_p.R8H	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	57	Required for interaction with TSC1.				acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)	p.R57H(2)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				CTCAACAATCGCATCCGGATG	0.468			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis																												p.R57H		.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"""E, O"""	TSC2_ENST00000219476,rectum,carcinoma,0,2	TSC2_ENST00000219476	0	2	Substitution - Missense(2)	large_intestine(2)	c.G170A						.						90.0	87.0	88.0					16																	2100432		2198	4300	6498	SO:0001583	missense	7249	exon3	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	ACAATCGCATCCG	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 160"""	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.170G>A	16.37:g.2100432G>A	ENSP00000219476:p.Arg57His	Somatic	58	0		WXS	Illumina HiSeq	.	46	2	NM_001114382	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Missense_Mutation	SNP	ENST00000219476.3	37	CCDS10458.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.802152	0.90538	.	.	ENSG00000103197	ENST00000219476;ENST00000432909;ENST00000401874;ENST00000353929;ENST00000439673;ENST00000382538;ENST00000350773;ENST00000445113	D;D;D;T;D;D	0.89196	-2.48;-2.48;-2.48;-0.14;-2.48;-2.48	4.78	4.78	0.61160	Armadillo-type fold (1);Tuberin, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.94427	0.8207	M	0.77486	2.375	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;0.999;0.917;1.0;0.998;0.996	D	0.95241	0.8351	10	0.87932	D	0	-21.1781	17.808	0.88607	0.0:0.0:1.0:0.0	.	8;57;57;57;57;57	B4DIL8;P49815-6;B7Z2B8;P49815-4;P49815-5;P49815	.;.;.;.;.;TSC2_HUMAN	H	57;8;57;57;57;8;57;68	ENSP00000219476:R57H;ENSP00000384468:R57H;ENSP00000248099:R57H;ENSP00000399232:R57H;ENSP00000371978:R8H;ENSP00000344383:R57H	ENSP00000219476:R57H	R	+	2	0	TSC2	2040433	1.000000	0.71417	1.000000	0.80357	0.711000	0.40976	8.804000	0.91921	2.195000	0.70347	0.407000	0.27541	CGC	.		0.468	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548	
HS3ST4	9951	hgsc.bcm.edu	37	16	26147016	26147016	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr16:26147016G>A	ENST00000331351.5	+	2	1210	c.818G>A	c.(817-819)cGc>cAc	p.R273H	HS3ST4_ENST00000475436.1_3'UTR	NM_006040.2	NP_006031.2	Q9Y661	HS3S4_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	273					heparan sulfate proteoglycan metabolic process (GO:0030201)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)	p.R273H(2)		breast(2)|endometrium(3)|large_intestine(1)|lung(9)	15				GBM - Glioblastoma multiforme(48;0.0988)		GCTCCCAAGCGCATTCACTCC	0.493																																					p.R273H		.											HS3ST4,NS,carcinoma,0,1	HS3ST4	0	2	Substitution - Missense(2)	lung(2)	c.G818A						.						118.0	107.0	110.0					16																	26147016		1568	3582	5150	SO:0001583	missense	9951	exon2			CCAAGCGCATTCA	AF105378	CCDS53995.1	16p11.2	2008-03-12			ENSG00000182601	ENSG00000182601	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5200	protein-coding gene	gene with protein product		604059				9988767	Standard	NM_006040		Approved	3OST4	uc002dof.3	Q9Y661	OTTHUMG00000059978	ENST00000331351.5:c.818G>A	16.37:g.26147016G>A	ENSP00000330606:p.Arg273His	Somatic	58	0		WXS	Illumina HiSeq	.	35	2	NM_006040	Q5QI42|Q8NDC2	Missense_Mutation	SNP	ENST00000331351.5	37	CCDS53995.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.583926	0.86748	.	.	ENSG00000182601	ENST00000331351	T	0.60424	0.19	5.45	5.45	0.79879	Sulfotransferase domain (1);	0.000000	0.64402	U	0.000001	D	0.84252	0.5431	H	0.96175	3.78	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89234	0.3579	10	0.87932	D	0	.	18.2672	0.90055	0.0:0.0:1.0:0.0	.	273	Q9Y661	HS3S4_HUMAN	H	273	ENSP00000330606:R273H	ENSP00000330606:R273H	R	+	2	0	HS3ST4	26054517	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.823000	0.86660	2.555000	0.86185	0.655000	0.94253	CGC	.		0.493	HS3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133286.2	NM_006040	
FOXP2	93986	hgsc.bcm.edu	37	7	114329937	114329937	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr7:114329937G>A	ENST00000393494.2	+	17	2383	c.2104G>A	c.(2104-2106)Gac>Aac	p.D702N	FOXP2_ENST00000408937.3_Missense_Mutation_p.D727N|FOXP2_ENST00000403559.4_Missense_Mutation_p.D719N|FOXP2_ENST00000350908.4_Missense_Mutation_p.D702N|FOXP2_ENST00000393489.3_Missense_Mutation_p.D610N|FOXP2_ENST00000393491.3_Missense_Mutation_p.D517N|FOXP2_ENST00000393498.2_Missense_Mutation_p.D681N			O15409	FOXP2_HUMAN	forkhead box P2	702					camera-type eye development (GO:0043010)|caudate nucleus development (GO:0021757)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|growth (GO:0040007)|lung alveolus development (GO:0048286)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of mesenchymal cell proliferation (GO:0002053)|post-embryonic development (GO:0009791)|putamen development (GO:0021758)|righting reflex (GO:0060013)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|vocal learning (GO:0042297)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|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 negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						ATTAGAAGACGACAGAGAGAT	0.443																																					p.D727N		.											FOXP2,colon,carcinoma,0,1	FOXP2	0	0			c.G2179A						.						141.0	129.0	133.0					7																	114329937		2203	4300	6503	SO:0001583	missense	93986	exon18			GAAGACGACAGAG	U80741	CCDS5760.1, CCDS5761.1, CCDS43635.1, CCDS5761.2, CCDS55154.1	7q31	2008-07-18			ENSG00000128573	ENSG00000128573		"""Forkhead boxes"""	13875	protein-coding gene	gene with protein product	"""trinucleotide repeat containing 10"", ""forkhead/winged-helix transcription factor"", ""speech and language disorder 1"", ""CAG repeat protein 44"""	605317		TNRC10, SPCH1		11586359, 9225980	Standard	NM_014491		Approved	CAGH44	uc003vgz.3	O15409	OTTHUMG00000023131	ENST00000393494.2:c.2104G>A	7.37:g.114329937G>A	ENSP00000377132:p.Asp702Asn	Somatic	48	0		WXS	Illumina HiSeq	.	48	2	NM_148898	A0AUV6|A4D0U8|A6NNW4|B4DLD9|Q6ZND1|Q75MJ3|Q8IZE0|Q8N0W2|Q8N6B7|Q8N6B8|Q8NFQ1|Q8NFQ2|Q8NFQ3|Q8NFQ4|Q8TD74	Missense_Mutation	SNP	ENST00000393494.2	37	CCDS5760.1	.	.	.	.	.	.	.	.	.	.	G	17.77	3.471259	0.63625	.	.	ENSG00000128573	ENST00000393494;ENST00000408937;ENST00000403559;ENST00000350908;ENST00000393498;ENST00000393489;ENST00000393491	D;D;D;D;D;D	0.92805	-2.81;-2.8;-2.85;-2.81;-2.91;-3.11	5.96	5.96	0.96718	.	0.042776	0.85682	D	0.000000	D	0.87337	0.6152	N	0.25485	0.75	0.80722	D	1	P;P;P;P;P	0.50943	0.94;0.94;0.94;0.94;0.468	B;B;B;B;B	0.37480	0.251;0.251;0.251;0.251;0.128	D	0.88814	0.3294	10	0.66056	D	0.02	.	20.4192	0.99033	0.0:0.0:1.0:0.0	.	701;719;517;702;727	B7ZLK5;B4DLD9;Q0PRL4;O15409;O15409-4	.;.;.;FOXP2_HUMAN;.	N	702;727;719;702;679;610;517	ENSP00000377132:D702N;ENSP00000386200:D727N;ENSP00000385069:D719N;ENSP00000265436:D702N;ENSP00000377129:D610N;ENSP00000377130:D517N	ENSP00000265436:D702N	D	+	1	0	FOXP2	114117173	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.476000	0.97823	2.831000	0.97527	0.650000	0.86243	GAC	.		0.443	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317366.1	NM_014491	
PDE1B	5153	hgsc.bcm.edu	37	12	54964077	54964077	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr12:54964077A>T	ENST00000243052.3	+	6	966	c.530A>T	c.(529-531)gAc>gTc	p.D177V	PDE1B_ENST00000394277.3_3'UTR|PDE1B_ENST00000538346.1_Missense_Mutation_p.D136V|PDE1B_ENST00000550620.1_Missense_Mutation_p.D157V	NM_000924.3	NP_000915.1	Q01064	PDE1B_HUMAN	phosphodiesterase 1B, calmodulin-dependent	177					activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cGMP catabolic process (GO:0046069)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|monocyte differentiation (GO:0030224)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of dopamine metabolic process (GO:0042053)|regulation of neurotransmitter levels (GO:0001505)|response to amphetamine (GO:0001975)|serotonin metabolic process (GO:0042428)|signal transduction (GO:0007165)|visual learning (GO:0008542)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity (GO:0048101)|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			endometrium(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(4)	31					Bepridil(DB01244)|Caffeine(DB00201)|Felodipine(DB01023)|Nicardipine(DB00622)	GCAGCAGATGACCATGCCCTG	0.498																																					p.D177V		.											PDE1B,NS,carcinoma,0,1	PDE1B	0	0			c.A530T						.						229.0	185.0	200.0					12																	54964077		2203	4300	6503	SO:0001583	missense	5153	exon6			CAGATGACCATGC	U56976	CCDS8882.1, CCDS53800.1, CCDS73477.1	12q13	2008-03-18				ENSG00000123360	3.1.4.17	"""Phosphodiesterases"""	8775	protein-coding gene	gene with protein product		171891		PDES1B		8855339, 9419816	Standard	NM_000924		Approved		uc001sgd.2	Q01064	OTTHUMG00000169844	ENST00000243052.3:c.530A>T	12.37:g.54964077A>T	ENSP00000243052:p.Asp177Val	Somatic	13	0		WXS	Illumina HiSeq	.	11	2	NM_000924	Q92825|Q96KP3	Missense_Mutation	SNP	ENST00000243052.3	37	CCDS8882.1	.	.	.	.	.	.	.	.	.	.	A	15.80	2.939426	0.52972	.	.	ENSG00000123360	ENST00000243052;ENST00000538346;ENST00000550620	T;T;T	0.70631	-0.5;-0.47;-0.48	3.84	3.84	0.44239	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.058783	0.64402	D	0.000005	T	0.76786	0.4036	L	0.54323	1.7	0.80722	D	1	D;D	0.54601	0.961;0.967	P;P	0.60541	0.876;0.756	T	0.78934	-0.2008	10	0.72032	D	0.01	.	11.2322	0.48918	1.0:0.0:0.0:0.0	.	157;177	Q01064-2;Q01064	.;PDE1B_HUMAN	V	177;136;157	ENSP00000243052:D177V;ENSP00000442559:D136V;ENSP00000448519:D157V	ENSP00000243052:D177V	D	+	2	0	PDE1B	53250344	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.921000	0.70028	1.970000	0.57323	0.459000	0.35465	GAC	.		0.498	PDE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406203.1		
GREB1L	80000	hgsc.bcm.edu	37	18	18981119	18981119	+	Nonsense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr18:18981119G>T	ENST00000580732.2	+	6	922	c.541G>T	c.(541-543)Gga>Tga	p.G181*	GREB1L_ENST00000269218.6_Nonsense_Mutation_p.G181*|RP11-296E23.1_ENST00000584611.1_RNA|GREB1L_ENST00000431264.1_Nonsense_Mutation_p.G181*|GREB1L_ENST00000400483.4_Nonsense_Mutation_p.G181*|GREB1L_ENST00000424526.1_Nonsense_Mutation_p.G181*|GREB1L_ENST00000578368.1_3'UTR			Q9C091	GRB1L_HUMAN	growth regulation by estrogen in breast cancer-like	181						integral component of membrane (GO:0016021)				breast(5)|endometrium(4)|kidney(6)|lung(1)|skin(1)	17						AGGGTTTTCTGGAAATTGTAT	0.378																																					p.G181X		.											.	.	.	0			c.G541T						.						81.0	65.0	70.0					18																	18981119		692	1591	2283	SO:0001587	stop_gained	80000	exon6			TTTTCTGGAAATT	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.541G>T	18.37:g.18981119G>T	ENSP00000464162:p.Gly181*	Somatic	76	0		WXS	Illumina HiSeq	.	66	4	NM_001142966	A4QN17|Q9H8F1	Nonsense_Mutation	SNP	ENST00000580732.2	37	CCDS45836.1	.	.	.	.	.	.	.	.	.	.	G	40	8.092909	0.98651	.	.	ENSG00000141449	ENST00000424526;ENST00000269218;ENST00000400483;ENST00000431264	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	.	19.7739	0.96383	0.0:0.0:1.0:0.0	.	.	.	.	X	181	.	ENSP00000269218:G181X	G	+	1	0	GREB1L	17235117	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.813000	0.99286	2.744000	0.94065	0.655000	0.94253	GGA	.		0.378	GREB1L-003	KNOWN	not_organism_supported|upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443782.2	NM_024935	
MUC4	4585	hgsc.bcm.edu	37	3	195515030	195515030	+	Missense_Mutation	SNP	C	C	T	rs538504516	byFrequency	TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr3:195515030C>T	ENST00000463781.3	-	2	3880	c.3421G>A	c.(3421-3423)Gac>Aac	p.D1141N	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D1141N	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	608					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGAAGTGTCGGTGACAGGA	0.572																																					p.D1141N		.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4_ENST00000463781	0	0			c.G3421A						.						8.0	6.0	7.0					3																	195515030		651	1358	2009	SO:0001583	missense	4585	exon2			AAGTGTCGGTGAC	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.3421G>A	3.37:g.195515030C>T	ENSP00000417498:p.Asp1141Asn	Somatic	96	0		WXS	Illumina HiSeq	.	52	3	NM_018406	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	.	.	.	.	.	.	.	.	.	.	-	6.340	0.430835	0.12045	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33654	1.4;1.41	0.663	-1.33	0.09172	.	.	.	.	.	T	0.30103	0.0754	N	0.14661	0.345	0.09310	N	1	D	0.65815	0.995	P	0.61132	0.884	T	0.15694	-1.0428	8	.	.	.	.	3.7507	0.08565	0.214:0.2493:0.5366:0.0	.	1141	E7ESK3	.	N	1141	ENSP00000417498:D1141N;ENSP00000420243:D1141N	.	D	-	1	0	MUC4	196999425	0.000000	0.05858	0.000000	0.03702	0.066000	0.16364	-2.687000	0.00833	-1.284000	0.02390	0.064000	0.15345	GAC	.		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
AGO3	192669	hgsc.bcm.edu	37	1	36501846	36501846	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr1:36501846G>T	ENST00000373191.4	+	14	2169	c.1820G>T	c.(1819-1821)gGa>gTa	p.G607V	AGO3_ENST00000246314.6_Missense_Mutation_p.G373V	NM_024852.3	NP_079128.2	Q9H9G7	AGO3_HUMAN	argonaute RISC catalytic component 3	607	Piwi. {ECO:0000255|HAMAP-Rule:MF_03032}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of stem cell proliferation (GO:0072091)	cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)										GCTGGTGATGGAAAGAAGCCT	0.398																																					p.G607V		.											EIF2C3,NS,carcinoma,0,1	EIF2C3	0	0			c.G1820T						.						167.0	157.0	160.0					1																	36501846		2203	4300	6503	SO:0001583	missense	192669	exon14			GTGATGGAAAGAA	AB046787	CCDS399.1, CCDS400.1	1p34	2013-06-03	2013-02-15	2013-02-15	ENSG00000126070	ENSG00000126070		"""Argonaute/PIWI family"""	18421	protein-coding gene	gene with protein product	"""argonaute 3"""	607355	"""eukaryotic translation initiation factor 2C, 3"""	EIF2C3		12906857	Standard	NM_024852		Approved	hAGO3, FLJ12765	uc001bzp.3	Q9H9G7	OTTHUMG00000184172	ENST00000373191.4:c.1820G>T	1.37:g.36501846G>T	ENSP00000362287:p.Gly607Val	Somatic	77	0		WXS	Illumina HiSeq	.	42	2	NM_024852	B1ALI0|Q5TA55|Q9H1U6	Missense_Mutation	SNP	ENST00000373191.4	37	CCDS399.1	.	.	.	.	.	.	.	.	.	.	G	19.34	3.809138	0.70797	.	.	ENSG00000126070	ENST00000373191;ENST00000246314	T;T	0.27256	1.68;1.68	5.51	5.51	0.81932	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.26340	0.0643	L	0.28776	0.89	0.80722	D	1	B	0.15141	0.012	B	0.28553	0.091	T	0.04029	-1.0983	10	0.49607	T	0.09	-40.6225	19.7828	0.96424	0.0:0.0:1.0:0.0	.	607	Q9H9G7	AGO3_HUMAN	V	607;373	ENSP00000362287:G607V;ENSP00000246314:G373V	ENSP00000246314:G373V	G	+	2	0	EIF2C3	36274433	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.850000	0.99511	2.747000	0.94245	0.650000	0.86243	GGA	.		0.398	AGO3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019831.4	NM_024852	
HLA-B	3106	hgsc.bcm.edu	37	6	31323974	31323974	+	Missense_Mutation	SNP	C	C	T	rs41545114		TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr6:31323974C>T	ENST00000412585.2	-	3	617	c.589G>A	c.(589-591)Gag>Aag	p.E197K		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	197	Alpha-2.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						TTCCCGTTCTCCAGGTATCTG	0.672									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.E197K		.											.	.	.	0			c.G589A						.						19.0	19.0	19.0					6																	31323974		2128	4141	6269	SO:0001583	missense	3106	exon3	Familial Cancer Database	;Lichen Sclerosis, Familial	CGTTCTCCAGGTA	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.589G>A	6.37:g.31323974C>T	ENSP00000399168:p.Glu197Lys	Somatic	37	0		WXS	Illumina HiSeq	.	37	7	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	12.16	1.853263	0.32699	.	.	ENSG00000234745	ENST00000412585;ENST00000428231;ENST00000452596;ENST00000434333	T;T	0.00864	5.6;5.6	3.18	1.3	0.21679	MHC class I, alpha chain, alpha1/alpha2 (4);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	0.866418	0.09417	U	0.805050	T	0.03305	0.0096	H	0.95260	3.645	0.28841	N	0.896629	D;P	0.64830	0.994;0.632	D;B	0.75020	0.985;0.417	T	0.12016	-1.0564	10	0.72032	D	0.01	.	7.4791	0.27393	0.0:0.7684:0.0:0.2316	rs41545114	197;197	P30480;P01889	1B42_HUMAN;1B07_HUMAN	K	197;76;76;208	ENSP00000399168:E197K;ENSP00000405931:E208K	ENSP00000399168:E197K	E	-	1	0	HLA-B	31431953	0.086000	0.21541	0.525000	0.27900	0.024000	0.10985	0.314000	0.19432	0.183000	0.20059	0.297000	0.19635	GAG	0.001		0.672	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
ZMYM4	9202	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	35824927	35824927	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr1:35824927A>C	ENST00000314607.6	+	3	567	c.487A>C	c.(487-489)Aaa>Caa	p.K163Q	ZMYM4_ENST00000373297.2_Missense_Mutation_p.K163Q|ZMYM4-AS1_ENST00000432683.1_RNA	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	163					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				AGAAAACAGCAAAGAGACATT	0.308																																					p.K163Q		.											.	.	.	0			c.A487C						.						35.0	36.0	35.0					1																	35824927		2199	4293	6492	SO:0001583	missense	9202	exon3			AACAGCAAAGAGA	AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"""Zinc fingers, MYM type"""	13055	protein-coding gene	gene with protein product		613568	"""zinc finger protein 262"""	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.487A>C	1.37:g.35824927A>C	ENSP00000322915:p.Lys163Gln	Somatic	118	0		WXS	Illumina HiSeq	.	82	28	NM_005095	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Missense_Mutation	SNP	ENST00000314607.6	37	CCDS389.1	.	.	.	.	.	.	.	.	.	.	A	10.10	1.257830	0.22965	.	.	ENSG00000146463	ENST00000314607;ENST00000373297	T;T	0.26223	1.8;1.75	5.54	5.54	0.83059	.	0.000000	0.64402	D	0.000010	T	0.14917	0.0360	N	0.17082	0.46	0.28744	N	0.901809	B	0.17038	0.02	B	0.12837	0.008	T	0.16217	-1.0410	10	0.13108	T	0.6	-12.9097	11.6618	0.51352	0.852:0.148:0.0:0.0	.	163	Q5VZL5	ZMYM4_HUMAN	Q	163	ENSP00000322915:K163Q;ENSP00000362394:K163Q	ENSP00000322915:K163Q	K	+	1	0	ZMYM4	35597514	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.294000	0.59043	2.101000	0.63845	0.528000	0.53228	AAA	.		0.308	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095	
ZMAT1	84460	hgsc.bcm.edu	37	X	101153157	101153157	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chrX:101153157G>T	ENST00000372782.3	-	4	312	c.265C>A	c.(265-267)Caa>Aaa	p.Q89K	ZMAT1_ENST00000540921.1_Missense_Mutation_p.Q89K|ZMAT1_ENST00000458570.1_5'UTR	NM_001011657.3	NP_001011657	Q5H9K5	ZMAT1_HUMAN	zinc finger, matrin-type 1	89						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22						CCATGCATTTGAAAATAAAAA	0.303																																					p.Q89K		.											.	.	.	0			c.C265A						.						94.0	77.0	83.0					X																	101153157		2203	4299	6502	SO:0001583	missense	84460	exon4			GCATTTGAAAATA	Z69304	CCDS35348.1	Xq21	2012-10-05	2010-09-15		ENSG00000166432	ENSG00000166432		"""Zinc fingers, matrin-type"""	29377	protein-coding gene	gene with protein product							Standard	NM_001011657		Approved	KIAA1789	uc011mrl.2	Q5H9K5	OTTHUMG00000022044	ENST00000372782.3:c.265C>A	X.37:g.101153157G>T	ENSP00000361868:p.Gln89Lys	Somatic	99	0		WXS	Illumina HiSeq	.	99	4	NM_001011657	Q8NDS3|Q96JN6	Missense_Mutation	SNP	ENST00000372782.3	37	CCDS35348.1	.	.	.	.	.	.	.	.	.	.	G	12.18	1.861611	0.32884	.	.	ENSG00000166432	ENST00000372782;ENST00000540921	T;T	0.16597	2.33;2.33	4.6	3.71	0.42584	.	0.650135	0.12979	N	0.423492	T	0.15132	0.0365	M	0.63843	1.955	0.80722	D	1	P	0.39282	0.666	B	0.30179	0.112	T	0.06954	-1.0798	10	0.13470	T	0.59	-0.7736	11.6171	0.51096	0.0:0.177:0.823:0.0	.	89	Q5H9K5	ZMAT1_HUMAN	K	89	ENSP00000361868:Q89K;ENSP00000437529:Q89K	ENSP00000361868:Q89K	Q	-	1	0	ZMAT1	101039813	1.000000	0.71417	0.979000	0.43373	0.802000	0.45316	4.782000	0.62396	1.072000	0.40860	0.424000	0.28305	CAA	.		0.303	ZMAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057598.1		
ZC3H11A	9877	hgsc.bcm.edu;bcgsc.ca	37	1	203766905	203766905	+	Intron	SNP	T	T	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr1:203766905T>A	ENST00000332127.4	+	2	293				ZC3H11A_ENST00000367212.3_Intron|ZBED6_ENST00000550078.1_Missense_Mutation_p.F85L|ZC3H11A_ENST00000545588.1_5'Flank|ZC3H11A_ENST00000367214.1_Intron|ZC3H11A_ENST00000466470.1_Intron			O75152	ZC11A_HUMAN	zinc finger CCCH-type containing 11A						poly(A)+ mRNA export from nucleus (GO:0016973)		metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)			CCAAAAAGTTTAGTAAGGATT	0.413																																					p.F85L		.											.	.	.	0			c.T255A						.																																			SO:0001627	intron_variant	100381270	exon1			AAAGTTTAGTAAG		CCDS30978.1	1q32.1	2012-07-05	2005-06-02	2005-06-02	ENSG00000058673	ENSG00000058673		"""Zinc fingers, CCCH-type domain containing"""	29093	protein-coding gene	gene with protein product		613513	"""zinc finger CCCH-type domain containing 11A"""	ZC3HDC11A		9734811	Standard	NM_014827		Approved	KIAA0663	uc001hac.3	O75152	OTTHUMG00000035909	ENST00000332127.4:c.-565+1281T>A	1.37:g.203766905T>A		Somatic	41	0		WXS	Illumina HiSeq	.	30	10	NM_001174108	Q6AHY4|Q6AHY9|Q6AW79|Q6AWA1|Q6PJK4|Q86XZ7	Missense_Mutation	SNP	ENST00000332127.4	37	CCDS30978.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.935071	0.73442	.	.	ENSG00000257315	ENST00000550078	.	.	.	5.86	-0.875	0.10628	.	.	.	.	.	T	0.12902	0.0313	N	0.08118	0	0.25228	N	0.989854	.	.	.	.	.	.	T	0.31724	-0.9933	6	0.06494	T	0.89	.	5.1708	0.15108	0.0:0.4189:0.177:0.4041	.	.	.	.	L	85	.	ENSP00000447879:F85L	F	+	3	2	ZBED6	202033528	0.931000	0.31567	0.980000	0.43619	0.802000	0.45316	-0.249000	0.08842	0.130000	0.18549	-0.400000	0.06385	TTT	.		0.413	ZC3H11A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087691.1	NM_014827	
HIST1H4I	8294	hgsc.bcm.edu	37	6	27107240	27107240	+	Silent	SNP	C	C	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr6:27107240C>A	ENST00000354348.2	+	1	165	c.153C>A	c.(151-153)atC>atA	p.I51I	HIST1H2BK_ENST00000396891.4_Intron	NM_003495.2	NP_003486.1	P62805	H4_HUMAN	histone cluster 1, H4i	51					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			lung(1)	1						CTGGCCTCATCTATGAGGAGA	0.637			T	BCL6	NHL																																p.I51I		.		Dom	yes		6	6p21.3	8294	"""histone 1, H4i (H4FM)"""		L	HIST1H4I_ENST00000354348,NS,lymphoid_neoplasm,0,2	HIST1H4I_ENST00000354348	0	0			c.C153A						.						67.0	67.0	67.0					6																	27107240		2203	4300	6503	SO:0001819	synonymous_variant	8294	exon1			CCTCATCTATGAG	AB000905	CCDS4620.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000198339	ENSG00000276180		"""Histones / Replication-dependent"""	4793	protein-coding gene	gene with protein product		602833	"""H4 histone family, member M"", ""histone 1, H4i"""	H4FM		8988030, 9439656, 12408966	Standard	NM_003495		Approved	H4/m	uc003niy.1	P62805	OTTHUMG00000014471	ENST00000354348.2:c.153C>A	6.37:g.27107240C>A		Somatic	60	0		WXS	Illumina HiSeq	.	37	2	NM_003495	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Silent	SNP	ENST00000354348.2	37	CCDS4620.1																																																																																			.		0.637	HIST1H4I-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040139.1	NM_003495	
CCT6P3	643180	hgsc.bcm.edu;ucsc.edu	37	7	64529883	64529883	+	RNA	SNP	C	C	T	rs2691644		TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr7:64529883C>T	ENST00000426828.1	+	0	858				SNORA15_ENST00000384334.1_RNA	NR_033416.1				chaperonin containing TCP1, subunit 6 (zeta) pseudogene 3																		TGGTTTTCAGCTGGTTGATGG	0.373																																					.		.											.	.	.	0			.						.																																					643180	.			TTTCAGCTGGTTG			7q11.21	2010-06-29			ENSG00000234585	ENSG00000234585			35137	pseudogene	pseudogene							Standard	NR_033416		Approved		uc010kzt.1		OTTHUMG00000156630		7.37:g.64529883C>T		Somatic	20	0		WXS	Illumina HiSeq	.	22	6	.		RNA	SNP	ENST00000426828.1	37																																																																																				.		0.373	CCT6P3-004	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000344862.1		
EXOC4	60412	hgsc.bcm.edu	37	7	133580353	133580353	+	Splice_Site	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr7:133580353G>T	ENST00000253861.4	+	12	1765	c.1736G>T	c.(1735-1737)aGc>aTc	p.S579I	EXOC4_ENST00000460346.1_3'UTR|EXOC4_ENST00000539845.1_Splice_Site_p.S478I|EXOC4_ENST00000545148.1_Splice_Site_p.S189I	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	579					cellular protein metabolic process (GO:0044267)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)	protein N-terminus binding (GO:0047485)	p.S579N(1)		NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(16)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	50		Esophageal squamous(399;0.129)				CATTTCCAGAGCACAATCATT	0.418																																					p.S579I		.											EXOC4,colon,carcinoma,+1,1	EXOC4	+1	1	Substitution - Missense(1)	ovary(1)	c.G1736T						.						194.0	170.0	178.0					7																	133580353		2203	4300	6503	SO:0001630	splice_region_variant	60412	exon12			TCCAGAGCACAAT	AL831989	CCDS5829.1, CCDS43648.1	7q31	2013-01-22	2005-11-01	2005-11-01	ENSG00000131558	ENSG00000131558			30389	protein-coding gene	gene with protein product		608185	"""SEC8-like 1 (S. cerevisiae)"""	SEC8L1		11214970, 12687004	Standard	XM_005250523		Approved	KIAA1699, MGC27170, SEC8, Sec8p	uc003vrk.3	Q96A65	OTTHUMG00000155259	ENST00000253861.4:c.1735-1G>T	7.37:g.133580353G>T		Somatic	49	0		WXS	Illumina HiSeq	.	42	2	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Missense_Mutation	SNP	ENST00000253861.4	37	CCDS5829.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.310024	0.81247	.	.	ENSG00000131558	ENST00000253861;ENST00000546185;ENST00000539845;ENST00000545148	.	.	.	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	D	0.83124	0.5186	M	0.73962	2.25	0.80722	D	1	D;D;D	0.89917	0.993;1.0;1.0	P;D;D	0.83275	0.84;0.996;0.982	T	0.82853	-0.0252	9	0.66056	D	0.02	.	20.6721	0.99693	0.0:0.0:1.0:0.0	.	111;189;579	B7Z689;F5GZT1;Q96A65	.;.;EXOC4_HUMAN	I	579;198;478;189	.	ENSP00000253861:S579I	S	+	2	0	EXOC4	133230893	1.000000	0.71417	1.000000	0.80357	0.136000	0.21042	9.841000	0.99482	2.894000	0.99253	0.591000	0.81541	AGC	.		0.418	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807	Missense_Mutation
MIRLET7BHG	400931	hgsc.bcm.edu	37	22	46494461	46494461	+	Intron	SNP	G	G	C			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr22:46494461G>C	ENST00000381051.2	+	3	202				FLJ27365_ENST00000360737.3_Intron																							TGTGAATGTTGATGAAAATTG	0.557																																					.		.											.	.	.	0			.						.						133.0	141.0	138.0					22																	46494461		692	1591	2283	SO:0001627	intron_variant	400931	.			AATGTTGATGAAA																												ENST00000381051.2:c.149+23G>C	22.37:g.46494461G>C		Somatic	43	0		WXS	Illumina HiSeq	.	43	7	.		RNA	SNP	ENST00000381051.2	37																																																																																				.		0.557	FLJ27365-003	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316783.1		
ENTPD1	953	hgsc.bcm.edu	37	10	97599460	97599460	+	Silent	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr10:97599460C>T	ENST00000371205.4	+	3	440	c.157C>T	c.(157-159)Ctg>Ttg	p.L53L	RP11-429G19.3_ENST00000433113.1_RNA|ENTPD1_ENST00000490659.1_3'UTR|ENTPD1_ENST00000453258.2_Silent_p.L60L|ENTPD1_ENST00000543964.1_5'UTR|ENTPD1_ENST00000539125.1_Intron|ENTPD1_ENST00000371203.5_5'UTR|ENTPD1_ENST00000371207.3_Silent_p.L65L|ENTPD1-AS1_ENST00000416301.1_RNA			P49961	ENTP1_HUMAN	ectonucleoside triphosphate diphosphohydrolase 1	53					ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|purine ribonucleoside diphosphate catabolic process (GO:0009181)	basal lamina (GO:0005605)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			cervix(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|skin(1)	16		Colorectal(252;0.0821)		Epithelial(162;1.31e-07)|all cancers(201;5.33e-06)		TGGGATTGTGCTGGATGCGGG	0.418																																					p.L65L		.											ENTPD1,NS,carcinoma,0,1	ENTPD1	0	0			c.C193T						.						210.0	203.0	206.0					10																	97599460		2203	4300	6503	SO:0001819	synonymous_variant	953	exon3			ATTGTGCTGGATG	S73813	CCDS7444.1, CCDS53556.1, CCDS53557.1, CCDS53558.1, CCDS41554.1	10q24.1	2014-03-03			ENSG00000138185	ENSG00000138185		"""CD molecules"""	3363	protein-coding gene	gene with protein product		601752		CD39		9226376, 24482476	Standard	NM_001098175		Approved	NTPDase-1, ATPDase, SPG64	uc010qoj.2	P49961	OTTHUMG00000018818	ENST00000371205.4:c.157C>T	10.37:g.97599460C>T		Somatic	66	0		WXS	Illumina HiSeq	.	50	2	NM_001164178	A9Z1X8|B4DWB9|B4E1X1|B7Z599|G3XAF6|Q5T561|Q5T562|Q86VV3|Q9UQQ9|Q9Y3Q9	Silent	SNP	ENST00000371205.4	37	CCDS7444.1																																																																																			.		0.418	ENTPD1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049566.1	NM_001776	
MTCL1	23255	hgsc.bcm.edu	37	18	8718506	8718506	+	Silent	SNP	C	C	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr18:8718506C>A	ENST00000306329.11	+	2	1138	c.1138C>A	c.(1138-1140)Cgg>Agg	p.R380R	SOGA2_ENST00000359865.3_Silent_p.R20R|Y_RNA_ENST00000516510.1_RNA|SOGA2_ENST00000517570.1_Silent_p.R20R|SOGA2_ENST00000306285.7_5'UTR|SOGA2_ENST00000400050.3_Silent_p.R20R																							GCAGGAACTTCGGCGAGAACT	0.488																																					p.R20R		.											CCDC165,NS,malignant_melanoma,0,1	CCDC165	0	0			c.C58A						.						107.0	100.0	103.0					18																	8718506		2203	4300	6503	SO:0001819	synonymous_variant	23255	exon3			GAACTTCGGCGAG																												ENST00000306329.11:c.1138C>A	18.37:g.8718506C>A		Somatic	58	0		WXS	Illumina HiSeq	.	32	2	NM_015210		Silent	SNP	ENST00000306329.11	37																																																																																				.		0.488	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1		
SETD8	387893	hgsc.bcm.edu	37	12	123879692	123879692	+	Missense_Mutation	SNP	C	C	A	rs371558123		TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr12:123879692C>A	ENST00000402868.3	+	4	814	c.388C>A	c.(388-390)Caa>Aaa	p.Q130K	SETD8_ENST00000478781.2_3'UTR|SETD8_ENST00000330479.4_Missense_Mutation_p.Q130K			Q9NQR1	SETD8_HUMAN	SET domain containing (lysine methyltransferase) 8	171					histone lysine methylation (GO:0034968)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|urinary_tract(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		TTTTCCAAACCAAAAATCTGA	0.502																																					p.Q130K		.											.	.	.	0			c.C388A						.						32.0	32.0	32.0					12																	123879692		2203	4300	6503	SO:0001583	missense	387893	exon4			CCAAACCAAAAAT	AY102937	CCDS9247.1	12q24.31	2011-07-01			ENSG00000183955	ENSG00000183955		"""Chromatin-modifying enzymes / K-methyltransferases"""	29489	protein-coding gene	gene with protein product		607240				15933070, 12086618, 12121615	Standard	NM_020382		Approved	SET8, SET07, PR-Set7, KMT5A	uc001uew.3	Q9NQR1	OTTHUMG00000150477	ENST00000402868.3:c.388C>A	12.37:g.123879692C>A	ENSP00000384629:p.Gln130Lys	Somatic	126	0		WXS	Illumina HiSeq	.	79	4	NM_020382	A8K9D0|Q86W83|Q8TD09	Missense_Mutation	SNP	ENST00000402868.3	37	CCDS9247.1	.	.	.	.	.	.	.	.	.	.	C	16.06	3.014970	0.54468	.	.	ENSG00000183955	ENST00000402868;ENST00000330479;ENST00000437502	D;D	0.98164	-4.76;-4.76	5.57	5.57	0.84162	.	0.136595	0.51477	D	0.000088	D	0.96256	0.8779	L	0.50333	1.59	0.42572	D	0.993184	B;B	0.30104	0.268;0.228	B;B	0.27796	0.056;0.083	D	0.95614	0.8675	10	0.14656	T	0.56	-27.5297	17.7337	0.88386	0.0:1.0:0.0:0.0	.	171;130	Q9NQR1;Q9NQR1-2	SETD8_HUMAN;.	K	130;130;121	ENSP00000384629:Q130K;ENSP00000332995:Q130K	ENSP00000332995:Q130K	Q	+	1	0	SETD8	122445645	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.682000	0.61671	2.642000	0.89623	0.462000	0.41574	CAA	.		0.502	SETD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318263.1	NM_020382	
TMC1	117531	hgsc.bcm.edu	37	9	75387387	75387387	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr9:75387387G>A	ENST00000297784.5	+	13	1340	c.800G>A	c.(799-801)gGa>gAa	p.G267E	TMC1_ENST00000396237.3_Missense_Mutation_p.G267E|TMC1_ENST00000340019.3_Missense_Mutation_p.G267E	NM_138691.2	NP_619636.2	Q8TDI8	TMC1_HUMAN	transmembrane channel-like 1	267					auditory receptor cell development (GO:0060117)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(21)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	36						CGAACAATTGGATGGATGAAT	0.403																																					p.G267E	Pancreas(75;173 1345 14232 34245 43413)	.											TMC1,NS,carcinoma,0,1	TMC1	0	0			c.G800A						.						221.0	216.0	218.0					9																	75387387		2203	4300	6503	SO:0001583	missense	117531	exon13			CAATTGGATGGAT	AF417578	CCDS6643.1	9q21	2014-01-28			ENSG00000165091	ENSG00000165091			16513	protein-coding gene	gene with protein product		606706	"""transmembrane, cochlear expressed, 1"""	DFNA36, DFNB7, DFNB11		11850618, 11850623	Standard	NM_138691		Approved		uc004aiz.1	Q8TDI8	OTTHUMG00000020014	ENST00000297784.5:c.800G>A	9.37:g.75387387G>A	ENSP00000297784:p.Gly267Glu	Somatic	71	0		WXS	Illumina HiSeq	.	47	2	NM_138691	A8MVZ2|B1AM91	Missense_Mutation	SNP	ENST00000297784.5	37	CCDS6643.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.027827	0.93518	.	.	ENSG00000165091	ENST00000297784;ENST00000340019;ENST00000396235;ENST00000537917;ENST00000538054;ENST00000542143;ENST00000396237	T;T;T	0.51071	0.72;0.72;0.72	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.71779	0.3380	M	0.80616	2.505	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.994;0.994;0.994	T	0.71915	-0.4448	10	0.48119	T	0.1	-25.4502	19.5228	0.95192	0.0:0.0:1.0:0.0	.	234;234;267	A5D8Y1;A4FUA6;Q8TDI8	.;.;TMC1_HUMAN	E	267;267;234;234;234;261;267	ENSP00000297784:G267E;ENSP00000341433:G267E;ENSP00000379538:G267E	ENSP00000297784:G267E	G	+	2	0	TMC1	74577207	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.983000	0.93477	2.770000	0.95276	0.650000	0.86243	GGA	.		0.403	TMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052655.1		
PHF20L1	51105	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	133816130	133816130	+	Nonsense_Mutation	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr8:133816130C>T	ENST00000395386.2	+	7	873	c.574C>T	c.(574-576)Cga>Tga	p.R192*	PHF20L1_ENST00000395376.1_Nonsense_Mutation_p.R196*|PHF20L1_ENST00000395390.2_Nonsense_Mutation_p.R166*|PHF20L1_ENST00000337920.4_Nonsense_Mutation_p.R166*|PHF20L1_ENST00000220847.7_5'UTR|PHF20L1_ENST00000395379.1_Nonsense_Mutation_p.R192*	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	192							zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2)	15	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)			GAGTAAACCTCGAACCAGCGC	0.408																																					p.R192X		.											.	.	.	0			c.C574T						.						67.0	66.0	66.0					8																	133816130		2203	4299	6502	SO:0001587	stop_gained	51105	exon7			AAACCTCGAACCA	AF230666	CCDS6367.2, CCDS6368.1, CCDS75791.1	8q24.22	2014-03-24			ENSG00000129292	ENSG00000129292		"""Tudor domain containing"", ""Zinc fingers, PHD-type"""	24280	protein-coding gene	gene with protein product	"""tudor domain containing 20B"""					10810093, 24492612	Standard	NM_016018		Approved	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B	uc003ytt.3	A8MW92	OTTHUMG00000148656	ENST00000395386.2:c.574C>T	8.37:g.133816130C>T	ENSP00000378784:p.Arg192*	Somatic	58	0		WXS	Illumina HiSeq	.	50	11	NM_016018	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Nonsense_Mutation	SNP	ENST00000395386.2	37	CCDS6367.2	.	.	.	.	.	.	.	.	.	.	C	39	7.719031	0.98450	.	.	ENSG00000129292	ENST00000395383;ENST00000395379;ENST00000361997;ENST00000395386;ENST00000315808;ENST00000337920;ENST00000395376;ENST00000395382;ENST00000395390;ENST00000395374	.	.	.	5.89	5.89	0.94794	.	0.163292	0.53938	D	0.000050	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.4745	12.7776	0.57457	0.2564:0.7436:0.0:0.0	.	.	.	.	X	196;192;166;192;192;166;196;62;166;31	.	ENSP00000324519:R192X	R	+	1	2	PHF20L1	133885312	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.511000	0.53400	2.788000	0.95919	0.585000	0.79938	CGA	.		0.408	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018	
KMT2C	58508	hgsc.bcm.edu	37	7	151921114	151921114	+	Nonsense_Mutation	SNP	A	A	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr7:151921114A>T	ENST00000262189.6	-	20	3527	c.3309T>A	c.(3307-3309)tgT>tgA	p.C1103*	KMT2C_ENST00000355193.2_Nonsense_Mutation_p.C1103*	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1103					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.C1103*(10)									CACATTGTCTACATTGCAGAA	0.338																																					p.C1103X		.											MLL3_ENST00000355193,NS,carcinoma,0,10	MLL3_ENST00000355193	0	10	Substitution - Nonsense(10)	kidney(6)|endometrium(4)	c.T3309A						.						56.0	51.0	52.0					7																	151921114		2203	4300	6503	SO:0001587	stop_gained	58508	exon20			TTGTCTACATTGC	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.3309T>A	7.37:g.151921114A>T	ENSP00000262189:p.Cys1103*	Somatic	109	2		WXS	Illumina HiSeq	.	88	5	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Nonsense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	A	41	8.814636	0.98964	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	.	.	.	5.39	-2.79	0.05841	.	0.000000	0.50627	D	0.000105	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.2367	0.59972	0.4373:0.0:0.5627:0.0	rs4024337	.	.	.	X	1103	.	ENSP00000262189:C1103X	C	-	3	2	MLL3	151552047	0.735000	0.28153	0.983000	0.44433	0.992000	0.81027	-0.154000	0.10130	-0.431000	0.07307	0.528000	0.53228	TGT	.		0.338	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
ROS1	6098	hgsc.bcm.edu	37	6	117715380	117715380	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr6:117715380G>T	ENST00000368508.3	-	10	1307	c.1109C>A	c.(1108-1110)tCt>tAt	p.S370Y	ROS1_ENST00000368507.3_Missense_Mutation_p.S379Y|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	370			S -> P (in dbSNP:rs56274823). {ECO:0000269|PubMed:17344846}.		cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.S370Y(1)	TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		GGAGATAGAAGAAATTAATCC	0.373			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""																																p.S370Y		.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"""O, E"""	ROS1_ENST00000368508,caecum,carcinoma,+1,1	ROS1_ENST00000368508	+1	1	Substitution - Missense(1)	ovary(1)	c.C1109A						.						52.0	55.0	54.0					6																	117715380		2202	4300	6502	SO:0001583	missense	6098	exon10			ATAGAAGAAATTA	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"""Fibronectin type III domain containing"""	10261	protein-coding gene	gene with protein product		165020	"""v-ros avian UR2 sarcoma virus oncogene homolog 1"", ""v-ros UR2 sarcoma virus oncogene homolog 1 (avian)"", ""c-ros oncogene 1 , receptor tyrosine kinase"""			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.1109C>A	6.37:g.117715380G>T	ENSP00000357494:p.Ser370Tyr	Somatic	67	0		WXS	Illumina HiSeq	.	48	2	NM_002944	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	G	14.38	2.518395	0.44763	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	D;D	0.91351	-2.83;-2.83	5.12	5.12	0.69794	.	0.300661	0.29152	N	0.012996	D	0.87358	0.6157	L	0.56769	1.78	0.80722	D	1	D	0.55385	0.971	P	0.50440	0.641	D	0.85647	0.1280	10	0.34782	T	0.22	.	9.4876	0.38940	0.0795:0.1454:0.775:0.0	.	370	P08922	ROS1_HUMAN	Y	370;379	ENSP00000357494:S370Y;ENSP00000357493:S379Y	ENSP00000357493:S379Y	S	-	2	0	ROS1	117822073	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	3.843000	0.55865	2.773000	0.95371	0.650000	0.86243	TCT	.		0.373	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		
C3orf52	79669	hgsc.bcm.edu	37	3	111835806	111835806	+	3'UTR	SNP	C	C	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr3:111835806C>A	ENST00000264848.5	+	0	1026				C3orf52_ENST00000431717.2_Missense_Mutation_p.F238L|C3orf52_ENST00000430855.1_Intron|C3orf52_ENST00000467942.2_Intron	NM_024616.2	NP_078892	Q5BVD1	TTMP_HUMAN	chromosome 3 open reading frame 52							endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4						tgttttgtttcgttttgtttt	0.517																																					p.F238L		.											C3orf52_ENST00000431717,NS,carcinoma,0,1	C3orf52_ENST00000431717	0	0			c.C714A						.						16.0	20.0	19.0					3																	111835806		692	1591	2283	SO:0001624	3_prime_UTR_variant	79669	exon4			TTGTTTCGTTTTG	AY830714	CCDS46887.1, CCDS54620.1	3q13.2	2006-01-30			ENSG00000114529	ENSG00000114529			26255	protein-coding gene	gene with protein product	"""TPA induced trans-membrane protein"""	611956				15737651	Standard	NM_024616		Approved	FLJ23186, TTMP	uc011bhs.2	Q5BVD1	OTTHUMG00000159230	ENST00000264848.5:c.*313C>A	3.37:g.111835806C>A		Somatic	33	0		WXS	Illumina HiSeq	.	17	2	NM_001171747	B4DNV2|B4E0Z2|Q96AJ4|Q9H5Q1	Missense_Mutation	SNP	ENST00000264848.5	37	CCDS46887.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	2.067|2.067	-0.414024|-0.414024	0.04799|0.04799	.|.	.|.	ENSG00000114529|ENSG00000114529	ENST00000431717|ENST00000484828	T|.	0.34667|.	1.35|.	0.714|0.714	-0.8|-0.8	0.10897|0.10897	.|.	.|.	.|.	.|.	.|.	T|T	0.10508|0.10508	0.0257|0.0257	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	P|.	0.44659|.	0.84|.	B|.	0.36719|.	0.231|.	T|T	0.21895|0.21895	-1.0232|-1.0232	8|4	0.87932|.	D|.	0|.	.|.	.|.	.|.	.|.	.|.	238|.	Q5BVD1-3|.	.|.	L|S	238|229	ENSP00000399392:F238L|.	ENSP00000399392:F238L|.	F|R	+|+	3|1	2|0	C3orf52|C3orf52	113318496|113318496	0.000000|0.000000	0.05858|0.05858	0.003000|0.003000	0.11579|0.11579	0.007000|0.007000	0.05969|0.05969	-5.306000|-5.306000	0.00133|0.00133	-1.879000|-1.879000	0.01126|0.01126	-2.843000|-2.843000	0.00104|0.00104	TTC|CGT	.		0.517	C3orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353961.1	NM_024616	
NLRP8	126205	hgsc.bcm.edu	37	19	56477640	56477640	+	Nonsense_Mutation	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr19:56477640C>T	ENST00000291971.3	+	5	2346	c.2275C>T	c.(2275-2277)Cag>Tag	p.Q759*	NLRP8_ENST00000590542.1_Nonsense_Mutation_p.Q759*	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	759					neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		GACGGGGAACCAGCATCTGAG	0.527																																					p.Q759X		.											.	.	.	0			c.C2275T						.						181.0	160.0	167.0					19																	56477640		2203	4300	6503	SO:0001587	stop_gained	126205	exon5			GGGAACCAGCATC	AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"""Nucleotide-binding domain and leucine rich repeat containing"""	22940	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"""	609659	"""NACHT, leucine rich repeat and PYD containing 8"""	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.2275C>T	19.37:g.56477640C>T	ENSP00000291971:p.Gln759*	Somatic	87	0		WXS	Illumina HiSeq	.	88	4	NM_176811	Q7RTR4	Nonsense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	.	.	.	.	.	.	.	.	.	.	C	18.90	3.721705	0.68959	.	.	ENSG00000179709	ENST00000291971	.	.	.	1.82	-3.65	0.04502	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	1.0317	0.01540	0.1824:0.3967:0.1602:0.2607	.	.	.	.	X	759	.	ENSP00000291971:Q759X	Q	+	1	0	NLRP8	61169452	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.091000	0.03369	-1.581000	0.01642	-3.398000	0.00039	CAG	.		0.527	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
RYR2	6262	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	1	237777618	237777618	+	Silent	SNP	G	G	A	rs397516541		TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr1:237777618G>A	ENST00000366574.2	+	37	5507	c.5190G>A	c.(5188-5190)acG>acA	p.T1730T	RYR2_ENST00000542537.1_Silent_p.T1714T|RYR2_ENST00000360064.6_Silent_p.T1728T	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1730	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TCCCCATGACGGAGGAGACGA	0.547																																					p.T1730T		.											.	.	.	0			c.G5190A						.						63.0	62.0	63.0					1																	237777618		2121	4237	6358	SO:0001819	synonymous_variant	6262	exon37			CATGACGGAGGAG	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.5190G>A	1.37:g.237777618G>A		Somatic	37	0		WXS	Illumina HiSeq	.	30	8	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	37	CCDS55691.1																																																																																			.		0.547	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
SH3BP5L	80851	hgsc.bcm.edu	37	1	249119038	249119038	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr1:249119038C>T	ENST00000366472.5	-	2	1326	c.97G>A	c.(97-99)Gca>Aca	p.A33T	MIR3124_ENST00000582636.1_RNA|SH3BP5L_ENST00000475978.1_5'UTR	NM_030645.1	NP_085148.1	Q7L8J4	3BP5L_HUMAN	SH3-binding domain protein 5-like	33										endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			GGCTCTTCTGCGACTGGGCTC	0.587																																					p.A33T		.											SH3BP5L,NS,carcinoma,0,1	SH3BP5L	0	0			c.G97A						.						149.0	151.0	150.0					1																	249119038		2203	4300	6503	SO:0001583	missense	80851	exon2			CTTCTGCGACTGG	AB051507	CCDS31126.1	1q44	2008-02-05			ENSG00000175137	ENSG00000175137			29360	protein-coding gene	gene with protein product							Standard	NM_030645		Approved	KIAA1720	uc001iew.1	Q7L8J4	OTTHUMG00000040389	ENST00000366472.5:c.97G>A	1.37:g.249119038C>T	ENSP00000355428:p.Ala33Thr	Somatic	41	0		WXS	Illumina HiSeq	.	34	2	NM_030645	B4DQ94|Q96FI5|Q9BQH8|Q9C0E3	Missense_Mutation	SNP	ENST00000366472.5	37	CCDS31126.1	.	.	.	.	.	.	.	.	.	.	C	7.378	0.628247	0.14257	.	.	ENSG00000175137	ENST00000366472	.	.	.	4.19	-3.36	0.04913	.	1.252050	0.05704	N	0.594686	T	0.14399	0.0348	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19614	-1.0300	9	0.08381	T	0.77	-0.0944	0.1798	0.00122	0.2965:0.2565:0.1457:0.3013	.	33	Q7L8J4	3BP5L_HUMAN	T	33	.	ENSP00000355428:A33T	A	-	1	0	SH3BP5L	247085661	0.000000	0.05858	0.003000	0.11579	0.667000	0.39255	-0.118000	0.10692	-0.402000	0.07633	-0.905000	0.02835	GCA	.		0.587	SH3BP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097140.1	NM_030645	
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	209113113	209113113	+	Missense_Mutation	SNP	G	G	A	rs121913499		TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr2:209113113G>A	ENST00000415913.1	-	4	775	c.394C>T	c.(394-396)Cgt>Tgt	p.R132C	IDH1_ENST00000446179.1_Missense_Mutation_p.R132C|IDH1_ENST00000345146.2_Missense_Mutation_p.R132C	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132C(446)|p.R132G(125)|p.R132S(106)|p.G131_R132>VL(1)|p.R132V(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		TAAGCATGACGACCTATGATG	0.398			Mis		gliobastoma																																p.R132C	Pancreas(158;264 1958 3300 35450 36047)	.		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	IDH1,NS,haematopoietic_neoplasm,0,788	IDH1	0	679	Substitution - Missense(678)|Complex - compound substitution(1)	haematopoietic_and_lymphoid_tissue(280)|central_nervous_system(181)|bone(177)|biliary_tract(21)|soft_tissue(12)|large_intestine(2)|skin(2)|autonomic_ganglia(1)|endometrium(1)|NS(1)|prostate(1)	c.C394T						.						81.0	74.0	76.0					2																	209113113		2203	4300	6503	SO:0001583	missense	3417	exon4			CATGACGACCTAT		CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.394C>T	2.37:g.209113113G>A	ENSP00000390265:p.Arg132Cys	Somatic	51	0		WXS	Illumina HiSeq	.	49	20	NM_005896	Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.550898	0.86127	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.87029	-2.2;-2.2;-2.2;-2.2	5.57	5.57	0.84162	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.94049	0.8093	H	0.99379	4.54	0.80722	D	1	B	0.29862	0.259	B	0.31245	0.126	D	0.94048	0.7315	10	0.87932	D	0	-20.0399	19.5341	0.95242	0.0:0.0:1.0:0.0	.	132	O75874	IDHC_HUMAN	C	132	ENSP00000260985:R132C;ENSP00000410513:R132C;ENSP00000390265:R132C;ENSP00000391075:R132C	ENSP00000260985:R132C	R	-	1	0	IDH1	208821358	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.074000	0.76791	2.616000	0.88540	0.555000	0.69702	CGT	.		0.398	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1		
CASKIN1	57524	hgsc.bcm.edu	37	16	2239059	2239059	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr16:2239059C>T	ENST00000343516.6	-	6	678	c.586G>A	c.(586-588)Gca>Aca	p.A196T		NM_020764.3	NP_065815.1	Q8WXD9	CSKI1_HUMAN	CASK interacting protein 1	196					signal transduction (GO:0007165)	cytoplasm (GO:0005737)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|liver(1)|lung(7)|ovary(4)|prostate(5)|skin(3)	28						TTTTTAGCTGCGAGGTGCAAA	0.657																																					p.A196T		.											CASKIN1_ENST00000382453,NS,carcinoma,0,2	CASKIN1_ENST00000382453	0	0			c.G586A						.						78.0	85.0	83.0					16																	2239059		2091	4208	6299	SO:0001583	missense	57524	exon6			TAGCTGCGAGGTG	AF451977	CCDS42103.1	16p13.3	2013-01-10				ENSG00000167971		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	20879	protein-coding gene	gene with protein product		612184				12040031	Standard	NM_020764		Approved	KIAA1306, ANKS5A	uc010bsg.1	Q8WXD9		ENST00000343516.6:c.586G>A	16.37:g.2239059C>T	ENSP00000345436:p.Ala196Thr	Somatic	68	0		WXS	Illumina HiSeq	.	44	2	NM_020764	Q9P2P0	Missense_Mutation	SNP	ENST00000343516.6	37	CCDS42103.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.529281	0.85706	.	.	ENSG00000167971	ENST00000343516;ENST00000382453	T	0.81163	-1.46	3.46	3.46	0.39613	Ankyrin repeat-containing domain (4);	.	.	.	.	D	0.91047	0.7183	M	0.93550	3.43	0.80722	D	1	D	0.67145	0.996	D	0.66196	0.942	D	0.93421	0.6777	9	0.87932	D	0	-9.7927	14.0324	0.64624	0.0:1.0:0.0:0.0	.	196	Q8WXD9	CSKI1_HUMAN	T	196;25	ENSP00000345436:A196T	ENSP00000345436:A196T	A	-	1	0	CASKIN1	2179060	1.000000	0.71417	1.000000	0.80357	0.615000	0.37417	5.734000	0.68580	1.954000	0.56735	0.561000	0.74099	GCA	.		0.657	CASKIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435055.1	NM_020764	
F5	2153	hgsc.bcm.edu	37	1	169500257	169500257	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr1:169500257G>T	ENST00000367797.3	-	15	5176	c.4975C>A	c.(4975-4977)Cgt>Agt	p.R1659S	F5_ENST00000367796.3_Missense_Mutation_p.R1664S	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	1659	F5/8 type A 3.|Plastocyanin-like 5.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	TTTTTAAAACGAACCTAGGAA	0.343																																					p.R1659S		.											F5,NS,carcinoma,0,1	F5	0	0			c.C4975A						.						72.0	72.0	72.0					1																	169500257		2203	4300	6503	SO:0001583	missense	2153	exon15			TAAAACGAACCTA	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.4975C>A	1.37:g.169500257G>T	ENSP00000356771:p.Arg1659Ser	Somatic	43	0		WXS	Illumina HiSeq	.	47	2	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	G	13.52	2.261753	0.39995	.	.	ENSG00000198734	ENST00000367797;ENST00000367796	D;D	0.99005	-5.32;-5.32	5.49	5.49	0.81192	Cupredoxin (2);Multicopper oxidase, type 3 (1);	0.506161	0.23638	N	0.046046	D	0.96134	0.8740	L	0.41492	1.28	0.27363	N	0.955915	B	0.25719	0.132	B	0.29785	0.107	D	0.94668	0.7854	9	0.29301	T	0.29	-2.1826	14.253	0.66033	0.0:0.0:0.8511:0.1489	.	1659	P12259	FA5_HUMAN	S	1659;1664	ENSP00000356771:R1659S;ENSP00000356770:R1664S	ENSP00000356770:R1664S	R	-	1	0	F5	167766881	0.999000	0.42202	0.997000	0.53966	0.919000	0.55068	4.489000	0.60309	2.586000	0.87340	0.655000	0.94253	CGT	.		0.343	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
ADAM28	10863	hgsc.bcm.edu	37	8	24199122	24199122	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr8:24199122G>T	ENST00000265769.4	+	16	1792	c.1682G>T	c.(1681-1683)tGt>tTt	p.C561F	ADAM28_ENST00000397649.3_Missense_Mutation_p.C308F|RP11-624C23.1_ENST00000523700.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000518988.1_RNA	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	561	Cys-rich.				spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.C561F(1)		central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		GATACCATGTGTGGGAAGTTG	0.388																																					p.C561F	NSCLC(193;488 2149 22258 34798 40734)	.											ADAM28,NS,carcinoma,0,1	ADAM28	0	1	Substitution - Missense(1)	endometrium(1)	c.G1682T						.						240.0	235.0	237.0					8																	24199122		2203	4300	6503	SO:0001583	missense	10863	exon16			CCATGTGTGGGAA	AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"""ADAM metallopeptidase domain containing"""	206	protein-coding gene	gene with protein product		606188	"""a disintegrin and metalloproteinase domain 28"""				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.1682G>T	8.37:g.24199122G>T	ENSP00000265769:p.Cys561Phe	Somatic	71	0		WXS	Illumina HiSeq	.	31	2	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Missense_Mutation	SNP	ENST00000265769.4	37	CCDS34865.1	.	.	.	.	.	.	.	.	.	.	G	18.62	3.662407	0.67700	.	.	ENSG00000042980	ENST00000265769;ENST00000397649	T;T	0.63580	-0.05;-0.05	5.84	5.84	0.93424	ADAM, cysteine-rich (2);	.	.	.	.	D	0.87438	0.6177	H	0.97806	4.08	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.91528	0.5240	9	0.87932	D	0	.	17.6318	0.88111	0.0:0.0:1.0:0.0	.	561;561	B2RMV5;Q9UKQ2	.;ADA28_HUMAN	F	561;308	ENSP00000265769:C561F;ENSP00000380770:C308F	ENSP00000265769:C561F	C	+	2	0	ADAM28	24255067	1.000000	0.71417	0.999000	0.59377	0.610000	0.37248	7.380000	0.79704	2.779000	0.95612	0.655000	0.94253	TGT	.		0.388	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778	
SDHA	6389	hgsc.bcm.edu	37	5	228322	228322	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr5:228322A>G	ENST00000264932.6	+	6	759	c.644A>G	c.(643-645)tAt>tGt	p.Y215C	SDHA_ENST00000504309.1_Missense_Mutation_p.Y215C|SDHA_ENST00000510361.1_Missense_Mutation_p.Y167C	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	215					cellular metabolic process (GO:0044237)|nervous system development (GO:0007399)|oxidation-reduction process (GO:0055114)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|tricarboxylic acid cycle (GO:0006099)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|succinate dehydrogenase (ubiquinone) activity (GO:0008177)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|liver(2)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	40			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	GATACCAGCTATTTTGTGGAG	0.438									Familial Paragangliomas																												p.Y215C		.											.	.	.	0			c.A644G						.						69.0	70.0	70.0					5																	228322		2203	4300	6503	SO:0001583	missense	6389	exon6	Familial Cancer Database	Hereditary Glomus Tumors, Familial Paragangliomas, Hereditary Paragangliomas, type 1-3: PGL1, PGL2, PGL3, incl. Familial Carotid Body Paraganglioma and Sensorineural Hearing Loss	CCAGCTATTTTGT	BC001380	CCDS3853.1	5p15	2014-09-17			ENSG00000073578	ENSG00000073578		"""Mitochondrial respiratory chain complex / Complex II"""	10680	protein-coding gene	gene with protein product		600857		SDH2		7798181	Standard	XM_005248329		Approved	FP, SDHF	uc003jao.4	P31040	OTTHUMG00000090275	ENST00000264932.6:c.644A>G	5.37:g.228322A>G	ENSP00000264932:p.Tyr215Cys	Somatic	115	0		WXS	Illumina HiSeq	.	91	4	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Missense_Mutation	SNP	ENST00000264932.6	37	CCDS3853.1	.	.	.	.	.	.	.	.	.	.	g	20.8	4.054712	0.75960	.	.	ENSG00000073578	ENST00000264932;ENST00000504309;ENST00000510361	T;T;T	0.70045	-0.45;-0.45;-0.45	5.23	5.23	0.72850	Fumarate reductase/succinate dehydrogenase flavoprotein, N-terminal (1);	0.000000	0.64402	U	0.000001	T	0.68229	0.2978	L	0.61218	1.895	0.80722	D	1	P;P;P;P;P	0.49559	0.496;0.767;0.925;0.525;0.525	B;P;P;B;B	0.46076	0.429;0.452;0.503;0.32;0.32	T	0.73668	-0.3910	10	0.87932	D	0	.	13.4155	0.60966	1.0:0.0:0.0:0.0	.	167;215;215;215;221	E9PBJ5;B4DYN5;D6RFM5;P31040;Q59GW8	.;.;.;DHSA_HUMAN;.	C	215;215;167	ENSP00000264932:Y215C;ENSP00000426514:Y215C;ENSP00000427703:Y167C	ENSP00000264932:Y215C	Y	+	2	0	SDHA	281322	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.156000	0.77453	2.127000	0.65507	0.524000	0.50904	TAT	.		0.438	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
PKP1	5317	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	201286846	201286846	+	Silent	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr1:201286846C>T	ENST00000352845.3	+	5	993	c.993C>T	c.(991-993)atC>atT	p.I331I	PKP1_ENST00000263946.3_Silent_p.I331I|PKP1_ENST00000367324.3_Silent_p.I331I|PKP1_ENST00000475988.1_3'UTR			Q13835	PKP1_HUMAN	plakophilin 1	331					apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intermediate filament bundle assembly (GO:0045110)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|lamin binding (GO:0005521)|signal transducer activity (GO:0004871)|structural constituent of epidermis (GO:0030280)			NS(2)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(5)|prostate(1)	22						AGAATGGGATCCGCGAGGCAG	0.657																																					p.I331I		.											.	.	.	0			c.C993T						.						34.0	36.0	35.0					1																	201286846		2203	4300	6503	SO:0001819	synonymous_variant	5317	exon5			TGGGATCCGCGAG	X79293	CCDS30966.1, CCDS30967.1	1q32	2014-06-18	2014-06-18		ENSG00000081277	ENSG00000081277		"""Armadillo repeat containing"""	9023	protein-coding gene	gene with protein product	"""ectodermal dysplasia/skin fragility syndrome"""	601975	"""plakophilin 1 (ectodermal dysplasia/skin fragility syndrome)"""			9272178	Standard	NM_001005337		Approved	B6P	uc001gwd.3	Q13835	OTTHUMG00000035729	ENST00000352845.3:c.993C>T	1.37:g.201286846C>T		Somatic	45	0		WXS	Illumina HiSeq	.	45	5	NM_001005337	O00645|Q14CA0|Q15152	Silent	SNP	ENST00000352845.3	37	CCDS30966.1																																																																																			.		0.657	PKP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086897.1	NM_000299	
WDR55	54853	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	140048015	140048015	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr5:140048015C>T	ENST00000358337.5	+	3	545	c.308C>T	c.(307-309)tCc>tTc	p.S103F		NM_017706.4	NP_060176	Q9H6Y2	WDR55_HUMAN	WD repeat domain 55	103					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)				NS(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATTACTGTCTCCAAGGACAAA	0.527																																					p.S103F		.											.	.	.	0			c.C308T						.						198.0	182.0	187.0					5																	140048015		2203	4300	6503	SO:0001583	missense	54853	exon3			CTGTCTCCAAGGA	AK000202	CCDS4235.1	5q31.3	2013-01-09			ENSG00000120314	ENSG00000120314		"""WD repeat domain containing"""	25971	protein-coding gene	gene with protein product						12477932	Standard	NM_017706		Approved	FLJ20195, FLJ21702	uc003lgr.4	Q9H6Y2	OTTHUMG00000129506	ENST00000358337.5:c.308C>T	5.37:g.140048015C>T	ENSP00000351100:p.Ser103Phe	Somatic	60	0		WXS	Illumina HiSeq	.	44	8	NM_017706	Q9NXK4	Missense_Mutation	SNP	ENST00000358337.5	37	CCDS4235.1	.	.	.	.	.	.	.	.	.	.	C	13.62	2.292964	0.40594	.	.	ENSG00000120314	ENST00000358337	T	0.74526	-0.85	4.98	4.98	0.66077	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.64402	D	0.000001	D	0.90363	0.6984	H	0.95294	3.65	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93101	0.6508	10	0.87932	D	0	-13.9723	17.1868	0.86868	0.0:1.0:0.0:0.0	.	103	Q9H6Y2	WDR55_HUMAN	F	103	ENSP00000351100:S103F	ENSP00000351100:S103F	S	+	2	0	WDR55	140028199	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	5.338000	0.65947	2.580000	0.87095	0.467000	0.42956	TCC	.		0.527	WDR55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251680.3	NM_017706	
PHKA2	5256	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	X	18924875	18924875	+	Silent	SNP	G	G	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chrX:18924875G>A	ENST00000379942.4	-	24	3320	c.2655C>T	c.(2653-2655)atC>atT	p.I885I		NM_000292.2	NP_000283.1	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)	885					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61	Hepatocellular(33;0.183)					CGGCAATGCTGATGTCCTGCC	0.597																																					p.I885I		.											.	.	.	0			c.C2655T						.						170.0	150.0	157.0					X																	18924875		2203	4300	6503	SO:0001819	synonymous_variant	5256	exon24			AATGCTGATGTCC		CCDS14190.1	Xp22.2-p22.1	2009-07-10			ENSG00000044446	ENSG00000044446	2.7.11.19		8926	protein-coding gene	gene with protein product		300798		PHK, PYK		2387090	Standard	NM_000292		Approved		uc004cyv.4	P46019	OTTHUMG00000021222	ENST00000379942.4:c.2655C>T	X.37:g.18924875G>A		Somatic	94	0		WXS	Illumina HiSeq	.	80	7	NM_000292	A8K1T1|Q6LAJ5|Q7Z6W0|Q96CR3|Q9UDA1	Silent	SNP	ENST00000379942.4	37	CCDS14190.1																																																																																			.		0.597	PHKA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055960.1	NM_000292	
F9	2158	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	138642998	138642998	+	Silent	SNP	A	A	G			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chrX:138642998A>G	ENST00000218099.2	+	7	829	c.822A>G	c.(820-822)aaA>aaG	p.K274K	F9_ENST00000394090.2_Silent_p.K236K	NM_000133.3	NP_000124.1	P00740	FA9_HUMAN	coagulation factor IX	274	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|blood coagulation, intrinsic pathway (GO:0007597)|cellular protein metabolic process (GO:0044267)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|skin(1)	35	Acute lymphoblastic leukemia(192;0.000127)				Antihemophilic Factor(DB00025)|Menadione(DB00170)	CTGGTGTTAAAATTACAGTTG	0.358																																					p.K274K		.											.	.	.	0			c.A822G						.						178.0	160.0	166.0					X																	138642998		2203	4300	6503	SO:0001819	synonymous_variant	2158	exon7			TGTTAAAATTACA	M11309	CCDS14666.1	Xq26.3-q27.1	2014-09-17	2008-08-01		ENSG00000101981	ENSG00000101981	3.4.21.22		3551	protein-coding gene	gene with protein product	"""Factor IX"", ""plasma thromboplastic component"", ""Christmas disease"", ""hemophilia B"""	300746					Standard	NM_000133		Approved	FIX	uc004fas.1	P00740	OTTHUMG00000022536	ENST00000218099.2:c.822A>G	X.37:g.138642998A>G		Somatic	163	0		WXS	Illumina HiSeq	.	136	15	NM_000133	A8K9N4|F2RM36|Q5FBE1|Q5JYJ8	Silent	SNP	ENST00000218099.2	37	CCDS14666.1																																																																																			.		0.358	F9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058557.1		
CUBN	8029	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	17164817	17164817	+	Silent	SNP	A	A	G			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr10:17164817A>G	ENST00000377833.4	-	6	635	c.570T>C	c.(568-570)tgT>tgC	p.C190C		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	190	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TTGTATTAACACATGTGCCTC	0.378																																					p.C190C		.											.	.	.	0			c.T570C						.						75.0	65.0	68.0					10																	17164817		2203	4300	6503	SO:0001819	synonymous_variant	8029	exon6			ATTAACACATGTG	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.570T>C	10.37:g.17164817A>G		Somatic	16	0		WXS	Illumina HiSeq	.	12	4	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																			.		0.378	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
RGS7	6000	hgsc.bcm.edu	37	1	240979680	240979680	+	Silent	SNP	G	G	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr1:240979680G>A	ENST00000407727.1	-	10	719	c.720C>T	c.(718-720)caC>caT	p.H240H	RGS7_ENST00000366564.1_Silent_p.H240H|RGS7_ENST00000331110.7_Silent_p.H214H|RGS7_ENST00000366565.1_Silent_p.H240H|RGS7_ENST00000348120.2_Silent_p.H187H|RGS7_ENST00000366562.4_Silent_p.H240H|RGS7_ENST00000401882.1_Silent_p.H187H|RGS7_ENST00000366563.1_Silent_p.H240H|RGS7_ENST00000446183.2_Silent_p.H156H			P49802	RGS7_HUMAN	regulator of G-protein signaling 7	240					G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite terminus (GO:0044292)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(51)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			GGGTAGGACTGTGACTTCTAA	0.348																																					p.H240H		.											.	.	.	0			c.C720T						.						302.0	272.0	282.0					1																	240979680		2203	4300	6503	SO:0001819	synonymous_variant	6000	exon11			AGGACTGTGACTT	BC022009	CCDS31071.1, CCDS60457.1, CCDS60458.1, CCDS60459.1	1q43	2008-02-05	2007-08-14		ENSG00000182901	ENSG00000182901		"""Regulators of G-protein signaling"""	10003	protein-coding gene	gene with protein product		602517	"""regulator of G-protein signalling 7"""			8548815	Standard	XM_005273218		Approved		uc001hyv.2	P49802	OTTHUMG00000040107	ENST00000407727.1:c.720C>T	1.37:g.240979680G>A		Somatic	115	0		WXS	Illumina HiSeq	.	100	4	NM_002924	Q5T3H4|Q8TD66|Q8TD67|Q8WW09|Q9UNU7|Q9Y6B9	Silent	SNP	ENST00000407727.1	37																																																																																				.		0.348	RGS7-204	KNOWN	basic	protein_coding	protein_coding		NM_002924	
GPRASP1	9737	hgsc.bcm.edu;bcgsc.ca	37	X	101910213	101910213	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chrX:101910213A>G	ENST00000361600.5	+	5	2173	c.1372A>G	c.(1372-1374)Agg>Ggg	p.R458G	GPRASP1_ENST00000537097.1_Missense_Mutation_p.R458G|RP4-769N13.7_ENST00000602441.1_RNA|GPRASP1_ENST00000415986.1_Missense_Mutation_p.R458G|GPRASP1_ENST00000444152.1_Missense_Mutation_p.R458G	NM_014710.4	NP_055525.3	Q5JY77	GASP1_HUMAN	G protein-coupled receptor associated sorting protein 1	458					endosome to lysosome transport (GO:0008333)|G-protein coupled receptor catabolic process (GO:1990172)	cytoplasm (GO:0005737)				NS(1)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						ATCCAGACCAAGGACTGATGG	0.502																																					p.R458G		.											.	.	.	0			c.A1372G						.						116.0	103.0	108.0					X																	101910213		2203	4300	6503	SO:0001583	missense	9737	exon3			AGACCAAGGACTG	AB007903	CCDS35352.1	Xq22.1	2014-03-21			ENSG00000198932	ENSG00000198932		"""Armadillo repeat containing"""	24834	protein-coding gene	gene with protein product		300417				9455477, 15086532, 16221301	Standard	NM_014710		Approved	GASP, GASP1	uc010nod.3	Q5JY77	OTTHUMG00000022061	ENST00000361600.5:c.1372A>G	X.37:g.101910213A>G	ENSP00000355146:p.Arg458Gly	Somatic	81	0		WXS	Illumina HiSeq	.	65	4	NM_001099411	O43168|Q96LA1	Missense_Mutation	SNP	ENST00000361600.5	37	CCDS35352.1	.	.	.	.	.	.	.	.	.	.	A	3.938	-0.014855	0.07681	.	.	ENSG00000198932	ENST00000415986;ENST00000444152;ENST00000361600;ENST00000537097	T;T;T;T	0.09538	2.97;2.97;2.97;2.97	2.58	-1.69	0.08186	.	.	.	.	.	T	0.06142	0.0159	L	0.38838	1.175	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.44467	-0.9326	9	0.18710	T	0.47	-3.5958	0.8594	0.01190	0.4877:0.193:0.1284:0.1908	.	458	Q5JY77	GASP1_HUMAN	G	458	ENSP00000393691:R458G;ENSP00000409420:R458G;ENSP00000355146:R458G;ENSP00000445683:R458G	ENSP00000355146:R458G	R	+	1	2	GPRASP1	101796869	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.476000	0.06591	-0.480000	0.06803	0.422000	0.28245	AGG	.		0.502	GPRASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057634.2	NM_014710	
MYBPC3	4607	hgsc.bcm.edu;bcgsc.ca	37	11	47360898	47360898	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr11:47360898C>T	ENST00000545968.1	-	22	2179	c.2125G>A	c.(2125-2127)Gat>Aat	p.D709N	MYBPC3_ENST00000399249.2_Missense_Mutation_p.D709N|MYBPC3_ENST00000256993.4_Missense_Mutation_p.D708N	NM_000256.3	NP_000247.2	Q14896	MYPC3_HUMAN	myosin binding protein C, cardiac	709	Ig-like C2-type 5.				cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|heart morphogenesis (GO:0003007)|muscle filament sliding (GO:0030049)|myosin filament assembly (GO:0031034)|positive regulation of ATPase activity (GO:0032781)|regulation of heart rate (GO:0002027)|regulation of muscle filament sliding (GO:0032971)|regulation of striated muscle contraction (GO:0006942)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	A band (GO:0031672)|C zone (GO:0014705)|cytosol (GO:0005829)|sarcomere (GO:0030017)|striated muscle myosin thick filament (GO:0005863)	ATPase activator activity (GO:0001671)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|myosin binding (GO:0017022)|myosin heavy chain binding (GO:0032036)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(3)|urinary_tract(2)	42				Lung(87;0.176)		ACCCACTCATCGCTGTCACCT	0.592																																					p.D709N		.											.	.	.	0			c.G2125A						.						156.0	177.0	170.0					11																	47360898		2124	4224	6348	SO:0001583	missense	4607	exon21			ACTCATCGCTGTC	X84075	CCDS53621.1	11p11.2	2014-09-17	2001-11-28			ENSG00000134571		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7551	protein-coding gene	gene with protein product		600958	"""myosin-binding protein C, cardiac"""	CMH4		7744002, 8358441	Standard	NM_000256		Approved	MYBP-C, FHC	uc021qis.1	Q14896		ENST00000545968.1:c.2125G>A	11.37:g.47360898C>T	ENSP00000442795:p.Asp709Asn	Somatic	66	0		WXS	Illumina HiSeq	.	50	4	NM_000256	A5PL00|Q16410|Q6R2F7|Q9UE27|Q9UM53	Missense_Mutation	SNP	ENST00000545968.1	37	CCDS53621.1	.	.	.	.	.	.	.	.	.	.	C	11.86	1.763426	0.31228	.	.	ENSG00000134571	ENST00000545968;ENST00000399249;ENST00000256993	T;T;T	0.74209	-0.82;-0.82;-0.82	5.29	3.08	0.35506	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.53818	0.1820	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.48043	-0.9069	9	0.52906	T	0.07	.	8.4413	0.32816	0.0:0.7919:0.0:0.2081	.	708	Q14896	MYPC3_HUMAN	N	709;709;708	ENSP00000442795:D709N;ENSP00000382193:D709N;ENSP00000256993:D708N	ENSP00000256993:D708N	D	-	1	0	MYBPC3	47317474	0.004000	0.15560	0.213000	0.23690	0.074000	0.17049	0.958000	0.29227	1.239000	0.43787	-0.254000	0.11334	GAT	.		0.592	MYBPC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392271.3		
GREB1	9687	hgsc.bcm.edu	37	2	11720942	11720942	+	Silent	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr2:11720942G>T	ENST00000381486.2	+	7	1185	c.885G>T	c.(883-885)ccG>ccT	p.P295P	GREB1_ENST00000234142.5_Silent_p.P295P|GREB1_ENST00000389825.3_Silent_p.P185P|GREB1_ENST00000381483.2_Silent_p.P295P|GREB1_ENST00000263834.5_Silent_p.P295P	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	295						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		TGGCCCTGCCGCGACCATCGG	0.592																																					p.P295P	Ovarian(39;850 945 2785 23371 33093)	.											GREB1_ENST00000381486,caecum,carcinoma,0,3	GREB1_ENST00000381486	0	0			c.G885T						.						48.0	47.0	47.0					2																	11720942		2203	4300	6503	SO:0001819	synonymous_variant	9687	exon7			CCTGCCGCGACCA		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"""gene regulated by estrogen in breast cancer"""	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.885G>T	2.37:g.11720942G>T		Somatic	56	0		WXS	Illumina HiSeq	.	53	3	NM_148903	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Silent	SNP	ENST00000381486.2	37	CCDS42655.1																																																																																			.		0.592	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668	
UBTF	7343	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	42294007	42294007	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr17:42294007C>A	ENST00000302904.4	-	3	616	c.124G>T	c.(124-126)Gac>Tac	p.D42Y	UBTF_ENST00000537550.1_5'UTR|UBTF_ENST00000526094.1_Missense_Mutation_p.D42Y|CTB-175E5.7_ENST00000586560.1_RNA|UBTF_ENST00000436088.1_Missense_Mutation_p.D42Y|UBTF_ENST00000527034.1_Missense_Mutation_p.D42Y|UBTF_ENST00000529383.1_Missense_Mutation_p.D42Y|UBTF_ENST00000533177.1_Missense_Mutation_p.D42Y|UBTF_ENST00000393606.3_Missense_Mutation_p.D42Y|UBTF_ENST00000343638.5_Missense_Mutation_p.D42Y			P17480	UBF1_HUMAN	upstream binding transcription factor, RNA polymerase I	42					chromatin silencing at rDNA (GO:0000183)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(10)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.114)		TTGGAGCTGTCATTGGATGGA	0.463																																					p.D42Y		.											.	.	.	0			c.G124T						.						200.0	182.0	188.0					17																	42294007		2203	4300	6503	SO:0001583	missense	7343	exon3			AGCTGTCATTGGA	BC042297	CCDS11480.1, CCDS42346.1	17q21.31	2014-03-25			ENSG00000108312	ENSG00000108312			12511	protein-coding gene	gene with protein product		600673				9126496	Standard	NM_001076683		Approved	UBF, NOR-90, UBF1, UBF2	uc010czs.3	P17480	OTTHUMG00000167585	ENST00000302904.4:c.124G>T	17.37:g.42294007C>A	ENSP00000302640:p.Asp42Tyr	Somatic	61	0		WXS	Illumina HiSeq	.	47	12	NM_014233	A8K6R8	Missense_Mutation	SNP	ENST00000302904.4	37	CCDS11480.1	.	.	.	.	.	.	.	.	.	.	c	23.4	4.415376	0.83449	.	.	ENSG00000108312	ENST00000343638;ENST00000302904;ENST00000527034;ENST00000533177;ENST00000436088;ENST00000393606;ENST00000526094;ENST00000529383;ENST00000530828	D;D;D;D;D;D;D;D;T	0.99311	-5.63;-4.83;-5.73;-5.63;-4.83;-5.63;-5.63;-4.83;-0.04	3.63	3.63	0.41609	.	0.000000	0.85682	D	0.000000	D	0.99236	0.9734	M	0.70595	2.14	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	D	0.98816	1.0745	10	0.87932	D	0	-29.0933	15.5339	0.75986	0.0:1.0:0.0:0.0	.	42;42;42	E9PKP7;P17480-2;P17480	.;.;UBF1_HUMAN	Y	42	ENSP00000345297:D42Y;ENSP00000302640:D42Y;ENSP00000431539:D42Y;ENSP00000437180:D42Y;ENSP00000390669:D42Y;ENSP00000377231:D42Y;ENSP00000432925:D42Y;ENSP00000435708:D42Y;ENSP00000433046:D42Y	ENSP00000302640:D42Y	D	-	1	0	UBTF	39649533	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.588000	0.82629	2.056000	0.61249	0.555000	0.69702	GAC	.		0.463	UBTF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395205.1	NM_014233	
PRRC2C	23215	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	171535854	171535854	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr1:171535854C>A	ENST00000338920.4	+	22	6661	c.6424C>A	c.(6424-6426)Cca>Aca	p.P2142T	PRRC2C_ENST00000426496.2_Missense_Mutation_p.P2142T|PRRC2C_ENST00000392078.3_Missense_Mutation_p.P2144T|PRRC2C_ENST00000367742.3_Missense_Mutation_p.P2144T	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	2142					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										ACAAGAGAAACCAAGCCCAGC	0.423																																					p.P2142T		.											.	.	.	0			c.C6424A						.						75.0	72.0	73.0					1																	171535854		2203	4300	6503	SO:0001583	missense	23215	exon22			GAGAAACCAAGCC	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"""BAT2 domain containing 1"", ""HLA-B associated transcript 2-like 2"""	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.6424C>A	1.37:g.171535854C>A	ENSP00000343629:p.Pro2142Thr	Somatic	83	0		WXS	Illumina HiSeq	.	63	15	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	37	CCDS1296.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	4.233|4.233	0.042170|0.042170	0.08196|0.08196	.|.	.|.	ENSG00000117523|ENSG00000117523	ENST00000495585|ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080	.|T;T;T;T	.|0.02067	.|4.53;4.47;4.54;4.54	5.46|5.46	-1.69|-1.69	0.08186|0.08186	.|.	.|0.484707	.|0.17303	.|N	.|0.179181	T|T	0.00412|0.00412	0.0013|0.0013	N|N	0.12182|0.12182	0.205|0.205	0.09310|0.09310	N|N	1|1	.|B	.|0.09022	.|0.002	.|B	.|0.09377	.|0.004	T|T	0.45469|0.45469	-0.9259|-0.9259	5|10	.|0.39692	.|T	.|0.17	.|.	2.5896|2.5896	0.04839|0.04839	0.1092:0.4069:0.2155:0.2684|0.1092:0.4069:0.2155:0.2684	.|.	.|2142	.|Q9Y520-4	.|.	K|T	689|2144;2096;2142;2144;2142;1899	.|ENSP00000375928:P2144T;ENSP00000410219:P2142T;ENSP00000356716:P2144T;ENSP00000343629:P2142T	.|ENSP00000343629:P2142T	N|P	+|+	3|1	2|0	PRRC2C|PRRC2C	169802478|169802478	0.921000|0.921000	0.31238|0.31238	0.529000|0.529000	0.27951|0.27951	0.568000|0.568000	0.35870|0.35870	0.206000|0.206000	0.17375|0.17375	0.021000|0.021000	0.15133|0.15133	-1.984000|-1.984000	0.00453|0.00453	AAC|CCA	.		0.423	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172	
RYR3	6263	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	33795931	33795931	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr15:33795931G>A	ENST00000389232.4	+	3	341	c.271G>A	c.(271-273)Ggc>Agc	p.G91S	RYR3_ENST00000415757.3_Missense_Mutation_p.G91S	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	91					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TGAAAATGGCGGCGAAGGGGT	0.483																																					p.G91S		.											RYR3,NS,carcinoma,0,1	RYR3	0	0			c.G271A						.						45.0	47.0	47.0					15																	33795931		1906	4128	6034	SO:0001583	missense	6263	exon3			AATGGCGGCGAAG		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.271G>A	15.37:g.33795931G>A	ENSP00000373884:p.Gly91Ser	Somatic	88	0		WXS	Illumina HiSeq	.	57	13	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	G	12.80	2.046216	0.36085	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.98178	-4.77;-4.77	5.5	2.15	0.27550	Inositol 1,4,5-trisphosphate/ryanodine receptor (1);	0.399541	0.22217	N	0.063020	D	0.91408	0.7289	N	0.08118	0	0.32465	N	0.543638	B;B	0.15141	0.012;0.003	B;B	0.11329	0.006;0.001	D	0.86200	0.1618	10	0.08381	T	0.77	.	6.1512	0.20313	0.4593:0.0:0.5407:0.0	.	91;91	Q15413-2;Q15413	.;RYR3_HUMAN	S	91	ENSP00000373884:G91S;ENSP00000399610:G91S	ENSP00000354735:G91S	G	+	1	0	RYR3	31583223	0.993000	0.37304	0.922000	0.36590	0.997000	0.91878	2.530000	0.45641	0.758000	0.33059	0.655000	0.94253	GGC	.		0.483	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
NUP205	23165	hgsc.bcm.edu;bcgsc.ca	37	7	135286256	135286256	+	Splice_Site	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr7:135286256G>T	ENST00000285968.6	+	17	2538		c.e17+1			NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa						carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						CCCTTTCCTGGTATATGCTTA	0.393																																					.		.											.	.	.	0			c.2512+1G>T						.						154.0	150.0	151.0					7																	135286256		2203	4300	6503	SO:0001630	splice_region_variant	23165	exon17			TTCCTGGTATATG	D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"""chromosome 7 open reading frame 14"""	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.2512+1G>T	7.37:g.135286256G>T		Somatic	68	0		WXS	Illumina HiSeq	.	54	4	NM_015135	A6H8X3|Q86YC1	Splice_Site	SNP	ENST00000285968.6	37	CCDS34759.1	.	.	.	.	.	.	.	.	.	.	G	17.87	3.494986	0.64186	.	.	ENSG00000155561	ENST00000285968	.	.	.	5.76	5.76	0.90799	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.9616	0.97254	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NUP205	134936796	1.000000	0.71417	0.998000	0.56505	0.491000	0.33493	9.687000	0.98667	2.724000	0.93272	0.561000	0.74099	.	.		0.393	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1		Intron
POLE	5426	hgsc.bcm.edu	37	12	133244235	133244235	+	Splice_Site	SNP	C	C	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr12:133244235C>A	ENST00000320574.5	-	20	2217		c.e20-1		POLE_ENST00000535270.1_Splice_Site	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit						base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)	p.?(1)		NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	CGGCAGTAATCTAAGCACGAC	0.567								DNA polymerases (catalytic subunits)																													.		.											POLE,NS,carcinoma,0,1	POLE	0	1	Unknown(1)	breast(1)	c.2174-1G>T						.						250.0	207.0	221.0					12																	133244235		2203	4300	6503	SO:0001630	splice_region_variant	5426	exon21			AGTAATCTAAGCA		CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"""DNA polymerases"""	9177	protein-coding gene	gene with protein product	"""DNA polymerase epsilon catalytic subunit A"""	174762	"""polymerase (DNA directed), epsilon"""			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.2174-1G>T	12.37:g.133244235C>A		Somatic	40	0		WXS	Illumina HiSeq	.	23	3	NM_006231	Q13533|Q86VH9	Splice_Site	SNP	ENST00000320574.5	37	CCDS9278.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.568743	0.86439	.	.	ENSG00000177084	ENST00000320574;ENST00000455752;ENST00000535270;ENST00000539006;ENST00000376577	.	.	.	5.86	5.86	0.93980	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.2526	0.98410	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	POLE	131754308	1.000000	0.71417	1.000000	0.80357	0.817000	0.46193	7.770000	0.85390	2.789000	0.95967	0.558000	0.71614	.	.		0.567	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231	Intron
KIAA0430	9665	hgsc.bcm.edu	37	16	15706433	15706433	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr16:15706433G>A	ENST00000396368.3	-	17	3661	c.3455C>T	c.(3454-3456)gCa>gTa	p.A1152V	KIAA0430_ENST00000540441.2_Missense_Mutation_p.A987V|CTB-193M12.1_ENST00000549756.1_RNA|KIAA0430_ENST00000551742.1_Missense_Mutation_p.A1152V|KIAA0430_ENST00000602337.1_Missense_Mutation_p.A1149V|KIAA0430_ENST00000344181.3_Missense_Mutation_p.A754V|KIAA0430_ENST00000548025.1_Missense_Mutation_p.A1149V	NM_001184998.1|NM_001184999.1|NM_014647.3	NP_001171927.1|NP_001171928.1|NP_055462.2	Q9Y4F3	MARF1_HUMAN	KIAA0430	1152	HTH OST-type 3. {ECO:0000255|PROSITE- ProRule:PRU00975}.				double-strand break repair (GO:0006302)|female meiotic division (GO:0007143)|negative regulation of phosphatase activity (GO:0010923)|oogenesis (GO:0048477)|regulation of gene expression (GO:0010468)	membrane (GO:0016020)|peroxisome (GO:0005777)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.A1152V(1)		breast(4)|endometrium(8)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(5)|skin(1)	40						ATGAGGCACTGCTTCTAATAA	0.458																																					p.A1152V		.											KIAA0430,NS,carcinoma,0,1	KIAA0430	0	1	Substitution - Missense(1)	breast(1)	c.C3455T						.						135.0	135.0	135.0					16																	15706433		2058	4218	6276	SO:0001583	missense	9665	exon17			GGCACTGCTTCTA	AB007890	CCDS10562.2, CCDS53990.1, CCDS55991.1	16p13.11	2013-01-11			ENSG00000166783	ENSG00000166783		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29562	protein-coding gene	gene with protein product	"""limkain b1"", ""protein phosphatase 1, regulatory subunit 34"", ""meiosis arrest female 1"""	614593				9455477, 10493829, 15932519, 22442484, 23090997	Standard	NM_014647		Approved	LKAP, PPP1R34, Marf1	uc010uzw.2	Q9Y4F3	OTTHUMG00000129884	ENST00000396368.3:c.3455C>T	16.37:g.15706433G>A	ENSP00000379654:p.Ala1152Val	Somatic	60	0		WXS	Illumina HiSeq	.	48	2	NM_014647	A8MSK2|B2RNX2|B4DYY9|B7ZMG1|B7ZMG2|F8VV09|Q6P1R6|Q8WYR2|Q9Y4J9	Missense_Mutation	SNP	ENST00000396368.3	37	CCDS10562.2	.	.	.	.	.	.	.	.	.	.	G	35	5.442334	0.96187	.	.	ENSG00000166783	ENST00000396368;ENST00000540441;ENST00000321370;ENST00000344181;ENST00000548025;ENST00000551742;ENST00000551298	T;T;T;T;T	0.52983	0.64;0.64;0.64;0.64;0.64	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.70055	0.3180	M	0.71206	2.165	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;0.999	D;D;D;D	0.91635	0.996;0.999;0.999;0.998	T	0.71381	-0.4610	10	0.62326	D	0.03	.	19.5965	0.95541	0.0:0.0:1.0:0.0	.	1151;1149;1148;1151	Q9Y4F3-5;F8VV09;Q9Y4F3-4;Q9Y4F3	.;.;.;LKAP_HUMAN	V	1152;987;1092;754;1149;1152;932	ENSP00000379654:A1152V;ENSP00000439819:A987V;ENSP00000341939:A754V;ENSP00000449376:A1149V;ENSP00000450309:A1152V	ENSP00000315718:A1092V	A	-	2	0	KIAA0430	15613934	1.000000	0.71417	0.976000	0.42696	0.993000	0.82548	8.951000	0.93025	2.627000	0.88993	0.643000	0.83706	GCA	.		0.458	KIAA0430-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252131.2	NM_014647	
KCMF1	56888	hgsc.bcm.edu	37	2	85280314	85280314	+	Nonsense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr2:85280314G>T	ENST00000409785.4	+	7	1287	c.928G>T	c.(928-930)Gaa>Taa	p.E310*		NM_020122.4	NP_064507.3	Q9P0J7	KCMF1_HUMAN	potassium channel modulatory factor 1	310							ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			ovary(3)	3						CCAGTCCATGGAAAGCGAGCG	0.463																																					p.E310X		.											KCMF1_ENST00000409785,NS,carcinoma,0,1	KCMF1_ENST00000409785	0	0			c.G928T						.						45.0	48.0	47.0					2																	85280314		1957	4160	6117	SO:0001587	stop_gained	56888	exon7			TCCATGGAAAGCG	AF155652	CCDS46350.1	2p11.2	2010-11-23			ENSG00000176407	ENSG00000176407		"""Zinc fingers, ZZ-type"""	20589	protein-coding gene	gene with protein product		614719					Standard	NM_020122		Approved	DEBT91, PCMF, DKFZP434L1021, ZZZ1	uc002sox.4	Q9P0J7	OTTHUMG00000153004	ENST00000409785.4:c.928G>T	2.37:g.85280314G>T	ENSP00000386738:p.Glu310*	Somatic	59	0		WXS	Illumina HiSeq	.	41	2	NM_020122	Q4ZG04|Q53SC7|Q9BWK2|Q9H8P5|Q9UFE8	Nonsense_Mutation	SNP	ENST00000409785.4	37	CCDS46350.1	.	.	.	.	.	.	.	.	.	.	G	41	8.572977	0.98868	.	.	ENSG00000176407	ENST00000409785	.	.	.	6.07	6.07	0.98685	.	0.095210	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-12.8005	18.1463	0.89656	0.0:0.0:1.0:0.0	.	.	.	.	X	310	.	ENSP00000386738:E310X	E	+	1	0	KCMF1	85133825	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	9.589000	0.98235	2.890000	0.99128	0.585000	0.79938	GAA	.		0.463	KCMF1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328942.4	NM_020122	
PSG6	5675	hgsc.bcm.edu	37	19	43421937	43421937	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr19:43421937G>A	ENST00000292125.2	-	1	52	c.8C>T	c.(7-9)cCc>cTc	p.P3L	PSG6_ENST00000187910.2_Missense_Mutation_p.P3L|PSG6_ENST00000402603.4_Missense_Mutation_p.P3L|PSG6_ENST00000601833.1_Intron	NM_002782.4	NP_002773.1	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6	3					female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(19)|ovary(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44		Prostate(69;0.00899)				GGCTGAGAGGGGTCCCATGGT	0.602																																					p.P3L		.											.	.	.	0			c.C8T						.						139.0	118.0	125.0					19																	43421937		2201	4300	6501	SO:0001583	missense	5675	exon1			GAGAGGGGTCCCA		CCDS12613.1, CCDS33038.1	19q13.2	2013-01-29			ENSG00000170848	ENSG00000170848		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9523	protein-coding gene	gene with protein product		176395				1690992	Standard	NM_002782		Approved			Q00889	OTTHUMG00000151127	ENST00000292125.2:c.8C>T	19.37:g.43421937G>A	ENSP00000292125:p.Pro3Leu	Somatic	122	0		WXS	Illumina HiSeq	.	75	4	NM_001031850	O75244|Q15224|Q15235|Q549K1	Missense_Mutation	SNP	ENST00000292125.2	37	CCDS12613.1	.	.	.	.	.	.	.	.	.	.	g	5.961	0.361349	0.11296	.	.	ENSG00000170848	ENST00000187910;ENST00000402603;ENST00000292125;ENST00000402456	T;T;T	0.29142	1.58;1.92;1.61	1.47	0.359	0.16088	.	.	.	.	.	T	0.24198	0.0586	L	0.59912	1.85	0.09310	N	1	B;B;B	0.15719	0.006;0.005;0.014	B;B;B	0.19946	0.009;0.018;0.027	T	0.30995	-0.9959	9	0.22109	T	0.4	.	3.3746	0.07233	0.3027:0.0:0.6973:0.0	.	3;3;3	Q00889;Q00889-2;B5MCE1	PSG6_HUMAN;.;.	L	3	ENSP00000187910:P3L;ENSP00000385736:P3L;ENSP00000292125:P3L	ENSP00000187910:P3L	P	-	2	0	PSG6	48113777	0.002000	0.14202	0.058000	0.19502	0.028000	0.11728	0.042000	0.13949	0.157000	0.19338	0.194000	0.17425	CCC	.		0.602	PSG6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321436.1	NM_002782	
MED13L	23389	hgsc.bcm.edu	37	12	116422008	116422008	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr12:116422008G>A	ENST00000281928.3	-	20	4714	c.4508C>T	c.(4507-4509)gCg>gTg	p.A1503V		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1503						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		GCAAACTTGCGCATAAAGTTT	0.438																																					p.A1503V		.											MED13L,NS,carcinoma,0,1	MED13L	0	0			c.C4508T						.						88.0	69.0	76.0					12																	116422008		2203	4300	6503	SO:0001583	missense	23389	exon20			ACTTGCGCATAAA	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"""thyroid hormone receptor associated protein 2"""	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.4508C>T	12.37:g.116422008G>A	ENSP00000281928:p.Ala1503Val	Somatic	74	1		WXS	Illumina HiSeq	.	39	2	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Missense_Mutation	SNP	ENST00000281928.3	37	CCDS9177.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.548263	0.86127	.	.	ENSG00000123066	ENST00000281928	T	0.71461	-0.57	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	D	0.86314	0.5903	M	0.85542	2.76	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.87922	0.2704	10	0.66056	D	0.02	.	19.2439	0.93895	0.0:0.0:1.0:0.0	.	1503	Q71F56	MD13L_HUMAN	V	1503	ENSP00000281928:A1503V	ENSP00000281928:A1503V	A	-	2	0	MED13L	114906391	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.471000	0.97696	2.538000	0.85594	0.655000	0.94253	GCG	.		0.438	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3		
GABRP	2568	hgsc.bcm.edu	37	5	170222402	170222402	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr5:170222402C>A	ENST00000518525.1	+	6	895	c.431C>A	c.(430-432)tCc>tAc	p.S144Y	GABRP_ENST00000519598.1_Missense_Mutation_p.S144Y|GABRP_ENST00000519385.1_Missense_Mutation_p.S144Y|GABRP_ENST00000265294.4_Missense_Mutation_p.S144Y			O00591	GBRP_HUMAN	gamma-aminobutyric acid (GABA) A receptor, pi	144					signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.S144F(1)		NS(1)|breast(1)|cervix(1)|endometrium(5)|large_intestine(4)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	29	Renal(175;0.000159)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CGCCTCTTCTCCAATGGCACG	0.557																																					p.S144Y		.											GABRP,trunk,malignant_melanoma,0,1	GABRP	0	1	Substitution - Missense(1)	skin(1)	c.C431A						.						92.0	83.0	86.0					5																	170222402		2203	4300	6503	SO:0001583	missense	2568	exon5			TCTTCTCCAATGG	U95367	CCDS4375.1, CCDS75368.1	5q35.1	2012-06-22			ENSG00000094755	ENSG00000094755		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4089	protein-coding gene	gene with protein product	"""GABA(A) receptor, pi"""	602729				9182563	Standard	NM_014211		Approved		uc003mau.3	O00591	OTTHUMG00000130443	ENST00000518525.1:c.431C>A	5.37:g.170222402C>A	ENSP00000430100:p.Ser144Tyr	Somatic	38	0		WXS	Illumina HiSeq	.	31	2	NM_014211	A8KA36|D3DQL2|Q32MJ1	Missense_Mutation	SNP	ENST00000518525.1	37	CCDS4375.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.191658	0.78902	.	.	ENSG00000094755	ENST00000521481;ENST00000522868;ENST00000518525;ENST00000539175;ENST00000265294;ENST00000519385;ENST00000519598	T;T;T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19;-1.19;-1.19	5.59	5.59	0.84812	Neurotransmitter-gated ion-channel ligand-binding (3);	0.138574	0.64402	D	0.000003	D	0.86920	0.6049	M	0.62154	1.92	0.53688	D	0.999978	D;D	0.76494	0.996;0.999	D;D	0.71870	0.948;0.975	D	0.86750	0.1960	10	0.59425	D	0.04	.	19.5561	0.95349	0.0:1.0:0.0:0.0	.	144;144	E7EWG0;O00591	.;GBRP_HUMAN	Y	144;144;144;42;144;144;144	ENSP00000428804:S144Y;ENSP00000430188:S144Y;ENSP00000430100:S144Y;ENSP00000265294:S144Y;ENSP00000430727:S144Y;ENSP00000430772:S144Y	ENSP00000265294:S144Y	S	+	2	0	GABRP	170154980	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	3.212000	0.51145	2.784000	0.95788	0.643000	0.83706	TCC	.		0.557	GABRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252834.3	NM_014211	
PMS2P3	5387	hgsc.bcm.edu	37	7	75155143	75155143	+	RNA	SNP	G	G	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr7:75155143G>A	ENST00000418756.1	-	0	618					NR_028059.1		Q13401	PM2P3_HUMAN	postmeiotic segregation increased 2 pseudogene 3						mismatch repair (GO:0006298)|regulation of transcription, DNA-templated (GO:0006355)	mismatch repair complex (GO:0032300)	nucleic acid binding (GO:0003676)			lung(1)	1						tgcatctcaagaaaaaaaaaa	0.423																																					.	NSCLC(70;602 1339 5301 18528 38453)	.											.	.	.	0			.						.						30.0	27.0	28.0					7																	75155143		692	1591	2283			5387	.			TCTCAAGAAAAAA	D38437		7q11.23	2010-10-26	2010-10-26	2010-10-26	ENSG00000127957	ENSG00000127957			9128	pseudogene	pseudogene			"""postmeiotic segregation increased 2-like 3"", ""postmeiotic segregation increased 2-like 3, pseudogene"""	PMS2L9, PMS2L3		8586419	Standard	NR_028059		Approved	PMS5, PMSR3	uc022agi.1	Q13401	OTTHUMG00000156049		7.37:g.75155143G>A		Somatic	39	0		WXS	Illumina HiSeq	.	28	4	.	A6NG70|Q3MJ29	RNA	SNP	ENST00000418756.1	37																																																																																				.		0.423	PMS2P3-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000342862.2	NR_028059	
DLGAP3	58512	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	1	35370532	35370532	+	Silent	SNP	C	C	G			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr1:35370532C>G	ENST00000373347.1	-	3	721	c.453G>C	c.(451-453)ggG>ggC	p.G151G	DLGAP3_ENST00000235180.4_Silent_p.G151G|DLGAP3_ENST00000495979.1_5'Flank			O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated protein 3	151					cell-cell signaling (GO:0007267)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(23)|ovary(4)|prostate(3)|skin(3)|urinary_tract(1)	46		Myeloproliferative disorder(586;0.0393)				CTGGCGCTGGCCCGGGCCCTG	0.617																																					p.G151G		.											.	.	.	0			c.G453C						.						17.0	18.0	17.0					1																	35370532		2197	4291	6488	SO:0001819	synonymous_variant	58512	exon1			CGCTGGCCCGGGC	AF131778	CCDS30670.1	1p35.3-p34.1	2008-02-05			ENSG00000116544	ENSG00000116544			30368	protein-coding gene	gene with protein product		611413				8619474, 9110174	Standard	NM_001080418		Approved	SAPAP3, DAP3	uc001byc.3	O95886	OTTHUMG00000004049	ENST00000373347.1:c.453G>C	1.37:g.35370532C>G		Somatic	17	0		WXS	Illumina HiSeq	.	13	4	NM_001080418	Q5TDD5|Q9H3X7	Silent	SNP	ENST00000373347.1	37	CCDS30670.1																																																																																			.		0.617	DLGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011554.1	NM_021234	
CHD4	1108	hgsc.bcm.edu	37	12	6680126	6680126	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr12:6680126C>T	ENST00000357008.2	-	39	5793	c.5630G>A	c.(5629-5631)cGa>cAa	p.R1877Q	CHD4_ENST00000309577.6_Missense_Mutation_p.R1905Q|NOP2_ENST00000542015.1_5'Flank|NOP2_ENST00000399466.2_5'Flank|NOP2_ENST00000540228.1_5'Flank|CHD4_ENST00000544040.1_Missense_Mutation_p.R1870Q|NOP2_ENST00000537442.1_5'Flank|CHD4_ENST00000544484.1_Missense_Mutation_p.R1902Q|NOP2_ENST00000545915.1_5'Flank|NOP2_ENST00000382421.3_5'Flank|NOP2_ENST00000541778.1_5'Flank|NOP2_ENST00000322166.5_5'Flank|NOP2_ENST00000545200.1_5'Flank	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	1877	Required for interaction with PCNT.				ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)	p.R1905Q(2)|p.R1877Q(2)		central_nervous_system(2)	2						TGGGGGAATTCGGGCAATGGT	0.537																																					p.R1877Q	Colon(32;586 792 4568 16848 45314)	.											CHD4_ENST00000357008,bladder,carcinoma,0,3	CHD4_ENST00000357008	0	4	Substitution - Missense(4)	urinary_tract(2)|endometrium(2)	c.G5630A						.						248.0	245.0	246.0					12																	6680126		2203	4300	6503	SO:0001583	missense	1108	exon39			GGAATTCGGGCAA	X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"""Zinc fingers, PHD-type"""	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.5630G>A	12.37:g.6680126C>T	ENSP00000349508:p.Arg1877Gln	Somatic	43	0		WXS	Illumina HiSeq	.	30	2	NM_001273	Q8IXZ5	Missense_Mutation	SNP	ENST00000357008.2	37	CCDS8552.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.993912	0.93167	.	.	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464	D;D;D;D	0.92099	-2.97;-2.89;-2.97;-2.9	5.68	5.68	0.88126	CHD, C-terminal 2 (1);	0.000000	0.85682	D	0.000000	D	0.95487	0.8534	M	0.64260	1.97	0.80722	D	1	D;D;P	0.76494	0.999;0.997;0.945	D;D;P	0.72982	0.975;0.979;0.567	D	0.95043	0.8180	10	0.54805	T	0.06	-2.3938	19.7959	0.96481	0.0:1.0:0.0:0.0	.	1905;1877;1870	Q14839-2;Q14839;F5GWX5	.;CHD4_HUMAN;.	Q	1902;1870;1905;1877;1851	ENSP00000440392:R1902Q;ENSP00000440542:R1870Q;ENSP00000312419:R1905Q;ENSP00000349508:R1877Q	ENSP00000312419:R1905Q	R	-	2	0	CHD4	6550387	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.487000	0.81328	2.689000	0.91719	0.655000	0.94253	CGA	.		0.537	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273	
ZNF385D	79750	hgsc.bcm.edu	37	3	21462759	21462759	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr3:21462759C>A	ENST00000281523.2	-	8	1653	c.1135G>T	c.(1135-1137)Gct>Tct	p.A379S		NM_024697.2	NP_078973.1	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	379						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(1)|prostate(1)|skin(4)	46						GGTCCAGGAGCTGGCCGCAGG	0.517																																					p.A379S		.											.	.	.	0			c.G1135T						.						49.0	47.0	48.0					3																	21462759		2203	4300	6503	SO:0001583	missense	79750	exon8			CAGGAGCTGGCCG	BC007212	CCDS2636.1	3p24.3	2012-10-05	2007-12-06	2007-12-06	ENSG00000151789	ENSG00000151789			26191	protein-coding gene	gene with protein product			"""zinc finger protein 659"""	ZNF659		12477932	Standard	NM_024697		Approved	FLJ22419	uc003cce.3	Q9H6B1	OTTHUMG00000130484	ENST00000281523.2:c.1135G>T	3.37:g.21462759C>A	ENSP00000281523:p.Ala379Ser	Somatic	98	0		WXS	Illumina HiSeq	.	51	4	NM_024697		Missense_Mutation	SNP	ENST00000281523.2	37	CCDS2636.1	.	.	.	.	.	.	.	.	.	.	C	17.18	3.324154	0.60634	.	.	ENSG00000151789	ENST00000281523	T	0.49720	0.77	5.95	5.95	0.96441	.	0.052183	0.85682	D	0.000000	T	0.44095	0.1277	L	0.49126	1.545	0.58432	D	0.999994	P	0.43094	0.799	B	0.33799	0.17	T	0.46359	-0.9197	10	0.51188	T	0.08	-31.2942	20.3747	0.98911	0.0:1.0:0.0:0.0	.	379	Q9H6B1	Z385D_HUMAN	S	379	ENSP00000281523:A379S	ENSP00000281523:A379S	A	-	1	0	ZNF385D	21437763	1.000000	0.71417	0.924000	0.36721	0.992000	0.81027	5.869000	0.69613	2.819000	0.97034	0.557000	0.71058	GCT	.		0.517	ZNF385D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252884.1	NM_024697	
ARID5A	10865	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	97217620	97217620	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr2:97217620C>T	ENST00000357485.3	+	7	1433	c.1355C>T	c.(1354-1356)gCt>gTt	p.A452V	ARID5A_ENST00000454558.2_Missense_Mutation_p.A384V	NM_212481.1	NP_997646.1	Q03989	ARI5A_HUMAN	AT rich interactive domain 5A (MRF1-like)	452					chondrocyte differentiation (GO:0002062)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)|skin(1)|urinary_tract(2)	14						GAAGAGGGTGCTGCCCACAGT	0.672																																					p.A452V		.											.	.	.	0			c.C1355T						.						26.0	26.0	26.0					2																	97217620		2203	4300	6503	SO:0001583	missense	10865	exon7			AGGGTGCTGCCCA	M62324	CCDS33251.1	2p11.1	2013-02-07			ENSG00000196843	ENSG00000196843		"""-"""	17361	protein-coding gene	gene with protein product	"""modulator recognition factor 1"""	611583				8649988	Standard	NM_212481		Approved	MRF-1, RP11-363D14	uc002swe.3	Q03989	OTTHUMG00000155229	ENST00000357485.3:c.1355C>T	2.37:g.97217620C>T	ENSP00000350078:p.Ala452Val	Somatic	20	0		WXS	Illumina HiSeq	.	16	4	NM_212481	Q6NX37	Missense_Mutation	SNP	ENST00000357485.3	37	CCDS33251.1	.	.	.	.	.	.	.	.	.	.	C	11.10	1.540544	0.27563	.	.	ENSG00000196843	ENST00000357485;ENST00000359765;ENST00000454558	T	0.62788	0.0	5.31	-0.121	0.13535	.	1.469050	0.04197	N	0.329295	T	0.36608	0.0973	N	0.08118	0	0.09310	N	1	B;B;B	0.22480	0.07;0.022;0.022	B;B;B	0.16289	0.015;0.01;0.01	T	0.10847	-1.0612	10	0.19147	T	0.46	0.2372	3.006	0.06028	0.3036:0.1787:0.0:0.5177	.	452;384;452	A6NM59;C9J1Q0;Q03989	.;.;ARI5A_HUMAN	V	452;452;384	ENSP00000350078:A452V	ENSP00000350078:A452V	A	+	2	0	ARID5A	96581347	0.225000	0.23685	0.002000	0.10522	0.239000	0.25481	0.203000	0.17315	-0.186000	0.10533	-0.312000	0.09012	GCT	.		0.672	ARID5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338888.2	NM_212481	
PCSK9	255738	hgsc.bcm.edu	37	1	55529044	55529044	+	Silent	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr1:55529044G>T	ENST00000302118.5	+	12	2156	c.1866G>T	c.(1864-1866)gtG>gtT	p.V622V	PCSK9_ENST00000543384.1_3'UTR|PCSK9_ENST00000490692.1_3'UTR	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	622	C-terminal domain.				apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|kidney development (GO:0001822)|lipoprotein metabolic process (GO:0042157)|liver development (GO:0001889)|low-density lipoprotein particle receptor catabolic process (GO:0032802)|lysosomal transport (GO:0007041)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of receptor recycling (GO:0001920)|neurogenesis (GO:0022008)|neuron differentiation (GO:0030182)|phospholipid metabolic process (GO:0006644)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of receptor internalization (GO:0002092)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)|regulation of neuron apoptotic process (GO:0043523)|regulation of receptor activity (GO:0010469)|triglyceride metabolic process (GO:0006641)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	apolipoprotein binding (GO:0034185)|apolipoprotein receptor binding (GO:0034190)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein particle receptor binding (GO:0050750)|poly(A) RNA binding (GO:0044822)|protein self-association (GO:0043621)|serine-type endopeptidase activity (GO:0004252)|sodium channel inhibitor activity (GO:0019871)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	32						TCTGGCAGGTGACCGTGGCCT	0.632																																					p.V622V	Pancreas(137;1454 1827 5886 22361 42375)	.											.	.	.	0			c.G1866T						.						29.0	30.0	30.0					1																	55529044		2203	4300	6503	SO:0001819	synonymous_variant	255738	exon12			GCAGGTGACCGTG	AX207686	CCDS603.1	1p34.1-p32	2014-09-17	2003-05-13		ENSG00000169174	ENSG00000169174			20001	protein-coding gene	gene with protein product		607786	"""hypercholesterolemia, autosomal dominant 3"""	HCHOLA3		12552133, 12730697	Standard	NM_174936		Approved	NARC-1, FH3	uc001cyf.2	Q8NBP7	OTTHUMG00000008136	ENST00000302118.5:c.1866G>T	1.37:g.55529044G>T		Somatic	117	0		WXS	Illumina HiSeq	.	83	4	NM_174936	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Silent	SNP	ENST00000302118.5	37	CCDS603.1																																																																																			.		0.632	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936	
PRPS1	5631	hgsc.bcm.edu	37	X	106885652	106885652	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chrX:106885652G>T	ENST00000372435.4	+	4	584	c.462G>T	c.(460-462)tgG>tgT	p.W154C	PRPS1_ENST00000372428.4_Missense_Mutation_p.W87C|PRPS1_ENST00000543248.1_Missense_Mutation_p.W154C|PRPS1_ENST00000372418.1_Missense_Mutation_p.W54C	NM_002764.3	NP_002755.1	P60891	PRPS1_HUMAN	phosphoribosyl pyrophosphate synthetase 1	154					5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|hypoxanthine biosynthetic process (GO:0046101)|nervous system development (GO:0007399)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|pyrimidine nucleotide biosynthetic process (GO:0006221)|ribonucleoside monophosphate biosynthetic process (GO:0009156)|small molecule metabolic process (GO:0044281)|urate biosynthetic process (GO:0034418)	cytosol (GO:0005829)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)|ribose phosphate diphosphokinase activity (GO:0004749)			breast(3)|endometrium(2)|kidney(3)|large_intestine(3)|lung(11)|upper_aerodigestive_tract(1)	23						TCCTAAAGTGGATAAGGGAGA	0.428																																					p.W154C		.											.	.	.	0			c.G462T						.						143.0	121.0	128.0					X																	106885652		2203	4300	6503	SO:0001583	missense	5631	exon4			AAAGTGGATAAGG	X15331	CCDS14529.1, CCDS76007.1	Xq22.3	2014-09-17			ENSG00000147224	ENSG00000147224	2.7.6.1		9462	protein-coding gene	gene with protein product	"""PRS I"", ""ribose-phosphate diphosphokinase 1"""	311850	"""deafness, X-linked 2, perceptive, congenital"""	DFN2		1962753, 20021999	Standard	NM_002764		Approved	CMTX5, DFNX1	uc004ene.4	P60891	OTTHUMG00000022167	ENST00000372435.4:c.462G>T	X.37:g.106885652G>T	ENSP00000361512:p.Trp154Cys	Somatic	95	0		WXS	Illumina HiSeq	.	90	5	NM_002764	B1ALA8|B2R6T7|B4DNL6|D3DUX6|P09329	Missense_Mutation	SNP	ENST00000372435.4	37	CCDS14529.1	.	.	.	.	.	.	.	.	.	.	G	19.56	3.849845	0.71603	.	.	ENSG00000147224	ENST00000372435;ENST00000372428;ENST00000543248;ENST00000372418	D;D;D;D	0.93076	-3.16;-2.88;-3.16;-2.55	4.51	4.51	0.55191	Phosphoribosyltransferase (1);	0.000000	0.85682	D	0.000000	D	0.94588	0.8256	M	0.90425	3.115	0.80722	D	1	B;B	0.31100	0.308;0.308	B;B	0.34779	0.189;0.189	D	0.94581	0.7779	10	0.46703	T	0.11	.	16.0202	0.80478	0.0:0.0:1.0:0.0	.	154;154	Q53FW2;P60891	.;PRPS1_HUMAN	C	154;87;154;54	ENSP00000361512:W154C;ENSP00000361505:W87C;ENSP00000443185:W154C;ENSP00000361495:W54C	ENSP00000361495:W54C	W	+	3	0	PRPS1	106772308	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	9.357000	0.97099	2.174000	0.68829	0.544000	0.68410	TGG	.		0.428	PRPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057840.1		
MT-ND4	4538	hgsc.bcm.edu	37	M	11192	11192	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chrM:11192G>A	ENST00000361381.2	+	1	433	c.433G>A	c.(433-435)Gca>Aca	p.A145T	MT-TH_ENST00000387441.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TS2_ENST00000387449.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	145					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						AACGCCTGAACGCAGGCACAT	0.468																																					p.A145T		.											.	.	.	0			c.G433A						.																																			SO:0001583	missense	0	exon1			CTGAACGCAGGCA			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.433G>A	M.37:g.11192G>A	ENSP00000354961:p.Ala145Thr	Somatic	6	0		WXS	Illumina HiSeq	.	20	5	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Missense_Mutation	SNP	ENST00000361381.2	37																																																																																				.		0.468	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
COL7A1	1294	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	48608557	48608557	+	Missense_Mutation	SNP	G	G	C			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr3:48608557G>C	ENST00000328333.8	-	93	7248	c.7141C>G	c.(7141-7143)Cct>Gct	p.P2381A	COL7A1_ENST00000454817.1_Missense_Mutation_p.P2349A	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	2381	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GGGCCAGGAGGCCCAGGGGAG	0.632																																					p.P2381A		.											.	.	.	0			c.C7141G						.						34.0	44.0	41.0					3																	48608557		2203	4299	6502	SO:0001583	missense	1294	exon93			CAGGAGGCCCAGG	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"""Collagens"", ""Fibronectin type III domain containing"""	2214	protein-coding gene	gene with protein product	"""collagen VII, alpha-1 polypeptide"", ""LC collagen"""	120120	"""epidermolysis bullosa, dystrophic, dominant and recessive"""	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.7141C>G	3.37:g.48608557G>C	ENSP00000332371:p.Pro2381Ala	Somatic	46	0		WXS	Illumina HiSeq	.	28	8	NM_000094	Q14054|Q16507	Missense_Mutation	SNP	ENST00000328333.8	37	CCDS2773.1	.	.	.	.	.	.	.	.	.	.	G	1.591	-0.529190	0.04112	.	.	ENSG00000114270	ENST00000328333;ENST00000454817;ENST00000422991	D;D;D	0.98633	-3.15;-3.15;-5.04	4.39	1.57	0.23409	.	0.150347	0.30428	N	0.009652	D	0.94634	0.8270	L	0.38692	1.165	0.09310	N	1	B	0.16396	0.017	B	0.22152	0.038	D	0.85055	0.0931	10	0.07644	T	0.81	.	4.9987	0.14253	0.1903:0.0:0.638:0.1717	.	2381	Q02388	CO7A1_HUMAN	A	2381;2349;46	ENSP00000332371:P2381A;ENSP00000412569:P2349A;ENSP00000391608:P46A	ENSP00000332371:P2381A	P	-	1	0	COL7A1	48583561	0.900000	0.30661	0.263000	0.24496	0.004000	0.04260	3.760000	0.55235	0.580000	0.29522	-0.181000	0.13052	CCT	.		0.632	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094	
SLC35F5	80255	hgsc.bcm.edu	37	2	114500277	114500277	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr2:114500277A>C	ENST00000245680.2	-	7	1155	c.742T>G	c.(742-744)Tgc>Ggc	p.C248G	SLC35F5_ENST00000409342.1_Missense_Mutation_p.C242G	NM_025181.2	NP_079457.2	Q8WV83	S35F5_HUMAN	solute carrier family 35, member F5	248					transport (GO:0006810)	integral component of membrane (GO:0016021)		p.C248fs*22(2)|p.?(1)		endometrium(1)|kidney(4)|large_intestine(2)|lung(7)|ovary(2)|prostate(3)|skin(1)	20						ACCACAAAGCAAAAAAAAAAG	0.343																																					p.C248G		.											SLC35F5,colon,carcinoma,+2,12	SLC35F5	+2	3	Deletion - Frameshift(2)|Unknown(1)	ovary(2)|skin(1)	c.T742G						.						105.0	103.0	104.0					2																	114500277		2203	4300	6503	SO:0001583	missense	80255	exon7			CAAAGCAAAAAAA	AF529364	CCDS2119.1	2q14.1	2013-05-22			ENSG00000115084	ENSG00000115084		"""Solute carriers"""	23617	protein-coding gene	gene with protein product							Standard	XM_005263799		Approved	FLJ22004	uc002tku.1	Q8WV83	OTTHUMG00000131361	ENST00000245680.2:c.742T>G	2.37:g.114500277A>C	ENSP00000245680:p.Cys248Gly	Somatic	52	0		WXS	Illumina HiSeq	.	69	3	NM_025181	Q9H6P8|Q9H7D8	Missense_Mutation	SNP	ENST00000245680.2	37	CCDS2119.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.447823	0.84101	.	.	ENSG00000115084	ENST00000245680;ENST00000409106;ENST00000409342	T;T	0.48522	0.81;0.81	5.0	5.0	0.66597	Drug/metabolite transporter (1);	0.000000	0.85682	D	0.000000	T	0.70613	0.3244	M	0.83223	2.63	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;0.997	D;D;D	0.87578	0.998;0.996;0.995	T	0.74529	-0.3635	10	0.52906	T	0.07	-2.4109	15.1644	0.72811	1.0:0.0:0.0:0.0	.	248;242;248	B2RDY0;B8ZZV6;Q8WV83	.;.;S35F5_HUMAN	G	248;242;242	ENSP00000245680:C248G;ENSP00000386754:C242G	ENSP00000245680:C248G	C	-	1	0	SLC35F5	114216747	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.439000	0.90308	2.232000	0.73038	0.528000	0.53228	TGC	.		0.343	SLC35F5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254150.1	NM_025181	
HSPA2	3306	hgsc.bcm.edu	37	14	65008064	65008064	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr14:65008064C>T	ENST00000394709.1	+	2	573	c.497C>T	c.(496-498)aCg>aTg	p.T166M	HSPA2_ENST00000554883.1_3'UTR|RP11-973N13.4_ENST00000554918.1_RNA|HSPA2_ENST00000247207.6_Missense_Mutation_p.T166M			P54652	HSP72_HUMAN	heat shock 70kDa protein 2	166					male meiosis (GO:0007140)|male meiosis I (GO:0007141)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle (GO:0031662)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)|spermatid development (GO:0007286)|synaptonemal complex disassembly (GO:0070194)	blood microparticle (GO:0072562)|CatSper complex (GO:0036128)|cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycolipid binding (GO:0051861)|unfolded protein binding (GO:0051082)	p.T166M(1)		breast(1)|endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00515)|OV - Ovarian serous cystadenocarcinoma(108;0.00584)|BRCA - Breast invasive adenocarcinoma(234;0.045)		GGCACCATCACGGGGCTCAAT	0.662																																					p.T166M	Pancreas(136;1211 1835 24894 31984 38227)	.											HSPA2,NS,carcinoma,0,1	HSPA2	0	1	Substitution - Missense(1)	endometrium(1)	c.C497T						.						51.0	52.0	52.0					14																	65008064		2203	4300	6503	SO:0001583	missense	3306	exon1			CCATCACGGGGCT	L26336, BC001752	CCDS9766.1	14q23	2012-10-02	2002-08-29		ENSG00000126803	ENSG00000126803		"""Heat shock proteins / HSP70"""	5235	protein-coding gene	gene with protein product		140560	"""heat shock 70kD protein 2"""				Standard	NM_021979		Approved		uc001xhk.4	P54652	OTTHUMG00000141311	ENST00000394709.1:c.497C>T	14.37:g.65008064C>T	ENSP00000378199:p.Thr166Met	Somatic	52	1		WXS	Illumina HiSeq	.	29	2	NM_021979	Q15508|Q53XM3|Q9UE78	Missense_Mutation	SNP	ENST00000394709.1	37	CCDS9766.1	.	.	.	.	.	.	.	.	.	.	C	19.15	3.772333	0.69992	.	.	ENSG00000126803	ENST00000394709;ENST00000247207	T;T	0.01015	5.44;5.44	5.18	5.18	0.71444	.	0.112431	0.38605	U	0.001623	T	0.01905	0.0060	N	0.08118	0	0.39563	D	0.969168	D	0.71674	0.998	P	0.62014	0.897	T	0.75505	-0.3294	10	0.87932	D	0	-7.4702	18.6851	0.91560	0.0:1.0:0.0:0.0	.	166	P54652	HSP72_HUMAN	M	166	ENSP00000378199:T166M;ENSP00000247207:T166M	ENSP00000247207:T166M	T	+	2	0	HSPA2	64077817	1.000000	0.71417	0.993000	0.49108	0.983000	0.72400	7.818000	0.86416	2.407000	0.81776	0.563000	0.77884	ACG	.		0.662	HSPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280651.1		
MAGEE1	57692	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	75650880	75650880	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chrX:75650880A>T	ENST00000361470.2	+	1	2835	c.2557A>T	c.(2557-2559)Agg>Tgg	p.R853W		NM_020932.2	NP_065983.1	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	853	Interaction with DTNA. {ECO:0000250}.|MAGE 2. {ECO:0000255|PROSITE- ProRule:PRU00127}.					dendrite (GO:0030425)|dystrophin-associated glycoprotein complex (GO:0016010)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	51						CAACCATGCCAGGGAGTCTGC	0.493																																					p.R853W		.											.	.	.	0			c.A2557T						.						52.0	46.0	48.0					X																	75650880		2203	4300	6503	SO:0001583	missense	57692	exon1			CATGCCAGGGAGT	AF490507	CCDS14433.1	Xq13	2008-02-05			ENSG00000198934	ENSG00000198934			24934	protein-coding gene	gene with protein product		300759				14623885	Standard	NM_020932		Approved	KIAA1587, DAMAGE	uc004ecm.2	Q9HCI5	OTTHUMG00000021879	ENST00000361470.2:c.2557A>T	X.37:g.75650880A>T	ENSP00000354912:p.Arg853Trp	Somatic	64	0		WXS	Illumina HiSeq	.	38	10	NM_020932	Q5JXC7|Q86TG0|Q8TD92|Q9H216	Missense_Mutation	SNP	ENST00000361470.2	37	CCDS14433.1	.	.	.	.	.	.	.	.	.	.	.	14.00	2.405607	0.42715	.	.	ENSG00000198934	ENST00000361470	T	0.05139	3.49	2.52	2.52	0.30459	.	.	.	.	.	T	0.13500	0.0327	L	0.42744	1.35	0.09310	N	1	D	0.61080	0.989	D	0.65233	0.933	T	0.09930	-1.0652	9	0.72032	D	0.01	.	6.0982	0.20033	1.0:0.0:0.0:0.0	.	853	Q9HCI5	MAGE1_HUMAN	W	853	ENSP00000354912:R853W	ENSP00000354912:R853W	R	+	1	2	MAGEE1	75567284	0.996000	0.38824	0.034000	0.17996	0.997000	0.91878	1.209000	0.32357	1.232000	0.43678	0.486000	0.48141	AGG	.		0.493	MAGEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057298.1	NM_020932	
LRP2	4036	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	170103393	170103393	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr2:170103393C>A	ENST00000263816.3	-	21	3297	c.3012G>T	c.(3010-3012)atG>atT	p.M1004I	LRP2_ENST00000443831.1_Missense_Mutation_p.M867I	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1004	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	AAGCCAGCCTCATTCCATAAG	0.527																																					p.M1004I		.											.	.	.	0			c.G3012T						.						93.0	85.0	87.0					2																	170103393		2203	4300	6503	SO:0001583	missense	4036	exon21			CAGCCTCATTCCA		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.3012G>T	2.37:g.170103393C>A	ENSP00000263816:p.Met1004Ile	Somatic	39	0		WXS	Illumina HiSeq	.	32	7	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.879897	0.91740	.	.	ENSG00000081479	ENST00000263816;ENST00000443831	T;T	0.40756	1.02;1.02	5.79	5.79	0.91817	Epidermal growth factor-like (1);	0.000000	0.85682	D	0.000000	T	0.63510	0.2517	M	0.65677	2.01	0.80722	D	1	D;D	0.62365	0.991;0.975	D;D	0.77004	0.989;0.942	T	0.54166	-0.8334	10	0.20046	T	0.44	.	20.0313	0.97540	0.0:1.0:0.0:0.0	.	867;1004	E9PC35;P98164	.;LRP2_HUMAN	I	1004;867	ENSP00000263816:M1004I;ENSP00000409813:M867I	ENSP00000263816:M1004I	M	-	3	0	LRP2	169811639	1.000000	0.71417	0.992000	0.48379	0.758000	0.43043	7.526000	0.81920	2.746000	0.94184	0.655000	0.94253	ATG	.		0.527	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
CASP8AP2	9994	hgsc.bcm.edu	37	6	90575684	90575684	+	RNA	SNP	C	C	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr6:90575684C>A	ENST00000551025.1	+	0	4112									caspase 8 associated protein 2											NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		GTGTTTTTACCAAATTCAGCT	0.279																																					p.P892Q	Colon(187;1656 2025 17045 31481 39901)	.											.	.	.	0			c.C2675A						.																																					9994	exon8			TTTTACCAAATTC	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"""FLICE-associated huge protein"""	606880	"""CASP8 associated protein 2"""			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		6.37:g.90575684C>A		Somatic	66	0		WXS	Illumina HiSeq	.	77	4	NM_001137667		Missense_Mutation	SNP	ENST00000551025.1	37																																																																																				.		0.279	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
FERD3L	222894	hgsc.bcm.edu	37	7	19184746	19184746	+	Silent	SNP	C	C	T	rs34966908|rs199985178|rs71017023	byFrequency	TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr7:19184746C>T	ENST00000275461.3	-	1	298	c.240G>A	c.(238-240)gaG>gaA	p.E80E	AC003986.5_ENST00000452700.1_RNA	NM_152898.2	NP_690862.1	Q96RJ6	FER3L_HUMAN	Fer3-like bHLH transcription factor	80	Poly-Glu.				cell development (GO:0048468)|floor plate development (GO:0033504)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of neurogenesis (GO:0050767)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E81_R82insE(1)		breast(1)|endometrium(4)|large_intestine(8)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	35						ttccgcgctcctcttcctcct	0.622																																					p.E80E		.											.,2	.	63	1	Insertion - In frame(1)	ovary(1)	c.G240A						.						72.0	54.0	60.0					7																	19184746		2203	4300	6503	SO:0001819	synonymous_variant	222894	exon1			GCGCTCCTCTTCC	AF369897	CCDS5368.1	7p21.3	2013-10-17	2013-10-17		ENSG00000146618	ENSG00000146618		"""Basic helix-loop-helix proteins"""	16660	protein-coding gene	gene with protein product			"""Fer3-like (Drosophila)"""			11472856, 12217327	Standard	NM_152898		Approved	NATO3, N-TWIST, bHLHa31	uc003suo.1	Q96RJ6	OTTHUMG00000090823	ENST00000275461.3:c.240G>A	7.37:g.19184746C>T		Somatic	14	0		WXS	Illumina HiSeq	.	13	2	NM_152898	Q495K0	Silent	SNP	ENST00000275461.3	37	CCDS5368.1																																																																																			.		0.622	FERD3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207627.1		
TRIM39	56658	hgsc.bcm.edu	37	6	30297399	30297399	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr6:30297399G>T	ENST00000396547.1	+	2	465	c.305G>T	c.(304-306)cGg>cTg	p.R102L	TRIM39_ENST00000540416.1_Missense_Mutation_p.R102L|HCG18_ENST00000412685.2_RNA|TRIM39_ENST00000396548.1_Missense_Mutation_p.R102L|HCG18_ENST00000426882.1_RNA|TRIM39_ENST00000396551.3_Missense_Mutation_p.R102L|TRIM39_ENST00000376659.5_Missense_Mutation_p.R102L|TRIM39_ENST00000376656.4_Missense_Mutation_p.R102L|HCG18_ENST00000413358.2_RNA|TRIM39-RPP21_ENST00000513556.1_Missense_Mutation_p.R14L			Q9HCM9	TRI39_HUMAN	tripartite motif containing 39	102					apoptotic process (GO:0006915)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|positive regulation of apoptotic signaling pathway (GO:2001235)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.R102Q(1)		ovary(3)	3						CGGAAGATCCGGGATGAGAGC	0.552																																					p.R102L		.											TRIM39_ENST00000376656,colon,carcinoma,+1,1	TRIM39_ENST00000376656	+1	1	Substitution - Missense(1)	large_intestine(1)	c.G305T						.						53.0	51.0	52.0					6																	30297399		1510	2707	4217	SO:0001583	missense	56658	exon3			AGATCCGGGATGA	BC034985	CCDS34377.1, CCDS34378.1	6p22.1	2013-01-09	2011-01-25	2002-06-07	ENSG00000204599	ENSG00000204599		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10065	protein-coding gene	gene with protein product		605700	"""ring finger protein 23"", ""tripartite motif-containing 39"""	RNF23		11006080	Standard	NM_021253		Approved			Q9HCM9	OTTHUMG00000031066	ENST00000396547.1:c.305G>T	6.37:g.30297399G>T	ENSP00000379796:p.Arg102Leu	Somatic	36	1		WXS	Illumina HiSeq	.	30	3	NM_172016	Q5STG3|Q5STG4|Q76BL3|Q8IYT9|Q96IB6	Missense_Mutation	SNP	ENST00000396547.1	37	CCDS34377.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.06|18.06	3.538913|3.538913	0.65085|0.65085	.|.	.|.	ENSG00000204599|ENSG00000204599;ENSG00000204599;ENSG00000204599;ENSG00000204599;ENSG00000204599;ENSG00000204599;ENSG00000204599;ENSG00000204599;ENSG00000204599;ENSG00000204599;ENSG00000204599;ENSG00000248167	ENST00000420746|ENST00000458516;ENST00000396551;ENST00000376656;ENST00000545104;ENST00000540416;ENST00000449040;ENST00000412529;ENST00000428728;ENST00000396548;ENST00000376659;ENST00000396547;ENST00000513556	.|T;T;T;T;T;T;T;T;T	.|0.54279	.|0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58	5.23|5.23	2.41|2.41	0.29592|0.29592	.|Zinc finger, B-box (2);	.|0.000000	.|0.43260	.|D	.|0.000582	T|T	0.16938|0.16938	0.0407|0.0407	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B;P;B	.|0.36199	.|0.002;0.543;0.44	.|B;P;B	.|0.46208	.|0.002;0.507;0.085	T|T	0.13255|0.13255	-1.0516|-1.0516	5|10	.|0.25106	.|T	.|0.35	.|.	4.9614|4.9614	0.14068|0.14068	0.178:0.0:0.6539:0.1681|0.178:0.0:0.6539:0.1681	.|.	.|16;102;102	.|F5H2V3;Q9HCM9;Q9HCM9-2	.|.;TRI39_HUMAN;.	W|L	32|102;102;102;102;102;102;16;102;102;102;102;14	.|ENSP00000405928:R102L;ENSP00000379800:R102L;ENSP00000365844:R102L;ENSP00000439400:R102L;ENSP00000406019:R102L;ENSP00000379797:R102L;ENSP00000365847:R102L;ENSP00000379796:R102L;ENSP00000424048:R14L	.|ENSP00000365844:R102L	G|R	+|+	1|2	0|0	TRIM39|TRIM39-RPP21;TRIM39	30405378|30405378	1.000000|1.000000	0.71417|0.71417	0.727000|0.727000	0.30756|0.30756	0.930000|0.930000	0.56654|0.56654	1.887000|1.887000	0.39698|0.39698	0.768000|0.768000	0.33290|0.33290	0.555000|0.555000	0.69702|0.69702	GGG|CGG	.		0.552	TRIM39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076086.2	NM_172016	
GHDC	84514	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	40344493	40344493	+	Nonsense_Mutation	SNP	C	C	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr17:40344493C>A	ENST00000301671.8	-	4	1096	c.655G>T	c.(655-657)Gag>Tag	p.E219*	GHDC_ENST00000414034.3_Nonsense_Mutation_p.E219*|GHDC_ENST00000436923.2_Nonsense_Mutation_p.E219*|GHDC_ENST00000593209.1_Nonsense_Mutation_p.E219*|GHDC_ENST00000587427.1_Nonsense_Mutation_p.E219*|GHDC_ENST00000428494.2_Nonsense_Mutation_p.E180*|GHDC_ENST00000590520.1_5'Flank			Q8N2G8	GHDC_HUMAN	GH3 domain containing	219						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		all_cancers(22;0.000229)|Breast(137;0.00104)|all_epithelial(22;0.00304)		BRCA - Breast invasive adenocarcinoma(366;0.124)		CCAGCTAGCTCTTCACCATCA	0.662																																					p.E219X		.											.	.	.	0			c.G655T						.						84.0	97.0	93.0					17																	40344493		2203	4298	6501	SO:0001587	stop_gained	84514	exon5			CTAGCTCTTCACC	AF316997, BC011056	CCDS11422.1, CCDS45682.1	17q21.2	2006-08-02				ENSG00000167925			24438	protein-coding gene	gene with protein product		608587				11161808, 11735219	Standard	NR_024573		Approved	LGP1	uc002hzf.4	Q8N2G8		ENST00000301671.8:c.655G>T	17.37:g.40344493C>A	ENSP00000301671:p.Glu219*	Somatic	51	0		WXS	Illumina HiSeq	.	36	10	NM_001142623	B4DQS4|E9PDB5|Q9BXM6	Nonsense_Mutation	SNP	ENST00000301671.8	37	CCDS11422.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.060271	0.76074	.	.	ENSG00000167925	ENST00000393854;ENST00000428494;ENST00000414034;ENST00000301671;ENST00000436923	.	.	.	4.52	3.48	0.39840	.	0.087618	0.43919	D	0.000519	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	-6.2613	8.8943	0.35453	0.0:0.8853:0.0:0.1147	.	.	.	.	X	163;180;219;219;219	.	ENSP00000301671:E219X	E	-	1	0	GHDC	37598019	0.023000	0.18921	0.937000	0.37676	0.084000	0.17831	2.007000	0.40883	0.996000	0.38943	0.561000	0.74099	GAG	.		0.662	GHDC-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449794.1	NM_032484	
ZFC3H1	196441	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	72024647	72024647	+	Silent	SNP	G	G	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr12:72024647G>A	ENST00000378743.3	-	17	3916	c.3558C>T	c.(3556-3558)tgC>tgT	p.C1186C		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	1186					RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						AATCAAAACGGCAGAAACACT	0.348																																					p.C1186C		.											.	.	.	0			c.C3558T						.						117.0	109.0	111.0					12																	72024647		1976	4173	6149	SO:0001819	synonymous_variant	196441	exon17			AAAACGGCAGAAA	AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"""Zinc finger, C3H1-type containing"""	28328	protein-coding gene	gene with protein product			"""proline/serine-rich coiled-coil 2"", ""coiled-coil domain containing 131"""	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.3558C>T	12.37:g.72024647G>A		Somatic	47	0		WXS	Illumina HiSeq	.	39	4	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Silent	SNP	ENST00000378743.3	37	CCDS41813.1																																																																																			.		0.348	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982	
HMCN1	83872	hgsc.bcm.edu	37	1	186064631	186064631	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr1:186064631G>T	ENST00000271588.4	+	68	10780	c.10551G>T	c.(10549-10551)aaG>aaT	p.K3517N	HMCN1_ENST00000367492.2_Missense_Mutation_p.K3517N	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3517					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)			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						AAGTCAGCAAGCACTTTATCC	0.403																																					p.K3517N		.											.	.	.	0			c.G10551T						.						99.0	93.0	95.0					1																	186064631		2203	4300	6503	SO:0001583	missense	83872	exon68			CAGCAAGCACTTT	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.10551G>T	1.37:g.186064631G>T	ENSP00000271588:p.Lys3517Asn	Somatic	76	0		WXS	Illumina HiSeq	.	70	3	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	17.94	3.511260	0.64522	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.68903	-0.36;-0.36	5.31	1.67	0.24075	Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.218606	0.47093	D	0.000258	T	0.58395	0.2119	M	0.70108	2.13	0.32384	N	0.554179	P	0.38395	0.629	B	0.37198	0.243	T	0.60316	-0.7287	10	0.19147	T	0.46	.	7.9142	0.29808	0.4557:0.0:0.5443:0.0	.	3517	Q96RW7	HMCN1_HUMAN	N	3517	ENSP00000271588:K3517N;ENSP00000356462:K3517N	ENSP00000271588:K3517N	K	+	3	2	HMCN1	184331254	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	0.634000	0.24614	0.498000	0.27948	-0.131000	0.14894	AAG	.		0.403	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
PLEKHH3	79990	hgsc.bcm.edu;broad.mit.edu	37	17	40823452	40823452	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr17:40823452G>A	ENST00000591022.1	-	8	1588	c.1201C>T	c.(1201-1203)Cgg>Tgg	p.R401W	PLEKHH3_ENST00000456950.2_5'UTR|PLEKHH3_ENST00000293349.6_Missense_Mutation_p.R401W|PLEKHH3_ENST00000412503.1_Missense_Mutation_p.R401W	NM_024927.4	NP_079203	Q7Z736	PKHH3_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 3	401					signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|skin(2)	13		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.14)		AGCTCCTGCCGTTGGCTCAAC	0.672																																					p.R401W		.											PLEKHH3,colon,carcinoma,0,1	PLEKHH3	0	0			c.C1201T						.						33.0	29.0	31.0					17																	40823452		2202	4299	6501	SO:0001583	missense	79990	exon8			CCTGCCGTTGGCT	BC052978	CCDS11434.1	17q21.2	2013-01-11				ENSG00000068137		"""Pleckstrin homology (PH) domain containing"""	26105	protein-coding gene	gene with protein product						12477932	Standard	NM_024927		Approved	FLJ21019	uc002iau.3	Q7Z736		ENST00000591022.1:c.1201C>T	17.37:g.40823452G>A	ENSP00000468678:p.Arg401Trp	Somatic	90	0		WXS	Illumina HiSeq	.	52	3	NM_024927	C9JQ76|Q59H20|Q96B28|Q9H7D6|Q9NT18	Missense_Mutation	SNP	ENST00000591022.1	37	CCDS11434.1	.	.	.	.	.	.	.	.	.	.	G	18.90	3.721684	0.68959	.	.	ENSG00000068137	ENST00000456950;ENST00000293349;ENST00000412503	T;T	0.75260	-0.92;-0.92	4.84	1.56	0.23342	Band 4.1 domain (1);	0.000000	0.41396	D	0.000887	T	0.81336	0.4801	M	0.67397	2.05	0.41884	D	0.990335	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.995	T	0.78725	-0.2092	10	0.87932	D	0	-23.2388	7.3521	0.26697	0.0772:0.0:0.4713:0.4516	.	401;401	Q7Z736-2;Q7Z736	.;PKHH3_HUMAN	W	63;401;401	ENSP00000293349:R401W;ENSP00000411885:R401W	ENSP00000293349:R401W	R	-	1	2	PLEKHH3	38076978	0.861000	0.29849	0.934000	0.37439	0.663000	0.39108	1.408000	0.34668	0.074000	0.16767	0.561000	0.74099	CGG	.		0.672	PLEKHH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452332.1	NM_024927	
REV3L	5980	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	111636540	111636540	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr6:111636540T>G	ENST00000358835.3	-	28	8850	c.8396A>C	c.(8395-8397)aAg>aCg	p.K2799T	REV3L_ENST00000462119.1_5'UTR|REV3L_ENST00000435970.1_Missense_Mutation_p.K2721T|REV3L_ENST00000368805.1_Missense_Mutation_p.K2799T|REV3L_ENST00000368802.3_Missense_Mutation_p.K2799T|RP5-1112D6.8_ENST00000607434.1_RNA			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2799					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		CTGACCAATCTTAAAAGACTG	0.333								DNA polymerases (catalytic subunits)																													p.K2799T		.											.	.	.	0			c.A8396C						.						80.0	72.0	75.0					6																	111636540		2203	4300	6503	SO:0001583	missense	5980	exon27			CCAATCTTAAAAG	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"""DNA polymerases"""	9968	protein-coding gene	gene with protein product	"""polymerase, DNA, zeta"""	602776	"""REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta"", ""REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"""			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.8396A>C	6.37:g.111636540T>G	ENSP00000351697:p.Lys2799Thr	Somatic	69	0		WXS	Illumina HiSeq	.	60	10	NM_002912	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	37	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	T	18.47	3.631442	0.67015	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	T;T;T;T	0.19250	2.16;2.16;2.16;2.16	5.33	5.33	0.75918	DNA polymerase, palm domain (1);DNA-directed DNA polymerase, family B, multifunctional domain (1);	0.124211	0.52532	D	0.000064	T	0.17662	0.0424	L	0.45581	1.43	0.39673	D	0.97078	B	0.33883	0.43	B	0.43990	0.438	T	0.03335	-1.1047	10	0.41790	T	0.15	.	15.2943	0.73891	0.0:0.0:0.0:1.0	.	2799	O60673	DPOLZ_HUMAN	T	2799;2799;2799;2721	ENSP00000357792:K2799T;ENSP00000357795:K2799T;ENSP00000351697:K2799T;ENSP00000402003:K2721T	ENSP00000351697:K2799T	K	-	2	0	REV3L	111743233	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.214000	0.58527	2.021000	0.59480	0.528000	0.53228	AAG	.		0.333	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912	
RBBP8NL	140893	hgsc.bcm.edu	37	20	60985985	60985985	+	Silent	SNP	G	G	A	rs151053015		TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr20:60985985G>A	ENST00000252998.1	-	14	2100	c.1944C>T	c.(1942-1944)gaC>gaT	p.D648D		NM_080833.2	NP_543023.2	Q8NC74	RB8NL_HUMAN	RBBP8 N-terminal like	648						extracellular space (GO:0005615)											GGTCCTCGGCGTCCCTTGGGC	0.677																																					p.D648D		.											C20orf151,lower_third,carcinoma,0,1	C20orf151	0	0			c.C1944T						.	G		1,4405	2.1+/-5.4	0,1,2202	93.0	91.0	92.0		1944	0.4	0.0	20	dbSNP_134	92	0,8600		0,0,4300	no	coding-synonymous	C20orf151	NM_080833.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		648/665	60985985	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	140893	exon14			CTCGGCGTCCCTT	AL121832	CCDS13498.1	20q13.33	2012-10-30	2012-10-30	2012-10-30	ENSG00000130701	ENSG00000130701			16144	protein-coding gene	gene with protein product	"""hypothetical protein LOC140893"""		"""chromosome 20 open reading frame 151"""	C20orf151		11780052	Standard	NM_080833		Approved	dJ908M14.3	uc002ycw.2	Q8NC74	OTTHUMG00000032913	ENST00000252998.1:c.1944C>T	20.37:g.60985985G>A		Somatic	80	0		WXS	Illumina HiSeq	.	48	2	NM_080833	B2RP98|Q8N4Z9|Q9BR75|Q9H0Y9	Silent	SNP	ENST00000252998.1	37	CCDS13498.1																																																																																			0.000		0.677	RBBP8NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080029.1	NM_080833	
PGBD1	84547	hgsc.bcm.edu	37	6	28251740	28251740	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr6:28251740C>A	ENST00000405948.2	+	2	570	c.150C>A	c.(148-150)ttC>ttA	p.F50L	PGBD1_ENST00000259883.3_Missense_Mutation_p.F50L	NM_001184743.1|NM_032507.3	NP_001171672.1|NP_115896.1	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	50	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.					membrane (GO:0016020)|nucleus (GO:0005634)	scavenger receptor activity (GO:0005044)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	41						TTCGGCACTTCTGCTACCAGG	0.567																																					p.F50L		.											PGBD1,right_lower_lobe,carcinoma,0,1	PGBD1	0	0			c.C150A						.						76.0	75.0	75.0					6																	28251740		2203	4300	6503	SO:0001583	missense	84547	exon2			GCACTTCTGCTAC	D88259	CCDS4648.1	6p22.1	2013-01-09			ENSG00000137338	ENSG00000137338		"""-"""	19398	protein-coding gene	gene with protein product							Standard	NM_001184743		Approved	HUCEP-4, dJ874C20.4, SCAND4	uc003nkz.3	Q96JS3	OTTHUMG00000014520	ENST00000405948.2:c.150C>A	6.37:g.28251740C>A	ENSP00000385213:p.Phe50Leu	Somatic	27	0		WXS	Illumina HiSeq	.	13	2	NM_001184743	Q53F43|Q6NTF5|Q8WWS4	Missense_Mutation	SNP	ENST00000405948.2	37	CCDS4648.1	.	.	.	.	.	.	.	.	.	.	C	14.09	2.432465	0.43224	.	.	ENSG00000137338	ENST00000405948;ENST00000259883	T;T	0.05199	3.48;3.48	4.65	2.88	0.33553	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	.	.	.	.	T	0.02047	0.0064	L	0.52206	1.635	0.25430	N	0.988197	B	0.18310	0.027	B	0.24006	0.05	T	0.45498	-0.9257	9	0.15499	T	0.54	1.5749	8.6373	0.33957	0.0:0.7472:0.0:0.2528	.	50	Q96JS3	PGBD1_HUMAN	L	50	ENSP00000385213:F50L;ENSP00000259883:F50L	ENSP00000259883:F50L	F	+	3	2	PGBD1	28359719	0.627000	0.27129	0.751000	0.31187	0.757000	0.42996	0.226000	0.17776	0.885000	0.36088	0.655000	0.94253	TTC	.		0.567	PGBD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040188.2		
C4orf29	80167	hgsc.bcm.edu	37	4	128904141	128904141	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr4:128904141C>T	ENST00000444616.1	+	2	278	c.31C>T	c.(31-33)Cgg>Tgg	p.R11W	C4orf29_ENST00000388795.5_5'UTR|C4orf29_ENST00000398965.1_Missense_Mutation_p.R11W			Q0P651	CD029_HUMAN	chromosome 4 open reading frame 29	11						extracellular region (GO:0005576)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	8						TATTCTATACCGGAGACTTCT	0.333																																					p.R11W		.											C4orf29_ENST00000398965,NS,carcinoma,0,2	C4orf29_ENST00000398965	0	0			c.C31T						.						61.0	54.0	56.0					4																	128904141		1801	4059	5860	SO:0001583	missense	80167	exon2			CTATACCGGAGAC	AK024759	CCDS47131.1	4q28.2	2008-02-05			ENSG00000164074	ENSG00000164074			26111	protein-coding gene	gene with protein product						12477932	Standard	XM_006714318		Approved	FLJ21106	uc021xrt.1	Q0P651	OTTHUMG00000133304	ENST00000444616.1:c.31C>T	4.37:g.128904141C>T	ENSP00000397229:p.Arg11Trp	Somatic	57	1		WXS	Illumina HiSeq	.	42	2	NM_001039717	A1A4W8|A1A4W9|Q9H7A7	Missense_Mutation	SNP	ENST00000444616.1	37		.	.	.	.	.	.	.	.	.	.	C	18.71	3.682644	0.68157	.	.	ENSG00000164074	ENST00000454347;ENST00000398965;ENST00000444616;ENST00000513371	.	.	.	5.42	5.42	0.78866	.	0.144833	0.43579	D	0.000549	T	0.76564	0.4005	M	0.73217	2.22	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.78700	-0.2102	9	0.87932	D	0	-16.7588	11.662	0.51352	0.2848:0.7152:0.0:0.0	.	11	Q0P651	CD029_HUMAN	W	11	.	ENSP00000381937:R11W	R	+	1	2	C4orf29	129123591	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	1.219000	0.32479	2.552000	0.86080	0.462000	0.41574	CGG	.		0.333	C4orf29-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257098.1	NM_001039717	
HTR5A	3361	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	154863304	154863304	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr7:154863304G>T	ENST00000287907.2	+	1	1271	c.695G>T	c.(694-696)gGc>gTc	p.G232V	HTR5A-AS1_ENST00000493904.1_5'Flank|HTR5A-AS1_ENST00000395731.2_5'Flank|HTR5A-AS1_ENST00000543018.1_5'Flank	NM_024012.3	NP_076917.1	P47898	5HT5A_HUMAN	5-hydroxytryptamine (serotonin) receptor 5A, G protein-coupled	232					cAMP-mediated signaling (GO:0019933)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hippocampus development (GO:0021766)|response to estradiol (GO:0032355)|serotonin receptor signaling pathway (GO:0007210)	dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	serotonin receptor activity (GO:0004993)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(3)|stomach(1)	48	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0238)	UCEC - Uterine corpus endometrioid carcinoma (81;0.171)	Asenapine(DB06216)|Loxapine(DB00408)|Olanzapine(DB00334)	TTCCGCGTGGGCTCCAGGAAG	0.532																																					p.G232V		.											.	.	.	0			c.G695T						.						75.0	72.0	73.0					7																	154863304		2203	4300	6503	SO:0001583	missense	3361	exon1			GCGTGGGCTCCAG		CCDS5936.1	7q36.1	2012-08-08	2012-02-03		ENSG00000157219	ENSG00000157219		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5300	protein-coding gene	gene with protein product		601305	"""5-hydroxytryptamine (serotonin) receptor 5A"""			7988681	Standard	NM_024012		Approved	5-HT5A	uc003wlu.2	P47898	OTTHUMG00000151327	ENST00000287907.2:c.695G>T	7.37:g.154863304G>T	ENSP00000287907:p.Gly232Val	Somatic	54	0		WXS	Illumina HiSeq	.	29	12	NM_024012	Q2M2D2	Missense_Mutation	SNP	ENST00000287907.2	37	CCDS5936.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.371314	0.82573	.	.	ENSG00000157219	ENST00000287907	T	0.36157	1.27	4.76	4.76	0.60689	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.54598	0.1868	L	0.52011	1.625	0.80722	D	1	D	0.67145	0.996	D	0.72982	0.979	T	0.52283	-0.8596	10	0.42905	T	0.14	.	17.9833	0.89148	0.0:0.0:1.0:0.0	.	232	P47898	5HT5A_HUMAN	V	232	ENSP00000287907:G232V	ENSP00000287907:G232V	G	+	2	0	HTR5A	154494237	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	9.173000	0.94815	2.485000	0.83878	0.650000	0.86243	GGC	.		0.532	HTR5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322240.1	NM_024012	
PCTP	58488	hgsc.bcm.edu	37	17	53852193	53852193	+	Silent	SNP	G	G	T	rs371579881		TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr17:53852193G>T	ENST00000268896.5	+	5	677	c.552G>T	c.(550-552)ccG>ccT	p.P184P	PCTP_ENST00000325214.6_Silent_p.P112P|PCTP_ENST00000573500.1_Silent_p.P184P|PCTP_ENST00000576221.1_3'UTR|PCTP_ENST00000576183.1_Silent_p.P184P	NM_021213.3	NP_067036.2	Q9UKL6	PPCT_HUMAN	phosphatidylcholine transfer protein	184	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|phospholipid transport (GO:0015914)	cytosol (GO:0005829)	phosphatidylcholine binding (GO:0031210)|phosphatidylcholine transporter activity (GO:0008525)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)	10			BRCA - Breast invasive adenocarcinoma(1;0.00207)			GCCAAATTCCGTCCTGGCTCA	0.498																																					p.P184P		.											PCTP,NS,malignant_melanoma,+1,1	PCTP	+1	0			c.G552T						.						87.0	86.0	86.0					17																	53852193		2203	4300	6503	SO:0001819	synonymous_variant	58488	exon5			AATTCCGTCCTGG	AK024667	CCDS11588.1, CCDS45741.1	17q21-q24	2011-09-13				ENSG00000141179		"""StAR-related lipid transfer (START) domain containing"""	8752	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 2"""	606055					Standard	NM_021213		Approved	STARD2	uc002iul.4	Q9UKL6		ENST00000268896.5:c.552G>T	17.37:g.53852193G>T		Somatic	78	0		WXS	Illumina HiSeq	.	66	4	NM_021213	Q9BSC9|Q9UIT3|Q9UKW7	Silent	SNP	ENST00000268896.5	37	CCDS11588.1																																																																																			.		0.498	PCTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439271.2	NM_021213	
FBN2	2201	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	127610310	127610310	+	Missense_Mutation	SNP	A	A	C			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr5:127610310A>C	ENST00000508053.1	-	66	8634	c.7660T>G	c.(7660-7662)Ttt>Gtt	p.F2554V	FBN2_ENST00000262464.4_Missense_Mutation_p.F2554V			P35556	FBN2_HUMAN	fibrillin 2	2554	EGF-like 43; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		TTACAGGTAAACCCCCCCAGG	0.418																																					p.F2554V		.											FBN2_ENST00000508053,NS,carcinoma,0,6	FBN2_ENST00000508053	0	0			c.T7660G						.						98.0	95.0	96.0					5																	127610310		2203	4300	6503	SO:0001583	missense	2201	exon60			AGGTAAACCCCCC	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"""fibrillin 5"""	612570	"""congenital contractural arachnodactyly"""	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.7660T>G	5.37:g.127610310A>C	ENSP00000424571:p.Phe2554Val	Somatic	77	0		WXS	Illumina HiSeq	.	54	7	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	37	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.717127	0.89205	.	.	ENSG00000138829	ENST00000262464;ENST00000508053	D;D	0.95918	-3.85;-3.85	4.92	4.92	0.64577	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.64402	D	0.000010	D	0.97620	0.9220	M	0.82193	2.58	0.58432	D	0.999996	D	0.62365	0.991	D	0.76575	0.988	D	0.98446	1.0589	10	0.87932	D	0	.	15.0181	0.71605	1.0:0.0:0.0:0.0	.	2554	P35556	FBN2_HUMAN	V	2554	ENSP00000262464:F2554V;ENSP00000424571:F2554V	ENSP00000262464:F2554V	F	-	1	0	FBN2	127638209	1.000000	0.71417	0.875000	0.34327	0.950000	0.60333	9.087000	0.94110	2.181000	0.69327	0.477000	0.44152	TTT	.		0.418	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	
TUFT1	7286	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	151553512	151553512	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr1:151553512C>T	ENST00000368849.3	+	12	1165	c.1103C>T	c.(1102-1104)cCg>cTg	p.P368L	TUFT1_ENST00000368848.2_Missense_Mutation_p.P343L|TUFT1_ENST00000538902.1_Missense_Mutation_p.P387L|TUFT1_ENST00000392712.3_Missense_Mutation_p.P313L|TUFT1_ENST00000353024.3_Missense_Mutation_p.P309L	NM_020127.2	NP_064512.1	Q9NNX1	TUFT1_HUMAN	tuftelin 1	368					bone mineralization (GO:0030282)|odontogenesis (GO:0042476)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	structural constituent of tooth enamel (GO:0030345)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)	13	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			ACAGAGAACCCGGGCAGGTGA	0.517																																					p.P368L		.											.	.	.	0			c.C1103T						.						51.0	52.0	51.0					1																	151553512		2203	4300	6503	SO:0001583	missense	7286	exon12			AGAACCCGGGCAG	AF254260	CCDS1000.1, CCDS44223.1	1q21	2008-02-05			ENSG00000143367	ENSG00000143367			12422	protein-coding gene	gene with protein product		600087				7919663	Standard	NM_020127		Approved		uc001eyl.3	Q9NNX1	OTTHUMG00000012536	ENST00000368849.3:c.1103C>T	1.37:g.151553512C>T	ENSP00000357842:p.Pro368Leu	Somatic	44	0		WXS	Illumina HiSeq	.	34	14	NM_020127	B2RD57|D3DV21|D3DV22|Q5T384|Q5T385|Q9BU28|Q9H5L1	Missense_Mutation	SNP	ENST00000368849.3	37	CCDS1000.1	.	.	.	.	.	.	.	.	.	.	C	4.379	0.069837	0.08436	.	.	ENSG00000143367	ENST00000368849;ENST00000392712;ENST00000353024;ENST00000368848;ENST00000538902	T;T;T;T;T	0.16897	2.35;2.36;2.35;2.35;2.31	4.96	-1.56	0.08532	.	0.595996	0.17158	N	0.184818	T	0.01765	0.0056	N	0.05383	-0.06	0.31332	N	0.684748	B;B;B	0.10296	0.001;0.001;0.003	B;B;B	0.09377	0.002;0.002;0.004	T	0.47100	-0.9143	10	0.20519	T	0.43	3.8478	5.2047	0.15285	0.0:0.4388:0.1771:0.3841	.	387;343;368	F5H607;Q9NNX1-2;Q9NNX1	.;.;TUFT1_HUMAN	L	368;313;309;343;387	ENSP00000357842:P368L;ENSP00000376476:P313L;ENSP00000343781:P309L;ENSP00000357841:P343L;ENSP00000437997:P387L	ENSP00000343781:P309L	P	+	2	0	TUFT1	149820136	0.548000	0.26473	0.759000	0.31340	0.685000	0.39939	-0.471000	0.06631	-0.432000	0.07297	0.655000	0.94253	CCG	.		0.517	TUFT1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035022.1	NM_020127	
TSC22D2	9819	hgsc.bcm.edu	37	3	150176395	150176395	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr3:150176395C>A	ENST00000361875.3	+	4	3331	c.2315C>A	c.(2314-2316)cCa>cAa	p.P772Q	TSC22D2_ENST00000361136.2_Missense_Mutation_p.P748Q	NM_014779.2	NP_055594.1	O75157	T22D2_HUMAN	TSC22 domain family, member 2	772					response to osmotic stress (GO:0006970)		sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	18			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			ACGCAACCTCCACAGCAGCCG	0.473																																					p.P772Q		.											TSC22D2,NS,malignant_melanoma,0,1	TSC22D2	0	0			c.C2315A						.						75.0	76.0	76.0					3																	150176395		2203	4300	6503	SO:0001583	missense	9819	exon4			AACCTCCACAGCA	AB014569	CCDS3149.1	3q25.1	2005-03-01			ENSG00000196428	ENSG00000196428			29095	protein-coding gene	gene with protein product						9734811	Standard	NM_014779		Approved	KIAA0669, TILZ4a, TILZ4b, TILZ4c	uc003exv.3	O75157	OTTHUMG00000159744	ENST00000361875.3:c.2315C>A	3.37:g.150176395C>A	ENSP00000354543:p.Pro772Gln	Somatic	40	0		WXS	Illumina HiSeq	.	36	2	NM_014779	D3DNI5|Q6PI50|Q9H2Z6|Q9H2Z7|Q9H2Z8	Missense_Mutation	SNP	ENST00000361875.3	37	CCDS3149.1	.	.	.	.	.	.	.	.	.	.	C	12.63	1.994541	0.35226	.	.	ENSG00000196428	ENST00000543241;ENST00000361875;ENST00000361136	T;T	0.28454	1.61;1.61	5.2	5.2	0.72013	.	0.404293	0.20321	N	0.094622	T	0.25568	0.0622	N	0.24115	0.695	0.33192	D	0.550969	B;B	0.24823	0.112;0.068	B;B	0.21151	0.033;0.015	T	0.25572	-1.0128	10	0.54805	T	0.06	.	18.6889	0.91576	0.0:1.0:0.0:0.0	.	748;772	O75157-2;O75157	.;T22D2_HUMAN	Q	221;772;748	ENSP00000354543:P772Q;ENSP00000354893:P748Q	ENSP00000354893:P748Q	P	+	2	0	TSC22D2	151659085	0.999000	0.42202	0.989000	0.46669	0.946000	0.59487	2.834000	0.48167	2.591000	0.87537	0.655000	0.94253	CCA	.		0.473	TSC22D2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357123.2	NM_014779	
PFDN1	5201	hgsc.bcm.edu	37	5	139680104	139680104	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr5:139680104G>T	ENST00000261813.4	-	2	144	c.97C>A	c.(97-99)Cag>Aag	p.Q33K	PFDN1_ENST00000524074.1_Missense_Mutation_p.Q33K|PFDN1_ENST00000510217.1_Intron|PFDN1_ENST00000514611.1_5'UTR	NM_002622.4	NP_002613.2	O60925	PFD1_HUMAN	prefoldin subunit 1	33					'de novo' posttranslational protein folding (GO:0051084)|actin cytoskeleton organization (GO:0030036)|B cell activation (GO:0042113)|cell cycle (GO:0007049)|cellular protein metabolic process (GO:0044267)|cerebellum development (GO:0021549)|protein folding (GO:0006457)|regulation of transcription, DNA-templated (GO:0006355)|telencephalon development (GO:0021537)	prefoldin complex (GO:0016272)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(3)|prostate(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGTTCAATCTGTATGTCTGCG	0.388																																					p.Q33K		.											.	.	.	0			c.C97A						.						245.0	200.0	215.0					5																	139680104		2203	4300	6503	SO:0001583	missense	5201	exon2			CAATCTGTATGTC	Y17392	CCDS4222.1	5q31	2008-02-05	2006-02-24		ENSG00000113068	ENSG00000113068			8866	protein-coding gene	gene with protein product		604897	"""prefoldin 1"""			9630229	Standard	XM_005268465		Approved	PFD1	uc003lff.1	O60925	OTTHUMG00000129249	ENST00000261813.4:c.97C>A	5.37:g.139680104G>T	ENSP00000261813:p.Gln33Lys	Somatic	70	0		WXS	Illumina HiSeq	.	56	4	NM_002622	B2RD02|Q53F95|Q96EX6	Missense_Mutation	SNP	ENST00000261813.4	37	CCDS4222.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.979685	0.74360	.	.	ENSG00000113068	ENST00000261813;ENST00000524074	T;T	0.45276	0.9;0.9	5.84	5.84	0.93424	Prefoldin beta-like (1);Prefoldin (1);	0.000000	0.85682	D	0.000000	T	0.53302	0.1788	M	0.69823	2.125	0.80722	D	1	P	0.42123	0.771	P	0.45428	0.48	T	0.49173	-0.8967	10	0.37606	T	0.19	-7.5902	20.1438	0.98071	0.0:0.0:1.0:0.0	.	33	O60925	PFD1_HUMAN	K	33	ENSP00000261813:Q33K;ENSP00000428707:Q33K	ENSP00000261813:Q33K	Q	-	1	0	PFDN1	139660288	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.236000	0.95360	2.768000	0.95171	0.650000	0.86243	CAG	.		0.388	PFDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251354.3	NM_002622	
NXF5	55998	hgsc.bcm.edu	37	X	101096287	101096287	+	Missense_Mutation	SNP	G	G	A	rs199849270		TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chrX:101096287G>A	ENST00000361708.2	-	7	696	c.337C>T	c.(337-339)Cgg>Tgg	p.R113W	NXF5_ENST00000537026.1_Missense_Mutation_p.R113W|NXF5_ENST00000473265.2_Missense_Mutation_p.R113W			Q9H1B4	NXF5_HUMAN	nuclear RNA export factor 5	113					mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|skin(1)	30						ACATTGTACCGTTTGTTCATG	0.547																																					p.R113W		.											.	.	.	0			c.C337T						.	G	TRP/ARG	1,3830		0,1,1629,571	34.0	34.0	34.0		337	-0.9	0.0	X		34	1,6673		0,1,2410,1852	no	missense	NXF5	NM_032946.2	101	0,2,4039,2423	AA,AG,GG,G		0.015,0.0261,0.019	probably-damaging	113/366	101096287	2,10503	2201	4263	6464	SO:0001583	missense	55998	exon7			TGTACCGTTTGTT	AJ277654	CCDS14491.1, CCDS14491.2	Xq22	2008-07-28			ENSG00000126952	ENSG00000126952			8075	protein-coding gene	gene with protein product		300319				11566096	Standard	NM_032946		Approved		uc011mrk.1	Q9H1B4	OTTHUMG00000022042	ENST00000361708.2:c.337C>T	X.37:g.101096287G>A	ENSP00000355286:p.Arg113Trp	Somatic	215	0		WXS	Illumina HiSeq	.	161	18	NM_032946	A2RRM0|B1AV82|B1AV83|B1AV84|B1AV85|Q9H1B0|Q9H1B1|Q9H1B2|Q9H1B3	Missense_Mutation	SNP	ENST00000361708.2	37		.	.	.	.	.	.	.	.	.	.	.	12.18	1.859693	0.32884	2.61E-4	1.5E-4	ENSG00000126952	ENST00000537026;ENST00000473265;ENST00000361708	T;T;T	0.58797	0.31;0.31;0.31	2.18	-0.91	0.10511	.	0.077917	0.50627	N	0.000108	T	0.52435	0.1734	M	0.91717	3.235	0.44807	D	0.997817	P	0.50443	0.935	B	0.37267	0.245	T	0.52495	-0.8568	10	0.87932	D	0	.	2.2335	0.04002	0.3224:0.0:0.4336:0.244	.	113	A2RRM0	.	W	113	ENSP00000442401:R113W;ENSP00000426978:R113W;ENSP00000355286:R113W	ENSP00000263032:R113W	R	-	1	2	NXF5	100982943	1.000000	0.71417	0.000000	0.03702	0.002000	0.02628	1.388000	0.34442	-0.338000	0.08413	-1.693000	0.00726	CGG	.		0.547	NXF5-201	KNOWN	basic	protein_coding	protein_coding			
ZC3H11A	9877	broad.mit.edu	37	1	203821508	203821508	+	Nonsense_Mutation	SNP	C	C	G			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr1:203821508C>G	ENST00000545588.1	+	17	6241	c.2414C>G	c.(2413-2415)tCa>tGa	p.S805*	ZC3H11A_ENST00000367212.3_Nonsense_Mutation_p.S805*|ZC3H11A_ENST00000367214.1_Nonsense_Mutation_p.S805*|ZC3H11A_ENST00000332127.4_Nonsense_Mutation_p.S805*|ZC3H11A_ENST00000367210.1_Nonsense_Mutation_p.S805*	NM_001271675.1	NP_001258604.1	O75152	ZC11A_HUMAN	zinc finger CCCH-type containing 11A	805					poly(A)+ mRNA export from nucleus (GO:0016973)		metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.S805*(3)		central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)			CTTGAGCTATCAGAAATGATT	0.378																																					p.S805X													ZC3H11A,NS,carcinoma,0,4	ZC3H11A	71	3	Substitution - Nonsense(3)	endometrium(2)|lung(1)	c.C2414G						.																																			SO:0001587	stop_gained	9877	exon20			AGCTATCAGAAAT		CCDS30978.1	1q32.1	2012-07-05	2005-06-02	2005-06-02	ENSG00000058673	ENSG00000058673		"""Zinc fingers, CCCH-type domain containing"""	29093	protein-coding gene	gene with protein product		613513	"""zinc finger CCCH-type domain containing 11A"""	ZC3HDC11A		9734811	Standard	NM_014827		Approved	KIAA0663	uc001hac.3	O75152	OTTHUMG00000035909	ENST00000545588.1:c.2414C>G	1.37:g.203821508C>G	ENSP00000438527:p.Ser805*	Somatic	251	1		WXS	Illumina GAIIx	Phase_I	218	4	NM_014827	Q6AHY4|Q6AHY9|Q6AW79|Q6AWA1|Q6PJK4|Q86XZ7	Nonsense_Mutation	SNP	ENST00000545588.1	37	CCDS30978.1	.	.	.	.	.	.	.	.	.	.	C	40	8.446087	0.98815	.	.	ENSG00000058673	ENST00000367214;ENST00000537080;ENST00000367212;ENST00000332127;ENST00000545588;ENST00000367210	.	.	.	5.9	4.99	0.66335	.	0.140252	0.49916	D	0.000132	.	.	.	.	.	.	0.45172	D	0.998181	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-4.7509	15.4578	0.75330	0.14:0.86:0.0:0.0	.	.	.	.	X	805;751;805;805;805;805	.	ENSP00000333253:S805X	S	+	2	0	ZC3H11A	202088131	1.000000	0.71417	0.920000	0.36463	0.858000	0.48976	6.206000	0.72154	1.492000	0.48499	-0.175000	0.13238	TCA	.		0.378	ZC3H11A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087471.3	NM_014827	
KCNK4	50801	broad.mit.edu	37	11	64060511	64060511	+	Silent	SNP	G	G	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr11:64060511G>A	ENST00000539216.1	+	1	381	c.21G>A	c.(19-21)ctG>ctA	p.L7L	KCNK4_ENST00000539651.1_Intron|KCNK4_ENST00000394525.2_Silent_p.L7L|KCNK4_ENST00000422670.2_Silent_p.L7L|RP11-783K16.10_ENST00000539086.1_RNA|Y_RNA_ENST00000384297.1_RNA|KCNK4_ENST00000538767.1_Intron			Q9NYG8	KCNK4_HUMAN	potassium channel, subfamily K, member 4	7					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			breast(2)|large_intestine(2)|lung(3)|prostate(2)|urinary_tract(1)	10						CCACGCTCCTGGCCCTGCTGG	0.736																																					p.L7L													.	KCNK4	22	0			c.G21A						.						19.0	21.0	20.0					11																	64060511		1846	3462	5308	SO:0001819	synonymous_variant	50801	exon2			GCTCCTGGCCCTG	AF247042	CCDS8067.1	11q13	2012-03-07			ENSG00000182450	ENSG00000182450		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6279	protein-coding gene	gene with protein product		605720				10767409, 16382106	Standard	NM_033310		Approved	K2p4.1, TRAAK	uc001nzk.1	Q9NYG8	OTTHUMG00000168006	ENST00000539216.1:c.21G>A	11.37:g.64060511G>A		Somatic	77	0		WXS	Illumina GAIIx	Phase_I	68	5	NM_033310	B5TJL1|Q96T94	Silent	SNP	ENST00000539216.1	37	CCDS8067.1																																																																																			.		0.736	KCNK4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396430.1	NM_033311	
RP11-146E13.4	0	broad.mit.edu	37	14	19857017	19857017	+	lincRNA	SNP	C	C	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr14:19857017C>A	ENST00000548109.1	+	0	72																											GTATTATACTCTCAGCATCCT	0.383																																					.													.	.	.	0			.						.																																					0	.			TATACTCTCAGCA																													14.37:g.19857017C>A		Somatic	84	0		WXS	Illumina GAIIx	Phase_I	67	16	.		RNA	SNP	ENST00000548109.1	37																																																																																				.		0.383	RP11-146E13.4-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000409408.1		
EMC4	51234	broad.mit.edu	37	15	34520740	34520740	+	Silent	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr15:34520740C>T	ENST00000267750.4	+	4	582	c.466C>T	c.(466-468)Ctg>Ttg	p.L156L	EMC4_ENST00000249209.4_Intron|EMC4_ENST00000559421.1_Intron|EMC4_ENST00000557879.1_3'UTR|EMC4_ENST00000559078.1_Intron	NM_016454.2	NP_057538.1	Q5J8M3	EMC4_HUMAN	ER membrane protein complex subunit 4	156					apoptotic process (GO:0006915)	ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)											GTCCATGGGACTGTTACCTAC	0.443																																					p.L156L													.	.	.	0			c.C466T						.						238.0	214.0	222.0					15																	34520740		2201	4298	6499	SO:0001819	synonymous_variant	51234	exon4			ATGGGACTGTTAC	BC016348	CCDS10035.1, CCDS66732.1	15q14	2012-05-23	2012-05-23	2012-05-23	ENSG00000128463	ENSG00000128463			28032	protein-coding gene	gene with protein product			"""transmembrane protein 85"""	TMEM85		18586032, 22119785	Standard	NM_001286420		Approved	FLJ90746, MGC24415, PIG17	uc001zhq.3	Q5J8M3	OTTHUMG00000129411	ENST00000267750.4:c.466C>T	15.37:g.34520740C>T		Somatic	100	0		WXS	Illumina GAIIx	Phase_I	40	3	NM_016454	A8K3A9|B4DJQ4|Q96KX9|Q9BUI5|Q9P0T9	Silent	SNP	ENST00000267750.4	37	CCDS10035.1																																																																																			.		0.443	EMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251568.1	NM_016454	
ABCC6	368	broad.mit.edu	37	16	16315466	16315466	+	Intron	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr16:16315466G>T	ENST00000205557.7	-	2	249				ABCC6_ENST00000575728.1_Silent_p.R87R|RP11-517A5.7_ENST00000574883.1_RNA|ABCC6_ENST00000574094.1_Intron	NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6						response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	TGCCTCCCCCGAACATTGCCT	0.542																																					p.R87R													.	ABCC6	110	0			c.C259A						.						22.0	22.0	22.0					16																	16315466		2197	4300	6497	SO:0001627	intron_variant	368	exon2			TCCCCCGAACATT	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"""ATP binding cassette transporters / subfamily C"""	57	protein-coding gene	gene with protein product		603234	"""pseudoxanthoma elasticum"""	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.219+39C>A	16.37:g.16315466G>T		Somatic	107	0		WXS	Illumina GAIIx	Phase_I	91	3	NM_001079528	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Silent	SNP	ENST00000205557.7	37	CCDS10568.1																																																																																			CAC|0.500;GAA|0.500		0.542	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		
SLC6A10PB	653562	broad.mit.edu	37	16	32895150	32895164	+	lincRNA	DEL	CCACTGACTCGGGCC	CCACTGACTCGGGCC	-	rs375921105		TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr16:32895150_32895164delCCACTGACTCGGGCC	ENST00000398669.2	+	0	0				SLC6A10P_ENST00000330048.5_RNA																							GTAGGGGTGGCCACTGACTCGGGCCCCACGTAGGG	0.642																																					.													.	.	.	0			.						.																																					0	.			GGGTGGCCACTGA																													16.37:g.32895150_32895164delCCACTGACTCGGGCC		Somatic	63	0		WXS	Illumina GAIIx	Phase_I	51	2	.		RNA	DEL	ENST00000398669.2	37																																																																																				CCACTGACTCGGGCC|0.500;-|0.500		0.642	RP11-989E6.3-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000432084.1		
ZNF18	7566	broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	11896084	11896084	+	Silent	SNP	G	G	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr17:11896084G>A	ENST00000322748.3	-	4	667	c.63C>T	c.(61-63)tcC>tcT	p.S21S	ZNF18_ENST00000454073.3_Silent_p.S21S|ZNF18_ENST00000580306.2_Silent_p.S21S	NM_144680.2	NP_653281.2	P17022	ZNF18_HUMAN	zinc finger protein 18	21					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)	14				Colorectal(4;3.33e-05)|COAD - Colon adenocarcinoma(4;0.000494)|READ - Rectum adenocarcinoma(10;0.233)		CTGAGAACTGGGAGTCCTCGG	0.577																																					p.S21S													.	ZNF18	42	0			c.C63T						.						58.0	54.0	56.0					17																	11896084		2203	4300	6503	SO:0001819	synonymous_variant	7566	exon4			GAACTGGGAGTCC	X52342	CCDS32568.1	17p12	2013-01-09	2006-05-10		ENSG00000154957	ENSG00000154957		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12969	protein-coding gene	gene with protein product		194524	"""zinc finger protein 18 (KOX 11)"""			15702252	Standard	XM_005256786		Approved	ZKSCAN6, KOX11, HDSG1, Zfp535, ZNF535, ZSCAN38	uc002gng.1	P17022	OTTHUMG00000178307	ENST00000322748.3:c.63C>T	17.37:g.11896084G>A		Somatic	63	1		WXS	Illumina GAIIx	Phase_I	31	4	NM_144680	Q5QHQ3|Q8IYC4|Q8NAH6	Silent	SNP	ENST00000322748.3	37	CCDS32568.1																																																																																			.		0.577	ZNF18-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441450.2	XM_085596	
HPN-AS1	100128675	broad.mit.edu	37	19	35566856	35566856	+	RNA	SNP	C	C	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr19:35566856C>A	ENST00000392227.2	-	0	404					NR_024562.1				HPN antisense RNA 1																		GGGGAACCCACAGGGGCCTCC	0.677																																					.													.	.	.	0			.						.																																					0	.			AACCCACAGGGGC			19q13.12	2013-04-25			ENSG00000227392	ENSG00000227392		"""Long non-coding RNAs"""	47041	non-coding RNA	RNA, long non-coding							Standard	NR_024561		Approved		uc010xsi.2		OTTHUMG00000182475		19.37:g.35566856C>A		Somatic	47	0		WXS	Illumina GAIIx	Phase_I	26	4	.		RNA	SNP	ENST00000392227.2	37																																																																																				.		0.677	HPN-AS1-001	KNOWN	basic	antisense	antisense	OTTHUMT00000461582.1		
SLC1A6	6511	broad.mit.edu;bcgsc.ca	37	19	15063766	15063766	+	Silent	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr19:15063766C>T	ENST00000221742.3	-	8	1480	c.1473G>A	c.(1471-1473)acG>acA	p.T491T	SLC1A6_ENST00000430939.2_Silent_p.T427T|SLC1A6_ENST00000600144.1_Silent_p.T413T	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	491					aspartate transport (GO:0015810)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						CAATGATGAGCGTGATGTCTT	0.607																																					p.T491T													.	SLC1A6	111	0			c.G1473A						.						199.0	150.0	167.0					19																	15063766		2203	4300	6503	SO:0001819	synonymous_variant	6511	exon8			GATGAGCGTGATG		CCDS12321.1, CCDS62578.1	19p13.12	2013-07-15			ENSG00000105143	ENSG00000105143		"""Solute carriers"""	10944	protein-coding gene	gene with protein product		600637				7791878	Standard	NM_005071		Approved	EAAT4	uc002naa.2	P48664	OTTHUMG00000183351	ENST00000221742.3:c.1473G>A	19.37:g.15063766C>T		Somatic	28	0		WXS	Illumina GAIIx	Phase_I	7	3	NM_005071	Q8N753	Silent	SNP	ENST00000221742.3	37	CCDS12321.1																																																																																			.		0.607	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071	
RUVBL2	10856	broad.mit.edu;bcgsc.ca	37	19	49518928	49518928	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr19:49518928C>A	ENST00000595090.1	+	14	1815	c.1351C>A	c.(1351-1353)Ctc>Atc	p.L451I	CTB-60B18.10_ENST00000600007.1_lincRNA|RUVBL2_ENST00000601968.1_3'UTR|RUVBL2_ENST00000413176.2_Missense_Mutation_p.L406I	NM_006666.1	NP_006657.1	Q9Y230	RUVB2_HUMAN	RuvB-like AAA ATPase 2	451					ATP catabolic process (GO:0006200)|cellular response to estradiol stimulus (GO:0071392)|cellular response to UV (GO:0034644)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|establishment of protein localization to chromatin (GO:0071169)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of estrogen receptor binding (GO:0071899)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein folding (GO:0006457)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)|transcriptional activation by promoter-enhancer looping (GO:0071733)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Ino80 complex (GO:0031011)|intracellular (GO:0005622)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|NuA4 histone acetyltransferase complex (GO:0035267)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|ATP-dependent DNA helicase activity (GO:0004003)|chromatin DNA binding (GO:0031490)|damaged DNA binding (GO:0003684)|DNA helicase activity (GO:0003678)|identical protein binding (GO:0042802)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|unfolded protein binding (GO:0051082)			large_intestine(1)|upper_aerodigestive_tract(1)	2		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000449)|OV - Ovarian serous cystadenocarcinoma(262;0.000555)|GBM - Glioblastoma multiforme(486;0.00585)|Epithelial(262;0.047)		GGACGCCTTCCTCTTCAACGA	0.587																																					p.L451I													.	RUVBL2	31	0			c.C1351A						.						84.0	90.0	88.0					19																	49518928		2101	4216	6317	SO:0001583	missense	10856	exon14			GCCTTCCTCTTCA	AF155138	CCDS42588.1	19q13.3	2013-09-12	2013-09-12					"""INO80 complex subunits"", ""ATPases / AAA-type"""	10475	protein-coding gene	gene with protein product	"""reptin"", ""INO80 complex subunit J"""	604788	"""RuvB (E coli homolog)-like 2"", ""RuvB-like 2 (E. coli)"""			10428817, 10998447	Standard	XM_005258426		Approved	RVB2, TIP48, TIP49b, Reptin52, ECP51, TIH2, INO80J, Rvb2	uc002plr.1	Q9Y230		ENST00000595090.1:c.1351C>A	19.37:g.49518928C>A	ENSP00000473172:p.Leu451Ile	Somatic	28	0		WXS	Illumina GAIIx	Phase_I	18	3	NM_006666	B3KQ59|E7ETE5|Q6FIB9|Q6PK27|Q9Y361	Missense_Mutation	SNP	ENST00000595090.1	37	CCDS42588.1	.	.	.	.	.	.	.	.	.	.	C	8.129	0.782672	0.16189	.	.	ENSG00000183207	ENST00000221413;ENST00000413176	T	0.47869	0.83	5.13	4.09	0.47781	.	0.075647	0.56097	D	0.000037	T	0.27933	0.0688	N	0.25957	0.775	0.54753	D	0.99998	B	0.02656	0.0	B	0.09377	0.004	T	0.06770	-1.0808	10	0.08599	T	0.76	-33.9841	6.9389	0.24483	0.1719:0.7386:0.0:0.0895	.	451	Q9Y230	RUVB2_HUMAN	I	451;406	ENSP00000413890:L406I	ENSP00000221413:L451I	L	+	1	0	RUVBL2	54210740	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.048000	0.49862	1.294000	0.44707	0.561000	0.74099	CTC	.		0.587	RUVBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466235.1		
MAP4K3	8491	broad.mit.edu	37	2	39564669	39564669	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr2:39564669G>T	ENST00000263881.3	-	5	688	c.364C>A	c.(364-366)Cag>Aag	p.Q122K	MAP4K3_ENST00000437545.1_Missense_Mutation_p.Q59K|MAP4K3_ENST00000341681.5_Missense_Mutation_p.Q122K	NM_003618.3	NP_003609.2	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase kinase 3	122	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)		ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			NS(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_hematologic(82;0.211)				TGATTTACCTGCAGTGTTTCT	0.313																																					p.Q122K													.	MAP4K3	109	0			c.C364A						.						119.0	116.0	117.0					2																	39564669		2203	4295	6498	SO:0001583	missense	8491	exon5			TTACCTGCAGTGT	AF000145	CCDS1803.1, CCDS58707.1	2p22.3	2011-06-09			ENSG00000011566	ENSG00000011566		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6865	protein-coding gene	gene with protein product		604921		RAB8IPL1		9275185	Standard	NM_003618		Approved	GLK, MAPKKKK3	uc002rro.4	Q8IVH8	OTTHUMG00000102127	ENST00000263881.3:c.364C>A	2.37:g.39564669G>T	ENSP00000263881:p.Gln122Lys	Somatic	88	0		WXS	Illumina GAIIx	Phase_I	70	3	NM_001270425	Q6IQ39|Q8IVH7|Q9UDM5|Q9Y6R5	Missense_Mutation	SNP	ENST00000263881.3	37	CCDS1803.1	.	.	.	.	.	.	.	.	.	.	G	13.88	2.369019	0.42003	.	.	ENSG00000011566	ENST00000263881;ENST00000437545;ENST00000341681	T;T;T	0.64085	-0.08;-0.08;-0.08	4.68	4.68	0.58851	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.47838	0.1467	N	0.04043	-0.29	0.80722	D	1	B;B	0.28880	0.032;0.226	B;B	0.41174	0.055;0.349	T	0.45963	-0.9225	9	.	.	.	.	16.7068	0.85374	0.0:0.0:1.0:0.0	.	122;122	Q8IVH8-3;Q8IVH8	.;M4K3_HUMAN	K	122;59;122	ENSP00000263881:Q122K;ENSP00000416958:Q59K;ENSP00000345434:Q122K	.	Q	-	1	0	MAP4K3	39418173	1.000000	0.71417	0.999000	0.59377	0.899000	0.52679	8.181000	0.89696	2.330000	0.79161	0.484000	0.47621	CAG	.		0.313	MAP4K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219966.2	NM_003618	
BMS1P20	96610	broad.mit.edu	37	22	22663052	22663052	+	RNA	SNP	T	T	C			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr22:22663052T>C	ENST00000426066.1	+	0	500					NR_027293.1				BMS1 pseudogene 20																		AATTTTGGGGTTCCTGTTAGC	0.308																																					.													.	.	.	0			.						.																																					0	.			TTGGGGTTCCTGT			22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22663052T>C		Somatic	226	0		WXS	Illumina GAIIx	Phase_I	256	6	.		RNA	SNP	ENST00000426066.1	37																																																																																				.		0.308	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473090.1		
EFCAB6	64800	broad.mit.edu	37	22	43985975	43985975	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr22:43985975T>C	ENST00000262726.7	-	24	3264	c.3011A>G	c.(3010-3012)gAg>gGg	p.E1004G	EFCAB6_ENST00000396231.2_Missense_Mutation_p.E852G	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	1004					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				ATGGGTCAGCTCCCCTTCGGT	0.408																																					p.E1004G													.	EFCAB6	177	0			c.A3011G						.						246.0	216.0	226.0					22																	43985975		2203	4300	6503	SO:0001583	missense	64800	exon24			GTCAGCTCCCCTT	Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"""EF-hand domain containing"""	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.3011A>G	22.37:g.43985975T>C	ENSP00000262726:p.Glu1004Gly	Somatic	65	0		WXS	Illumina GAIIx	Phase_I	52	3	NM_022785	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Missense_Mutation	SNP	ENST00000262726.7	37	CCDS14049.1	.	.	.	.	.	.	.	.	.	.	T	14.73	2.622278	0.46840	.	.	ENSG00000186976	ENST00000396231;ENST00000262726	D;D	0.85629	-2.01;-2.01	4.73	4.73	0.59995	EF-hand-like domain (1);	0.344456	0.26380	N	0.024719	D	0.91081	0.7193	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.972	D	0.91897	0.5528	10	0.72032	D	0.01	-29.3854	13.1111	0.59275	0.0:0.0:0.0:1.0	.	852;1004	Q5THR3-2;Q5THR3	.;EFCB6_HUMAN	G	852;1004	ENSP00000379533:E852G;ENSP00000262726:E1004G	ENSP00000262726:E1004G	E	-	2	0	EFCAB6	42317308	1.000000	0.71417	0.983000	0.44433	0.093000	0.18481	4.531000	0.60602	1.902000	0.55061	0.454000	0.30748	GAG	.		0.408	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785	
UROC1	131669	broad.mit.edu	37	3	126208213	126208213	+	Silent	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr3:126208213C>T	ENST00000290868.2	-	17	1667	c.1614G>A	c.(1612-1614)ccG>ccA	p.P538P	UROC1_ENST00000383579.3_Silent_p.P598P	NM_144639.2	NP_653240.1	Q96N76	HUTU_HUMAN	urocanate hydratase 1	538					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	urocanate hydratase activity (GO:0016153)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(1)|skin(1)	39				GBM - Glioblastoma multiforme(114;0.17)		TCAGGACCACCGGCGCCTGTG	0.597																																					p.P598P													.	UROC1	150	0			c.G1794A						.						105.0	93.0	97.0					3																	126208213		2203	4300	6503	SO:0001819	synonymous_variant	131669	exon18			GACCACCGGCGCC	AK055862	CCDS3038.1, CCDS54636.1	3q21.2	2012-08-21	2012-08-21		ENSG00000159650	ENSG00000159650	4.2.1.49		26444	protein-coding gene	gene with protein product	"""urocanase 1"""	613012	"""urocanase domain containing 1"""			19304569	Standard	NM_144639		Approved	FLJ31300, HMFN0320	uc010hsi.2	Q96N76	OTTHUMG00000162753	ENST00000290868.2:c.1614G>A	3.37:g.126208213C>T		Somatic	27	0		WXS	Illumina GAIIx	Phase_I	13	3	NM_001165974	E9PE13|Q14C64|Q68CJ7	Silent	SNP	ENST00000290868.2	37	CCDS3038.1																																																																																			.		0.597	UROC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370325.2	NM_144639	
GTF2H2B	653238	broad.mit.edu	37	5	69719461	69719461	+	RNA	DEL	T	T	-			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr5:69719461delT	ENST00000513202.1	+	0	468					NR_033417.1				general transcription factor IIH, polypeptide 2B (pseudogene)																		ttttctttccttttttttttt	0.353																																					.													.	.	.	0			.						.																																					0	.			CTTTCCTTTTTTT			5q13.2	2011-09-01	2011-09-01		ENSG00000226259	ENSG00000226259		"""General transcription factors"""	31393	pseudogene	pseudogene			"""general transcription factor IIH, polypeptide 2B"""				Standard	NR_033417		Approved	DKFZP686M0199	uc021yab.1		OTTHUMG00000162394		5.37:g.69719461delT		Somatic	23	0		WXS	Illumina GAIIx	Phase_I	21	2	.		RNA	DEL	ENST00000513202.1	37																																																																																				.		0.353	GTF2H2B-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000396209.1	NM_001098729	
LARP1	23367	broad.mit.edu	37	5	154190824	154190824	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr5:154190824T>C	ENST00000336314.4	+	17	2654	c.2630T>C	c.(2629-2631)cTt>cCt	p.L877P		NM_015315.3	NP_056130.2	Q6PKG0	LARP1_HUMAN	La ribonucleoprotein domain family, member 1	954					cell proliferation (GO:0008283)|positive regulation of macroautophagy (GO:0016239)|positive regulation of translation (GO:0045727)|TOR signaling (GO:0031929)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation activator activity (GO:0008494)|translation initiation factor binding (GO:0031369)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TTGGAGTGCCTTTTTCGATAC	0.433																																					p.L877P													.	LARP1	187	0			c.T2630C						.						114.0	107.0	109.0					5																	154190824		2203	4300	6503	SO:0001583	missense	23367	exon17			AGTGCCTTTTTCG	AB018274	CCDS4328.1	5q33.2	2014-02-12			ENSG00000155506	ENSG00000155506		"""La ribonucleoprotein domain containing"""	29531	protein-coding gene	gene with protein product		612059				9872452, 10878606	Standard	NM_015315		Approved	LARP, KIAA0731, MGC19556	uc003lvo.4	Q6PKG0	OTTHUMG00000130191	ENST00000336314.4:c.2630T>C	5.37:g.154190824T>C	ENSP00000336721:p.Leu877Pro	Somatic	56	0		WXS	Illumina GAIIx	Phase_I	55	3	NM_015315	O94836|Q8N4M2|Q8NB73|Q9UFD7	Missense_Mutation	SNP	ENST00000336314.4	37	CCDS4328.1	.	.	.	.	.	.	.	.	.	.	T	27.2	4.813757	0.90790	.	.	ENSG00000155506	ENST00000336314	T	0.63580	-0.05	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	D	0.83755	0.5323	M	0.91140	3.18	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.87349	0.2336	10	0.87932	D	0	-16.1477	16.5763	0.84648	0.0:0.0:0.0:1.0	.	954;877	Q6PKG0;Q6PKG0-3	LARP1_HUMAN;.	P	877	ENSP00000336721:L877P	ENSP00000336721:L877P	L	+	2	0	LARP1	154171017	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.975000	0.88055	2.317000	0.78254	0.459000	0.35465	CTT	.		0.433	LARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252509.1	NM_033551	
DNAH8	1769	broad.mit.edu	37	6	38890868	38890868	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr6:38890868A>G	ENST00000359357.3	+	70	10300	c.10046A>G	c.(10045-10047)aAg>aGg	p.K3349R	RP1-207H1.3_ENST00000418399.1_RNA|DNAH8_ENST00000449981.2_Missense_Mutation_p.K3566R|DNAH8_ENST00000441566.1_Missense_Mutation_p.K3313R|RP1-207H1.3_ENST00000416948.1_RNA			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	3349					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TGCCGGAAAAAGATGCAGGCC	0.433																																					p.K3566R													.	DNAH8	1239	0			c.A10697G						.						57.0	59.0	59.0					6																	38890868		2203	4300	6503	SO:0001583	missense	1769	exon72			GGAAAAAGATGCA	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.10046A>G	6.37:g.38890868A>G	ENSP00000352312:p.Lys3349Arg	Somatic	77	1		WXS	Illumina GAIIx	Phase_I	66	3	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	A	22.6	4.308244	0.81247	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.74209	-0.82;-0.82;-0.82	5.33	5.33	0.75918	Dynein heavy chain, coiled coil stalk (1);	0.000000	0.85682	D	0.000000	T	0.71484	0.3345	M	0.69248	2.105	0.58432	D	0.999999	P	0.41848	0.763	P	0.48571	0.582	T	0.70901	-0.4746	10	0.27785	T	0.31	.	15.5898	0.76517	1.0:0.0:0.0:0.0	.	3349	Q96JB1	DYH8_HUMAN	R	3554;3554;3349;3313	ENSP00000333363:K3554R;ENSP00000352312:K3349R;ENSP00000402294:K3313R	ENSP00000333363:K3554R	K	+	2	0	DNAH8	38998846	1.000000	0.71417	1.000000	0.80357	0.571000	0.35966	9.243000	0.95416	2.136000	0.66102	0.533000	0.62120	AAG	.		0.433	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
LINC00472	79940	broad.mit.edu	37	6	72084709	72084712	+	lincRNA	DEL	ATAA	ATAA	-			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr6:72084709_72084712delATAA	ENST00000602823.1	-	0	267				MIR30C2_ENST00000362224.1_RNA																							atgtaaatatataaatatatgtaa	0.059																																					.													.	.	.	0			.						.																																					0	.			AAATATATAAATA																													6.37:g.72084709_72084712delATAA		Somatic	16	0		WXS	Illumina GAIIx	Phase_I	9	3	.		RNA	DEL	ENST00000602823.1	37																																																																																				.		0.059	RP3-331H24.5-001	KNOWN	basic|readthrough_transcript	lincRNA	lincRNA	OTTHUMT00000467928.1		
KCP	375616	broad.mit.edu	37	7	128546870	128546874	+	RNA	DEL	AAAGT	AAAGT	-	rs145152760	byFrequency	TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr7:128546870_128546874delAAAGT	ENST00000476647.2	-	0	530				AC025594.1_ENST00000408474.1_RNA			Q6ZWJ8	KCP_HUMAN	kielin/chordin-like protein							extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)	4						tttgccattaaaagtcatgtcaaaa	0.468																																					.													.	KCP	16	0			.						.																																					375616	.			CCATTAAAAGTCA	AK122706		7q32.3	2009-11-06	2009-02-18	2009-02-18	ENSG00000135253	ENSG00000135253			17585	protein-coding gene	gene with protein product	"""kielin"""	609344	"""cysteine rich BMP regulator 2 (chordin-like)"""	CRIM2		15793581	Standard	NM_001135914		Approved	FLJ33365, NET67	uc011kor.2	Q6ZWJ8	OTTHUMG00000158363		7.37:g.128546870_128546874delAAAGT		Somatic	31	0		WXS	Illumina GAIIx	Phase_I	35	6	.	Q8NBE0	RNA	DEL	ENST00000476647.2	37																																																																																				.		0.468	KCP-006	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000403051.1	NM_199349	
LOC101928283	101928283	broad.mit.edu	37	7	124985954	124985954	+	lincRNA	DEL	T	T	-			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr7:124985954delT	ENST00000424515.2	+	0	1024																											ACTTTTGTGCTTTGGGAACTG	0.438																																					.													.	.	.	0			.						.																																					0	.			TTGTGCTTTGGGA																													7.37:g.124985954delT		Somatic	7	0		WXS	Illumina GAIIx	Phase_I	6	2	.		RNA	DEL	ENST00000424515.2	37																																																																																				.		0.438	RP11-3B12.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000347734.2		
ADCY8	114	broad.mit.edu	37	8	131812682	131812682	+	Missense_Mutation	SNP	T	T	C	rs539555378		TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr8:131812682T>C	ENST00000286355.5	-	15	5142	c.3050A>G	c.(3049-3051)gAc>gGc	p.D1017G	ADCY8_ENST00000377928.3_Missense_Mutation_p.D886G	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	1017					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			CTCATCGAAGTCAGCAATGAT	0.403										HNSCC(32;0.087)			T|||	1	0.000199681	0.0	0.0	5008	,	,		22355	0.0		0.0	False		,,,				2504	0.001				p.D1017G													ADCY8,NS,carcinoma,+1,1	ADCY8	291	0			c.A3050G						.						181.0	164.0	170.0					8																	131812682		2203	4300	6503	SO:0001583	missense	114	exon15			TCGAAGTCAGCAA	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"""Adenylate cyclases"""	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.3050A>G	8.37:g.131812682T>C	ENSP00000286355:p.Asp1017Gly	Somatic	92	0		WXS	Illumina GAIIx	Phase_I	89	3	NM_001115		Missense_Mutation	SNP	ENST00000286355.5	37	CCDS6363.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.056704	0.76074	.	.	ENSG00000155897	ENST00000286355;ENST00000377928	D;D	0.81739	-1.53;-1.53	5.31	5.31	0.75309	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.048033	0.85682	D	0.000000	D	0.84483	0.5482	L	0.33137	0.985	0.38897	D	0.957243	P;B	0.34892	0.474;0.433	P;P	0.56398	0.682;0.797	D	0.86645	0.1894	10	0.72032	D	0.01	.	14.4386	0.67301	0.0:0.0:0.0:1.0	.	886;1017	E7EVL1;P40145	.;ADCY8_HUMAN	G	1017;886	ENSP00000286355:D1017G;ENSP00000367161:D886G	ENSP00000286355:D1017G	D	-	2	0	ADCY8	131881864	1.000000	0.71417	0.997000	0.53966	0.914000	0.54420	4.270000	0.58896	1.997000	0.58415	0.455000	0.32223	GAC	.		0.403	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1		
MLLT3	4300	broad.mit.edu	37	9	20414379	20414379	+	Silent	SNP	G	G	A	rs373338988		TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr9:20414379G>A	ENST00000380338.4	-	5	751	c.465C>T	c.(463-465)agC>agT	p.S155S	MLLT3_ENST00000429426.2_Silent_p.S152S|MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000475957.1_5'UTR	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	155	Poly-Ser.				anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)		p.S155S(4)		central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		tgctgctactgctgctgctgc	0.532			T	MLL	ALL																																p.S155S				Dom	yes		9	9p22	4300	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"""		L	MLLT3,NS,carcinoma,0,8	MLLT3	125	4	Substitution - coding silent(4)	urinary_tract(1)|large_intestine(1)|lung(1)|kidney(1)	c.C465T						.						10.0	15.0	14.0					9																	20414379		1871	3851	5722	SO:0001819	synonymous_variant	4300	exon5			GCTACTGCTGCTG	L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"""			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.465C>T	9.37:g.20414379G>A		Somatic	106	1		WXS	Illumina GAIIx	Phase_I	87	5	NM_004529	B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Silent	SNP	ENST00000380338.4	37	CCDS6494.1																																																																																			.		0.532	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529	
C9orf50	375759	broad.mit.edu	37	9	132377802	132377802	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr9:132377802G>T	ENST00000372478.4	-	4	1042	c.841C>A	c.(841-843)Cag>Aag	p.Q281K	NTMT1_ENST00000372486.1_Intron	NM_199350.3	NP_955382.3	Q5SZB4	CI050_HUMAN	chromosome 9 open reading frame 50	281										central_nervous_system(1)|endometrium(4)|large_intestine(2)|ovary(1)|skin(1)|urinary_tract(1)	10		Ovarian(14;0.00556)				GTTGTGTCCTGCAGGGTCTCG	0.642																																					p.Q281K													.	C9orf50	25	0			c.C841A						.						68.0	59.0	62.0					9																	132377802		2203	4300	6503	SO:0001583	missense	375759	exon4			TGTCCTGCAGGGT	AK093122	CCDS35159.1	9q34.2	2012-03-15			ENSG00000179058	ENSG00000179058			23677	protein-coding gene	gene with protein product							Standard	NM_199350		Approved	FLJ35803	uc004byc.4	Q5SZB4	OTTHUMG00000020786	ENST00000372478.4:c.841C>A	9.37:g.132377802G>T	ENSP00000361556:p.Gln281Lys	Somatic	69	0		WXS	Illumina GAIIx	Phase_I	48	3	NM_199350	Q2M1I2|Q8NA65	Missense_Mutation	SNP	ENST00000372478.4	37	CCDS35159.1	.	.	.	.	.	.	.	.	.	.	g	4.182	0.032329	0.08101	.	.	ENSG00000179058	ENST00000372478	T	0.19938	2.11	3.17	1.17	0.20885	.	0.481828	0.15435	N	0.262506	T	0.11324	0.0276	N	0.24115	0.695	0.09310	N	1	B	0.28850	0.225	B	0.26969	0.075	T	0.33137	-0.9880	10	0.17832	T	0.49	-9.2012	7.75	0.28892	0.0:0.0:0.5463:0.4537	.	281	Q5SZB4	CI050_HUMAN	K	281	ENSP00000361556:Q281K	ENSP00000361556:Q281K	Q	-	1	0	C9orf50	131417623	0.001000	0.12720	0.007000	0.13788	0.529000	0.34654	0.062000	0.14389	0.316000	0.23135	0.434000	0.28630	CAG	.		0.642	C9orf50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054593.1	NM_199350	
BRWD3	254065	broad.mit.edu;bcgsc.ca	37	X	79946606	79946606	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chrX:79946606G>T	ENST00000373275.4	-	31	3764	c.3548C>A	c.(3547-3549)gCt>gAt	p.A1183D	BRWD3_ENST00000473691.1_5'UTR	NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	1183	Bromo 1. {ECO:0000255|PROSITE- ProRule:PRU00035}.				cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)					breast(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(39)|ovary(4)|prostate(2)|skin(3)	87						AGTTGGATAAGCAACTACAGT	0.358																																					p.A1183D													.	BRWD3	251	0			c.C3548A						.						78.0	75.0	76.0					X																	79946606		2202	4299	6501	SO:0001583	missense	254065	exon31			GGATAAGCAACTA		CCDS14447.1	Xq21.1	2013-01-09			ENSG00000165288	ENSG00000165288		"""WD repeat domain containing"""	17342	protein-coding gene	gene with protein product		300553				15543602, 16094372	Standard	NM_153252		Approved	FLJ38568, MRX93	uc004edt.3	Q6RI45	OTTHUMG00000021908	ENST00000373275.4:c.3548C>A	X.37:g.79946606G>T	ENSP00000362372:p.Ala1183Asp	Somatic	225	2		WXS	Illumina GAIIx	Phase_I	138	7	NM_153252	C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Missense_Mutation	SNP	ENST00000373275.4	37	CCDS14447.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.957549	0.73902	.	.	ENSG00000165288	ENST00000373275	T	0.18174	2.23	4.81	4.81	0.61882	Bromodomain (5);	0.051832	0.85682	D	0.000000	T	0.31513	0.0799	L	0.37897	1.145	0.58432	D	0.999999	D	0.71674	0.998	D	0.70487	0.969	T	0.02075	-1.1218	9	.	.	.	-14.8958	17.0235	0.86440	0.0:0.0:1.0:0.0	.	1183	Q6RI45	BRWD3_HUMAN	D	1183	ENSP00000362372:A1183D	.	A	-	2	0	BRWD3	79833262	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.263000	0.95617	2.197000	0.70478	0.600000	0.82982	GCT	.		0.358	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	NM_153252	
ATP11C	286410	broad.mit.edu;bcgsc.ca	37	X	138899055	138899055	+	Silent	SNP	A	A	G			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chrX:138899055A>G	ENST00000327569.3	-	4	392	c.294T>C	c.(292-294)ctT>ctC	p.L98L	ATP11C_ENST00000361648.2_Silent_p.L98L|ATP11C_ENST00000370543.1_Silent_p.L98L|ATP11C_ENST00000359686.2_Silent_p.L98L|ATP11C_ENST00000370557.1_Silent_p.L95L	NM_173694.4	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C	98					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|positive regulation of B cell differentiation (GO:0045579)|pre-B cell differentiation (GO:0002329)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(31)|ovary(5)|prostate(1)|skin(3)	75	Acute lymphoblastic leukemia(192;0.000127)					TAACAAAGAAAAGTGGAAGTC	0.353																																					p.L98L													.	ATP11C	319	0			c.T294C						.						84.0	78.0	80.0					X																	138899055		2203	4300	6503	SO:0001819	synonymous_variant	286410	exon4			AAAGAAAAGTGGA	AJ580094	CCDS14668.1, CCDS35410.1	Xq27.1	2011-06-09	2007-09-19		ENSG00000101974	ENSG00000101974		"""ATPases / P-type"""	13554	protein-coding gene	gene with protein product		300516	"""ATPase, Class VI, type 11C"""			11015572	Standard	NM_173694		Approved	ATPIG, ATPIQ	uc004faz.3	Q8NB49	OTTHUMG00000022538	ENST00000327569.3:c.294T>C	X.37:g.138899055A>G		Somatic	232	0		WXS	Illumina GAIIx	Phase_I	190	6	NM_001010986	Q5JT69|Q5JT70|Q5JT71|Q5JT72|Q5JT73|Q6ZND5|Q6ZU50|Q6ZUP7|Q70IJ9|Q70IK0|Q8WX24	Silent	SNP	ENST00000327569.3	37	CCDS14668.1																																																																																			.		0.353	ATP11C-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354945.1	NM_173694	
FN1	2335	ucsc.edu;bcgsc.ca	37	2	216271210	216271210	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr2:216271210G>T	ENST00000359671.1	-	19	3002	c.2737C>A	c.(2737-2739)Ctg>Atg	p.L913M	FN1_ENST00000357009.2_Missense_Mutation_p.L913M|FN1_ENST00000356005.4_Missense_Mutation_p.L913M|FN1_ENST00000323926.6_Missense_Mutation_p.L913M|FN1_ENST00000357867.4_Missense_Mutation_p.L913M|FN1_ENST00000354785.4_Missense_Mutation_p.L913M|FN1_ENST00000345488.5_Missense_Mutation_p.L913M|FN1_ENST00000446046.1_Missense_Mutation_p.L913M|FN1_ENST00000432072.2_Missense_Mutation_p.L913M|FN1_ENST00000421182.1_Missense_Mutation_p.L913M|FN1_ENST00000443816.1_Missense_Mutation_p.L913M|FN1_ENST00000346544.3_Missense_Mutation_p.L913M|FN1_ENST00000336916.4_Missense_Mutation_p.L913M			P02751	FINC_HUMAN	fibronectin 1	913	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316, ECO:0000255|PROSITE-ProRule:PRU00478, ECO:0000255|PROSITE-ProRule:PRU00479}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	ACAAACTGCAGGTCCCTGGGA	0.502																																					p.L913M													.	FN1	521	0			c.C2737A						.						63.0	54.0	57.0					2																	216271210		2203	4300	6503	SO:0001583	missense	2335	exon19			ACTGCAGGTCCCT		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"""Fibronectin type III domain containing"", ""Endogenous ligands"""	3778	protein-coding gene	gene with protein product	"""migration-stimulating factor"", ""cold-insoluble globulin"""	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.2737C>A	2.37:g.216271210G>T	ENSP00000352696:p.Leu913Met	Somatic	34	0		WXS	Illumina HiSeq		27	4	NM_212476	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	37		.	.	.	.	.	.	.	.	.	.	G	22.7	4.321389	0.81580	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005	T;T;T;T;T;T;T;T;T;T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14;-0.14;-0.14;-0.14;-0.14;-0.14;-0.14;-0.14;-0.14;-0.14	5.93	5.93	0.95920	.	0.000000	0.49916	D	0.000140	T	0.79393	0.4438	M	0.82056	2.57	0.80722	D	1	D;D;D;P;D;D;D;P;P;D	0.89917	0.999;0.995;1.0;0.832;0.998;0.995;1.0;0.832;0.832;0.999	D;D;D;P;D;D;D;P;P;D	0.87578	0.986;0.979;0.996;0.857;0.985;0.979;0.995;0.857;0.857;0.998	T	0.80564	-0.1326	10	0.59425	D	0.04	.	13.5241	0.61584	0.0709:0.0:0.9291:0.0	.	913;913;913;913;913;913;913;913;913;913	P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.	M	913	ENSP00000394423:L913M;ENSP00000323534:L913M;ENSP00000338200:L913M;ENSP00000350534:L913M;ENSP00000346839:L913M;ENSP00000352696:L913M;ENSP00000265312:L913M;ENSP00000273049:L913M;ENSP00000349509:L913M;ENSP00000410422:L913M;ENSP00000415018:L913M;ENSP00000399538:L913M;ENSP00000348285:L913M	ENSP00000265313:L913M	L	-	1	2	FN1	215979455	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	4.954000	0.63631	2.805000	0.96524	0.655000	0.94253	CTG	.		0.502	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476	
OR13H1	347468	ucsc.edu	37	X	130678378	130678378	+	Nonsense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chrX:130678378G>T	ENST00000338616.3	+	1	429	c.331G>T	c.(331-333)Gag>Tag	p.E111*		NM_001004486.1	NP_001004486.1	Q8NG92	O13H1_HUMAN	olfactory receptor, family 13, subfamily H, member 1	111						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	15	Acute lymphoblastic leukemia(192;0.000636)					GGCCACAGCAGAGTGCCTCCT	0.527																																					p.E111X													.	OR13H1	41	0			c.G331T						.						152.0	122.0	132.0					X																	130678378		2203	4300	6503	SO:0001587	stop_gained	347468	exon1			ACAGCAGAGTGCC		CCDS35396.1	Xq26.2	2012-08-23			ENSG00000171054	ENSG00000171054		"""GPCR / Class A : Olfactory receptors"""	14755	protein-coding gene	gene with protein product							Standard	NM_001004486		Approved		uc011muw.2	Q8NG92	OTTHUMG00000022411	ENST00000338616.3:c.331G>T	X.37:g.130678378G>T	ENSP00000340748:p.Glu111*	Somatic	38	0		WXS	Illumina HiSeq		35	4	NM_001004486	B2RNQ3|Q6IET8|Q96R12	Nonsense_Mutation	SNP	ENST00000338616.3	37	CCDS35396.1	.	.	.	.	.	.	.	.	.	.	G	13.11	2.138069	0.37728	.	.	ENSG00000171054	ENST00000338616	.	.	.	4.87	3.04	0.35103	.	0.000000	0.39909	U	0.001237	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	7.9412	0.29959	0.0954:0.1591:0.7454:0.0	.	.	.	.	X	111	.	ENSP00000340748:E111X	E	+	1	0	OR13H1	130506059	0.810000	0.29049	0.447000	0.26932	0.020000	0.10135	1.457000	0.35212	1.031000	0.39867	0.600000	0.82982	GAG	.		0.527	OR13H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058297.1		
PLEKHM2	23207	bcgsc.ca	37	1	16056369	16056369	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr1:16056369C>T	ENST00000375799.3	+	14	2380	c.2153C>T	c.(2152-2154)gCc>gTc	p.A718V	PLEKHM2_ENST00000477849.1_3'UTR|RP11-288I21.1_ENST00000453804.1_RNA|PLEKHM2_ENST00000375793.2_Missense_Mutation_p.A698V	NM_015164.2	NP_055979.2	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 2	718					Golgi organization (GO:0007030)	cytoplasm (GO:0005737)	kinesin binding (GO:0019894)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000259)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00057)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		CTGACGGATGCCACCATGGAG	0.537																																					p.A718V													.	PLEKHM2	94	0			c.C2153T						.						67.0	70.0	69.0					1																	16056369		1982	4169	6151	SO:0001583	missense	23207	exon14			CGGATGCCACCAT	AB020649	CCDS44063.1	1p36.13	2013-01-10			ENSG00000116786	ENSG00000116786		"""Pleckstrin homology (PH) domain containing"""	29131	protein-coding gene	gene with protein product		609613				10048485	Standard	NM_015164		Approved	KIAA0842	uc010obo.2	Q8IWE5	OTTHUMG00000003062	ENST00000375799.3:c.2153C>T	1.37:g.16056369C>T	ENSP00000364956:p.Ala718Val	Somatic	53	0		WXS	Illumina HiSeq	Phase_1	23	3	NM_015164	O94928|Q5VT65|Q6NUH9|Q7L8G1|Q8IVT7|Q8N2T4|Q96AY0|Q9NTF7	Missense_Mutation	SNP	ENST00000375799.3	37	CCDS44063.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.325274	0.81580	.	.	ENSG00000116786	ENST00000375799;ENST00000375793	T;T	0.52526	0.67;0.66	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.40670	0.1126	L	0.32530	0.975	0.80722	D	1	P	0.39809	0.689	B	0.35312	0.2	T	0.43228	-0.9404	10	0.66056	D	0.02	-27.3525	19.3302	0.94283	0.0:1.0:0.0:0.0	.	718	Q8IWE5	PKHM2_HUMAN	V	718;698	ENSP00000364956:A718V;ENSP00000364950:A698V	ENSP00000364950:A698V	A	+	2	0	PLEKHM2	15928956	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.263000	0.78421	2.572000	0.86782	0.591000	0.81541	GCC	.		0.537	PLEKHM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008463.1	NM_015164	
RAD54L	8438	bcgsc.ca	37	1	46733249	46733249	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr1:46733249G>T	ENST00000371975.4	+	9	1684	c.1010G>T	c.(1009-1011)aGc>aTc	p.S337I	RAD54L_ENST00000442598.1_Missense_Mutation_p.S337I|RAD54L_ENST00000473251.1_3'UTR	NM_003579.3	NP_003570.2	Q92698	RAD54_HUMAN	RAD54-like (S. cerevisiae)	337	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				chromosome organization (GO:0051276)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|meiotic nuclear division (GO:0007126)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			breast(2)|cervix(1)|kidney(3)|large_intestine(5)|liver(1)|lung(6)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	25	Acute lymphoblastic leukemia(166;0.155)	Breast(1374;0.0634)		KIRC - Kidney renal clear cell carcinoma(1967;0.000896)		GAGTATTTCAGCTTGGTACAT	0.493								Direct reversal of damage;Homologous recombination																													p.S337I													.	RAD54L	64	0			c.G1010T						.						74.0	73.0	73.0					1																	46733249		2203	4300	6503	SO:0001583	missense	8438	exon9			ATTTCAGCTTGGT	X97795	CCDS532.1	1p32	2008-02-05	2001-11-28		ENSG00000085999	ENSG00000085999			9826	protein-coding gene	gene with protein product		603615	"""RAD54 (S.cerevisiae)-like"""			8805304	Standard	NM_003579		Approved	hHR54, hRAD54, RAD54A	uc009vye.2	Q92698	OTTHUMG00000007772	ENST00000371975.4:c.1010G>T	1.37:g.46733249G>T	ENSP00000361043:p.Ser337Ile	Somatic	54	0		WXS	Illumina HiSeq	Phase_1	54	5	NM_003579	Q5TE31|Q6IUY3	Missense_Mutation	SNP	ENST00000371975.4	37	CCDS532.1	.	.	.	.	.	.	.	.	.	.	G	34	5.404941	0.96051	.	.	ENSG00000085999	ENST00000442598;ENST00000371975;ENST00000535499	D;D	0.94576	-3.46;-3.46	5.34	5.34	0.76211	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.98381	0.9462	H	0.97158	3.95	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.976;0.999	D	0.99628	1.0985	10	0.87932	D	0	-14.3922	19.0329	0.92965	0.0:0.0:1.0:0.0	.	157;337	G3V1N0;Q92698	.;RAD54_HUMAN	I	337;337;157	ENSP00000396113:S337I;ENSP00000361043:S337I	ENSP00000361043:S337I	S	+	2	0	RAD54L	46505836	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.524000	0.98036	2.486000	0.83907	0.561000	0.74099	AGC	.		0.493	RAD54L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021272.1	NM_003579	
Unknown	0	bcgsc.ca	37	2	229216901	229216901	+	IGR	SNP	G	G	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr2:229216901G>A								SPHKAP (170540 upstream) : AC009410.1 (131075 downstream)																							AAGAGAGCTGGCAGCCAGTAG	0.552																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			GAGCTGGCAGCCA																													2.37:g.229216901G>A		Somatic	42	0		WXS	Illumina HiSeq	Phase_1	26	10	.		RNA	SNP		37																																																																																				.	0	0.552								
FILIP1L	11259	bcgsc.ca	37	3	99568935	99568935	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr3:99568935G>T	ENST00000354552.3	-	5	2055	c.1585C>A	c.(1585-1587)Caa>Aaa	p.Q529K	FILIP1L_ENST00000383694.2_Missense_Mutation_p.Q289K|FILIP1L_ENST00000471562.1_Missense_Mutation_p.Q289K|FILIP1L_ENST00000331335.5_Missense_Mutation_p.Q529K|CMSS1_ENST00000496116.1_Intron|FILIP1L_ENST00000476723.1_Intron|FILIP1L_ENST00000487087.1_Missense_Mutation_p.Q105K|CMSS1_ENST00000421999.2_Intron	NM_182909.2	NP_878913.2	Q4L180	FIL1L_HUMAN	filamin A interacting protein 1-like	529						cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	35						ACTTTATTTTGCTCCACTTGA	0.348																																					p.Q529K													.	FILIP1L	154	0			c.C1585A						.						84.0	71.0	75.0					3																	99568935		1823	4084	5907	SO:0001583	missense	11259	exon5			TATTTTGCTCCAC		CCDS43117.1, CCDS43118.1, CCDS43119.1, CCDS63700.1, CCDS74969.1	3q12.1	2011-10-21			ENSG00000168386	ENSG00000168386			24589	protein-coding gene	gene with protein product	"""downregulated in ovarian cancer 1"", ""GPBP-interacting protein of 130 kDa"""	612993				8314147, 15935955, 21832087	Standard	NM_001282793		Approved	DOC-1, GIP130	uc003dtm.3	Q4L180	OTTHUMG00000159055	ENST00000354552.3:c.1585C>A	3.37:g.99568935G>T	ENSP00000346560:p.Gln529Lys	Somatic	34	0		WXS	Illumina HiSeq	Phase_1	21	3	NM_182909	B2CNV7|B2CNV8|Q13597|Q2YDY5|Q6KFX5|Q6KFX6|Q6KFX7|Q8IUM3|Q8N6Z0	Missense_Mutation	SNP	ENST00000354552.3	37	CCDS43117.1	.	.	.	.	.	.	.	.	.	.	G	14.59	2.582080	0.46006	.	.	ENSG00000168386	ENST00000354552;ENST00000487087;ENST00000471562;ENST00000331335;ENST00000383694;ENST00000441620;ENST00000495625	T;T;T;T;T;T	0.41758	0.99;1.72;1.69;0.99;1.69;1.69	5.87	4.97	0.65823	.	0.000000	0.50627	D	0.000107	T	0.34687	0.0906	L	0.53780	1.695	0.47276	D	0.999372	B;B	0.32526	0.374;0.257	B;B	0.33254	0.16;0.077	T	0.15178	-1.0446	10	0.02654	T	1	-8.705	13.0511	0.58954	0.0:0.1233:0.7486:0.1281	.	529;529	Q4L180-2;Q4L180	.;FIL1L_HUMAN	K	529;105;289;529;289;275;289	ENSP00000346560:Q529K;ENSP00000417774:Q105K;ENSP00000419642:Q289K;ENSP00000327880:Q529K;ENSP00000373192:Q289K;ENSP00000419874:Q289K	ENSP00000327880:Q529K	Q	-	1	0	FILIP1L	101051625	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.709000	0.74665	1.436000	0.47453	0.655000	0.94253	CAA	.		0.348	FILIP1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353069.1	NM_014890	
Unknown	0	bcgsc.ca	37	4	135967761	135967761	+	IGR	SNP	G	G	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr4:135967761G>A								RP11-192C21.2 (112475 upstream) : RP11-553P9.2 (20626 downstream)																							ATTGATTGCCGTTCTGGTAAA	0.478																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			ATTGCCGTTCTGG																													4.37:g.135967761G>A		Somatic	72	0		WXS	Illumina HiSeq	Phase_1	26	6	.		RNA	SNP		37																																																																																				.	0	0.478								
STOX2	56977	bcgsc.ca	37	4	184931278	184931278	+	Silent	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr4:184931278G>T	ENST00000308497.4	+	3	2722	c.1287G>T	c.(1285-1287)gtG>gtT	p.V429V	STOX2_ENST00000438269.1_Silent_p.V429V	NM_020225.1	NP_064610.1	Q9P2F5	STOX2_HUMAN	storkhead box 2	429					embryo development (GO:0009790)|maternal placenta development (GO:0001893)					breast(1)|endometrium(7)|lung(6)	14		all_lung(41;1.89e-12)|Lung NSC(41;3.48e-12)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|all_hematologic(60;0.027)|Prostate(90;0.0283)		all cancers(43;2.85e-26)|Epithelial(43;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-10)|Colorectal(24;8.23e-06)|GBM - Glioblastoma multiforme(59;1.64e-05)|STAD - Stomach adenocarcinoma(60;3.6e-05)|COAD - Colon adenocarcinoma(29;4.37e-05)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.227)		ACACAAACGTgctcgagtccc	0.483																																					p.V429V													.	STOX2	142	0			c.G1287T						.						51.0	53.0	52.0					4																	184931278		2039	4197	6236	SO:0001819	synonymous_variant	56977	exon3			AAACGTGCTCGAG	AB037813	CCDS47167.1	4q35.1	2014-09-11			ENSG00000173320	ENSG00000173320			25450	protein-coding gene	gene with protein product							Standard	XM_005263142		Approved	DKFZp762K222	uc003ivz.1	Q9P2F5	OTTHUMG00000160618	ENST00000308497.4:c.1287G>T	4.37:g.184931278G>T		Somatic	52	0		WXS	Illumina HiSeq	Phase_1	19	3	NM_020225	A6H8U4|Q9NPS8	Silent	SNP	ENST00000308497.4	37	CCDS47167.1																																																																																			.		0.483	STOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361433.3	NM_020225	
DHX16	8449	bcgsc.ca	37	6	30638651	30638651	+	Silent	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr6:30638651C>T	ENST00000376442.3	-	3	720	c.525G>A	c.(523-525)ctG>ctA	p.L175L		NM_001164239.1|NM_003587.4	NP_001157711.1|NP_003578.2	O60231	DHX16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 16	175					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			kidney(2)|ovary(2)	4						CACGCTCCTCCAGGTCCTGAA	0.567																																					p.L175L													.	DHX16	119	0			c.G525A						.						151.0	110.0	124.0					6																	30638651		1511	2709	4220	SO:0001819	synonymous_variant	8449	exon3			CTCCTCCAGGTCC	AB001601	CCDS4685.1	6p21.3	2010-02-17	2003-06-13	2003-06-20	ENSG00000204560	ENSG00000204560		"""DEAH-boxes"""	2739	protein-coding gene	gene with protein product		603405	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 16"""	DDX16		9547260	Standard	NM_003587		Approved	DBP2, Prp2, PRPF2	uc003nqz.3	O60231	OTTHUMG00000031060	ENST00000376442.3:c.525G>A	6.37:g.30638651C>T		Somatic	27	0		WXS	Illumina HiSeq	Phase_1	22	3	NM_003587	O60322|Q5JP45|Q969X7|Q96QC1	Silent	SNP	ENST00000376442.3	37	CCDS4685.1																																																																																			.		0.567	DHX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076076.2	NM_003587	
RPL23AP48	728567	bcgsc.ca	37	6	122001472	122001472	+	IGR	SNP	C	C	T	rs200498403|rs562728329		TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr6:122001472C>T								RNU2-8P (99805 upstream) : RNU1-18P (531321 downstream)																							ctttttttttctttttttttt	0.463																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			TTTTTTCTTTTTT																													6.37:g.122001472C>T		Somatic	78	1		WXS	Illumina HiSeq	Phase_1	42	4	.		RNA	SNP		37																																																																																				.	0	0.463								
Unknown	0	bcgsc.ca	37	6	138028222	138028222	+	IGR	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr6:138028222G>T								RP11-95M15.1 (32531 upstream) : AL357060.1 (9862 downstream)																							AATGGAACATGTGAAGTCTCC	0.458																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			GAACATGTGAAGT																													6.37:g.138028222G>T		Somatic	41	0		WXS	Illumina HiSeq	Phase_1	26	4	.		RNA	SNP		37																																																																																				.	0	0.458								
PAXIP1	22976	bcgsc.ca	37	7	154753289	154753289	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr7:154753289C>T	ENST00000404141.1	-	11	2351	c.2197G>A	c.(2197-2199)Gcc>Acc	p.A733T	PAXIP1_ENST00000473219.1_5'UTR|PAXIP1_ENST00000397192.1_Missense_Mutation_p.A733T			Q6ZW49	PAXI1_HUMAN	PAX interacting (with transcription-activation domain) protein 1	733	BRCT 4. {ECO:0000255|PROSITE- ProRule:PRU00033}.|Interaction with TP53BP1.				adipose tissue development (GO:0060612)|chorion development (GO:0060717)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|endothelial cell migration (GO:0043542)|histone H3-K4 methylation (GO:0051568)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K36 methylation (GO:0000416)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of isotype switching (GO:0045830)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	33	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0296)	UCEC - Uterine corpus endometrioid carcinoma (81;0.178)		GTATATTTGGCACCTGCCAAA	0.333																																					p.A733T													.	PAXIP1	150	0			c.G2197A						.						50.0	48.0	49.0					7																	154753289		1837	4093	5930	SO:0001583	missense	22976	exon11			ATTTGGCACCTGC	U80735	CCDS47753.1	7q36	2007-07-06	2005-04-05	2005-04-05	ENSG00000157212	ENSG00000157212			8624	protein-coding gene	gene with protein product		608254	"""PAX transcription activation domain interacting protein 1 like"""	PAXIP1L		9225980	Standard	XM_005249539		Approved	CAGF29, CAGF28, TNRC2, PTIP	uc022aqf.1	Q6ZW49	OTTHUMG00000151322	ENST00000404141.1:c.2197G>A	7.37:g.154753289C>T	ENSP00000384048:p.Ala733Thr	Somatic	60	0		WXS	Illumina HiSeq	Phase_1	66	4	NM_007349	O15404|Q6N099|Q6ZWH9|Q7Z315|Q86UN0|Q8N4P9|Q96HP2	Missense_Mutation	SNP	ENST00000404141.1	37	CCDS47753.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.110057	0.77210	.	.	ENSG00000157212	ENST00000404141;ENST00000397192;ENST00000357094;ENST00000323199	T;T	0.57107	0.42;0.42	5.08	5.08	0.68730	BRCT (3);	0.000000	0.52532	U	0.000062	T	0.81108	0.4754	H	0.94222	3.51	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	D	0.86610	0.1872	10	0.72032	D	0.01	-24.234	18.8369	0.92167	0.0:1.0:0.0:0.0	.	686;699;733	B4DEQ6;Q6ZW49-1;Q6ZW49	.;.;PAXI1_HUMAN	T	733;733;557;686	ENSP00000384048:A733T;ENSP00000380376:A733T	ENSP00000319149:A686T	A	-	1	0	PAXIP1	154384222	1.000000	0.71417	0.976000	0.42696	0.693000	0.40251	7.158000	0.77470	2.504000	0.84457	0.655000	0.94253	GCC	.		0.333	PAXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322223.1	NM_007349	
PHYHD1	254295	bcgsc.ca	37	9	131704026	131704026	+	3'UTR	SNP	C	C	T	rs141466531		TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr9:131704026C>T	ENST00000372592.3	+	0	1843				PHYHD1_ENST00000353176.5_3'UTR|PHYHD1_ENST00000308941.5_Silent_p.P296P|PHYHD1_ENST00000421063.2_3'UTR|RP11-101E3.5_ENST00000482796.1_Intron	NM_001100876.1	NP_001094346.1	Q5SRE7	PHYD1_HUMAN	phytanoyl-CoA dioxygenase domain containing 1								dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|skin(1)|stomach(3)	10						TCGCCCCTCCCGGGTGAAGCT	0.607																																					p.P296P													.	PHYHD1	29	0			c.C888T						.	C	,,	1,4405	2.1+/-5.4	0,1,2202	42.0	43.0	42.0		,,888	-10.1	0.0	9	dbSNP_134	42	0,8600		0,0,4300	no	utr-3,utr-3,coding-synonymous	PHYHD1	NM_001100876.1,NM_001100877.1,NM_174933.3	,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,	,,296/298	131704026	1,13005	2203	4300	6503	SO:0001624	3_prime_UTR_variant	254295	exon12			CCCTCCCGGGTGA	BC051300	CCDS6914.1, CCDS43885.1, CCDS43886.1	9q34.13	2010-08-13			ENSG00000175287	ENSG00000175287			23396	protein-coding gene	gene with protein product						12477932	Standard	NM_174933		Approved	MGC16638	uc004bwp.2	Q5SRE7	OTTHUMG00000020764	ENST00000372592.3:c.*34C>T	9.37:g.131704026C>T		Somatic	30	0		WXS	Illumina HiSeq	Phase_1	15	3	NM_174933	A6PWN9|A6PWP0|B3KT57|B4E3X8|Q5SRE9|Q5SRF0|Q7Z623|Q7Z7P9|Q96GM4	Silent	SNP	ENST00000372592.3	37	CCDS43885.1																																																																																			C|1.000;T|0.000		0.607	PHYHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054506.2	NM_174933	
ATG2A	23130	bcgsc.ca	37	11	64676552	64676552	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr11:64676552G>T	ENST00000377264.3	-	16	2387	c.2275C>A	c.(2275-2277)Ctg>Atg	p.L759M	ATG2A_ENST00000421419.2_Missense_Mutation_p.L759M	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	759					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						GACAGCTCCAGTTCCTCTCCC	0.617																																					p.L759M													.	ATG2A	133	0			c.C2275A						.						88.0	60.0	69.0					11																	64676552		2200	4297	6497	SO:0001583	missense	23130	exon16			GCTCCAGTTCCTC		CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"""ATG2 autophagy related 2 homolog A (S. cerevisiae)"""			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.2275C>A	11.37:g.64676552G>T	ENSP00000366475:p.Leu759Met	Somatic	84	0		WXS	Illumina HiSeq	Phase_1	51	5	NM_015104	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Missense_Mutation	SNP	ENST00000377264.3	37	CCDS31602.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.56|13.56	2.274449|2.274449	0.40194|0.40194	.|.	.|.	ENSG00000110046|ENSG00000110046	ENST00000421419;ENST00000377264|ENST00000418259	T;T|.	0.07567|.	3.18;3.18|.	4.77|4.77	4.77|4.77	0.60923|0.60923	.|.	0.570926|.	0.17286|.	N|.	0.179822|.	T|T	0.48502|0.48502	0.1503|0.1503	L|L	0.47716|0.47716	1.5|1.5	0.29615|0.29615	N|N	0.846661|0.846661	P|.	0.34977|.	0.478|.	B|.	0.27887|.	0.084|.	T|T	0.44574|0.44574	-0.9319|-0.9319	10|5	0.35671|.	T|.	0.21|.	.|.	10.7062|10.7062	0.45956|0.45956	0.0:0.0:0.8098:0.1902|0.0:0.0:0.8098:0.1902	.|.	759|.	Q2TAZ0|.	ATG2A_HUMAN|.	M|N	759|560	ENSP00000410522:L759M;ENSP00000366475:L759M|.	ENSP00000366475:L759M|.	L|T	-|-	1|2	2|0	ATG2A|ATG2A	64433128|64433128	0.991000|0.991000	0.36638|0.36638	0.992000|0.992000	0.48379|0.48379	0.397000|0.397000	0.30659|0.30659	2.062000|2.062000	0.41413|0.41413	2.644000|2.644000	0.89710|0.89710	0.655000|0.655000	0.94253|0.94253	CTG|ACT	.		0.617	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104	
MRPL48	51642	bcgsc.ca	37	11	73536794	73536794	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr11:73536794C>T	ENST00000310614.7	+	4	810	c.154C>T	c.(154-156)Ccc>Tcc	p.P52S	MRPL48_ENST00000411840.2_5'UTR|MRPL48_ENST00000542303.1_Missense_Mutation_p.P52S|MRPL48_ENST00000535529.1_Missense_Mutation_p.P34S|MRPL48_ENST00000398483.3_5'UTR	NM_016055.5	NP_057139.1	Q96GC5	RM48_HUMAN	mitochondrial ribosomal protein L48	52						mitochondrial ribosome (GO:0005761)				kidney(1)	1						CAAGACAAAGCCCACCCACGG	0.398																																					p.P52S													.	MRPL48	16	0			c.C154T						.						42.0	42.0	42.0					11																	73536794		1848	4076	5924	SO:0001583	missense	51642	exon4			ACAAAGCCCACCC	AF151876	CCDS44676.1	11q13.4	2012-09-13			ENSG00000175581	ENSG00000175581		"""Mitochondrial ribosomal proteins / large subunits"""	16653	protein-coding gene	gene with protein product		611853				10810093	Standard	NM_016055		Approved	CGI-118	uc001ouh.4	Q96GC5	OTTHUMG00000168048	ENST00000310614.7:c.154C>T	11.37:g.73536794C>T	ENSP00000308717:p.Pro52Ser	Somatic	63	0		WXS	Illumina HiSeq	Phase_1	61	4	NM_016055	B4DN34|Q49AK7|Q4U2Q4|Q9P091|Q9Y5J0	Missense_Mutation	SNP	ENST00000310614.7	37	CCDS44676.1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.443545	0.43429	.	.	ENSG00000175581	ENST00000310614;ENST00000535529;ENST00000542303	T;T	0.79033	-0.91;-1.23	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.88005	0.6321	M	0.81497	2.545	0.49915	D	0.999836	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.87880	0.2677	10	0.52906	T	0.07	-28.465	14.8661	0.70416	0.0:1.0:0.0:0.0	.	34;52	B4DN34;Q96GC5	.;RM48_HUMAN	S	52;34;52	ENSP00000308717:P52S;ENSP00000443685:P52S	ENSP00000308717:P52S	P	+	1	0	MRPL48	73214442	1.000000	0.71417	0.994000	0.49952	0.716000	0.41182	1.976000	0.40579	2.890000	0.99128	0.585000	0.79938	CCC	.		0.398	MRPL48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397733.1	NM_016055	
Unknown	0	bcgsc.ca	37	12	75057793	75057793	+	IGR	SNP	C	C	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr12:75057793C>A								ATXN7L3B (122570 upstream) : RP11-81K13.1 (356955 downstream)																							GGACAGGAAGCTGCTTCTCAC	0.458																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			AGGAAGCTGCTTC																													12.37:g.75057793C>A		Somatic	20	0		WXS	Illumina HiSeq	Phase_1	14	3	.		RNA	SNP		37																																																																																				.	0	0.458								
Unknown	0	bcgsc.ca	37	14	19443807	19443807	+	IGR	SNP	A	A	G			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr14:19443807A>G								RP11-536C10.16 (29909 upstream) : MED15P1 (56038 downstream)																							ATCTCTCACCATCTTGACTGC	0.418																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			CTCACCATCTTGA																													14.37:g.19443807A>G		Somatic	24	0		WXS	Illumina HiSeq	Phase_1	19	5	.		RNA	SNP		37																																																																																				.	0	0.418								
TRDC	28526	bcgsc.ca	37	14	22932181	22932181	+	RNA	SNP	G	G	T			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr14:22932181G>T	ENST00000390477.2	+	0	258				AE000661.37_ENST00000514473.2_RNA|AE000661.37_ENST00000556777.1_RNA			B7Z8K6	TRDC_HUMAN	T cell receptor delta constant							integral component of membrane (GO:0016021)											CACTGACTTTGAAGTGAAGAC	0.408																																					.													.	.	.	0			.						.						76.0	75.0	75.0					14																	22932181		1866	4120	5986			0	.			GACTTTGAAGTGA	M22148		14q11.2	2012-02-07			ENSG00000211829	ENSG00000211829		"""T cell receptors / TRD locus"""	12253	other	T cell receptor gene		186810					Standard	NG_001332		Approved			B7Z8K6	OTTHUMG00000170905		14.37:g.22932181G>T		Somatic	42	0		WXS	Illumina HiSeq	Phase_1	54	4	.		RNA	SNP	ENST00000390477.2	37																																																																																				.		0.408	TRDC-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	TR_C_gene	TR_C_gene	OTTHUMT00000410936.1	NG_001332	
ZNF821	55565	bcgsc.ca	37	16	71894006	71894006	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr16:71894006T>C	ENST00000565601.1	-	7	1561	c.1154A>G	c.(1153-1155)cAg>cGg	p.Q385R	ZNF821_ENST00000446827.2_Missense_Mutation_p.Q343R|ATXN1L_ENST00000569119.1_Intron|ZNF821_ENST00000313565.6_Missense_Mutation_p.Q343R|ZNF821_ENST00000564134.1_3'UTR|ZNF821_ENST00000425432.1_Missense_Mutation_p.Q385R	NM_001201553.1	NP_001188482.1	O75541	ZN821_HUMAN	zinc finger protein 821	385					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(2)	13						TACAGGCAGCTGGAAGAAGTT	0.547																																					p.Q385R													.	ZNF821	25	0			c.A1154G						.						71.0	59.0	63.0					16																	71894006		2198	4300	6498	SO:0001583	missense	55565	exon7			GGCAGCTGGAAGA	AF070588	CCDS32481.1, CCDS56006.1, CCDS73911.1	16q22.3	2008-05-02				ENSG00000102984		"""Zinc fingers, C2H2-type"""	28043	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_017530		Approved		uc021tlb.1	O75541		ENST00000565601.1:c.1154A>G	16.37:g.71894006T>C	ENSP00000455648:p.Gln385Arg	Somatic	31	0		WXS	Illumina HiSeq	Phase_1	17	3	NM_001201553	A6NK48|B4DKK4|D3DWS3	Missense_Mutation	SNP	ENST00000565601.1	37	CCDS56006.1	.	.	.	.	.	.	.	.	.	.	T	17.60	3.429009	0.62844	.	.	ENSG00000102984	ENST00000425432;ENST00000313565;ENST00000446827	T;T;T	0.01613	6.34;4.73;4.73	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.02267	0.0070	N	0.19112	0.55	0.48341	D	0.999635	D;P;D	0.55385	0.971;0.718;0.971	P;B;P	0.45712	0.491;0.277;0.491	T	0.63563	-0.6609	10	0.87932	D	0	-19.1509	13.2153	0.59856	0.0:0.0:0.1324:0.8676	.	385;343;385	B4DKK4;O75541-2;O75541	.;.;ZN821_HUMAN	R	385;343;343	ENSP00000398089:Q385R;ENSP00000313822:Q343R;ENSP00000405908:Q343R	ENSP00000313822:Q343R	Q	-	2	0	ZNF821	70451507	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	4.731000	0.62022	2.367000	0.80283	0.528000	0.53228	CAG	.		0.547	ZNF821-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434180.1	NM_017530	
SPATA20	64847	bcgsc.ca	37	17	48625960	48625960	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr17:48625960C>A	ENST00000356488.4	+	3	377	c.294C>A	c.(292-294)aaC>aaA	p.N98K	SPATA20_ENST00000393244.3_Missense_Mutation_p.N54K|SPATA20_ENST00000511937.1_3'UTR|SPATA20_ENST00000006658.6_Missense_Mutation_p.N114K	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	98					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			GGAAGGAAAACAAGCCGATTT	0.642																																					p.N114K													.	SPATA20	59	0			c.C342A						.						80.0	91.0	87.0					17																	48625960		2203	4300	6503	SO:0001583	missense	64847	exon4			GGAAAACAAGCCG		CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"""hypothetical protein FLJ21347"""	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.294C>A	17.37:g.48625960C>A	ENSP00000348878:p.Asn98Lys	Somatic	74	0		WXS	Illumina HiSeq	Phase_1	55	4	NM_022827	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Missense_Mutation	SNP	ENST00000356488.4	37	CCDS58563.1	.	.	.	.	.	.	.	.	.	.	C	17.28	3.350880	0.61183	.	.	ENSG00000006282	ENST00000006658;ENST00000356488;ENST00000393244	T;T;T	0.50277	0.75;0.75;0.75	4.59	3.59	0.41128	Thioredoxin-like fold (2);Domain of unknown function DUF255 (1);	0.152960	0.56097	D	0.000021	T	0.58323	0.2114	M	0.90759	3.145	0.45354	D	0.998349	P;P;P	0.48350	0.792;0.834;0.909	P;B;B	0.47251	0.542;0.407;0.355	T	0.65952	-0.6043	10	0.54805	T	0.06	-17.0743	9.0329	0.36269	0.0:0.8324:0.0:0.1676	.	98;98;114	B4DZC5;Q8TB22;Q8TB22-2	.;SPT20_HUMAN;.	K	114;98;54	ENSP00000006658:N114K;ENSP00000348878:N98K;ENSP00000376935:N54K	ENSP00000006658:N114K	N	+	3	2	SPATA20	45980959	1.000000	0.71417	1.000000	0.80357	0.773000	0.43773	1.623000	0.37008	2.368000	0.80403	0.561000	0.74099	AAC	.		0.642	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827	
LPHN1	22859	bcgsc.ca	37	19	14267774	14267774	+	Missense_Mutation	SNP	C	C	T	rs560004956		TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr19:14267774C>T	ENST00000340736.6	-	16	3241	c.2944G>A	c.(2944-2946)Gct>Act	p.A982T	CTB-55O6.12_ENST00000592086.1_RNA|CTB-55O6.12_ENST00000588387.1_RNA|CTB-55O6.12_ENST00000588658.1_RNA|LPHN1_ENST00000361434.3_Missense_Mutation_p.A977T	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	982					calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|heterophilic cell-cell adhesion (GO:0007157)|neuropeptide signaling pathway (GO:0007218)|positive regulation of synapse maturation (GO:0090129)	axon (GO:0030424)|cell junction (GO:0030054)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TCAATGGCAGCCGCGATGCCC	0.627																																					p.A982T													.	LPHN1	107	0			c.G2944A						.						47.0	38.0	41.0					19																	14267774		2202	4300	6502	SO:0001583	missense	22859	exon16			TGGCAGCCGCGAT	AB020628	CCDS12307.1, CCDS32928.1	19p13.2	2014-08-08				ENSG00000072071		"""-"", ""GPCR / Class B : Orphans"""	20973	protein-coding gene	gene with protein product						10994649	Standard	NM_014921		Approved	KIAA0821, CIRL1, LEC2	uc010xnn.2	O94910		ENST00000340736.6:c.2944G>A	19.37:g.14267774C>T	ENSP00000340688:p.Ala982Thr	Somatic	63	0		WXS	Illumina HiSeq	Phase_1	46	4	NM_001008701	Q96IE7|Q9BU07|Q9HAR3	Missense_Mutation	SNP	ENST00000340736.6	37	CCDS32928.1	.	.	.	.	.	.	.	.	.	.	C	17.59	3.426772	0.62733	.	.	ENSG00000072071	ENST00000340736;ENST00000361434	T;T	0.37058	1.22;1.22	4.83	3.79	0.43588	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.42381	0.1200	L	0.60455	1.87	0.58432	D	0.999991	P;P	0.50066	0.454;0.931	B;P	0.49085	0.347;0.6	T	0.42310	-0.9459	10	0.87932	D	0	.	11.1369	0.48378	0.0:0.9088:0.0:0.0912	.	977;982	O94910-2;O94910	.;LPHN1_HUMAN	T	982;977	ENSP00000340688:A982T;ENSP00000355328:A977T	ENSP00000340688:A982T	A	-	1	0	LPHN1	14128774	1.000000	0.71417	0.058000	0.19502	0.828000	0.46876	5.992000	0.70609	1.164000	0.42652	0.561000	0.74099	GCT	.		0.627	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921	
ZNF546	339327	bcgsc.ca	37	19	40520472	40520472	+	Missense_Mutation	SNP	G	G	A	rs199852460		TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr19:40520472G>A	ENST00000347077.4	+	7	1511	c.1295G>A	c.(1294-1296)cGt>cAt	p.R432H	ZNF546_ENST00000600094.1_Missense_Mutation_p.R406H|ZNF546_ENST00000596894.1_Intron	NM_178544.3	NP_848639.2	Q86UE3	ZN546_HUMAN	zinc finger protein 546	432					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(15)|lung(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)	34	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					GCTCGACATCGTAGAATTCAT	0.388																																					p.R432H													ZNF546,NS,carcinoma,0,2	ZNF546	93	0			c.G1295A						.						48.0	51.0	50.0					19																	40520472		2203	4299	6502	SO:0001583	missense	339327	exon7			GACATCGTAGAAT	BC045649	CCDS12548.1	19q13.2	2013-01-08				ENSG00000187187		"""Zinc fingers, C2H2-type"", ""-"""	28671	protein-coding gene	gene with protein product				ZNF49		12477932	Standard	XM_005258853		Approved	MGC43537	uc002oms.2	Q86UE3		ENST00000347077.4:c.1295G>A	19.37:g.40520472G>A	ENSP00000339823:p.Arg432His	Somatic	51	0		WXS	Illumina HiSeq	Phase_1	43	4	NM_178544	A8K913	Missense_Mutation	SNP	ENST00000347077.4	37	CCDS12548.1	.	.	.	.	.	.	.	.	.	.	a	8.172	0.791803	0.16258	.	.	ENSG00000187187	ENST00000347077;ENST00000392042	T	0.07688	3.17	2.69	1.62	0.23740	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06508	0.0167	L	0.31120	0.905	0.09310	N	1	B;B	0.09022	0.002;0.0	B;B	0.11329	0.006;0.0	T	0.36648	-0.9739	9	0.49607	T	0.09	.	6.2676	0.20936	0.7535:0.0:0.2465:0.0	.	406;432	B3KVL3;Q86UE3	.;ZN546_HUMAN	H	432;69	ENSP00000339823:R432H	ENSP00000339823:R432H	R	+	2	0	ZNF546	45212312	0.000000	0.05858	0.619000	0.29118	0.984000	0.73092	-0.310000	0.08135	0.007000	0.14760	-0.254000	0.11334	CGT	.		0.388	ZNF546-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462495.2	NM_178544	
ANKRD30BP1	642460	bcgsc.ca	37	21	14768303	14768303	+	IGR	SNP	T	T	C			TCGA-W5-AA2G-01A-11D-A417-09	TCGA-W5-AA2G-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	47619547-f613-400f-9d49-51447acdff69	41c0feef-88a9-4742-9c2b-15c3851dba8d	g.chr21:14768303T>C								AL050302.1 (22917 upstream) : MIR3156-3 (10401 downstream)																							TATTTTGCCATTTGTTGTCTT	0.294																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	642460	.			TTGCCATTTGTTG																													21.37:g.14768303T>C		Somatic	56	0		WXS	Illumina HiSeq	Phase_1	43	6	.		RNA	SNP		37																																																																																				.	0	0.294								
