#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
MAGEA1	4100	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	X	152482527	152482527	+	Frame_Shift_Del	DEL	C	C	-			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chrX:152482527delC	ENST00000356661.5	-	3	702	c.484delG	c.(484-486)gcafs	p.A162fs		NM_004988.4	NP_004979.3	P43355	MAGA1_HUMAN	melanoma antigen family A, 1 (directs expression of antigen MZ2-E)	162	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone deacetylase binding (GO:0042826)			breast(1)|central_nervous_system(7)|kidney(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GTGGGGTCTGCTTCCTTCACG	0.517																																					p.A162fs		.											.	.	.	0			c.485delC						.						122.0	113.0	116.0					X																	152482527		2203	4300	6503	SO:0001589	frameshift_variant	4100	exon3			GGTCTGCTTCCTT		CCDS76051.1	Xq28	2010-05-26			ENSG00000198681	ENSG00000198681			6796	protein-coding gene	gene with protein product	"""melanoma-associated antigen 1"", ""melanoma-associated antigen MZ2-E"", ""melanoma antigen MAGE-1"", ""melanoma antigen family A 1"", ""cancer/testis antigen family 1, member 1"""	300016		MAGE1		1840703	Standard	NM_004988		Approved	MGC9326, CT1.1	uc004fhf.2	P43355	OTTHUMG00000024192	ENST00000356661.5:c.484delG	X.37:g.152482527delC	ENSP00000349085:p.Ala162fs	Somatic	63	0		WXS	Illumina HiSeq	.	71	24	NM_004988	B2RC81|O00346	Frame_Shift_Del	DEL	ENST00000356661.5	37	CCDS14720.1																																																																																			.		0.517	MAGEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060940.1	NM_004988	
CLIP4	79745	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	2	29366790	29366792	+	In_Frame_Del	DEL	TGT	TGT	-			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr2:29366790_29366792delTGT	ENST00000320081.5	+	7	1119_1121	c.864_866delTGT	c.(862-867)cgtgtt>cgt	p.V290del	CLIP4_ENST00000401617.2_In_Frame_Del_p.V183del|CLIP4_ENST00000404424.1_In_Frame_Del_p.V290del|CLIP4_ENST00000401605.1_In_Frame_Del_p.V290del	NM_024692.4	NP_078968.3	Q8N3C7	CLIP4_HUMAN	CAP-GLY domain containing linker protein family, member 4	290										endometrium(4)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(1)	26	Acute lymphoblastic leukemia(172;0.155)					TGGGGGATCGTGTTGTTATTGCA	0.458																																					p.288_289del		.											.	.	.	0			c.863_865del						.																																			SO:0001651	inframe_deletion	79745	exon7			GGATCGTGTTGTT	AK024722	CCDS1770.1, CCDS74502.1	2p23	2013-01-10	2007-01-04	2007-01-04	ENSG00000115295	ENSG00000115295		"""Ankyrin repeat domain containing"""	26108	protein-coding gene	gene with protein product			"""restin-like 2"""	RSNL2			Standard	XM_005264562		Approved	FLJ21069	uc002rmv.3	Q8N3C7	OTTHUMG00000097837	ENST00000320081.5:c.864_866delTGT	2.37:g.29366793_29366795delTGT	ENSP00000327009:p.Val290del	Somatic	35	0		WXS	Illumina HiSeq	.	61	16	NM_024692	A0AV10|B2RMQ3|B7Z7N8|Q7Z4U3|Q96BR7|Q96MA5|Q9H7C0	In_Frame_Del	DEL	ENST00000320081.5	37	CCDS1770.1																																																																																			.		0.458	CLIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215123.2	NM_024692	
IBSP	3381	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	4	88732730	88732732	+	In_Frame_Del	DEL	GGA	GGA	-			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr4:88732730_88732732delGGA	ENST00000226284.5	+	7	689_691	c.622_624delGGA	c.(622-624)ggadel	p.G208del		NM_004967.3	NP_004958.2	P21815	SIAL_HUMAN	integrin-binding sialoprotein	208					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cellular response to growth factor stimulus (GO:0071363)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|membrane-bounded vesicle (GO:0031988)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)	21		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000333)|COAD - Colon adenocarcinoma(81;0.154)		AAGTGTCACTGGAGCCAATGCAG	0.547																																					p.207_208del		.											IBSP,NS,carcinoma,0,1	IBSP	0	0			c.621_623del						.																																			SO:0001651	inframe_deletion	3381	exon7			GTCACTGGAGCCA		CCDS3624.1	4q21.1	2008-07-28	2008-07-28		ENSG00000029559	ENSG00000029559			5341	protein-coding gene	gene with protein product	"""bone sialoprotein"", ""bone sialoprotein II"""	147563				8406493	Standard	NM_004967		Approved	BSP, SP-II, BSP-II	uc003hqx.4	P21815	OTTHUMG00000130600	ENST00000226284.5:c.622_624delGGA	4.37:g.88732730_88732732delGGA	ENSP00000226284:p.Gly208del	Somatic	39	0		WXS	Illumina HiSeq	.	54	18	NM_004967		In_Frame_Del	DEL	ENST00000226284.5	37	CCDS3624.1																																																																																			.		0.547	IBSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253050.2		
LINC00304	283860	hgsc.bcm.edu	37	16	89226805	89226873	+	lincRNA	DEL	CCCCCGCTTCCTCACCCGAAGACCCCCCGCTTCCTCACCCAAAGACCCCCCGCTTCCTTGCCCCGAAGA	CCCCCGCTTCCTCACCCGAAGACCCCCCGCTTCCTCACCCAAAGACCCCCCGCTTCCTTGCCCCGAAGA	-	rs377040896|rs199592398|rs113949453|rs570349537|rs202035945|rs537874533|rs117495642|rs200619525	byFrequency	TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	CCCCCGCTTCCTCACCCGAAGACCCCCCGCTTCCTCACCCAAAGACCCCCCGCTTCCTTGCCCCGAAGA	CCCCCGCTTCCTCACCCGAAGACCCCCCGCTTCCTCACCCAAAGACCCCCCGCTTCCTTGCCCCGAAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr16:89226805_89226873delCCCCCGCTTCCTCACCCGAAGACCCCCCGCTTCCTCACCCAAAGACCCCCCGCTTCCTTGCCCCGAAGA	ENST00000321214.2	+	0	527_595					NR_024347.2		Q8N9R0	CP081_HUMAN	long intergenic non-protein coding RNA 304																		ACCCGAAGACCCCCCGCTTCCTCACCCGAAGACCCCCCGCTTCCTCACCCAAAGACCCCCCGCTTCCTTGCCCCGAAGACCCCGCTTCC	0.665																																					.		.											.	.	.	0			.						.																																					283860	.			GAAGACCCCCCGC	AK094020		16q24.3	2012-11-19	2011-08-10	2011-08-10	ENSG00000180422	ENSG00000180422		"""Long non-coding RNAs"""	26713	non-coding RNA	RNA, long non-coding			"""chromosome 16 open reading frame 81"", ""non-protein coding RNA 304"""	C16orf81, NCRNA00304			Standard	NR_024347		Approved	FLJ36701	uc002fms.3	Q8N9R0	OTTHUMG00000175524		16.37:g.89226805_89226873delCCCCCGCTTCCTCACCCGAAGACCCCCCGCTTCCTCACCCAAAGACCCCCCGCTTCCTTGCCCCGAAGA		Somatic	95	0		WXS	Illumina HiSeq	.	139	0	.		RNA	DEL	ENST00000321214.2	37																																																																																				.		0.665	LINC00304-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000430368.1	NR_024347	
MAGEA1	4100	hgsc.bcm.edu	37	X	152482527	152482528	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chrX:152482527_152482528delCT	ENST00000356661.5	-	3	701_702	c.483_484delAG	c.(481-486)gaagcafs	p.EA161fs		NM_004988.4	NP_004979.3	P43355	MAGA1_HUMAN	melanoma antigen family A, 1 (directs expression of antigen MZ2-E)	161	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone deacetylase binding (GO:0042826)			breast(1)|central_nervous_system(7)|kidney(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GTGGGGTCTGCTTCCTTCACGT	0.515																																					p.162_162del		.											.	.	.	0			c.484_485del						.																																			SO:0001589	frameshift_variant	4100	exon3			GGTCTGCTTCCTT		CCDS76051.1	Xq28	2010-05-26			ENSG00000198681	ENSG00000198681			6796	protein-coding gene	gene with protein product	"""melanoma-associated antigen 1"", ""melanoma-associated antigen MZ2-E"", ""melanoma antigen MAGE-1"", ""melanoma antigen family A 1"", ""cancer/testis antigen family 1, member 1"""	300016		MAGE1		1840703	Standard	NM_004988		Approved	MGC9326, CT1.1	uc004fhf.2	P43355	OTTHUMG00000024192	ENST00000356661.5:c.483_484delAG	X.37:g.152482527_152482528delCT	ENSP00000349085:p.Glu161fs	Somatic	63	0		WXS	Illumina HiSeq	.	71	0	NM_004988	B2RC81|O00346	Frame_Shift_Del	DEL	ENST00000356661.5	37	CCDS14720.1																																																																																			.		0.515	MAGEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060940.1	NM_004988	
MT-CO1	4512	hgsc.bcm.edu	37	M	5801	5801	+	5'Flank	SNP	T	T	C			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chrM:5801T>C	ENST00000361624.2	+	0	0				MT-RNR2_ENST00000387347.2_RNA|MT-TW_ENST00000387382.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-TA_ENST00000387392.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-ATP8_ENST00000361851.1_5'Flank|MT-TL1_ENST00000386347.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-CO2_ENST00000361739.1_5'Flank|MT-TQ_ENST00000387372.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-TI_ENST00000387365.1_RNA|MT-ATP6_ENST00000361899.2_5'Flank			P00395	COX1_HUMAN	mitochondrially encoded cytochrome c oxidase I						aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidative phosphorylation (GO:0006119)|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 IV (GO:0005751)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(4)|endometrium(25)|kidney(19)|lung(3)|prostate(3)	54						CGAATTTGCAATTCAATATGA	0.483																																					.		.											.	.	.	0			.						.																																			SO:0001631	upstream_gene_variant	0	.			TTGCAATTCAATA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198804	ENSG00000198804		"""Mitochondrial respiratory chain complex / Complex IV"""	7419	protein-coding gene	gene with protein product		516030	"""cytochrome c oxidase I"""	MTCO1		7219534	Standard			Approved	COX1, COI		P00395			M.37:g.5801T>C	Exception_encountered	Somatic	173	0		WXS	Illumina HiSeq	.	654	593	.	Q34770	RNA	SNP	ENST00000361624.2	37																																																																																				.		0.483	MT-CO1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024028	
DOCK9	23348	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	13	99554100	99554100	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr13:99554100C>T	ENST00000376460.1	-	13	1515	c.1435G>A	c.(1435-1437)Gaa>Aaa	p.E479K	DOCK9_ENST00000448493.2_Missense_Mutation_p.E491K|DOCK9_ENST00000339416.2_Missense_Mutation_p.E480K|DOCK9_ENST00000442173.1_Missense_Mutation_p.E479K	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9	480					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					AGGACTTTTTCAATTCTGGCC	0.413																																					p.E480K		.											.	.	.	0			c.G1438A						.						60.0	56.0	57.0					13																	99554100		1863	4098	5961	SO:0001583	missense	23348	exon13			CTTTTTCAATTCT	AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"""Pleckstrin homology (PH) domain containing"""	14132	protein-coding gene	gene with protein product	"""zizimin1"""	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.1435G>A	13.37:g.99554100C>T	ENSP00000365643:p.Glu479Lys	Somatic	50	0		WXS	Illumina HiSeq	.	68	8	NM_001130049	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Missense_Mutation	SNP	ENST00000376460.1	37	CCDS45062.1	.	.	.	.	.	.	.	.	.	.	C	35	5.522042	0.96416	.	.	ENSG00000088387	ENST00000376460;ENST00000357329;ENST00000376455;ENST00000400235;ENST00000428223;ENST00000339416;ENST00000448493;ENST00000442173	T;T;T;T	0.51817	0.69;0.69;0.69;0.69	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.74435	0.3716	M	0.86420	2.815	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;0.998;1.0;1.0	D;D;D;D;D	0.85130	0.987;0.979;0.992;0.997;0.994	T	0.76953	-0.2768	9	.	.	.	.	19.6436	0.95767	0.0:1.0:0.0:0.0	.	480;479;479;479;480	A6H8Z6;E9PFM9;B3KX25;Q9BZ29-5;Q9BZ29	.;.;.;.;DOCK9_HUMAN	K	479;480;480;480;479;480;491;479	ENSP00000365643:E479K;ENSP00000341086:E480K;ENSP00000401958:E491K;ENSP00000406883:E479K	.	E	-	1	0	DOCK9	98352101	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.410000	0.80065	2.712000	0.92718	0.650000	0.86243	GAA	.		0.413	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296	
PUM1	9698	hgsc.bcm.edu	37	1	31465481	31465481	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr1:31465481G>T	ENST00000257075.5	-	7	1007	c.914C>A	c.(913-915)tCt>tAt	p.S305Y	PUM1_ENST00000423018.2_Missense_Mutation_p.S209Y|PUM1_ENST00000424085.2_Intron|PUM1_ENST00000373742.2_Missense_Mutation_p.S245Y|PUM1_ENST00000426105.2_Missense_Mutation_p.S305Y|PUM1_ENST00000440538.2_Missense_Mutation_p.S305Y|PUM1_ENST00000373747.3_Missense_Mutation_p.S305Y|PUM1_ENST00000373741.4_Missense_Mutation_p.S341Y	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	305					membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)	p.S305F(1)		breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		TTCATTAGCAGAGTTCTGGCA	0.493																																					p.S305Y		.											PUM1,NS,carcinoma,0,1	PUM1	0	1	Substitution - Missense(1)	endometrium(1)	c.C914A						.						75.0	70.0	72.0					1																	31465481		2203	4300	6503	SO:0001583	missense	9698	exon7			TTAGCAGAGTTCT	AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644			14957	protein-coding gene	gene with protein product		607204	"""pumilio (Drosophila) homolog 1"", ""pumilio homolog 1 (Drosophila)"""				Standard	NM_001020658		Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.914C>A	1.37:g.31465481G>T	ENSP00000257075:p.Ser305Tyr	Somatic	28	0		WXS	Illumina HiSeq	.	31	2	NM_014676	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Missense_Mutation	SNP	ENST00000257075.5	37	CCDS338.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.823798	0.90873	.	.	ENSG00000134644	ENST00000257075;ENST00000373747;ENST00000426105;ENST00000440538;ENST00000373741;ENST00000423018;ENST00000373742;ENST00000543952	T;T;T;T;T;T;T	0.32753	1.44;1.75;1.73;1.72;1.71;1.8;1.62	5.56	5.56	0.83823	.	0.165679	0.64402	D	0.000016	T	0.57330	0.2046	M	0.68317	2.08	0.80722	D	1	D;B;D;P;D;D;D	0.76494	0.96;0.38;0.999;0.514;0.999;0.999;0.999	P;B;D;B;D;D;D	0.83275	0.723;0.248;0.996;0.431;0.996;0.996;0.996	T	0.57940	-0.7724	10	0.87932	D	0	-6.8642	19.8898	0.96926	0.0:0.0:1.0:0.0	.	245;209;341;305;305;305;305	B4DG92;E7EWT3;Q5T1Z8;Q14671-2;Q14671;E9PCJ0;Q5T1Z4	.;.;.;.;PUM1_HUMAN;.;.	Y	305;305;305;305;341;209;245;305	ENSP00000257075:S305Y;ENSP00000362852:S305Y;ENSP00000391723:S305Y;ENSP00000401777:S305Y;ENSP00000362846:S341Y;ENSP00000399440:S209Y;ENSP00000362847:S245Y	ENSP00000257075:S305Y	S	-	2	0	PUM1	31238068	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.378000	0.97191	2.775000	0.95449	0.655000	0.94253	TCT	.		0.493	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1		
FAM169A	26049	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	74091907	74091907	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr5:74091907G>T	ENST00000389156.4	-	11	1298	c.1208C>A	c.(1207-1209)gCa>gAa	p.A403E	FAM169A_ENST00000380515.3_3'UTR|FAM169A_ENST00000510496.1_Missense_Mutation_p.A343E	NM_015566.2	NP_056381.1	Q9Y6X4	F169A_HUMAN	family with sequence similarity 169, member A	403	Asp/Glu-rich.					membrane (GO:0016020)|nucleus (GO:0005634)		p.A403E(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(12)|prostate(2)|urinary_tract(1)	27						TGCTGGCCGTGCATCTCTATC	0.428																																					p.A403E		.											FAM169A,NS,carcinoma,0,1	FAM169A	0	1	Substitution - Missense(1)	lung(1)	c.C1208A						.						216.0	205.0	209.0					5																	74091907		1975	4164	6139	SO:0001583	missense	26049	exon11			GGCCGTGCATCTC		CCDS43330.1	5q13.3	2008-08-08			ENSG00000198780	ENSG00000198780			29138	protein-coding gene	gene with protein product		615769				10048485	Standard	NM_015566		Approved	KIAA0888	uc003kdm.4	Q9Y6X4	OTTHUMG00000162930	ENST00000389156.4:c.1208C>A	5.37:g.74091907G>T	ENSP00000373808:p.Ala403Glu	Somatic	30	0		WXS	Illumina HiSeq	.	36	15	NM_015566	A8K1T9|Q6MZT0|Q9H989	Missense_Mutation	SNP	ENST00000389156.4	37	CCDS43330.1	.	.	.	.	.	.	.	.	.	.	G	0.208	-1.038663	0.02013	.	.	ENSG00000198780	ENST00000389156;ENST00000510496	T	0.42131	0.98	4.53	2.7	0.31948	.	0.608195	0.14472	N	0.317481	T	0.24005	0.0581	L	0.27053	0.805	0.09310	N	1	B;B	0.26809	0.082;0.16	B;B	0.24394	0.053;0.037	T	0.20273	-1.0280	10	0.11794	T	0.64	-2.8569	6.1873	0.20503	0.2335:0.0:0.7665:0.0	.	343;403	D6RB01;Q9Y6X4	.;F169A_HUMAN	E	403;343	ENSP00000373808:A403E	ENSP00000373808:A403E	A	-	2	0	FAM169A	74127663	0.000000	0.05858	0.005000	0.12908	0.063000	0.16089	0.308000	0.19314	0.804000	0.34136	0.655000	0.94253	GCA	.		0.428	FAM169A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371092.2		
PLEKHA3	65977	hgsc.bcm.edu	37	2	179367333	179367333	+	Intron	SNP	T	T	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr2:179367333T>A	ENST00000234453.5	+	8	1177					NM_019091.3	NP_061964.3	Q9HB20	PKHA3_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3							Golgi apparatus (GO:0005794)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)			TTTTTTTTTTTAAGGGGATCA	0.289																																					.		.											.	.	.	0			.						.						17.0	14.0	15.0					2																	179367333		692	1567	2259	SO:0001627	intron_variant	100302152	.			TTTTTTTAAGGGG	AF286162	CCDS33336.1	2q31.2	2013-01-10	2002-01-14		ENSG00000116095	ENSG00000116095		"""Pleckstrin homology (PH) domain containing"""	14338	protein-coding gene	gene with protein product	"""four-phosphate-adaptor protein 1"""	607774	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3"""			11001876, 15107860	Standard	NM_019091		Approved	FAPP1	uc002umn.3	Q9HB20	OTTHUMG00000154446	ENST00000234453.5:c.776-1154T>A	2.37:g.179367333T>A		Somatic	54	0		WXS	Illumina HiSeq	.	93	4	.	Q4ZG69|Q86TQ1|Q9NXT3	RNA	SNP	ENST00000234453.5	37	CCDS33336.1																																																																																			.		0.289	PLEKHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335241.2	NM_019091	
Unknown	0	hgsc.bcm.edu	37	6	29855595	29855595	+	IGR	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr6:29855595C>T								HLA-G (56693 upstream) : HLA-A (53441 downstream)														p.Q23*(1)									GACCCTGACCCAGACCTGGGC	0.726																																					.		.											ENSG00000196306,brain,glioma,0,1	ENSG00000196306	0	1	Substitution - Nonsense(1)	central_nervous_system(1)	.						.																																			SO:0001628	intergenic_variant	3136	.			CTGACCCAGACCT																													6.37:g.29855595C>T		Somatic	35	1		WXS	Illumina HiSeq	.	55	6	.		RNA	SNP		37																																																																																				.	0	0.726								
LRRCC1	85444	hgsc.bcm.edu	37	8	86038933	86038933	+	Nonsense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr8:86038933G>T	ENST00000360375.3	+	9	1431	c.1282G>T	c.(1282-1284)Gaa>Taa	p.E428*	LRRCC1_ENST00000414626.2_Nonsense_Mutation_p.E408*	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	428					mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						GTCCCTTGTTGAACAGCTAGA	0.368																																					p.E428X		.											.	.	.	0			c.G1282T						.						66.0	64.0	64.0					8																	86038933		1867	4100	5967	SO:0001587	stop_gained	85444	exon9			CTTGTTGAACAGC	BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"""centrosomal leucine-rich repeat and coiled-coil containing protein"", ""variable number of flagella 1 homolog (Chlamydomonas)"""		"""leucine rich repeat and coiled-coil domain containing 1"""			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.1282G>T	8.37:g.86038933G>T	ENSP00000353538:p.Glu428*	Somatic	46	0		WXS	Illumina HiSeq	.	85	3	NM_033402	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Nonsense_Mutation	SNP	ENST00000360375.3	37	CCDS43750.1	.	.	.	.	.	.	.	.	.	.	G	38	6.780504	0.97833	.	.	ENSG00000133739	ENST00000360375;ENST00000414626	.	.	.	5.56	3.71	0.42584	.	0.000000	0.37095	N	0.002257	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	-10.4777	14.2094	0.65755	0.0:0.5668:0.4332:0.0	.	.	.	.	X	428;408	.	ENSP00000353538:E428X	E	+	1	0	LRRCC1	86226185	1.000000	0.71417	0.968000	0.41197	0.962000	0.63368	3.306000	0.51881	1.347000	0.45714	0.655000	0.94253	GAA	.		0.368	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402	
TLR1	7096	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	38798332	38798332	+	Missense_Mutation	SNP	G	G	C			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr4:38798332G>C	ENST00000502213.2	-	3	2350	c.2121C>G	c.(2119-2121)tgC>tgG	p.C707W	TLR1_ENST00000308979.2_Missense_Mutation_p.C707W|TLR1_ENST00000510552.1_5'Flank			Q15399	TLR1_HUMAN	toll-like receptor 1	707	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.C707C(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						GTTCATAATGGCACCATTCAC	0.418																																					p.C707W	GBM(5;216 373 40795 46382)	.											TLR1,NS,carcinoma,0,1	TLR1	0	1	Substitution - coding silent(1)	lung(1)	c.C2121G						.						173.0	167.0	169.0					4																	38798332		2203	4300	6503	SO:0001583	missense	7096	exon4			ATAATGGCACCAT	U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"""CD molecules"""	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.2121C>G	4.37:g.38798332G>C	ENSP00000421259:p.Cys707Trp	Somatic	56	0		WXS	Illumina HiSeq	.	99	34	NM_003263	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Missense_Mutation	SNP	ENST00000502213.2	37	CCDS33973.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.775283	0.49786	.	.	ENSG00000174125	ENST00000308979;ENST00000502213	T;T	0.03801	3.8;3.8	5.2	2.5	0.30297	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.000000	0.64402	D	0.000001	T	0.30103	0.0754	H	0.96633	3.855	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.20940	-1.0260	10	0.87932	D	0	.	10.0152	0.42010	0.3029:0.0:0.6971:0.0	.	707	Q15399	TLR1_HUMAN	W	707	ENSP00000354932:C707W;ENSP00000421259:C707W	ENSP00000354932:C707W	C	-	3	2	TLR1	38474727	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.885000	0.28227	0.285000	0.22329	0.563000	0.77884	TGC	.		0.418	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3		
HEATR2	54919	hgsc.bcm.edu	37	7	814755	814755	+	Nonsense_Mutation	SNP	C	C	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr7:814755C>A	ENST00000297440.6	+	11	2215	c.2195C>A	c.(2194-2196)tCg>tAg	p.S732*	HEATR2_ENST00000403952.3_Nonsense_Mutation_p.S157*|HEATR2_ENST00000313147.5_Nonsense_Mutation_p.S732*	NM_017802.3	NP_060272.3	Q86Y56	HEAT2_HUMAN	HEAT repeat containing 2	732						cytoplasm (GO:0005737)				breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|prostate(4)|skin(1)	22		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0182)|Epithelial(4;5.48e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.95e-16)|all cancers(6;2.98e-14)		TTAAAAACCTCGGGCGGCATG	0.512											OREG0017814|OREG0026740	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S732X		.											HEATR2,NS,carcinoma,0,1	HEATR2	0	0			c.C2195A						.						116.0	109.0	111.0					7																	814755		2203	4300	6503	SO:0001587	stop_gained	54919	exon11			AAACCTCGGGCGG	AL832914, AK000404, NM_017802, AK056233	CCDS34580.1	7p22.3	2014-05-06	2006-05-19		ENSG00000164818	ENSG00000164818			26013	protein-coding gene	gene with protein product		614864				23040496	Standard	NM_017802		Approved	FLJ20397, FLJ31671, FLJ39381, FLJ25564, CILD18	uc010krz.1	Q86Y56	OTTHUMG00000151416	ENST00000297440.6:c.2195C>A	7.37:g.814755C>A	ENSP00000297440:p.Ser732*	Somatic	28	0	591	WXS	Illumina HiSeq	.	46	4	NM_017802	Q69YL1|Q96FI9|Q9NX75	Nonsense_Mutation	SNP	ENST00000297440.6	37	CCDS34580.1	.	.	.	.	.	.	.	.	.	.	C	35	5.441559	0.96187	.	.	ENSG00000164818	ENST00000297440;ENST00000313147;ENST00000537862;ENST00000403952	.	.	.	5.15	2.22	0.28083	.	0.444655	0.26460	N	0.024252	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	-10.0216	8.7596	0.34667	0.0:0.3871:0.516:0.0969	.	.	.	.	X	732;732;478;157	.	ENSP00000297440:S732X	S	+	2	0	HEATR2	781281	0.922000	0.31269	0.000000	0.03702	0.004000	0.04260	1.602000	0.36783	0.545000	0.28902	-0.254000	0.11334	TCG	.		0.512	HEATR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322542.1	NM_017802	
LRP1B	53353	hgsc.bcm.edu	37	2	141812690	141812690	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr2:141812690C>T	ENST00000389484.3	-	10	2518	c.1547G>A	c.(1546-1548)tGc>tAc	p.C516Y		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	516	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.			C -> Y (in Ref. 2; AAL38107). {ECO:0000305}.	protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CATACTTTTGCATGACCTGCC	0.428										TSP Lung(27;0.18)																											p.C516Y	Colon(99;50 2074 2507 20106)	.											LRP1B,NS,carcinoma,0,1	LRP1B	0	0			c.G1547A						.						95.0	83.0	87.0					2																	141812690		2203	4300	6503	SO:0001583	missense	53353	exon10			CTTTTGCATGACC	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.1547G>A	2.37:g.141812690C>T	ENSP00000374135:p.Cys516Tyr	Somatic	35	0		WXS	Illumina HiSeq	.	41	2	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.038855	0.75617	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.99042	-5.36	5.45	4.56	0.56223	Growth factor, receptor (1);Epidermal growth factor-like (1);EGF-like region, conserved site (1);	0.000000	0.85682	U	0.000000	D	0.98839	0.9608	H	0.94306	3.52	0.58432	D	0.999995	P	0.46277	0.875	B	0.41440	0.357	D	0.98408	1.0571	10	0.87932	D	0	.	15.4826	0.75539	0.1398:0.8602:0.0:0.0	.	516	Q9NZR2	LRP1B_HUMAN	Y	516;454	ENSP00000374135:C516Y	ENSP00000374135:C516Y	C	-	2	0	LRP1B	141529160	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.726000	0.84824	1.282000	0.44496	0.557000	0.71058	TGC	.		0.428	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
WDFY3	23001	hgsc.bcm.edu	37	4	85716106	85716106	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr4:85716106G>T	ENST00000295888.4	-	20	3601	c.3194C>A	c.(3193-3195)cCt>cAt	p.P1065H	WDFY3_ENST00000322366.6_Missense_Mutation_p.P1065H	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	1065					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		AGCATTATGAGGGGCCAAACT	0.393																																					p.P1065H		.											.	.	.	0			c.C3194A						.						70.0	68.0	69.0					4																	85716106		2203	4300	6503	SO:0001583	missense	23001	exon20			TTATGAGGGGCCA	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.3194C>A	4.37:g.85716106G>T	ENSP00000295888:p.Pro1065His	Somatic	59	0		WXS	Illumina HiSeq	.	86	4	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Missense_Mutation	SNP	ENST00000295888.4	37	CCDS3609.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.630317	0.87660	.	.	ENSG00000163625	ENST00000322366;ENST00000295888	T;T	0.60920	0.15;0.15	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.76737	0.4029	M	0.74647	2.275	0.80722	D	1	D	0.89917	1.0	D	0.69307	0.963	T	0.78763	-0.2077	10	0.87932	D	0	.	19.6264	0.95679	0.0:0.0:1.0:0.0	.	1065	Q8IZQ1	WDFY3_HUMAN	H	1065	ENSP00000318466:P1065H;ENSP00000295888:P1065H	ENSP00000295888:P1065H	P	-	2	0	WDFY3	85935130	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	9.420000	0.97426	2.717000	0.92951	0.655000	0.94253	CCT	.		0.393	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991	
SLC18A2	6571	hgsc.bcm.edu	37	10	119003781	119003781	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr10:119003781G>T	ENST00000298472.5	+	3	564	c.421G>T	c.(421-423)Gtc>Ttc	p.V141F	SLC18A2_ENST00000497497.1_3'UTR|RP11-501J20.5_ENST00000425264.1_RNA	NM_003054.4	NP_003045.2	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 2	141					aging (GO:0007568)|cellular response to ammonium ion (GO:0071242)|cellular response to drug (GO:0035690)|death (GO:0016265)|dopamine transport (GO:0015872)|endocytic recycling (GO:0032456)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|negative regulation of neurotransmitter transport (GO:0051589)|neurotransmitter loading into synaptic vesicle (GO:0098700)|neurotransmitter secretion (GO:0007269)|post-embryonic development (GO:0009791)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to corticosterone (GO:0051412)|response to herbicide (GO:0009635)|response to starvation (GO:0042594)|response to zinc ion (GO:0010043)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|dense core granule (GO:0031045)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)|terminal bouton (GO:0043195)	amine transmembrane transporter activity (GO:0005275)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)|serotonin transmembrane transporter activity (GO:0015222)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)	29		Colorectal(252;0.19)		all cancers(201;0.029)	Amphetamine(DB00182)|Benzphetamine(DB00865)|Deserpidine(DB01089)|Dextroamphetamine(DB01576)|Ephedra(DB01363)|Ephedrine(DB01364)|Isometheptene(DB06706)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Propylhexedrine(DB06714)|Reserpine(DB00206)|Tetrabenazine(DB04844)	GAAAGCCACCGTCCAGCTCAT	0.478																																					p.V141F		.											SLC18A2,NS,haematopoietic_neoplasm,0,1	SLC18A2	0	0			c.G421T						.						63.0	59.0	60.0					10																	119003781		2203	4300	6503	SO:0001583	missense	6571	exon3			GCCACCGTCCAGC	L14269	CCDS7599.1	10q25	2013-07-18	2013-07-18		ENSG00000165646	ENSG00000165646		"""Solute carriers"""	10935	protein-coding gene	gene with protein product		193001		VMAT2			Standard	NM_003054		Approved	SVMT, SVAT	uc001ldd.2	Q05940	OTTHUMG00000019121	ENST00000298472.5:c.421G>T	10.37:g.119003781G>T	ENSP00000298472:p.Val141Phe	Somatic	20	0		WXS	Illumina HiSeq	.	37	2	NM_003054	B2RC96|D3DRC4|Q15876|Q4G147|Q5VW49|Q9H3P6	Missense_Mutation	SNP	ENST00000298472.5	37	CCDS7599.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.168853	0.78339	.	.	ENSG00000165646	ENST00000298472	T	0.57436	0.4	5.71	2.31	0.28768	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.122077	0.53938	D	0.000041	T	0.63248	0.2495	M	0.72894	2.215	0.58432	D	0.999999	P	0.46512	0.879	P	0.57009	0.811	T	0.62305	-0.6882	10	0.42905	T	0.14	-24.6891	10.5411	0.45033	0.2478:0.0:0.7522:0.0	.	141	Q05940	VMAT2_HUMAN	F	141	ENSP00000298472:V141F	ENSP00000298472:V141F	V	+	1	0	SLC18A2	118993771	1.000000	0.71417	0.672000	0.29872	0.978000	0.69477	3.545000	0.53648	0.726000	0.32339	0.655000	0.94253	GTC	.		0.478	SLC18A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050563.1	NM_003054	
WDR26	80232	hgsc.bcm.edu	37	1	224599141	224599141	+	Nonsense_Mutation	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr1:224599141C>T	ENST00000414423.2	-	7	1339	c.1146G>A	c.(1144-1146)tgG>tgA	p.W382*	WDR26_ENST00000366852.2_3'UTR|WDR26_ENST00000295024.6_Nonsense_Mutation_p.W235*	NM_001115113.2|NM_025160.6	NP_001108585.2|NP_079436.4	Q9H7D7	WDR26_HUMAN	WD repeat domain 26	382						cytoplasm (GO:0005737)|nucleus (GO:0005634)				biliary_tract(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)	18				GBM - Glioblastoma multiforme(131;0.0104)		GATCAACTTGCCATATGATAA	0.313																																					p.W382X		.											.	.	.	0			c.G1146A						.						141.0	118.0	126.0					1																	224599141		2203	4300	6503	SO:0001587	stop_gained	80232	exon7			AACTTGCCATATG	AK024669	CCDS31037.1, CCDS31037.2	1q42.13	2013-01-09			ENSG00000162923	ENSG00000162923		"""WD repeat domain containing"""	21208	protein-coding gene	gene with protein product	"""GID complex subunit 7 homolog (S. cerevisiae)"""						Standard	NM_001115113		Approved	FLJ21016, GID7	uc001hop.4	Q9H7D7	OTTHUMG00000037636	ENST00000414423.2:c.1146G>A	1.37:g.224599141C>T	ENSP00000408108:p.Trp382*	Somatic	62	0		WXS	Illumina HiSeq	.	79	3	NM_025160	A0MNN3|Q4G100|Q59EC4|Q5GLZ9|Q86UY4|Q9H3C2	Nonsense_Mutation	SNP	ENST00000414423.2	37	CCDS31037.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	41|41	9.156159|9.156159	0.99084|0.99084	.|.	.|.	ENSG00000162923|ENSG00000162923	ENST00000480676|ENST00000414423;ENST00000295024	.|.	.|.	.|.	5.54|5.54	5.54|5.54	0.83059|0.83059	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.48003|.	0.1476|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.35968|.	-0.9767|.	4|.	.|0.02654	.|T	.|1	.|.	19.8424|19.8424	0.96695|0.96695	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	T|X	16|382;235	.|.	.|ENSP00000295024:W235X	A|W	-|-	1|3	0|0	WDR26|WDR26	222665764|222665764	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.776000|7.776000	0.85560|0.85560	2.764000|2.764000	0.94973|0.94973	0.655000|0.655000	0.94253|0.94253	GCA|TGG	.		0.313	WDR26-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091760.2	NM_025160	
ABCA8	10351	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	66878815	66878815	+	Silent	SNP	T	T	G			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr17:66878815T>G	ENST00000269080.2	-	28	3770	c.3633A>C	c.(3631-3633)ccA>ccC	p.P1211P	ABCA8_ENST00000586539.1_Silent_p.P1251P|ABCA8_ENST00000430352.2_Silent_p.P1251P	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	1211					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					CCTCTCCTTCTGGTTCTTCTG	0.343																																					p.P1211P		.											.	.	.	0			c.A3633C						.						186.0	165.0	172.0					17																	66878815		2203	4299	6502	SO:0001819	synonymous_variant	10351	exon28			TCCTTCTGGTTCT	AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"""ATP binding cassette transporters / subfamily A"""	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.3633A>C	17.37:g.66878815T>G		Somatic	38	0		WXS	Illumina HiSeq	.	59	6	NM_007168	A1L3U3|C9JQE6|Q86WW0	Silent	SNP	ENST00000269080.2	37	CCDS11680.1																																																																																			.		0.343	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168	
WDR33	55339	hgsc.bcm.edu;broad.mit.edu	37	2	128522166	128522166	+	Intron	SNP	C	C	T	rs557391879		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr2:128522166C>T	ENST00000322313.4	-	6	785				WDR33_ENST00000393006.1_Intron|WDR33_ENST00000409658.3_Missense_Mutation_p.A288T	NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33						mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		GTGCAAAATGCGGCAGACAGT	0.343																																					p.A288T		.											WDR33_ENST00000409658,NS,carcinoma,0,1	WDR33_ENST00000409658	0	0			c.G862A						.						44.0	43.0	43.0					2																	128522166		1116	2180	3296	SO:0001627	intron_variant	55339	exon6			AAAATGCGGCAGA		CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"""WD repeat domain containing"""	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.626+235G>A	2.37:g.128522166C>T		Somatic	30	0		WXS	Illumina HiSeq	.	44	3	NM_001006622	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Missense_Mutation	SNP	ENST00000322313.4	37	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	C	1.183	-0.637615	0.03557	.	.	ENSG00000136709	ENST00000409658	T	0.38240	1.15	5.91	2.69	0.31865	.	.	.	.	.	T	0.17534	0.0421	.	.	.	0.23162	N	0.998193	B	0.12630	0.006	B	0.08055	0.003	T	0.31475	-0.9942	8	0.09338	T	0.73	.	8.1008	0.30857	0.0:0.6402:0.0:0.3598	.	288	Q9C0J8-2	.	T	288	ENSP00000387186:A288T	ENSP00000387186:A288T	A	-	1	0	WDR33	128238636	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.096000	0.30976	0.233000	0.21120	0.655000	0.94253	GCA	.		0.343	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383	
GAL3ST2	64090	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	2	242741335	242741335	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr2:242741335G>A	ENST00000192314.6	+	3	390	c.259G>A	c.(259-261)Ggc>Agc	p.G87S	AC114730.5_ENST00000437438.1_RNA	NM_022134.2	NP_071417.2	Q9H3Q3	G3ST2_HUMAN	galactose-3-O-sulfotransferase 2	87					biosynthetic process (GO:0009058)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	galactosylceramide sulfotransferase activity (GO:0001733)|sulfotransferase activity (GO:0008146)			endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|prostate(1)|skin(1)	14		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)		GCTGCCCGCCGGCTCACGCGT	0.642																																					p.G87S		.											.	.	.	0			c.G259A						.						58.0	53.0	55.0					2																	242741335		2203	4298	6501	SO:0001583	missense	64090	exon3			CCCGCCGGCTCAC	AB040610	CCDS33427.1	2q37.2	2014-05-19			ENSG00000154252	ENSG00000154252		"""Sulfotransferases, membrane-bound"""	24869	protein-coding gene	gene with protein product		608237				11029462	Standard	NM_022134		Approved	GP3ST	uc002wcj.1	Q9H3Q3	OTTHUMG00000151473	ENST00000192314.6:c.259G>A	2.37:g.242741335G>A	ENSP00000192314:p.Gly87Ser	Somatic	17	0		WXS	Illumina HiSeq	.	48	9	NM_022134	Q17RK0|Q57Z52	Missense_Mutation	SNP	ENST00000192314.6	37	CCDS33427.1	.	.	.	.	.	.	.	.	.	.	G	15.21	2.764779	0.49574	.	.	ENSG00000154252	ENST00000192314	T	0.14893	2.47	3.8	3.8	0.43715	.	0.092462	0.47093	D	0.000241	T	0.29061	0.0722	L	0.53729	1.69	0.27689	N	0.946173	D	0.89917	1.0	D	0.71184	0.972	T	0.07046	-1.0793	10	0.08381	T	0.77	-48.0285	11.4681	0.50252	0.0:0.0:0.82:0.18	.	87	Q9H3Q3	G3ST2_HUMAN	S	87	ENSP00000192314:G87S	ENSP00000192314:G87S	G	+	1	0	GAL3ST2	242390008	0.940000	0.31905	0.267000	0.24556	0.016000	0.09150	1.952000	0.40343	2.118000	0.64928	0.306000	0.20318	GGC	.		0.642	GAL3ST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322792.1	NM_022134	
SLC12A6	9990	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	34628712	34628712	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr15:34628712C>T	ENST00000354181.3	-	2	662	c.170G>A	c.(169-171)aGt>aAt	p.S57N	SLC12A6_ENST00000558589.1_Missense_Mutation_p.S48N|SLC12A6_ENST00000558667.1_Missense_Mutation_p.S57N|SLC12A6_ENST00000397702.2_De_novo_Start_OutOfFrame|SLC12A6_ENST00000458406.2_De_novo_Start_OutOfFrame|SLC12A6_ENST00000560611.1_Missense_Mutation_p.S57N|SLC12A6_ENST00000397707.2_Missense_Mutation_p.S57N			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6	57					angiogenesis (GO:0001525)|cellular hypotonic response (GO:0071476)|cellular hypotonic salinity response (GO:0071477)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|rubidium ion transport (GO:0035826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium ion transmembrane transporter activity (GO:0015079)|potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)|rubidium ion transmembrane transporter activity (GO:0035827)			central_nervous_system(5)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|skin(3)	45		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	CATAGGCTCACTCCGGCTTGT	0.562																																					p.S57N		.											.	.	.	0			c.G170A						.						65.0	72.0	70.0					15																	34628712		2181	4289	6470	SO:0001583	missense	9990	exon1			GGCTCACTCCGGC	AF108831	CCDS10036.1, CCDS42010.1, CCDS42011.1, CCDS42012.1, CCDS58352.1	15q13	2014-09-17	2013-07-18		ENSG00000140199	ENSG00000140199		"""Solute carriers"""	10914	protein-coding gene	gene with protein product		604878	"""agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome)"""	KCC3, ACCPN		10187864, 10347194	Standard	NM_133647		Approved		uc001zhw.3	Q9UHW9	OTTHUMG00000129441	ENST00000354181.3:c.170G>A	15.37:g.34628712C>T	ENSP00000346112:p.Ser57Asn	Somatic	32	0		WXS	Illumina HiSeq	.	77	29	NM_133647	A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Missense_Mutation	SNP	ENST00000354181.3	37	CCDS58352.1	.	.	.	.	.	.	.	.	.	.	C	17.66	3.445763	0.63178	.	.	ENSG00000140199	ENST00000397707;ENST00000354181	D	0.84516	-1.86	4.89	4.89	0.63831	.	0.361406	0.27134	N	0.020764	T	0.72803	0.3506	N	0.08118	0	0.80722	D	1	B;B	0.29085	0.232;0.149	B;B	0.28139	0.086;0.039	T	0.70799	-0.4774	10	0.31617	T	0.26	.	16.9856	0.86339	0.0:1.0:0.0:0.0	.	57;57	Q9UHW9-3;Q9UHW9	.;S12A6_HUMAN	N	57;48	ENSP00000380819:S57N	ENSP00000346112:S48N	S	-	2	0	SLC12A6	32416004	1.000000	0.71417	0.798000	0.32154	0.995000	0.86356	6.014000	0.70784	2.540000	0.85666	0.563000	0.77884	AGT	.		0.562	SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135	
MYH10	4628	hgsc.bcm.edu	37	17	8408136	8408136	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr17:8408136C>T	ENST00000269243.4	-	26	3520	c.3382G>A	c.(3382-3384)Gaa>Aaa	p.E1128K	MYH10_ENST00000379980.4_Missense_Mutation_p.E1144K|MYH10_ENST00000360416.3_Missense_Mutation_p.E1159K|MYH10_ENST00000396239.1_Missense_Mutation_p.E1149K	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	1128					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						TTCTCGGATTCAAAGTCTTCC	0.468																																					p.E1159K		.											MYH10,NS,carcinoma,0,1	MYH10	0	0			c.G3475A						.						196.0	184.0	188.0					17																	8408136		2203	4300	6503	SO:0001583	missense	4628	exon28			CGGATTCAAAGTC	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"""Myosins / Myosin superfamily : Class II"""	7568	protein-coding gene	gene with protein product		160776	"""myosin, heavy polypeptide 10, non-muscle"""			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.3382G>A	17.37:g.8408136C>T	ENSP00000269243:p.Glu1128Lys	Somatic	29	0		WXS	Illumina HiSeq	.	30	2	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Missense_Mutation	SNP	ENST00000269243.4	37	CCDS11144.1	.	.	.	.	.	.	.	.	.	.	C	34	5.409163	0.96072	.	.	ENSG00000133026	ENST00000269243;ENST00000360416;ENST00000396239;ENST00000379980	D;D;D;D	0.82344	-1.6;-1.6;-1.6;-1.6	4.9	4.9	0.64082	Myosin tail (1);	0.000000	0.85682	D	0.000000	D	0.92737	0.7691	M	0.91300	3.195	0.80722	D	1	D;D;D	0.62365	0.991;0.989;0.991	D;D;D	0.68039	0.955;0.925;0.928	D	0.94261	0.7502	10	0.87932	D	0	.	18.2878	0.90120	0.0:1.0:0.0:0.0	.	1137;1159;1128	B2RWP9;F8VTL3;P35580	.;.;MYH10_HUMAN	K	1128;1159;1149;1144	ENSP00000269243:E1128K;ENSP00000353590:E1159K;ENSP00000379539:E1149K;ENSP00000369315:E1144K	ENSP00000269243:E1128K	E	-	1	0	MYH10	8348861	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	7.609000	0.82925	2.551000	0.86045	0.563000	0.77884	GAA	.		0.468	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2		
IQGAP2	10788	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	75969392	75969392	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr5:75969392A>T	ENST00000274364.6	+	25	3484	c.3187A>T	c.(3187-3189)Att>Ttt	p.I1063F	IQGAP2_ENST00000396234.3_Missense_Mutation_p.I559F|IQGAP2_ENST00000502745.1_Missense_Mutation_p.I559F|IQGAP2_ENST00000379730.3_Missense_Mutation_p.I565F	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	1063	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		GAATTCTATCATTTCTTCCCT	0.418																																					p.I1063F		.											.	.	.	0			c.A3187T						.						149.0	143.0	145.0					5																	75969392		2203	4300	6503	SO:0001583	missense	10788	exon25			TCTATCATTTCTT	U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.3187A>T	5.37:g.75969392A>T	ENSP00000274364:p.Ile1063Phe	Somatic	44	0		WXS	Illumina HiSeq	.	60	20	NM_006633	A8K4V1|B7Z8A4|J3KR91	Missense_Mutation	SNP	ENST00000274364.6	37	CCDS34188.1	.	.	.	.	.	.	.	.	.	.	A	13.43	2.233987	0.39498	.	.	ENSG00000145703	ENST00000274364;ENST00000379730;ENST00000505766;ENST00000396234;ENST00000502745	T;T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19;-1.19	5.75	1.73	0.24493	Rho GTPase activation protein (1);Ras GTPase-activating protein (4);	0.236165	0.45867	D	0.000332	T	0.63663	0.2530	L	0.41824	1.3	0.37601	D	0.920558	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.15052	0.008;0.012;0.005	T	0.56709	-0.7934	10	0.45353	T	0.12	-8.0325	4.0953	0.09988	0.4955:0.0:0.1823:0.3222	.	565;559;1063	F5H7S7;Q13576-2;Q13576	.;.;IQGA2_HUMAN	F	1063;565;1013;559;559	ENSP00000274364:I1063F;ENSP00000442313:I565F;ENSP00000421097:I1013F;ENSP00000379535:I559F;ENSP00000426027:I559F	ENSP00000274364:I1063F	I	+	1	0	IQGAP2	76005148	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	1.481000	0.35476	0.423000	0.26033	0.482000	0.46254	ATT	.		0.418	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633	
USP48	84196	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	22063114	22063114	+	Silent	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr1:22063114C>T	ENST00000308271.9	-	9	1644	c.996G>A	c.(994-996)ggG>ggA	p.G332G	USP48_ENST00000529637.1_Silent_p.G332G|USP48_ENST00000421625.2_Silent_p.G332G|USP48_ENST00000400301.1_Silent_p.G332G	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	332	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			NS(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(14)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		ACACGTAGGACCCACCTGGAG	0.433																																					p.G332G		.											.	.	.	0			c.G996A						.						74.0	67.0	69.0					1																	22063114		2203	4300	6503	SO:0001819	synonymous_variant	84196	exon9			GTAGGACCCACCT	AF502942	CCDS30623.1, CCDS44084.1	1p36.12	2008-02-05	2005-08-08	2004-04-07	ENSG00000090686	ENSG00000090686		"""Ubiquitin-specific peptidases"""	18533	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"", ""ubiquitin specific protease 48"""	USP31		12838346	Standard	XM_005246009		Approved	FLJ23277, FLJ11328, FLJ20103, FLJ23054, MGC14879	uc001bfb.3	Q86UV5	OTTHUMG00000007798	ENST00000308271.9:c.996G>A	1.37:g.22063114C>T		Somatic	49	0		WXS	Illumina HiSeq	.	40	17	NM_001032730	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Silent	SNP	ENST00000308271.9	37	CCDS30623.1																																																																																			.		0.433	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236	
TGM1	7051	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	24729730	24729730	+	Nonsense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr14:24729730G>T	ENST00000206765.6	-	4	806	c.683C>A	c.(682-684)tCa>tAa	p.S228*	TGM1_ENST00000544573.1_Intron	NM_000359.2	NP_000350.1	P22735	TGM1_HUMAN	transglutaminase 1	228					cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|organ morphogenesis (GO:0009887)|peptide cross-linking (GO:0018149)	cell-cell adherens junction (GO:0005913)|cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|intrinsic component of membrane (GO:0031224)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)	24				GBM - Glioblastoma multiforme(265;0.0186)	L-Glutamine(DB00130)	CCCAGCGTCTGATTGTGTGCG	0.592																																					p.S228X		.											.	.	.	0			c.C683A						.						181.0	155.0	164.0					14																	24729730		2203	4300	6503	SO:0001587	stop_gained	7051	exon4			GCGTCTGATTGTG	D90287	CCDS9622.1	14q11.2	2013-05-02	2013-05-02		ENSG00000092295	ENSG00000092295	2.3.2.13	"""Transglutaminases"""	11777	protein-coding gene	gene with protein product	"""K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase"""	190195	"""transglutaminase 1 (K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase)"""	ICR2		11390390	Standard	NM_000359		Approved	TGASE, TGK, LI, LI1	uc001wod.3	P22735	OTTHUMG00000029329	ENST00000206765.6:c.683C>A	14.37:g.24729730G>T	ENSP00000206765:p.Ser228*	Somatic	33	0		WXS	Illumina HiSeq	.	23	16	NM_000359	B4DWR7|Q197M4	Nonsense_Mutation	SNP	ENST00000206765.6	37	CCDS9622.1	.	.	.	.	.	.	.	.	.	.	G	18.32	3.598157	0.66332	.	.	ENSG00000092295	ENST00000206765	.	.	.	6.02	3.07	0.35406	.	0.887861	0.09011	U	0.861569	.	.	.	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	-0.5526	11.0411	0.47831	0.0713:0.5255:0.4031:0.0	.	.	.	.	X	228	.	ENSP00000206765:S228X	S	-	2	0	TGM1	23799570	0.000000	0.05858	0.003000	0.11579	0.089000	0.18198	0.313000	0.19415	0.374000	0.24650	0.655000	0.94253	TCA	.		0.592	TGM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073160.6	NM_000359	
NCOR1	9611	hgsc.bcm.edu	37	17	15971432	15971432	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr17:15971432G>T	ENST00000268712.3	-	32	4774	c.4517C>A	c.(4516-4518)aCa>aAa	p.T1506K	NCOR1_ENST00000395857.3_Missense_Mutation_p.T90K|NCOR1_ENST00000395851.1_Missense_Mutation_p.T1522K	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1506	Interaction with C1D. {ECO:0000250}.|Interaction with ETO.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|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)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		AGAAGAAATTGTAACTGGAAA	0.398																																					p.T1522K		.											.	.	.	0			c.C4565A						.						32.0	32.0	32.0					17																	15971432		2203	4300	6503	SO:0001583	missense	9611	exon31			GAAATTGTAACTG	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"""thyroid hormone- and retinoic acid receptor-associated corepressor 1"", ""protein phosphatase 1, regulatory subunit 109"""	600849	"""nuclear receptor co-repressor 1"""			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.4517C>A	17.37:g.15971432G>T	ENSP00000268712:p.Thr1506Lys	Somatic	54	0		WXS	Illumina HiSeq	.	84	4	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	37	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	G	13.18	2.161650	0.38119	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395857	T;T;T	0.39997	1.05;1.64;1.05	5.76	5.76	0.90799	.	0.458541	0.22630	N	0.057581	T	0.32912	0.0845	N	0.22421	0.69	0.35047	D	0.760241	B;B;B;B	0.26195	0.144;0.02;0.034;0.034	B;B;B;B	0.28232	0.087;0.016;0.036;0.036	T	0.43556	-0.9384	10	0.62326	D	0.03	.	13.8568	0.63531	0.0:0.2537:0.7463:0.0	.	317;1506;1522;27	B4DZ48;O75376;O75376-2;Q86YY1	.;NCOR1_HUMAN;.;.	K	1506;1522;90	ENSP00000268712:T1506K;ENSP00000379192:T1522K;ENSP00000379198:T90K	ENSP00000268712:T1506K	T	-	2	0	NCOR1	15912157	0.997000	0.39634	0.785000	0.31869	0.930000	0.56654	3.073000	0.50057	2.715000	0.92844	0.563000	0.77884	ACA	.		0.398	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311	
GLRA3	8001	hgsc.bcm.edu	37	4	175580272	175580272	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr4:175580272G>A	ENST00000274093.3	-	8	1506	c.1004C>T	c.(1003-1005)gCa>gTa	p.A335V	GLRA3_ENST00000340217.5_Missense_Mutation_p.A335V	NM_006529.2	NP_006520.2	O75311	GLRA3_HUMAN	glycine receptor, alpha 3	335					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)			endometrium(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	35		Prostate(90;0.00601)|Breast(14;0.0091)|Melanoma(52;0.00959)|Renal(120;0.0183)|all_neural(102;0.0891)|all_hematologic(60;0.107)		all cancers(43;4.99e-18)|Epithelial(43;1.18e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.88e-09)|STAD - Stomach adenocarcinoma(60;0.00442)|GBM - Glioblastoma multiforme(59;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0421)	Glycine(DB00145)|Ivermectin(DB00602)|Lindane(DB00431)	ATTTACAGCTGCATACTCCAG	0.373																																					p.A335V		.											GLRA3,colon,carcinoma,0,1	GLRA3	0	0			c.C1004T						.						123.0	115.0	118.0					4																	175580272		2203	4300	6503	SO:0001583	missense	8001	exon8			ACAGCTGCATACT	AF017724	CCDS3822.1, CCDS43283.1	4q34.1	2012-02-07			ENSG00000145451	ENSG00000145451		"""Ligand-gated ion channels / Glycine receptors"""	4328	protein-coding gene	gene with protein product		600421				9677400	Standard	NM_001042543		Approved		uc003ity.1	O75311	OTTHUMG00000149816	ENST00000274093.3:c.1004C>T	4.37:g.175580272G>A	ENSP00000274093:p.Ala335Val	Somatic	34	0		WXS	Illumina HiSeq	.	38	2	NM_001042543	D3DP44|O75816|Q5D0E3	Missense_Mutation	SNP	ENST00000274093.3	37	CCDS3822.1	.	.	.	.	.	.	.	.	.	.	G	36	5.673262	0.96754	.	.	ENSG00000145451	ENST00000274093;ENST00000340217	D;D	0.89939	-2.59;-2.59	5.35	5.35	0.76521	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.92286	0.7553	L	0.58969	1.84	0.80722	D	1	P;P	0.44877	0.814;0.845	P;P	0.54924	0.652;0.764	D	0.92872	0.6315	10	0.87932	D	0	.	19.0501	0.93039	0.0:0.0:1.0:0.0	.	335;335	O75311-2;O75311	.;GLRA3_HUMAN	V	335	ENSP00000274093:A335V;ENSP00000345284:A335V	ENSP00000274093:A335V	A	-	2	0	GLRA3	175816847	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.813000	0.99286	2.523000	0.85059	0.650000	0.86243	GCA	.		0.373	GLRA3-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313427.1		
UBTF	7343	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	42293340	42293340	+	Silent	SNP	T	T	G			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr17:42293340T>G	ENST00000302904.4	-	4	744	c.252A>C	c.(250-252)acA>acC	p.T84T	CTB-175E5.7_ENST00000586560.1_RNA|UBTF_ENST00000533177.1_Silent_p.T84T|UBTF_ENST00000537550.1_5'UTR|UBTF_ENST00000436088.1_Silent_p.T84T|UBTF_ENST00000343638.5_Silent_p.T84T|UBTF_ENST00000393606.3_Silent_p.T84T|UBTF_ENST00000527034.1_Silent_p.T84T|UBTF_ENST00000526094.1_Silent_p.T84T|UBTF_ENST00000529383.1_Silent_p.T84T			P17480	UBF1_HUMAN	upstream binding transcription factor, RNA polymerase I	84					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)		ATTCTGTCAATGTACGGAACT	0.468																																					p.T84T		.											.	.	.	0			c.A252C						.						114.0	107.0	110.0					17																	42293340		2203	4300	6503	SO:0001819	synonymous_variant	7343	exon4			TGTCAATGTACGG	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.252A>C	17.37:g.42293340T>G		Somatic	31	0		WXS	Illumina HiSeq	.	57	7	NM_014233	A8K6R8	Silent	SNP	ENST00000302904.4	37	CCDS11480.1																																																																																			.		0.468	UBTF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395205.1	NM_014233	
GGTLC1	92086	hgsc.bcm.edu	37	20	23967157	23967157	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr20:23967157A>G	ENST00000335694.4	-	2	296	c.92T>C	c.(91-93)aTg>aCg	p.M31T	GGTLC1_ENST00000286890.4_Missense_Mutation_p.M31T|GGTLC1_ENST00000278765.4_Missense_Mutation_p.M31T	NM_178311.2	NP_842563.1	Q9BX51	GGTL1_HUMAN	gamma-glutamyltransferase light chain 1	31					glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)	gamma-glutamyltransferase activity (GO:0003840)	p.M31T(6)		NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	15						GTCATCCGGCATGTAGAACTC	0.622																																					p.M31T		.											GGTLC1,NS,carcinoma,0,12	GGTLC1	0	6	Substitution - Missense(6)	lung(4)|NS(2)	c.T92C						.						67.0	61.0	63.0					20																	23967157		2203	4300	6503	SO:0001583	missense	92086	exon2			TCCGGCATGTAGA	AL133466	CCDS13163.1	20p11.21	2010-07-14	2008-03-10	2008-03-10	ENSG00000149435	ENSG00000149435		"""Gamma-glutamyltransferases"""	16437	protein-coding gene	gene with protein product		612338	"""gamma-glutamyltransferase-like activity 4"", ""gamma-glutamyltransferase-like activity 3"""	GGTLA4, GGTLA3		10843999, 18357469	Standard	NM_178311		Approved	dJ831C21.2, dJ831C21.1	uc002wtu.3	Q9BX51	OTTHUMG00000032095	ENST00000335694.4:c.92T>C	20.37:g.23967157A>G	ENSP00000337587:p.Met31Thr	Somatic	81	2		WXS	Illumina HiSeq	.	132	6	NM_178311	D3DW43|Q08246	Missense_Mutation	SNP	ENST00000335694.4	37	CCDS13163.1	.	.	.	.	.	.	.	.	.	.	a	0	-2.745202	0.00087	.	.	ENSG00000149435	ENST00000286890;ENST00000278765;ENST00000335694	T;T;T	0.05786	3.39;3.39;3.39	0.844	-1.69	0.08186	.	0.459428	0.22918	N	0.054055	T	0.01092	0.0036	N	0.00332	-1.63	0.20403	N	0.999909	B	0.02656	0.0	B	0.01281	0.0	T	0.28996	-1.0026	10	0.02654	T	1	-29.1837	4.9338	0.13930	0.5039:0.0:0.4961:0.0	.	31	Q9BX51	GGTL1_HUMAN	T	31	ENSP00000286890:M31T;ENSP00000278765:M31T;ENSP00000337587:M31T	ENSP00000278765:M31T	M	-	2	0	GGTLC1	23915157	0.993000	0.37304	0.024000	0.17045	0.024000	0.10985	1.453000	0.35167	-1.885000	0.01118	-1.888000	0.00539	ATG	.		0.622	GGTLC1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078366.2	NM_178311.2	
FAM127A	8933	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	134166535	134166535	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chrX:134166535C>A	ENST00000257013.7	+	1	203	c.122C>A	c.(121-123)cCg>cAg	p.P41Q	FAM127A_ENST00000464369.1_3'UTR	NM_001078171.1	NP_001071639.1	O15255	CXX1_HUMAN	family with sequence similarity 127, member A	0						plasma membrane (GO:0005886)				endometrium(3)|urinary_tract(1)	4	Acute lymphoblastic leukemia(192;0.000127)					GACCGACTCCCGGAGTTCATC	0.622																																					p.P41Q		.											.	.	.	0			c.C122A						.						102.0	105.0	104.0					X																	134166535		2169	4245	6414	SO:0001583	missense	8933	exon1			GACTCCCGGAGTT	Y13374	CCDS43997.1	Xq26	2014-05-16	2006-11-16	2006-11-16	ENSG00000134590	ENSG00000134590			2569	protein-coding gene	gene with protein product		300213	"""CAAX box 1"""	CXX1		9403077, 15716091, 16093683	Standard	NM_001078171		Approved	Mart8, Mar8, MAR8C	uc004eyd.3	A6ZKI3	OTTHUMG00000022465	ENST00000257013.7:c.122C>A	X.37:g.134166535C>A	ENSP00000257013:p.Pro41Gln	Somatic	87	0		WXS	Illumina HiSeq	.	101	28	NM_001078171	Q6IBF1	Missense_Mutation	SNP	ENST00000257013.7	37	CCDS43997.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.204558	0.79127	.	.	ENSG00000134590	ENST00000257013	T	0.32272	1.46	3.95	3.95	0.45737	.	.	.	.	.	T	0.38241	0.1033	L	0.52759	1.655	0.28050	N	0.933384	D	0.55385	0.971	P	0.55999	0.789	T	0.09079	-1.0691	9	0.15499	T	0.54	.	10.4135	0.44307	0.0:1.0:0.0:0.0	.	41	A6ZKI3	F127A_HUMAN	Q	41	ENSP00000257013:P41Q	ENSP00000257013:P41Q	P	+	2	0	FAM127A	133994201	1.000000	0.71417	0.999000	0.59377	0.711000	0.40976	2.563000	0.45922	2.215000	0.71742	0.538000	0.68166	CCG	.		0.622	FAM127A-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058391.2	NM_001078171	
NELFCD	51497	hgsc.bcm.edu;ucsc.edu	37	20	57568731	57568731	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr20:57568731G>T	ENST00000344018.3	+	13	1547	c.1520G>T	c.(1519-1521)gGt>gTt	p.G507V	NELFCD_ENST00000479207.1_Splice_Site|NELFCD_ENST00000602795.1_Missense_Mutation_p.G516V			Q8IXH7	NELFD_HUMAN	negative elongation factor complex member C/D	507					gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	membrane (GO:0016020)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)											CTGAGTCGAGGTTATGTACTT	0.493																																					p.G516V		.											.	.	.	0			c.G1547T						.						188.0	167.0	174.0					20																	57568731		2203	4300	6503	SO:0001583	missense	51497	exon13			GTCGAGGTTATGT	AF161479	CCDS13473.1, CCDS13473.2	20q13	2013-01-31	2013-01-31	2013-01-31	ENSG00000101158	ENSG00000101158			15934	protein-coding gene	gene with protein product	"""trihydrophobin 1"""	605297	"""TH1-like (Drosophila homolog)"", ""TH1-like (Drosophila)"""	TH1L		11030415, 11042152	Standard	NM_198976		Approved	HSPC130, TH1, NELF-C, NELF-D	uc002yag.4	Q8IXH7	OTTHUMG00000032861	ENST00000344018.3:c.1520G>T	20.37:g.57568731G>T	ENSP00000342300:p.Gly507Val	Somatic	24	0		WXS	Illumina HiSeq	.	39	4	NM_198976	B4DE06|Q9BYL2|Q9H405|Q9H888|Q9H8T3|Q9NVX5|Q9P029|Q9UGN1|Q9UGN2|Q9UGN3	Missense_Mutation	SNP	ENST00000344018.3	37		.	.	.	.	.	.	.	.	.	.	G	22.2	4.255003	0.80135	.	.	ENSG00000101158	ENST00000344018	.	.	.	4.73	4.73	0.59995	.	0.000000	0.85682	D	0.000000	D	0.84410	0.5466	M	0.87827	2.91	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87330	0.2324	9	0.87932	D	0	-30.6017	18.2473	0.89991	0.0:0.0:1.0:0.0	.	507	Q8IXH7	NELFD_HUMAN	V	507	.	ENSP00000342300:G507V	G	+	2	0	TH1L	57002126	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	9.563000	0.98148	2.622000	0.88805	0.557000	0.71058	GGT	.		0.493	NELFCD-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198976	
MAST4	375449	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	66391445	66391445	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr5:66391445C>G	ENST00000403625.2	+	7	1149	c.854C>G	c.(853-855)tCg>tGg	p.S285W	MAST4_ENST00000261569.7_Missense_Mutation_p.S91W|MAST4_ENST00000490016.2_Missense_Mutation_p.S96W|MAST4_ENST00000405643.1_Missense_Mutation_p.S106W|MAST4_ENST00000404260.3_Missense_Mutation_p.S288W|MAST4_ENST00000403666.1_Missense_Mutation_p.S96W	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	288						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		CGCCGCTGGTCGTTGGCTTCT	0.473																																					p.S285W		.											.	.	.	0			c.C854G						.						81.0	87.0	85.0					5																	66391445		1975	4165	6140	SO:0001583	missense	375449	exon7			GCTGGTCGTTGGC	AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.854C>G	5.37:g.66391445C>G	ENSP00000385727:p.Ser285Trp	Somatic	44	0		WXS	Illumina HiSeq	.	75	33	NM_001164664	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	37	CCDS54861.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.732024	0.89390	.	.	ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000490016;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569;ENST00000436277;ENST00000432399	T;T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92;0.92	6.04	6.04	0.98038	Microtubule-associated serine/threonine-protein kinase, domain (1);	0.000000	0.50627	U	0.000113	T	0.75148	0.3810	M	0.92459	3.31	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;0.999	T	0.79820	-0.1642	10	0.87932	D	0	-11.1109	20.5948	0.99439	0.0:1.0:0.0:0.0	.	106;288;91;96;96	E7EWQ5;O15021;O15021-2;O15021-3;D6RAK1	.;MAST4_HUMAN;.;.;.	W	288;285;96;96;106;106;91;91;91	ENSP00000385048:S288W;ENSP00000385727:S285W;ENSP00000421739:S96W;ENSP00000384313:S96W;ENSP00000384099:S106W;ENSP00000261569:S91W;ENSP00000392478:S91W	ENSP00000261569:S91W	S	+	2	0	MAST4	66427201	1.000000	0.71417	0.970000	0.41538	0.930000	0.56654	7.487000	0.81328	2.873000	0.98535	0.563000	0.77884	TCG	.		0.473	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2		
SLC25A32	81034	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	8	104413805	104413805	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr8:104413805G>T	ENST00000297578.4	-	6	917	c.751C>A	c.(751-753)Cgt>Agt	p.R251S	SLC25A32_ENST00000543107.1_Missense_Mutation_p.R119S|SLC25A32_ENST00000523701.1_5'UTR	NM_030780.3	NP_110407.2	Q9H2D1	MFTC_HUMAN	solute carrier family 25 (mitochondrial folate carrier), member 32	251					folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	folic acid transporter activity (GO:0008517)	p.R251S(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	9			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)		Folic Acid(DB00158)	TCCTGAAGACGAGCTCTTACG	0.388																																					p.R251S		.											.	.	.	1	Substitution - Missense(1)	lung(1)	c.C751A						.						172.0	155.0	161.0					8																	104413805		2203	4300	6503	SO:0001583	missense	81034	exon6			GAAGACGAGCTCT	AF283645	CCDS6300.1	8q22.3	2013-05-22	2013-03-15		ENSG00000164933	ENSG00000164933		"""Solute carriers"""	29683	protein-coding gene	gene with protein product		610815	"""solute carrier family 25, member 32"""			10978331	Standard	NM_030780		Approved	MFTC	uc003yll.4	Q9H2D1	OTTHUMG00000164790	ENST00000297578.4:c.751C>A	8.37:g.104413805G>T	ENSP00000297578:p.Arg251Ser	Somatic	38	0		WXS	Illumina HiSeq	.	93	4	NM_030780	Q96JZ6|Q96SU7	Missense_Mutation	SNP	ENST00000297578.4	37	CCDS6300.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.766460	0.90020	.	.	ENSG00000164933	ENST00000297578;ENST00000424899;ENST00000543107	D;D	0.83992	-1.79;-1.79	5.72	5.72	0.89469	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.94860	0.8339	H	0.98818	4.34	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96416	0.9308	10	0.87932	D	0	-4.5331	14.6799	0.69009	0.0:0.0:0.8548:0.1452	.	251	Q9H2D1	MFTC_HUMAN	S	251;235;119	ENSP00000297578:R251S;ENSP00000443497:R119S	ENSP00000297578:R251S	R	-	1	0	SLC25A32	104482981	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.500000	0.81588	2.690000	0.91761	0.655000	0.94253	CGT	.		0.388	SLC25A32-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380290.2	NM_030780	
SCAI	286205	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	9	127762184	127762184	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr9:127762184G>T	ENST00000336505.6	-	13	1288	c.1230C>A	c.(1228-1230)caC>caA	p.H410Q	SCAI_ENST00000487795.1_5'Flank|SCAI_ENST00000373549.4_Missense_Mutation_p.H433Q	NM_001144877.2	NP_001138349.1	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion	410					negative regulation of cell migration (GO:0030336)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(5)|stomach(1)|urinary_tract(1)	35						GCATTTCCTTGTGGGACTGAT	0.323																																					p.H433Q		.											.	.	.	0			c.C1299A						.						161.0	158.0	159.0					9																	127762184		1835	4085	5920	SO:0001583	missense	286205	exon14			TTCCTTGTGGGAC	AK093983	CCDS43877.1, CCDS48017.1	9q34.11	2009-11-06	2009-07-09	2009-07-09	ENSG00000173611	ENSG00000173611			26709	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 126"""	C9orf126			Standard	NM_173690		Approved	FLJ36664, NET40	uc004bpd.3	Q8N9R8	OTTHUMG00000020667	ENST00000336505.6:c.1230C>A	9.37:g.127762184G>T	ENSP00000336756:p.His410Gln	Somatic	52	0		WXS	Illumina HiSeq	.	81	4	NM_173690	Q3SXZ1|Q3SXZ2|Q5T163|Q8N1I4	Missense_Mutation	SNP	ENST00000336505.6	37	CCDS48017.1	.	.	.	.	.	.	.	.	.	.	G	11.89	1.774866	0.31411	.	.	ENSG00000173611	ENST00000336505;ENST00000373549	T;T	0.41065	1.02;1.01	6.17	2.95	0.34219	.	0.196102	0.56097	N	0.000035	T	0.21347	0.0514	N	0.13235	0.315	0.32084	N	0.592749	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.11324	-1.0592	10	0.28530	T	0.3	-10.1319	5.5634	0.17157	0.2551:0.1568:0.5881:0.0	.	410;433	Q8N9R8;Q8N9R8-2	SCAI_HUMAN;.	Q	410;433	ENSP00000336756:H410Q;ENSP00000362650:H433Q	ENSP00000336756:H410Q	H	-	3	2	SCAI	126802005	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.967000	0.40491	0.902000	0.36520	0.655000	0.94253	CAC	.		0.323	SCAI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054055.3	NM_173690	
DDR1	780	hgsc.bcm.edu	37	6	30858814	30858814	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr6:30858814C>T	ENST00000324771.8	+	7	1030	c.482C>T	c.(481-483)gCc>gTc	p.A161V	DDR1_ENST00000376569.3_Missense_Mutation_p.A161V|DDR1_ENST00000452441.1_Missense_Mutation_p.A161V|DDR1_ENST00000513240.1_Missense_Mutation_p.A161V|DDR1_ENST00000508312.1_Missense_Mutation_p.A179V|MIR4640_ENST00000581824.1_RNA|DDR1_ENST00000376575.3_Missense_Mutation_p.A161V|DDR1_ENST00000376568.3_Missense_Mutation_p.A161V|DDR1_ENST00000376567.2_Missense_Mutation_p.A161V|DDR1_ENST00000376570.4_Missense_Mutation_p.A161V|DDR1_ENST00000446312.1_Missense_Mutation_p.A161V|DDR1_ENST00000361741.4_5'Flank|DDR1_ENST00000454612.2_Missense_Mutation_p.A161V|DDR1_ENST00000508472.1_3'UTR|DDR1_ENST00000418800.2_Missense_Mutation_p.A161V			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	161	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|ear development (GO:0043583)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine autophosphorylation (GO:0038083)|protein autophosphorylation (GO:0046777)|regulation of cell growth (GO:0001558)|regulation of cell-matrix adhesion (GO:0001952)|regulation of extracellular matrix disassembly (GO:0010715)|smooth muscle cell migration (GO:0014909)|smooth muscle cell-matrix adhesion (GO:0061302)|wound healing, spreading of cells (GO:0044319)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(1)|prostate(1)|skin(1)	29					Imatinib(DB00619)	CCCATGGTTGCCCGACTGGTT	0.637																																					p.A179V		.											.	.	.	0			c.C536T						.						63.0	64.0	64.0					6																	30858814		1510	2709	4219	SO:0001583	missense	780	exon5			TGGTTGCCCGACT	X99031	CCDS4690.1, CCDS34385.1, CCDS47396.1, CCDS56411.1, CCDS75419.1	6p21.33	2010-02-17	2008-01-23		ENSG00000204580	ENSG00000204580	2.7.10.1	"""CD molecules"""	2730	protein-coding gene	gene with protein product		600408	"""discoidin domain receptor family, member 1"""	NTRK4, PTK3A, NEP, CAK, EDDR1		7789998	Standard	NM_001954		Approved	RTK6, CD167	uc003nrv.3	Q08345	OTTHUMG00000031236	ENST00000324771.8:c.482C>T	6.37:g.30858814C>T	ENSP00000318217:p.Ala161Val	Somatic	39	0		WXS	Illumina HiSeq	.	62	4	NM_001202523	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Missense_Mutation	SNP	ENST00000324771.8	37	CCDS34385.1	.	.	.	.	.	.	.	.	.	.	C	31	5.094521	0.94149	.	.	ENSG00000204580	ENST00000460944;ENST00000324771;ENST00000418800;ENST00000454612;ENST00000512694;ENST00000376569;ENST00000376575;ENST00000376570;ENST00000446312;ENST00000428153;ENST00000376568;ENST00000452441;ENST00000515219;ENST00000508312;ENST00000421124;ENST00000503495;ENST00000376567;ENST00000513240	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.99732	-6.57;-6.57;-6.57;-6.57;-6.57;-6.57;-6.57;-6.57;-6.57;-6.57;-6.57;-6.57;-6.57;-6.57;-6.57;-6.57;-6.57;-6.57	4.81	4.81	0.61882	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	D	0.99694	0.9884	M	0.86178	2.8	0.80722	D	1	D;D;D;D;D	0.89917	0.999;0.999;0.999;1.0;1.0	D;D;D;D;D	0.87578	0.93;0.958;0.973;0.973;0.998	D	0.97518	1.0071	10	0.87932	D	0	.	15.4086	0.74900	0.0:1.0:0.0:0.0	.	161;187;179;161;161	Q08345-4;B7Z3A2;B7Z2K0;Q08345-5;Q08345	.;.;.;.;DDR1_HUMAN	V	161;161;161;161;161;161;161;161;161;161;161;161;3;179;161;187;161;161	ENSP00000426420:A161V;ENSP00000318217:A161V;ENSP00000407699:A161V;ENSP00000406091:A161V;ENSP00000426229:A161V;ENSP00000365753:A161V;ENSP00000365759:A161V;ENSP00000365754:A161V;ENSP00000405998:A161V;ENSP00000390593:A161V;ENSP00000365752:A161V;ENSP00000405039:A161V;ENSP00000421152:A3V;ENSP00000422442:A179V;ENSP00000409682:A161V;ENSP00000423749:A187V;ENSP00000365751:A161V;ENSP00000427552:A161V	ENSP00000318217:A161V	A	+	2	0	DDR1	30966793	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.544000	0.67231	2.502000	0.84385	0.467000	0.42956	GCC	.		0.637	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994	
HSPG2	3339	hgsc.bcm.edu	37	1	22214554	22214554	+	Nonsense_Mutation	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr1:22214554G>A	ENST00000374695.3	-	7	659	c.580C>T	c.(580-582)Cag>Tag	p.Q194*		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	194					angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	CTTGGGAACTGGGGCACTGCA	0.647																																					p.Q194X		.											HSPG2,NS,malignant_melanoma,0,2	HSPG2	0	0			c.C580T						.						59.0	53.0	55.0					1																	22214554		2203	4300	6503	SO:0001587	stop_gained	3339	exon7			GGAACTGGGGCAC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.580C>T	1.37:g.22214554G>A	ENSP00000363827:p.Gln194*	Somatic	29	0		WXS	Illumina HiSeq	.	30	2	NM_005529	Q16287|Q5SZI3|Q9H3V5	Nonsense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.161651	0.78226	.	.	ENSG00000142798	ENST00000374695	.	.	.	5.32	5.32	0.75619	.	0.252388	0.21699	N	0.070444	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.23302	T	0.38	.	16.4889	0.84193	0.0:0.0:1.0:0.0	.	.	.	.	X	194	.	ENSP00000363827:Q194X	Q	-	1	0	HSPG2	22087141	1.000000	0.71417	1.000000	0.80357	0.550000	0.35303	5.467000	0.66737	2.504000	0.84457	0.462000	0.41574	CAG	.		0.647	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
MUC4	4585	hgsc.bcm.edu	37	3	195511212	195511212	+	Missense_Mutation	SNP	G	G	C	rs549429405	byFrequency	TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr3:195511212G>C	ENST00000463781.3	-	2	7698	c.7239C>G	c.(7237-7239)caC>caG	p.H2413Q	MUC4_ENST00000475231.1_Missense_Mutation_p.H2413Q|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			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)		GATGGGTGGCGTGACCTGTGG	0.592																																					p.H2413Q		.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4_ENST00000463781	0	0			c.C7239G						.						42.0	42.0	42.0					3																	195511212		668	1587	2255	SO:0001583	missense	4585	exon2			GGTGGCGTGACCT	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.7239C>G	3.37:g.195511212G>C	ENSP00000417498:p.His2413Gln	Somatic	125	0		WXS	Illumina HiSeq	.	169	7	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	.	.	.	.	.	.	.	.	.	.	G	5.745	0.321952	0.10900	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.26810	1.71;1.75	.	.	.	.	.	.	.	.	T	0.13586	0.0329	N	0.19112	0.55	0.09310	N	1	B	0.18610	0.029	B	0.04013	0.001	T	0.30909	-0.9962	7	.	.	.	.	6.6894	0.23163	2.0E-4:0.0:0.9998:0.0	.	2413	E7ESK3	.	Q	2413	ENSP00000417498:H2413Q;ENSP00000420243:H2413Q	.	H	-	3	2	MUC4	196995607	0.000000	0.05858	0.003000	0.11579	0.000000	0.00434	0.313000	0.19415	0.482000	0.27582	0.000000	0.15137	CAC	.		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
RIMS1	22999	hgsc.bcm.edu	37	6	72892048	72892048	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr6:72892048C>T	ENST00000521978.1	+	6	874	c.874C>T	c.(874-876)Cgc>Tgc	p.R292C	RIMS1_ENST00000491071.2_Missense_Mutation_p.R292C|RIMS1_ENST00000522291.1_Missense_Mutation_p.R292C|RIMS1_ENST00000264839.7_Missense_Mutation_p.R292C|RIMS1_ENST00000348717.5_Missense_Mutation_p.R292C|RIMS1_ENST00000517960.1_Missense_Mutation_p.R292C|RIMS1_ENST00000518273.1_Missense_Mutation_p.R292C|RIMS1_ENST00000520567.1_Missense_Mutation_p.R292C	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	292					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				CGAGCGGAAACGCGTGCCAAA	0.552																																					p.R292C		.											RIMS1,colon,carcinoma,0,1	RIMS1	0	0			c.C874T						.						35.0	41.0	39.0					6																	72892048		1889	4119	6008	SO:0001583	missense	22999	exon6			CGGAAACGCGTGC	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"""Rab3-interacting molecule"""	606629	"""RAB3 interacting protein 2"""	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.874C>T	6.37:g.72892048C>T	ENSP00000428417:p.Arg292Cys	Somatic	35	0		WXS	Illumina HiSeq	.	38	2	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	37	CCDS47449.1	.	.	.	.	.	.	.	.	.	.	C	18.89	3.720460	0.68959	.	.	ENSG00000079841	ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978	T;T;T;T;T;T;T;T	0.17213	2.29;2.43;2.34;2.43;2.43;2.43;2.43;2.35	5.28	4.41	0.53225	.	0.000000	0.56097	D	0.000025	T	0.20088	0.0483	M	0.63843	1.955	0.80722	D	1	D	0.89917	1.0	P	0.58873	0.847	T	0.01920	-1.1247	10	0.87932	D	0	-5.9565	8.7448	0.34580	0.1497:0.7743:0.0:0.0759	.	292	Q86UR5	RIMS1_HUMAN	C	292	ENSP00000430101:R292C;ENSP00000275037:R292C;ENSP00000264839:R292C;ENSP00000429959:R292C;ENSP00000430408:R292C;ENSP00000430502:R292C;ENSP00000430932:R292C;ENSP00000428417:R292C	ENSP00000264839:R292C	R	+	1	0	RIMS1	72948769	1.000000	0.71417	0.997000	0.53966	0.871000	0.50021	5.383000	0.66219	1.238000	0.43771	0.462000	0.41574	CGC	.		0.552	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1		
PAPPA2	60676	hgsc.bcm.edu	37	1	176759060	176759060	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr1:176759060G>T	ENST00000367662.3	+	18	5995	c.4831G>T	c.(4831-4833)Ggc>Tgc	p.G1611C		NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	1611	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						ATGTACCAATGGCTTCAGCCT	0.483																																					p.G1611C		.											.	.	.	0			c.G4831T						.						142.0	140.0	141.0					1																	176759060		1997	4167	6164	SO:0001583	missense	60676	exon18			ACCAATGGCTTCA	BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"""placenta-specific 3"""	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.4831G>T	1.37:g.176759060G>T	ENSP00000356634:p.Gly1611Cys	Somatic	59	0		WXS	Illumina HiSeq	.	88	4	NM_020318	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	ENST00000367662.3	37	CCDS41438.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.241085	0.79912	.	.	ENSG00000116183	ENST00000367662	T	0.02216	4.39	5.51	5.51	0.81932	Complement control module (1);Sushi/SCR/CCP (2);	0.052843	0.85682	D	0.000000	T	0.14399	0.0348	M	0.83953	2.67	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.00047	-1.2209	10	0.87932	D	0	-26.2527	16.3531	0.83224	0.0:0.0:1.0:0.0	.	1611	Q9BXP8	PAPP2_HUMAN	C	1611	ENSP00000356634:G1611C	ENSP00000356634:G1611C	G	+	1	0	PAPPA2	175025683	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.743000	0.74848	2.582000	0.87167	0.557000	0.71058	GGC	.		0.483	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1		
PTPRC	5788	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	198710997	198710997	+	Splice_Site	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr1:198710997G>T	ENST00000367376.2	+	24	2568		c.e24-1		PTPRC_ENST00000348564.6_Splice_Site|PTPRC_ENST00000594404.1_Splice_Site|PTPRC_ENST00000442510.2_Splice_Site|PTPRC_ENST00000352140.3_Splice_Site	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C						axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						CTCTTGACTAGAAAAAAGAAA	0.408																																					.		.											.	.	.	0			c.1921-1G>T						.						30.0	32.0	31.0					1																	198710997		2203	4299	6502	SO:0001630	splice_region_variant	5788	exon21			TGACTAGAAAAAA	Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237		"""CD molecules"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9666	protein-coding gene	gene with protein product		151460		CD45		2169617	Standard	NM_001267798		Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000367376.2:c.2398-1G>T	1.37:g.198710997G>T		Somatic	16	0		WXS	Illumina HiSeq	.	30	13	NM_080921	A8K7W6|Q16614|Q9H0Y6	Splice_Site	SNP	ENST00000367376.2	37		.	.	.	.	.	.	.	.	.	.	G	26.0	4.697611	0.88830	.	.	ENSG00000081237	ENST00000367376;ENST00000352140;ENST00000442510;ENST00000348564	.	.	.	5.95	5.95	0.96441	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.3854	0.98941	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PTPRC	196977620	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	8.692000	0.91284	2.825000	0.97269	0.655000	0.94253	.	.		0.408	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding			Intron
RIOK2	55781	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	96503500	96503500	+	Silent	SNP	C	C	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr5:96503500C>A	ENST00000283109.3	-	8	1136	c.1068G>T	c.(1066-1068)cgG>cgT	p.R356R	RIOK2_ENST00000508447.1_Silent_p.R356R|CTD-2215E18.1_ENST00000509481.1_Intron	NM_018343.2	NP_060813.2	Q9BVS4	RIOK2_HUMAN	RIO kinase 2	356	Protein kinase.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|urinary_tract(2)	23		all_cancers(142;0.000125)|all_epithelial(76;8.48e-07)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0676)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0657)		CTAGACAGTTCCGTTCACTTT	0.403																																					p.R356R		.											.	.	.	0			c.G1068T						.						139.0	137.0	138.0					5																	96503500		2203	4300	6503	SO:0001819	synonymous_variant	55781	exon8			ACAGTTCCGTTCA	AK002021	CCDS4089.1, CCDS54884.1	5q14	2012-12-10	2012-12-10		ENSG00000058729	ENSG00000058729			18999	protein-coding gene	gene with protein product			"""RIO kinase 2 (yeast)"""				Standard	NM_018343		Approved	FLJ11159	uc003kmz.3	Q9BVS4	OTTHUMG00000128723	ENST00000283109.3:c.1068G>T	5.37:g.96503500C>A		Somatic	31	0		WXS	Illumina HiSeq	.	35	17	NM_001159749	D6RDI3|Q9NUT0	Silent	SNP	ENST00000283109.3	37	CCDS4089.1																																																																																			.		0.403	RIOK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250628.1	NM_018343	
LRP12	29967	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	105510177	105510177	+	Silent	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr8:105510177G>A	ENST00000276654.5	-	5	711	c.603C>T	c.(601-603)gcC>gcT	p.A201A	LRP12_ENST00000424843.2_Silent_p.A182A|LRP12_ENST00000518375.1_5'Flank	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	201	LDL-receptor class A 1. {ECO:0000255|PROSITE-ProRule:PRU00124}.				endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			TTGCTTCTTTGGCACAGATCT	0.438																																					p.A201A		.											.	.	.	0			c.C603T						.						204.0	182.0	189.0					8																	105510177		2203	4300	6503	SO:0001819	synonymous_variant	29967	exon5			TTCTTTGGCACAG	AF166350	CCDS6303.1, CCDS47907.1	8q22.2	2013-02-27	2010-01-26		ENSG00000147650	ENSG00000147650		"""Low density lipoprotein receptors"""	31708	protein-coding gene	gene with protein product						12809483, 14676824	Standard	NM_013437		Approved	ST7, FLJ12929	uc003yma.3	Q9Y561	OTTHUMG00000164892	ENST00000276654.5:c.603C>T	8.37:g.105510177G>A		Somatic	46	0		WXS	Illumina HiSeq	.	97	23	NM_013437	A8K137|B4DRQ2	Silent	SNP	ENST00000276654.5	37	CCDS6303.1																																																																																			.		0.438	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1	NM_013437	
SH2D3A	10045	hgsc.bcm.edu	37	19	6755188	6755188	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr19:6755188T>C	ENST00000245908.6	-	5	904	c.635A>G	c.(634-636)aAg>aGg	p.K212R	SH2D3A_ENST00000599563.1_5'UTR|SH2D3A_ENST00000437152.3_Missense_Mutation_p.K90R	NM_005490.2	NP_005481.2	Q9BRG2	SH23A_HUMAN	SH2 domain containing 3A	212					JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|urinary_tract(1)	24						CCGGGGGGGCTTCGTTGGTGC	0.647																																					p.K212R		.											SH2D3A,NS,carcinoma,0,1	SH2D3A	0	0			c.A635G						.						93.0	106.0	101.0					19																	6755188		2203	4300	6503	SO:0001583	missense	10045	exon5			GGGGGCTTCGTTG	AF124249	CCDS12173.1	19p13.3	2013-02-14	2002-01-14			ENSG00000125731		"""SH2 domain containing"""	16885	protein-coding gene	gene with protein product		604721	"""SH2 domain-containing 3A"""			10187783	Standard	NM_005490		Approved	NSP1	uc002mft.3	Q9BRG2		ENST00000245908.6:c.635A>G	19.37:g.6755188T>C	ENSP00000245908:p.Lys212Arg	Somatic	60	0		WXS	Illumina HiSeq	.	79	3	NM_005490	A8K9R6|B4DRS7|Q9Y2X4	Missense_Mutation	SNP	ENST00000245908.6	37	CCDS12173.1	.	.	.	.	.	.	.	.	.	.	T	11.25	1.582253	0.28180	.	.	ENSG00000125731	ENST00000245908;ENST00000437152	T;T	0.39229	2.54;1.09	4.53	4.53	0.55603	Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.40469	N	0.001089	T	0.61751	0.2372	M	0.77313	2.365	0.34311	D	0.685493	P;D	0.76494	0.859;0.999	B;D	0.68765	0.274;0.96	T	0.73522	-0.3956	10	0.44086	T	0.13	-28.5372	11.8134	0.52195	0.0:0.0:0.0:1.0	.	90;212	B4DRS7;Q9BRG2	.;SH23A_HUMAN	R	212;90	ENSP00000245908:K212R;ENSP00000393303:K90R	ENSP00000245908:K212R	K	-	2	0	SH2D3A	6706188	1.000000	0.71417	0.995000	0.50966	0.097000	0.18754	4.542000	0.60677	1.677000	0.50941	0.379000	0.24179	AAG	.		0.647	SH2D3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458016.1	NM_005490	
BLK	640	hgsc.bcm.edu	37	8	11415529	11415529	+	Silent	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr8:11415529G>T	ENST00000259089.4	+	10	1603	c.1011G>T	c.(1009-1011)ctG>ctT	p.L337L	RP11-148O21.2_ENST00000533322.1_RNA|RP11-148O21.4_ENST00000528629.1_RNA|BLK_ENST00000529894.1_Silent_p.L266L	NM_001715.2	NP_001706.2	P51451	BLK_HUMAN	BLK proto-oncogene, Src family tyrosine kinase	337	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell receptor signaling pathway (GO:0050853)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of insulin secretion (GO:0032024)	plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)	p.L337L(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(4)|stomach(1)	27			STAD - Stomach adenocarcinoma(15;0.00391)	COAD - Colon adenocarcinoma(149;0.207)		TCCCAAGGCTGATTGACATGT	0.542																																					p.L337L		.											BLK,NS,carcinoma,+2,1	BLK	+2	1	Substitution - coding silent(1)	lung(1)	c.G1011T						.						140.0	106.0	117.0					8																	11415529		2203	4300	6503	SO:0001819	synonymous_variant	640	exon10			AAGGCTGATTGAC	BC004473	CCDS5982.1	8p23-p22	2014-06-25	2014-06-25		ENSG00000136573	ENSG00000136573		"""SH2 domain containing"""	1057	protein-coding gene	gene with protein product		191305	"""B lymphoid tyrosine kinase"""			7845672	Standard	NM_001715		Approved	MGC10442	uc003wty.3	P51451	OTTHUMG00000090729	ENST00000259089.4:c.1011G>T	8.37:g.11415529G>T		Somatic	16	0		WXS	Illumina HiSeq	.	22	2	NM_001715	Q16291|Q96IN1	Silent	SNP	ENST00000259089.4	37	CCDS5982.1																																																																																			.		0.542	BLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207460.1		
AHNAK	79026	hgsc.bcm.edu	37	11	62300279	62300279	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr11:62300279T>A	ENST00000378024.4	-	5	1884	c.1610A>T	c.(1609-1611)aAa>aTa	p.K537I	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	537					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TCTGGAGCCTTTAAGTGCCAC	0.512																																					p.K537I		.											AHNAK,NS,carcinoma,0,1	AHNAK	0	0			c.A1610T						.						111.0	120.0	117.0					11																	62300279		2202	4299	6501	SO:0001583	missense	79026	exon5			GAGCCTTTAAGTG	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.1610A>T	11.37:g.62300279T>A	ENSP00000367263:p.Lys537Ile	Somatic	12	0		WXS	Illumina HiSeq	.	26	2	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	T	15.53	2.859929	0.51482	.	.	ENSG00000124942	ENST00000378024	T	0.00682	5.86	4.76	3.55	0.40652	.	2.113380	0.02361	N	0.076860	T	0.06781	0.0173	M	0.89163	3.01	0.21147	N	0.999777	D	0.76494	0.999	D	0.91635	0.999	T	0.33343	-0.9872	10	0.41790	T	0.15	-2.4238	11.192	0.48690	0.0:0.0:0.1523:0.8477	.	537	Q09666	AHNK_HUMAN	I	537	ENSP00000367263:K537I	ENSP00000367263:K537I	K	-	2	0	AHNAK	62056855	0.996000	0.38824	0.914000	0.36105	0.860000	0.49131	2.318000	0.43779	1.916000	0.55485	0.454000	0.30748	AAA	.		0.512	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
ZNF157	7712	hgsc.bcm.edu	37	X	47272743	47272743	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chrX:47272743G>T	ENST00000377073.3	+	4	1357	c.1271G>T	c.(1270-1272)aGt>aTt	p.S424I		NM_003446.3	NP_003437.2	P51786	ZN157_HUMAN	zinc finger protein 157	424					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|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)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	11						AAAATCTTCAGTATGAAGAAA	0.418																																					p.S424I		.											.	.	.	0			c.G1271T						.						77.0	69.0	72.0					X																	47272743		2203	4300	6503	SO:0001583	missense	7712	exon4			TCTTCAGTATGAA	U28687	CCDS14278.1	Xp11.2	2013-01-08	2006-08-22		ENSG00000147117	ENSG00000147117		"""Zinc fingers, C2H2-type"", ""-"""	12942	protein-coding gene	gene with protein product		300024	"""zinc finger protein 157 (HZF22)"""			8586441	Standard	NM_003446		Approved	HZF22	uc004dhr.1	P51786	OTTHUMG00000021443	ENST00000377073.3:c.1271G>T	X.37:g.47272743G>T	ENSP00000366273:p.Ser424Ile	Somatic	43	0		WXS	Illumina HiSeq	.	79	4	NM_003446	Q96LE9	Missense_Mutation	SNP	ENST00000377073.3	37	CCDS14278.1	.	.	.	.	.	.	.	.	.	.	G	11.72	1.721438	0.30503	.	.	ENSG00000147117	ENST00000377073	T	0.19938	2.11	3.29	2.39	0.29439	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.21186	0.0510	L	0.47190	1.495	0.09310	N	1	D	0.52996	0.957	P	0.45794	0.493	T	0.08066	-1.0740	9	0.38643	T	0.18	.	8.64	0.33972	0.0:0.4579:0.5421:0.0	.	424	P51786	ZN157_HUMAN	I	424	ENSP00000366273:S424I	ENSP00000366273:S424I	S	+	2	0	ZNF157	47157687	0.001000	0.12720	0.054000	0.19295	0.990000	0.78478	0.236000	0.17967	0.738000	0.32606	0.600000	0.82982	AGT	.		0.418	ZNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056415.1	NM_003446	
NTRK3	4916	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	88678415	88678415	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr15:88678415C>G	ENST00000360948.2	-	9	1282	c.1121G>C	c.(1120-1122)gGc>gCc	p.G374A	NTRK3_ENST00000317501.3_Missense_Mutation_p.G374A|NTRK3_ENST00000542733.2_Missense_Mutation_p.G276A|NTRK3_ENST00000355254.2_Missense_Mutation_p.G374A|NTRK3_ENST00000540489.2_Missense_Mutation_p.G374A|NTRK3_ENST00000394480.2_Missense_Mutation_p.G374A|NTRK3_ENST00000558676.1_Missense_Mutation_p.G374A|NTRK3_ENST00000357724.2_Missense_Mutation_p.G374A|NTRK3_ENST00000557856.1_Missense_Mutation_p.G374A	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	374	Ig-like C2-type 2.				activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			GGTATAGTTGCCATTGTTGTA	0.542			T	ETV6	"""congenital fibrosarcoma, Secretory breast """					TSP Lung(13;0.10)																											p.G374A		.		Dom	yes		15	15q25	4916	"""neurotrophic tyrosine kinase, receptor, type 3"""		"""E, M"""	.	.	.	0			c.G1121C						.						258.0	232.0	241.0					15																	88678415		2201	4299	6500	SO:0001583	missense	4916	exon10			TAGTTGCCATTGT	U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"""	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.1121G>C	15.37:g.88678415C>G	ENSP00000354207:p.Gly374Ala	Somatic	43	0		WXS	Illumina HiSeq	.	103	34	NM_001243101	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	37	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.647695	0.87958	.	.	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254;ENST00000542733;ENST00000540489;ENST00000317501	T;T;T;T;T;T;T	0.80738	-1.41;-1.41;-1.41;-1.41;-1.41;-1.41;-1.41	5.02	5.02	0.67125	Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.91851	0.7421	M	0.91768	3.24	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;0.999;1.0;1.0;0.999;0.999	D	0.93739	0.7048	10	0.87932	D	0	.	17.3435	0.87304	0.0:1.0:0.0:0.0	.	276;374;374;374;374;374	B7Z7U4;E9PG56;B7Z4C5;Q96CY4;Q16288-3;Q16288	.;.;.;.;.;NTRK3_HUMAN	A	374;374;374;374;276;374;374	ENSP00000377990:G374A;ENSP00000354207:G374A;ENSP00000350356:G374A;ENSP00000347397:G374A;ENSP00000437773:G276A;ENSP00000444673:G374A;ENSP00000318328:G374A	ENSP00000318328:G374A	G	-	2	0	NTRK3	86479419	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.459000	0.80802	2.324000	0.78689	0.563000	0.77884	GGC	.		0.542	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding			
BCL3	602	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	45262071	45262071	+	Nonsense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr19:45262071G>T	ENST00000164227.5	+	8	1394	c.1150G>T	c.(1150-1152)Gag>Tag	p.E384*		NM_005178.4	NP_005169.2	P20749	BCL3_HUMAN	B-cell CLL/lymphoma 3	384	Pro/Ser-rich.				antimicrobial humoral response (GO:0019730)|cellular response to DNA damage stimulus (GO:0006974)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|extracellular matrix organization (GO:0030198)|follicular dendritic cell differentiation (GO:0002268)|germinal center formation (GO:0002467)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 biosynthetic process (GO:0045082)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|protein import into nucleus, translocation (GO:0000060)|regulation of apoptotic process (GO:0042981)|regulation of DNA binding (GO:0051101)|regulation of NF-kappaB import into nucleus (GO:0042345)|response to UV-C (GO:0010225)|response to virus (GO:0009615)|spleen development (GO:0048536)|T-helper 1 type immune response (GO:0042088)|T-helper 2 cell differentiation (GO:0045064)|transcription, DNA-templated (GO:0006351)	Bcl3-Bcl10 complex (GO:0032996)|Bcl3/NF-kappaB2 complex (GO:0033257)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	Lung NSC(12;0.000698)|all_lung(12;0.002)	Ovarian(192;0.0728)				CACCTCCCCCGAGAGCAGCAG	0.662			T	IGH@	CLL																																p.E384X		.		Dom	yes		19	19q13	602	B-cell CLL/lymphoma 3		L	.	.	.	0			c.G1150T						.						38.0	37.0	38.0					19																	45262071		2191	4295	6486	SO:0001587	stop_gained	602	exon8			TCCCCCGAGAGCA	M31732	CCDS12642.2	19q13.1-q13.2	2013-01-10			ENSG00000069399	ENSG00000069399		"""Ankyrin repeat domain containing"""	998	protein-coding gene	gene with protein product	"""B-cell lymphoma 3-encoded protein"", ""B-cell leukemia/lymphoma 3"", ""chronic lymphatic leukemia protein"""	109560		D19S37, BCL4		1501714, 2180580	Standard	NM_005178		Approved		uc010xxe.2	P20749	OTTHUMG00000151517	ENST00000164227.5:c.1150G>T	19.37:g.45262071G>T	ENSP00000164227:p.Glu384*	Somatic	14	0		WXS	Illumina HiSeq	.	20	8	NM_005178		Nonsense_Mutation	SNP	ENST00000164227.5	37	CCDS12642.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	38|38	6.873146|6.873146	0.97901|0.97901	.|.	.|.	ENSG00000069399|ENSG00000069399	ENST00000164227|ENST00000444487	.|.	.|.	.|.	4.11|4.11	4.11|4.11	0.48088|0.48088	.|.	0.513537|.	0.16071|.	N|.	0.231001|.	.|T	.|0.60457	.|0.2270	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.58578	.|-0.7612	.|4	0.25106|.	T|.	0.35|.	-3.0933|-3.0933	10.0426|10.0426	0.42166|0.42166	0.0:0.2065:0.7935:0.0|0.0:0.2065:0.7935:0.0	.|.	.|.	.|.	.|.	X|L	384|287	.|.	ENSP00000164227:E384X|.	E|R	+|+	1|2	0|0	BCL3|BCL3	49953911|49953911	1.000000|1.000000	0.71417|0.71417	0.782000|0.782000	0.31804|0.31804	0.765000|0.765000	0.43378|0.43378	4.900000|4.900000	0.63252|0.63252	1.841000|1.841000	0.53522|0.53522	0.485000|0.485000	0.47835|0.47835	GAG|CGA	.		0.662	BCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322976.1	NM_005178	
PLEC	5339	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	8	144991673	144991673	+	Nonsense_Mutation	SNP	C	C	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr8:144991673C>A	ENST00000322810.4	-	32	12896	c.12727G>T	c.(12727-12729)Gag>Tag	p.E4243*	PLEC_ENST00000357649.2_Nonsense_Mutation_p.E4110*|PLEC_ENST00000345136.3_Nonsense_Mutation_p.E4106*|PLEC_ENST00000436759.2_Nonsense_Mutation_p.E4133*|PLEC_ENST00000398774.2_Nonsense_Mutation_p.E4074*|PLEC_ENST00000356346.3_Nonsense_Mutation_p.E4092*|PLEC_ENST00000354958.2_Nonsense_Mutation_p.E4084*|PLEC_ENST00000354589.3_Nonsense_Mutation_p.E4106*|PLEC_ENST00000527096.1_Nonsense_Mutation_p.E4129*	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	4243	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)	p.E4243*(1)|p.E4133*(1)|p.E4106*(1)		NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						ATACAACGCTCCATCAGCTGC	0.597																																					p.E4243X		.											PLEC_ENST00000436759,NS,carcinoma,0,3	PLEC_ENST00000436759	0	3	Substitution - Nonsense(3)	kidney(3)	c.G12727T						.						55.0	60.0	58.0					8																	144991673		2085	4216	6301	SO:0001587	stop_gained	5339	exon32			AACGCTCCATCAG	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.12727G>T	8.37:g.144991673C>A	ENSP00000323856:p.Glu4243*	Somatic	29	0		WXS	Illumina HiSeq	.	60	13	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Nonsense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	C	54	22.160543	0.99946	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	.	.	.	5.14	4.26	0.50523	.	0.081026	0.46758	U	0.000274	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	15.4199	0.75003	0.0:0.8602:0.1398:0.0	.	.	.	.	X	4106;4110;4106;4074;4243;4084;4092;4133;4129	.	ENSP00000323856:E4243X	E	-	1	0	PLEC	145063661	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.796000	0.69080	1.373000	0.46208	0.549000	0.68633	GAG	.		0.597	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
CDH26	60437	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	58564141	58564141	+	Silent	SNP	T	T	C			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr20:58564141T>C	ENST00000244047.5	+	9	1517	c.1206T>C	c.(1204-1206)atT>atC	p.I402I	CDH26_ENST00000348616.4_Silent_p.I402I			Q8IXH8	CAD26_HUMAN	cadherin 26	402	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(11)|lung(14)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	44	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)			AGAGCTTCATTGTCAATAAAG	0.572																																					p.I402I		.											.	.	.	0			c.T1206C						.						146.0	171.0	162.0					20																	58564141		2203	4300	6503	SO:0001819	synonymous_variant	60437	exon9			CTTCATTGTCAAT	AF169690, AK055202	CCDS13485.1, CCDS13486.1	20q13.33	2010-01-26	2009-11-20		ENSG00000124215	ENSG00000124215		"""Cadherins / Major cadherins"""	15902	protein-coding gene	gene with protein product			"""cadherin-like 26"""				Standard	NM_177980		Approved	VR20	uc002ybe.3	Q8IXH8	OTTHUMG00000032874	ENST00000244047.5:c.1206T>C	20.37:g.58564141T>C		Somatic	60	0		WXS	Illumina HiSeq	.	100	34	NM_177980	A2A2M5|B3KNX3|Q6P5Y6|Q8TCH3|Q9BQN4|Q9NRU1	Silent	SNP	ENST00000244047.5	37																																																																																				.		0.572	CDH26-201	KNOWN	basic	protein_coding	protein_coding		NM_177980	
CHADL	150356	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	41633412	41633412	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr22:41633412T>C	ENST00000216241.9	-	3	1716	c.1664A>G	c.(1663-1665)aAc>aGc	p.N555S		NM_138481.1	NP_612490.1	Q6NUI6	CHADL_HUMAN	chondroadherin-like	555						proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|kidney(1)|skin(1)	4						GGTGATGCGGTTTCCACTCAG	0.662																																					p.N555S		.											.	.	.	0			c.A1664G						.						11.0	15.0	14.0					22																	41633412		691	1586	2277	SO:0001583	missense	150356	exon3			ATGCGGTTTCCAC	BC012882	CCDS46715.1	22q13.2	2008-10-31			ENSG00000100399	ENSG00000100399			25165	protein-coding gene	gene with protein product						12477932	Standard	NM_138481		Approved	SLRR4B	uc003azq.4	Q6NUI6	OTTHUMG00000150936	ENST00000216241.9:c.1664A>G	22.37:g.41633412T>C	ENSP00000216241:p.Asn555Ser	Somatic	65	0		WXS	Illumina HiSeq	.	103	34	NM_138481	Q05CY2|Q4G0S0|Q5JY13|Q86XY1|Q96E60	Missense_Mutation	SNP	ENST00000216241.9	37	CCDS46715.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	21.5|21.5	4.159344|4.159344	0.78226|0.78226	.|.	.|.	ENSG00000100399|ENSG00000100399	ENST00000216241;ENST00000455425|ENST00000417999	T;T|.	0.72505|.	-0.66;-0.07|.	5.22|5.22	4.17|4.17	0.49024|0.49024	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.76716|0.76716	0.4026|0.4026	M|M	0.86573|0.86573	2.825|2.825	0.45118|0.45118	D|D	0.998135|0.998135	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.998;0.999|.	T|T	0.79669|0.79669	-0.1707|-0.1707	10|5	0.72032|.	D|.	0.01|.	.|.	11.148|11.148	0.48442|0.48442	0.0:0.0739:0.0:0.9261|0.0:0.0739:0.0:0.9261	.|.	555;555|.	Q6NUI6-2;Q6NUI6|.	.;CHADL_HUMAN|.	S|A	555;52|553	ENSP00000216241:N555S;ENSP00000412359:N52S|.	ENSP00000216241:N555S|.	N|T	-|-	2|1	0|0	CHADL|CHADL	39963358|39963358	1.000000|1.000000	0.71417|0.71417	0.953000|0.953000	0.39169|0.39169	0.866000|0.866000	0.49608|0.49608	5.860000|5.860000	0.69546|0.69546	1.972000|1.972000	0.57404|0.57404	0.454000|0.454000	0.30748|0.30748	AAC|ACC	.		0.662	CHADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320597.1	NM_138481	
HNRNPM	4670	hgsc.bcm.edu	37	19	8528546	8528546	+	Silent	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr19:8528546C>T	ENST00000325495.4	+	5	455	c.414C>T	c.(412-414)agC>agT	p.S138S	HNRNPM_ENST00000348943.3_Silent_p.S138S	NM_005968.4	NP_005959.2	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M	138	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|RNA binding (GO:0003723)	p.S138S(1)		endometrium(5)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)	25						ATAGTCTGAGCGGAAGACCAC	0.418																																					p.S138S		.											HNRNPM,caecum,carcinoma,0,1	HNRNPM	0	1	Substitution - coding silent(1)	large_intestine(1)	c.C414T						.						114.0	93.0	100.0					19																	8528546		2203	4300	6503	SO:0001819	synonymous_variant	4670	exon5			TCTGAGCGGAAGA	L03532	CCDS12203.1, CCDS12204.1	19p13.2	2013-06-12		2008-04-18	ENSG00000099783	ENSG00000099783		"""RNA binding motif (RRM) containing"""	5046	protein-coding gene	gene with protein product	"""CEA receptor"""	160994		NAGR1, HNRPM		8441656, 7558047	Standard	NM_005968		Approved	HTGR1, HNRNPM4, HNRPM4, CEAR	uc010dwe.3	P52272	OTTHUMG00000182383	ENST00000325495.4:c.414C>T	19.37:g.8528546C>T		Somatic	33	0		WXS	Illumina HiSeq	.	50	2	NM_031203	Q15584|Q8WZ44|Q96H56|Q9BWL9|Q9Y492	Silent	SNP	ENST00000325495.4	37	CCDS12203.1																																																																																			.		0.418	HNRNPM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460894.1		
HRH3	11255	hgsc.bcm.edu;broad.mit.edu	37	20	60791534	60791534	+	Missense_Mutation	SNP	G	G	A	rs374571202		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr20:60791534G>A	ENST00000340177.5	-	3	1150	c.866C>T	c.(865-867)gCg>gTg	p.A289V	HRH3_ENST00000317393.6_Missense_Mutation_p.A289V	NM_007232.2	NP_009163.2	Q9Y5N1	HRH3_HUMAN	histamine receptor H3	289					brain development (GO:0007420)|drinking behavior (GO:0042756)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|learning (GO:0007612)|memory (GO:0007613)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of gamma-aminobutyric acid secretion (GO:0014053)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of serotonin secretion (GO:0014063)|neurotransmitter secretion (GO:0007269)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of epithelial cell proliferation (GO:0050679)|regulation of norepinephrine secretion (GO:0014061)|response to organic cyclic compound (GO:0014070)	integral component of plasma membrane (GO:0005887)|myelin sheath (GO:0043209)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|histamine receptor activity (GO:0004969)			breast(1)|endometrium(1)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	9	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;7.08e-07)		Betahistine(DB06698)|Histamine Phosphate(DB00667)|Mirtazapine(DB00370)	CCCGAGGGTCGCCTCCCCGGC	0.736																																					p.A289V		.											.	.	.	0			c.C866T						.																																			SO:0001583	missense	11255	exon3			AGGGTCGCCTCCC	AF140538	CCDS13493.1	20q13.33	2013-09-19			ENSG00000101180	ENSG00000101180		"""GPCR / Class A : Histamine receptors"""	5184	protein-coding gene	gene with protein product		604525				10347254	Standard	NM_007232		Approved	GPCR97	uc002ycf.2	Q9Y5N1	OTTHUMG00000032899	ENST00000340177.5:c.866C>T	20.37:g.60791534G>A	ENSP00000342560:p.Ala289Val	Somatic	14	0		WXS	Illumina HiSeq	.	16	7	NM_007232	Q4QRI7|Q9GZX2|Q9H4K8	Missense_Mutation	SNP	ENST00000340177.5	37	CCDS13493.1	.	.	.	.	.	.	.	.	.	.	G	3.448	-0.112710	0.06881	.	.	ENSG00000101180	ENST00000340177;ENST00000317393;ENST00000370797	T;T	0.67865	-0.25;-0.29	4.15	-3.37	0.04898	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.42337	0.1198	N	0.22421	0.69	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.15321	-1.0441	9	0.28530	T	0.3	0.04	2.0362	0.03540	0.2262:0.2577:0.3974:0.1187	.	289;289	Q9Y5N1-2;Q9Y5N1	.;HRH3_HUMAN	V	289;289;259	ENSP00000342560:A289V;ENSP00000321482:A289V	ENSP00000321482:A289V	A	-	2	0	HRH3	60224929	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.032000	0.03574	-0.941000	0.03700	-1.026000	0.02426	GCG	.		0.736	HRH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079994.1	NM_007232	
RALGAPA1	253959	hgsc.bcm.edu	37	14	36123575	36123575	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr14:36123575G>T	ENST00000389698.3	-	29	4477	c.4087C>A	c.(4087-4089)Caa>Aaa	p.Q1363K	RALGAPA1_ENST00000258840.6_Missense_Mutation_p.Q1410K|RALGAPA1_ENST00000382366.3_Missense_Mutation_p.Q1376K|RALGAPA1_ENST00000307138.6_Missense_Mutation_p.Q1363K	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	1363	Minimal domain that binds to TCF3/E12. {ECO:0000250}.				activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						TTACTTACTTGAATAATTTTC	0.274																																					p.Q1363K		.											.	.	.	0			c.C4087A						.						37.0	38.0	37.0					14																	36123575		2203	4296	6499	SO:0001583	missense	253959	exon29			TTACTTGAATAAT	AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"""tuberin-like protein 1"", ""GAP-related interacting protein to E12"""	608884	"""GTPase activating RANGAP domain-like 1"", ""GTPase activating Rap/RanGAP domain-like 1"""	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.4087C>A	14.37:g.36123575G>T	ENSP00000374348:p.Gln1363Lys	Somatic	22	0		WXS	Illumina HiSeq	.	48	4	NM_194301	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Missense_Mutation	SNP	ENST00000389698.3	37	CCDS32065.1	.	.	.	.	.	.	.	.	.	.	G	16.70	3.194880	0.58017	.	.	ENSG00000174373	ENST00000389698;ENST00000307138;ENST00000335518;ENST00000258840;ENST00000382366;ENST00000553892	T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18	5.93	5.93	0.95920	.	0.056727	0.64402	D	0.000001	T	0.51924	0.1703	N	0.24115	0.695	0.44995	D	0.998018	B;B;B;B	0.29988	0.264;0.107;0.141;0.107	B;B;B;B	0.32805	0.153;0.065;0.078;0.041	T	0.51419	-0.8708	10	0.48119	T	0.1	-11.9849	15.7803	0.78255	0.0:0.1355:0.8645:0.0	.	1410;1376;1363;1363	Q6GYQ0-6;B9EK38;Q6GYQ0-2;Q6GYQ0	.;.;.;RGPA1_HUMAN	K	1363;1363;1363;1410;1376;1410	ENSP00000374348:Q1363K;ENSP00000302647:Q1363K;ENSP00000258840:Q1410K;ENSP00000371803:Q1376K;ENSP00000451877:Q1410K	ENSP00000258840:Q1410K	Q	-	1	0	RALGAPA1	35193326	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	4.547000	0.60712	2.812000	0.96745	0.555000	0.69702	CAA	.		0.274	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022	
CSRP3	8048	hgsc.bcm.edu	37	11	19206570	19206570	+	Missense_Mutation	SNP	C	C	T	rs377066670		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr11:19206570C>T	ENST00000533783.1	-	6	677	c.437G>A	c.(436-438)cGc>cAc	p.R146H	CSRP3_ENST00000265968.3_Missense_Mutation_p.R146H	NM_003476.4	NP_003467.1	P50461	CSRP3_HUMAN	cysteine and glycine-rich protein 3 (cardiac LIM protein)	146	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue development (GO:0048738)|cardiac myofibril assembly (GO:0055003)|cellular calcium ion homeostasis (GO:0006874)|detection of muscle stretch (GO:0035995)|protein localization to organelle (GO:0033365)|regulation of the force of heart contraction (GO:0002026)|skeletal muscle tissue development (GO:0007519)	cytoskeleton (GO:0005856)|nucleus (GO:0005634)|Z disc (GO:0030018)	actinin binding (GO:0042805)|structural constituent of muscle (GO:0008307)|telethonin binding (GO:0031433)|zinc ion binding (GO:0008270)			kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(2)	10						GATGGCACAGCGGAAACAGGT	0.458																																					p.R146H		.											CSRP3,NS,malignant_melanoma,0,1	CSRP3	0	0			c.G437A						.	C	HIS/ARG,HIS/ARG	0,4398		0,0,2199	100.0	89.0	93.0		437,437	5.4	1.0	11		93	1,8585	1.2+/-3.3	0,1,4292	no	missense,missense	CSRP3	NM_001127656.1,NM_003476.3	29,29	0,1,6491	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	146/195,146/195	19206570	1,12983	2199	4293	6492	SO:0001583	missense	8048	exon6			GCACAGCGGAAAC	U20324	CCDS7848.1	11p15.1	2014-09-17				ENSG00000129170			2472	protein-coding gene	gene with protein product		600824				7490106	Standard	NM_003476		Approved	CLP, MLP, CMD1M	uc001mpk.3	P50461		ENST00000533783.1:c.437G>A	11.37:g.19206570C>T	ENSP00000431813:p.Arg146His	Somatic	44	1		WXS	Illumina HiSeq	.	68	3	NM_003476	Q9P131	Missense_Mutation	SNP	ENST00000533783.1	37	CCDS7848.1	.	.	.	.	.	.	.	.	.	.	C	33	5.246411	0.95305	0.0	1.16E-4	ENSG00000129170	ENST00000265968;ENST00000533783	D;D	0.91295	-2.82;-2.82	5.41	5.41	0.78517	Zinc finger, LIM-type (5);	0.000000	0.85682	D	0.000000	D	0.95430	0.8516	M	0.83384	2.64	0.80722	D	1	D	0.62365	0.991	D	0.64506	0.926	D	0.95733	0.8776	10	0.72032	D	0.01	-7.824	18.7893	0.91966	0.0:1.0:0.0:0.0	.	146	P50461	CSRP3_HUMAN	H	146	ENSP00000265968:R146H;ENSP00000431813:R146H	ENSP00000265968:R146H	R	-	2	0	CSRP3	19163146	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.794000	0.85869	2.552000	0.86080	0.655000	0.94253	CGC	.		0.458	CSRP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394484.1	NM_003476	
C1orf94	84970	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	34663014	34663014	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr1:34663014G>A	ENST00000488417.1	+	2	629	c.509G>A	c.(508-510)aGt>aAt	p.S170N	C1orf94_ENST00000373374.3_5'UTR	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94	170										central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)				GTGGCAGGCAGTAATGAGCGC	0.602																																					p.S170N		.											.	.	.	0			c.G509A						.						19.0	23.0	21.0					1																	34663014		692	1591	2283	SO:0001583	missense	84970	exon2			CAGGCAGTAATGA	AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698			28250	protein-coding gene	gene with protein product						12477932	Standard	NM_001134734		Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.509G>A	1.37:g.34663014G>A	ENSP00000435634:p.Ser170Asn	Somatic	23	0		WXS	Illumina HiSeq	.	29	13	NM_001134734	B3KVT1|D3DPR3|E9PJ76|Q96IC8	Missense_Mutation	SNP	ENST00000488417.1	37	CCDS44108.1	.	.	.	.	.	.	.	.	.	.	G	6.225	0.409666	0.11812	.	.	ENSG00000142698	ENST00000488417	T	0.26067	1.76	5.35	3.48	0.39840	.	.	.	.	.	T	0.20373	0.0490	L	0.36672	1.1	0.09310	N	1	B	0.10296	0.003	B	0.11329	0.006	T	0.19353	-1.0308	9	0.51188	T	0.08	-25.6678	8.0901	0.30795	0.1865:0.0:0.8135:0.0	.	170	Q6P1W5	CA094_HUMAN	N	170	ENSP00000435634:S170N	ENSP00000435634:S170N	S	+	2	0	C1orf94	34435601	0.084000	0.21492	0.001000	0.08648	0.019000	0.09904	2.091000	0.41691	0.630000	0.30394	0.655000	0.94253	AGT	.		0.602	C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2	NM_032884	
Unknown	0	hgsc.bcm.edu	37	16	33546482	33546482	+	IGR	SNP	G	G	C			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr16:33546482G>C								BMS1P8 (47390 upstream) : IGHV3OR16-12 (58748 downstream)																							GAATTACACTGTAGAAAACAG	0.348																																					.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	100873777	.			TACACTGTAGAAA																													16.37:g.33546482G>C		Somatic	29	0		WXS	Illumina HiSeq	.	52	16	.		RNA	SNP		37																																																																																				.	0	0.348								
ZNF527	84503	hgsc.bcm.edu	37	19	37879856	37879856	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr19:37879856A>G	ENST00000436120.2	+	5	1012	c.905A>G	c.(904-906)tAt>tGt	p.Y302C	ZNF527_ENST00000587349.1_Intron	NM_032453.1	NP_115829.1	Q8NB42	ZN527_HUMAN	zinc finger protein 527	302					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Y302>?(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	33			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GAAAAACCATATGCATGCAAT	0.393																																					p.Y302C		.											.,1	.	78	1	Complex(1)	lung(1)	c.A905G						.						105.0	96.0	99.0					19																	37879856		2093	4241	6334	SO:0001583	missense	84503	exon5			AACCATATGCATG	AB058732, AK091585	CCDS42559.1	19q13.1	2013-01-08			ENSG00000189164	ENSG00000189164		"""Zinc fingers, C2H2-type"", ""-"""	29385	protein-coding gene	gene with protein product						11347906	Standard	NM_032453		Approved	KIAA1829	uc010efk.1	Q8NB42	OTTHUMG00000048173	ENST00000436120.2:c.905A>G	19.37:g.37879856A>G	ENSP00000390179:p.Tyr302Cys	Somatic	30	1		WXS	Illumina HiSeq	.	40	3	NM_032453	B4DVL5	Missense_Mutation	SNP	ENST00000436120.2	37	CCDS42559.1	.	.	.	.	.	.	.	.	.	.	A	2.120	-0.401673	0.04865	.	.	ENSG00000189164	ENST00000356178;ENST00000317566;ENST00000436120	.	.	.	4.19	2.11	0.27256	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.557068	0.13635	N	0.373399	T	0.49983	0.1589	M	0.88704	2.975	0.09310	N	0.999999	B;B	0.17038	0.02;0.016	B;B	0.16722	0.016;0.009	T	0.53704	-0.8401	9	0.72032	D	0.01	.	3.9384	0.09316	0.6603:0.0:0.1838:0.1559	.	302;270	Q8NB42;Q8NB42-2	ZN527_HUMAN;.	C	302;270;250	.	ENSP00000325231:Y270C	Y	+	2	0	ZNF527	42571696	0.000000	0.05858	0.042000	0.18584	0.284000	0.27059	-0.422000	0.07043	0.193000	0.20303	-0.274000	0.10170	TAT	.		0.393	ZNF527-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458434.1	NM_032453	
GRM3	2913	hgsc.bcm.edu	37	7	86394780	86394780	+	Nonsense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr7:86394780G>T	ENST00000361669.2	+	2	1418	c.319G>T	c.(319-321)Gag>Tag	p.E107*	GRM3_ENST00000546348.1_Intron|GRM3_ENST00000394720.2_Nonsense_Mutation_p.E105*|GRM3_ENST00000439827.1_Nonsense_Mutation_p.E107*|GRM3_ENST00000536043.1_Intron	NM_000840.2	NP_000831.2	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3	107					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|axon (GO:0030424)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)	p.E107Q(1)		NS(2)|breast(6)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(43)|ovary(3)|pancreas(2)|prostate(4)|skin(25)|upper_aerodigestive_tract(5)	109	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)					CTATGCATTGGAGCAATCACT	0.408																																					p.E107X	GBM(52;969 1098 3139 52280)	.											GRM3,NS,carcinoma,-2,1	GRM3	-2	1	Substitution - Missense(1)	lung(1)	c.G319T						.						198.0	180.0	186.0					7																	86394780		2203	4300	6503	SO:0001587	stop_gained	2913	exon2			GCATTGGAGCAAT		CCDS5600.1	7q21.1-q21.2	2012-08-29			ENSG00000198822	ENSG00000198822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4595	protein-coding gene	gene with protein product		601115				8824806	Standard	NM_000840		Approved	GPRC1C, mGlu3, MGLUR3	uc003uid.3	Q14832	OTTHUMG00000022884	ENST00000361669.2:c.319G>T	7.37:g.86394780G>T	ENSP00000355316:p.Glu107*	Somatic	31	0		WXS	Illumina HiSeq	.	43	2	NM_000840	Q2PNZ6|Q75MV4|Q75N17|Q86YG6|Q8TBH9	Nonsense_Mutation	SNP	ENST00000361669.2	37	CCDS5600.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.783955	0.90282	.	.	ENSG00000198822	ENST00000361669;ENST00000439827;ENST00000394720	.	.	.	5.24	4.35	0.52113	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.4394	0.67306	0.0:0.0:0.8517:0.1483	.	.	.	.	X	107;107;105	.	ENSP00000355316:E107X	E	+	1	0	GRM3	86232716	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	9.648000	0.98483	1.434000	0.47414	0.655000	0.94253	GAG	.		0.408	GRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253362.2		
CFTR	1080	hgsc.bcm.edu	37	7	117232262	117232262	+	Nonsense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr7:117232262G>T	ENST00000003084.6	+	14	2173	c.2041G>T	c.(2041-2043)Gaa>Taa	p.E681*	CFTR_ENST00000454343.1_Nonsense_Mutation_p.E620*	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	681					cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	CTCCTGGACAGAAACAAAAAA	0.358									Cystic Fibrosis																												p.E681X		.											CFTR,NS,carcinoma,0,1	CFTR	0	0			c.G2041T						.						40.0	41.0	41.0					7																	117232262		2203	4300	6503	SO:0001587	stop_gained	1080	exon14	Familial Cancer Database	CF	TGGACAGAAACAA	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"""Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators"", ""ATP binding cassette transporters / subfamily C"""	1884	protein-coding gene	gene with protein product	"""ATP-binding cassette sub-family C, member 7"""	602421	"""cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"""	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.2041G>T	7.37:g.117232262G>T	ENSP00000003084:p.Glu681*	Somatic	25	0		WXS	Illumina HiSeq	.	40	2	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Nonsense_Mutation	SNP	ENST00000003084.6	37	CCDS5773.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.952566	0.92660	.	.	ENSG00000001626	ENST00000003084;ENST00000454343;ENST00000426809	.	.	.	5.63	4.74	0.60224	.	0.181977	0.64402	D	0.000017	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	-10.1405	13.9763	0.64275	0.074:0.0:0.926:0.0	.	.	.	.	X	681;620;651	.	ENSP00000003084:E681X	E	+	1	0	CFTR	117019498	1.000000	0.71417	0.068000	0.19968	0.222000	0.24845	4.899000	0.63245	1.478000	0.48253	0.563000	0.77884	GAA	.		0.358	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492	
KTI12	112970	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	52498812	52498812	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr1:52498812G>T	ENST00000371614.1	-	1	676	c.622C>A	c.(622-624)Ctc>Atc	p.L208I	RP11-91A18.4_ENST00000425802.1_RNA|TXNDC12_ENST00000371626.4_Intron	NM_138417.2	NP_612426.1	Q96EK9	KTI12_HUMAN	KTI12 homolog, chromatin associated (S. cerevisiae)	208							ATP binding (GO:0005524)			central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)|ovary(1)|stomach(2)|urinary_tract(1)	12						GCCTCCAGGAGTTCGGGAGAG	0.587																																					p.L208I		.											.	.	.	0			c.C622A						.						48.0	54.0	52.0					1																	52498812		2203	4300	6503	SO:0001583	missense	112970	exon1			CCAGGAGTTCGGG		CCDS562.1	1p32.3	2008-02-05			ENSG00000198841	ENSG00000198841			25160	protein-coding gene	gene with protein product						11929532	Standard	NM_138417		Approved	TOT4, MGC20419, SBBI81	uc001ctj.1	Q96EK9	OTTHUMG00000008630	ENST00000371614.1:c.622C>A	1.37:g.52498812G>T	ENSP00000360676:p.Leu208Ile	Somatic	63	0		WXS	Illumina HiSeq	.	88	27	NM_138417		Missense_Mutation	SNP	ENST00000371614.1	37	CCDS562.1	.	.	.	.	.	.	.	.	.	.	G	2.277	-0.365624	0.05069	.	.	ENSG00000198841	ENST00000371614	T	0.33654	1.4	4.5	2.6	0.31112	.	0.170837	0.34200	U	0.004170	T	0.16257	0.0391	N	0.21545	0.675	0.09310	N	0.999999	P	0.38223	0.623	B	0.34301	0.179	T	0.26538	-1.0100	10	0.02654	T	1	.	6.7454	0.23458	0.0956:0.3431:0.5613:0.0	.	208	Q96EK9	KTI12_HUMAN	I	208	ENSP00000360676:L208I	ENSP00000360676:L208I	L	-	1	0	KTI12	52271400	0.986000	0.35501	0.878000	0.34440	0.481000	0.33189	1.741000	0.38238	0.503000	0.28060	0.557000	0.71058	CTC	.		0.587	KTI12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023821.1	NM_138417	
SRPX2	27286	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	99921900	99921900	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chrX:99921900C>A	ENST00000373004.3	+	8	1359	c.931C>A	c.(931-933)Cag>Aag	p.Q311K		NM_014467.2	NP_055282.1	O60687	SRPX2_HUMAN	sushi-repeat containing protein, X-linked 2	311	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				angiogenesis (GO:0001525)|cell motility (GO:0048870)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of synapse assembly (GO:0051965)|regulation of phosphorylation (GO:0042325)|single organismal cell-cell adhesion (GO:0016337)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|excitatory synapse (GO:0060076)|extracellular space (GO:0005615)|synaptic membrane (GO:0097060)	hepatocyte growth factor binding (GO:0036458)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(10)|ovary(2)|upper_aerodigestive_tract(1)	19						GTCCAGCCGCCAGTGGTCAGG	0.582																																					p.Q311K		.											.	.	.	0			c.C931A						.						31.0	26.0	28.0					X																	99921900		2203	4300	6503	SO:0001583	missense	27286	exon8			AGCCGCCAGTGGT	AF393649	CCDS14471.1	Xq21.33-q23	2011-01-25	2011-01-25		ENSG00000102359	ENSG00000102359			30668	protein-coding gene	gene with protein product		300642	"""sushi-repeat-containing protein, X-linked 2"""			9864177	Standard	NM_014467		Approved	SRPUL	uc004egb.3	O60687	OTTHUMG00000022003	ENST00000373004.3:c.931C>A	X.37:g.99921900C>A	ENSP00000362095:p.Gln311Lys	Somatic	44	0		WXS	Illumina HiSeq	.	60	27	NM_014467	B3KQT3|Q8WW85	Missense_Mutation	SNP	ENST00000373004.3	37	CCDS14471.1	.	.	.	.	.	.	.	.	.	.	C	6.837	0.523732	0.13066	.	.	ENSG00000102359	ENST00000373004	T	0.65364	-0.15	5.26	5.26	0.73747	Complement control module (2);Sushi/SCR/CCP (3);	0.344881	0.34133	N	0.004222	T	0.51075	0.1653	L	0.38649	1.16	0.36192	D	0.850169	B	0.23128	0.08	B	0.22880	0.042	T	0.54886	-0.8226	9	.	.	.	-11.0505	13.2756	0.60186	0.1583:0.8417:0.0:0.0	.	311	O60687	SRPX2_HUMAN	K	311	ENSP00000362095:Q311K	.	Q	+	1	0	SRPX2	99808556	0.998000	0.40836	1.000000	0.80357	0.992000	0.81027	1.523000	0.35932	2.343000	0.79666	0.529000	0.55759	CAG	.		0.582	SRPX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057486.1	NM_014467	
RAB44	401258	hgsc.bcm.edu	37	6	36690143	36690143	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr6:36690143C>T	ENST00000229824.8	+	6	1913	c.1913C>T	c.(1912-1914)gCt>gTt	p.A638V		NM_001257357.1	NP_001244286.1	Q7Z6P3	RAB44_HUMAN	RAB44, member RAS oncogene family	0					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)			kidney(1)	1						CTCCAAGGGGCTCTCCTCCCA	0.637																																					p.G744G		.											.	.	.	0			c.C2232T						.																																			SO:0001583	missense	401258	exon9			AAGGGGCTCTCCT		CCDS75442.1	6p21.31-p21.2	2012-04-20	2004-02-03	2004-07-01	ENSG00000255587	ENSG00000255587		"""RAB, member RAS oncogene"""	21068	protein-coding gene	gene with protein product			"""RASD family, member 3"""	RASD3, RASL13			Standard	NM_001257357		Approved	dJ431A14.3	uc010jwm.2	Q7Z6P3	OTTHUMG00000016308	ENST00000229824.8:c.1913C>T	6.37:g.36690143C>T	ENSP00000229824:p.Ala638Val	Somatic	17	0		WXS	Illumina HiSeq	.	34	10	NM_001257357		Silent	SNP	ENST00000229824.8	37																																																																																				.		0.637	RAB44-001	PUTATIVE	not_organism_supported|mRNA_start_NF|cds_start_NF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043674.3	XM_003403440	
GRM5	2915	hgsc.bcm.edu;bcgsc.ca	37	11	88323785	88323785	+	Silent	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr11:88323785G>T	ENST00000305447.4	-	6	1823	c.1674C>A	c.(1672-1674)ccC>ccA	p.P558P	GRM5_ENST00000455756.2_Silent_p.P558P|GRM5_ENST00000393297.1_Silent_p.P558P|GRM5_ENST00000305432.5_Silent_p.P558P|GRM5_ENST00000418177.2_Silent_p.P558P	NM_001143831.2	NP_001137303.1	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5	558					activation of MAPKKK activity (GO:0000185)|cognition (GO:0050890)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|learning (GO:0007612)|locomotory behavior (GO:0007626)|negative regulation of locomotion (GO:0040013)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(1)|breast(5)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(18)|lung(40)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)|Rufinamide(DB06201)	GATCATCAGTGGGCCAAGACC	0.468																																					p.P558P		.											.	.	.	0			c.C1674A						.						128.0	98.0	108.0					11																	88323785		2201	4299	6500	SO:0001819	synonymous_variant	2915	exon7			ATCAGTGGGCCAA	D28538	CCDS8283.1, CCDS44694.1	11q14.3	2014-06-12			ENSG00000168959	ENSG00000168959		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4597	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 86"""	604102				7908515	Standard	NM_001143831		Approved	MGLUR5, GPRC1E, mGlu5, PPP1R86	uc001pcq.3	P41594	OTTHUMG00000134306	ENST00000305447.4:c.1674C>A	11.37:g.88323785G>T		Somatic	35	0		WXS	Illumina HiSeq	.	51	4	NM_000842	Q6J164	Silent	SNP	ENST00000305447.4	37	CCDS44694.1																																																																																			.		0.468	GRM5-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259226.1	NM_000842	
PPFIBP1	8496	hgsc.bcm.edu	37	12	27832995	27832995	+	Splice_Site	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr12:27832995G>T	ENST00000318304.8	+	20	2196		c.e20+1		PPFIBP1_ENST00000228425.6_Splice_Site|PPFIBP1_ENST00000542629.1_Splice_Site|PPFIBP1_ENST00000537927.1_Splice_Site	NM_001198916.1|NM_177444.2	NP_001185845.1|NP_803193	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)						cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)			PPFIBP1/ALK(3)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(13)|prostate(2)|skin(1)	32	Lung SC(9;0.0873)					AGTCTAACAGGTAAGAAGAGC	0.478																																					.		.											.	.	.	0			c.1454+1G>T						.						67.0	73.0	71.0					12																	27832995		2203	4300	6503	SO:0001630	splice_region_variant	8496	exon18			TAACAGGTAAGAA	AF034802	CCDS8713.1, CCDS55812.1, CCDS55813.1, CCDS55814.1	12p12.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"""	9249	protein-coding gene	gene with protein product		603141				9624153, 11836260	Standard	NM_003622		Approved	L2, hSGT2, hSgt2p, SGT2	uc001ric.2	Q86W92		ENST00000318304.8:c.1913+1G>T	12.37:g.27832995G>T		Somatic	62	0		WXS	Illumina HiSeq	.	87	4	NM_001198915	O75336|Q86X70|Q9NY03|Q9ULJ0	Splice_Site	SNP	ENST00000318304.8	37	CCDS55812.1	.	.	.	.	.	.	.	.	.	.	G	16.78	3.218870	0.58560	.	.	ENSG00000110841	ENST00000540114;ENST00000537927;ENST00000318304;ENST00000542629;ENST00000228425	.	.	.	5.91	5.91	0.95273	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.9003	0.96983	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PPFIBP1	27724262	1.000000	0.71417	1.000000	0.80357	0.473000	0.32948	9.029000	0.93718	2.808000	0.96608	0.655000	0.94253	.	.		0.478	PPFIBP1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402877.1	NM_003622	Intron
CPVL	54504	hgsc.bcm.edu	37	7	29111505	29111505	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr7:29111505C>T	ENST00000409850.1	-	13	1394	c.748G>A	c.(748-750)Gca>Aca	p.A250T	CPVL_ENST00000265394.5_Missense_Mutation_p.A250T|CPVL_ENST00000396276.3_Missense_Mutation_p.A250T			Q9H3G5	CPVL_HUMAN	carboxypeptidase, vitellogenic-like	250						extracellular vesicular exosome (GO:0070062)	serine-type carboxypeptidase activity (GO:0004185)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(1)	28						AGGAATTCTGCATAGCCCCCT	0.418																																					p.A250T		.											.	.	.	0			c.G748A						.						115.0	104.0	108.0					7																	29111505		2203	4300	6503	SO:0001583	missense	54504	exon9			ATTCTGCATAGCC	AF106704	CCDS5419.1	7p15.1	2012-02-10			ENSG00000106066	ENSG00000106066			14399	protein-coding gene	gene with protein product	"""carboxypeptidase WUG"", ""vitellogenic carboxypeptidase-like protein"", ""CP-Mac carboxypeptidase"""	609780				11401439	Standard	XM_005249786		Approved		uc003szw.3	Q9H3G5	OTTHUMG00000023669	ENST00000409850.1:c.748G>A	7.37:g.29111505C>T	ENSP00000387164:p.Ala250Thr	Somatic	55	0		WXS	Illumina HiSeq	.	98	3	NM_019029	A4D1A4|Q6UX20|Q8NBL7|Q96AR7|Q9HB41	Missense_Mutation	SNP	ENST00000409850.1	37	CCDS5419.1	.	.	.	.	.	.	.	.	.	.	C	15.20	2.763059	0.49574	.	.	ENSG00000106066	ENST00000265394;ENST00000396276;ENST00000455893;ENST00000409850;ENST00000542995;ENST00000448959	D;D;T;D;D	0.85629	-2.01;-2.01;1.44;-2.01;-2.01	5.54	3.64	0.41730	.	0.100619	0.64402	D	0.000003	D	0.89663	0.6780	M	0.69823	2.125	0.46376	D	0.999018	D	0.60575	0.988	P	0.62435	0.902	D	0.87741	0.2585	10	0.21540	T	0.41	-1.8315	15.2938	0.73888	0.0:0.6163:0.3837:0.0	.	250	Q9H3G5	CPVL_HUMAN	T	250;250;6;250;134;180	ENSP00000265394:A250T;ENSP00000379572:A250T;ENSP00000403580:A6T;ENSP00000387164:A250T;ENSP00000409036:A180T	ENSP00000265394:A250T	A	-	1	0	CPVL	29078030	0.999000	0.42202	0.971000	0.41717	0.218000	0.24690	1.399000	0.34566	1.309000	0.44985	0.591000	0.81541	GCA	.		0.418	CPVL-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328305.1	NM_019029	
DNAJA3	9093	hgsc.bcm.edu	37	16	4484495	4484495	+	Nonsense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr16:4484495G>T	ENST00000262375.6	+	2	399	c.322G>T	c.(322-324)Gag>Tag	p.E108*	DNAJA3_ENST00000355296.4_Nonsense_Mutation_p.E108*|DNAJA3_ENST00000431375.2_Intron|DNAJA3_ENST00000572139.1_3'UTR	NM_005147.5	NP_005138.3	Q96EY1	DNJA3_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 3	108	J.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation-induced cell death of T cells (GO:0006924)|cell aging (GO:0007569)|mitochondrial DNA replication (GO:0006264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of programmed cell death (GO:0043069)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell proliferation (GO:0042102)|protein folding (GO:0006457)|protein stabilization (GO:0050821)|response to heat (GO:0009408)|response to interferon-gamma (GO:0034341)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|small GTPase mediated signal transduction (GO:0007264)|T cell differentiation in thymus (GO:0033077)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of plasma membrane (GO:0019897)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|interferon-gamma receptor binding (GO:0005133)|metal ion binding (GO:0046872)|NF-kappaB binding (GO:0051059)|protein kinase binding (GO:0019901)|small GTPase regulator activity (GO:0005083)|transcription factor binding (GO:0008134)			NS(1)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|upper_aerodigestive_tract(2)	15						CAGCCAGAAAGAGATCAAGAA	0.428																																					p.E108X		.											.	.	.	0			c.G322T						.						169.0	157.0	161.0					16																	4484495		2197	4300	6497	SO:0001587	stop_gained	9093	exon2			CAGAAAGAGATCA	AF061749	CCDS10515.1, CCDS45400.1, CCDS66930.1	16p13.3	2011-09-02			ENSG00000103423	ENSG00000103423		"""Heat shock proteins / DNAJ (HSP40)"""	11808	protein-coding gene	gene with protein product		608382		TID1		9683573	Standard	NM_005147		Approved	hTid-1	uc002cwk.3	Q96EY1	OTTHUMG00000129470	ENST00000262375.6:c.322G>T	16.37:g.4484495G>T	ENSP00000262375:p.Glu108*	Somatic	48	0		WXS	Illumina HiSeq	.	62	4	NM_001135110	B2RAJ5|B4DI33|E7ES32|O75472|Q8WUJ6|Q8WXJ3|Q96D76|Q96IV1|Q9NYH8	Nonsense_Mutation	SNP	ENST00000262375.6	37	CCDS10515.1	.	.	.	.	.	.	.	.	.	.	G	38	6.671268	0.97751	.	.	ENSG00000103423	ENST00000262375;ENST00000355296	.	.	.	5.2	5.2	0.72013	.	0.232378	0.43579	D	0.000548	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-8.9504	17.7256	0.88364	0.0:0.0:1.0:0.0	.	.	.	.	X	108	.	ENSP00000262375:E108X	E	+	1	0	DNAJA3	4424496	1.000000	0.71417	0.995000	0.50966	0.988000	0.76386	9.682000	0.98655	2.413000	0.81919	0.655000	0.94253	GAG	.		0.428	DNAJA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251633.1		
EPHA7	2045	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	94068073	94068073	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr6:94068073G>A	ENST00000369303.4	-	4	1073	c.889C>T	c.(889-891)Cca>Tca	p.P297S		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	297	Cys-rich.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		CTGTGAGTTGGACAACGAGAG	0.463																																					p.P297S		.											.	.	.	0			c.C889T						.						97.0	90.0	92.0					6																	94068073		2203	4300	6503	SO:0001583	missense	2045	exon4			GAGTTGGACAACG	L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3390	protein-coding gene	gene with protein product		602190	"""EphA7"""			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.889C>T	6.37:g.94068073G>A	ENSP00000358309:p.Pro297Ser	Somatic	27	0		WXS	Illumina HiSeq	.	21	9	NM_004440	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Missense_Mutation	SNP	ENST00000369303.4	37	CCDS5031.1	.	.	.	.	.	.	.	.	.	.	G	32	5.154546	0.94686	.	.	ENSG00000135333	ENST00000369303	T	0.23950	1.88	5.62	5.62	0.85841	Tyrosine-protein kinase ephrin type A/B receptor-like (1);Growth factor, receptor (1);	0.053444	0.85682	D	0.000000	T	0.54287	0.1849	M	0.88906	2.99	0.80722	D	1	D;P;P	0.67145	0.996;0.905;0.846	D;P;P	0.75484	0.986;0.474;0.524	T	0.62946	-0.6746	10	0.87932	D	0	.	19.6472	0.95784	0.0:0.0:1.0:0.0	.	297;297;297	Q15375-4;Q15375-2;Q15375	.;.;EPHA7_HUMAN	S	297	ENSP00000358309:P297S	ENSP00000358309:P297S	P	-	1	0	EPHA7	94124794	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.835000	0.99442	2.652000	0.90054	0.655000	0.94253	CCA	.		0.463	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1		
RYR1	6261	hgsc.bcm.edu	37	19	39062862	39062862	+	Silent	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr19:39062862G>A	ENST00000359596.3	+	95	13950	c.13950G>A	c.(13948-13950)ctG>ctA	p.L4650L	RYR1_ENST00000360985.3_Silent_p.L4645L|RYR1_ENST00000355481.4_Silent_p.L4645L			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4650			L -> P (in CCD; autosomal recessive form). {ECO:0000269|PubMed:12937085}.		calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|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)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.L4650L(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	TGAGCCTCCTGCATACACTGG	0.567																																					p.L4650L		.											RYR1,NS,carcinoma,0,2	RYR1	0	1	Substitution - coding silent(1)	lung(1)	c.G13950A						.						122.0	105.0	111.0					19																	39062862		2203	4300	6503	SO:0001819	synonymous_variant	6261	exon95			CCTCCTGCATACA	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.13950G>A	19.37:g.39062862G>A		Somatic	32	0		WXS	Illumina HiSeq	.	39	2	NM_000540	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			.		0.567	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
TMEM59	9528	hgsc.bcm.edu	37	1	54512947	54512947	+	Silent	SNP	A	A	G			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr1:54512947A>G	ENST00000234831.5	-	2	537	c.288T>C	c.(286-288)tgT>tgC	p.C96C	TMEM59_ENST00000371348.1_5'UTR|TMEM59_ENST00000371341.1_5'UTR|TMEM59_ENST00000371344.1_5'Flank|TMEM59_ENST00000371337.3_Silent_p.C96C	NM_004872.3	NP_004863.2	Q9BXS4	TMM59_HUMAN	transmembrane protein 59	96					autophagy (GO:0006914)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of protein glycosylation in Golgi (GO:0090285)|negative regulation of protein processing (GO:0010955)|positive regulation of autophagy (GO:0010508)	extracellular vesicular exosome (GO:0070062)|Golgi cis cisterna (GO:0000137)|Golgi medial cisterna (GO:0005797)|Golgi trans cisterna (GO:0000138)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	endopeptidase activity (GO:0004175)			kidney(3)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7						TACCAGATTCACATTCCAATT	0.363																																					p.C96C		.											.	.	.	0			c.T288C						.						115.0	102.0	106.0					1																	54512947		2203	4300	6503	SO:0001819	synonymous_variant	9528	exon2			AGATTCACATTCC	AF047439	CCDS586.1	1p32.3	2008-05-14	2005-07-22	2005-07-22	ENSG00000116209	ENSG00000116209			1239	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 8"""	C1orf8		9653160	Standard	NM_004872		Approved	HSPC001	uc001cwp.3	Q9BXS4	OTTHUMG00000008437	ENST00000234831.5:c.288T>C	1.37:g.54512947A>G		Somatic	49	0		WXS	Illumina HiSeq	.	69	4	NM_004872	B3KQL7|O75393|Q4VBP9|Q5T705|Q96KX7	Silent	SNP	ENST00000234831.5	37	CCDS586.1																																																																																			.		0.363	TMEM59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023254.2	NM_004872	
UBR1	197131	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	43281074	43281074	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr15:43281074C>A	ENST00000290650.4	-	35	4018	c.3940G>T	c.(3940-3942)Gat>Tat	p.D1314Y	UBR1_ENST00000382177.2_3'UTR	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	1314					cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		ACTCGAGGATCCCTTTCATCA	0.398																																					p.D1314Y		.											.	.	.	0			c.G3940T						.						110.0	110.0	110.0					15																	43281074		2203	4299	6502	SO:0001583	missense	197131	exon35			GAGGATCCCTTTC		CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"""Ubiquitin protein ligase E3 component n-recognins"""	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.3940G>T	15.37:g.43281074C>A	ENSP00000290650:p.Asp1314Tyr	Somatic	45	0		WXS	Illumina HiSeq	.	78	36	NM_174916	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	37	CCDS10091.1	.	.	.	.	.	.	.	.	.	.	C	16.09	3.024211	0.54683	.	.	ENSG00000159459	ENST00000290650	T	0.59638	0.25	5.07	4.15	0.48705	.	0.162296	0.56097	D	0.000032	T	0.73289	0.3568	M	0.77313	2.365	0.80722	D	1	D	0.76494	0.999	D	0.64042	0.921	T	0.77744	-0.2473	10	0.87932	D	0	-24.1218	13.2721	0.60167	0.0:0.9244:0.0:0.0756	.	1314	Q8IWV7	UBR1_HUMAN	Y	1314	ENSP00000290650:D1314Y	ENSP00000290650:D1314Y	D	-	1	0	UBR1	41068366	0.977000	0.34250	0.856000	0.33681	0.575000	0.36095	2.446000	0.44908	1.352000	0.45808	0.655000	0.94253	GAT	.		0.398	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916	
ROR2	4920	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	9	94487167	94487167	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr9:94487167C>T	ENST00000375708.3	-	9	1807	c.1609G>A	c.(1609-1611)Gtc>Atc	p.V537I	ROR2_ENST00000375715.1_Missense_Mutation_p.V397I|ROR2_ENST00000550066.1_5'UTR	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	537	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						AGCAGGCAGACGACGTTGGGG	0.627																																					p.V537I		.											.	.	.	0			c.G1609A						.						72.0	72.0	72.0					9																	94487167		2203	4300	6503	SO:0001583	missense	4920	exon9			GGCAGACGACGTT	M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"""Immunoglobulin superfamily / I-set domain containing"""	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.1609G>A	9.37:g.94487167C>T	ENSP00000364860:p.Val537Ile	Somatic	19	0		WXS	Illumina HiSeq	.	9	7	NM_004560	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Missense_Mutation	SNP	ENST00000375708.3	37	CCDS6691.1	.	.	.	.	.	.	.	.	.	.	C	13.49	2.254016	0.39896	.	.	ENSG00000169071	ENST00000375715;ENST00000375708	D;D	0.91996	-2.95;-2.95	4.56	2.69	0.31865	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.38005	N	0.001852	D	0.86272	0.5893	L	0.35593	1.075	0.58432	D	0.999999	B;B	0.12630	0.003;0.006	B;B	0.22152	0.013;0.038	T	0.79035	-0.1968	10	0.33141	T	0.24	.	10.941	0.47273	0.0:0.847:0.0:0.153	.	537;397	Q01974;B1APY4	ROR2_HUMAN;.	I	397;537	ENSP00000364867:V397I;ENSP00000364860:V537I	ENSP00000364860:V537I	V	-	1	0	ROR2	93526988	0.748000	0.28294	0.883000	0.34634	0.946000	0.59487	1.462000	0.35266	0.639000	0.30564	0.561000	0.74099	GTC	.		0.627	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1		
RAB11B	9230	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	8467101	8467101	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr19:8467101G>A	ENST00000328024.6	+	3	586	c.368G>A	c.(367-369)gGc>gAc	p.G123D	RAB11B_ENST00000594216.1_Missense_Mutation_p.G123D|RAB11B_ENST00000601897.1_Missense_Mutation_p.G4D	NM_004218.3	NP_004209.2	Q15907	RB11B_HUMAN	RAB11B, member RAS oncogene family	123					cellular response to acidic pH (GO:0071468)|constitutive secretory pathway (GO:0045054)|establishment of protein localization to membrane (GO:0090150)|GTP catabolic process (GO:0006184)|insulin secretion involved in cellular response to glucose stimulus (GO:0035773)|melanosome transport (GO:0032402)|receptor recycling (GO:0001881)|regulated secretory pathway (GO:0045055)|regulation of anion transport (GO:0044070)|regulation of endocytic recycling (GO:2001135)|regulation of protein localization to cell surface (GO:2000008)|retrograde transport, endosome to plasma membrane (GO:1990126)|small GTPase mediated signal transduction (GO:0007264)|transferrin transport (GO:0033572)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|phagocytic vesicle (GO:0045335)|recycling endosome (GO:0055037)|recycling endosome membrane (GO:0055038)|synaptic vesicle (GO:0008021)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			large_intestine(2)|lung(1)|ovary(1)	4						ATGCTGGTGGGCAACAAGAGT	0.627																																					p.G123D		.											.	.	.	0			c.G368A						.						62.0	35.0	44.0					19																	8467101		2200	4294	6494	SO:0001583	missense	9230	exon3			TGGTGGGCAACAA	X79780	CCDS12201.1	19p13.2	2012-07-02			ENSG00000185236	ENSG00000185236		"""RAB, member RAS oncogene"""	9761	protein-coding gene	gene with protein product		604198				7811277	Standard	NM_004218		Approved	H-YPT3	uc002mju.4	Q15907		ENST00000328024.6:c.368G>A	19.37:g.8467101G>A	ENSP00000333547:p.Gly123Asp	Somatic	11	0		WXS	Illumina HiSeq	.	25	13	NM_004218	A5YM50|B2R7I4|B4DMK0|D6W671|Q2YDT2|Q5U0I1|Q6FHR0|Q6FI42|Q8NI07	Missense_Mutation	SNP	ENST00000328024.6	37	CCDS12201.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.627253	0.87560	.	.	ENSG00000185236	ENST00000328024	D	0.85861	-2.04	4.84	3.79	0.43588	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.95692	0.8599	H	0.99435	4.565	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	D	0.97010	0.9735	10	0.87932	D	0	.	13.5197	0.61561	0.0:0.0:0.8425:0.1575	.	123;123	B4DMK0;Q15907	.;RB11B_HUMAN	D	123	ENSP00000333547:G123D	ENSP00000333547:G123D	G	+	2	0	RAB11B	8373101	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	9.657000	0.98554	1.379000	0.46325	0.561000	0.74099	GGC	.		0.627	RAB11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460343.2	NM_004218	
POLA1	5422	hgsc.bcm.edu	37	X	24741359	24741359	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chrX:24741359C>T	ENST00000379059.3	+	11	1172	c.1157C>T	c.(1156-1158)aCg>aTg	p.T386M	POLA1_ENST00000379068.3_Missense_Mutation_p.T392M	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	386					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	ATCGAGCGAACGCTTTACTTC	0.428																																					p.T386M		.											.	.	.	0			c.C1157T						.						193.0	174.0	180.0					X																	24741359		2203	4300	6503	SO:0001583	missense	5422	exon11			AGCGAACGCTTTA		CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	2.7.7.7	"""DNA polymerases"""	9173	protein-coding gene	gene with protein product		312040	"""polymerase (DNA directed), alpha"", ""polymerase (DNA directed), alpha 1"", ""N syndrome (mental retardation, malformations, chromosome breakage)"""	POLA, NSX		1689958	Standard	NM_016937		Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.1157C>T	X.37:g.24741359C>T	ENSP00000368349:p.Thr386Met	Somatic	51	0		WXS	Illumina HiSeq	.	91	4	NM_016937	Q86UQ7	Missense_Mutation	SNP	ENST00000379059.3	37	CCDS14214.1	.	.	.	.	.	.	.	.	.	.	C	8.394	0.840410	0.16891	.	.	ENSG00000101868	ENST00000379068;ENST00000379059	T;T	0.09723	2.95;2.95	5.25	3.49	0.39957	DNA-directed DNA polymerase, family B, exonuclease domain (1);	0.279996	0.39475	N	0.001350	T	0.16938	0.0407	M	0.82517	2.595	0.58432	D	0.999997	B;B	0.25105	0.074;0.118	B;B	0.27500	0.067;0.08	T	0.01566	-1.1323	10	0.37606	T	0.19	-0.422	10.6638	0.45717	0.0:0.8424:0.0:0.1576	.	392;386	A6NMQ1;P09884	.;DPOLA_HUMAN	M	392;386	ENSP00000368358:T392M;ENSP00000368349:T386M	ENSP00000368349:T386M	T	+	2	0	POLA1	24651280	0.991000	0.36638	0.061000	0.19648	0.061000	0.15899	2.927000	0.48900	0.591000	0.29711	0.600000	0.82982	ACG	.		0.428	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937	
TENM4	26011	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	78498091	78498091	+	Silent	SNP	G	G	A	rs376356209	byFrequency	TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr11:78498091G>A	ENST00000278550.7	-	16	2679	c.2217C>T	c.(2215-2217)tgC>tgT	p.C739C		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	739	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										TGCCCCCTACGCACACGCCAT	0.701													G|||	2	0.000399361	0.0008	0.0	5008	,	,		14414	0.001		0.0	False		,,,				2504	0.0				p.C739C		.											.	.	.	0			c.C2217T						.	G		0,4040		0,0,2020	6.0	8.0	8.0		2217	1.1	0.9	11		8	1,8167		0,1,4083	no	coding-synonymous	ODZ4	NM_001098816.2		0,1,6103	AA,AG,GG		0.0122,0.0,0.0082		739/2770	78498091	1,12207	2020	4084	6104	SO:0001819	synonymous_variant	26011	exon16			CCCTACGCACACG	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"""odz, odd Oz/ten-m homolog 4 (Drosophila)"""	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.2217C>T	11.37:g.78498091G>A		Somatic	33	0		WXS	Illumina HiSeq	.	34	12	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Silent	SNP	ENST00000278550.7	37	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	G	0.840	-0.742175	0.03088	0.0	1.22E-4	ENSG00000149256	ENST00000533525	.	.	.	5.07	1.07	0.20283	.	.	.	.	.	T	0.65821	0.2728	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60372	-0.7276	4	.	.	.	.	12.7952	0.57556	0.3655:0.0:0.6345:0.0	.	.	.	.	V	53	.	.	A	-	2	0	ODZ4	78175739	0.951000	0.32395	0.930000	0.37139	0.021000	0.10359	0.230000	0.17852	-0.147000	0.11254	-2.069000	0.00389	GCG	.		0.701	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
PDE4A	5141	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	10568639	10568639	+	Missense_Mutation	SNP	C	C	T	rs200742358		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr19:10568639C>T	ENST00000352831.6	+	8	1072	c.962C>T	c.(961-963)cCg>cTg	p.P321L	PDE4A_ENST00000380702.2_Missense_Mutation_p.P299L|PDE4A_ENST00000344979.3_Missense_Mutation_p.P82L|PDE4A_ENST00000293683.5_Missense_Mutation_p.P295L|PDE4A_ENST00000592685.1_Missense_Mutation_p.P299L|PDE4A_ENST00000440014.2_Missense_Mutation_p.P260L	NM_001111307.1	NP_001104777.1	P27815	PDE4A_HUMAN	phosphodiesterase 4A, cAMP-specific	321					cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06)		Caffeine(DB00201)|Dipyridamole(DB00975)|Drotaverine(DB06751)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theophylline(DB00277)|Tofisopam(DB08811)	CCCTCCCAGCCGCCCCCGCCC	0.527													c|||	1	0.000199681	0.0	0.0	5008	,	,		11986	0.0		0.0	False		,,,				2504	0.001				p.P321L		.											.	.	.	0			c.C962T						.						65.0	75.0	71.0					19																	10568639		2203	4300	6503	SO:0001583	missense	5141	exon8			CCCAGCCGCCCCC		CCDS12238.1, CCDS45961.1, CCDS45962.1, CCDS45963.1, CCDS58649.1	19p13.2	2010-06-24	2010-06-24			ENSG00000065989	3.1.4.17	"""Phosphodiesterases"""	8780	protein-coding gene	gene with protein product	"""phosphodiesterase E2 dunce homolog (Drosophila)"""	600126	"""phosphodiesterase 4A, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E2)"""	DPDE2		8009369	Standard	NM_006202		Approved		uc002moj.2	P27815		ENST00000352831.6:c.962C>T	19.37:g.10568639C>T	ENSP00000270474:p.Pro321Leu	Somatic	37	0		WXS	Illumina HiSeq	.	59	22	NM_001111307	O75522|O76092|Q16255|Q16691|Q5DM53|Q6PMT2|Q8IVA7|Q8WUQ3|Q9H3H2	Missense_Mutation	SNP	ENST00000352831.6	37	CCDS45961.1	.	.	.	.	.	.	.	.	.	.	c	8.471	0.857449	0.17106	.	.	ENSG00000065989	ENST00000380702;ENST00000352831;ENST00000293683;ENST00000440014;ENST00000344979	T;T;T;T;T	0.66280	-0.19;-0.19;-0.2;-0.19;0.11	4.14	3.12	0.35913	.	1.049540	0.07645	N	0.930888	T	0.40956	0.1138	N	0.19112	0.55	0.45634	D	0.99856	P;P;B;B	0.50617	0.937;0.846;0.171;0.035	B;B;B;B	0.39706	0.307;0.131;0.018;0.003	T	0.41251	-0.9519	10	0.06365	T	0.9	.	7.7742	0.29026	0.7717:0.2283:0.0:0.0	.	82;260;295;321	P27815-4;P27815-6;P27815-2;P27815	.;.;.;PDE4A_HUMAN	L	299;321;295;260;82	ENSP00000370078:P299L;ENSP00000270474:P321L;ENSP00000293683:P295L;ENSP00000394754:P260L;ENSP00000341007:P82L	ENSP00000293683:P295L	P	+	2	0	PDE4A	10429639	1.000000	0.71417	0.990000	0.47175	0.326000	0.28443	1.407000	0.34657	0.942000	0.37525	-0.269000	0.10298	CCG	.		0.527	PDE4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451244.1		
SCG5	6447	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	15	32988766	32988766	+	Nonsense_Mutation	SNP	A	A	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr15:32988766A>T	ENST00000300175.4	+	6	705	c.595A>T	c.(595-597)Aag>Tag	p.K199*	SCG5_ENST00000413748.2_Nonsense_Mutation_p.K198*|SCG5_ENST00000494364.1_Nonsense_Mutation_p.K180*|SCG5_ENST00000497208.1_Nonsense_Mutation_p.K181*|SCG5_ENST00000498069.1_3'UTR	NM_001144757.1	NP_001138229.1	P05408	7B2_HUMAN	secretogranin V (7B2 protein)	199					intracellular protein transport (GO:0006886)|neuropeptide signaling pathway (GO:0007218)|peptide hormone processing (GO:0016486)|regulation of hormone secretion (GO:0046883)	extracellular region (GO:0005576)|secretory granule (GO:0030141)	enzyme inhibitor activity (GO:0004857)|GTP binding (GO:0005525)|unfolded protein binding (GO:0051082)			lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	6		all_lung(180;7.32e-08)		all cancers(64;6.48e-17)|Epithelial(43;1.23e-11)|GBM - Glioblastoma multiforme(186;1.39e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0212)		TGTTGCAAAGAAGTCTGTCCC	0.403																																					p.K199X		.											.	.	.	0			c.A595T						.						97.0	90.0	92.0					15																	32988766		1907	4127	6034	SO:0001587	stop_gained	6447	exon6			GCAAAGAAGTCTG	Y00757	CCDS45207.1, CCDS45208.1	15q13-q14	2006-03-20	2006-03-20	2006-03-20	ENSG00000166922	ENSG00000166922			10816	protein-coding gene	gene with protein product	"""prohormone convertase chaperone"""	173120	"""secretory granule, neuroendocrine protein 1 (7B2 protein)"""	SGNE1		8162254, 12646671	Standard	NM_003020		Approved	7B2, SgV	uc001zha.2	P05408	OTTHUMG00000159447	ENST00000300175.4:c.595A>T	15.37:g.32988766A>T	ENSP00000300175:p.Lys199*	Somatic	39	0		WXS	Illumina HiSeq	.	43	20	NM_001144757	P01164|Q6FHD0|Q9BS38	Nonsense_Mutation	SNP	ENST00000300175.4	37	CCDS45207.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.307608	0.81247	.	.	ENSG00000166922	ENST00000300175;ENST00000413748;ENST00000494364;ENST00000497208	.	.	.	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.0072	0.71522	1.0:0.0:0.0:0.0	.	.	.	.	X	199;198;180;181	.	ENSP00000300175:K199X	K	+	1	0	SCG5	30776058	1.000000	0.71417	1.000000	0.80357	0.740000	0.42216	7.606000	0.82863	2.131000	0.65755	0.460000	0.39030	AAG	.		0.403	SCG5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355438.1	NM_003020	
APP	351	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	21	27277339	27277339	+	Missense_Mutation	SNP	G	G	C			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr21:27277339G>C	ENST00000346798.3	-	15	1993	c.1960C>G	c.(1960-1962)Cca>Gca	p.P654A	APP_ENST00000358918.3_Intron|APP_ENST00000448388.2_Missense_Mutation_p.P544A|APP_ENST00000354192.3_Missense_Mutation_p.P523A|APP_ENST00000359726.3_Missense_Mutation_p.P598A|APP_ENST00000357903.3_Missense_Mutation_p.P635A|APP_ENST00000440126.3_Missense_Mutation_p.P630A|APP_ENST00000439274.2_Missense_Mutation_p.P598A|APP_ENST00000348990.5_Missense_Mutation_p.P579A	NM_000484.3	NP_000475.1	P05067	A4_HUMAN	amyloid beta (A4) precursor protein	654					adult locomotory behavior (GO:0008344)|axon cargo transport (GO:0008088)|axon midline choice point recognition (GO:0016199)|axonogenesis (GO:0007409)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|collateral sprouting in absence of injury (GO:0048669)|dendrite development (GO:0016358)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|ionotropic glutamate receptor signaling pathway (GO:0035235)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|mRNA polyadenylation (GO:0006378)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron differentiation (GO:0045665)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of multicellular organism growth (GO:0040014)|regulation of protein binding (GO:0043393)|regulation of synapse structure and activity (GO:0050803)|regulation of translation (GO:0006417)|response to oxidative stress (GO:0006979)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|suckling behavior (GO:0001967)|synaptic growth at neuromuscular junction (GO:0051124)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|ciliary rootlet (GO:0035253)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endosome (GO:0005768)|ER to Golgi transport vesicle (GO:0030134)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|receptor complex (GO:0043235)|spindle midzone (GO:0051233)|synapse (GO:0045202)	acetylcholine receptor binding (GO:0033130)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|peptidase activator activity (GO:0016504)|PTB domain binding (GO:0051425)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			endometrium(5)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(209;0.00295)				CTGATACCTGGTCGAGTGGTC	0.527																																					p.P654A		.											.	.	.	0			c.C1960G						.						146.0	129.0	135.0					21																	27277339		2203	4300	6503	SO:0001583	missense	351	exon15			TACCTGGTCGAGT	M15533	CCDS13576.1, CCDS13577.1, CCDS33523.1, CCDS46638.1, CCDS46639.1, CCDS56211.1, CCDS56212.1, CCDS56213.1	21q21.2	2014-01-30	2008-07-31		ENSG00000142192	ENSG00000142192		"""Endogenous ligands"""	620	protein-coding gene	gene with protein product	"""peptidase nexin-II"""	104760	"""Alzheimer disease"""	AD1		1679289	Standard	NM_001136130		Approved		uc002ylz.3	P05067	OTTHUMG00000078438	ENST00000346798.3:c.1960C>G	21.37:g.27277339G>C	ENSP00000284981:p.Pro654Ala	Somatic	32	0		WXS	Illumina HiSeq	.	25	13	NM_000484	B2R5V1|B4DII8|D3DSD1|D3DSD2|D3DSD3|P09000|P78438|Q13764|Q13778|Q13793|Q16011|Q16014|Q16019|Q16020|Q6GSC0|Q8WZ99|Q9BT38|Q9UC33|Q9UCA9|Q9UCB6|Q9UCC8|Q9UCD1|Q9UQ58	Missense_Mutation	SNP	ENST00000346798.3	37	CCDS13576.1	.	.	.	.	.	.	.	.	.	.	G	16.86	3.238246	0.58886	.	.	ENSG00000142192	ENST00000346798;ENST00000354192;ENST00000348990;ENST00000357903;ENST00000359726;ENST00000448388;ENST00000440126;ENST00000439274	D;D;D;D;D;D;D;D	0.96073	-1.95;-3.89;-3.89;-1.96;-3.9;-3.89;-1.96;-1.95	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	D	0.96935	0.8999	L	0.50333	1.59	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.993;1.0;0.996;0.996;1.0	D;D;D;D;D;D;D	0.91635	0.997;0.997;0.956;0.999;0.981;0.981;0.997	D	0.96788	0.9580	10	0.54805	T	0.06	.	19.0554	0.93062	0.0:0.0:1.0:0.0	.	544;598;630;523;579;635;654	E9PEV0;E9PG40;B4DII8;P05067-10;P05067-4;P05067-8;P05067	.;.;.;.;.;.;A4_HUMAN	A	654;523;579;635;598;544;630;598	ENSP00000284981:P654A;ENSP00000346129:P523A;ENSP00000345463:P579A;ENSP00000350578:P635A;ENSP00000352760:P598A;ENSP00000388538:P544A;ENSP00000387483:P630A;ENSP00000398879:P598A	ENSP00000284981:P654A	P	-	1	0	APP	26199210	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.449000	0.80643	2.837000	0.97791	0.655000	0.94253	CCA	.		0.527	APP-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171340.1	NM_000484	
SUPT20H	55578	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	13	37595675	37595675	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr13:37595675G>A	ENST00000350612.6	-	21	1946	c.1726C>T	c.(1726-1728)Cct>Tct	p.P576S	SUPT20H_ENST00000464744.1_Missense_Mutation_p.P577S|SUPT20H_ENST00000475892.1_Missense_Mutation_p.P655S|SUPT20H_ENST00000360252.4_Missense_Mutation_p.P577S|SUPT20H_ENST00000356185.3_Missense_Mutation_p.P577S	NM_001014286.2	NP_001014308.2	Q8NEM7	SP20H_HUMAN	suppressor of Ty 20 homolog (S. cerevisiae)	576					autophagy (GO:0006914)|chromatin organization (GO:0006325)|gastrulation (GO:0007369)	SAGA complex (GO:0000124)|SAGA-type complex (GO:0070461)	transcription cofactor activity (GO:0003712)										ATTCCTGCAGGAGTTATGGCA	0.517																																					p.P577S		.											.	.	.	0			c.C1729T						.						59.0	51.0	54.0					13																	37595675		2203	4300	6503	SO:0001583	missense	55578	exon21			CTGCAGGAGTTAT	AF093250	CCDS9362.1, CCDS31959.1, CCDS61311.1	13q13	2012-11-29	2012-11-29	2012-11-29	ENSG00000102710	ENSG00000102710			20596	protein-coding gene	gene with protein product	"""p38 interacting protein"", ""transcription factor (p38 interacting protein)"""	613417	"""chromosome 13 open reading frame 19"", ""family with sequence similarity 48, member A"""	C13orf19, FAM48A		12070015 , 16685401	Standard	NM_001278480		Approved	SPT20, bA421P11.4, P38IP	uc001uwg.3	Q8NEM7	OTTHUMG00000016747	ENST00000350612.6:c.1726C>T	13.37:g.37595675G>A	ENSP00000218894:p.Pro576Ser	Somatic	31	0		WXS	Illumina HiSeq	.	22	15	NM_017569	E7ER46|Q71RF3|Q9Y6A6	Missense_Mutation	SNP	ENST00000350612.6	37	CCDS31959.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.602702	0.87157	.	.	ENSG00000102710	ENST00000360252;ENST00000475892;ENST00000350612;ENST00000356185;ENST00000536874;ENST00000464744	T;T;T;T;T	0.56275	0.52;0.47;1.04;0.52;0.52	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.74068	0.3668	M	0.77313	2.365	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.999	D;D;D;D;D	0.69479	0.922;0.921;0.964;0.921;0.964	T	0.73994	-0.3807	10	0.49607	T	0.09	-13.5477	19.888	0.96917	0.0:0.0:1.0:0.0	.	655;577;577;576;576	E7ER46;A8K8L1;Q8NEM7-2;Q8NEM7;F5GX46	.;.;.;FA48A_HUMAN;.	S	577;655;576;577;576;577	ENSP00000353388:P577S;ENSP00000417510:P655S;ENSP00000218894:P576S;ENSP00000348512:P577S;ENSP00000419754:P577S	ENSP00000218894:P576S	P	-	1	0	FAM48A	36493675	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.169000	0.50809	2.720000	0.93068	0.591000	0.81541	CCT	.		0.517	SUPT20H-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354766.1	NM_017569	
FAM47C	442444	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	X	37028705	37028705	+	Missense_Mutation	SNP	A	A	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chrX:37028705A>T	ENST00000358047.3	+	1	2274	c.2222A>T	c.(2221-2223)gAg>gTg	p.E741V		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	741										breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						CTCCGCCCAGAGCCTCCCAAG	0.627																																					p.E741V		.											.	.	.	0			c.A2222T						.						47.0	46.0	46.0					X																	37028705		2202	4300	6502	SO:0001583	missense	442444	exon1			GCCCAGAGCCTCC	AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.2222A>T	X.37:g.37028705A>T	ENSP00000367913:p.Glu741Val	Somatic	149	0		WXS	Illumina HiSeq	.	219	14	NM_001013736	Q6ZU46	Missense_Mutation	SNP	ENST00000358047.3	37	CCDS35227.1	.	.	.	.	.	.	.	.	.	.	-	8.065	0.769062	0.15983	.	.	ENSG00000198173	ENST00000358047	T	0.16196	2.36	.	.	.	.	.	.	.	.	T	0.23094	0.0558	M	0.74881	2.28	0.23113	N	0.998274	D	0.58620	0.983	P	0.51170	0.661	T	0.13442	-1.0509	8	0.27785	T	0.31	.	2.9621	0.05896	0.5166:0.483:1.0E-4:2.0E-4	.	741	Q5HY64	FA47C_HUMAN	V	741	ENSP00000367913:E741V	ENSP00000367913:E741V	E	+	2	0	FAM47C	36938626	0.040000	0.19996	0.018000	0.16275	0.018000	0.09664	0.144000	0.16135	0.215000	0.20761	0.213000	0.17768	GAG	.		0.627	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736	
GUCY1A3	2982	hgsc.bcm.edu	37	4	156632290	156632290	+	Nonsense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr4:156632290G>T	ENST00000296518.7	+	6	1182	c.973G>T	c.(973-975)Gaa>Taa	p.E325*	GUCY1A3_ENST00000511507.1_Nonsense_Mutation_p.E325*|GUCY1A3_ENST00000393832.3_Nonsense_Mutation_p.E67*|GUCY1A3_ENST00000506455.1_Nonsense_Mutation_p.E325*|GUCY1A3_ENST00000455639.2_Nonsense_Mutation_p.E325*|GUCY1A3_ENST00000513574.1_Nonsense_Mutation_p.E325*|GUCY1A3_ENST00000511108.1_Nonsense_Mutation_p.E325*			Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3	325					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of cGMP biosynthetic process (GO:0030828)|regulation of blood pressure (GO:0008217)|relaxation of vascular smooth muscle (GO:0060087)|response to defense-related host nitric oxide production (GO:0052565)	guanylate cyclase complex, soluble (GO:0008074)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|receptor activity (GO:0004872)	p.E325K(1)		central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|liver(2)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)		AGAATACTTTGAAATTCTGAC	0.393																																					p.E325X		.											GUCY1A3,scalp,carcinoma,0,1	GUCY1A3	0	1	Substitution - Missense(1)	skin(1)	c.G973T						.						69.0	72.0	71.0					4																	156632290		2203	4300	6503	SO:0001587	stop_gained	2982	exon6			TACTTTGAAATTC		CCDS34085.1, CCDS54812.1	4q31.3-q33	2008-03-18				ENSG00000164116	4.6.1.2		4685	protein-coding gene	gene with protein product		139396		GUC1A3		1352257	Standard	NM_001130687		Approved	GC-SA3	uc003iow.3	Q02108		ENST00000296518.7:c.973G>T	4.37:g.156632290G>T	ENSP00000296518:p.Glu325*	Somatic	42	0		WXS	Illumina HiSeq	.	50	2	NM_001130687	D3DP19|D6RDW3|O43843|Q8TAH3	Nonsense_Mutation	SNP	ENST00000296518.7	37	CCDS34085.1	.	.	.	.	.	.	.	.	.	.	G	40	8.158619	0.98683	.	.	ENSG00000164116	ENST00000506455;ENST00000511108;ENST00000511507;ENST00000455639;ENST00000393832;ENST00000296518;ENST00000513574	.	.	.	5.76	5.76	0.90799	.	0.084050	0.50627	D	0.000102	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	.	20.3219	0.98684	0.0:0.0:1.0:0.0	.	.	.	.	X	325;325;325;325;67;325;325	.	ENSP00000296518:E325X	E	+	1	0	GUCY1A3	156851740	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.148000	0.58085	2.876000	0.98609	0.643000	0.83706	GAA	.		0.393	GUCY1A3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365786.2		
IRX1	79192	hgsc.bcm.edu	37	5	3599509	3599509	+	Silent	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr5:3599509C>T	ENST00000302006.3	+	2	499	c.447C>T	c.(445-447)caC>caT	p.H149H	CTD-2012M11.3_ENST00000559410.1_RNA	NM_024337.3	NP_077313.3	P78414	IRX1_HUMAN	iroquois homeobox 1	149					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			biliary_tract(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|pancreas(1)|prostate(5)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						TCAACGAGCACCGCAAGAATC	0.632																																					p.H149H		.											.,1	.	106	0			c.C447T						.						141.0	112.0	122.0					5																	3599509		2203	4300	6503	SO:0001819	synonymous_variant	79192	exon2			CGAGCACCGCAAG	U90307	CCDS34132.1	5p15.33	2011-12-16	2007-07-13		ENSG00000170549	ENSG00000170549		"""Homeoboxes / TALE class"""	14358	protein-coding gene	gene with protein product		606197					Standard	NM_024337		Approved	IRX-5	uc003jde.3	P78414	OTTHUMG00000161632	ENST00000302006.3:c.447C>T	5.37:g.3599509C>T		Somatic	44	0		WXS	Illumina HiSeq	.	39	2	NM_024337	Q7Z2F8|Q8N312	Silent	SNP	ENST00000302006.3	37	CCDS34132.1																																																																																			.		0.632	IRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365546.1	NM_024337	
NBPF22P	285622	hgsc.bcm.edu	37	5	85580175	85580175	+	RNA	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr5:85580175G>A	ENST00000590707.1	+	0	484					NR_003719.2				neuroblastoma breakpoint family, member 22, pseudogene																		TTCTCAGAGTGTGAAGAGTAC	0.468																																					.		.											.	.	.	0			.						.																																					285622	.			CAGAGTGTGAAGA	BC050328		5q14.3	2013-01-17	2011-04-15		ENSG00000205449	ENSG00000205449		"""neuroblastoma breakpoint family"""	28731	pseudogene	pseudogene						16079250	Standard	NR_003719		Approved	MGC48637	uc003kiq.3		OTTHUMG00000162585		5.37:g.85580175G>A		Somatic	36	0		WXS	Illumina HiSeq	.	58	19	.		RNA	SNP	ENST00000590707.1	37																																																																																				.		0.468	NBPF22P-004	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000453100.1	XM_208333	
MYH15	22989	hgsc.bcm.edu;bcgsc.ca	37	3	108174599	108174599	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr3:108174599C>T	ENST00000273353.3	-	21	2362	c.2306G>A	c.(2305-2307)cGa>cAa	p.R769Q	MYH15_ENST00000495753.2_5'Flank	NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	769	Actin-binding. {ECO:0000250}.|Myosin motor.					cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						GATTCCAAATCGGTACTGGGT	0.418																																					p.R769Q		.											.	.	.	0			c.G2306A						.						186.0	179.0	182.0					3																	108174599		1858	4100	5958	SO:0001583	missense	22989	exon21			CCAAATCGGTACT	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"""Myosins / Myosin superfamily : Class II"""	31073	protein-coding gene	gene with protein product		609929	"""myosin, heavy polypeptide 15"""			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.2306G>A	3.37:g.108174599C>T	ENSP00000273353:p.Arg769Gln	Somatic	48	0		WXS	Illumina HiSeq	.	55	4	NM_014981		Missense_Mutation	SNP	ENST00000273353.3	37	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	C	14.32	2.500876	0.44455	.	.	ENSG00000144821	ENST00000273353	D	0.87491	-2.26	6.06	-5.93	0.02254	Myosin head, motor domain (2);	.	.	.	.	T	0.77572	0.4150	N	0.20766	0.605	0.09310	N	1	B	0.20671	0.047	B	0.21917	0.037	T	0.56553	-0.7960	9	0.34782	T	0.22	.	17.2958	0.87170	0.0:0.763:0.0:0.237	.	769	Q9Y2K3	MYH15_HUMAN	Q	769	ENSP00000273353:R769Q	ENSP00000273353:R769Q	R	-	2	0	MYH15	109657289	0.001000	0.12720	0.022000	0.16811	0.946000	0.59487	-0.792000	0.04594	-0.864000	0.04078	-1.084000	0.02203	CGA	.		0.418	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	
LDLRAD1	388633	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	54474764	54474764	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr1:54474764C>A	ENST00000371360.1	-	6	526	c.509G>T	c.(508-510)tGt>tTt	p.C170F	LDLRAD1_ENST00000420619.1_Missense_Mutation_p.C131F|LDLRAD1_ENST00000371362.3_Missense_Mutation_p.C81F|LDLRAD1_ENST00000545928.1_Missense_Mutation_p.C127F	NM_001010978.2	NP_001010978.2	Q5T700	LRAD1_HUMAN	low density lipoprotein receptor class A domain containing 1	170	LDL-receptor class A 3; atypical. {ECO:0000255|PROSITE-ProRule:PRU00124}.					integral component of membrane (GO:0016021)				large_intestine(3)|prostate(1)|skin(3)	7						GGTTGAAGGACAGCGCCACCA	0.592																																					p.C170F		.											.	.	.	0			c.G509T						.						114.0	107.0	110.0					1																	54474764		2203	4300	6503	SO:0001583	missense	388633	exon6			GAAGGACAGCGCC		CCDS30725.1, CCDS60145.1, CCDS60146.1, CCDS60147.1	1p32.3	2008-02-05	2005-10-07		ENSG00000203985	ENSG00000203985			32069	protein-coding gene	gene with protein product			"""low density lipoprotein receptor A domain containing 1"""				Standard	NM_001010978		Approved		uc001cwm.2	Q5T700	OTTHUMG00000008433	ENST00000371360.1:c.509G>T	1.37:g.54474764C>A	ENSP00000360411:p.Cys170Phe	Somatic	13	0		WXS	Illumina HiSeq	.	14	4	NM_001010978	A0PJY0|B7ZME3|Q5T6Z9	Missense_Mutation	SNP	ENST00000371360.1	37	CCDS30725.1	.	.	.	.	.	.	.	.	.	.	C	13.21	2.170324	0.38315	.	.	ENSG00000203985	ENST00000371362;ENST00000371360;ENST00000545928;ENST00000420619	D;D;D;D	0.99784	-6.74;-6.74;-6.74;-6.74	4.5	4.5	0.54988	.	0.000000	0.64402	D	0.000004	D	0.99674	0.9878	M	0.71581	2.175	0.50813	D	0.99989	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.97291	0.9924	10	0.87932	D	0	-23.7599	16.1603	0.81700	0.0:1.0:0.0:0.0	.	127;170	B7ZME3;Q5T700	.;LRAD1_HUMAN	F	81;170;127;131	ENSP00000360413:C81F;ENSP00000360411:C170F;ENSP00000445871:C127F;ENSP00000411017:C131F	ENSP00000360411:C170F	C	-	2	0	LDLRAD1	54247352	1.000000	0.71417	0.512000	0.27736	0.007000	0.05969	5.081000	0.64444	2.348000	0.79779	0.655000	0.94253	TGT	.		0.592	LDLRAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023243.1	NM_001010978	
SF3B1	23451	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	198266713	198266713	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr2:198266713C>T	ENST00000335508.6	-	15	2310	c.2219G>A	c.(2218-2220)gGa>gAa	p.G740E	SF3B1_ENST00000462613.1_5'Flank|SNORA4_ENST00000365564.1_RNA	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	740					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)	p.G740E(1)		NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			ATTTACCTTTCCTCTGTGTTG	0.343			Mis		myelodysplastic syndrome																																p.G740E		.		Dom	yes		2	2q33.1	23451	"""splicing factor 3b, subunit 1, 155kDa"""		L	SF3B1,right_upper_lobe,carcinoma,0,5	SF3B1	0	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2219A						.						87.0	83.0	85.0					2																	198266713		2203	4300	6503	SO:0001583	missense	23451	exon15			ACCTTTCCTCTGT	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"""splicing factor 3b, subunit 1, 155kD"""			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.2219G>A	2.37:g.198266713C>T	ENSP00000335321:p.Gly740Glu	Somatic	53	0		WXS	Illumina HiSeq	.	101	31	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	37	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.036521	0.93630	.	.	ENSG00000115524	ENST00000335508	T	0.62364	0.03	5.58	5.58	0.84498	Armadillo-like helical (1);Armadillo-type fold (1);	0.107844	0.64402	D	0.000005	T	0.76449	0.3989	M	0.83692	2.655	0.80722	D	1	D	0.55800	0.973	P	0.51974	0.686	T	0.80183	-0.1488	10	0.66056	D	0.02	.	19.5659	0.95393	0.0:1.0:0.0:0.0	.	740	O75533	SF3B1_HUMAN	E	740	ENSP00000335321:G740E	ENSP00000335321:G740E	G	-	2	0	SF3B1	197974958	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.359000	0.79477	2.619000	0.88677	0.563000	0.77884	GGA	.		0.343	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2		
OC90	729330	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	133044207	133044207	+	Silent	SNP	G	G	T	rs199706785		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr8:133044207G>T	ENST00000443356.2	-	13	1086	c.1000C>A	c.(1000-1002)Cgg>Agg	p.R334R	OC90_ENST00000254627.3_Silent_p.R318R|OC90_ENST00000262283.5_Silent_p.R530R|OC90_ENST00000603859.1_Silent_p.R318R			Q02509	OC90_HUMAN	otoconin 90	334	Phospholipase A2-like 2.				lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(23)|ovary(2)|prostate(1)|skin(1)	37	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)			TCCGGGCACCGGGATGTCAGA	0.542																																					p.R318R		.											.	.	.	0			c.C952A						.						88.0	88.0	88.0					8																	133044207		2019	4180	6199	SO:0001819	synonymous_variant	729330	exon12			GGCACCGGGATGT	Z14310	CCDS47919.1	8q24.22	2011-03-01			ENSG00000253117	ENSG00000253117			8100	protein-coding gene	gene with protein product		601658		PLA2L		10329003, 9860971	Standard	NM_001080399		Approved		uc011lix.1	Q02509	OTTHUMG00000164672	ENST00000443356.2:c.1000C>A	8.37:g.133044207G>T		Somatic	21	0		WXS	Illumina HiSeq	.	35	11	NM_001080399	B4DNG8	Silent	SNP	ENST00000443356.2	37																																																																																				.		0.542	OC90-201	KNOWN	basic	protein_coding	protein_coding		NM_001080399	
PTPRF	5792	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	44085499	44085499	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr1:44085499A>G	ENST00000359947.4	+	29	5421	c.5081A>G	c.(5080-5082)tAc>tGc	p.Y1694C	PTPRF_ENST00000372413.3_Missense_Mutation_p.Y1685C|PTPRF_ENST00000372414.3_Missense_Mutation_p.Y1694C|PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000422171.2_Missense_Mutation_p.Y1053C|PTPRF_ENST00000438120.1_Missense_Mutation_p.Y1685C	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1694	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GGCTCTGACTACATCAATGCC	0.587																																					p.Y1694C		.											.	.	.	0			c.A5081G						.						132.0	108.0	116.0					1																	44085499		2203	4300	6503	SO:0001583	missense	5792	exon29			CTGACTACATCAA	Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.5081A>G	1.37:g.44085499A>G	ENSP00000353030:p.Tyr1694Cys	Somatic	20	0		WXS	Illumina HiSeq	.	27	10	NM_002840	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Missense_Mutation	SNP	ENST00000359947.4	37	CCDS489.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.57|19.57	3.853051|3.853051	0.71719|0.71719	.|.	.|.	ENSG00000142949|ENSG00000142949	ENST00000429895|ENST00000359947;ENST00000438120;ENST00000372414;ENST00000372413;ENST00000422171;ENST00000372407	.|T;T;T;T;T;T	.|0.38077	.|1.16;1.16;1.16;1.16;1.16;1.16	5.33|5.33	5.33|5.33	0.75918|0.75918	.|Protein-tyrosine phosphatase, receptor/non-receptor type (3);	.|0.000000	.|0.31381	.|N	.|0.007759	T|T	0.77565|0.77565	0.4149|0.4149	H|H	0.99379|0.99379	4.54|4.54	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D	.|0.97110	.|0.999;1.0;1.0;0.999;1.0	D|D	0.87838|0.87838	0.2649|0.2649	5|10	.|0.87932	.|D	.|0	.|.	16.0164|16.0164	0.80443|0.80443	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|1339;1053;1271;1685;1694	.|Q59FI2;F2Z3B8;Q5W9G3;P10586-2;P10586	.|.;.;.;.;PTPRF_HUMAN	A|C	1340|1694;1685;1694;1685;1053;766	.|ENSP00000353030:Y1694C;ENSP00000398822:Y1685C;ENSP00000361491:Y1694C;ENSP00000361490:Y1685C;ENSP00000387885:Y1053C;ENSP00000361484:Y766C	.|ENSP00000353030:Y1694C	T|Y	+|+	1|2	0|0	PTPRF|PTPRF	43858086|43858086	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.905000|0.905000	0.53344|0.53344	9.281000|9.281000	0.95811|0.95811	2.322000|2.322000	0.78497|0.78497	0.528000|0.528000	0.53228|0.53228	ACA|TAC	.		0.587	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1		
PREX2	80243	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	69129946	69129946	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr8:69129946G>A	ENST00000288368.4	+	38	4977	c.4700G>A	c.(4699-4701)cGg>cAg	p.R1567Q		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	1567					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)	p.R1567Q(1)		NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						GATGTGATGCGGAAGCAGGTA	0.527																																					p.R1567Q		.											PREX2,NS,carcinoma,0,1	PREX2	0	1	Substitution - Missense(1)	prostate(1)	c.G4700A						.						140.0	99.0	113.0					8																	69129946		2203	4300	6503	SO:0001583	missense	80243	exon38			TGATGCGGAAGCA	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.4700G>A	8.37:g.69129946G>A	ENSP00000288368:p.Arg1567Gln	Somatic	29	0		WXS	Illumina HiSeq	.	19	8	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	37	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	G	36	5.751501	0.96890	.	.	ENSG00000046889	ENST00000288368	T	0.76839	-1.05	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	D	0.83876	0.5349	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84785	0.0775	10	0.87932	D	0	.	19.2235	0.93808	0.0:0.0:1.0:0.0	.	1567	Q70Z35	PREX2_HUMAN	Q	1567	ENSP00000288368:R1567Q	ENSP00000288368:R1567Q	R	+	2	0	PREX2	69292500	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.973000	0.93428	2.838000	0.97847	0.591000	0.81541	CGG	.		0.527	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
KRTAP1-4	728255	hgsc.bcm.edu;bcgsc.ca	37	17	39186078	39186078	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr17:39186078G>T	ENST00000377747.4	-	1	278	c.253C>A	c.(253-255)Cca>Aca	p.P85T	KRTAP1-5_ENST00000361883.5_5'Flank	NM_001257305.1	NP_001244234.1	P0C5Y4	KRA14_HUMAN	keratin associated protein 1-4	85						keratin filament (GO:0045095)				lung(1)	1						CAGCAGGATGGGGGTGTGCAG	0.672																																					p.P85T		.											.	.	.	0			c.C253A						.																																			SO:0001583	missense	728255	exon1			AGGATGGGGGTGT	AC007455	CCDS58548.1	17q21.2	2010-06-22			ENSG00000204887	ENSG00000204887		"""Keratin associated proteins"""	18904	protein-coding gene	gene with protein product		608821					Standard	NM_001257305		Approved	KAP1.4	uc031raf.1	P0C5Y4	OTTHUMG00000133631	ENST00000377747.4:c.253C>A	17.37:g.39186078G>T	ENSP00000366976:p.Pro85Thr	Somatic	67	0		WXS	Illumina HiSeq	.	139	7	NM_001257305	A6NJ92	Missense_Mutation	SNP	ENST00000377747.4	37	CCDS58548.1	.	.	.	.	.	.	.	.	.	.	G	17.29	3.350910	0.61183	.	.	ENSG00000204887	ENST00000377747	T	0.30714	1.52	4.6	4.6	0.57074	.	0.000000	0.40640	N	0.001055	T	0.46541	0.1398	.	.	.	.	.	.	.	.	.	.	.	.	T	0.59700	-0.7405	6	0.62326	D	0.03	.	13.6272	0.62173	0.0:0.0:1.0:0.0	.	.	.	.	T	85	ENSP00000366976:P85T	ENSP00000366976:P85T	P	-	1	0	KRTAP1-4	36439604	1.000000	0.71417	0.981000	0.43875	0.812000	0.45895	3.110000	0.50352	2.482000	0.83794	0.655000	0.94253	CCA	.		0.672	KRTAP1-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257776.3		
WDPCP	51057	hgsc.bcm.edu;bcgsc.ca	37	2	63609210	63609210	+	Silent	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr2:63609210C>T	ENST00000272321.7	-	11	1982	c.1455G>A	c.(1453-1455)caG>caA	p.Q485Q	WDPCP_ENST00000409835.1_5'UTR|WDPCP_ENST00000409120.1_Silent_p.Q293Q|WDPCP_ENST00000409562.3_Silent_p.Q485Q|WDPCP_ENST00000409199.1_Silent_p.Q293Q|WDPCP_ENST00000398544.3_Silent_p.Q326Q	NM_015910.5	NP_056994.3	O95876	FRITZ_HUMAN	WD repeat containing planar cell polarity effector	485					auditory receptor cell morphogenesis (GO:0002093)|camera-type eye development (GO:0043010)|cardiovascular system development (GO:0072358)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|digestive system development (GO:0055123)|embryonic digit morphogenesis (GO:0042733)|establishment of protein localization (GO:0045184)|glomerular visceral epithelial cell migration (GO:0090521)|kidney development (GO:0001822)|palate development (GO:0060021)|regulation of embryonic cell shape (GO:0016476)|regulation of establishment of cell polarity (GO:2000114)|regulation of fibroblast migration (GO:0010762)|regulation of focal adhesion assembly (GO:0051893)|regulation of protein localization (GO:0032880)|regulation of ruffle assembly (GO:1900027)|respiratory system development (GO:0060541)|septin cytoskeleton organization (GO:0032185)|smoothened signaling pathway (GO:0007224)	axonemal basal plate (GO:0097541)|axoneme (GO:0005930)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(19)|ovary(1)|skin(1)	35						TCAGGCCCAGCTGTCCTCGAG	0.398																																					p.Q485Q		.											.	.	.	0			c.G1455A						.						69.0	66.0	67.0					2																	63609210		1923	4138	6061	SO:0001819	synonymous_variant	51057	exon11			GCCCAGCTGTCCT		CCDS42688.1, CCDS46301.1	2p15	2014-04-24	2011-02-01	2011-02-01	ENSG00000143951	ENSG00000143951			28027	protein-coding gene	gene with protein product		613580	"""chromosome 2 open reading frame 86"""	C2orf86		15654087, 20671153	Standard	NM_015910		Approved	hFrtz, fritz, BBS15	uc002sch.3	O95876	OTTHUMG00000152566	ENST00000272321.7:c.1455G>A	2.37:g.63609210C>T		Somatic	38	0		WXS	Illumina HiSeq	.	66	4	NM_015910	Q53RW4|Q7Z2Z3	Silent	SNP	ENST00000272321.7	37	CCDS42688.1																																																																																			.		0.398	WDPCP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326820.1	NM_015910	
KIAA0922	23240	hgsc.bcm.edu	37	4	154525248	154525248	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr4:154525248G>T	ENST00000409663.3	+	25	3133	c.3081G>T	c.(3079-3081)gaG>gaT	p.E1027D	KIAA0922_ENST00000440693.1_Missense_Mutation_p.E944D|KIAA0922_ENST00000409959.3_Missense_Mutation_p.E1028D	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	1027						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				CCATGCGTGAGAACTGGATCA	0.468																																					p.E1028D		.											KIAA0922_ENST00000409959,NS,carcinoma,0,2	KIAA0922_ENST00000409959	0	0			c.G3084T						.						78.0	78.0	78.0					4																	154525248		2203	4300	6503	SO:0001583	missense	23240	exon25			GCGTGAGAACTGG	AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.3081G>T	4.37:g.154525248G>T	ENSP00000386574:p.Glu1027Asp	Somatic	38	0		WXS	Illumina HiSeq	.	46	2	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	37	CCDS3783.2	.	.	.	.	.	.	.	.	.	.	G	12.48	1.951597	0.34471	.	.	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487	T;T;T;T	0.21191	2.3;2.02;2.3;2.02	5.86	1.89	0.25635	.	0.578481	0.20355	N	0.093969	T	0.38374	0.1038	L	0.56769	1.78	0.28138	N	0.929917	D;D;D	0.76494	0.999;0.993;0.995	D;P;P	0.79784	0.993;0.897;0.826	T	0.16276	-1.0408	10	0.41790	T	0.15	-14.2551	11.5339	0.50626	0.0677:0.4962:0.4361:0.0	.	944;1028;1027	A2VDJ0-3;A2VDJ0-5;A2VDJ0	.;.;T131L_HUMAN	D	1027;944;1028;805	ENSP00000386574:E1027D;ENSP00000409663:E944D;ENSP00000386787:E1028D;ENSP00000240487:E805D	ENSP00000240487:E805D	E	+	3	2	KIAA0922	154744698	1.000000	0.71417	0.852000	0.33557	0.459000	0.32528	2.079000	0.41577	0.328000	0.23435	0.655000	0.94253	GAG	.		0.468	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196	
DDX39B	7919	hgsc.bcm.edu	37	6	31498987	31498987	+	Intron	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr6:31498987G>A	ENST00000396172.1	-	9	1608				ATP6V1G2-DDX39B_ENST00000376185.1_Intron|DDX39B_ENST00000415382.2_Intron|DDX39B_ENST00000376177.2_Intron|DDX39B_ENST00000417556.2_Intron|DDX39B_ENST00000458640.1_Intron|DDX39B_ENST00000462421.1_5'Flank	NM_004640.6	NP_004631.1	Q13838	DX39B_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B						ATP catabolic process (GO:0006200)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|RNA secondary structure unwinding (GO:0010501)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|transcription export complex (GO:0000346)	ATP binding (GO:0005524)|ATP-dependent protein binding (GO:0043008)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)|RNA-dependent ATPase activity (GO:0008186)|U4 snRNA binding (GO:0030621)|U6 snRNA binding (GO:0017070)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19						TTGTGAGAAAGGAAATTTAAA	0.448																																					.		.											.	.	.	0			.						.						62.0	62.0	62.0					6																	31498987		2203	4300	6503	SO:0001627	intron_variant	100532737	.			GAGAAAGGAAATT	Z37166	CCDS4697.1	6p21.33	2011-02-09	2011-02-08	2011-02-08	ENSG00000198563	ENSG00000198563		"""DEAD-boxes"""	13917	protein-coding gene	gene with protein product	"""U2AF65-associated protein 56"""	142560	"""HLA-B associated transcript 1"""	BAT1		7601445, 2813433	Standard	NM_004640		Approved	D6S81E, UAP56	uc003ntu.3	Q13838	OTTHUMG00000031165	ENST00000396172.1:c.978-13C>T	6.37:g.31498987G>A		Somatic	32	0		WXS	Illumina HiSeq	.	40	20	.	B0S8C0|O43496|Q0EFA1|Q2L6F9|Q53GL9|Q5RJ64|Q5RJ66|Q5ST94|Q5STB4|Q5STB5|Q5STB7|Q5STB8|Q5STU4|Q5STU5|Q5STU6|Q5STU8|Q71V76	RNA	SNP	ENST00000396172.1	37	CCDS4697.1																																																																																			.		0.448	DDX39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259083.1	NM_004640	
GUCY2F	2986	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	108641914	108641914	+	Silent	SNP	C	C	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chrX:108641914C>A	ENST00000218006.2	-	11	2430	c.2139G>T	c.(2137-2139)acG>acT	p.T713T		NM_001522.2	NP_001513.2	P51841	GUC2F_HUMAN	guanylate cyclase 2F, retinal	713	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(6)|large_intestine(14)|lung(33)|prostate(3)|skin(1)	67						GTTCAGGGGCCGTCCACAGCA	0.478																																					p.T713T		.											.	.	.	0			c.G2139T						.						75.0	64.0	68.0					X																	108641914		2203	4300	6503	SO:0001819	synonymous_variant	2986	exon11			AGGGGCCGTCCAC	L37378	CCDS14545.1	Xq22	2008-08-01			ENSG00000101890	ENSG00000101890			4691	protein-coding gene	gene with protein product	"""guanylate cyclase 2D-like, membrane (retina-specific)"""	300041				8838319, 7777544	Standard	NM_001522		Approved	GUC2DL, GC-F, RetGC-2, ROS-GC2, CYGF	uc004eod.4	P51841	OTTHUMG00000022184	ENST00000218006.2:c.2139G>T	X.37:g.108641914C>A		Somatic	51	0		WXS	Illumina HiSeq	.	56	8	NM_001522	Q9UJF1	Silent	SNP	ENST00000218006.2	37	CCDS14545.1																																																																																			.		0.478	GUCY2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057884.1	NM_001522	
SRPR	6734	hgsc.bcm.edu	37	11	126135636	126135636	+	Missense_Mutation	SNP	G	G	T	rs565989865		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr11:126135636G>T	ENST00000332118.6	-	9	1288	c.1134C>A	c.(1132-1134)ttC>ttA	p.F378L	SRPR_ENST00000532259.1_Missense_Mutation_p.F350L|SRPR_ENST00000530680.1_5'Flank	NM_003139.3	NP_003130.2	P08240	SRPR_HUMAN	signal recognition particle receptor (docking protein)	378					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|signal recognition particle receptor complex (GO:0005785)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			endometrium(7)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)	21	all_hematologic(175;0.145)			BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0736)		ACTTACTGCTGAACGTCCCCA	0.473																																					p.F378L		.											SRPR,NS,carcinoma,0,1	SRPR	0	0			c.C1134A						.						134.0	102.0	113.0					11																	126135636		2201	4299	6500	SO:0001583	missense	6734	exon9			ACTGCTGAACGTC	BC001162	CCDS31717.1, CCDS53722.1	11q24-q25	2012-10-02	2008-10-29		ENSG00000182934	ENSG00000182934			11307	protein-coding gene	gene with protein product		182180	"""signal recognition particle receptor ('docking protein')"""			3340536, 1312991	Standard	NM_001177842		Approved	SRP-alpha, Sralpha	uc001qdh.3	P08240	OTTHUMG00000165826	ENST00000332118.6:c.1134C>A	11.37:g.126135636G>T	ENSP00000328023:p.Phe378Leu	Somatic	18	0		WXS	Illumina HiSeq	.	31	2	NM_003139	A6NIB3|B2R5Z8|B4E0H3|E9PJS4|Q9BVJ4	Missense_Mutation	SNP	ENST00000332118.6	37	CCDS31717.1	.	.	.	.	.	.	.	.	.	.	G	18.15	3.559122	0.65538	.	.	ENSG00000182934	ENST00000332118;ENST00000532259	.	.	.	5.25	3.22	0.36961	Signal recognition particle, SRP54 subunit, helical bundle (4);	0.000000	0.85682	D	0.000000	T	0.71813	0.3384	M	0.80616	2.505	0.80722	D	1	D;D	0.71674	0.998;0.995	D;D	0.70016	0.967;0.967	T	0.72616	-0.4239	9	0.51188	T	0.08	-13.3663	8.1058	0.30885	0.2629:0.0:0.7371:0.0	.	350;378	E9PJS4;P08240	.;SRPR_HUMAN	L	378;350	.	ENSP00000328023:F378L	F	-	3	2	SRPR	125640846	1.000000	0.71417	0.999000	0.59377	0.541000	0.35023	1.075000	0.30716	1.423000	0.47198	0.655000	0.94253	TTC	.		0.473	SRPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386425.2	NM_003139	
HOXB6	3216	hgsc.bcm.edu	37	17	46673137	46673137	+	3'UTR	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr17:46673137G>A	ENST00000484302.2	-	0	1935				HOXB-AS3_ENST00000492897.3_RNA|HOXB-AS3_ENST00000465846.2_RNA|HOXB-AS3_ENST00000480872.1_RNA|HOXB-AS3_ENST00000466037.2_RNA|HOXB-AS3_ENST00000481995.1_RNA|HOXB-AS3_ENST00000476204.1_RNA|HOXB6_ENST00000490419.1_5'Flank|HOXB-AS3_ENST00000460041.1_RNA|HOXB6_ENST00000225648.3_3'UTR|HOXB-AS3_ENST00000477144.1_RNA|HOXB-AS3_ENST00000474040.1_RNA|HOXB-AS3_ENST00000474324.1_RNA|HOXB-AS3_ENST00000467155.2_RNA|HOXB-AS3_ENST00000429755.4_RNA|HOXB-AS3_ENST00000487849.3_RNA|HOXB5_ENST00000239151.5_5'Flank|HOXB3_ENST00000552000.2_Intron			P17509	HXB6_HUMAN	homeobox B6						anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|erythrocyte homeostasis (GO:0034101)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(1)|lung(4)	7						CTttattattgttgttgttgt	0.408																																					.		.											.	.	.	0			.						.																																			SO:0001624	3_prime_UTR_variant	3216	.			ATTATTGTTGTTG		CCDS11531.1	17q21.32	2011-06-20	2005-12-22		ENSG00000108511	ENSG00000108511		"""Homeoboxes / ANTP class : HOXL subclass"""	5117	protein-coding gene	gene with protein product		142961	"""homeo box B6"""	HOX2, HOX2B		1973146, 1358459	Standard	XM_005257284		Approved		uc002ins.1	P17509	OTTHUMG00000159912	ENST00000484302.2:c.*638C>T	17.37:g.46673137G>A		Somatic	21	0		WXS	Illumina HiSeq	.	36	4	.	A8K835|D3DTV5|P09068|Q9HB11|Q9UGH2	RNA	SNP	ENST00000484302.2	37	CCDS11531.1																																																																																			.		0.408	HOXB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358146.2		
THPO	7066	hgsc.bcm.edu	37	3	184090419	184090419	+	Missense_Mutation	SNP	G	G	T	rs562029329		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr3:184090419G>T	ENST00000204615.7	-	6	1158	c.944C>A	c.(943-945)aCc>aAc	p.T315N	THPO_ENST00000421442.2_Missense_Mutation_p.H276Q|EIF2B5_ENST00000444495.1_Intron|THPO_ENST00000477594.1_5'Flank|THPO_ENST00000445696.2_Missense_Mutation_p.T311N	NM_000460.2|NM_001177597.1|NM_001177598.1	NP_000451.1|NP_001171068.1|NP_001171069.1	P40225	TPO_HUMAN	thrombopoietin	315	Pro-rich.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|myeloid cell differentiation (GO:0030099)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|thrombopoietin-mediated signaling pathway (GO:0038163)	extracellular space (GO:0005615)	growth factor activity (GO:0008083)			NS(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)	16	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GACCACAGGGGTGGGCAAGGT	0.597																																					p.T315N		.											THPO,colon,carcinoma,0,1	THPO	0	0			c.C944A						.						134.0	143.0	140.0					3																	184090419		2203	4300	6503	SO:0001583	missense	7066	exon6			ACAGGGGTGGGCA		CCDS3265.1, CCDS54693.1	3q27	2014-01-30	2008-07-31		ENSG00000090534	ENSG00000090534		"""Endogenous ligands"""	11795	protein-coding gene	gene with protein product	"""prepro-thrombopoietin"", ""megakaryocyte stimulating factor"", ""myeloproliferative leukemia virus oncogene ligand"", ""megakaryocyte growth and development factor"", ""MPL ligand"", ""megakaryocyte colony-stimulating factor"", ""c-mpl ligand"", ""thrombopoietin nirs variant 1"""	600044		MGDF		8202154	Standard	XM_006713738		Approved	TPO, MPLLG	uc003fol.1	P40225	OTTHUMG00000156745	ENST00000204615.7:c.944C>A	3.37:g.184090419G>T	ENSP00000204615:p.Thr315Asn	Somatic	19	0		WXS	Illumina HiSeq	.	27	2	NM_000460	A1L3Y0|B7ZLR8|B9EGA8|Q13020|Q15790|Q15791|Q15792	Missense_Mutation	SNP	ENST00000204615.7	37	CCDS3265.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.67|10.67	1.416008|1.416008	0.25552|0.25552	.|.	.|.	ENSG00000090534|ENSG00000090534	ENST00000421442|ENST00000204615;ENST00000445696;ENST00000353488	T|T;T	0.36520|0.48836	1.25|0.8;0.82	4.09|4.09	2.19|2.19	0.27852|0.27852	.|Four-helical cytokine, core (1);	.|0.559314	.|0.16126	.|N	.|0.228426	T|T	0.30665|0.30665	0.0772|0.0772	L|L	0.32530|0.32530	0.975|0.975	0.09310|0.09310	N|N	1|1	B|P;P	0.13145|0.48016	0.007|0.904;0.845	B|B;B	0.10450|0.38683	0.005|0.279;0.145	T|T	0.19353|0.19353	-1.0308|-1.0308	9|10	0.45353|0.72032	T|D	0.12|0.01	-17.4699|-17.4699	4.8077|4.8077	0.13328|0.13328	0.1327:0.2503:0.617:0.0|0.1327:0.2503:0.617:0.0	.|.	276|311;315	F8W6L1|P40225-2;P40225	.|.;TPO_HUMAN	Q|N	276|315;311;276	ENSP00000411704:H276Q|ENSP00000204615:T315N;ENSP00000410763:T311N	ENSP00000411704:H276Q|ENSP00000204615:T315N	H|T	-|-	3|2	2|0	THPO|THPO	185573113|185573113	0.748000|0.748000	0.28294|0.28294	0.014000|0.014000	0.15608|0.15608	0.096000|0.096000	0.18686|0.18686	0.767000|0.767000	0.26575|0.26575	0.321000|0.321000	0.23259|0.23259	0.467000|0.467000	0.42956|0.42956	CAC|ACC	.		0.597	THPO-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345554.1	NM_000460	
ZCWPW1	55063	hgsc.bcm.edu;bcgsc.ca	37	7	100000187	100000187	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr7:100000187G>A	ENST00000398027.2	-	16	1670	c.1423C>T	c.(1423-1425)Ccc>Tcc	p.P475S	ZCWPW1_ENST00000324725.6_Missense_Mutation_p.P355S|ZCWPW1_ENST00000360951.4_Intron|ZCWPW1_ENST00000490721.1_Missense_Mutation_p.P355S	NM_017984.4	NP_060454.3	Q9H0M4	ZCPW1_HUMAN	zinc finger, CW type with PWWP domain 1	475							zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)	16	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TTACGAATGGGCAAAATTGGG	0.438																																					p.P475S		.											.	.	.	0			c.C1423T						.						401.0	374.0	383.0					7																	100000187		1884	4127	6011	SO:0001583	missense	55063	exon16			GAATGGGCAAAAT	AK000919	CCDS43623.1, CCDS59067.1	7q22.1	2012-02-10	2004-11-03		ENSG00000078487	ENSG00000078487			23486	protein-coding gene	gene with protein product			"""zinc finger, CW-type with PWWP domain 1"""			11230166, 14607086, 20826339	Standard	NM_017984		Approved	FLJ10057, DKFZp434N0510, ZCW1	uc003uut.4	Q9H0M4	OTTHUMG00000159537	ENST00000398027.2:c.1423C>T	7.37:g.100000187G>A	ENSP00000381109:p.Pro475Ser	Somatic	30	0		WXS	Illumina HiSeq	.	57	4	NM_017984	A8MVF5|B4DUQ2|Q8NA98|Q9BUD0|Q9NWF7	Missense_Mutation	SNP	ENST00000398027.2	37	CCDS43623.1	.	.	.	.	.	.	.	.	.	.	G	10.47	1.358435	0.24598	.	.	ENSG00000078487	ENST00000398027;ENST00000490721;ENST00000324725	T;T;T	0.50548	0.86;0.74;0.74	4.46	3.53	0.40419	.	0.751758	0.11886	N	0.520027	T	0.54046	0.1834	L	0.46157	1.445	0.20926	N	0.99983	D;D;D	0.63046	0.961;0.961;0.992	P;P;P	0.59357	0.617;0.617;0.856	T	0.36016	-0.9765	9	.	.	.	0.0417	7.7084	0.28663	0.1212:0.0:0.8788:0.0	.	436;475;355	B4DXS7;Q9H0M4;Q9H0M4-4	.;ZCPW1_HUMAN;.	S	475;355;355	ENSP00000381109:P475S;ENSP00000419187:P355S;ENSP00000314880:P355S	.	P	-	1	0	ZCWPW1	99838123	0.819000	0.29175	0.248000	0.24265	0.063000	0.16089	1.487000	0.35540	1.373000	0.46208	-0.345000	0.07892	CCC	.		0.438	ZCWPW1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356083.1	NM_017984	
VGLL4	9686	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	11744451	11744451	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr3:11744451C>T	ENST00000273038.3	-	2	423	c.58G>A	c.(58-60)Gaa>Aaa	p.E20K	VGLL4_ENST00000404339.1_5'UTR	NM_001284391.1|NM_014667.2	NP_001271320.1|NP_055482.2	Q14135	VGLL4_HUMAN	vestigial-like family member 4	20					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|endometrium(1)|large_intestine(1)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10				LUSC - Lung squamous cell carcinoma(1;0.089)|Lung(1;0.111)		TTACGTTTTTCGTCATCAGCA	0.398																																					p.E20K		.											.	.	.	0			c.G58A						.						62.0	63.0	63.0					3																	11744451		2203	4300	6503	SO:0001583	missense	9686	exon2			GTTTTTCGTCATC	D50911	CCDS2606.1, CCDS46754.1, CCDS46755.1, CCDS46756.1, CCDS68342.1, CCDS68343.1	3p25.2	2014-03-03	2014-03-03		ENSG00000144560	ENSG00000144560			28966	protein-coding gene	gene with protein product			"""vestigial like 4 (Drosophila)"""			8590280, 15140898	Standard	NM_001284390		Approved	KIAA0121	uc010hdx.1	Q14135	OTTHUMG00000129739	ENST00000273038.3:c.58G>A	3.37:g.11744451C>T	ENSP00000273038:p.Glu20Lys	Somatic	92	0		WXS	Illumina HiSeq	.	105	70	NM_014667	B4DTS7|J3KN68|Q7L5V0|Q9BQ78	Missense_Mutation	SNP	ENST00000273038.3	37	CCDS2606.1	.	.	.	.	.	.	.	.	.	.	C	13.77	2.337245	0.41398	.	.	ENSG00000144560	ENST00000273038;ENST00000445411;ENST00000418000;ENST00000417206;ENST00000419541	T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01	5.28	4.38	0.52667	.	0.000000	0.43110	D	0.000616	T	0.34542	0.0901	N	0.22421	0.69	0.80722	D	1	D	0.55800	0.973	P	0.48089	0.566	T	0.05419	-1.0886	10	0.30854	T	0.27	.	11.9948	0.53196	0.0:0.8254:0.1746:0.0	.	20	Q14135	VGLL4_HUMAN	K	20	ENSP00000273038:E20K;ENSP00000412923:E20K;ENSP00000394439:E20K;ENSP00000391932:E20K;ENSP00000395557:E20K	ENSP00000273038:E20K	E	-	1	0	VGLL4	11719451	1.000000	0.71417	0.966000	0.40874	0.903000	0.53119	3.859000	0.55987	1.304000	0.44892	0.462000	0.41574	GAA	.		0.398	VGLL4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251950.2	NM_014667	
SPNS1	83985	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	28993745	28993745	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr16:28993745G>A	ENST00000311008.11	+	8	1411	c.1034G>A	c.(1033-1035)cGc>cAc	p.R345H	LAT_ENST00000395456.2_5'Flank|SPNS1_ENST00000565975.1_Missense_Mutation_p.R390H|LAT_ENST00000395461.3_5'Flank|LAT_ENST00000564277.1_5'Flank|SPNS1_ENST00000334536.8_Missense_Mutation_p.R293H|SPNS1_ENST00000352260.7_Missense_Mutation_p.R271H|LAT_ENST00000566177.1_5'Flank|LAT_ENST00000354453.4_5'Flank|SPNS1_ENST00000323081.8_Missense_Mutation_p.R272H|LAT_ENST00000454369.2_5'Flank|LAT_ENST00000360872.5_5'Flank|RP11-264B17.3_ENST00000569969.1_RNA	NM_032038.2	NP_114427.1	Q9H2V7	SPNS1_HUMAN	spinster homolog 1 (Drosophila)	345					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrial inner membrane (GO:0005743)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)|urinary_tract(1)	21						GAGATCAGCCGCCGGCTCCGC	0.652																																					p.R345H		.											.	.	.	0			c.G1034A						.						63.0	64.0	64.0					16																	28993745		2197	4300	6497	SO:0001583	missense	83985	exon9			TCAGCCGCCGGCT	BC006156	CCDS10646.1, CCDS45452.1, CCDS45453.1, CCDS45454.1	16p11.2	2007-04-12			ENSG00000169682	ENSG00000169682			30621	protein-coding gene	gene with protein product		612583				11340170, 12815463	Standard	NM_032038		Approved	HSpin1, nrs, SPINL, PP2030, SPIN1, LAT	uc010vdi.1	Q9H2V7	OTTHUMG00000131762	ENST00000311008.11:c.1034G>A	16.37:g.28993745G>A	ENSP00000309945:p.Arg345His	Somatic	27	0		WXS	Illumina HiSeq	.	31	9	NM_001142448	B5MDM9|Q6P182|Q71RB5|Q7L541|Q86VU7|Q8N953|Q8TCS5|Q9BRN5	Missense_Mutation	SNP	ENST00000311008.11	37	CCDS10646.1	.	.	.	.	.	.	.	.	.	.	G	18.26	3.584116	0.65992	.	.	ENSG00000169682	ENST00000311008;ENST00000334536;ENST00000352260;ENST00000323081	T;T;T;T	0.59502	0.26;0.26;0.26;0.26	4.32	4.32	0.51571	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.136830	0.44902	D	0.000415	T	0.71550	0.3353	M	0.79475	2.455	0.49389	D	0.99978	D;D;D;D	0.89917	0.998;0.999;0.999;1.0	D;D;D;D	0.68943	0.921;0.947;0.953;0.961	T	0.74523	-0.3637	10	0.87932	D	0	.	8.0356	0.30491	0.1084:0.0:0.8916:0.0	.	272;271;345;293	Q9H2V7-4;Q9H2V7-3;Q9H2V7;Q9H2V7-2	.;.;SPNS1_HUMAN;.	H	345;293;271;272	ENSP00000309945:R345H;ENSP00000335494:R293H;ENSP00000306050:R271H;ENSP00000318228:R272H	ENSP00000309945:R345H	R	+	2	0	SPNS1	28901246	0.997000	0.39634	1.000000	0.80357	0.531000	0.34715	2.514000	0.45503	2.244000	0.73946	0.462000	0.41574	CGC	.		0.652	SPNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254690.2	NM_032038	
OR2J3	442186	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	29080455	29080455	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr6:29080455T>G	ENST00000377169.1	+	1	788	c.788T>G	c.(787-789)cTc>cGc	p.L263R		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	263						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24						TGCATGTATCTCCAGCCACCA	0.448																																					p.L263R		.											.	.	.	0			c.T788G						.						111.0	111.0	111.0					6																	29080455		1251	2555	3806	SO:0001583	missense	442186	exon1			TGTATCTCCAGCC		CCDS43433.1	6p22.2-p21.31	2012-08-09			ENSG00000204701	ENSG00000204701		"""GPCR / Class A : Olfactory receptors"""	8261	protein-coding gene	gene with protein product		615016					Standard	NM_001005216		Approved	OR6-6	uc011dll.2	O76001	OTTHUMG00000031092	ENST00000377169.1:c.788T>G	6.37:g.29080455T>G	ENSP00000366374:p.Leu263Arg	Somatic	25	0		WXS	Illumina HiSeq	.	27	12	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Missense_Mutation	SNP	ENST00000377169.1	37	CCDS43433.1	.	.	.	.	.	.	.	.	.	.	T	10.18	1.280454	0.23392	.	.	ENSG00000204701	ENST00000377169	T	0.44083	0.93	2.78	2.78	0.32641	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.61451	0.2348	H	0.94698	3.57	0.19945	N	0.999941	D	0.89917	1.0	D	0.91635	0.999	T	0.53408	-0.8443	9	0.87932	D	0	.	9.3572	0.38173	0.0:0.0:0.0:1.0	.	263	O76001	OR2J3_HUMAN	R	263	ENSP00000366374:L263R	ENSP00000366374:L263R	L	+	2	0	OR2J3	29188434	0.000000	0.05858	0.972000	0.41901	0.258000	0.26162	-0.035000	0.12205	1.268000	0.44264	0.358000	0.22013	CTC	.		0.448	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2		
PERM1	84808	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	1	916538	916538	+	Silent	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr1:916538G>T	ENST00000341290.2	-	2	44	c.9C>A	c.(7-9)ccC>ccA	p.P3P	C1orf170_ENST00000433179.2_Silent_p.P23P			Q5SV97	PERM1_HUMAN		0					regulation of transcription, DNA-templated (GO:0006355)|response to muscle activity (GO:0014850)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											CACCGCCTCGGGGCTCCATCC	0.632																																					.		.											.	.	.	0			.						.																																			SO:0001819	synonymous_variant	84808	.			GCCTCGGGGCTCC																												ENST00000341290.2:c.9C>A	1.37:g.916538G>T		Somatic	30	0		WXS	Illumina HiSeq	.	34	6	.	Q6ZVZ7|Q9BRF2|S5G239	RNA	SNP	ENST00000341290.2	37																																																																																				.		0.632	C1orf170-001	PUTATIVE	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000097943.2		
GLRA2	2742	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	14748367	14748367	+	Silent	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chrX:14748367C>T	ENST00000218075.4	+	9	1649	c.1119C>T	c.(1117-1119)agC>agT	p.S373S	GLRA2_ENST00000443437.2_Silent_p.S284S|GLRA2_ENST00000355020.4_Silent_p.S373S	NM_002063.3	NP_002054.1	P23416	GLRA2_HUMAN	glycine receptor, alpha 2	373					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)|synapse assembly (GO:0007416)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(22)|ovary(1)|prostate(1)|skin(2)	37	Hepatocellular(33;0.128)				Ethanol(DB00898)|Glycine(DB00145)|Lindane(DB00431)	TTAATTTTAGCGGTTATGGGA	0.473																																					p.S373S		.											.	.	.	0			c.C1119T						.						223.0	222.0	222.0					X																	14748367		2203	4300	6503	SO:0001819	synonymous_variant	2742	exon10			TTTTAGCGGTTAT		CCDS14160.1, CCDS48085.1, CCDS55371.1	Xp22.2	2012-02-07			ENSG00000101958	ENSG00000101958		"""Ligand-gated ion channels / Glycine receptors"""	4327	protein-coding gene	gene with protein product		305990		GLR			Standard	NM_002063		Approved		uc010nep.3	P23416	OTTHUMG00000021166	ENST00000218075.4:c.1119C>T	X.37:g.14748367C>T		Somatic	75	0		WXS	Illumina HiSeq	.	89	29	NM_001118885	A8K0J6|B2R6I8|B7Z4F5|J3KQ59|Q53YX7|Q6ICQ0|Q99862	Silent	SNP	ENST00000218075.4	37	CCDS14160.1																																																																																			.		0.473	GLRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055829.1		
GMPR	2766	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	16290801	16290801	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr6:16290801T>A	ENST00000259727.4	+	8	920	c.806T>A	c.(805-807)aTg>aAg	p.M269K	GMPR_ENST00000544145.1_3'UTR	NM_006877.3	NP_006868.3	P36959	GMPR1_HUMAN	guanosine monophosphate reductase	269	GMP binding.				nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to cold (GO:0009409)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|GMP reductase complex (GO:1902560)	GMP reductase activity (GO:0003920)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	20	Breast(50;0.0427)|Ovarian(93;0.103)	all_hematologic(90;0.0895)				TTCTACGGGATGAGCTCTGAC	0.567																																					p.M269K		.											.	.	.	0			c.T806A						.						167.0	150.0	155.0					6																	16290801		2203	4300	6503	SO:0001583	missense	2766	exon8			ACGGGATGAGCTC		CCDS4537.1	6p23	2009-07-10			ENSG00000137198	ENSG00000137198	1.7.1.7		4376	protein-coding gene	gene with protein product		139265				2194676	Standard	NM_006877		Approved		uc003nbs.3	P36959	OTTHUMG00000014302	ENST00000259727.4:c.806T>A	6.37:g.16290801T>A	ENSP00000259727:p.Met269Lys	Somatic	34	0		WXS	Illumina HiSeq	.	45	16	NM_006877	Q96HQ6	Missense_Mutation	SNP	ENST00000259727.4	37	CCDS4537.1	.	.	.	.	.	.	.	.	.	.	T	18.16	3.561809	0.65538	.	.	ENSG00000137198	ENST00000259727	D	0.81908	-1.55	5.4	5.4	0.78164	Aldolase-type TIM barrel (1);IMP dehydrogenase/GMP reductase (1);	0.075806	0.85682	D	0.000000	D	0.95066	0.8402	H	0.99770	4.765	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.97442	1.0022	10	0.87932	D	0	-8.4891	15.4288	0.75075	0.0:0.0:0.0:1.0	.	269	P36959	GMPR1_HUMAN	K	269	ENSP00000259727:M269K	ENSP00000259727:M269K	M	+	2	0	GMPR	16398780	1.000000	0.71417	1.000000	0.80357	0.131000	0.20780	8.036000	0.88901	2.027000	0.59764	0.533000	0.62120	ATG	.		0.567	GMPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039942.2		
MIRLET7BHG	400931	hgsc.bcm.edu;broad.mit.edu	37	22	46501415	46501415	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr22:46501415C>T	ENST00000381051.2	+	5	387	c.334C>T	c.(334-336)Cac>Tac	p.H112Y	FLJ27365_ENST00000360737.3_Intron																							ACCTGCCGGGCACCCAGCCAA	0.657																																					.		.											.	.	.	0			.						.																																			SO:0001583	missense	400931	.			GCCGGGCACCCAG																												ENST00000381051.2:c.334C>T	22.37:g.46501415C>T	ENSP00000370439:p.His112Tyr	Somatic	31	0		WXS	Illumina HiSeq	.	51	5	.		RNA	SNP	ENST00000381051.2	37		.	.	.	.	.	.	.	.	.	.	C	3.952	-0.012040	0.07727	.	.	ENSG00000197182	ENST00000381051	.	.	.	1.29	0.0918	0.14469	.	.	.	.	.	T	0.18759	0.0450	.	.	.	.	.	.	P	0.43024	0.798	B	0.28385	0.089	T	0.18085	-1.0348	6	0.87932	D	0	.	5.0567	0.14537	0.0:0.6168:0.3832:0.0	.	112	B1AKH7	.	Y	112	.	ENSP00000370439:H112Y	H	+	1	0	MIRLET7BHG	44880079	0.000000	0.05858	0.005000	0.12908	0.002000	0.02628	-1.242000	0.02908	0.067000	0.16545	0.561000	0.74099	CAC	.		0.657	FLJ27365-003	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316783.1		
MT-ND5	4540	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	M	12736	12736	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chrM:12736G>A	ENST00000361567.2	+	1	400	c.400G>A	c.(400-402)Gct>Act	p.A134T	MT-TE_ENST00000387459.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TR_ENST00000387439.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TG_ENST00000387429.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	134					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(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						TCTTAGTTACCGCTAACAACC	0.388																																					p.A134T		.											.	.	.	0			c.G400A						.																																			SO:0001583	missense	0	exon1			GTTACCGCTAACA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.400G>A	M.37:g.12736G>A	ENSP00000354813:p.Ala134Thr	Somatic	41	0		WXS	Illumina HiSeq	.	14	13	ENST00000361567	Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	37																																																																																				.		0.388	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
HDAC4	9759	hgsc.bcm.edu;bcgsc.ca	37	2	240048352	240048352	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr2:240048352C>T	ENST00000345617.3	-	12	2109	c.1318G>A	c.(1318-1320)Gca>Aca	p.A440T	HDAC4_ENST00000541256.1_Missense_Mutation_p.A414T|HDAC4_ENST00000543185.1_Missense_Mutation_p.A24T	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	440					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|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)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		AAGGACTGTGCGTGGAGGGGC	0.622																																					p.A440T		.											.	.	.	0			c.G1318A						.						40.0	47.0	45.0					2																	240048352		2203	4300	6503	SO:0001583	missense	9759	exon12			ACTGTGCGTGGAG	AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"""brachydactyly-mental retardation syndrome"""	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.1318G>A	2.37:g.240048352C>T	ENSP00000264606:p.Ala440Thr	Somatic	52	0		WXS	Illumina HiSeq	.	66	4	NM_006037	Q9UND6	Missense_Mutation	SNP	ENST00000345617.3	37	CCDS2529.1	.	.	.	.	.	.	.	.	.	.	C	10.68	1.418311	0.25552	.	.	ENSG00000068024	ENST00000345617;ENST00000456922;ENST00000543185;ENST00000541256;ENST00000393621	T;T;T	0.63913	0.39;-0.07;1.56	4.46	0.516	0.17019	.	0.788660	0.11343	N	0.573862	T	0.48960	0.1529	L	0.51422	1.61	0.29628	N	0.845693	B;B;B;B;B;B	0.10296	0.0;0.0;0.001;0.003;0.0;0.001	B;B;B;B;B;B	0.08055	0.001;0.001;0.003;0.001;0.0;0.0	T	0.39014	-0.9634	9	.	.	.	.	3.966	0.09431	0.2819:0.4863:0.0:0.2317	.	440;323;414;414;408;440	B7Z8G5;F5H0Q9;F5H5W4;B7Z8I2;Q53SM2;P56524	.;.;.;.;.;HDAC4_HUMAN	T	440;328;24;414;323	ENSP00000264606:A440T;ENSP00000440481:A24T;ENSP00000443057:A414T	.	A	-	1	0	HDAC4	239713289	0.926000	0.31397	0.973000	0.42090	0.961000	0.63080	0.039000	0.13884	-0.123000	0.11745	0.563000	0.77884	GCA	.		0.622	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037	
TOP2A	7153	hgsc.bcm.edu	37	17	38560515	38560515	+	Silent	SNP	T	T	C			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr17:38560515T>C	ENST00000423485.1	-	19	2330	c.2172A>G	c.(2170-2172)ccA>ccG	p.P724P		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	724					apoptotic chromosome condensation (GO:0030263)|ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA ligation (GO:0006266)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|embryonic cleavage (GO:0040016)|hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cell cycle (GO:0000278)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|positive regulation of apoptotic process (GO:0043065)|positive regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral genome replication (GO:0045070)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|DNA-dependent ATPase activity (GO:0008094)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(9)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	39		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00183)		Amsacrine(DB00276)|Ciprofloxacin(DB00537)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Doxorubicin(DB00997)|Enoxacin(DB00467)|Epirubicin(DB00445)|Etoposide(DB00773)|Fleroxacin(DB04576)|Idarubicin(DB01177)|Levofloxacin(DB01137)|Lomefloxacin(DB00978)|Lucanthone(DB04967)|Mitoxantrone(DB01204)|Moxifloxacin(DB00218)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Pefloxacin(DB00487)|Podofilox(DB01179)|Sparfloxacin(DB01208)|Teniposide(DB00444)|Trovafloxacin(DB00685)|Valrubicin(DB00385)	TTCTCTGACCTGGTTTCAAAC	0.353																																					p.P724P		.											.	.	.	0			c.A2172G						.						122.0	114.0	117.0					17																	38560515		1870	4112	5982	SO:0001819	synonymous_variant	7153	exon19			CTGACCTGGTTTC		CCDS45672.1	17q21-q22	2008-08-06	2002-08-29		ENSG00000131747	ENSG00000131747	5.99.1.2		11989	protein-coding gene	gene with protein product		126430	"""topoisomerase (DNA) II alpha (170kD)"""	TOP2			Standard	NM_001067		Approved		uc002huq.3	P11388	OTTHUMG00000155008	ENST00000423485.1:c.2172A>G	17.37:g.38560515T>C		Somatic	66	0		WXS	Illumina HiSeq	.	93	4	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Silent	SNP	ENST00000423485.1	37	CCDS45672.1																																																																																			.		0.353	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1		
ATP13A5	344905	hgsc.bcm.edu;bcgsc.ca	37	3	193081945	193081945	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr3:193081945C>T	ENST00000342358.4	-	2	305	c.188G>A	c.(187-189)tGc>tAc	p.C63Y		NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	63						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		GCATGGGATGCAGTTGGCCCA	0.522																																					p.C63Y		.											.	.	.	0			c.G188A						.						171.0	162.0	165.0					3																	193081945		2203	4300	6503	SO:0001583	missense	344905	exon2			GGGATGCAGTTGG	AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"""ATPases / P-type"""	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.188G>A	3.37:g.193081945C>T	ENSP00000341942:p.Cys63Tyr	Somatic	31	0		WXS	Illumina HiSeq	.	57	4	NM_198505	Q6UWS4|Q6ZWL0	Missense_Mutation	SNP	ENST00000342358.4	37	CCDS33914.1	.	.	.	.	.	.	.	.	.	.	C	14.53	2.564381	0.45694	.	.	ENSG00000187527	ENST00000342358;ENST00000446087	T;T	0.22539	1.95;1.95	5.5	5.5	0.81552	.	0.085538	0.51477	D	0.000087	T	0.40862	0.1134	M	0.67569	2.06	0.38502	D	0.948269	D	0.89917	1.0	D	0.97110	1.0	T	0.26189	-1.0110	10	0.05351	T	0.99	-12.2749	17.2713	0.87103	0.0:1.0:0.0:0.0	.	63	Q4VNC0	AT135_HUMAN	Y	63;85	ENSP00000341942:C63Y;ENSP00000389416:C85Y	ENSP00000341942:C63Y	C	-	2	0	ATP13A5	194564639	0.996000	0.38824	0.137000	0.22149	0.077000	0.17291	5.054000	0.64275	2.765000	0.95021	0.650000	0.86243	TGC	.		0.522	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505	
DLGAP2	9228	hgsc.bcm.edu	37	8	1626409	1626409	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr8:1626409T>C	ENST00000421627.2	+	9	2212	c.2078T>C	c.(2077-2079)gTc>gCc	p.V693A		NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	772					neuron-neuron synaptic transmission (GO:0007270)	cell junction (GO:0030054)|neurofilament (GO:0005883)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(6)|lung(31)|prostate(3)	41		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		TCTAACAGCGTCACGGCCGCC	0.557																																					p.V693A		.											.	.	.	0			c.T2078C						.						53.0	58.0	56.0					8																	1626409		2091	4192	6283	SO:0001583	missense	9228	exon9			ACAGCGTCACGGC	AB000275	CCDS47760.1, CCDS75689.1	8p23	2007-12-06	2001-11-28		ENSG00000198010	ENSG00000198010			2906	protein-coding gene	gene with protein product		605438	"""discs, large (Drosophila) homolog-associated protein 2"""			9286858, 10854099	Standard	NM_004745		Approved	DAP-2	uc003wpl.4	Q9P1A6	OTTHUMG00000163599	ENST00000421627.2:c.2078T>C	8.37:g.1626409T>C	ENSP00000400258:p.Val693Ala	Somatic	41	0		WXS	Illumina HiSeq	.	77	4	NM_004745	A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	Missense_Mutation	SNP	ENST00000421627.2	37	CCDS47760.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.3|25.3	4.627428|4.627428	0.87560|0.87560	.|.	.|.	ENSG00000198010|ENSG00000198010	ENST00000520901|ENST00000356067;ENST00000421627	.|T	.|0.20598	.|2.06	4.85|4.85	4.85|4.85	0.62838|0.62838	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.47563|0.47563	0.1452|0.1452	M|M	0.81942|0.81942	2.565|2.565	0.48087|0.48087	D|D	0.999588|0.999588	.|D;D	.|0.76494	.|0.999;0.991	.|D;D	.|0.69307	.|0.957;0.963	T|T	0.53781|0.53781	-0.8390|-0.8390	5|10	.|0.66056	.|D	.|0.02	-13.8981|-13.8981	14.4352|14.4352	0.67277|0.67277	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|758;772	.|Q9P1A6-2;Q9P1A6	.|.;DLGP2_HUMAN	P|A	696|724;693	.|ENSP00000400258:V693A	.|ENSP00000348366:V724A	S|V	+|+	1|2	0|0	DLGAP2|DLGAP2	1613816|1613816	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.925000|0.925000	0.55904|0.55904	7.559000|7.559000	0.82265|0.82265	1.810000|1.810000	0.52873|0.52873	0.455000|0.455000	0.32223|0.32223	TCA|GTC	.		0.557	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374478.1	NM_004745	
ADAM20	8748	hgsc.bcm.edu	37	14	70990328	70990328	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr14:70990328G>T	ENST00000256389.3	-	2	1541	c.1297C>A	c.(1297-1299)Caa>Aaa	p.Q433K	RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003814.4	NP_003805.3	O43506	ADA20_HUMAN	ADAM metallopeptidase domain 20	383	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(2)	27			KIRC - Kidney renal clear cell carcinoma(12;0.133)|Kidney(31;0.188)	all cancers(60;0.00294)|BRCA - Breast invasive adenocarcinoma(234;0.00668)|OV - Ovarian serous cystadenocarcinoma(108;0.0344)		TCCCAATATTGGGCATAACTG	0.423																																					p.Q433K		.											ADAM20,NS,carcinoma,0,1	ADAM20	0	0			c.C1297A						.						240.0	134.0	170.0					14																	70990328		2203	4300	6503	SO:0001583	missense	8748	exon2			AATATTGGGCATA	AF029899	CCDS32111.1	14q24.2	2012-04-30	2005-08-18		ENSG00000134007	ENSG00000134007		"""ADAM metallopeptidase domain containing"""	199	protein-coding gene	gene with protein product		603712	"""a disintegrin and metalloproteinase domain 20"""			9469942	Standard	NM_003814		Approved		uc001xme.3	O43506	OTTHUMG00000167548	ENST00000256389.3:c.1297C>A	14.37:g.70990328G>T	ENSP00000256389:p.Gln433Lys	Somatic	65	0		WXS	Illumina HiSeq	.	47	2	NM_003814	Q6GTZ1|Q9UKJ9	Missense_Mutation	SNP	ENST00000256389.3	37	CCDS32111.1	.	.	.	.	.	.	.	.	.	.	G	9.147	1.015392	0.19355	.	.	ENSG00000134007	ENST00000256389	T	0.63096	-0.02	3.99	-7.97	0.01139	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	3.213270	0.01609	U	0.022446	T	0.63486	0.2515	M	0.77616	2.38	0.09310	N	1	B	0.20780	0.048	B	0.29440	0.102	T	0.51293	-0.8724	10	0.31617	T	0.26	.	12.5035	0.55968	0.0:0.2137:0.6491:0.1371	.	383	O43506	ADA20_HUMAN	K	433	ENSP00000256389:Q433K	ENSP00000256389:Q433K	Q	-	1	0	ADAM20	70060081	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	-3.054000	0.00626	-2.339000	0.00626	0.460000	0.39030	CAA	.		0.423	ADAM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395004.2		
PCDHA11	56138	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	140250727	140250727	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr5:140250727G>A	ENST00000398640.2	+	1	2039	c.2039G>A	c.(2038-2040)cGg>cAg	p.R680Q	PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018902.3	NP_061725.1	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11	680					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)			breast(1)|lung(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCTCTTCCCGGACTTTGGCG	0.652																																					p.R680Q		.											.	.	.	0			c.G2039A						.						29.0	35.0	33.0					5																	140250727		2197	4296	6493	SO:0001583	missense	56138	exon1			CTTCCCGGACTTT	AF152476	CCDS47284.1, CCDS75326.1	5q31	2010-11-26			ENSG00000249158	ENSG00000249158		"""Cadherins / Protocadherins : Clustered"""	8665	other	complex locus constituent	"""KIAA0345-like 3"", ""ortholog of mouse CNR7"""	606317		CNRS7		10380929, 10662547	Standard	NM_018902		Approved	CNR7, CRNR7, CNRN7, PCDH-ALPHA11		Q9Y5I1	OTTHUMG00000163369	ENST00000398640.2:c.2039G>A	5.37:g.140250727G>A	ENSP00000381636:p.Arg680Gln	Somatic	38	0		WXS	Illumina HiSeq	.	114	27	NM_018902	B2RN58|O75279	Missense_Mutation	SNP	ENST00000398640.2	37	CCDS47284.1	.	.	.	.	.	.	.	.	.	.	G	12.11	1.839885	0.32513	.	.	ENSG00000249158	ENST00000398640	T	0.51325	0.71	4.42	1.53	0.23141	.	.	.	.	.	T	0.35595	0.0937	L	0.48642	1.525	0.09310	N	1	B;B	0.27286	0.174;0.064	B;B	0.24269	0.052;0.011	T	0.21759	-1.0236	9	0.22109	T	0.4	.	6.9412	0.24494	0.1814:0.4399:0.3787:0.0	.	680;680	Q9Y5I1-2;Q9Y5I1	.;PCDAB_HUMAN	Q	680	ENSP00000381636:R680Q	ENSP00000381636:R680Q	R	+	2	0	PCDHA11	140230911	0.000000	0.05858	0.015000	0.15790	0.009000	0.06853	0.688000	0.25422	0.068000	0.16574	0.655000	0.94253	CGG	.		0.652	PCDHA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372885.2	NM_018902	
SNTG2	54221	hgsc.bcm.edu	37	2	1168797	1168797	+	Silent	SNP	C	C	T	rs374240224		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr2:1168797C>T	ENST00000308624.5	+	8	648	c.519C>T	c.(517-519)agC>agT	p.S173S	SNTG2_ENST00000467759.1_3'UTR|SNTG2_ENST00000407292.1_Intron	NM_018968.3	NP_061841.2	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	173					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|syntrophin complex (GO:0016013)	PDZ domain binding (GO:0030165)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		GGCCATCCAGCGACCACAGCA	0.498																																					p.S173S		.											SNTG2,NS,neuroblastoma,0,1	SNTG2	0	0			c.C519T						.						129.0	136.0	134.0					2																	1168797		1988	4166	6154	SO:0001819	synonymous_variant	54221	exon8			ATCCAGCGACCAC	AJ003029	CCDS46220.1	2p25	2008-05-23			ENSG00000172554	ENSG00000172554			13741	protein-coding gene	gene with protein product		608715				10747910	Standard	NM_018968		Approved	SYN5, G2SYN	uc002qwq.3	Q9NY99	OTTHUMG00000151370	ENST00000308624.5:c.519C>T	2.37:g.1168797C>T		Somatic	54	0		WXS	Illumina HiSeq	.	86	4	NM_018968	Q05AH5	Silent	SNP	ENST00000308624.5	37	CCDS46220.1																																																																																			.		0.498	SNTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322454.1	NM_018968	
PLOD2	5352	hgsc.bcm.edu	37	3	145788922	145788922	+	Nonsense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr3:145788922G>T	ENST00000360060.3	-	18	2142	c.1965C>A	c.(1963-1965)taC>taA	p.Y655*	RP11-274H2.2_ENST00000480247.1_RNA|RP11-274H2.3_ENST00000490375.1_RNA|RP11-274H2.2_ENST00000494745.2_RNA|PLOD2_ENST00000282903.5_Nonsense_Mutation_p.Y676*|PLOD2_ENST00000461497.1_Nonsense_Mutation_p.Y336*|PLOD2_ENST00000494950.1_Nonsense_Mutation_p.Y621*	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	655	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.				cellular protein modification process (GO:0006464)|extracellular matrix organization (GO:0030198)|response to hypoxia (GO:0001666)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-lysine 5-dioxygenase activity (GO:0008475)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29					Vitamin C(DB00126)	GTTCAGGGGAGTATTTTACTA	0.353																																					p.Y676X		.											.	.	.	0			c.C2028A						.						72.0	75.0	74.0					3																	145788922		2201	4300	6501	SO:0001587	stop_gained	5352	exon19			AGGGGAGTATTTT	U84573	CCDS3131.1, CCDS3132.1	3q24	2011-08-24	2005-01-04		ENSG00000152952	ENSG00000152952			9082	protein-coding gene	gene with protein product	"""lysyl hydroxlase 2"""	601865	"""procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2"""			9054364	Standard	XM_005247535		Approved	LH2	uc003evr.1	O00469	OTTHUMG00000159417	ENST00000360060.3:c.1965C>A	3.37:g.145788922G>T	ENSP00000353170:p.Tyr655*	Somatic	78	0		WXS	Illumina HiSeq	.	109	5	NM_182943	B3KWS3|Q59ED2|Q8N170	Nonsense_Mutation	SNP	ENST00000360060.3	37	CCDS3131.1	.	.	.	.	.	.	.	.	.	.	G	37	6.009720	0.97200	.	.	ENSG00000152952	ENST00000461497;ENST00000282903;ENST00000360060;ENST00000494950	.	.	.	4.9	-3.46	0.04767	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.2259	13.6264	0.62168	0.5343:0.0:0.4657:0.0	.	.	.	.	X	336;676;655;621	.	ENSP00000282903:Y676X	Y	-	3	2	PLOD2	147271612	0.751000	0.28327	0.913000	0.36048	0.506000	0.33950	-0.102000	0.10956	-0.646000	0.05452	-0.998000	0.02512	TAC	.		0.353	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935	
ZSCAN2	54993	hgsc.bcm.edu	37	15	85164298	85164298	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr15:85164298C>T	ENST00000448803.2	+	3	1164	c.872C>T	c.(871-873)gCc>gTc	p.A291V	ZSCAN2_ENST00000541040.1_Intron|ZSCAN2_ENST00000485222.2_Intron|ZSCAN2_ENST00000358472.3_Missense_Mutation_p.A141V|ZSCAN2_ENST00000327179.6_Missense_Mutation_p.A290V|ZSCAN2_ENST00000546148.1_Missense_Mutation_p.A291V|ZSCAN2_ENST00000538076.1_Intron	NM_181877.3	NP_870992.2	Q7Z7L9	ZSCA2_HUMAN	zinc finger and SCAN domain containing 2	291					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|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)|kidney(2)|large_intestine(7)|liver(2)|lung(4)|ovary(1)|pancreas(1)	19				UCEC - Uterine corpus endometrioid carcinoma (272;0.168)|all cancers(203;5.43e-22)		AGCCGGAGTGCCAACCTCATA	0.522																																					p.A291V		.											ZSCAN2,NS,lymphoid_neoplasm,0,1	ZSCAN2	0	0			c.C872T						.						58.0	59.0	59.0					15																	85164298		2203	4299	6502	SO:0001583	missense	54993	exon3			GGAGTGCCAACCT	BC041620	CCDS10329.2, CCDS32315.1, CCDS32316.1	15q25.2	2013-01-08	2004-11-01	2004-11-02	ENSG00000176371	ENSG00000176371		"""-"", ""Zinc fingers, C2H2-type"""	20994	protein-coding gene	gene with protein product			"""zinc finger protein 29"""	ZFP29		1937051	Standard	NM_017894		Approved	FLJ20595, ZNF854	uc002bkr.3	Q7Z7L9	OTTHUMG00000074027	ENST00000448803.2:c.872C>T	15.37:g.85164298C>T	ENSP00000410198:p.Ala291Val	Somatic	30	0		WXS	Illumina HiSeq	.	47	2	NM_181877	A6NG83|B2RMQ9|Q6ZQY9|Q9NWU4	Missense_Mutation	SNP	ENST00000448803.2	37	CCDS10329.2	.	.	.	.	.	.	.	.	.	.	C	17.71	3.457075	0.63401	.	.	ENSG00000176371	ENST00000448803;ENST00000546148;ENST00000358472;ENST00000327179;ENST00000379353	T;T;T;T	0.15372	2.43;2.43;3.14;2.43	4.78	4.78	0.61160	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.56097	D	0.000027	T	0.09598	0.0236	N	0.04355	-0.22	0.24854	N	0.99239	P;D	0.53745	0.823;0.962	B;B	0.43018	0.145;0.405	T	0.23190	-1.0195	9	.	.	.	-24.104	15.6428	0.77020	0.0:1.0:0.0:0.0	.	291;291	A8K5A9;Q7Z7L9	.;ZSCA2_HUMAN	V	291;291;141;290;272	ENSP00000410198:A291V;ENSP00000445451:A291V;ENSP00000351257:A141V;ENSP00000325123:A290V	.	A	+	2	0	ZSCAN2	82965302	0.124000	0.22315	0.367000	0.25926	0.989000	0.77384	2.172000	0.42463	2.355000	0.79922	0.655000	0.94253	GCC	.		0.522	ZSCAN2-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396956.1	NM_017894	
ZNF449	203523	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	134494603	134494603	+	Nonsense_Mutation	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chrX:134494603C>T	ENST00000339249.4	+	5	1299	c.1159C>T	c.(1159-1161)Cga>Tga	p.R387*		NM_152695.5	NP_689908.3	Q6P9G9	ZN449_HUMAN	zinc finger protein 449	387					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(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					ATGTAAAAAGCGATTCACTCG	0.428																																					p.R387X		.											.	.	.	0			c.C1159T						.						103.0	100.0	101.0					X																	134494603		2203	4298	6501	SO:0001587	stop_gained	203523	exon5			AAAAAGCGATTCA	AY280801	CCDS14649.1	Xq26.3	2013-01-09			ENSG00000173275	ENSG00000173275		"""-"", ""Zinc fingers, C2H2-type"""	21039	protein-coding gene	gene with protein product		300627					Standard	NM_152695		Approved	ZSCAN19, FLJ23614	uc004eys.3	Q6P9G9	OTTHUMG00000022478	ENST00000339249.4:c.1159C>T	X.37:g.134494603C>T	ENSP00000339585:p.Arg387*	Somatic	28	0		WXS	Illumina HiSeq	.	75	32	NM_152695	Q5JRZ7|Q5JRZ8|Q6NZX2|Q8N3Q1|Q8TED7	Nonsense_Mutation	SNP	ENST00000339249.4	37	CCDS14649.1	.	.	.	.	.	.	.	.	.	.	C	18.09	3.546768	0.65198	.	.	ENSG00000173275	ENST00000339249	.	.	.	4.49	3.55	0.40652	.	0.000000	0.35936	N	0.002881	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	.	8.4042	0.32605	0.349:0.651:0.0:0.0	.	.	.	.	X	387	.	ENSP00000339585:R387X	R	+	1	2	ZNF449	134322269	0.340000	0.24792	0.997000	0.53966	0.128000	0.20619	0.183000	0.16919	2.228000	0.72767	0.600000	0.82982	CGA	.		0.428	ZNF449-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058411.1	NM_152695	
MYO5C	55930	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	52517156	52517156	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr15:52517156G>A	ENST00000261839.7	-	28	3549	c.3388C>T	c.(3388-3390)Cat>Tat	p.H1130Y		NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	1130						extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		TCATTTAAATGTTCCAGATCT	0.343																																					p.H1130Y		.											.	.	.	0			c.C3388T						.						120.0	114.0	116.0					15																	52517156		1826	4075	5901	SO:0001583	missense	55930	exon28			TTAAATGTTCCAG	AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"""Myosins / Myosin superfamily : Class V"""	7604	protein-coding gene	gene with protein product	"""myosin 5C"""	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.3388C>T	15.37:g.52517156G>A	ENSP00000261839:p.His1130Tyr	Somatic	49	0		WXS	Illumina HiSeq	.	123	44	NM_018728	Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	37	CCDS42036.1	.	.	.	.	.	.	.	.	.	.	G	11.80	1.746149	0.30955	.	.	ENSG00000128833	ENST00000261839	T	0.16196	2.36	5.89	5.89	0.94794	.	0.320114	0.34088	N	0.004277	T	0.10981	0.0268	N	0.22421	0.69	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.05852	-1.0860	10	0.02654	T	1	.	15.0262	0.71671	0.0:0.0:0.8578:0.1422	.	1130	Q9NQX4	MYO5C_HUMAN	Y	1130	ENSP00000261839:H1130Y	ENSP00000261839:H1130Y	H	-	1	0	MYO5C	50304448	1.000000	0.71417	1.000000	0.80357	0.625000	0.37756	4.397000	0.59690	2.783000	0.95769	0.655000	0.94253	CAT	.		0.343	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728	
NXF4	55999	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	101822176	101822176	+	RNA	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chrX:101822176C>T	ENST00000360035.2	+	0	1929					NR_002216.1				nuclear RNA export factor 4 pseudogene											endometrium(2)|lung(8)	10						ACTCCAAGAACTCTCTCAGCT	0.458																																					.		.											.	.	.	0			.						.																																					55999	.			CAAGAACTCTCTC	AK124700		Xq22	2005-01-24			ENSG00000196970	ENSG00000196970			8074	pseudogene	pseudogene		300318	"""nuclear RNA export factor 4"""			11566096	Standard	NR_002216		Approved		uc004ejf.1		OTTHUMG00000039695		X.37:g.101822176C>T		Somatic	11	0		WXS	Illumina HiSeq	.	27	12	.		RNA	SNP	ENST00000360035.2	37																																																																																				.		0.458	NXF4-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000095720.1		
CHL1	10752	hgsc.bcm.edu	37	3	383704	383704	+	Silent	SNP	T	T	G			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr3:383704T>G	ENST00000256509.2	+	7	1260	c.618T>G	c.(616-618)gcT>gcG	p.A206A	CHL1_ENST00000397491.2_Silent_p.A206A	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0	Glu-rich.|Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.A206A(1)		NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		GTTGCTTTGCTGCATTTCCAA	0.373																																					p.A206A		.											CHL1,NS,carcinoma,0,1	CHL1	0	1	Substitution - coding silent(1)	lung(1)	c.T618G						.						99.0	95.0	96.0					3																	383704		2203	4300	6503	SO:0001819	synonymous_variant	10752	exon5			CTTTGCTGCATTT	AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	1939	protein-coding gene	gene with protein product	"""neural cell adhesion molecule"", ""close homolog of L1"""	607416	"""cell adhesion molecule with homology to L1CAM (close homologue of L1)"", ""cell adhesion molecule with homology to L1CAM (close homolog of L1)"""			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.618T>G	3.37:g.383704T>G		Somatic	29	0		WXS	Illumina HiSeq	.	39	2	NM_001253388	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Silent	SNP	ENST00000256509.2	37	CCDS2556.1																																																																																			.		0.373	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614	
UBE4B	10277	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	10205034	10205034	+	Nonsense_Mutation	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr1:10205034G>A	ENST00000253251.8	+	17	2852	c.2013G>A	c.(2011-2013)tgG>tgA	p.W671*	UBE4B_ENST00000377157.3_Nonsense_Mutation_p.W555*|UBE4B_ENST00000343090.6_Nonsense_Mutation_p.W800*					ubiquitination factor E4B											NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		AAAGCCAATGGAAAGATTCCC	0.388																																					p.W800X		.											.	.	.	0			c.G2400A						.						72.0	70.0	71.0					1																	10205034		2203	4300	6503	SO:0001587	stop_gained	10277	exon18			CCAATGGAAAGAT	AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"""U-box domain containing"""	12500	protein-coding gene	gene with protein product		613565	"""ubiquitination factor E4B (homologous to yeast UFD2)"", ""ubiquitination factor E4B (UFD2 homolog, yeast)"""			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.2013G>A	1.37:g.10205034G>A	ENSP00000253251:p.Trp671*	Somatic	55	0		WXS	Illumina HiSeq	.	51	33	NM_001105562		Nonsense_Mutation	SNP	ENST00000253251.8	37	CCDS110.1	.	.	.	.	.	.	.	.	.	.	G	47	13.862914	0.99767	.	.	ENSG00000130939	ENST00000253251;ENST00000377157;ENST00000343090	.	.	.	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.1466	20.1047	0.97888	0.0:0.0:1.0:0.0	.	.	.	.	X	671;555;800	.	ENSP00000253251:W671X	W	+	3	0	UBE4B	10127621	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.183000	0.94887	2.762000	0.94881	0.655000	0.94253	TGG	.		0.388	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048	
VPS13A	23230	hgsc.bcm.edu	37	9	79890501	79890501	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr9:79890501G>T	ENST00000360280.3	+	25	2860	c.2600G>T	c.(2599-2601)aGa>aTa	p.R867I	VPS13A_ENST00000376634.4_Missense_Mutation_p.R867I|VPS13A_ENST00000357409.5_Missense_Mutation_p.R867I|VPS13A_ENST00000376636.3_Missense_Mutation_p.R867I	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	867					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						ATTCGAACCAGAAAGTTACAA	0.348																																					p.R867I		.											.	.	.	0			c.G2600T						.						103.0	112.0	109.0					9																	79890501		2203	4299	6502	SO:0001583	missense	23230	exon25			GAACCAGAAAGTT	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"""chorein"""	605978	"""chorea acanthocytosis"", ""vacuolar protein sorting 13A (yeast)"""	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.2600G>T	9.37:g.79890501G>T	ENSP00000353422:p.Arg867Ile	Somatic	93	0		WXS	Illumina HiSeq	.	95	4	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	37	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	G	12.45	1.941396	0.34283	.	.	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.49432	0.95;0.78;0.86;0.95	5.6	-4.27	0.03744	.	0.820473	0.11188	N	0.590268	T	0.24967	0.0606	N	0.08118	0	0.09310	N	0.999996	B;B;B;B	0.26002	0.074;0.047;0.139;0.06	B;B;B;B	0.28553	0.091;0.015;0.047;0.047	T	0.17258	-1.0375	10	0.38643	T	0.18	.	10.8663	0.46858	0.69:0.1014:0.2086:0.0	.	867;867;867;867	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	I	867	ENSP00000365821:R867I;ENSP00000365823:R867I;ENSP00000353422:R867I;ENSP00000349985:R867I	ENSP00000349985:R867I	R	+	2	0	VPS13A	79080321	0.004000	0.15560	0.000000	0.03702	0.091000	0.18340	-0.333000	0.07894	-1.323000	0.02275	-0.378000	0.06908	AGA	.		0.348	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	
CLCN4	1183	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	X	10176631	10176631	+	Splice_Site	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chrX:10176631G>A	ENST00000380833.4	+	9	1780		c.e9+1		CLCN4_ENST00000421085.2_Splice_Site|CLCN4_ENST00000380829.1_Splice_Site	NM_001256944.1|NM_001830.3	NP_001243873.1|NP_001821.2	P51793	CLCN4_HUMAN	chloride channel, voltage-sensitive 4						chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						TGGCATGAAGGTAAGTGAAAG	0.517																																					.	Melanoma(74;1050 1296 1576 30544 38374)	.											.	.	.	0			c.1389+1G>A						.						43.0	42.0	43.0					X																	10176631		2188	4254	6442	SO:0001630	splice_region_variant	1183	exon9			ATGAAGGTAAGTG	X77197	CCDS14137.1, CCDS59159.1	Xp22.3	2012-09-26	2012-02-23		ENSG00000073464	ENSG00000073464		"""Ion channels / Chloride channels : Voltage-sensitive"""	2022	protein-coding gene	gene with protein product		302910	"""chloride channel 4"""			8069296	Standard	NM_001830		Approved	CLC4, ClC-4	uc004csy.4	P51793	OTTHUMG00000021125	ENST00000380833.4:c.1389+1G>A	X.37:g.10176631G>A		Somatic	61	0		WXS	Illumina HiSeq	.	49	7	NM_001830	A1L3U1|B7Z5Z4|Q9UBU1	Splice_Site	SNP	ENST00000380833.4	37	CCDS14137.1	.	.	.	.	.	.	.	.	.	.	g	24.2	4.505160	0.85282	.	.	ENSG00000073464	ENST00000380833;ENST00000380829;ENST00000421085	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.4525	0.90709	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CLCN4	10136631	1.000000	0.71417	0.995000	0.50966	0.998000	0.95712	9.667000	0.98616	2.299000	0.77371	0.596000	0.82720	.	.		0.517	CLCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055730.1		Intron
SRBD1	55133	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	45807033	45807033	+	Silent	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr2:45807033G>A	ENST00000263736.4	-	7	1115	c.1053C>T	c.(1051-1053)taC>taT	p.Y351Y		NM_018079.4	NP_060549.4	Q8N5C6	SRBD1_HUMAN	S1 RNA binding domain 1	351					nucleobase-containing compound metabolic process (GO:0006139)		hydrolase activity, acting on ester bonds (GO:0016788)|RNA binding (GO:0003723)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(13)|large_intestine(8)|lung(15)|skin(2)|stomach(1)|urinary_tract(1)	49		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)			CAGGCCTAATGTACGATAGCA	0.398																																					p.Y351Y		.											.	.	.	0			c.C1053T						.						188.0	182.0	184.0					2																	45807033		2203	4300	6503	SO:0001819	synonymous_variant	55133	exon7			CCTAATGTACGAT	AK056536	CCDS1823.1	2p21	2008-02-05			ENSG00000068784	ENSG00000068784			25521	protein-coding gene	gene with protein product						12477932	Standard	NM_018079		Approved	FLJ10379	uc002rus.3	Q8N5C6	OTTHUMG00000128814	ENST00000263736.4:c.1053C>T	2.37:g.45807033G>A		Somatic	41	0		WXS	Illumina HiSeq	.	76	42	NM_018079	Q53T56|Q96TA4|Q9NW11	Silent	SNP	ENST00000263736.4	37	CCDS1823.1																																																																																			.		0.398	SRBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250747.3	NM_018079	
PSMD6	9861	hgsc.bcm.edu	37	3	63996509	63996509	+	Intron	SNP	C	C	T	rs372965754	byFrequency	TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr3:63996509C>T	ENST00000295901.4	-	7	1214				PSMD6_ENST00000482510.1_Intron|PSMD6_ENST00000394431.2_Intron|PSMD6_ENST00000492933.1_Intron|RP11-245J9.5_ENST00000607115.1_lincRNA|PSMD6-AS2_ENST00000472046.1_RNA|RP11-245J9.4_ENST00000462717.1_RNA	NM_014814.1	NP_055629.1	Q15008	PSMD6_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 6						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATPase activity (GO:0016887)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|pancreas(1)|prostate(1)|skin(1)	13		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000805)|Kidney(15;0.00188)|KIRC - Kidney renal clear cell carcinoma(15;0.00212)		AGTTGACCTACTTTTAAAATT	0.338																																					.		.											.	.	.	0			.						.						68.0	70.0	69.0					3																	63996509		2202	4298	6500	SO:0001627	intron_variant	100507062	.			GACCTACTTTTAA	AF215935	CCDS2901.1, CCDS63677.1, CCDS63678.1, CCDS63679.1	3p14.1	2008-05-22			ENSG00000163636	ENSG00000163636		"""Proteasome (prosome, macropain) subunits"""	9564	protein-coding gene	gene with protein product						10723133	Standard	NM_001271779		Approved	S10, p44S10, KIAA0107, Rpn7	uc003dmb.2	Q15008	OTTHUMG00000158765	ENST00000295901.4:c.1073+44G>A	3.37:g.63996509C>T		Somatic	76	0		WXS	Illumina HiSeq	.	96	2	.	A8K2E0|E9PHI9|Q6UV22	RNA	SNP	ENST00000295901.4	37	CCDS2901.1																																																																																			.		0.338	PSMD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352082.1	NM_014814	
EEFSEC	60678	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	128060585	128060585	+	Silent	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr3:128060585G>A	ENST00000254730.6	+	5	1350	c.1296G>A	c.(1294-1296)agG>agA	p.R432R	EEFSEC_ENST00000483569.1_3'UTR|EEFSEC_ENST00000483457.1_Silent_p.R377R	NM_021937.3	NP_068756.2	P57772	SELB_HUMAN	eukaryotic elongation factor, selenocysteine-tRNA-specific	432					selenocysteine incorporation (GO:0001514)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ribonucleoprotein complex binding (GO:0043021)|selenocysteine insertion sequence binding (GO:0035368)|translation elongation factor activity (GO:0003746)|tRNA binding (GO:0000049)			NS(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(10)|ovary(1)	25						TTGGCTCCAGGCTAGATGCGG	0.632																																					p.R432R		.											.	.	.	0			c.G1296A						.						75.0	70.0	72.0					3																	128060585		2203	4300	6503	SO:0001819	synonymous_variant	60678	exon5			CTCCAGGCTAGAT		CCDS33849.1	3q21.3	2007-05-25			ENSG00000132394	ENSG00000132394			24614	protein-coding gene	gene with protein product	"""elongation factor for selenoprotein translation"""	607695				10970870, 15229221	Standard	XM_005247696		Approved	SELB, EFSEC	uc003eki.3	P57772	OTTHUMG00000159659	ENST00000254730.6:c.1296G>A	3.37:g.128060585G>A		Somatic	22	0		WXS	Illumina HiSeq	.	25	7	NM_021937	Q96HZ6	Silent	SNP	ENST00000254730.6	37	CCDS33849.1																																																																																			.		0.632	EEFSEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356738.2	NM_021937	
SCLY	51540	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	238990809	238990809	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr2:238990809G>A	ENST00000555827.1	+	6	800	c.736G>A	c.(736-738)Gag>Aag	p.E246K	SCLY_ENST00000429612.2_Intron|SCLY_ENST00000254663.6_Missense_Mutation_p.E254K|SCLY_ENST00000409736.2_Missense_Mutation_p.E246K|SCLY_ENST00000373332.3_Missense_Mutation_p.E164K|SCLY_ENST00000422984.2_Missense_Mutation_p.E152K			Q96I15	SCLY_HUMAN	selenocysteine lyase	246					cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)	pyridoxal phosphate binding (GO:0030170)|selenocysteine lyase activity (GO:0009000)|transferase activity (GO:0016740)			endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	22		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285)		CGTGGATGTGGAGGACCTGGG	0.607																																					p.E254K	Melanoma(24;424 891 11947 32582 36034)|Ovarian(46;648 1065 26199 32764 45893)	.											.	.	.	0			c.G760A						.						82.0	75.0	77.0					2																	238990809		2203	4300	6503	SO:0001583	missense	51540	exon6			GATGTGGAGGACC	AF175767	CCDS2524.1, CCDS2524.2	2q37.3	2008-02-05			ENSG00000132330	ENSG00000132330			18161	protein-coding gene	gene with protein product	"""putative selenocysteine lyase"""	611056				10692412	Standard	NM_016510		Approved	SCL	uc010fyv.4	Q96I15	OTTHUMG00000133336	ENST00000555827.1:c.736G>A	2.37:g.238990809G>A	ENSP00000450613:p.Glu246Lys	Somatic	11	0		WXS	Illumina HiSeq	.	28	10	NM_016510	B9A068|J3KN06|Q53SN1|Q53SN8|Q7L670|Q9NVT7|Q9NZR7	Missense_Mutation	SNP	ENST00000555827.1	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	24.2|24.2|24.2	4.510393|4.510393|4.510393	0.85389|0.85389|0.85389	.|.|.	.|.|.	ENSG00000132330|ENSG00000132330|ENSG00000132330	ENST00000254663;ENST00000555827;ENST00000373332;ENST00000413463;ENST00000409736;ENST00000422984;ENST00000450965|ENST00000437134;ENST00000440143|ENST00000431487	D;D;D;D;D;D;D|.|.	0.85773|.|.	-2.03;-2.03;-2.03;-2.03;-2.03;-2.03;-2.03|.|.	5.48|5.48|5.48	3.64|3.64|3.64	0.41730|0.41730|0.41730	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);|.|.	0.443591|.|.	0.27206|.|.	N|.|.	0.020435|.|.	T|T|.	0.48314|0.48314|.	0.1493|0.1493|.	N|N|N	0.17764|0.17764|0.17764	0.52|0.52|0.52	0.80722|0.80722|0.80722	D|D|D	1|1|1	B;B;B|.|.	0.16603|.|.	0.002;0.0;0.018|.|.	B;B;B|.|.	0.13407|.|.	0.007;0.005;0.009|.|.	T|T|.	0.39522|0.39522|.	-0.9610|-0.9610|.	10|5|.	0.02654|.|.	T|.|.	1|.|.	-7.2726|-7.2726|-7.2726	13.787|13.787|13.787	0.63117|0.63117|0.63117	0.0:0.5958:0.4042:0.0|0.0:0.5958:0.4042:0.0|0.0:0.5958:0.4042:0.0	.|.|.	152;246;246|.|.	E7ESG3;Q96I15;Q96I15-2|.|.	.;SCLY_HUMAN;.|.|.	K|E|X	254;246;164;160;246;152;76|89;23|91	ENSP00000254663:E254K;ENSP00000450613:E246K;ENSP00000362429:E164K;ENSP00000414165:E160K;ENSP00000387162:E246K;ENSP00000416865:E152K;ENSP00000414053:E76K|.|.	ENSP00000254663:E246K|.|.	E|G|W	+|+|+	1|2|3	0|0|0	SCLY|SCLY|SCLY	238655548|238655548|238655548	0.951000|0.951000|0.951000	0.32395|0.32395|0.32395	0.979000|0.979000|0.979000	0.43373|0.43373|0.43373	0.952000|0.952000|0.952000	0.60782|0.60782|0.60782	0.401000|0.401000|0.401000	0.20948|0.20948|0.20948	1.318000|1.318000|1.318000	0.45170|0.45170|0.45170	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GAG|GGA|TGG	.		0.607	SCLY-204	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_016510	
HPS5	11234	hgsc.bcm.edu	37	11	18339303	18339303	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr11:18339303G>T	ENST00000349215.3	-	2	380	c.103C>A	c.(103-105)Cta>Ata	p.L35I	HPS5_ENST00000531848.1_Intron|HPS5_ENST00000438420.2_Intron|HPS5_ENST00000396253.3_Intron	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	35					blood coagulation (GO:0007596)|organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)		p.L35V(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						TTCACCTTTAGACGACTGGAG	0.473									Hermansky-Pudlak syndrome																												p.L35I		.											HPS5,NS,carcinoma,0,1	HPS5	0	1	Substitution - Missense(1)	breast(1)	c.C103A						.						59.0	53.0	55.0					11																	18339303		2199	4293	6492	SO:0001583	missense	11234	exon2	Familial Cancer Database	HPS, HPS1-8	CCTTTAGACGACT	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.103C>A	11.37:g.18339303G>T	ENSP00000265967:p.Leu35Ile	Somatic	43	0		WXS	Illumina HiSeq	.	58	3	NM_181507	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Missense_Mutation	SNP	ENST00000349215.3	37	CCDS7836.1	.	.	.	.	.	.	.	.	.	.	G	13.93	2.383866	0.42308	.	.	ENSG00000110756	ENST00000349215	T	0.63096	-0.02	5.05	4.14	0.48551	WD40 repeat-like-containing domain (1);	0.075577	0.53938	D	0.000051	T	0.51839	0.1698	N	0.17082	0.46	0.80722	D	1	P;P	0.51351	0.859;0.944	B;P	0.54460	0.41;0.753	T	0.45934	-0.9227	10	0.08179	T	0.78	.	9.9396	0.41572	0.1566:0.0:0.8434:0.0	.	51;35	Q8IZE8;Q9UPZ3	.;HPS5_HUMAN	I	35	ENSP00000265967:L35I	ENSP00000265967:L35I	L	-	1	2	HPS5	18295879	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.647000	0.46639	1.112000	0.41740	0.591000	0.81541	CTA	.		0.473	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1	NM_181507	
CDC37L1	55664	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	9	4685133	4685133	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr9:4685133C>T	ENST00000381854.3	+	2	591	c.389C>T	c.(388-390)gCc>gTc	p.A130V	CDC37L1_ENST00000479095.1_3'UTR|CDC37L1_ENST00000381858.1_Missense_Mutation_p.A130V	NM_017913.2	NP_060383.2	Q7L3B6	CD37L_HUMAN	cell division cycle 37-like 1	130	Self-association.					cytoplasm (GO:0005737)				breast(1)|kidney(1)|lung(2)	4	all_hematologic(13;0.137)	Breast(48;0.238)		GBM - Glioblastoma multiforme(50;0.0318)		AGCACGGATGCCATTAGCAAG	0.418																																					p.A130V		.											.	.	.	0			c.C389T						.						137.0	142.0	140.0					9																	4685133		2203	4300	6503	SO:0001583	missense	55664	exon2			CGGATGCCATTAG	AK000497	CCDS6454.1	9p24.1	2013-01-17	2013-01-17		ENSG00000106993	ENSG00000106993			17179	protein-coding gene	gene with protein product		610346	"""CDC37 cell division cycle 37 homolog (S. cerevisiae)-like 1"", ""cell division cycle 37 homolog (S. cerevisiae)-like 1"""				Standard	NM_017913		Approved	HARC, FLJ20639, CDC37B	uc003zio.3	Q7L3B6	OTTHUMG00000019465	ENST00000381854.3:c.389C>T	9.37:g.4685133C>T	ENSP00000371278:p.Ala130Val	Somatic	72	0		WXS	Illumina HiSeq	.	59	5	NM_017913	B1AL70|Q9NWS3|Q9NX16	Missense_Mutation	SNP	ENST00000381854.3	37	CCDS6454.1	.	.	.	.	.	.	.	.	.	.	C	13.26	2.184309	0.38609	.	.	ENSG00000106993	ENST00000381858;ENST00000381854	T;T	0.44083	0.93;0.94	5.28	4.36	0.52297	.	0.458490	0.25497	N	0.030274	T	0.25195	0.0612	N	0.14661	0.345	0.28487	N	0.914672	B	0.10296	0.003	B	0.16722	0.016	T	0.13361	-1.0512	10	0.51188	T	0.08	-15.8115	7.7911	0.29121	0.0:0.6082:0.2749:0.117	.	130	Q7L3B6	CD37L_HUMAN	V	130	ENSP00000371282:A130V;ENSP00000371278:A130V	ENSP00000371278:A130V	A	+	2	0	CDC37L1	4675133	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.524000	0.35942	1.322000	0.45245	0.467000	0.42956	GCC	.		0.418	CDC37L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051564.1	NM_017913	
MAATS1	89876	hgsc.bcm.edu	37	3	119466657	119466657	+	Splice_Site	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr3:119466657G>T	ENST00000273390.5	+	16	2128		c.e16-1		RP11-169N13.4_ENST00000489428.2_RNA	NM_033364.3	NP_203528	Q7Z4T9	MAAT1_HUMAN	MYCBP-associated, testis expressed 1							mitochondrion (GO:0005739)											ATATTTTTTAGCCGAACCTAT	0.368																																					.		.											.	.	.	0			c.2052-1G>T						.						76.0	78.0	77.0					3																	119466657		2202	4300	6502	SO:0001630	splice_region_variant	89876	exon16			TTTTTAGCCGAAC	AB063296	CCDS2994.1	3q12-q13.3	2014-07-31	2012-12-07	2012-09-26	ENSG00000183833	ENSG00000183833			24010	protein-coding gene	gene with protein product	"""AMY-1-associating protein expressed in testis 1"", ""MYCBP-binding protein"", ""spermatogenesis associated 26"""	609910	"""chromosome 3 open reading frame 15"", ""MYCBP/AMY-1-associated, testis expressed 1"""	C3orf15		12223483, 14551891, 17967944	Standard	NM_033364		Approved	AAT1, AAT1alpha, SPATA26, CaM-IP2	uc003ede.4	Q7Z4T9	OTTHUMG00000159422	ENST00000273390.5:c.2052-1G>T	3.37:g.119466657G>T		Somatic	50	0		WXS	Illumina HiSeq	.	65	4	NM_033364	A0AVK2|A8K1J9|B3KP23|B4DG52|B4DZ14|C9JUG4|Q68DX2|Q8TD41|Q96A45|Q96JE8	Splice_Site	SNP	ENST00000273390.5	37	CCDS2994.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.154973	0.78114	.	.	ENSG00000183833	ENST00000273390	.	.	.	5.43	4.55	0.56014	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5987	0.68424	0.0703:0.0:0.9297:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C3orf15	120949347	1.000000	0.71417	0.391000	0.26233	0.755000	0.42902	6.627000	0.74258	1.505000	0.48720	0.650000	0.86243	.	.		0.368	MAATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355222.1	NM_033364	Intron
CCDC129	223075	hgsc.bcm.edu	37	7	31617535	31617535	+	Silent	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr7:31617535G>T	ENST00000407970.3	+	8	695	c.657G>T	c.(655-657)ctG>ctT	p.L219L	CCDC129_ENST00000409210.1_Silent_p.L127L|CCDC129_ENST00000319386.3_Silent_p.L219L|CCDC129_ENST00000451887.2_Silent_p.L245L	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	219								p.L219L(2)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						CATCTCTGCTGAGTGATGTCA	0.488																																					p.L245L		.											LOC223075,NS,carcinoma,0,2	LOC223075	0	2	Substitution - coding silent(2)	endometrium(2)	c.G735T						.						68.0	52.0	58.0					7																	31617535		2203	4300	6503	SO:0001819	synonymous_variant	223075	exon8			TCTGCTGAGTGAT	AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347			27363	protein-coding gene	gene with protein product						14702039	Standard	NM_001257967		Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000407970.3:c.657G>T	7.37:g.31617535G>T		Somatic	28	0		WXS	Illumina HiSeq	.	53	3	NM_001257968	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Silent	SNP	ENST00000407970.3	37	CCDS5435.2																																																																																			.		0.488	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300	
EYS	346007	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	65300622	65300622	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr6:65300622G>A	ENST00000370621.3	-	26	5664	c.5138C>T	c.(5137-5139)cCc>cTc	p.P1713L	EYS_ENST00000370616.2_Missense_Mutation_p.P1713L|EYS_ENST00000503581.1_Missense_Mutation_p.P1713L			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1713					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						TACCTCAGTGGGTCCCATAGT	0.333																																					p.P1713L		.											.	.	.	0			c.C5138T						.						26.0	23.0	24.0					6																	65300622		692	1590	2282	SO:0001583	missense	346007	exon26			TCAGTGGGTCCCA		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.5138C>T	6.37:g.65300622G>A	ENSP00000359655:p.Pro1713Leu	Somatic	38	0		WXS	Illumina HiSeq	.	68	25	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	37		.	.	.	.	.	.	.	.	.	.	G	10.52	1.373242	0.24857	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	D;D;D	0.84800	-1.9;-1.87;-1.87	6.08	0.178	0.15058	.	.	.	.	.	T	0.46288	0.1385	N	0.08118	0	0.09310	N	1	B;B	0.17852	0.024;0.007	B;B	0.17979	0.02;0.005	T	0.40887	-0.9539	9	0.66056	D	0.02	.	1.5685	0.02609	0.3224:0.1403:0.3954:0.1419	.	1713;1713	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	L	1713	ENSP00000424243:P1713L;ENSP00000359655:P1713L;ENSP00000359650:P1713L	ENSP00000359650:P1713L	P	-	2	0	EYS	65357343	0.000000	0.05858	0.005000	0.12908	0.180000	0.23129	0.642000	0.24735	0.080000	0.16959	0.591000	0.81541	CCC	.		0.333	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
PATL1	219988	hgsc.bcm.edu	37	11	59418265	59418265	+	Silent	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr11:59418265G>T	ENST00000300146.9	-	13	1630	c.1546C>A	c.(1546-1548)Cga>Aga	p.R516R		NM_152716.2	NP_689929.2	Q86TB9	PATL1_HUMAN	protein associated with topoisomerase II homolog 1 (yeast)	516	Involved in nuclear spleckles localization.|Region C.				cytoplasmic mRNA processing body assembly (GO:0033962)|deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(2)|lung(5)|ovary(1)|prostate(2)	11						CTCTTGTCTCGAACTTGTTTT	0.303																																					p.R516R		.											.	.	.	0			c.C1546A						.						86.0	75.0	78.0					11																	59418265		1785	4043	5828	SO:0001819	synonymous_variant	219988	exon13			TGTCTCGAACTTG	AK094193	CCDS44613.1	11q12.1	2012-06-07	2007-10-18		ENSG00000166889	ENSG00000166889			26721	protein-coding gene	gene with protein product		614660				17936923	Standard	NM_152716		Approved	FLJ36874, Pat1b	uc001noe.4	Q86TB9	OTTHUMG00000167423	ENST00000300146.9:c.1546C>A	11.37:g.59418265G>T		Somatic	76	0		WXS	Illumina HiSeq	.	91	4	NM_152716	B3KXT9|Q2TA86|Q6P166|Q8N9M6|Q8NI63	Silent	SNP	ENST00000300146.9	37	CCDS44613.1																																																																																			.		0.303	PATL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394559.1	NM_152716	
ANKHD1	54882	hgsc.bcm.edu;broad.mit.edu	37	5	139781730	139781730	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr5:139781730G>A	ENST00000360839.2	+	1	332	c.178G>A	c.(178-180)Ggc>Agc	p.G60S	ANKHD1-EIF4EBP3_ENST00000532219.1_Missense_Mutation_p.G60S|CTC-329D1.2_ENST00000507521.1_RNA|ANKHD1_ENST00000394722.3_Missense_Mutation_p.G60S|ANKHD1_ENST00000394723.3_Missense_Mutation_p.G60S|ANKHD1_ENST00000297183.6_Missense_Mutation_p.G60S	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	60	Gly-rich.					cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			cggcagcagcggcggcggcgg	0.756																																					p.G60S		.											ANKHD1-EIF4EBP3,NS,carcinoma,0,2	ANKHD1-EIF4EBP3	0	0			c.G178A						.																																			SO:0001583	missense	54882	exon1			AGCAGCGGCGGCG	AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"""Ankyrin repeat domain containing"""	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.178G>A	5.37:g.139781730G>A	ENSP00000354085:p.Gly60Ser	Somatic	14	0		WXS	Illumina HiSeq	.	33	3	NM_017978	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Missense_Mutation	SNP	ENST00000360839.2	37	CCDS4225.1	.	.	.	.	.	.	.	.	.	.	G	14.87	2.663652	0.47572	.	.	ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996	ENST00000360839;ENST00000422011;ENST00000297183;ENST00000253810;ENST00000421134;ENST00000394723;ENST00000511151;ENST00000394722;ENST00000532219	T;T;T;T;T;T;T	0.66815	-0.12;-0.17;-0.14;-0.1;-0.23;-0.01;-0.17	4.8	1.98	0.26296	.	0.127893	0.34555	N	0.003870	T	0.61451	0.2348	N	0.24115	0.695	0.22366	N	0.999162	D;D;D;D;P	0.71674	0.998;0.996;0.996;0.998;0.836	D;P;P;D;B	0.65443	0.935;0.862;0.862;0.935;0.038	T	0.52586	-0.8556	10	0.17369	T	0.5	.	6.4517	0.21908	0.4177:0.0:0.5823:0.0	.	60;60;60;60;60	Q8IWZ3-5;Q8IWZ2;Q8IWZ3;Q8IWZ3-3;Q8IWZ3-2	.;.;ANKH1_HUMAN;.;.	S	60;74;60;60;60;60;60;60;60	ENSP00000354085:G60S;ENSP00000297183:G60S;ENSP00000394489:G60S;ENSP00000378212:G60S;ENSP00000421069:G60S;ENSP00000378211:G60S;ENSP00000432016:G60S	ENSP00000432016:G60S	G	+	1	0	ANKHD1-EIF4EBP3;ANKHD1	139761914	0.926000	0.31397	0.971000	0.41717	0.367000	0.29736	0.608000	0.24223	0.224000	0.20940	0.505000	0.49811	GGC	.		0.756	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747	
EIF4EBP3	8637	hgsc.bcm.edu	37	5	139931630	139931630	+	IGR	SNP	A	A	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr5:139931630A>T	ENST00000310331.2	+	0	691				SRA1_ENST00000520427.1_5'UTR|SRA1_ENST00000336283.6_Silent_p.A109A	NM_003732.2	NP_003723.1	O60516	4EBP3_HUMAN	eukaryotic translation initiation factor 4E binding protein 3						negative regulation of translational initiation (GO:0045947)	eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	translation repressor activity (GO:0030371)			endometrium(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTCCATCACAGCCTCAGACT	0.597																																					p.A109A		.											.,1	.	24	0			c.T327A						.						83.0	61.0	68.0					5																	139931630		2202	4298	6500	SO:0001628	intergenic_variant	10011	exon3			CATCACAGCCTCA	AF038869	CCDS4226.1	5q31.3	2007-07-18			ENSG00000243056	ENSG00000243056			3290	protein-coding gene	gene with protein product		603483				9593750	Standard	NM_003732		Approved	4E-BP3	uc003lfy.1	O60516	OTTHUMG00000129498		5.37:g.139931630A>T		Somatic	23	0		WXS	Illumina HiSeq	.	97	3	NM_001035235		Silent	SNP	ENST00000310331.2	37	CCDS4226.1																																																																																			.		0.597	EIF4EBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251668.2	NM_003732	
USP28	57646	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	113674003	113674003	+	Splice_Site	SNP	C	C	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr11:113674003C>A	ENST00000003302.4	-	23	2807	c.2739G>T	c.(2737-2739)aaG>aaT	p.K913N	USP28_ENST00000260188.5_Splice_Site_p.K881N|USP28_ENST00000545540.1_Splice_Site_p.K756N|USP28_ENST00000544967.1_Splice_Site_p.K589N	NM_020886.2	NP_065937.1	Q96RU2	UBP28_HUMAN	ubiquitin specific peptidase 28	913					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|protein deubiquitination (GO:0016579)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	59		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		CCTCTTGGTACCTTAGAAAAA	0.483																																					p.K913N	Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)	.											.	.	.	0			c.G2739T						.						52.0	55.0	54.0					11																	113674003		2201	4296	6497	SO:0001630	splice_region_variant	57646	exon23			TTGGTACCTTAGA	AB040948	CCDS31680.1, CCDS73394.1	11q23	2008-04-11	2005-08-08		ENSG00000048028	ENSG00000048028		"""Ubiquitin-specific peptidases"""	12625	protein-coding gene	gene with protein product		610748	"""ubiquitin specific protease 28"""			12838346, 11597335	Standard	XM_005271630		Approved	KIAA1515	uc001poh.3	Q96RU2	OTTHUMG00000168205	ENST00000003302.4:c.2739-1G>T	11.37:g.113674003C>A		Somatic	87	0		WXS	Illumina HiSeq	.	67	36	NM_020886	B0YJC0|B0YJC1|Q9P213	Missense_Mutation	SNP	ENST00000003302.4	37	CCDS31680.1	.	.	.	.	.	.	.	.	.	.	C	15.43	2.831661	0.50845	.	.	ENSG00000048028	ENST00000003302;ENST00000260188;ENST00000544967;ENST00000545540	T;T;T;T	0.49139	1.3;1.37;0.79;1.37	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	T	0.55353	0.1915	L	0.48642	1.525	0.49582	D	0.999804	D;B;D	0.71674	0.989;0.103;0.998	P;B;P	0.62885	0.797;0.034;0.908	T	0.49978	-0.8881	10	0.34782	T	0.22	.	10.3107	0.43706	0.0:0.8489:0.0:0.1511	.	756;913;589	B4E3L3;Q96RU2;G3V1N5	.;UBP28_HUMAN;.	N	913;881;589;756	ENSP00000003302:K913N;ENSP00000260188:K881N;ENSP00000442431:K589N;ENSP00000444991:K756N	ENSP00000003302:K913N	K	-	3	2	USP28	113179213	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	2.397000	0.44477	2.641000	0.89580	0.563000	0.77884	AAG	.		0.483	USP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398789.1		Missense_Mutation
SRPR	6734	hgsc.bcm.edu	37	11	126134929	126134929	+	Missense_Mutation	SNP	G	G	T	rs142997401		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr11:126134929G>T	ENST00000332118.6	-	11	1604	c.1450C>A	c.(1450-1452)Cgc>Agc	p.R484S	SRPR_ENST00000532259.1_Missense_Mutation_p.R456S|SRPR_ENST00000530680.1_5'Flank	NM_003139.3	NP_003130.2	P08240	SRPR_HUMAN	signal recognition particle receptor (docking protein)	484					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|signal recognition particle receptor complex (GO:0005785)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			endometrium(7)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)	21	all_hematologic(175;0.145)			BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0736)		ACCATGGTGCGGCCACCATGC	0.567																																					p.R484S		.											SRPR,NS,carcinoma,0,1	SRPR	0	0			c.C1450A						.						65.0	59.0	61.0					11																	126134929		2201	4299	6500	SO:0001583	missense	6734	exon11			TGGTGCGGCCACC	BC001162	CCDS31717.1, CCDS53722.1	11q24-q25	2012-10-02	2008-10-29		ENSG00000182934	ENSG00000182934			11307	protein-coding gene	gene with protein product		182180	"""signal recognition particle receptor ('docking protein')"""			3340536, 1312991	Standard	NM_001177842		Approved	SRP-alpha, Sralpha	uc001qdh.3	P08240	OTTHUMG00000165826	ENST00000332118.6:c.1450C>A	11.37:g.126134929G>T	ENSP00000328023:p.Arg484Ser	Somatic	46	0		WXS	Illumina HiSeq	.	44	2	NM_003139	A6NIB3|B2R5Z8|B4E0H3|E9PJS4|Q9BVJ4	Missense_Mutation	SNP	ENST00000332118.6	37	CCDS31717.1	.	.	.	.	.	.	.	.	.	.	G	32	5.178730	0.94846	.	.	ENSG00000182934	ENST00000332118;ENST00000532259	.	.	.	5.26	5.26	0.73747	ATPase, AAA+ type, core (1);Signal recognition particle, SRP54 subunit, GTPase (2);	0.106362	0.64402	D	0.000003	T	0.68430	0.3000	L	0.36672	1.1	0.80722	D	1	P;P	0.42973	0.796;0.796	P;P	0.53593	0.73;0.73	T	0.70360	-0.4893	9	0.72032	D	0.01	-9.2626	19.0619	0.93096	0.0:0.0:1.0:0.0	.	456;484	E9PJS4;P08240	.;SRPR_HUMAN	S	484;456	.	ENSP00000328023:R484S	R	-	1	0	SRPR	125640139	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.562000	0.82300	2.744000	0.94065	0.650000	0.86243	CGC	.		0.567	SRPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386425.2	NM_003139	
CDK12	51755	hgsc.bcm.edu	37	17	37665977	37665977	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr17:37665977G>T	ENST00000447079.4	+	7	2662	c.2629G>T	c.(2629-2631)Gat>Tat	p.D877Y	CDK12_ENST00000430627.2_Missense_Mutation_p.D877Y	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	877	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						CAAACTAGCAGATTTTGGACT	0.363			"""Mis, N, F"""		serous ovarian					TCGA Ovarian(9;0.13)																											p.D877Y		.		Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	.	.	.	0			c.G2629T						.						129.0	129.0	129.0					17																	37665977		2203	4300	6503	SO:0001583	missense	51755	exon7			CTAGCAGATTTTG	AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"""Cyclin-dependent kinases"""	24224	protein-coding gene	gene with protein product	"""CDC2 related protein kinase 7"""	615514	"""Cdc2-related kinase, arginine/serine-rich"""	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.2629G>T	17.37:g.37665977G>T	ENSP00000398880:p.Asp877Tyr	Somatic	52	0		WXS	Illumina HiSeq	.	89	4	NM_016507	A7E2B2|B4DYX4|B9EIQ6|O94978	Missense_Mutation	SNP	ENST00000447079.4	37	CCDS11337.1	.	.	.	.	.	.	.	.	.	.	G	19.55	3.849604	0.71603	.	.	ENSG00000167258	ENST00000430627;ENST00000447079	D;D	0.93076	-3.16;-3.16	5.35	5.35	0.76521	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	0.47455	D	0.000231	D	0.98495	0.9498	H	0.99454	4.575	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.99552	1.0966	10	0.87932	D	0	-9.8158	19.4455	0.94844	0.0:0.0:1.0:0.0	.	876;877;877	E7EUM9;Q9NYV4;Q9NYV4-2	.;CDK12_HUMAN;.	Y	877	ENSP00000407720:D877Y;ENSP00000398880:D877Y	ENSP00000407720:D877Y	D	+	1	0	CDK12	34919503	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.813000	0.99286	2.666000	0.90696	0.650000	0.86243	GAT	.		0.363	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507	
MAGEC1	9947	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	140995729	140995729	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chrX:140995729C>A	ENST00000285879.4	+	4	2825	c.2539C>A	c.(2539-2541)Cct>Act	p.P847T	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	847										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					CAAGAGTTCCCCTGAGAGTCC	0.522										HNSCC(15;0.026)																											p.P847T		.											.	.	.	0			c.C2539A						.						122.0	128.0	126.0					X																	140995729		2203	4300	6503	SO:0001583	missense	9947	exon4			AGTTCCCCTGAGA	AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 1"""	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.2539C>A	X.37:g.140995729C>A	ENSP00000285879:p.Pro847Thr	Somatic	43	0		WXS	Illumina HiSeq	.	71	22	NM_005462	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	.	.	.	.	.	.	.	.	.	.	-	9.849	1.193154	0.22037	.	.	ENSG00000155495	ENST00000285879	T	0.02121	4.44	0.548	-1.1	0.09872	.	.	.	.	.	T	0.02304	0.0071	N	0.14661	0.345	0.09310	N	1	P	0.48350	0.909	P	0.50440	0.641	T	0.46176	-0.9210	9	0.66056	D	0.02	.	4.8033	0.13307	0.3498:0.6502:0.0:1.0E-4	.	847	O60732	MAGC1_HUMAN	T	847	ENSP00000285879:P847T	ENSP00000285879:P847T	P	+	1	0	MAGEC1	140823395	0.001000	0.12720	0.005000	0.12908	0.149000	0.21700	-0.135000	0.10420	-0.635000	0.05531	0.171000	0.16805	CCT	.		0.522	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462	
GPR87	53836	hgsc.bcm.edu	37	3	151012036	151012036	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr3:151012036G>T	ENST00000260843.4	-	3	1462	c.998C>A	c.(997-999)aCc>aAc	p.T333N	MED12L_ENST00000273432.4_Intron|MED12L_ENST00000491549.1_Intron|MED12L_ENST00000474524.1_Intron	NM_023915.3	NP_076404.3	Q9BY21	GPR87_HUMAN	G protein-coupled receptor 87	333					negative regulation of adenylate cyclase activity (GO:0007194)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(6)|large_intestine(6)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	19			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TTCACTCCTGGTTCTGATATT	0.363																																					p.T333N		.											.	.	.	0			c.C998A						.						156.0	158.0	157.0					3																	151012036		2203	4300	6503	SO:0001583	missense	53836	exon3			CTCCTGGTTCTGA	AF237763	CCDS3157.1	3q24	2012-08-21			ENSG00000138271	ENSG00000138271		"""GPCR / Class A : Orphans"""	4538	protein-coding gene	gene with protein product		606379		GPR95		11273702	Standard	NM_023915		Approved		uc003eyt.2	Q9BY21	OTTHUMG00000159858	ENST00000260843.4:c.998C>A	3.37:g.151012036G>T	ENSP00000260843:p.Thr333Asn	Somatic	54	0		WXS	Illumina HiSeq	.	85	4	NM_023915	Q5KU35|Q96JZ8|Q9BXC2	Missense_Mutation	SNP	ENST00000260843.4	37	CCDS3157.1	.	.	.	.	.	.	.	.	.	.	G	14.21	2.468073	0.43839	.	.	ENSG00000138271	ENST00000260843	T	0.37058	1.22	5.24	5.24	0.73138	.	0.149168	0.47093	D	0.000247	T	0.23014	0.0556	N	0.08118	0	0.41368	D	0.987476	P	0.49090	0.919	B	0.42882	0.401	T	0.06232	-1.0838	10	0.13470	T	0.59	-12.3313	19.1984	0.93699	0.0:0.0:1.0:0.0	.	333	Q9BY21	GPR87_HUMAN	N	333	ENSP00000260843:T333N	ENSP00000260843:T333N	T	-	2	0	GPR87	152494726	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.065000	0.71176	2.609000	0.88269	0.655000	0.94253	ACC	.		0.363	GPR87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357788.1		
ACSBG2	81616	hgsc.bcm.edu	37	19	6187825	6187825	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr19:6187825G>T	ENST00000586696.1	+	13	2172	c.1896G>T	c.(1894-1896)gaG>gaT	p.E632D	ACSBG2_ENST00000588304.1_Missense_Mutation_p.E582D|ACSBG2_ENST00000591403.1_Missense_Mutation_p.E632D|ACSBG2_ENST00000252669.5_Missense_Mutation_p.E632D|ACSBG2_ENST00000591741.1_3'UTR|ACSBG2_ENST00000588485.1_Missense_Mutation_p.E445D|RFX2_ENST00000587700.1_5'Flank			Q5FVE4	ACBG2_HUMAN	acyl-CoA synthetase bubblegum family member 2	632					cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid metabolic process (GO:0001676)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(3)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TCATCTTGGAGAAGGACTTTT	0.512																																					p.E632D		.											ACSBG2,NS,carcinoma,0,1	ACSBG2	0	0			c.G1896T						.						198.0	182.0	188.0					19																	6187825		2203	4300	6503	SO:0001583	missense	81616	exon13			CTTGGAGAAGGAC		CCDS12159.1, CCDS74269.1	19p13.3	2012-10-02			ENSG00000130377	ENSG00000130377		"""Acyl-CoA synthetase family"""	24174	protein-coding gene	gene with protein product	"""bubblegum related protein"""	614363				11230166	Standard	XM_005259653		Approved	BGR, PRTD-NY3, DKFZp434K1635	uc002meh.1	Q5FVE4	OTTHUMG00000180754	ENST00000586696.1:c.1896G>T	19.37:g.6187825G>T	ENSP00000465589:p.Glu632Asp	Somatic	30	0		WXS	Illumina HiSeq	.	39	2	NM_030924	B3KSF2|Q6UWJ3|Q7Z5A0|Q8WW03|Q96M36|Q9BYZ3|Q9H0C4	Missense_Mutation	SNP	ENST00000586696.1	37	CCDS12159.1	.	.	.	.	.	.	.	.	.	.	G	10.80	1.452870	0.26161	.	.	ENSG00000130377	ENST00000252669	T	0.09350	2.99	5.46	0.705	0.18127	.	0.503904	0.16998	N	0.191033	T	0.06325	0.0163	N	0.17764	0.52	0.35851	D	0.826797	B;B	0.14012	0.001;0.009	B;B	0.15052	0.003;0.012	T	0.28235	-1.0050	10	0.33141	T	0.24	-35.0069	7.5801	0.27959	0.1457:0.3811:0.4732:0.0	.	604;632	B4DYU1;Q5FVE4	.;ACBG2_HUMAN	D	632	ENSP00000252669:E632D	ENSP00000252669:E632D	E	+	3	2	ACSBG2	6138825	0.155000	0.22806	0.998000	0.56505	0.839000	0.47603	-0.666000	0.05280	0.249000	0.21456	0.655000	0.94253	GAG	.		0.512	ACSBG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452898.1	NM_030924	
PSMB10	5699	hgsc.bcm.edu	37	16	67968568	67968568	+	Silent	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr16:67968568G>T	ENST00000358514.4	-	8	1054	c.717C>A	c.(715-717)ggC>ggA	p.G239G	CTRL_ENST00000574481.1_5'Flank|CTC-479C5.12_ENST00000573493.1_3'UTR|CTRL_ENST00000576408.1_5'Flank	NM_002801.3	NP_002792.1	P40306	PSB10_HUMAN	proteasome (prosome, macropain) subunit, beta type, 10	239					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cell morphogenesis (GO:0000902)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|humoral immune response (GO:0006959)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|T cell proliferation (GO:0042098)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)	p.G239G(2)		NS(2)|endometrium(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00415)|Epithelial(162;0.0182)|all cancers(182;0.119)	Carfilzomib(DB08889)	AGTGGTAGCGGCCAGACCTGG	0.597																																					p.G239G		.											PSMB10,NS,carcinoma,0,2	PSMB10	0	2	Substitution - coding silent(2)	lung(1)|endometrium(1)	c.C717A						.						111.0	109.0	109.0					16																	67968568		2198	4300	6498	SO:0001819	synonymous_variant	5699	exon8			GTAGCGGCCAGAC	Y13640	CCDS10853.1	16q22.1	2008-02-05			ENSG00000205220	ENSG00000205220		"""Proteasome (prosome, macropain) subunits"""	9538	protein-coding gene	gene with protein product		176847		MECL1		8268911	Standard	NM_002801		Approved	LMP10, MGC1665, beta2i	uc002eux.2	P40306	OTTHUMG00000137553	ENST00000358514.4:c.717C>A	16.37:g.67968568G>T		Somatic	43	0		WXS	Illumina HiSeq	.	42	2	NM_002801	B2R5J4|Q5U098	Silent	SNP	ENST00000358514.4	37	CCDS10853.1																																																																																			.		0.597	PSMB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268887.1	NM_002801	
Unknown	0	hgsc.bcm.edu	37	2	91963899	91963899	+	IGR	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr2:91963899C>T								AC027612.2 (11855 upstream) : SLC9B1P2 (116598 downstream)																							CTGTGCCCTGCTGGGGAGGTG	0.607																																					.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	645367	.			GCCCTGCTGGGGA																													2.37:g.91963899C>T		Somatic	29	0		WXS	Illumina HiSeq	.	68	4	.		RNA	SNP		37																																																																																				.	0	0.607								
MAP9	79884	hgsc.bcm.edu	37	4	156281387	156281387	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr4:156281387G>T	ENST00000311277.4	-	7	1246	c.983C>A	c.(982-984)aCa>aAa	p.T328K	AC097467.2_ENST00000609716.1_RNA|AC097467.2_ENST00000608544.1_RNA|AC097467.2_ENST00000594492.1_RNA|AC097467.2_ENST00000596165.1_RNA|AC097467.2_ENST00000417474.1_RNA|AC097467.2_ENST00000598890.1_RNA|AC097467.2_ENST00000608762.1_RNA|AC097467.2_ENST00000608406.1_RNA|AC097467.2_ENST00000594666.1_RNA|AC097467.2_ENST00000609254.1_RNA|AC097467.2_ENST00000597831.1_RNA|AC097467.2_ENST00000600928.1_RNA|AC097467.2_ENST00000598252.1_RNA|AC097467.2_ENST00000596754.1_RNA|MAP9_ENST00000515654.1_Missense_Mutation_p.T304K	NM_001039580.1	NP_001034669.1	Q49MG5	MAP9_HUMAN	microtubule-associated protein 9	328					cytokinesis (GO:0000910)|regulation of mitosis (GO:0007088)|spindle assembly involved in mitosis (GO:0090307)	astral microtubule (GO:0000235)|mitotic spindle midzone (GO:1990023)		p.T328K(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)		TGGATCAACTGTTCTGTCATC	0.368																																					p.T328K		.											MAP9,NS,carcinoma,0,1	MAP9	0	1	Substitution - Missense(1)	lung(1)	c.C983A						.						153.0	141.0	145.0					4																	156281387		2203	4300	6503	SO:0001583	missense	79884	exon7			TCAACTGTTCTGT	AK024812	CCDS35493.1	4q32.1	2008-02-05			ENSG00000164114	ENSG00000164114			26118	protein-coding gene	gene with protein product	"""aster-associated protein"""	610070				16049101	Standard	XM_006714306		Approved	ASAP, FLJ21159	uc003ios.3	Q49MG5	OTTHUMG00000133628	ENST00000311277.4:c.983C>A	4.37:g.156281387G>T	ENSP00000310593:p.Thr328Lys	Somatic	67	0		WXS	Illumina HiSeq	.	75	3	NM_001039580	Q4W5I7|Q68DU1|Q9H781|Q9H7B6	Missense_Mutation	SNP	ENST00000311277.4	37	CCDS35493.1	.	.	.	.	.	.	.	.	.	.	G	13.67	2.305786	0.40795	.	.	ENSG00000164114	ENST00000311277;ENST00000515654;ENST00000433024;ENST00000393836	T;T;T	0.30981	2.27;2.17;1.51	4.77	3.84	0.44239	.	0.516808	0.17659	N	0.166401	T	0.35158	0.0922	L	0.42245	1.32	0.20638	N	0.99988	B;D;D	0.59357	0.009;0.985;0.985	B;P;P	0.54270	0.023;0.747;0.747	T	0.06807	-1.0806	10	0.32370	T	0.25	-9.8757	9.5276	0.39173	0.0:0.0:0.7902:0.2098	.	303;328;328	B4DVG9;B9EJB6;Q49MG5	.;.;MAP9_HUMAN	K	328;304;327;328	ENSP00000310593:T328K;ENSP00000427402:T304K;ENSP00000394048:T327K	ENSP00000310593:T328K	T	-	2	0	MAP9	156500837	0.006000	0.16342	0.007000	0.13788	0.009000	0.06853	1.684000	0.37649	2.565000	0.86533	0.591000	0.81541	ACA	.		0.368	MAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257771.3	NM_001039580	
TRMT12	55039	hgsc.bcm.edu;bcgsc.ca	37	8	125464268	125464268	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr8:125464268C>T	ENST00000328599.3	+	1	1221	c.1100C>T	c.(1099-1101)aCc>aTc	p.T367I	TRMT12_ENST00000521443.1_Intron	NM_017956.3	NP_060426.2	Q53H54	TYW2_HUMAN	tRNA methyltransferase 12 homolog (S. cerevisiae)	367					tRNA processing (GO:0008033)		transferase activity (GO:0016740)			breast(2)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15	Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			CAGCAAATTACCACCAACCAA	0.473																																					p.T367I		.											.	.	.	0			c.C1100T						.						61.0	59.0	59.0					8																	125464268		2203	4300	6503	SO:0001583	missense	55039	exon1			AAATTACCACCAA	AF313041	CCDS6349.1	8q24.13	2011-05-09	2006-11-16		ENSG00000183665	ENSG00000183665			26091	protein-coding gene	gene with protein product	"""tRNA-yW synthesizing protein 2"""	611244	"""tRNA methyltranferase 12 homolog (S. cerevisiae)"""			16005430, 17150819	Standard	NM_017956		Approved	FLJ20772, Trm12, TYW2	uc003yra.4	Q53H54	OTTHUMG00000165022	ENST00000328599.3:c.1100C>T	8.37:g.125464268C>T	ENSP00000329858:p.Thr367Ile	Somatic	57	0		WXS	Illumina HiSeq	.	80	4	NM_017956	Q6PKB9|Q96F21|Q9NWK6	Missense_Mutation	SNP	ENST00000328599.3	37	CCDS6349.1	.	.	.	.	.	.	.	.	.	.	C	0.104	-1.148425	0.01714	.	.	ENSG00000183665	ENST00000328599	T	0.46063	0.88	4.81	-2.03	0.07365	.	1.156040	0.06525	N	0.740352	T	0.14270	0.0345	N	0.01267	-0.92	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16660	-1.0395	10	0.36615	T	0.2	-0.3166	4.1944	0.10437	0.1789:0.4232:0.0:0.3979	.	367	Q53H54	TYW2_HUMAN	I	367	ENSP00000329858:T367I	ENSP00000329858:T367I	T	+	2	0	TRMT12	125533449	0.000000	0.05858	0.045000	0.18777	0.204000	0.24138	-0.493000	0.06459	-0.157000	0.11059	-0.459000	0.05422	ACC	.		0.473	TRMT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381465.1	NM_017956	
GYG2	8908	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	X	2799129	2799129	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chrX:2799129G>A	ENST00000381163.3	+	12	1663	c.1381G>A	c.(1381-1383)Gaa>Aaa	p.E461K	GYG2_ENST00000398806.3_Missense_Mutation_p.E430K|GYG2_ENST00000381161.1_3'UTR|GYG2_ENST00000338623.5_Missense_Mutation_p.E425K|GYG2_ENST00000542787.1_Missense_Mutation_p.E390K	NM_001079855.1|NM_001184702.1|NM_003918.2	NP_001073324.1|NP_001171631.1|NP_003909.2	O15488	GLYG2_HUMAN	glycogenin 2	461					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	glycogenin glucosyltransferase activity (GO:0008466)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)	13		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GATCTCCATCGAAGAGAAGGT	0.542																																					p.E461K		.											.	.	.	0			c.G1381A						.						120.0	81.0	94.0					X																	2799129		2203	4298	6501	SO:0001583	missense	8908	exon12			TCCATCGAAGAGA	U94361	CCDS14121.1, CCDS48074.1	Xp22.3	2013-02-22			ENSG00000056998	ENSG00000056998	2.4.1.186	"""Glycosyltransferase family 8 domain containing"""	4700	protein-coding gene	gene with protein product	"""glycogenin glucosyltransferase"""	300198				9857012	Standard	NM_001079855		Approved	GN-2	uc004cqs.1	O15488	OTTHUMG00000021079	ENST00000381163.3:c.1381G>A	X.37:g.2799129G>A	ENSP00000370555:p.Glu461Lys	Somatic	23	0		WXS	Illumina HiSeq	.	44	18	NM_003918	B7WNN6|O15485|O15486|O15487|O15489|O15490	Missense_Mutation	SNP	ENST00000381163.3	37	CCDS14121.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	3.162|3.162	-0.171924|-0.171924	0.06421|0.06421	.|.	.|.	ENSG00000056998|ENSG00000056998	ENST00000398806;ENST00000381163;ENST00000338623;ENST00000542787|ENST00000381157	T;T;T;T|.	0.43294|.	0.95;1.27;1.27;1.29|.	4.03|4.03	-5.68|-5.68	0.02436|0.02436	.|.	2.478110|.	0.01761|.	N|.	0.030583|.	T|T	0.06826|0.06826	0.0174|0.0174	N|N	0.00926|0.00926	-1.1|-1.1	0.09310|0.09310	N|N	1|1	B;B;B;B;B;B|.	0.18166|.	0.001;0.002;0.009;0.002;0.011;0.026|.	B;B;B;B;B;B|.	0.10450|.	0.002;0.003;0.005;0.001;0.003;0.001|.	T|T	0.31998|0.31998	-0.9923|-0.9923	10|5	0.12103|.	T|.	0.63|.	.|.	3.2847|3.2847	0.06927|0.06927	0.3626:0.4082:0.1297:0.0995|0.3626:0.4082:0.1297:0.0995	.|.	425;390;421;430;430;461|.	O15488-6;O15488-4;O15488-3;A8K8Y1;O15488-2;O15488|.	.;.;.;.;.;GLYG2_HUMAN|.	K|Q	430;461;425;390|243	ENSP00000381786:E430K;ENSP00000370555:E461K;ENSP00000341273:E425K;ENSP00000446092:E390K|.	ENSP00000341273:E425K|.	E|R	+|+	1|2	0|0	GYG2|GYG2	2809129|2809129	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.018000|0.018000	0.09664|0.09664	-0.289000|-0.289000	0.08365|0.08365	-0.955000|-0.955000	0.03636|0.03636	-0.235000|-0.235000	0.12190|0.12190	GAA|CGA	.		0.542	GYG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055645.1	NM_003918	
UNC79	57578	hgsc.bcm.edu;bcgsc.ca	37	14	94084687	94084687	+	Silent	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr14:94084687C>T	ENST00000393151.2	+	29	4374	c.4374C>T	c.(4372-4374)agC>agT	p.S1458S	UNC79_ENST00000555664.1_Silent_p.S1458S|UNC79_ENST00000256339.4_Silent_p.S1281S|UNC79_ENST00000553484.1_Silent_p.S1480S			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	1458					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						GCAGATACAGCGAAAAAGAAA	0.393																																					p.S1281S		.											.	.	.	0			c.C3843T						.						80.0	71.0	74.0					14																	94084687		2203	4300	6503	SO:0001819	synonymous_variant	57578	exon29			ATACAGCGAAAAA	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"""KIAA1409"""	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.4374C>T	14.37:g.94084687C>T		Somatic	81	0		WXS	Illumina HiSeq	.	63	4	NM_020818	B5MDL6|Q6ZUT7	Silent	SNP	ENST00000393151.2	37																																																																																				.		0.393	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395	
BCAN	63827	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	156622711	156622711	+	Intron	SNP	C	C	G			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr1:156622711C>G	ENST00000329117.5	+	8	2278				RP11-284F21.7_ENST00000448869.1_RNA|BCAN_ENST00000361588.5_Missense_Mutation_p.L657V	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican						carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)	p.L657I(1)		cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CTCAACTGCCCTCTCTATCCT	0.587																																					p.L657V		.											.	.	.	1	Substitution - Missense(1)	lung(1)	c.C1969G						.						112.0	84.0	94.0					1																	156622711		2162	4242	6404	SO:0001627	intron_variant	63827	exon8			ACTGCCCTCTCTA	BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	23059	protein-coding gene	gene with protein product	"""chondroitin sulfate proteoglycan 7"", ""brevican proteoglycan"""	600347				11054543, 11873941	Standard	NM_021948		Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.1942+27C>G	1.37:g.156622711C>G		Somatic	21	0		WXS	Illumina HiSeq	.	29	11	NM_198427	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Missense_Mutation	SNP	ENST00000329117.5	37	CCDS1149.1	.	.	.	.	.	.	.	.	.	.	C	3.504	-0.101288	0.06967	.	.	ENSG00000132692	ENST00000361588	T	0.05382	3.45	4.0	-0.258	0.12975	.	.	.	.	.	T	0.00998	0.0033	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.47911	-0.9080	7	.	.	.	.	5.6596	0.17662	0.0:0.4869:0.3191:0.1941	.	657	Q96GW7-2	.	V	657	ENSP00000354925:L657V	.	L	+	1	0	BCAN	154889335	0.003000	0.15002	0.001000	0.08648	0.203000	0.24098	0.251000	0.18257	0.085000	0.17107	0.455000	0.32223	CTC	.		0.587	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948	
ERLEC1	27248	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	54035592	54035592	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr2:54035592C>T	ENST00000185150.4	+	9	1167	c.1036C>T	c.(1036-1038)Cgt>Tgt	p.R346C	GPR75-ASB3_ENST00000352846.3_Intron|ASB3_ENST00000406625.2_Intron|ERLEC1_ENST00000378239.5_Intron|ERLEC1_ENST00000405123.3_Missense_Mutation_p.R346C|ASB3_ENST00000498475.2_Intron	NM_015701.4	NP_056516.2	Q96DZ1	ERLEC_HUMAN	endoplasmic reticulum lectin 1	346	PRKCSH 2.				ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum lumen (GO:0005788)	glycoprotein binding (GO:0001948)			endometrium(2)|large_intestine(4)|lung(8)|ovary(2)|stomach(1)|urinary_tract(1)	18						TTACTGCTTTCGTGGGGTGAG	0.403																																					p.R346C		.											ERLEC1,NS,carcinoma,0,1	ERLEC1	0	0			c.C1036T						.						95.0	98.0	97.0					2																	54035592		2203	4300	6503	SO:0001583	missense	27248	exon9			TGCTTTCGTGGGG	AF131849	CCDS1848.1, CCDS46283.1, CCDS46284.1	2p16	2010-03-19	2009-08-26	2009-08-26	ENSG00000068912	ENSG00000068912			25222	protein-coding gene	gene with protein product	"""erlectin 1"""	611229	"""chromosome 2 open reading frame 30"""	C2orf30		9110174, 8619474, 16531414, 18264092	Standard	NM_015701		Approved	CL25084, XTP3TPB, XTP3-B, ERLECTIN	uc002rxl.3	Q96DZ1	OTTHUMG00000129281	ENST00000185150.4:c.1036C>T	2.37:g.54035592C>T	ENSP00000185150:p.Arg346Cys	Somatic	64	0		WXS	Illumina HiSeq	.	93	20	NM_015701	B2RDB4|B5MC72|O95901|Q6UWN7|Q9NUY7|Q9UQL4	Missense_Mutation	SNP	ENST00000185150.4	37	CCDS1848.1	.	.	.	.	.	.	.	.	.	.	C	18.95	3.732573	0.69189	.	.	ENSG00000068912	ENST00000405123;ENST00000185150	T;T	0.03982	3.74;3.74	5.02	5.02	0.67125	Mannose-6-phosphate receptor, binding (1);Glucosidase II beta subunit-like (1);	0.141227	0.64402	D	0.000005	T	0.12092	0.0294	.	.	.	0.80722	D	1	D;P	0.57571	0.98;0.951	B;P	0.49887	0.17;0.625	T	0.01639	-1.1306	9	0.45353	T	0.12	-8.8904	18.6995	0.91615	0.0:1.0:0.0:0.0	.	346;346	B5MC72;Q96DZ1	.;ERLEC_HUMAN	C	346	ENSP00000385629:R346C;ENSP00000185150:R346C	ENSP00000185150:R346C	R	+	1	0	ERLEC1	53889096	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	7.615000	0.83006	2.479000	0.83701	0.491000	0.48974	CGT	.		0.403	ERLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251404.1	NM_015701	
ZDHHC6	64429	hgsc.bcm.edu	37	10	114200370	114200370	+	Silent	SNP	A	A	G			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr10:114200370A>G	ENST00000369405.3	-	5	1026	c.603T>C	c.(601-603)gcT>gcC	p.A201A	ZDHHC6_ENST00000369404.3_Silent_p.A197A	NM_022494.1	NP_071939.1	Q9H6R6	ZDHC6_HUMAN	zinc finger, DHHC-type containing 6	201					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Colorectal(252;0.198)		Epithelial(162;0.0291)|all cancers(201;0.117)		TAGCAAATGCAGCTAATCCAA	0.443																																					p.A201A		.											.	.	.	0			c.T603C						.						173.0	156.0	161.0					10																	114200370		2203	4300	6503	SO:0001819	synonymous_variant	64429	exon5			AAATGCAGCTAAT	AK025605	CCDS7574.1	10q26.11	2008-05-02			ENSG00000023041	ENSG00000023041		"""Zinc fingers, DHHC-type"""	19160	protein-coding gene	gene with protein product							Standard	NM_022494		Approved	ZNF376, FLJ21952	uc001kzv.3	Q9H6R6	OTTHUMG00000019062	ENST00000369405.3:c.603T>C	10.37:g.114200370A>G		Somatic	68	0		WXS	Illumina HiSeq	.	82	2	NM_022494	D3DRB6|Q53G45|Q96IV7|Q9H605	Silent	SNP	ENST00000369405.3	37	CCDS7574.1																																																																																			.		0.443	ZDHHC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050393.1	NM_022494	
CCDC57	284001	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	17	80151670	80151670	+	Silent	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr17:80151670C>T	ENST00000389641.4	-	6	849	c.813G>A	c.(811-813)caG>caA	p.Q271Q	CCDC57_ENST00000392347.1_Silent_p.Q271Q|CCDC57_ENST00000392343.3_Silent_p.Q271Q			Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	271										endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	16	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			TCCTGGTTAGCTGCACAGAGT	0.453																																					p.Q271Q		.											.	.	.	0			c.G813A						.						106.0	100.0	102.0					17																	80151670		1951	4151	6102	SO:0001819	synonymous_variant	284001	exon6			GGTTAGCTGCACA	BC040264		17q25.3	2006-03-08			ENSG00000176155	ENSG00000176155			27564	protein-coding gene	gene with protein product						12477932	Standard	XM_006722279		Approved	FLJ00130, FLJ23754	uc002kdx.1	Q2TAC2	OTTHUMG00000140396	ENST00000389641.4:c.813G>A	17.37:g.80151670C>T		Somatic	38	0		WXS	Illumina HiSeq	.	76	4	NM_198082	A6NP51|A8MQC7|Q8IWG2|Q8TER3	Silent	SNP	ENST00000389641.4	37																																																																																				.		0.453	CCDC57-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000277182.3	NM_198082	
SCLY	51540	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	238990770	238990770	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr2:238990770G>A	ENST00000555827.1	+	6	761	c.697G>A	c.(697-699)Gat>Aat	p.D233N	SCLY_ENST00000429612.2_Intron|SCLY_ENST00000254663.6_Missense_Mutation_p.D241N|SCLY_ENST00000409736.2_Missense_Mutation_p.D233N|SCLY_ENST00000373332.3_Missense_Mutation_p.D151N|SCLY_ENST00000422984.2_Missense_Mutation_p.D139N			Q96I15	SCLY_HUMAN	selenocysteine lyase	233					cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)	pyridoxal phosphate binding (GO:0030170)|selenocysteine lyase activity (GO:0009000)|transferase activity (GO:0016740)			endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	22		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285)		CGTGCACACGGATGCTGCACA	0.597																																					p.D241N	Melanoma(24;424 891 11947 32582 36034)|Ovarian(46;648 1065 26199 32764 45893)	.											.	.	.	0			c.G721A						.						98.0	87.0	91.0					2																	238990770		2203	4300	6503	SO:0001583	missense	51540	exon6			CACACGGATGCTG	AF175767	CCDS2524.1, CCDS2524.2	2q37.3	2008-02-05			ENSG00000132330	ENSG00000132330			18161	protein-coding gene	gene with protein product	"""putative selenocysteine lyase"""	611056				10692412	Standard	NM_016510		Approved	SCL	uc010fyv.4	Q96I15	OTTHUMG00000133336	ENST00000555827.1:c.697G>A	2.37:g.238990770G>A	ENSP00000450613:p.Asp233Asn	Somatic	11	0		WXS	Illumina HiSeq	.	35	12	NM_016510	B9A068|J3KN06|Q53SN1|Q53SN8|Q7L670|Q9NVT7|Q9NZR7	Missense_Mutation	SNP	ENST00000555827.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.1|21.1	4.090162|4.090162	0.76756|0.76756	.|.	.|.	ENSG00000132330|ENSG00000132330	ENST00000254663;ENST00000555827;ENST00000373332;ENST00000413463;ENST00000409736;ENST00000422984;ENST00000450965|ENST00000437134;ENST00000440143	T;T;D;D;D;T;D|.	0.98996|.	-1.48;-1.48;-1.77;-5.31;-1.77;-1.48;-1.77|.	5.48|5.48	5.48|5.48	0.80851|0.80851	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.88051|0.88051	0.6333|0.6333	H|H	0.96430|0.96430	3.82|3.82	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	1.0;1.0;1.0|.	D|D	0.91618|0.91618	0.5308|0.5308	10|5	0.87932|.	D|.	0|.	-10.9898|-10.9898	18.1424|18.1424	0.89644|0.89644	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	139;233;233|.	E7ESG3;Q96I15;Q96I15-2|.	.;SCLY_HUMAN;.|.	N|E	241;233;151;147;233;139;63|76;10	ENSP00000254663:D241N;ENSP00000450613:D233N;ENSP00000362429:D151N;ENSP00000414165:D147N;ENSP00000387162:D233N;ENSP00000416865:D139N;ENSP00000414053:D63N|.	ENSP00000254663:D233N|.	D|G	+|+	1|2	0|0	SCLY|SCLY	238655509|238655509	1.000000|1.000000	0.71417|0.71417	0.109000|0.109000	0.21407|0.21407	0.029000|0.029000	0.11900|0.11900	9.752000|9.752000	0.98900|0.98900	2.576000|2.576000	0.86940|0.86940	0.655000|0.655000	0.94253|0.94253	GAT|GGA	.		0.597	SCLY-204	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_016510	
CLCN5	1184	hgsc.bcm.edu	37	X	49840560	49840560	+	Nonsense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chrX:49840560G>T	ENST00000307367.2	+	4	607	c.316G>T	c.(316-318)Gag>Tag	p.E106*	CLCN5_ENST00000376088.3_Nonsense_Mutation_p.E176*|CLCN5_ENST00000376091.3_Nonsense_Mutation_p.E176*|CLCN5_ENST00000376108.3_Nonsense_Mutation_p.E106*			P51795	CLCN5_HUMAN	chloride channel, voltage-sensitive 5	106					chloride transmembrane transport (GO:1902476)|endocytosis (GO:0006897)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)	30	Ovarian(276;0.236)					CTGGAACTCTGAGCATGTCAC	0.418																																					p.E176X		.											.	.	.	0			c.G526T						.						158.0	130.0	139.0					X																	49840560		2203	4300	6503	SO:0001587	stop_gained	1184	exon7			AACTCTGAGCATG	X91906	CCDS14328.1, CCDS48115.1, CCDS69763.1	Xp11.23-p11.22	2012-09-26	2012-02-23		ENSG00000171365	ENSG00000171365		"""Ion channels / Chloride channels : Voltage-sensitive"""	2023	protein-coding gene	gene with protein product	"""Dent disease"""	300008	"""nephrolithiasis 2, X-linked"", ""nephrolithiasis 1 (X-linked)"", ""chloride channel 5"""	NPHL2, NPHL1		7874126, 8111383, 8099916, 8559248, 9602200	Standard	NM_001272102		Approved	DENTS, XLRH, hClC-K2, hCIC-K2, CLC5, XRN, ClC-5	uc004doq.1	P51795	OTTHUMG00000021514	ENST00000307367.2:c.316G>T	X.37:g.49840560G>T	ENSP00000304257:p.Glu106*	Somatic	46	0		WXS	Illumina HiSeq	.	97	4	NM_001127898	A1L475|B3KPN6|Q5JQD5|Q7RTN8	Nonsense_Mutation	SNP	ENST00000307367.2	37	CCDS14328.1	.	.	.	.	.	.	.	.	.	.	G	37	6.051323	0.97236	.	.	ENSG00000171365	ENST00000376088;ENST00000376091;ENST00000376108;ENST00000307367	.	.	.	5.0	-3.64	0.04515	.	0.817091	0.10929	N	0.618551	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	-6.5404	6.3468	0.21353	0.4037:0.3263:0.27:0.0	.	.	.	.	X	176;176;106;106	.	ENSP00000304257:E106X	E	+	1	0	CLCN5	49727300	0.716000	0.27956	0.000000	0.03702	0.978000	0.69477	1.696000	0.37773	-0.945000	0.03681	0.529000	0.55759	GAG	.		0.418	CLCN5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056544.1		
RPL36A	6173	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	100646777	100646777	+	Nonsense_Mutation	SNP	T	T	G			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chrX:100646777T>G	ENST00000553110.3	+	3	228	c.144T>G	c.(142-144)taT>taG	p.Y48*	RPL36A_ENST00000471855.1_De_novo_Start_OutOfFrame|RPL36A_ENST00000427805.2_Nonsense_Mutation_p.Y84*|RPL36A-HNRNPH2_ENST00000409170.3_Missense_Mutation_p.M59R			P83881	RL36A_HUMAN	ribosomal protein L36a	48					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			liver(4)|lung(1)|prostate(1)	6						AGAGTGGCTATGGTGGGCAAA	0.413																																					p.Y84X		.											.	.	.	0			c.T252G						.						149.0	127.0	135.0					X																	100646777		2203	4300	6503	SO:0001587	stop_gained	0	exon3			TGGCTATGGTGGG	BC001781	CCDS14483.1, CCDS14483.2	Xq22.1	2011-04-06	2002-01-15	2002-01-18	ENSG00000241343	ENSG00000241343		"""L ribosomal proteins"""	10359	protein-coding gene	gene with protein product		300902	"""ribosomal protein L44"""	RPL44		3461443	Standard	NM_021029		Approved	L36A		P83881	OTTHUMG00000022027	ENST00000553110.3:c.144T>G	X.37:g.100646777T>G	ENSP00000446503:p.Tyr48*	Somatic	58	0		WXS	Illumina HiSeq	.	106	27	NM_001199973	P09896|P10661|Q08ES5|Q5J9I6	Nonsense_Mutation	SNP	ENST00000553110.3	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	29.0|29.0|29.0	4.965194|4.965194|4.965194	0.92855|0.92855|0.92855	.|.|.	.|.|.	ENSG00000257529|ENSG00000241343|ENSG00000241343;ENSG00000241343;ENSG00000257529	ENST00000409170|ENST00000392994|ENST00000427805;ENST00000553110;ENST00000409338	.|.|.	.|.|.	.|.|.	5.85|5.85|5.85	-1.65|-1.65|-1.65	0.08291|0.08291|0.08291	.|.|.	.|.|0.000000	.|.|0.56097	.|.|U	.|.|0.000034	T|T|.	0.36552|0.36552|.	0.0971|0.0971|.	.|.|.	.|.|.	.|.|.	0.80722|0.80722|0.80722	A|A|A	1|1|1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|.	0.39440|0.39440|.	-0.9614|-0.9614|.	3|3|.	.|.|.	.|.|.	.|.|.	-22.4825|-22.4825|-22.4825	6.3926|6.3926|6.3926	0.21595|0.21595|0.21595	0.11:0.3316:0.0:0.5585|0.11:0.3316:0.0:0.5585|0.11:0.3316:0.0:0.5585	.|.|.	.|.|.	.|.|.	.|.|.	R|G|X	59|67|84;48;59	.|.|.	.|.|.	M|W|Y	+|+|+	2|1|3	0|0|2	RP1-164F3.9|RPL36A|RPL36A;RP1-164F3.9	100533433|100533433|100533433	0.992000|0.992000|0.992000	0.36948|0.36948|0.36948	0.905000|0.905000|0.905000	0.35620|0.35620|0.35620	0.995000|0.995000|0.995000	0.86356|0.86356|0.86356	0.205000|0.205000|0.205000	0.17356|0.17356|0.17356	-0.713000|-0.713000|-0.713000	0.04981|0.04981|0.04981	0.381000|0.381000|0.381000	0.24937|0.24937|0.24937	ATG|TGG|TAT	.		0.413	RPL36A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_021029	
ELF4	2000	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	129201166	129201166	+	Nonsense_Mutation	SNP	C	C	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chrX:129201166C>A	ENST00000308167.5	-	9	1901	c.1522G>T	c.(1522-1524)Gga>Tga	p.G508*	ELF4_ENST00000335997.7_Nonsense_Mutation_p.G508*	NM_001421.3	NP_001412.1			E74-like factor 4 (ets domain transcription factor)											breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	22						CCTGCTGGTCCAGCCCCTGTG	0.667			T	ERG	AML																																p.G508X		.		Dom	yes		X	Xq26	2000	E74-like factor 4 (ets domain transcription factor)		L	.	.	.	0			c.G1522T						.						25.0	27.0	27.0					X																	129201166		2199	4289	6488	SO:0001587	stop_gained	2000	exon9			CTGGTCCAGCCCC	U32645	CCDS14617.1	Xq26	2014-09-17			ENSG00000102034	ENSG00000102034			3319	protein-coding gene	gene with protein product		300775				8895518	Standard	NM_001421		Approved	MEF, ELFR	uc004eve.4	Q99607	OTTHUMG00000022390	ENST00000308167.5:c.1522G>T	X.37:g.129201166C>A	ENSP00000311280:p.Gly508*	Somatic	29	0		WXS	Illumina HiSeq	.	66	19	NM_001421		Nonsense_Mutation	SNP	ENST00000308167.5	37	CCDS14617.1	.	.	.	.	.	.	.	.	.	.	c	38	6.647086	0.97730	.	.	ENSG00000102034	ENST00000335997;ENST00000308167	.	.	.	3.38	1.55	0.23275	.	0.435423	0.20999	N	0.081890	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	.	3.2972	0.06970	0.2575:0.5994:0.0:0.1431	.	.	.	.	X	508	.	ENSP00000311280:G508X	G	-	1	0	ELF4	129028847	0.287000	0.24315	0.012000	0.15200	0.994000	0.84299	0.250000	0.18235	0.274000	0.22072	0.509000	0.49947	GGA	.		0.667	ELF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058243.1	NM_001421	
LRRC52	440699	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	1	165513519	165513519	+	5'UTR	SNP	T	T	C			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr1:165513519T>C	ENST00000294818.1	+	0	276				RP11-280O1.2_ENST00000438275.1_RNA|RP11-280O1.2_ENST00000416424.1_RNA|RP11-280O1.2_ENST00000421273.1_RNA	NM_001005214.3	NP_001005214.2	Q8N7C0	LRC52_HUMAN	leucine rich repeat containing 52						ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)	18	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)					AGGAGGGTGGTTGTGGCTTCT	0.572																																					.		.											.	.	.	0			.						.						96.0	91.0	92.0					1																	165513519		2203	4300	6503	SO:0001623	5_prime_UTR_variant	440699	.			GGGTGGTTGTGGC	AK098677	CCDS30930.1	1q23.3	2008-02-05			ENSG00000162763	ENSG00000162763			32156	protein-coding gene	gene with protein product		615218					Standard	NM_001005214		Approved	FLJ25811	uc001gde.2	Q8N7C0	OTTHUMG00000034625	ENST00000294818.1:c.-15T>C	1.37:g.165513519T>C		Somatic	67	0		WXS	Illumina HiSeq	.	107	18	.	A2RUN7|Q5T9K5	RNA	SNP	ENST00000294818.1	37	CCDS30930.1																																																																																			.		0.572	LRRC52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083793.1	NM_001005214	
CCDC88C	440193	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	14	91883098	91883098	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr14:91883098G>T	ENST00000389857.6	-	2	231	c.145C>A	c.(145-147)Caa>Aaa	p.Q49K	CCDC88C_ENST00000553403.1_Missense_Mutation_p.Q49K|CCDC88C_ENST00000389856.5_Missense_Mutation_p.Q41K|RP11-895M11.3_ENST00000557524.1_lincRNA|CCDC88C_ENST00000554165.1_5'UTR	NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	49					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				AGCATAATTTGGTTCAAAAAG	0.478																																					p.Q49K		.											.	.	.	0			c.C145A						.						56.0	53.0	54.0					14																	91883098		1935	4126	6061	SO:0001583	missense	440193	exon2			TAATTTGGTTCAA		CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"""Dvl-associating protein with a high frequency of leucine residues"", ""spinocerebellar ataxia 40"""	611204	"""KIAA1509"""	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.145C>A	14.37:g.91883098G>T	ENSP00000374507:p.Gln49Lys	Somatic	34	0		WXS	Illumina HiSeq	.	38	4	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Missense_Mutation	SNP	ENST00000389857.6	37	CCDS45151.1	.	.	.	.	.	.	.	.	.	.	G	12.02	1.813277	0.32053	.	.	ENSG00000015133	ENST00000389857;ENST00000541408;ENST00000389856;ENST00000553403	T;T;T	0.43688	2.0;0.94;0.94	5.18	4.16	0.48862	.	0.251811	0.20735	U	0.086646	T	0.22044	0.0531	N	0.05383	-0.06	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.11329	0.006;0.001	T	0.06481	-1.0824	10	0.26408	T	0.33	-7.7523	10.4269	0.44385	0.0:0.0:0.6309:0.3691	.	49;49	Q9P219;G3V3S0	DAPLE_HUMAN;.	K	49;13;41;49	ENSP00000374507:Q49K;ENSP00000374506:Q41K;ENSP00000451392:Q49K	ENSP00000374506:Q41K	Q	-	1	0	CCDC88C	90952851	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.281000	0.65609	2.569000	0.86673	0.462000	0.41574	CAA	.		0.478	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353	
APAF1	317	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	99106135	99106135	+	Silent	SNP	T	T	C			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr12:99106135T>C	ENST00000551964.1	+	21	3616	c.2880T>C	c.(2878-2880)acT>acC	p.T960T	APAF1_ENST00000339433.3_Silent_p.T917T|APAF1_ENST00000333991.1_Intron|APAF1_ENST00000359972.2_Silent_p.T906T|APAF1_ENST00000549007.1_Silent_p.T917T|APAF1_ENST00000550527.1_Silent_p.T949T|APAF1_ENST00000357310.1_Silent_p.T917T|APAF1_ENST00000547045.1_Silent_p.T917T|APAF1_ENST00000552268.1_Intron	NM_181861.1	NP_863651.1	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1	960					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway (GO:0097193)|nervous system development (GO:0007399)|neural tube closure (GO:0001843)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|response to G1 DNA damage checkpoint signaling (GO:0072432)	apoptosome (GO:0043293)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(1)	42					Adenosine triphosphate(DB00171)	ATTATCTGACTGAAGCTCAAG	0.388																																					p.T960T		.											.	.	.	0			c.T2880C						.						127.0	112.0	117.0					12																	99106135		2203	4300	6503	SO:0001819	synonymous_variant	317	exon21			TCTGACTGAAGCT	AF013263	CCDS9069.1, CCDS9070.1, CCDS9071.1, CCDS55862.1, CCDS55863.1	12q23	2013-01-10	2006-10-23			ENSG00000120868		"""WD repeat domain containing"""	576	protein-coding gene	gene with protein product		602233	"""apoptotic protease activating factor"", ""apoptotic peptidase activating factor"""			9267021, 10702682	Standard	NM_181861		Approved	CED4, APAF-1	uc001tfz.3	O14727	OTTHUMG00000170214	ENST00000551964.1:c.2880T>C	12.37:g.99106135T>C		Somatic	31	0		WXS	Illumina HiSeq	.	27	18	NM_181861	B2RMX8|O43297|Q7Z438|Q9BXZ6|Q9UBZ5|Q9UGN8|Q9UGN9|Q9UGP0|Q9UJ58|Q9UJ59|Q9UJ60|Q9UJ61|Q9UJ62|Q9UJ63|Q9UJ64|Q9UJ65|Q9UJ66|Q9UJ67|Q9UNC9	Silent	SNP	ENST00000551964.1	37	CCDS9069.1																																																																																			.		0.388	APAF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408006.1	NM_181861.1	
EP400	57634	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	12	132530051	132530051	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr12:132530051G>T	ENST00000333577.4	+	39	7189	c.7080G>T	c.(7078-7080)gaG>gaT	p.E2360D	EP400_ENST00000389562.2_Missense_Mutation_p.E2323D|EP400_ENST00000332482.4_Missense_Mutation_p.E2287D|EP400_ENST00000330386.6_Missense_Mutation_p.E2243D|EP400_ENST00000389561.2_Missense_Mutation_p.E2324D			Q96L91	EP400_HUMAN	E1A binding protein p400	2360	Myb-like. {ECO:0000255|PROSITE- ProRule:PRU00133}.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		CCACAGCTGAGCCTGGTCAAG	0.562																																					p.E2324D		.											.	.	.	0			c.G6972T						.						64.0	63.0	63.0					12																	132530051		2203	4300	6503	SO:0001583	missense	57634	exon38			AGCTGAGCCTGGT	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.7080G>T	12.37:g.132530051G>T	ENSP00000333602:p.Glu2360Asp	Somatic	23	0		WXS	Illumina HiSeq	.	26	4	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	37		.	.	.	.	.	.	.	.	.	.	G	7.906	0.735497	0.15574	.	.	ENSG00000183495	ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000541296	D;D;D;D;D	0.92199	-2.98;-2.97;-2.99;-2.98;-2.97	5.61	2.71	0.32032	.	0.049151	0.85682	N	0.000000	D	0.88937	0.6573	M	0.69248	2.105	0.30894	N	0.730033	B;B;B	0.18863	0.031;0.031;0.031	B;B;B	0.25140	0.058;0.058;0.058	D	0.83881	0.0279	10	0.72032	D	0.01	.	4.561	0.12160	0.2982:0.0:0.5578:0.1439	.	2324;2243;2323	Q96L91-2;Q96L91-4;Q96L91-5	.;.;.	D	2360;2324;2323;2287;2243;2324	ENSP00000333602:E2360D;ENSP00000374212:E2324D;ENSP00000374213:E2323D;ENSP00000331737:E2287D;ENSP00000330620:E2243D	ENSP00000330620:E2243D	E	+	3	2	EP400	131096004	0.528000	0.26314	0.148000	0.22405	0.136000	0.21042	0.869000	0.27996	0.284000	0.22305	0.655000	0.94253	GAG	.		0.562	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
SPHK2	56848	hgsc.bcm.edu	37	19	49132111	49132111	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr19:49132111G>T	ENST00000245222.4	+	7	1412	c.1046G>T	c.(1045-1047)cGc>cTc	p.R349L	SPHK2_ENST00000340932.3_Intron|SPHK2_ENST00000599029.1_Missense_Mutation_p.R313L|SPHK2_ENST00000600537.1_Missense_Mutation_p.R290L|SPHK2_ENST00000599748.1_Missense_Mutation_p.R313L|SPHK2_ENST00000443164.1_Missense_Mutation_p.R411L|SPHK2_ENST00000598088.1_Missense_Mutation_p.R349L	NM_001204158.2|NM_001243876.1|NM_020126.4	NP_001191087.1|NP_001230805.1|NP_064511.2	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2	349					blood vessel development (GO:0001568)|brain development (GO:0007420)|cell proliferation (GO:0008283)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|small molecule metabolic process (GO:0044281)|sphinganine-1-phosphate biosynthetic process (GO:0006669)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	ATP binding (GO:0005524)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|Ras GTPase binding (GO:0017016)|sphinganine kinase activity (GO:0008481)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	19		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		CAGAGCGAGCGCTTCAGGGCC	0.662																																					p.R349L		.											SPHK2,caecum,carcinoma,0,1	SPHK2	0	0			c.G1046T						.						71.0	72.0	72.0					19																	49132111		2203	4300	6503	SO:0001583	missense	56848	exon7			GCGAGCGCTTCAG	AF245447	CCDS12727.1, CCDS59404.1, CCDS59405.1, CCDS74414.1	19q13.33	2013-09-20			ENSG00000063176	ENSG00000063176			18859	protein-coding gene	gene with protein product		607092				10751414, 17895250	Standard	NM_020126		Approved		uc002pjs.3	Q9NRA0	OTTHUMG00000183318	ENST00000245222.4:c.1046G>T	19.37:g.49132111G>T	ENSP00000245222:p.Arg349Leu	Somatic	45	0		WXS	Illumina HiSeq	.	47	2	NM_020126	A0T4C8|B4DU87|Q9BRN1|Q9H0Q2|Q9NWU7	Missense_Mutation	SNP	ENST00000245222.4	37	CCDS12727.1	.	.	.	.	.	.	.	.	.	.	G	15.38	2.816473	0.50527	.	.	ENSG00000063176	ENST00000245222;ENST00000406269;ENST00000443164	T;T	0.14266	2.52;2.52	4.13	4.13	0.48395	.	0.061034	0.56097	D	0.000023	T	0.17152	0.0412	M	0.87381	2.88	0.80722	D	1	B;P;P	0.50066	0.18;0.931;0.704	B;B;B	0.35607	0.081;0.1;0.206	T	0.06607	-1.0817	10	0.72032	D	0.01	-43.7105	7.9713	0.30130	0.1116:0.0:0.8884:0.0	.	290;411;349	B4DU87;A0T4C8;Q9NRA0	.;.;SPHK2_HUMAN	L	349;322;411	ENSP00000245222:R349L;ENSP00000413369:R411L	ENSP00000245222:R349L	R	+	2	0	SPHK2	53823923	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	3.665000	0.54532	2.317000	0.78254	0.655000	0.94253	CGC	.		0.662	SPHK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466153.1		
GXYLT1	283464	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	42512815	42512815	+	Missense_Mutation	SNP	C	C	G			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr12:42512815C>G	ENST00000398675.3	-	3	705	c.473G>C	c.(472-474)aGc>aCc	p.S158T	GXYLT1_ENST00000280876.6_Missense_Mutation_p.S127T	NM_001099650.1|NM_173601.1	NP_001093120.1|NP_775872.1	Q4G148	GXLT1_HUMAN	glucoside xylosyltransferase 1	158					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|O-glycan processing (GO:0016266)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	UDP-xylosyltransferase activity (GO:0035252)			kidney(2)|large_intestine(4)|liver(3)|lung(8)	17						GCCTTTAAAGCTATGATGTAG	0.323																																					p.S158T		.											.	.	.	0			c.G473C						.						70.0	63.0	65.0					12																	42512815		1854	4093	5947	SO:0001583	missense	283464	exon3			TTAAAGCTATGAT	BC015597	CCDS41771.1, CCDS41772.1	12q12	2013-10-11	2009-11-17	2009-11-17	ENSG00000151233	ENSG00000151233		"""Glycosyltransferase family 8 domain containing"""	27482	protein-coding gene	gene with protein product		613321	"""glycosyltransferase 8 domain containing 3"""	GLT8D3		19940119	Standard	NM_001099650		Approved	FLJ43151	uc001rms.4	Q4G148	OTTHUMG00000169379	ENST00000398675.3:c.473G>C	12.37:g.42512815C>G	ENSP00000381666:p.Ser158Thr	Somatic	60	0		WXS	Illumina HiSeq	.	100	40	NM_173601	B3KWJ2|Q8IXV1|Q96BH4	Missense_Mutation	SNP	ENST00000398675.3	37	CCDS41772.1	.	.	.	.	.	.	.	.	.	.	C	12.27	1.886608	0.33348	.	.	ENSG00000151233	ENST00000398675;ENST00000280876	T;T	0.22134	1.97;1.97	5.77	4.88	0.63580	.	0.199524	0.56097	D	0.000030	T	0.22627	0.0546	M	0.71581	2.175	0.32128	N	0.587187	B;B	0.33345	0.356;0.409	B;B	0.36030	0.138;0.216	T	0.17258	-1.0375	10	0.10636	T	0.68	-5.4156	9.4303	0.38606	0.0:0.7862:0.0:0.2138	.	127;158	Q4G148-2;Q4G148	.;GXLT1_HUMAN	T	158;127	ENSP00000381666:S158T;ENSP00000280876:S127T	ENSP00000280876:S127T	S	-	2	0	GXYLT1	40799082	0.994000	0.37717	0.996000	0.52242	0.963000	0.63663	2.067000	0.41461	1.445000	0.47624	0.591000	0.81541	AGC	.		0.323	GXYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403778.1	XM_290597	
COL6A6	131873	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	130287118	130287118	+	Missense_Mutation	SNP	C	C	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr3:130287118C>A	ENST00000358511.6	+	5	2102	c.2071C>A	c.(2071-2073)Caa>Aaa	p.Q691K	COL6A6_ENST00000453409.2_Missense_Mutation_p.Q691K	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	691	Nonhelical region.|VWFA 4. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						TGCAATAGACCAAATGGCTCA	0.493																																					p.Q691K		.											.	.	.	0			c.C2071A						.						132.0	132.0	132.0					3																	130287118		1957	4144	6101	SO:0001583	missense	131873	exon5			ATAGACCAAATGG	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"""Collagens"""	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.2071C>A	3.37:g.130287118C>A	ENSP00000351310:p.Gln691Lys	Somatic	41	0		WXS	Illumina HiSeq	.	72	28	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	C	2.386	-0.340886	0.05243	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.77098	-1.07;-1.07	5.51	1.21	0.21127	von Willebrand factor, type A (3);	1.168170	0.06378	N	0.714674	T	0.49729	0.1574	N	0.02973	-0.45	0.09310	N	1	B	0.18461	0.028	B	0.14023	0.01	T	0.41270	-0.9518	10	0.18276	T	0.48	.	2.542	0.04728	0.3436:0.3064:0.2613:0.0888	.	691	A6NMZ7	CO6A6_HUMAN	K	691	ENSP00000351310:Q691K;ENSP00000399236:Q691K	ENSP00000351310:Q691K	Q	+	1	0	COL6A6	131769808	0.000000	0.05858	0.342000	0.25602	0.020000	0.10135	-0.204000	0.09425	0.662000	0.31006	0.655000	0.94253	CAA	.		0.493	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
BMPR2	659	hgsc.bcm.edu	37	2	203383553	203383553	+	Silent	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr2:203383553C>T	ENST00000374580.4	+	6	1169	c.630C>T	c.(628-630)ggC>ggT	p.G210G	BMPR2_ENST00000374574.2_Silent_p.G210G	NM_001204.6	NP_001195.2	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor, type II (serine/threonine kinase)	210	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	42						AGCTGATTGGCCGAGGTCGAT	0.343																																					p.G210G		.											.	.	.	0			c.C630T						.						75.0	70.0	71.0					2																	203383553		2203	4300	6503	SO:0001819	synonymous_variant	659	exon6			GATTGGCCGAGGT	Z48923	CCDS33361.1	2q33-q34	2014-09-17			ENSG00000204217	ENSG00000204217			1078	protein-coding gene	gene with protein product		600799	"""primary pulmonary hypertension 1"""	PPH1		7791754	Standard	NM_001204		Approved	BRK-3, T-ALK, BMPR3, BMPR-II	uc002uzf.4	Q13873	OTTHUMG00000133617	ENST00000374580.4:c.630C>T	2.37:g.203383553C>T		Somatic	54	0		WXS	Illumina HiSeq	.	95	4	NM_001204	Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8	Silent	SNP	ENST00000374580.4	37	CCDS33361.1																																																																																			.		0.343	BMPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257743.1	NM_001204	
FZD1	8321	hgsc.bcm.edu	37	7	90894459	90894459	+	Silent	SNP	A	A	G	rs71292991|rs139480179	byFrequency	TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr7:90894459A>G	ENST00000287934.2	+	1	677	c.264A>G	c.(262-264)caA>caG	p.Q88Q		NM_003505.1	NP_003496.1	Q9UP38	FZD1_HUMAN	frizzled class receptor 1	88					autocrine signaling (GO:0035425)|axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation (GO:0044338)|canonical Wnt signaling pathway involved in osteoblast differentiation (GO:0044339)|cell-cell signaling (GO:0007267)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hard palate development (GO:0060022)|lung alveolus development (GO:0048286)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.Q88_P89insP(2)|p.Q88_P89insA(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(62;3.1e-10)|all_epithelial(64;1.66e-08)|Breast(17;0.000635)|Lung NSC(181;0.153)|all_lung(186;0.154)|all_hematologic(106;0.215)		STAD - Stomach adenocarcinoma(171;0.0134)			cggggcAGCAACCGCCGCCGC	0.741																																					p.Q88Q		.											.,4	.	64	3	Insertion - In frame(3)	breast(2)|liver(1)	c.A264G						.						10.0	11.0	11.0					7																	90894459		2176	4257	6433	SO:0001819	synonymous_variant	8321	exon1			GCAGCAACCGCCG	AB017363	CCDS5620.1	7q21	2014-01-29	2014-01-29		ENSG00000157240	ENSG00000157240		"""GPCR / Class F : Frizzled receptors"""	4038	protein-coding gene	gene with protein product	"""Wnt receptor"", ""frizzled, Drosophila, homolog of, 1"""	603408	"""frizzled (Drosophila) homolog 1"", ""frizzled homolog 1 (Drosophila)"", ""frizzled 1, seven transmembrane spanning receptor"", ""frizzled family receptor 1"""			9813155	Standard	NM_003505		Approved	DKFZp564G072	uc003ula.3	Q9UP38	OTTHUMG00000023046	ENST00000287934.2:c.264A>G	7.37:g.90894459A>G		Somatic	7	0		WXS	Illumina HiSeq	.	20	4	NM_003505	A4D1E8|O94815|Q549T8	Silent	SNP	ENST00000287934.2	37	CCDS5620.1																																																																																			.		0.741	FZD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059367.2	NM_003505	
PXDNL	137902	hgsc.bcm.edu	37	8	52361599	52361599	+	Missense_Mutation	SNP	G	G	T	rs377262954		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr8:52361599G>T	ENST00000356297.4	-	11	1429	c.1329C>A	c.(1327-1329)gaC>gaA	p.D443E	PXDNL_ENST00000543296.1_Missense_Mutation_p.D443E	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	443	Ig-like C2-type 3.				hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.D443D(1)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				GTGGGTTGCCGTCAGCTTCAC	0.428																																					p.D443E		.											PXDNL_ENST00000356297,NS,carcinoma,0,1	PXDNL_ENST00000356297	0	1	Substitution - coding silent(1)	breast(1)	c.C1329A						.						54.0	56.0	56.0					8																	52361599		1919	4072	5991	SO:0001583	missense	137902	exon11			GTTGCCGTCAGCT		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.1329C>A	8.37:g.52361599G>T	ENSP00000348645:p.Asp443Glu	Somatic	23	0		WXS	Illumina HiSeq	.	35	3	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	G	0.262	-0.998631	0.02128	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.64438	-0.1;-0.1	4.69	-9.38	0.00623	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.24699	0.0599	N	0.03268	-0.37	0.09310	N	1	B	0.12013	0.005	B	0.19391	0.025	T	0.17653	-1.0362	9	0.08837	T	0.75	.	2.9422	0.05834	0.2779:0.4386:0.1154:0.1681	.	443	A1KZ92	PXDNL_HUMAN	E	443	ENSP00000348645:D443E;ENSP00000444865:D443E	ENSP00000348645:D443E	D	-	3	2	PXDNL	52524152	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.271000	0.01166	-1.397000	0.02068	-1.909000	0.00523	GAC	.		0.428	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
AMBRA1	55626	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	46529852	46529852	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr11:46529852T>C	ENST00000458649.2	-	9	2646	c.2228A>G	c.(2227-2229)cAg>cGg	p.Q743R	AMBRA1_ENST00000426438.1_Missense_Mutation_p.Q714R|AMBRA1_ENST00000314845.3_Missense_Mutation_p.Q653R|AMBRA1_ENST00000528950.1_Missense_Mutation_p.Q714R|AMBRA1_ENST00000534300.1_Intron|AMBRA1_ENST00000298834.3_Intron|AMBRA1_ENST00000533727.1_Missense_Mutation_p.Q624R			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	743					autophagy (GO:0006914)|cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neural tube development (GO:0021915)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|phagocytic vesicle (GO:0045335)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	39				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		CATGGAGCGCTGGCGAATACT	0.512																																					p.Q746R		.											.	.	.	0			c.A2237G						.						108.0	96.0	100.0					11																	46529852		2201	4299	6500	SO:0001583	missense	55626	exon11			GAGCGCTGGCGAA	AB051523	CCDS31475.1, CCDS58132.1, CCDS73281.1	11p11.2	2013-01-09			ENSG00000110497	ENSG00000110497		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	25990	protein-coding gene	gene with protein product	"""WD repeat domain 94"", ""DDB1 and CUL4 associated factor 3"""	611359				17622796, 17603510, 17589504	Standard	NM_001267782		Approved	FLJ20294, KIAA1736, WDR94, DCAF3	uc001ncv.3	Q9C0C7	OTTHUMG00000166500	ENST00000458649.2:c.2228A>G	11.37:g.46529852T>C	ENSP00000415327:p.Gln743Arg	Somatic	37	0		WXS	Illumina HiSeq	.	49	18	NM_001267782	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Missense_Mutation	SNP	ENST00000458649.2	37		.	.	.	.	.	.	.	.	.	.	T	34	5.293414	0.95546	.	.	ENSG00000110497	ENST00000314845;ENST00000533727;ENST00000426438;ENST00000458649;ENST00000528950	D;D;D;D;D	0.90261	-2.64;-2.64;-2.64;-2.64;-2.64	6.17	6.17	0.99709	.	.	.	.	.	D	0.92596	0.7648	L	0.32530	0.975	0.80722	D	1	D;D;D;D;D	0.63046	0.987;0.992;0.992;0.992;0.992	D;D;D;D;D	0.72982	0.953;0.979;0.979;0.979;0.979	D	0.92854	0.6300	9	0.51188	T	0.08	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	743;714;624;746;653	Q9C0C7;Q9C0C7-3;G3V193;Q9C0C7-5;Q9C0C7-4	AMRA1_HUMAN;.;.;.;.	R	653;624;714;743;714	ENSP00000318313:Q653R;ENSP00000433372:Q624R;ENSP00000410899:Q714R;ENSP00000415327:Q743R;ENSP00000433945:Q714R	ENSP00000318313:Q653R	Q	-	2	0	AMBRA1	46486428	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.546000	0.82137	2.371000	0.80710	0.533000	0.62120	CAG	.		0.512	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749	
ZFP92	139735	hgsc.bcm.edu;broad.mit.edu	37	X	152686855	152686855	+	Silent	SNP	C	C	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chrX:152686855C>A	ENST00000338647.5	+	4	1021	c.1020C>A	c.(1018-1020)cgC>cgA	p.R340R	U82695.10_ENST00000569962.1_lincRNA	NM_001136273.1	NP_001129745.1	A6NM28	ZFP92_HUMAN	ZFP92 zinc finger protein	340					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(4)	6						AGCACCGGCGCGTGCACAGCG	0.711																																					p.R340R		.											.	.	.	0			c.C1020A						.						8.0	9.0	9.0					X																	152686855		676	1561	2237	SO:0001819	synonymous_variant	139735	exon4			CCGGCGCGTGCAC	U82695	CCDS59177.1	Xq28	2013-01-08	2012-11-27		ENSG00000189420	ENSG00000189420		"""Zinc fingers, C2H2-type"", ""-"""	12865	protein-coding gene	gene with protein product			"""zinc finger protein homologous to Zfp92 in mouse"", ""zinc finger protein 92 homolog (mouse)"""				Standard	NM_001136273		Approved	ZNF897	uc011myo.2	A6NM28	OTTHUMG00000024198	ENST00000338647.5:c.1020C>A	X.37:g.152686855C>A		Somatic	6	0		WXS	Illumina HiSeq	.	20	5	NM_001136273		Silent	SNP	ENST00000338647.5	37	CCDS59177.1																																																																																			.		0.711	ZFP92-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332220.2		
GLG1	2734	hgsc.bcm.edu	37	16	74496020	74496020	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr16:74496020G>T	ENST00000422840.2	-	22	3007	c.3008C>A	c.(3007-3009)cCt>cAt	p.P1003H	GLG1_ENST00000205061.5_Missense_Mutation_p.P1003H|Y_RNA_ENST00000384794.1_RNA|GLG1_ENST00000447066.2_Missense_Mutation_p.P992H	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	1003					blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						CTGGAGCTGAGGATCCAGGCG	0.522																																					p.P1003H		.											.,1	.	106	0			c.C3008A						.						74.0	72.0	72.0					16																	74496020		2198	4300	6498	SO:0001583	missense	2734	exon22			AGCTGAGGATCCA		CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"""golgi apparatus protein 1"""			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.3008C>A	16.37:g.74496020G>T	ENSP00000405984:p.Pro1003His	Somatic	38	0		WXS	Illumina HiSeq	.	45	2	NM_001145667	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Missense_Mutation	SNP	ENST00000422840.2	37	CCDS45527.1	.	.	.	.	.	.	.	.	.	.	G	32	5.166525	0.94768	.	.	ENSG00000090863	ENST00000205061;ENST00000447066;ENST00000422840	.	.	.	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.83234	0.5210	M	0.76838	2.35	0.80722	D	1	D;D;D;D	0.89917	0.993;0.999;0.996;1.0	P;D;D;D	0.87578	0.889;0.988;0.967;0.998	D	0.84690	0.0722	9	0.87932	D	0	-17.8264	19.6588	0.95855	0.0:0.0:1.0:0.0	.	133;1003;1003;992	Q6ZMF1;Q92896;Q92896-2;B7Z8Y4	.;GSLG1_HUMAN;.;.	H	1003;992;1003	.	ENSP00000205061:P1003H	P	-	2	0	GLG1	73053521	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	9.869000	0.99810	2.648000	0.89879	0.563000	0.77884	CCT	.		0.522	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1	NM_012201	
MAP1B	4131	hgsc.bcm.edu	37	5	71491850	71491850	+	Nonsense_Mutation	SNP	G	G	T	rs139604402		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr5:71491850G>T	ENST00000296755.7	+	5	2966	c.2668G>T	c.(2668-2670)Gag>Tag	p.E890*		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	890					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		AGGTCCTGCCGAGTCCCCTGA	0.542																																					p.E890X	Melanoma(17;367 822 11631 31730 47712)	.											.	.	.	0			c.G2668T						.						106.0	109.0	108.0					5																	71491850		2203	4300	6503	SO:0001587	stop_gained	4131	exon5			CCTGCCGAGTCCC	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 102"""	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.2668G>T	5.37:g.71491850G>T	ENSP00000296755:p.Glu890*	Somatic	34	0		WXS	Illumina HiSeq	.	42	3	NM_005909	A2BDK5	Nonsense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	G	43	9.974874	0.99308	.	.	ENSG00000131711	ENST00000296755	.	.	.	5.44	5.44	0.79542	.	0.187730	0.37761	N	0.001952	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-21.0008	19.2467	0.93905	0.0:0.0:1.0:0.0	.	.	.	.	X	890	.	ENSP00000296755:E890X	E	+	1	0	MAP1B	71527606	1.000000	0.71417	0.999000	0.59377	0.822000	0.46500	8.012000	0.88631	2.557000	0.86248	0.591000	0.81541	GAG	.		0.542	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909	
SPATA31E1	286234	hgsc.bcm.edu	37	9	90502147	90502147	+	Silent	SNP	C	C	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr9:90502147C>A	ENST00000325643.5	+	4	2811	c.2745C>A	c.(2743-2745)acC>acA	p.T915T		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	915					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.T915T(3)									CAGTCCCGACCGTGAGTGGCC	0.587																																					p.T915T		.											C9orf79,NS,carcinoma,0,3	C9orf79	0	3	Substitution - coding silent(3)	upper_aerodigestive_tract(1)|lung(1)|endometrium(1)	c.C2745A						.						53.0	54.0	54.0					9																	90502147		2203	4300	6503	SO:0001819	synonymous_variant	286234	exon4			CCCGACCGTGAGT	AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 79"", ""family with sequence similarity 75, member E1"""	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.2745C>A	9.37:g.90502147C>A		Somatic	55	0		WXS	Illumina HiSeq	.	37	2	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Silent	SNP	ENST00000325643.5	37	CCDS6676.1																																																																																			.		0.587	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828	
RP11-196E1.3	0	broad.mit.edu	37	11	119489814	119489814	+	RNA	DEL	T	T	-	rs10592023|rs138713709		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr11:119489814delT	ENST00000532153.1	+	0	117																											TGGGAGTTACTTTTTTTTTTT	0.353																																					.													.	.	.	0			.						.																																					0	.			AGTTACTTTTTTT																													11.37:g.119489814delT		Somatic	5	0		WXS	Illumina GAIIx	Phase_I	6	2	.		RNA	DEL	ENST00000532153.1	37																																																																																				.		0.353	RP11-196E1.3-001	KNOWN	basic	antisense	antisense	OTTHUMT00000388380.1		
PRB2	653247	broad.mit.edu	37	12	11546320	11546322	+	In_Frame_Del	DEL	TTG	TTG	-			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr12:11546320_11546322delTTG	ENST00000389362.4	-	3	725_727	c.690_692delCAA	c.(688-693)aacaag>aag	p.N230del	PRB1_ENST00000546254.1_Intron|PRB2_ENST00000545829.1_5'Flank	NM_006248.3	NP_006239.3	P02812	PRB2_HUMAN	proline-rich protein BstNI subfamily 2	230	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-P-Q-G-[GD]-[NKS]-[KSQ]- [PRS]-[QRS] [GPS]-[PSAR]-[PSR].					extracellular region (GO:0005576)				NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(5)|skin(4)|stomach(2)|urinary_tract(1)	37		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			ACTTTGGGACTTGTTGTCTCCTT	0.601																																					p.230_231del													.	PRB2	168	0			c.690_692del						.																																			SO:0001651	inframe_deletion	653247	exon3			TGGGACTTGTTGT	K03208	CCDS41757.2	12p13.2	2012-10-02			ENSG00000121335	ENSG00000121335			9338	protein-coding gene	gene with protein product		168810				8554050	Standard	NM_006248		Approved	PRPPRB1, Ps, cP7	uc010shk.1	P02812	OTTHUMG00000156975	ENST00000389362.4:c.690_692delCAA	12.37:g.11546323_11546325delTTG	ENSP00000374013:p.Asn230del	Somatic	84	0		WXS	Illumina GAIIx	Phase_I	141	7	NM_006248	O00599|P02811|P04281	In_Frame_Del	DEL	ENST00000389362.4	37	CCDS41757.2																																																																																			.		0.601	PRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346925.2	NM_006248	
NIPA1	123606	broad.mit.edu	37	15	23100429	23100430	+	5'Flank	DEL	GG	GG	-	rs201620838|rs201243920		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr15:23100429_23100430delGG	ENST00000437912.2	-	0	0				RP11-566K19.6_ENST00000557922.1_RNA|RP11-566K19.5_ENST00000559740.1_RNA			Q7RTP0	NIPA1_HUMAN	non imprinted in Prader-Willi/Angelman syndrome 1						cell death (GO:0008219)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	magnesium ion transmembrane transporter activity (GO:0015095)			endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|skin(1)	15		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;4.18e-06)|Epithelial(43;3.97e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00165)		ACAtgtacgtgggtgtgtgtgt	0.391																																					.													.	.	.	0			.						.																																			SO:0001631	upstream_gene_variant	0	.			GTACGTGGGTGTG	BK001020	CCDS73691.1, CCDS73692.1	15q11.2	2006-10-06			ENSG00000170113	ENSG00000170113			17043	protein-coding gene	gene with protein product		608145	"""spastic paraplegia 6 (autosomal dominant)"""	SPG6		14508710	Standard	NM_144599		Approved	MGC35570	uc001yvc.3	Q7RTP0	OTTHUMG00000129099		15.37:g.23100429_23100430delGG	Exception_encountered	Somatic	5	0		WXS	Illumina GAIIx	Phase_I	9	3	.	B2RA76|Q5HYA9|Q7KZB0|Q86XW4	RNA	DEL	ENST00000437912.2	37	CCDS45190.1																																																																																			.		0.391	NIPA1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000415890.1	NM_144599	
KIF7	374654	broad.mit.edu	37	15	90196148	90196148	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr15:90196148G>T	ENST00000394412.3	-	2	90	c.14C>A	c.(13-15)gCt>gAt	p.A5D		NM_198525.2	NP_940927.2	Q2M1P5	KIF7_HUMAN	kinesin family member 7	5					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|kinesin complex (GO:0005871)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	25	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)			CAGCCTCTGAGCCTCCAGCCC	0.662																																					p.A5D													.	KIF7	130	0			c.C14A						.						5.0	8.0	7.0					15																	90196148		654	1539	2193	SO:0001583	missense	374654	exon2			CTCTGAGCCTCCA	AY358384	CCDS32325.2	15q26.1	2011-06-02			ENSG00000166813	ENSG00000166813		"""Kinesins"""	30497	protein-coding gene	gene with protein product		611254				11416179, 15547730	Standard	NM_198525		Approved	JBTS12	uc002bof.2	Q2M1P5	OTTHUMG00000157177	ENST00000394412.3:c.14C>A	15.37:g.90196148G>T	ENSP00000377934:p.Ala5Asp	Somatic	12	0		WXS	Illumina GAIIx	Phase_I	18	3	NM_198525	Q3SXY0|Q6UXE9|Q8IW72	Missense_Mutation	SNP	ENST00000394412.3	37	CCDS32325.2	.	.	.	.	.	.	.	.	.	.	G	20.7	4.035193	0.75617	.	.	ENSG00000166813	ENST00000394412	T	0.71222	-0.55	4.45	4.45	0.53987	.	.	.	.	.	T	0.57607	0.2065	L	0.29908	0.895	0.33356	D	0.571725	P	0.36065	0.535	B	0.31290	0.127	T	0.69235	-0.5198	9	0.42905	T	0.14	.	13.9843	0.64324	0.0:0.0:1.0:0.0	.	5	Q2M1P5	KIF7_HUMAN	D	5	ENSP00000377934:A5D	ENSP00000377934:A5D	A	-	2	0	KIF7	87997152	.	.	1.000000	0.80357	0.879000	0.50718	.	.	2.013000	0.59113	0.655000	0.94253	GCT	.		0.662	KIF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347782.1	NM_198525	
PSMD7	5713	broad.mit.edu	37	16	74342857	74342857	+	IGR	DEL	A	A	-	rs573542468	byFrequency	TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr16:74342857delA	ENST00000219313.4	+	0	1670				AC009120.6_ENST00000561921.1_RNA|AC009120.6_ENST00000565313.1_RNA|AC009120.6_ENST00000566411.1_RNA	NM_002811.4	NP_002802.2	P51665	PSMD7_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 7						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	protein homodimerization activity (GO:0042803)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)	15						actctgtctcaaaaaaaaaaa	0.418													|||unknown(NO_COVERAGE)	785	0.156749	0.1657	0.1628	5008	,	,		16887	0.1399		0.1451	False		,,,				2504	0.1697				.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			TGTCTCAAAAAAA	D50063	CCDS10910.1	16q22.3	2010-10-15	2007-07-06		ENSG00000103035	ENSG00000103035		"""Proteasome (prosome, macropain) subunits"""	9565	protein-coding gene	gene with protein product	"""Mov34 homolog"""	157970	"""proteasome (prosome, macropain) 26S subunit, non-ATPase, 7 (Mov34 homolog)"""			7755639	Standard	NM_002811		Approved	S12, P40, MOV34, Rpn8	uc002fcq.3	P51665	OTTHUMG00000137601		16.37:g.74342857delA		Somatic	4	0		WXS	Illumina GAIIx	Phase_I	4	1	.	D3DWS9|Q6PKI2|Q96E97	RNA	DEL	ENST00000219313.4	37	CCDS10910.1																																																																																			.		0.418	PSMD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269010.2	NM_002811	
SMG1	23049	broad.mit.edu	37	16	18882689	18882689	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr16:18882689T>C	ENST00000446231.2	-	16	2711	c.2299A>G	c.(2299-2301)Aac>Gac	p.N767D	SMG1_ENST00000389467.3_Missense_Mutation_p.N767D|snoU13_ENST00000459248.1_RNA			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	767	Interaction with SMG8 and SMG9.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						GTCTTACTGTTGGCTAAAAGG	0.363																																					p.N767D													.	SMG1	401	0			c.A2299G						.						33.0	31.0	31.0					16																	18882689		1799	4058	5857	SO:0001583	missense	23049	exon16			TACTGTTGGCTAA	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase-related kinase"""	607032	"""smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"""			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.2299A>G	16.37:g.18882689T>C	ENSP00000402515:p.Asn767Asp	Somatic	183	0		WXS	Illumina GAIIx	Phase_I	301	7	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	37	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.399615	0.83120	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.11604	2.76;2.76	5.36	5.36	0.76844	Armadillo-type fold (1);	0.000000	0.64402	U	0.000017	T	0.14013	0.0339	L	0.44542	1.39	0.41984	D	0.990811	D	0.55172	0.97	P	0.48704	0.587	T	0.10337	-1.0634	10	0.09843	T	0.71	.	15.6517	0.77099	0.0:0.0:0.0:1.0	.	767	Q96Q15	SMG1_HUMAN	D	767	ENSP00000402515:N767D;ENSP00000374118:N767D	ENSP00000374118:N767D	N	-	1	0	SMG1	18790190	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.060000	0.71141	2.158000	0.67659	0.454000	0.30748	AAC	.		0.363	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092	
TTC25	83538	broad.mit.edu	37	17	40100452	40100452	+	RNA	DEL	A	A	-	rs548959105	byFrequency	TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr17:40100452delA	ENST00000591658.1	+	0	1126							Q96NG3	TTC25_HUMAN	tetratricopeptide repeat domain 25							cytoplasm (GO:0005737)				endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	12		all_cancers(22;8.16e-06)|Breast(137;0.000143)|all_epithelial(22;0.000236)				actccgtctcaaaaaaaaaaa	0.517													|||unknown(HR)	734	0.146565	0.2307	0.1527	5008	,	,		13823	0.0972		0.0845	False		,,,				2504	0.1431				.													.	TTC25	37	0			.						.						1.0	1.0	1.0					17																	40100452		255	674	929			83538	.			CGTCTCAAAAAAA	AK055498	CCDS74063.1	17q21.2	2014-08-12			ENSG00000204815	ENSG00000204815		"""Tetratricopeptide (TTC) repeat domain containing"""	25280	protein-coding gene	gene with protein product							Standard	XM_006722129		Approved	DKFZP434H0115	uc002hyj.4	Q96NG3	OTTHUMG00000175837		17.37:g.40100452delA		Somatic	6	0		WXS	Illumina GAIIx	Phase_I	8	2	.	Q6NX40|Q6PJ04|Q9H0K5	RNA	DEL	ENST00000591658.1	37																																																																																				.		0.517	TTC25-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000449237.1	NM_031421	
ZNF826P	664701	broad.mit.edu	37	19	20594818	20594818	+	RNA	DEL	T	T	-	rs58933790|rs113384451|rs200861949		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr19:20594818delT	ENST00000502675.1	-	0	171					NR_036455.1		Q6ZT77	ZN826_HUMAN	zinc finger protein 826, pseudogene						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(4)	4						AAGAGAAGCCTTTTTTTTTTT	0.433																																					.													.	ZNF826P	5	0			.						.																																					0	.			GAAGCCTTTTTTT	BC016785		19p12	2010-08-03	2010-08-03	2010-08-03	ENSG00000231205	ENSG00000231205			33875	pseudogene	pseudogene			"""zinc finger protein 826"""	ZNF826			Standard	NR_036455		Approved	FLJ44894	uc021urn.2	Q6ZT77	OTTHUMG00000162773		19.37:g.20594818delT		Somatic	4	0		WXS	Illumina GAIIx	Phase_I	7	2	.		RNA	DEL	ENST00000502675.1	37																																																																																				.		0.433	ZNF826P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000370365.1	NM_001039884	
HNRNPUL1	11100	broad.mit.edu	37	19	41798301	41798301	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr19:41798301G>T	ENST00000392006.3	+	8	1324	c.1151G>T	c.(1150-1152)gGa>gTa	p.G384V	HNRNPUL1_ENST00000593587.1_Missense_Mutation_p.G284V|HNRNPUL1_ENST00000263367.3_Missense_Mutation_p.G295V|HNRNPUL1_ENST00000352456.3_Missense_Mutation_p.G284V|HNRNPUL1_ENST00000378215.4_Missense_Mutation_p.G270V|HNRNPUL1_ENST00000595018.1_Missense_Mutation_p.G284V|HNRNPUL1_ENST00000602130.1_Missense_Mutation_p.G384V	NM_007040.3	NP_008971.2	Q9BUJ2	HNRL1_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 1	384	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.|Necessary for interaction with TP53.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	29						TTCAACTTCGGACAGAGAGCA	0.562																																					p.G384V													.	HNRNPUL1	73	0			c.G1151T						.						135.0	127.0	130.0					19																	41798301		2203	4300	6503	SO:0001583	missense	11100	exon8			ACTTCGGACAGAG	AJ007509	CCDS12576.1, CCDS12577.1	19q13.2	2013-06-12		2008-04-18	ENSG00000105323	ENSG00000105323			17011	protein-coding gene	gene with protein product	"""E1B 55kDa associated protein 5"""	605800		HNRPUL1		9733834, 12489984	Standard	XM_005258459		Approved	E1B-AP5, E1BAP5, FLJ12944	uc002oqb.4	Q9BUJ2	OTTHUMG00000182740	ENST00000392006.3:c.1151G>T	19.37:g.41798301G>T	ENSP00000375863:p.Gly384Val	Somatic	34	0		WXS	Illumina GAIIx	Phase_I	42	3	NM_007040	B3KMW7|O76022|Q6ZSZ0|Q7L8P4|Q8N6Z4|Q96G37|Q9HAL3|Q9UG75	Missense_Mutation	SNP	ENST00000392006.3	37	CCDS12576.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.994253	0.93167	.	.	ENSG00000105323	ENST00000352456;ENST00000392006;ENST00000378215;ENST00000263367	T;T;T;T	0.73363	-0.74;-0.74;-0.74;-0.74	6.04	6.04	0.98038	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.85682	D	0.000000	D	0.91553	0.7332	H	0.97023	3.925	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.999;1.0;0.999;1.0;0.999;0.999	D	0.93486	0.6831	10	0.87932	D	0	-18.9152	19.3663	0.94464	0.0:0.0:1.0:0.0	.	295;284;384;270;384;284	B7Z4B8;A8K3W4;Q9BUJ2-2;Q9BUJ2-3;Q9BUJ2;Q9BUJ2-4	.;.;.;.;HNRL1_HUMAN;.	V	284;384;270;295	ENSP00000340857:G284V;ENSP00000375863:G384V;ENSP00000367460:G270V;ENSP00000263367:G295V	ENSP00000263367:G295V	G	+	2	0	HNRNPUL1	46490141	1.000000	0.71417	0.984000	0.44739	0.927000	0.56198	9.808000	0.99193	2.873000	0.98535	0.563000	0.77884	GGA	.		0.562	HNRNPUL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463406.1	NM_144732, NM_007040	
LOC101927533	101927533	broad.mit.edu	37	2	65894933	65894933	+	lincRNA	DEL	A	A	-			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr2:65894933delA	ENST00000377977.3	+	0	862				AC007389.4_ENST00000583614.1_RNA																							TCAGAGGTTTAAAAAAAAAAA	0.517																																					.													.	.	.	0			.						.																																					0	.			AGGTTTAAAAAAA																													2.37:g.65894933delA		Somatic	8	0		WXS	Illumina GAIIx	Phase_I	12	3	.		RNA	DEL	ENST00000377977.3	37																																																																																				.		0.517	AC074391.1-010	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000470883.1		
SPTBN1	6711	broad.mit.edu	37	2	54877117	54877117	+	Silent	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr2:54877117G>T	ENST00000356805.4	+	26	5849	c.5568G>T	c.(5566-5568)ctG>ctT	p.L1856L	SPTBN1_ENST00000333896.5_Silent_p.L1843L	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1856	Interaction with ANK2.				actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			TCCAGGCTCTGGGCACACAGG	0.512																																					p.L1856L													.	SPTBN1	378	0			c.G5568T						.						68.0	70.0	69.0					2																	54877117		2203	4300	6503	SO:0001819	synonymous_variant	0	exon26			GGCTCTGGGCACA		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"""Pleckstrin homology (PH) domain containing"""	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.5568G>T	2.37:g.54877117G>T		Somatic	26	0		WXS	Illumina GAIIx	Phase_I	36	3	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Silent	SNP	ENST00000356805.4	37	CCDS33198.1																																																																																			.		0.512	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3		
IGKV1-9	28941	broad.mit.edu;bcgsc.ca	37	2	89309651	89309651	+	RNA	SNP	T	T	C	rs547763453	byFrequency	TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr2:89309651T>C	ENST00000493819.1	-	0	236									immunoglobulin kappa variable 1-9																		CCCTGGTTTTTGCTGATACCA	0.522													N|||	2	0.000399361	0.0008	0.0	5008	,	,		9375	0.0		0.001	False		,,,				2504	0.0				.													.	.	.	0			.						.						119.0	114.0	116.0					2																	89309651		1850	4066	5916			0	.			GGTTTTTGCTGAT	Z00013		2p11.2	2012-02-10			ENSG00000241755	ENSG00000241755		"""Immunoglobulins / IGK locus"""	5744	other	immunoglobulin gene							Standard	NG_000834		Approved	IGKV19, L8			OTTHUMG00000151637		2.37:g.89309651T>C		Somatic	95	0		WXS	Illumina GAIIx	Phase_I	183	64	.		RNA	SNP	ENST00000493819.1	37																																																																																				.		0.522	IGKV1-9-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	IG_V_gene	OTTHUMT00000323361.1	NG_000834	
ERBB4	2066	broad.mit.edu	37	2	212530115	212530115	+	Missense_Mutation	SNP	T	T	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr2:212530115T>A	ENST00000342788.4	-	15	2114	c.1804A>T	c.(1804-1806)Agt>Tgt	p.S602C	ERBB4_ENST00000436443.1_Missense_Mutation_p.S602C|ERBB4_ENST00000402597.1_Missense_Mutation_p.S602C	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	602	Cys-rich.				cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|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)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	AAAATGAAACTGTTTGCCCCC	0.483										TSP Lung(8;0.080)																											p.S602C													.	ERBB4	480	0			c.A1804T						.						159.0	141.0	147.0					2																	212530115		2203	4300	6503	SO:0001583	missense	2066	exon15			TGAAACTGTTTGC	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"""v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"""			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.1804A>T	2.37:g.212530115T>A	ENSP00000342235:p.Ser602Cys	Somatic	87	1		WXS	Illumina GAIIx	Phase_I	102	5	NM_001042599	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	37	CCDS2394.1	.	.	.	.	.	.	.	.	.	.	T	16.50	3.139448	0.56936	.	.	ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597	T;T;T	0.46451	0.87;0.87;0.87	5.56	5.56	0.83823	Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	T	0.57301	0.2044	L	0.58101	1.795	0.58432	D	0.999999	D;D;P;D;D	0.71674	0.997;0.99;0.921;0.998;0.997	P;P;B;P;P	0.59056	0.753;0.608;0.355;0.851;0.714	T	0.60905	-0.7170	10	0.72032	D	0.01	.	15.7153	0.77663	0.0:0.0:0.0:1.0	.	602;602;461;602;602	Q15303-4;Q15303-2;Q53QS8;Q15303-3;Q15303	.;.;.;.;ERBB4_HUMAN	C	602	ENSP00000342235:S602C;ENSP00000403204:S602C;ENSP00000385565:S602C	ENSP00000342235:S602C	S	-	1	0	ERBB4	212238360	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.283000	0.72646	2.127000	0.65507	0.533000	0.62120	AGT	.		0.483	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599	
FAM182B	728882	broad.mit.edu	37	20	25755510	25755510	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr20:25755510C>T	ENST00000376403.1	-	3	824	c.446G>A	c.(445-447)cGc>cAc	p.R149H	FAM182B_ENST00000478164.1_Intron|FAM182B_ENST00000376404.2_Intron			Q5T319	F182B_HUMAN	family with sequence similarity 182, member B	149										lung(1)	1						CCTTCCATCGCGGCCACCATG	0.706																																					.													.	FAM182B	6	0			.						.																																			SO:0001583	missense	0	.			CCATCGCGGCCAC			20p11.1	2010-07-14			ENSG00000175170	ENSG00000175170			34503	pseudogene	pseudogene							Standard	NR_027061		Approved			Q5T319	OTTHUMG00000032136	ENST00000376403.1:c.446G>A	20.37:g.25755510C>T	ENSP00000365585:p.Arg149His	Somatic	118	1		WXS	Illumina GAIIx	Phase_I	148	9	.	Q4G0Q1	Missense_Mutation	SNP	ENST00000376403.1	37		.	.	.	.	.	.	.	.	.	.	.	2.423	-0.332565	0.05314	.	.	ENSG00000175170	ENST00000376403	.	.	.	.	.	.	.	.	.	.	.	T	0.18425	0.0442	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.30822	-0.9965	3	0.15066	T	0.55	.	.	.	.	.	.	.	.	H	149	.	ENSP00000365585:R149H	R	-	2	0	FAM182B	25703510	0.001000	0.12720	0.047000	0.18901	0.048000	0.14542	-1.599000	0.02085	0.064000	0.16427	0.064000	0.15345	CGC	.		0.706	FAM182B-003	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000078463.2	NR_026714	
MUC4	4585	broad.mit.edu	37	3	195505763	195505763	+	Missense_Mutation	SNP	G	G	A	rs534260673	byFrequency	TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr3:195505763G>A	ENST00000463781.3	-	2	13147	c.12688C>T	c.(12688-12690)Ctt>Ttt	p.L4230F	MUC4_ENST00000475231.1_Missense_Mutation_p.L4230F|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	987					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.L4230F(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACTGAGGAAAGGCTGGTGACA	0.582																																					p.L4230F													MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	2	Substitution - Missense(2)	kidney(2)	c.C12688T						.						42.0	42.0	42.0					3																	195505763		2092	4200	6292	SO:0001583	missense	4585	exon2			AGGAAAGGCTGGT	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.12688C>T	3.37:g.195505763G>A	ENSP00000417498:p.Leu4230Phe	Somatic	76	0		WXS	Illumina GAIIx	Phase_I	91	5	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	.	.	.	.	.	.	.	.	.	.	N	10.21	1.286628	0.23478	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31769	1.48;1.49	1.78	0.849	0.18972	.	.	.	.	.	T	0.13756	0.0333	N	0.19112	0.55	0.09310	N	1	P	0.35139	0.486	B	0.19946	0.027	T	0.16276	-1.0408	8	.	.	.	.	6.3726	0.21489	0.0:0.3086:0.6914:0.0	.	4102	E7ESK3	.	F	4230	ENSP00000417498:L4230F;ENSP00000420243:L4230F	.	L	-	1	0	MUC4	196990542	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.092000	0.11129	0.347000	0.23924	-0.229000	0.12294	CTT	.		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
LOC101243545	101243545	broad.mit.edu	37	3	161146937	161146937	+	lincRNA	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr3:161146937G>A	ENST00000473595.1	+	0	1231				RP11-3P17.5_ENST00000602890.1_lincRNA	NR_102265.1																						AATTTTGTTGGCAACATCCAA	0.378																																					.													.	.	.	0			.						.						71.0	81.0	77.0					3																	161146937		1442	2583	4025			0	.			TTGTTGGCAACAT																													3.37:g.161146937G>A		Somatic	32	0		WXS	Illumina GAIIx	Phase_I	57	7	.		RNA	SNP	ENST00000473595.1	37																																																																																				.		0.378	RP11-3P17.4-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000353185.1		
MUC4	4585	broad.mit.edu	37	3	195515290	195515290	+	Missense_Mutation	SNP	C	C	G	rs78535324		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr3:195515290C>G	ENST00000463781.3	-	2	3620	c.3161G>C	c.(3160-3162)aGc>aCc	p.S1054T	MUC4_ENST00000475231.1_Missense_Mutation_p.S1054T|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	484					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.S1054T(4)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AAGAGGGGTGCTGTCACCTGT	0.572																																					p.S1054T													MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	4	Substitution - Missense(4)	NS(2)|kidney(1)|endometrium(1)	c.G3161C						.						16.0	11.0	13.0					3																	195515290		689	1583	2272	SO:0001583	missense	4585	exon2			GGGGTGCTGTCAC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3161G>C	3.37:g.195515290C>G	ENSP00000417498:p.Ser1054Thr	Somatic	66	2		WXS	Illumina GAIIx	Phase_I	107	9	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	.	.	.	.	.	.	.	.	.	.	-	1.980	-0.434268	0.04669	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30714	1.53;1.52	1.0	-2.01	0.07410	.	.	.	.	.	T	0.12433	0.0302	N	0.08118	0	0.09310	N	1	B	0.13594	0.008	B	0.08055	0.003	T	0.20706	-1.0267	8	.	.	.	.	5.9202	0.19078	0.1903:0.2487:0.561:0.0	.	1054	E7ESK3	.	T	1054	ENSP00000417498:S1054T;ENSP00000420243:S1054T	.	S	-	2	0	MUC4	196999685	.	.	0.001000	0.08648	0.010000	0.07245	.	.	-2.658000	0.00420	-2.332000	0.00249	AGC	.		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TMPRSS11F	389208	broad.mit.edu	37	4	68918905	68918905	+	IGR	DEL	T	T	-	rs34085122|rs371429078|rs398083174|rs397796455	byFrequency	TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr4:68918905delT	ENST00000356291.2	-	0	2088				UBA6-AS1_ENST00000500538.2_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F							extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(4)	39						AGAGTCTTAATTTTTTTTTTT	0.358													|||unknown(HR)	3489	0.696685	0.5711	0.5692	5008	,	,		18343	0.8621		0.7316	False		,,,				2504	0.7505				.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			TCTTAATTTTTTT	AK122625	CCDS3520.1	4q13.2	2010-04-13			ENSG00000198092	ENSG00000198092		"""Serine peptidases / Transmembrane"""	29994	protein-coding gene	gene with protein product							Standard	NM_207407		Approved	FLJ16046	uc003hdt.1	Q6ZWK6	OTTHUMG00000129307		4.37:g.68918905delT		Somatic	8	0		WXS	Illumina GAIIx	Phase_I	18	8	.	A8MXX2	RNA	DEL	ENST00000356291.2	37	CCDS3520.1																																																																																			T|0.750;-|0.250		0.358	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407	
LOC100653061	100653061	broad.mit.edu	37	5	34189325	34189325	+	RNA	DEL	T	T	-	rs372858629		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr5:34189325delT	ENST00000514048.1	-	0	43																											tttctttttctttttttttat	0.517																																					.													.	.	.	0			.						.																																					0	.			TTTTTCTTTTTTT																													5.37:g.34189325delT		Somatic	6	0		WXS	Illumina GAIIx	Phase_I	8	3	.		RNA	DEL	ENST00000514048.1	37																																																																																				.		0.517	RP11-1023L17.1-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000367775.1		
FAT2	2196	broad.mit.edu;ucsc.edu	37	5	150948137	150948137	+	Missense_Mutation	SNP	A	A	G			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr5:150948137A>G	ENST00000261800.5	-	1	368	c.356T>C	c.(355-357)aTc>aCc	p.I119T		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	119	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGTGGCTTGGATGATGAGGGT	0.517																																					p.I119T													.	FAT2	465	0			c.T356C						.						121.0	119.0	120.0					5																	150948137		2203	4300	6503	SO:0001583	missense	2196	exon1			GCTTGGATGATGA	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.356T>C	5.37:g.150948137A>G	ENSP00000261800:p.Ile119Thr	Somatic	21	5		WXS	Illumina GAIIx	Phase_I	40	11	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	A	15.99	2.994409	0.54041	.	.	ENSG00000086570	ENST00000261800	T	0.66638	-0.22	5.45	5.45	0.79879	Cadherin (3);Cadherin-like (1);	0.541443	0.18142	N	0.150374	T	0.73048	0.3537	M	0.91663	3.23	0.43527	D	0.995803	B	0.32245	0.361	B	0.24541	0.054	T	0.77466	-0.2577	10	0.87932	D	0	.	15.5309	0.75960	1.0:0.0:0.0:0.0	.	119	Q9NYQ8	FAT2_HUMAN	T	119	ENSP00000261800:I119T	ENSP00000261800:I119T	I	-	2	0	FAT2	150928330	1.000000	0.71417	0.995000	0.50966	0.982000	0.71751	9.262000	0.95591	2.065000	0.61736	0.454000	0.30748	ATC	.		0.517	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
AC136604.1	0	broad.mit.edu	37	5	179078735	179078735	+	Missense_Mutation	SNP	T	T	C	rs571082086		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr5:179078735T>C	ENST00000425471.1	+	2	218	c.218T>C	c.(217-219)cTg>cCg	p.L73P	AC136604.1_ENST00000418535.2_Missense_Mutation_p.L73P																kidney(1)	1						CGGGCTCCCCTGGCTCCTCTG	0.632																																					.													.	.	.	0			.						.																																			SO:0001583	missense	0	.			CTCCCCTGGCTCC																												ENST00000425471.1:c.218T>C	5.37:g.179078735T>C	ENSP00000388857:p.Leu73Pro	Somatic	51	1		WXS	Illumina GAIIx	Phase_I	102	5	.		Missense_Mutation	SNP	ENST00000425471.1	37		.	.	.	.	.	.	.	.	.	.	C	2.694	-0.272460	0.05716	.	.	ENSG00000228259	ENST00000418535;ENST00000425471	T;T	0.51817	0.69;1.88	1.1	-0.77	0.11005	.	.	.	.	.	T	0.18002	0.0432	.	.	.	.	.	.	.	.	.	.	.	.	T	0.36841	-0.9731	5	0.02654	T	1	.	4.9002	0.13771	0.0:0.3733:0.0:0.6267	.	.	.	.	P	73	ENSP00000404996:L73P;ENSP00000388857:L73P	ENSP00000404996:L73P	L	+	2	0	AC136604.1	179011341	0.040000	0.19996	0.000000	0.03702	0.009000	0.06853	-0.477000	0.06583	-0.891000	0.03940	-0.479000	0.04858	CTG	.		0.632	AC136604.1-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding			
HLA-A	3105	broad.mit.edu;bcgsc.ca	37	6	29910607	29910607	+	Silent	SNP	G	G	C	rs72555397		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr6:29910607G>C	ENST00000396634.1	+	4	488	c.147G>C	c.(145-147)gtG>gtC	p.V49V	HLA-A_ENST00000376809.5_Silent_p.V49V|HLA-A_ENST00000376806.5_Silent_p.V49V|HLA-A_ENST00000376802.2_Silent_p.V49V			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	49	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)	p.V49V(2)		central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						TCATCGCCGTGGGCTACGTGG	0.692									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.V49V													HLA-A,NS,carcinoma,0,5	HLA-A	89	2	Substitution - coding silent(2)	lung(1)|kidney(1)	c.G147C						.																																			SO:0001819	synonymous_variant	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CGCCGTGGGCTAC	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.147G>C	6.37:g.29910607G>C		Somatic	54	1		WXS	Illumina GAIIx	Phase_I	74	11	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			.		0.692	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
CEP162	22832	broad.mit.edu	37	6	84894963	84894963	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr6:84894963G>T	ENST00000403245.3	-	13	1719	c.1605C>A	c.(1603-1605)gaC>gaA	p.D535E	KIAA1009_ENST00000461137.1_5'UTR|KIAA1009_ENST00000257766.4_Missense_Mutation_p.D459E	NM_014895.2	NP_055710.2														breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	43		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)		TTTTTATAATGTCCTCTGAAG	0.353																																					p.D535E													.	KIAA1009	119	0			c.C1605A						.						100.0	97.0	98.0					6																	84894963		2203	4300	6503	SO:0001583	missense	22832	exon13			TATAATGTCCTCT																												ENST00000403245.3:c.1605C>A	6.37:g.84894963G>T	ENSP00000385215:p.Asp535Glu	Somatic	94	0		WXS	Illumina GAIIx	Phase_I	61	3	NM_014895		Missense_Mutation	SNP	ENST00000403245.3	37	CCDS34494.2	.	.	.	.	.	.	.	.	.	.	G	0.016	-1.529084	0.00951	.	.	ENSG00000135315	ENST00000257766;ENST00000403245	T;T	0.14893	2.47;2.47	5.34	-1.36	0.09085	.	0.161303	0.43416	D	0.000574	T	0.03305	0.0096	L	0.50333	1.59	0.09310	N	0.999999	B;P	0.35155	0.037;0.487	B;B	0.34779	0.039;0.189	T	0.46707	-0.9172	10	0.09590	T	0.72	-17.7728	5.9246	0.19101	0.566:0.0:0.2986:0.1354	.	535;535	Q5TB80;C9JFM9	QN1_HUMAN;.	E	459;535	ENSP00000257766:D459E;ENSP00000385215:D535E	ENSP00000257766:D459E	D	-	3	2	KIAA1009	84951682	0.000000	0.05858	0.018000	0.16275	0.002000	0.02628	-0.732000	0.04904	-0.522000	0.06417	-0.377000	0.06932	GAC	.		0.353	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1		
SOBP	55084	broad.mit.edu;ucsc.edu	37	6	107827478	107827478	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr6:107827478G>T	ENST00000317357.5	+	3	927	c.268G>T	c.(268-270)Gac>Tac	p.D90Y		NM_018013.3	NP_060483.3			sine oculis binding protein homolog (Drosophila)											endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	26		all_cancers(87;5.26e-06)|Acute lymphoblastic leukemia(125;2.87e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.00193)|Colorectal(196;0.156)		BRCA - Breast invasive adenocarcinoma(108;0.026)|all cancers(137;0.087)|Epithelial(106;0.104)|OV - Ovarian serous cystadenocarcinoma(136;0.154)		ATTACCCGAGGACAGTGTTAT	0.388																																					p.D90Y													.	SOBP	53	0			c.G268T						.						121.0	116.0	118.0					6																	107827478		1847	4102	5949	SO:0001583	missense	55084	exon3			CCCGAGGACAGTG	AK001021	CCDS43488.1	6q21	2007-03-15			ENSG00000112320	ENSG00000112320			29256	protein-coding gene	gene with protein product		613667					Standard	NM_018013		Approved	FLJ10159	uc003prx.3	A7XYQ1	OTTHUMG00000015312	ENST00000317357.5:c.268G>T	6.37:g.107827478G>T	ENSP00000318900:p.Asp90Tyr	Somatic	53	1		WXS	Illumina GAIIx	Phase_I	50	5	NM_018013		Missense_Mutation	SNP	ENST00000317357.5	37	CCDS43488.1	.	.	.	.	.	.	.	.	.	.	G	19.34	3.808372	0.70797	.	.	ENSG00000112320	ENST00000317357	T	0.13196	2.61	5.02	5.02	0.67125	.	0.219560	0.46758	D	0.000265	T	0.12646	0.0307	N	0.08118	0	0.48571	D	0.999672	D	0.71674	0.998	D	0.65443	0.935	T	0.39981	-0.9587	10	0.72032	D	0.01	-15.8462	18.7119	0.91661	0.0:0.0:1.0:0.0	.	90	A7XYQ1	SOBP_HUMAN	Y	90	ENSP00000318900:D90Y	ENSP00000318900:D90Y	D	+	1	0	SOBP	107934171	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.867000	0.75511	2.497000	0.84241	0.655000	0.94253	GAC	.		0.388	SOBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041693.2	NM_018013	
PHYHIP	9796	broad.mit.edu	37	8	22079030	22079030	+	Missense_Mutation	SNP	G	G	T	rs199574600		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr8:22079030G>T	ENST00000321613.3	-	6	1285	c.829C>A	c.(829-831)Cgc>Agc	p.R277S	PHYHIP_ENST00000454243.2_Missense_Mutation_p.R277S	NM_001099335.1	NP_001092805.1	Q92561	PHYIP_HUMAN	phytanoyl-CoA 2-hydroxylase interacting protein	277										endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(1)	10				Colorectal(74;0.0152)|COAD - Colon adenocarcinoma(73;0.0629)		TGGGCGTGGCGGAAGACCAGC	0.642																																					p.R277S													.	PHYHIP	24	0			c.C829A						.						71.0	87.0	82.0					8																	22079030		2135	4242	6377	SO:0001583	missense	9796	exon5			CGTGGCGGAAGAC	D87463	CCDS43723.1	8p21.2	2010-02-17	2006-01-09		ENSG00000168490	ENSG00000168490			16865	protein-coding gene	gene with protein product		608511	"""phytanoyl-CoA hydroxylase interacting protein"", ""DYRK1A interacting protein 3"""	DYRK1AP3		9039502, 10686344	Standard	NM_014759		Approved	KIAA0273, PAHX-AP	uc003xbj.4	Q92561	OTTHUMG00000163776	ENST00000321613.3:c.829C>A	8.37:g.22079030G>T	ENSP00000320017:p.Arg277Ser	Somatic	17	0		WXS	Illumina GAIIx	Phase_I	26	3	NM_014759	D3DSR1|Q8N4I9	Missense_Mutation	SNP	ENST00000321613.3	37	CCDS43723.1	.	.	.	.	.	.	.	.	.	.	G	12.46	1.943811	0.34283	.	.	ENSG00000168490	ENST00000321613;ENST00000454243;ENST00000456132;ENST00000523252	T;T	0.28895	1.59;1.59	5.48	5.48	0.80851	.	0.160851	0.56097	D	0.000022	T	0.16257	0.0391	N	0.08118	0	0.43919	D	0.996564	B	0.22541	0.071	B	0.20184	0.028	T	0.10636	-1.0621	10	0.27785	T	0.31	-41.0255	11.5865	0.50920	0.083:0.0:0.917:0.0	.	277	Q92561	PHYIP_HUMAN	S	277;277;184;229	ENSP00000320017:R277S;ENSP00000415491:R277S	ENSP00000320017:R277S	R	-	1	0	PHYHIP	22134975	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.213000	0.58520	2.580000	0.87095	0.555000	0.69702	CGC	.		0.642	PHYHIP-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000375388.1	NM_014759	
NBN	4683	broad.mit.edu	37	8	90983510	90983510	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr8:90983510G>T	ENST00000265433.3	-	6	747	c.593C>A	c.(592-594)cCa>cAa	p.P198Q	NBN_ENST00000409330.1_Missense_Mutation_p.P116Q	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin	198	Mediates interaction with SP100. {ECO:0000250}.				blastocyst growth (GO:0001832)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|DNA damage checkpoint (GO:0000077)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intrinsic apoptotic signaling pathway (GO:0097193)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G2 DNA damage checkpoint (GO:0007095)|neuromuscular process controlling balance (GO:0050885)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|telomere maintenance (GO:0000723)	Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nuclear inclusion body (GO:0042405)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|replication fork (GO:0005657)|site of double-strand break (GO:0035861)	damaged DNA binding (GO:0003684)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(11;0.0344)			ATCAAGAGGTGGGTAAAAACT	0.299								Homologous recombination																													p.P198Q													.	NBN	86	0			c.C593A						.						45.0	46.0	46.0					8																	90983510		2201	4294	6495	SO:0001583	missense	4683	exon6			AGAGGTGGGTAAA	AF058696	CCDS6249.1	8q21-q24	2014-09-17	2005-06-02	2005-06-02	ENSG00000104320	ENSG00000104320			7652	protein-coding gene	gene with protein product		602667	"""Nijmegen breakage syndrome 1 (nibrin)"""	NBS, NBS1		9590181, 9590180	Standard	XM_005250923		Approved	ATV, AT-V2, AT-V1	uc003yej.1	O60934	OTTHUMG00000153546	ENST00000265433.3:c.593C>A	8.37:g.90983510G>T	ENSP00000265433:p.Pro198Gln	Somatic	112	0		WXS	Illumina GAIIx	Phase_I	222	4	NM_002485	B2R626|B2RNC5|O60672|Q32NF7|Q53FM6|Q63HR6|Q7LDM2	Missense_Mutation	SNP	ENST00000265433.3	37	CCDS6249.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.382702	0.82792	.	.	ENSG00000104320	ENST00000265433;ENST00000409330;ENST00000452387;ENST00000519426;ENST00000517772	T;T;T;T	0.79940	-1.32;-1.11;1.31;-1.14	5.84	5.84	0.93424	.	0.050989	0.85682	D	0.000000	D	0.91633	0.7356	M	0.86953	2.85	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92172	0.5744	10	0.87932	D	0	-17.6889	20.1346	0.98019	0.0:0.0:1.0:0.0	.	198;198	A6H8Y5;O60934	.;NBN_HUMAN	Q	198;116;198;110;116	ENSP00000265433:P198Q;ENSP00000386924:P116Q;ENSP00000430983:P110Q;ENSP00000428717:P116Q	ENSP00000265433:P198Q	P	-	2	0	NBN	91052686	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.987000	0.76206	2.765000	0.95021	0.655000	0.94253	CCA	.		0.299	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3	NM_001024688	
SLC7A2	6542	broad.mit.edu	37	8	17415880	17415880	+	Silent	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr8:17415880G>T	ENST00000494857.1	+	9	1490	c.1272G>T	c.(1270-1272)ctG>ctT	p.L424L	SLC7A2_ENST00000004531.10_Silent_p.L464L|SLC7A2_ENST00000470360.1_Silent_p.L463L|SLC7A2_ENST00000522656.1_Silent_p.L424L|SLC7A2_ENST00000398090.3_Silent_p.L463L	NM_001008539.3	NP_001008539.3	P52569	CTR2_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	424					amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|macrophage activation (GO:0042116)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide production involved in inflammatory response (GO:0002537)|regulation of inflammatory response (GO:0050727)|regulation of macrophage activation (GO:0043030)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	basic amino acid transmembrane transporter activity (GO:0015174)|high-affinity arginine transmembrane transporter activity (GO:0005289)|L-lysine transmembrane transporter activity (GO:0015189)|L-ornithine transmembrane transporter activity (GO:0000064)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|stomach(1)	25				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	L-Lysine(DB00123)|L-Ornithine(DB00129)	CCTACTCTCTGGTGGCAGCCT	0.532																																					p.L464L													.	SLC7A2	157	0			c.G1392T						.						176.0	136.0	150.0					8																	17415880		2203	4300	6503	SO:0001819	synonymous_variant	6542	exon8			CTCTCTGGTGGCA	D29990	CCDS6002.2, CCDS34852.1, CCDS55203.1	8p22	2013-05-22			ENSG00000003989	ENSG00000003989		"""Solute carriers"""	11060	protein-coding gene	gene with protein product		601872		ATRC2		8954799	Standard	NM_001164771		Approved	CAT-2, HCAT2	uc011kye.2	P52569	OTTHUMG00000130819	ENST00000494857.1:c.1272G>T	8.37:g.17415880G>T		Somatic	23	0		WXS	Illumina GAIIx	Phase_I	50	4	NM_001164771	B7ZL54|O15291|O15292|Q14CQ6|Q6NSZ7|Q86TC6	Silent	SNP	ENST00000494857.1	37	CCDS34852.1																																																																																			.		0.532	SLC7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253367.3	NM_003046	
SLC39A4	55630	broad.mit.edu	37	8	145640396	145640396	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr8:145640396G>T	ENST00000301305.3	-	4	871	c.766C>A	c.(766-768)Ctc>Atc	p.L256I	SLC39A4_ENST00000531013.1_5'Flank|SLC39A4_ENST00000276833.5_Missense_Mutation_p.L231I	NM_130849.2	NP_570901	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter), member 4	256					cellular response to zinc ion starvation (GO:0034224)|cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	14	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;1.12e-40)|all cancers(56;8.17e-36)|BRCA - Breast invasive adenocarcinoma(115;0.0407)|Colorectal(110;0.055)			GAGCTGATGAGGGGCACAGGG	0.667																																					p.L256I													.	SLC39A4	54	0			c.C766A						.						40.0	45.0	43.0					8																	145640396		2203	4300	6503	SO:0001583	missense	55630	exon4			TGATGAGGGGCAC	AK025537	CCDS6424.1, CCDS43782.1	8q24.3	2013-05-22			ENSG00000147804	ENSG00000147804		"""Solute carriers"""	17129	protein-coding gene	gene with protein product		607059	"""acrodermatitis enteropathica, zinc-deficiency type"""	AEZ		12801924, 12659941, 14709598	Standard	NM_017767		Approved	ZIP4, AWMS2	uc003zcq.3	Q6P5W5		ENST00000301305.3:c.766C>A	8.37:g.145640396G>T	ENSP00000301305:p.Leu256Ile	Somatic	26	0		WXS	Illumina GAIIx	Phase_I	64	4	NM_130849	Q7L5S5|Q9H6T8|Q9NXC4	Missense_Mutation	SNP	ENST00000301305.3	37	CCDS6424.1	.	.	.	.	.	.	.	.	.	.	G	13.21	2.169376	0.38315	.	.	ENSG00000147804	ENST00000276833;ENST00000301305;ENST00000526658	T;T;T	0.61627	0.09;0.09;0.09	5.0	3.2	0.36748	.	3.221490	0.00766	N	0.001170	T	0.54854	0.1884	L	0.47716	1.5	0.09310	N	1	B;B	0.33073	0.396;0.396	B;B	0.34722	0.188;0.099	T	0.38023	-0.9680	10	0.37606	T	0.19	0.2389	7.6052	0.28097	0.1978:0.0:0.8022:0.0	.	256;231	Q6P5W5;A6NDY5	S39A4_HUMAN;.	I	231;256;162	ENSP00000276833:L231I;ENSP00000301305:L256I;ENSP00000434512:L162I	ENSP00000276833:L231I	L	-	1	0	SLC39A4	145611204	0.312000	0.24545	0.001000	0.08648	0.028000	0.11728	1.212000	0.32394	0.540000	0.28808	0.543000	0.68304	CTC	.		0.667	SLC39A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382688.1		
CELP	1057	broad.mit.edu	37	9	135962591	135962593	+	RNA	DEL	TGT	TGT	-	rs11243995	byFrequency	TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr9:135962591_135962593delTGT	ENST00000411440.2	+	0	1098_1100					NR_001275.2				carboxyl ester lipase pseudogene																		AGGCTGCCCCTGTGTCCCCCACA	0.626																																					.													.	.	.	0			.						.																																					0	.			TGCCCCTGTGTCC	L14813		9q34.2	2014-03-18	2003-02-28	2003-03-07	ENSG00000170827	ENSG00000170827			1849	pseudogene	pseudogene			"""carboxyl ester lipase-like (bile salt-stimulated lipase-like)"""	CELL		1639390	Standard	NR_001275		Approved		uc011mcu.1		OTTHUMG00000020857		9.37:g.135962591_135962593delTGT		Somatic	7	0		WXS	Illumina GAIIx	Phase_I	8	3	.		RNA	DEL	ENST00000411440.2	37																																																																																				.		0.626	CELP-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000339837.1	NM_001808	
MT-CO2	4513	broad.mit.edu;bcgsc.ca	37	M	7929	7929	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chrM:7929G>A	ENST00000361739.1	+	1	344	c.344G>A	c.(343-345)gGa>gAa	p.G115E	MT-TW_ENST00000387382.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-TN_ENST00000387400.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-TR_ENST00000387439.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-TC_ENST00000387405.1_RNA|MT-ATP8_ENST00000361851.1_5'Flank|MT-CO3_ENST00000362079.2_5'Flank|MT-ND3_ENST00000361227.2_5'Flank|MT-TD_ENST00000387419.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ATP6_ENST00000361899.2_5'Flank|MT-TG_ENST00000387429.1_RNA			P00403	COX2_HUMAN	mitochondrially encoded cytochrome c oxidase II	115					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|respiratory chain complex IV (GO:0045277)	copper ion binding (GO:0005507)|cytochrome-c oxidase activity (GO:0004129)			endometrium(5)|kidney(8)|lung(2)|pancreas(3)|prostate(1)	19						CGACTACGGCGGACTAATCTT	0.488																																					p.G115E													.	.	.	0			c.G344A						.																																			SO:0001583	missense	4513	exon1			ACGGCGGACTAAT			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198712	ENSG00000198712		"""Mitochondrial respiratory chain complex / Complex IV"""	7421	protein-coding gene	gene with protein product		516040	"""cytochrome c oxidase II"""	MTCO2		1712754, 1989603	Standard			Approved	COX2, CO2		P00403		ENST00000361739.1:c.344G>A	M.37:g.7929G>A	ENSP00000354876:p.Gly115Glu	Somatic	268	0		WXS	Illumina GAIIx	Phase_I	1157	30	ENST00000361739	Q37526	Missense_Mutation	SNP	ENST00000361739.1	37																																																																																				.		0.488	MT-CO2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024029	
BCOR	54880	broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	39933623	39933623	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chrX:39933623G>T	ENST00000378444.4	-	4	1204	c.976C>A	c.(976-978)Ccg>Acg	p.P326T	BCOR_ENST00000397354.3_Missense_Mutation_p.P326T|BCOR_ENST00000378455.4_Missense_Mutation_p.P326T|BCOR_ENST00000342274.4_Missense_Mutation_p.P326T	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	326					heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						GTGTCCCCCGGCAGGCCACTG	0.637			"""F, N, S, T"""	RARA	"""retinoblastoma, AML, APL(translocation)"""		oculo-facio-cardio-dental genetic																														p.P326T				Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	0			c.C976A						.						28.0	25.0	26.0					X																	39933623		2202	4299	6501	SO:0001583	missense	54880	exon4			CCCCCGGCAGGCC	AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"""Ankyrin repeat domain containing"""	20893	protein-coding gene	gene with protein product		300485	"""BCL6 co-repressor"""			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.976C>A	X.37:g.39933623G>T	ENSP00000367705:p.Pro326Thr	Somatic	32	0		WXS	Illumina GAIIx	Phase_I	45	5	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Missense_Mutation	SNP	ENST00000378444.4	37	CCDS48093.1	.	.	.	.	.	.	.	.	.	.	G	13.54	2.268785	0.40095	.	.	ENSG00000183337	ENST00000378455;ENST00000397354;ENST00000378444;ENST00000342274;ENST00000406200	T;T;T;T;T	0.21361	2.01;2.01;2.01;2.01;2.01	5.56	5.56	0.83823	.	.	.	.	.	T	0.28699	0.0711	N	0.24115	0.695	0.33254	D	0.558915	D;D;D;D	0.71674	0.971;0.998;0.991;0.995	P;D;P;D	0.65987	0.779;0.94;0.873;0.94	T	0.38499	-0.9658	9	0.87932	D	0	-13.3399	9.2956	0.37813	0.0788:0.1421:0.779:0.0	.	326;326;326;326	Q6W2J9-3;Q6W2J9-4;Q6W2J9;Q6W2J9-2	.;.;BCOR_HUMAN;.	T	326	ENSP00000367716:P326T;ENSP00000380512:P326T;ENSP00000367705:P326T;ENSP00000345923:P326T;ENSP00000384485:P326T	ENSP00000345923:P326T	P	-	1	0	BCOR	39818567	1.000000	0.71417	0.996000	0.52242	0.970000	0.65996	1.178000	0.31981	2.331000	0.79229	0.600000	0.82982	CCG	.		0.637	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745	
PGD	5226	ucsc.edu;bcgsc.ca	37	1	10478978	10478978	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr1:10478978G>A	ENST00000270776.8	+	11	1243	c.1205G>A	c.(1204-1206)tGc>tAc	p.C402Y	PGD_ENST00000498356.1_3'UTR|PGD_ENST00000538557.1_Missense_Mutation_p.C389Y|PGD_ENST00000541529.1_Missense_Mutation_p.C380Y	NM_002631.2	NP_002622.2	P52209	6PGD_HUMAN	phosphogluconate dehydrogenase	402					carbohydrate metabolic process (GO:0005975)|D-gluconate metabolic process (GO:0019521)|oxidation-reduction process (GO:0055114)|pentose biosynthetic process (GO:0019322)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, oxidative branch (GO:0009051)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	NADP binding (GO:0050661)|phosphogluconate dehydrogenase (decarboxylating) activity (GO:0004616)			NS(1)|breast(1)|cervix(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	14	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.14e-07)|COAD - Colon adenocarcinoma(227;7.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000294)|Kidney(185;0.000728)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.00832)|READ - Rectum adenocarcinoma(331;0.0487)	Dacarbazine(DB00851)|Furosemide(DB00695)|Gadopentetate dimeglumine(DB00789)|Ketotifen(DB00920)|Meloxicam(DB00814)|Methotrexate(DB00563)|Ritodrine(DB00867)	GTTGAAAACTGCCAGGTATGT	0.423																																					p.C402Y													.	PGD	39	0			c.G1205A						.						97.0	94.0	95.0					1																	10478978		2203	4300	6503	SO:0001583	missense	5226	exon11			AAAACTGCCAGGT	BC000368	CCDS113.1	1p36.22	2012-10-02			ENSG00000142657	ENSG00000142657	1.1.1.43		8891	protein-coding gene	gene with protein product		172200					Standard	NM_002631		Approved		uc001arc.3	P52209	OTTHUMG00000001905	ENST00000270776.8:c.1205G>A	1.37:g.10478978G>A	ENSP00000270776:p.Cys402Tyr	Somatic	41	0		WXS	Illumina HiSeq		38	4	NM_002631	A8K2Y9|B4DQJ8|Q9BWD8	Missense_Mutation	SNP	ENST00000270776.8	37	CCDS113.1	.	.	.	.	.	.	.	.	.	.	g	24.5	4.540396	0.85917	.	.	ENSG00000142657	ENST00000541529;ENST00000543846;ENST00000270776;ENST00000538557	T;T;T	0.39997	1.05;1.05;1.05	5.08	5.08	0.68730	6-phosphogluconate dehydrogenase, C-terminal (1);Dehydrogenase, multihelical (1);6-phosphogluconate dehydrogenase, C-terminal-like (1);	0.000000	0.85682	D	0.000000	T	0.56499	0.1989	L	0.41824	1.3	0.80722	D	1	D;D;D	0.71674	0.989;0.998;0.998	P;D;D	0.75484	0.902;0.986;0.986	T	0.50457	-0.8826	10	0.31617	T	0.26	-28.9237	18.8956	0.92421	0.0:0.0:1.0:0.0	.	380;402;402	F5H7U0;A8K2Y9;P52209	.;.;6PGD_HUMAN	Y	380;348;402;389	ENSP00000442285:C380Y;ENSP00000270776:C402Y;ENSP00000437822:C389Y	ENSP00000270776:C402Y	C	+	2	0	PGD	10401565	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	6.651000	0.74372	2.531000	0.85337	0.645000	0.84053	TGC	.		0.423	PGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005398.1	NM_002631	
IL22RA1	58985	ucsc.edu	37	1	24460734	24460734	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr1:24460734G>T	ENST00000270800.1	-	4	536	c.498C>A	c.(496-498)caC>caA	p.H166Q		NM_021258.3	NP_067081.2	Q8N6P7	I22R1_HUMAN	interleukin 22 receptor, alpha 1	166	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)	integral component of membrane (GO:0016021)	interferon receptor activity (GO:0004904)			breast(2)|endometrium(2)|large_intestine(4)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000992)|all_lung(284;0.00138)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-24)|Colorectal(126;6.43e-08)|COAD - Colon adenocarcinoma(152;3.51e-06)|GBM - Glioblastoma multiforme(114;5.06e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00911)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.148)		GGAGCTCTAAGTGGTAGAACA	0.527																																					p.H166Q													.	IL22RA1	62	0			c.C498A						.						106.0	87.0	93.0					1																	24460734		2203	4300	6503	SO:0001583	missense	58985	exon4			CTCTAAGTGGTAG	AF286095	CCDS247.1	1p36.11	2009-10-06	2002-12-02	2002-12-06	ENSG00000142677	ENSG00000142677		"""Interleukins and interleukin receptors"""	13700	protein-coding gene	gene with protein product		605457	"""interleukin 22 receptor"""	IL22R		10875937	Standard	NM_021258		Approved	CRF2-9	uc001biq.2	Q8N6P7	OTTHUMG00000003041	ENST00000270800.1:c.498C>A	1.37:g.24460734G>T	ENSP00000270800:p.His166Gln	Somatic	49	0		WXS	Illumina HiSeq		43	4	NM_021258	A8K839|B2R9Y9|Q9HB22	Missense_Mutation	SNP	ENST00000270800.1	37	CCDS247.1	.	.	.	.	.	.	.	.	.	.	G	14.47	2.544557	0.45280	.	.	ENSG00000142677	ENST00000270800	T	0.40756	1.02	4.98	4.06	0.47325	Interferon alpha/beta receptor, beta chain (1);Immunoglobulin-like fold (1);	0.701271	0.14351	N	0.325085	T	0.27594	0.0678	N	0.24115	0.695	0.29850	N	0.828511	B;B	0.18741	0.03;0.03	B;B	0.17098	0.017;0.017	T	0.09751	-1.0660	10	0.23891	T	0.37	-18.1229	9.7927	0.40715	0.0995:0.0:0.9005:0.0	.	58;166	B4E2V9;Q8N6P7	.;I22R1_HUMAN	Q	166	ENSP00000270800:H166Q	ENSP00000270800:H166Q	H	-	3	2	IL22RA1	24333321	0.004000	0.15560	0.916000	0.36221	0.935000	0.57460	0.378000	0.20569	2.313000	0.78055	0.561000	0.74099	CAC	.		0.527	IL22RA1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008412.1		
CFHR1	3078	ucsc.edu	37	1	196797357	196797357	+	Silent	SNP	A	A	G	rs3201739	byFrequency	TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr1:196797357A>G	ENST00000320493.5	+	4	676	c.588A>G	c.(586-588)acA>acG	p.T196T	CFHR1_ENST00000367424.4_Intron|CFHR2_ENST00000367421.3_Intron	NM_002113.2	NP_002104.2	Q03591	FHR1_HUMAN	complement factor H-related 1	196	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|kidney(1)|large_intestine(2)|lung(7)	11						GAAACTGGACAGAACCACCTC	0.348																																					p.T196T													CFHR1,NS,carcinoma,0,1	CFHR1	47	0			c.A588G						.	A		1322,2228		545,232,998	66.0	100.0	90.0		588	0.6	1.0	1	dbSNP_105	90	1631,6527		669,293,3117	no	coding-synonymous	CFHR1	NM_002113.2		1214,525,4115	GG,GA,AA		19.9926,37.2394,25.2221		196/331	196797357	2953,8755	1775	4079	5854	SO:0001819	synonymous_variant	3078	exon4			CTGGACAGAACCA	M65292	CCDS1386.1	1q32	2014-09-17	2004-08-09	2006-02-28	ENSG00000244414	ENSG00000244414		"""Complement system"""	4888	protein-coding gene	gene with protein product		134371	"""H factor (complement)-like 1"", ""complement factor H-related 1 pseudogene"", ""H factor (complement)-like 2"""	HFL1, CFHL1, CFHR1P, HFL2, CFHL1P		1711047, 1826708	Standard	NM_002113		Approved	H36-1, FHR1, CFHL, H36-2		Q03591	OTTHUMG00000036276	ENST00000320493.5:c.588A>G	1.37:g.196797357A>G		Somatic	25	1		WXS	Illumina HiSeq		63	13	NM_002113	A8K465|Q3B774|Q9UJ17	Silent	SNP	ENST00000320493.5	37	CCDS1386.1																																																																																			A|0.500;G|0.500		0.348	CFHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088251.2	NM_002113	
ERVW-1	30816	ucsc.edu	37	7	92098628	92098628	+	Silent	SNP	C	C	A	rs200174854		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr7:92098628C>A	ENST00000493463.2	-	1	1991	c.1068G>T	c.(1066-1068)ggG>ggT	p.G356G	ERVW-1_ENST00000603053.1_Silent_p.G356G|AC007566.10_ENST00000427458.1_RNA|ERVW-1_ENST00000604270.1_Intron	NM_014590.3	NP_055405.3	Q9UQF0	SYCY1_HUMAN	endogenous retrovirus group W, member 1	356					anatomical structure morphogenesis (GO:0009653)|syncytium formation (GO:0006949)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|viral envelope (GO:0019031)				endometrium(1)|large_intestine(1)|lung(15)	17						gttccatgtccccatttagtt	0.468																																					.													.	.	.	0			.						.						72.0	72.0	72.0					7																	92098628		2203	4300	6503	SO:0001819	synonymous_variant	30816	.			CATGTCCCCATTT	AF208161	CCDS5626.1	7q21.2	2011-06-16	2011-05-05	2011-05-05	ENSG00000242950	ENSG00000242950			13525	other	endogenous retrovirus	"""envelope protein"", ""HERV-W Env glycoprotein"", ""enverin"", ""syncytin-1"", ""HERV-tryptophan envelope protein"", ""HERV-W{7q21.1} provirus ancestral Env polyprotein"", ""HERV-7q envelope protein"", ""envelope glycoprotein"", ""syncytin"""	604659	"""endogenous retroviral family W, env(C7), member 1"""	ERVWE1		9835022, 9882319, 21542922	Standard	NM_001130925		Approved	HERV-W, HERV-W-ENV, HERVW, HERV-7q	uc022ahe.1	Q9UQF0	OTTHUMG00000131249	ENST00000493463.2:c.1068G>T	7.37:g.92098628C>A		Somatic	23	2		WXS	Illumina HiSeq		66	15	.	B2RPD4|O95244|O95245|Q8NHY7|Q9NRZ2|Q9NZG3	Silent	SNP	ENST00000493463.2	37	CCDS5626.1																																																																																			.		0.468	ERVW-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254009.2	NM_014590	
LMO2	4005	ucsc.edu	37	11	33881017	33881017	+	Missense_Mutation	SNP	T	T	C	rs570458390		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr11:33881017T>C	ENST00000395833.3	-	3	791	c.362A>G	c.(361-363)aAa>aGa	p.K121R	LMO2_ENST00000257818.2_Missense_Mutation_p.K190R	NM_001142315.1|NM_001142316.1	NP_001135787.1|NP_001135788.1	P25791	RBTN2_HUMAN	LIM domain only 2 (rhombotin-like 1)	121	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cellular response to thyroid hormone stimulus (GO:0097067)|embryonic hemopoiesis (GO:0035162)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|multicellular organismal development (GO:0007275)|negative regulation of erythrocyte differentiation (GO:0045647)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|cofactor binding (GO:0048037)|E-box binding (GO:0070888)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)|urinary_tract(1)	14						GGCGGCGCATTTGAAACATTC	0.488			T	TRD@	T-ALL								T|||	1	0.000199681	0.0	0.0	5008	,	,		20133	0.001		0.0	False		,,,				2504	0.0				p.K190R				Dom	yes		11	11p13	4005	LIM domain only 2 (rhombotin-like 1) (RBTN2)		L	LMO2,NS,carcinoma,-1,2	LMO2	21	0			c.A569G						.						136.0	115.0	123.0					11																	33881017		2202	4298	6500	SO:0001583	missense	4005	exon6			GCGCATTTGAAAC	X61118	CCDS7888.2, CCDS44567.1	11p13	2008-07-18			ENSG00000135363	ENSG00000135363			6642	protein-coding gene	gene with protein product	"""T-cell translocation gene 2"", ""rhombotin-like 1"""	180385		RBTNL1		2034676	Standard	NM_005574		Approved	TTG2, RHOM2, RBTN2	uc010rem.2	P25791	OTTHUMG00000157176	ENST00000395833.3:c.362A>G	11.37:g.33881017T>C	ENSP00000379175:p.Lys121Arg	Somatic	33	0		WXS	Illumina HiSeq		42	4	NM_005574	Q9HD58	Missense_Mutation	SNP	ENST00000395833.3	37	CCDS44567.1	.	.	.	.	.	.	.	.	.	.	T	19.03	3.748602	0.69533	.	.	ENSG00000135363	ENST00000395833;ENST00000257818	D;D	0.87256	-2.23;-2.23	5.15	5.15	0.70609	Zinc finger, LIM-type (5);	0.000000	0.85682	D	0.000000	D	0.87030	0.6076	N	0.13043	0.29	0.80722	D	1	D;D	0.59357	0.985;0.974	P;D	0.67103	0.728;0.949	D	0.88263	0.2924	10	0.45353	T	0.12	.	15.286	0.73828	0.0:0.0:0.0:1.0	.	190;121	P25791-3;P25791	.;RBTN2_HUMAN	R	121;190	ENSP00000379175:K121R;ENSP00000257818:K190R	ENSP00000257818:K190R	K	-	2	0	LMO2	33837593	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.792000	0.85828	2.087000	0.62958	0.402000	0.26972	AAA	.		0.488	LMO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347777.1	NM_005574	
WDTC1	23038	bcgsc.ca	37	1	27609889	27609889	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr1:27609889G>T	ENST00000319394.3	+	5	775	c.240G>T	c.(238-240)aaG>aaT	p.K80N	WDTC1_ENST00000361771.3_Missense_Mutation_p.K80N	NM_001276252.1|NM_015023.3	NP_001263181.1|NP_055838.2	Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1	80					cellular chemical homeostasis (GO:0055082)|cellular response to insulin stimulus (GO:0032869)|glucose metabolic process (GO:0006006)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|regulation of cell size (GO:0008361)	cytosol (GO:0005829)|nucleus (GO:0005634)	enzyme inhibitor activity (GO:0004857)			central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|skin(1)	21		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)		TGCACCACAAGAAGCTGCTCT	0.532																																					p.K80N													WDTC1,NS,carcinoma,+2,1	WDTC1	69	0			c.G240T						.						117.0	100.0	106.0					1																	27609889		2203	4300	6503	SO:0001583	missense	23038	exon5			CCACAAGAAGCTG	AK023778	CCDS296.1, CCDS60044.1	1p35.3	2013-01-11			ENSG00000142784	ENSG00000142784		"""DDB1 and CUL4 associated factors"", ""WD repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29175	protein-coding gene	gene with protein product	"""adipose homolog (Drosophila)"", ""DDB1 and CUL4 associated factor 9"""					12717455, 19238144	Standard	NM_015023		Approved	KIAA1037, ADP, DCAF9	uc009vst.3	Q8N5D0	OTTHUMG00000004273	ENST00000319394.3:c.240G>T	1.37:g.27609889G>T	ENSP00000317971:p.Lys80Asn	Somatic	27	0		WXS	Illumina HiSeq	Phase_1	15	3	NM_015023	D3DPL5|Q5SSC5|Q9NV87|Q9UPW4	Missense_Mutation	SNP	ENST00000319394.3	37		.	.	.	.	.	.	.	.	.	.	G	17.46	3.395221	0.62066	.	.	ENSG00000142784	ENST00000319394;ENST00000361771	D;D	0.82081	-1.57;-1.57	5.35	5.35	0.76521	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.189087	0.56097	D	0.000029	D	0.89083	0.6614	M	0.88310	2.945	0.80722	D	1	P;P	0.48998	0.918;0.835	P;B	0.49192	0.602;0.318	D	0.89446	0.3727	10	0.38643	T	0.18	.	18.0683	0.89398	0.0:0.0:1.0:0.0	.	80;80	Q8N5D0;Q8N5D0-4	WDTC1_HUMAN;.	N	80	ENSP00000317971:K80N;ENSP00000355317:K80N	ENSP00000317971:K80N	K	+	3	2	WDTC1	27482476	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.278000	0.65592	2.510000	0.84645	0.655000	0.94253	AAG	.		0.532	WDTC1-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015023	
PDE4DIPP1	728920	bcgsc.ca	37	1	146019699	146019699	+	IGR	SNP	T	T	C			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr1:146019699T>C								RNVU1-7 (50266 upstream) : NBPF11 (12947 downstream)																							TTTTTCAGGCTTGGGTTTGGA	0.443																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			TCAGGCTTGGGTT																													1.37:g.146019699T>C		Somatic	99	0		WXS	Illumina HiSeq	Phase_1	144	18	.		RNA	SNP		37																																																																																				.	0	0.443								
BIRC6	57448	bcgsc.ca	37	2	32631613	32631613	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr2:32631613G>T	ENST00000421745.2	+	9	1599	c.1465G>T	c.(1465-1467)Gat>Tat	p.D489Y		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	489					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TTCCAGATCAGATTCTGTGAC	0.284																																					p.D489Y	Pancreas(94;175 1509 16028 18060 45422)												.	BIRC6	838	0			c.G1465T						.						70.0	77.0	75.0					2																	32631613		2203	4300	6503	SO:0001583	missense	57448	exon9			AGATCAGATTCTG	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.1465G>T	2.37:g.32631613G>T	ENSP00000393596:p.Asp489Tyr	Somatic	51	0		WXS	Illumina HiSeq	Phase_1	101	4	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	G	17.08	3.296606	0.60086	.	.	ENSG00000115760	ENST00000421745	T	0.76186	-1.0	5.63	5.63	0.86233	.	0.132923	0.49305	D	0.000152	T	0.60314	0.2259	N	0.08118	0	0.58432	D	0.999997	P	0.43094	0.799	B	0.39617	0.305	T	0.68209	-0.5469	10	0.59425	D	0.04	.	19.6961	0.96026	0.0:0.0:1.0:0.0	.	489	Q9NR09	BIRC6_HUMAN	Y	489	ENSP00000393596:D489Y	ENSP00000393596:D489Y	D	+	1	0	BIRC6	32485117	1.000000	0.71417	1.000000	0.80357	0.848000	0.48234	9.414000	0.97362	2.654000	0.90174	0.650000	0.86243	GAT	.		0.284	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
SNX25	83891	bcgsc.ca	37	4	186185626	186185626	+	Missense_Mutation	SNP	G	G	A	rs529369855		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr4:186185626G>A	ENST00000504273.1	+	4	568	c.274G>A	c.(274-276)Gca>Aca	p.A92T	SNX25_ENST00000264694.8_Missense_Mutation_p.A92T			Q9H3E2	SNX25_HUMAN	sorting nexin 25	92	PXA. {ECO:0000255|PROSITE- ProRule:PRU00147, ECO:0000255|PROSITE- ProRule:PRU00553}.				negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein transport (GO:0015031)|receptor catabolic process (GO:0032801)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			NS(1)|breast(4)|endometrium(2)|kidney(4)|large_intestine(8)|lung(13)|ovary(2)|pancreas(2)|prostate(2)|urinary_tract(2)	40		all_lung(41;1.03e-13)|Lung NSC(41;2.5e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;2.13e-24)|Epithelial(43;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.6e-11)|BRCA - Breast invasive adenocarcinoma(30;0.00013)|Colorectal(24;0.000165)|GBM - Glioblastoma multiforme(59;0.000357)|COAD - Colon adenocarcinoma(29;0.000887)|STAD - Stomach adenocarcinoma(60;0.00118)|LUSC - Lung squamous cell carcinoma(40;0.0129)|READ - Rectum adenocarcinoma(43;0.228)		TGTGTTGCACGCATGCTTGAG	0.398																																					p.A92T													.	SNX25	100	0			c.G274A						.						166.0	153.0	158.0					4																	186185626		2203	4300	6503	SO:0001583	missense	83891	exon4			TTGCACGCATGCT	AF113223	CCDS34116.1	4q35.1	2011-05-03			ENSG00000109762	ENSG00000109762		"""Sorting nexins"""	21883	protein-coding gene	gene with protein product						12461558	Standard	NM_031953		Approved	SBBI31	uc003ixh.3	Q9H3E2	OTTHUMG00000160475	ENST00000504273.1:c.274G>A	4.37:g.186185626G>A	ENSP00000426255:p.Ala92Thr	Somatic	45	0		WXS	Illumina HiSeq	Phase_1	121	5	NM_031953	Q3ZT30|Q8N6K3	Missense_Mutation	SNP	ENST00000504273.1	37	CCDS34116.1	.	.	.	.	.	.	.	.	.	.	G	11.66	1.703845	0.30232	.	.	ENSG00000109762	ENST00000504273;ENST00000264694	T;T	0.09723	2.95;2.95	5.27	-1.78	0.07957	Phox-associated domain (2);	0.647857	0.15679	N	0.250006	T	0.04679	0.0127	N	0.22421	0.69	0.21950	N	0.999451	B	0.06786	0.001	B	0.06405	0.002	T	0.37842	-0.9688	10	0.23891	T	0.37	0.1488	0.115	0.00060	0.339:0.1937:0.1919:0.2754	.	92	Q9H3E2	SNX25_HUMAN	T	92	ENSP00000426255:A92T;ENSP00000264694:A92T	ENSP00000264694:A92T	A	+	1	0	SNX25	186422620	0.055000	0.20627	0.045000	0.18777	0.972000	0.66771	0.089000	0.15002	-0.674000	0.05253	-0.126000	0.14955	GCA	.		0.398	SNX25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360756.1	NM_031953	
ELOVL7	79993	bcgsc.ca	37	5	60067809	60067809	+	Missense_Mutation	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr5:60067809C>T	ENST00000508821.1	-	4	490	c.176G>A	c.(175-177)cGc>cAc	p.R59H	ELOVL7_ENST00000425382.1_Missense_Mutation_p.R59H|ELOVL7_ENST00000505959.1_Missense_Mutation_p.R46H|ELOVL7_ENST00000438340.1_Missense_Mutation_p.R59H	NM_024930.2	NP_079206.2	A1L3X0	ELOV7_HUMAN	ELOVL fatty acid elongase 7	59					cellular lipid metabolic process (GO:0044255)|fatty acid elongation, polyunsaturated fatty acid (GO:0034626)|fatty acid elongation, saturated fatty acid (GO:0019367)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity (GO:0016740)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(1)	9		Lung NSC(810;2.56e-06)|Prostate(74;0.0115)|Breast(144;0.0244)|Ovarian(174;0.0481)				AAAGGGCTTGCGATTTTCCAT	0.413																																					p.R59H													ELOVL7,NS,lymphoid_neoplasm,0,1	ELOVL7	24	0			c.G176A						.						84.0	79.0	81.0					5																	60067809		2203	4300	6503	SO:0001583	missense	79993	exon3			GGCTTGCGATTTT	AK027216	CCDS34164.1	5q12	2011-05-25	2011-05-25			ENSG00000164181			26292	protein-coding gene	gene with protein product		614451	"""ELOVL family member 7, elongation of long chain fatty acids (yeast)"""			19826053	Standard	NM_024930		Approved	FLJ23563	uc010iwk.3	A1L3X0		ENST00000508821.1:c.176G>A	5.37:g.60067809C>T	ENSP00000424123:p.Arg59His	Somatic	42	0		WXS	Illumina HiSeq	Phase_1	58	4	NM_001104558	Q589T3|Q9H5D0|Q9NT66	Missense_Mutation	SNP	ENST00000508821.1	37	CCDS34164.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.701681	0.88924	.	.	ENSG00000164181	ENST00000508821;ENST00000438340;ENST00000425382;ENST00000505959;ENST00000507047;ENST00000511799	T;T;T;T;T;T	0.27104	1.69;1.69;1.69;1.69;1.69;1.69	5.73	5.73	0.89815	.	0.059805	0.64402	D	0.000004	T	0.51907	0.1702	M	0.93978	3.48	0.80722	D	1	P;D	0.59357	0.907;0.985	P;P	0.52159	0.477;0.691	T	0.63778	-0.6560	10	0.66056	D	0.02	-6.6369	13.9375	0.64034	0.0:0.9216:0.0:0.0784	.	46;59	D6RHD0;A1L3X0	.;ELOV7_HUMAN	H	59;59;59;46;59;59	ENSP00000424123:R59H;ENSP00000411255:R59H;ENSP00000402634:R59H;ENSP00000421043:R46H;ENSP00000426400:R59H;ENSP00000424081:R59H	ENSP00000402634:R59H	R	-	2	0	ELOVL7	60103566	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.726000	0.68515	2.868000	0.98415	0.557000	0.71058	CGC	.		0.413	ELOVL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368195.1		
BCLAF1P1	728366	bcgsc.ca	37	5	110284092	110284092	+	IGR	SNP	A	A	G	rs367881369		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr5:110284092A>G								SLC25A46 (183235 upstream) : CTC-551A13.1 (22557 downstream)																							AAGGTTCCTCATGGTTGGCTA	0.378																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			TTCCTCATGGTTG																													5.37:g.110284092A>G		Somatic	32	0		WXS	Illumina HiSeq	Phase_1	53	10	.		RNA	SNP		37																																																																																				.	0	0.378								
BCLAF1P1	728366	bcgsc.ca	37	5	110284097	110284097	+	IGR	SNP	T	T	C	rs370268370		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr5:110284097T>C								SLC25A46 (183240 upstream) : CTC-551A13.1 (22552 downstream)																							TCCTCATGGTTGGCTAACTCC	0.388																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			CATGGTTGGCTAA																													5.37:g.110284097T>C		Somatic	33	1		WXS	Illumina HiSeq	Phase_1	52	10	.		RNA	SNP		37																																																																																				.	0	0.388								
HAUS6P1	653175	bcgsc.ca	37	7	53255583	53255583	+	IGR	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr7:53255583G>T								POM121L12 (150966 upstream) : RNU1-14P (178167 downstream)																							CGGTCTTTGTGGGCTTCAGTG	0.353																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	653175	.			CTTTGTGGGCTTC																													7.37:g.53255583G>T		Somatic	67	0		WXS	Illumina HiSeq	Phase_1	97	31	.		RNA	SNP		37																																																																																				.	0	0.353								
ZAN	7455	bcgsc.ca	37	7	100349919	100349919	+	RNA	SNP	T	T	C	rs200193075	byFrequency	TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr7:100349919T>C	ENST00000348028.3	+	0	2356				ZAN_ENST00000546292.1_RNA|ZAN_ENST00000421100.1_RNA|ZAN_ENST00000427578.1_RNA|ZAN_ENST00000538115.1_RNA|ZAN_ENST00000449052.1_RNA|ZAN_ENST00000542585.1_RNA|ZAN_ENST00000546213.1_RNA|ZAN_ENST00000349350.6_RNA|ZAN_ENST00000443370.1_RNA			Q9Y493	ZAN_HUMAN	zonadhesin (gene/pseudogene)						binding of sperm to zona pellucida (GO:0007339)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.S731P(1)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(21)|kidney(6)|large_intestine(18)|lung(60)|ovary(4)|pancreas(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)	139	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			CACAGAAAAATCCACCATCTC	0.517													N|||	80	0.0159744	0.0091	0.0144	5008	,	,		14946	0.0377		0.0159	False		,,,				2504	0.0041				.													ZAN,trunk,malignant_melanoma,0,1	ZAN	658	1	Substitution - Missense(1)	skin(1)	.						.						141.0	157.0	152.0					7																	100349919		1822	4070	5892			7455	.			GAAAAATCCACCA	U83191		7q22.1	2013-10-10	2013-10-10		ENSG00000146839	ENSG00000146839			12857	protein-coding gene	gene with protein product		602372	"""zonadhesin"""			9799793, 17033959	Standard	NM_003386		Approved		uc003uwk.3	Q9Y493	OTTHUMG00000157037		7.37:g.100349919T>C		Somatic	133	9		WXS	Illumina HiSeq	Phase_1	182	24	.	A0FKC8|D6W5W4|O00218|Q96L85|Q96L86|Q96L87|Q96L88|Q96L89|Q96L90|Q9BXN9|Q9BZ83|Q9BZ84|Q9BZ85|Q9BZ86|Q9BZ87|Q9BZ88	Missense_Mutation	SNP	ENST00000348028.3	37		.	.	.	.	.	.	.	.	.	.	N	4.049	0.006856	0.07866	.	.	ENSG00000146839	ENST00000546292;ENST00000538115;ENST00000542585	T;T;T	0.64085	-0.08;-0.02;-0.08	3.93	-7.86	0.01187	.	.	.	.	.	T	0.34337	0.0894	N	0.02539	-0.55	0.19300	N	0.999976	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.61530	-0.7044	9	0.30078	T	0.28	.	16.8785	0.86058	0.1313:0.7109:0.0:0.1578	.	731;731	F5H0T8;Q9Y493	.;ZAN_HUMAN	P	731	ENSP00000445943:S731P;ENSP00000445091:S731P;ENSP00000444427:S731P	ENSP00000423579:S731P	S	+	1	0	ZAN	100187855	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-10.783000	0.00005	-6.293000	0.00005	-3.776000	0.00021	TCC	T|0.996;C|0.004		0.517	ZAN-006	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000347214.1	NM_003386	
PRSS1	5644	bcgsc.ca	37	7	142458938	142458938	+	Intron	SNP	T	T	A	rs374770738		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr7:142458938T>A	ENST00000311737.7	+	2	206				PRSS1_ENST00000486171.1_Missense_Mutation_p.F73L	NM_002769.4	NP_002760.1	P07477	TRY1_HUMAN	protease, serine, 1 (trypsin 1)						cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(24)|prostate(2)	38	Melanoma(164;0.047)	all_cancers(3;2.14e-49)|Acute lymphoblastic leukemia(3;7.3e-185)|all_hematologic(3;1.1e-165)	all cancers(2;0.000126)|Colorectal(2;0.000157)|Epithelial(2;0.000191)|COAD - Colon adenocarcinoma(2;0.00189)		Aprotinin(DB06692)	agtcaaaattttcaggAAGAG	0.388																																					.													.	PRSS1	68	0			.						.																																			SO:0001627	intron_variant	5644	.			AAAATTTTCAGGA	M22612	CCDS5872.1	7q34	2012-10-02			ENSG00000204983	ENSG00000204983	3.4.21.4	"""Serine peptidases / Serine peptidases"""	9475	protein-coding gene	gene with protein product		276000		TRY1			Standard	NM_002769		Approved		uc003wak.2	P07477	OTTHUMG00000158923	ENST00000311737.7:c.200+373T>A	7.37:g.142458938T>A		Somatic	38	0		WXS	Illumina HiSeq	Phase_1	55	6	.	A1A509|A6NJ71|B2R5I5|Q5NV57|Q7M4N3|Q7M4N4|Q92955|Q9HAN4|Q9HAN5|Q9HAN6|Q9HAN7	Missense_Mutation	SNP	ENST00000311737.7	37	CCDS5872.1	.	.	.	.	.	.	.	.	.	.	t	5.014	0.188341	0.09547	.	.	ENSG00000204983	ENST00000486171	D	0.92199	-2.99	1.97	0.784	0.18578	.	.	.	.	.	T	0.75019	0.3793	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.63817	-0.6551	6	0.02654	T	1	.	3.9587	0.09401	0.0:0.1879:0.0:0.8121	.	.	.	.	L	73	ENSP00000417854:F73L	ENSP00000417854:F73L	F	+	3	2	PRSS1	142138512	0.000000	0.05858	0.032000	0.17829	0.031000	0.12232	0.210000	0.17455	0.222000	0.20900	-0.849000	0.03036	TTT	.		0.388	PRSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352538.2		
CDK2AP2P3	401525	bcgsc.ca	37	9	68370776	68370776	+	IGR	SNP	G	G	A	rs112484539		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr9:68370776G>A								RP11-149F8.5 (30132 upstream) : RP11-764K9.1 (27101 downstream)																							GGAGCCCTGGGCACCAGGTGG	0.632																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	401525	.			CCCTGGGCACCAG																													9.37:g.68370776G>A		Somatic	74	3		WXS	Illumina HiSeq	Phase_1	98	25	.		RNA	SNP		37																																																																																				G|0.500;A|0.500	0	0.632								
CDK2AP2P3	401525	bcgsc.ca	37	9	68370821	68370821	+	IGR	SNP	C	C	T	rs113256212		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr9:68370821C>T								RP11-149F8.5 (30177 upstream) : RP11-764K9.1 (27056 downstream)																							GGTAGGCGGTCCAAAGTCTTT	0.647																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	401525	.			GGCGGTCCAAAGT																													9.37:g.68370821C>T		Somatic	102	2		WXS	Illumina HiSeq	Phase_1	129	24	.		RNA	SNP		37																																																																																				C|0.500;T|0.500	0	0.647								
LCN1P1	286310	bcgsc.ca	37	9	136102181	136102181	+	IGR	SNP	C	C	T	rs533219721		TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr9:136102181C>T								OBP2B (17551 upstream) : ABO (23606 downstream)																							TTTCCCGGCTCGTCAGTTTTC	0.592													c|||	1	0.000199681	0.0	0.0	5008	,	,		13759	0.0		0.0	False		,,,				2504	0.001				.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	286310	.			CCGGCTCGTCAGT																													9.37:g.136102181C>T		Somatic	160	0		WXS	Illumina HiSeq	Phase_1	118	66	.		RNA	SNP		37																																																																																				.	0	0.592								
MARCH8	220972	bcgsc.ca	37	10	46028613	46028613	+	Missense_Mutation	SNP	G	G	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr10:46028613G>A	ENST00000319836.3	-	2	796	c.47C>T	c.(46-48)gCc>gTc	p.A16V	MARCH8_ENST00000453424.2_Missense_Mutation_p.A16V|MARCH8_ENST00000395771.3_Missense_Mutation_p.A16V|MARCH8_ENST00000395769.2_Missense_Mutation_p.A16V	NM_145021.4	NP_659458.2	Q5T0T0	MARH8_HUMAN	membrane-associated ring finger (C3HC4) 8, E3 ubiquitin protein ligase	16					immune system process (GO:0002376)|protein polyubiquitination (GO:0000209)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(5)|lung(4)	12						AGCAGAGATGGCATCCTGGGA	0.428																																					p.A16V	NSCLC(102;658 1594 2173 16344 34808)												.	MARCH8	29	0			c.C47T						.						112.0	105.0	107.0					10																	46028613		2203	4300	6503	SO:0001583	missense	220972	exon2			GAGATGGCATCCT	AL833316	CCDS7213.1, CCDS60519.1	10q11.22	2013-01-09	2012-02-23	2005-01-27	ENSG00000165406	ENSG00000165406		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	23356	protein-coding gene	gene with protein product		613335	"""c-mir, cellular modulator of immune recognition"", ""membrane-associated ring finger (C3HC4) 8"""	MIR		12582153, 14722266	Standard	XM_005271804		Approved	c-MIR, MARCH-VIII, RNF178	uc001jch.2	Q5T0T0	OTTHUMG00000019345	ENST00000319836.3:c.47C>T	10.37:g.46028613G>A	ENSP00000317087:p.Ala16Val	Somatic	45	0		WXS	Illumina HiSeq	Phase_1	58	4	NM_001002266	B2R8E7|H0Y7C6|Q5T0S8|Q8TC72	Missense_Mutation	SNP	ENST00000319836.3	37	CCDS7213.1	.	.	.	.	.	.	.	.	.	.	G	9.838	1.190265	0.21954	.	.	ENSG00000165406	ENST00000395771;ENST00000319836;ENST00000395769;ENST00000453980	T;T;T	0.10960	2.82;2.82;2.82	5.04	2.17	0.27698	.	.	.	.	.	T	0.06280	0.0162	N	0.22421	0.69	0.21064	N	0.999791	B	0.06786	0.001	B	0.04013	0.001	T	0.44802	-0.9304	9	0.12766	T	0.61	.	6.4049	0.21658	0.3035:0.0:0.6965:0.0	.	16	Q5T0T0	MARH8_HUMAN	V	16	ENSP00000379118:A16V;ENSP00000317087:A16V;ENSP00000379116:A16V	ENSP00000317087:A16V	A	-	2	0	MARCH8	45348619	0.959000	0.32827	0.973000	0.42090	0.974000	0.67602	1.548000	0.36201	0.523000	0.28482	0.563000	0.77884	GCC	.		0.428	MARCH8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051217.1	NM_145021	
MUC2	4583	bcgsc.ca	37	11	1093134	1093134	+	Silent	SNP	C	C	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr11:1093134C>A	ENST00000441003.2	+	30	4980	c.4953C>A	c.(4951-4953)acC>acA	p.T1651T	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Silent_p.T1618T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	agaccccaaccacgacaccca	0.627																																					p.T1651T													.	MUC2	614	0			c.C4953A						.						102.0	166.0	144.0					11																	1093134		1800	3370	5170	SO:0001819	synonymous_variant	4583	exon30			CCCAACCACGACA	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4953C>A	11.37:g.1093134C>A		Somatic	174	10		WXS	Illumina HiSeq	Phase_1	339	34	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
CD163L1	283316	bcgsc.ca	37	12	7519849	7519849	+	Missense_Mutation	SNP	T	T	C			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr12:7519849T>C	ENST00000313599.3	-	18	4319	c.4262A>G	c.(4261-4263)cAt>cGt	p.H1421R	CD163L1_ENST00000396630.1_Intron|CD163L1_ENST00000416109.2_Missense_Mutation_p.H1431R			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	1421						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						TCTTGTCCCATGTGGGTCCTC	0.512																																					p.H1421R													.	CD163L1	238	0			c.A4262G						.						69.0	61.0	64.0					12																	7519849		2203	4300	6503	SO:0001583	missense	283316	exon18			GTCCCATGTGGGT	AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"""CD163 antigen-like 1"""			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.4262A>G	12.37:g.7519849T>C	ENSP00000315945:p.His1421Arg	Somatic	31	0		WXS	Illumina HiSeq	Phase_1	42	4	NM_174941	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Missense_Mutation	SNP	ENST00000313599.3	37	CCDS8577.1	.	.	.	.	.	.	.	.	.	.	T	6.006	0.369598	0.11352	.	.	ENSG00000177675	ENST00000313599;ENST00000416109	T;T	0.01304	5.03;5.03	1.93	-2.3	0.06785	.	.	.	.	.	T	0.00906	0.0030	N	0.08118	0	0.09310	N	1	B;P	0.49185	0.329;0.92	B;B	0.44224	0.038;0.444	T	0.49916	-0.8888	9	0.23891	T	0.37	.	5.1907	0.15209	0.0:0.4004:0.0:0.5996	.	1431;1421	E7EVK4;Q9NR16	.;C163B_HUMAN	R	1421;1431	ENSP00000315945:H1421R;ENSP00000393474:H1431R	ENSP00000315945:H1421R	H	-	2	0	CD163L1	7411116	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.411000	0.21115	-0.668000	0.05296	-0.375000	0.07067	CAT	.		0.512	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941	
SLC17A8	246213	bcgsc.ca	37	12	100774620	100774620	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr12:100774620G>T	ENST00000323346.5	+	2	556	c.243G>T	c.(241-243)atG>atT	p.M81I	SLC17A8_ENST00000392989.3_Missense_Mutation_p.M81I	NM_001145288.1|NM_139319.2	NP_001138760.1|NP_647480.1	Q8NDX2	VGLU3_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 8	81					ion transport (GO:0006811)|neurotransmitter transport (GO:0006836)|sensory perception of sound (GO:0007605)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|synaptic vesicle membrane (GO:0030672)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(25)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	44						TTGCTATCATGAGTGGGCTGG	0.527																																					p.M81I													.	SLC17A8	89	0			c.G243T						.						202.0	182.0	189.0					12																	100774620		2203	4300	6503	SO:0001583	missense	246213	exon2			TATCATGAGTGGG	AJ459241	CCDS9077.1, CCDS44957.1	12q23.1	2013-07-18	2013-07-18		ENSG00000179520	ENSG00000179520		"""Solute carriers"""	20151	protein-coding gene	gene with protein product	"""vesicular glutamate transporter 3"""	607557	"""deafness, autosomal dominant 25"", ""solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 8"""	DFNA25		12151341	Standard	NM_139319		Approved	VGLUT3	uc010svi.2	Q8NDX2	OTTHUMG00000170358	ENST00000323346.5:c.243G>T	12.37:g.100774620G>T	ENSP00000316909:p.Met81Ile	Somatic	49	0		WXS	Illumina HiSeq	Phase_1	45	4	NM_001145288	B3KXZ6|B7ZKV4|Q17RQ8	Missense_Mutation	SNP	ENST00000323346.5	37	CCDS9077.1	.	.	.	.	.	.	.	.	.	.	G	16.66	3.184213	0.57800	.	.	ENSG00000179520	ENST00000323346;ENST00000392989	T;T	0.56941	0.43;0.43	5.27	5.27	0.74061	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.102276	0.64402	D	0.000001	T	0.54095	0.1837	L	0.45137	1.4	0.58432	D	0.999999	B;B	0.31752	0.018;0.338	B;B	0.38755	0.057;0.281	T	0.57653	-0.7774	10	0.72032	D	0.01	.	18.8896	0.92392	0.0:0.0:1.0:0.0	.	81;81	Q8NDX2;Q8NDX2-2	VGLU3_HUMAN;.	I	81	ENSP00000316909:M81I;ENSP00000376715:M81I	ENSP00000316909:M81I	M	+	3	0	SLC17A8	99298751	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.053000	0.71089	2.466000	0.83321	0.591000	0.81541	ATG	.		0.527	SLC17A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408673.2	NM_139319	
PEX12P1	121727	bcgsc.ca	37	13	90644559	90644559	+	IGR	SNP	C	C	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr13:90644559C>A								SNORD38 (155068 upstream) : LINC00559 (67946 downstream)																							CCCTTCCTGGCAGCCTACCCA	0.458																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	121727	.			TCCTGGCAGCCTA																													13.37:g.90644559C>A		Somatic	28	0		WXS	Illumina HiSeq	Phase_1	15	3	.		RNA	SNP		37																																																																																				.	0	0.458								
DYNLL1P1	246720	bcgsc.ca	37	14	81712881	81712881	+	IGR	SNP	T	T	A			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr14:81712881T>A								GTF2A1 (25306 upstream) : STON2 (14118 downstream)																							TGTCCGCATTTTTGATCACGG	0.567																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	246720	.			CGCATTTTTGATC																													14.37:g.81712881T>A		Somatic	42	0		WXS	Illumina HiSeq	Phase_1	44	28	.		RNA	SNP		37																																																																																				.	0	0.567								
ZNF676	163223	bcgsc.ca	37	19	22363737	22363737	+	Missense_Mutation	SNP	C	C	G	rs572031376	byFrequency	TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr19:22363737C>G	ENST00000397121.2	-	3	1099	c.782G>C	c.(781-783)gGa>gCa	p.G261A		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	261					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				GCTACTAAATCCTTTGCCACA	0.393													G|||	17	0.00339457	0.0015	0.0029	5008	,	,		24868	0.0089		0.003	False		,,,				2504	0.001				p.G261A													.	ZNF676	146	0			c.G782C						.						89.0	96.0	93.0					19																	22363737		2158	4274	6432	SO:0001583	missense	163223	exon3			CTAAATCCTTTGC	AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"""Zinc fingers, C2H2-type"""	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.782G>C	19.37:g.22363737C>G	ENSP00000380310:p.Gly261Ala	Somatic	58	1		WXS	Illumina HiSeq	Phase_1	71	8	NM_001001411	A8MVX5	Missense_Mutation	SNP	ENST00000397121.2	37	CCDS42539.1	.	.	.	.	.	.	.	.	.	.	.	0.001	-3.455683	0.00012	.	.	ENSG00000196109	ENST00000397121	T	0.35236	1.32	0.81	-1.62	0.08372	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09247	0.0228	N	0.00788	-1.185	0.09310	N	1	B	0.11235	0.004	B	0.14023	0.01	T	0.28996	-1.0026	9	0.02654	T	1	.	8.4431	0.32826	0.0:0.685:0.315:0.0	.	261	Q8N7Q3	ZN676_HUMAN	A	261	ENSP00000380310:G261A	ENSP00000380310:G261A	G	-	2	0	ZNF676	22155577	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.024000	0.12435	-1.409000	0.02038	-1.398000	0.01145	GGA	.		0.393	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411	
CYP2A7P1	1550	bcgsc.ca	37	19	41532038	41532038	+	IGR	SNP	C	C	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr19:41532038C>T								CYP2B6 (7735 upstream) : CYP2A13 (62338 downstream)																							CGGCTTGGTGCGCTCCCAGGT	0.667																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	1550	.			TTGGTGCGCTCCC																													19.37:g.41532038C>T		Somatic	45	0		WXS	Illumina HiSeq	Phase_1	64	4	.		Missense_Mutation	SNP		37		.	.	.	.	.	.	.	.	.	.	c	15.65	2.896386	0.52121	.	.	ENSG00000213908	ENST00000301171	.	.	.	3.21	3.21	0.36854	.	0.000000	0.85682	U	0.000000	T	0.67552	0.2905	.	.	.	0.09310	N	1.0	.	.	.	.	.	.	T	0.78964	-0.1996	5	0.72032	D	0.01	.	13.522	0.61574	0.0:1.0:0.0:0.0	.	.	.	.	H	119	.	ENSP00000301171:R119H	R	-	2	0	CYP2A7P1	46223878	0.904000	0.30761	0.997000	0.53966	0.009000	0.06853	1.535000	0.36061	1.504000	0.48704	0.194000	0.17425	CGC	.	0	0.667								
BRSK1	84446	bcgsc.ca	37	19	55817627	55817627	+	Missense_Mutation	SNP	G	G	T			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr19:55817627G>T	ENST00000309383.1	+	17	2175	c.1898G>T	c.(1897-1899)aGc>aTc	p.S633I	BRSK1_ENST00000326848.7_Missense_Mutation_p.S328I|BRSK1_ENST00000590333.1_Missense_Mutation_p.S649I	NM_032430.1	NP_115806.1	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1	633					axonogenesis (GO:0007409)|cellular response to DNA damage stimulus (GO:0006974)|centrosome duplication (GO:0051298)|establishment of cell polarity (GO:0030010)|G2 DNA damage checkpoint (GO:0031572)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|protein phosphorylation (GO:0006468)|response to UV (GO:0009411)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(15)|ovary(2)|prostate(2)|skin(6)|stomach(1)	48		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0474)		CAGATCCCCAGCCTGAGTCAC	0.612																																					p.S633I													.	BRSK1	192	0			c.G1898T						.						55.0	57.0	57.0					19																	55817627		2203	4300	6503	SO:0001583	missense	84446	exon17			TCCCCAGCCTGAG	AB058714	CCDS12921.1	19q13.4	2008-02-05				ENSG00000160469			18994	protein-coding gene	gene with protein product		609235				14976552	Standard	NM_032430		Approved	KIAA1811	uc002qkg.3	Q8TDC3		ENST00000309383.1:c.1898G>T	19.37:g.55817627G>T	ENSP00000310649:p.Ser633Ile	Somatic	30	0		WXS	Illumina HiSeq	Phase_1	54	4	NM_032430	F1DG44|Q5J5B5|Q8NDD0|Q8NDR4|Q8TDC2|Q96AV4|Q96JL4	Missense_Mutation	SNP	ENST00000309383.1	37	CCDS12921.1	.	.	.	.	.	.	.	.	.	.	.	16.16	3.045385	0.55110	.	.	ENSG00000160469	ENST00000309383;ENST00000543410;ENST00000326848	T;T	0.73258	-0.73;1.78	5.11	5.11	0.69529	.	0.140194	0.48286	D	0.000195	D	0.82559	0.5063	L	0.61218	1.895	0.47778	D	0.999514	D;D	0.69078	0.995;0.997	D;D	0.80764	0.986;0.994	D	0.84294	0.0501	10	0.87932	D	0	.	17.7465	0.88422	0.0:0.0:1.0:0.0	.	633;649	Q8TDC3;Q8TDC3-2	BRSK1_HUMAN;.	I	633;328;328	ENSP00000310649:S633I;ENSP00000320853:S328I	ENSP00000310649:S633I	S	+	2	0	BRSK1	60509439	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.520000	0.67080	2.572000	0.86782	0.555000	0.69702	AGC	.		0.612	BRSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452787.1	NM_032430	
MAGEA1	4100	bcgsc.ca	37	X	152482528	152482528	+	Missense_Mutation	SNP	T	T	G			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chrX:152482528T>G	ENST00000356661.5	-	3	701	c.483A>C	c.(481-483)gaA>gaC	p.E161D		NM_004988.4	NP_004979.3	P43355	MAGA1_HUMAN	melanoma antigen family A, 1 (directs expression of antigen MZ2-E)	161	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone deacetylase binding (GO:0042826)			breast(1)|central_nervous_system(7)|kidney(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TGGGGTCTGCTTCCTTCACGT	0.517																																					p.E161D													.	MAGEA1	57	0			c.A483C						.						123.0	114.0	117.0					X																	152482528		2203	4300	6503	SO:0001583	missense	4100	exon3			GTCTGCTTCCTTC		CCDS76051.1	Xq28	2010-05-26			ENSG00000198681	ENSG00000198681			6796	protein-coding gene	gene with protein product	"""melanoma-associated antigen 1"", ""melanoma-associated antigen MZ2-E"", ""melanoma antigen MAGE-1"", ""melanoma antigen family A 1"", ""cancer/testis antigen family 1, member 1"""	300016		MAGE1		1840703	Standard	NM_004988		Approved	MGC9326, CT1.1	uc004fhf.2	P43355	OTTHUMG00000024192	ENST00000356661.5:c.483A>C	X.37:g.152482528T>G	ENSP00000349085:p.Glu161Asp	Somatic	65	0		WXS	Illumina HiSeq	Phase_1	69	24	NM_004988	B2RC81|O00346	Missense_Mutation	SNP	ENST00000356661.5	37	CCDS14720.1	.	.	.	.	.	.	.	.	.	.	T	7.416	0.635719	0.14322	.	.	ENSG00000198681	ENST00000356661	T	0.08720	3.06	1.28	-1.83	0.07833	.	0.254655	0.43919	N	0.000504	T	0.11324	0.0276	M	0.89287	3.02	0.09310	N	1	B	0.11235	0.004	B	0.20767	0.031	T	0.29305	-1.0016	10	0.66056	D	0.02	.	2.2218	0.03974	0.0:0.2316:0.3158:0.4526	.	161	P43355	MAGA1_HUMAN	D	161	ENSP00000349085:E161D	ENSP00000349085:E161D	E	-	3	2	MAGEA1	152135722	0.009000	0.17119	0.002000	0.10522	0.003000	0.03518	-0.083000	0.11286	-0.595000	0.05828	-1.314000	0.01303	GAA	.		0.517	MAGEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060940.1	NM_004988	
KCNN3	3782	hgsc.bcm.edu	37	1	154842252	154842253	+	Missense_Mutation	DNP	AG	AG	CT			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr1:154842252_154842253AG>CT	ENST00000271915.4	-	1	503_504	c.188_189CT>AG	c.(187-189)cCT>cAG	p.P63Q	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	63	Gln-rich.|Pro-rich.				potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	gaagctgcggaggctgaggctg	0.698																																					p.P63Q		.											.	.	.	0			c.C188A						.																																			SO:0001583	missense	3782	exon1			TGCGGAGGCTGAG	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.188_189delinsCT	1.37:g.154842252_154842253delinsCT	ENSP00000271915:p.Pro63Gln	Somatic	27	0		WXS	Illumina HiSeq	.	44	6	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	Missense_Mutation	DNP	ENST00000271915.4	37	CCDS30880.1																																																																																			.		0.698	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249	
THOC5	8563	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	29913065	29913066	+	Missense_Mutation	DNP	GC	GC	TA			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr22:29913065_29913066GC>TA	ENST00000490103.1	-	17	1755_1756	c.1633_1634GC>TA	c.(1633-1635)GCt>TAt	p.A545Y	THOC5_ENST00000397872.1_Missense_Mutation_p.A545Y|THOC5_ENST00000397873.2_Missense_Mutation_p.A545Y|CTA-256D12.11_ENST00000411969.1_RNA|THOC5_ENST00000397871.1_Missense_Mutation_p.A545Y	NM_003678.4	NP_003669.4	Q13769	THOC5_HUMAN	THO complex 5	545					blastocyst development (GO:0001824)|cell morphogenesis (GO:0000902)|monocyte differentiation (GO:0030224)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of macrophage differentiation (GO:0045650)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|primitive hemopoiesis (GO:0060215)|regulation of mRNA export from nucleus (GO:0010793)|regulation of stem cell division (GO:2000035)|RNA splicing (GO:0008380)|stem cell division (GO:0017145)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	mRNA binding (GO:0003729)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(4)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GGTGTCCCCAGCCAGTCCCGCA	0.535																																					p.A545Y		.											.	.	.	0			c.G1633T						.																																			SO:0001583	missense	8563	exon18			CCCCAGCCAGTCC	AB023200	CCDS13859.1	22q12	2013-02-11			ENSG00000100296	ENSG00000100296		"""THO complex subunits"""	19074	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 79"""	612733	"""chromosome 22 open reading frame 19"""	C22orf19		11979277, 8242058, 10231032, 19015024, 18373705	Standard	NM_003678		Approved	PK1.3, KIAA0983, Fmip, fSAP79	uc003afs.3	Q13769	OTTHUMG00000151291	ENST00000490103.1:c.1633_1634delinsTA	22.37:g.29913065_29913066delinsTA	ENSP00000420306:p.Ala545Tyr	Somatic	37	0		WXS	Illumina HiSeq	.	71	10	NM_001002878	O60839|Q9UPZ5	Missense_Mutation	DNP	ENST00000490103.1	37	CCDS13859.1																																																																																			.		0.535	THOC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322097.1	NM_003678	
UHRF1	29128	hgsc.bcm.edu	37	19	4954681	4954681	+	RNA	SNP	G	G	C			TCGA-W5-AA2U-01A-11D-A417-09	TCGA-W5-AA2U-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	0792d270-49b3-4526-9045-86541d7cb765	b017d225-02d9-4581-be93-d2341687c3da	g.chr19:4954681G>C	ENST00000592666.1	+	0	2553							Q96T88	UHRF1_HUMAN	ubiquitin-like with PHD and ring finger domains 1						cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA repair (GO:0006281)|histone monoubiquitination (GO:0010390)|histone ubiquitination (GO:0016574)|maintenance of DNA methylation (GO:0010216)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity (GO:2000373)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autoubiquitination (GO:0051865)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|replication fork (GO:0005657)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|hemi-methylated DNA-binding (GO:0044729)|histone binding (GO:0042393)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|methyl-CpG binding (GO:0008327)|methylated histone binding (GO:0035064)|nucleosomal histone binding (GO:0031493)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|upper_aerodigestive_tract(2)	16				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0276)		CGAGCAGGGCGGGTCCCCGCG	0.682																																					.		.											.	.	.	0			.						.						8.0	10.0	9.0					19																	4954681		1813	4040	5853			29128	p.A672A			CAGGGCGGGTCCC	AF129507	CCDS74262.1, CCDS74263.1	19p13.3	2012-04-20	2008-08-14		ENSG00000034063	ENSG00000276043		"""RING-type (C3HC4) zinc fingers"""	12556	protein-coding gene	gene with protein product		607990				10646863	Standard	NM_001048201		Approved	ICBP90, Np95, FLJ21925, RNF106	uc002mbo.3	Q96T88			19.37:g.4954681G>C		Somatic	30	0		WXS	Illumina HiSeq	Phase_I	42	5	.	A0JBR2|A8K024|B2RBA9|Q2HIX7|Q8J022|Q9H6S6|Q9P115|Q9P1U7	Silent	SNP	ENST00000592666.1	37																																																																																				.		0.682	UHRF1-006	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000450444.1	NM_001048201	
