#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_NTotCov	i_NVarCov	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TranscriptID	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
AAR2	25980	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	20	34828481	34828481	+	Missense_Mutation	SNP	G	G	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr20:34828481G>A	ENST00000373932.3	+	2	1037	c.691G>A	c.(691-693)Gac>Aac	p.D231N	AAR2_ENST00000320849.4_Missense_Mutation_p.D231N|AAR2_ENST00000397286.3_Missense_Mutation_p.D231N	NM_015511.3	NP_056326.2	Q9Y312	AAR2_HUMAN	AAR2 splicing factor homolog (S. cerevisiae)	231																	GCACAGCATGGACCTGAGCTA	0.592																																					p.D231N		.											.	.	.	0			c.G691A						.						36.0	36.0	36.0					20																	34828481		2203	4300	6503	SO:0001583	missense	25980	exon2			AGCATGGACCTGA		CCDS13273.1	20q11.23	2012-07-20	2012-07-20	2012-07-20	ENSG00000131043	ENSG00000131043			15886	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 4"""	C20orf4			Standard	NM_015511		Approved	bA234K24.2	uc002xfc.3	Q9Y312	OTTHUMG00000032380	ENST00000373932.3:c.691G>A	20.37:g.34828481G>A	ENSP00000363043:p.Asp231Asn	55.0	0.0		40.0	13.0	NM_001271874	E1P5S7|Q9H4F9|Q9P1P3|Q9UFK9	Missense_Mutation	SNP	ENST00000373932.3	37	CCDS13273.1	.	.	.	.	.	.	.	.	.	.	G	32	5.184603	0.94885	.	.	ENSG00000131043	ENST00000397286;ENST00000320849;ENST00000373932	T;T;T	0.70045	-0.45;-0.45;-0.45	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	D	0.84862	0.5566	M	0.89353	3.025	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.87452	0.2402	10	0.87932	D	0	.	17.8963	0.88890	0.0:0.0:1.0:0.0	.	231;231	A2A2Q9;Q9Y312	.;CT004_HUMAN	N	231	ENSP00000380455:D231N;ENSP00000313674:D231N;ENSP00000363043:D231N	ENSP00000313674:D231N	D	+	1	0	C20orf4	34291895	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.959000	0.93110	2.775000	0.95449	0.655000	0.94253	GAC	.		0.592	AAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079001.2	NM_015511	
ACAD8	27034	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	134131730	134131730	+	Silent	SNP	T	T	C			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr11:134131730T>C	ENST00000281182.4	+	9	1144	c.1038T>C	c.(1036-1038)gaT>gaC	p.D346D	ACAD8_ENST00000374752.4_Silent_p.D219D|ACAD8_ENST00000524547.1_3'UTR|ACAD8_ENST00000537423.1_Silent_p.D269D|ACAD8_ENST00000543332.1_3'UTR	NM_014384.2	NP_055199.1	Q9UKU7	ACAD8_HUMAN	acyl-CoA dehydrogenase family, member 8	346					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|lipid metabolic process (GO:0006629)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|valine catabolic process (GO:0006574)	mitochondrial matrix (GO:0005759)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	14	all_hematologic(175;0.127)	all_cancers(12;8e-23)|all_epithelial(12;2.59e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|all_neural(223;0.0189)|Medulloblastoma(222;0.0245)|Esophageal squamous(93;0.0559)		Epithelial(10;1.92e-10)|all cancers(11;2.26e-09)|BRCA - Breast invasive adenocarcinoma(10;8.73e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00154)|Lung(977;0.21)	Flavin adenine dinucleotide(DB03147)	AGAGGAAGGATGCAGTGGCCT	0.562																																					p.D346D	GBM(65;238 1125 33403 41853 48889)	.											.	ACAD8	90	0			c.T1038C						.						140.0	102.0	115.0					11																	134131730		2201	4297	6498	SO:0001819	synonymous_variant	27034	exon9			GAAGGATGCAGTG	AF126245	CCDS8498.1	11q25	2014-09-17	2010-04-30		ENSG00000151498	ENSG00000151498			87	protein-coding gene	gene with protein product		604773	"""acyl-Coenzyme A dehydrogenase family, member 8"""			10524212	Standard	NM_014384		Approved		uc001qhk.3	Q9UKU7	OTTHUMG00000167177	ENST00000281182.4:c.1038T>C	11.37:g.134131730T>C		61.0	0.0		25.0	13.0	NM_014384	B7Z5W4|Q6ZWP6|Q9BUS8	Silent	SNP	ENST00000281182.4	37	CCDS8498.1																																																																																			.		0.562	ACAD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393607.1	NM_014384	
ADAMTS9	56999	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	64666990	64666990	+	Missense_Mutation	SNP	T	T	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr3:64666990T>A	ENST00000498707.1	-	3	908	c.566A>T	c.(565-567)cAg>cTg	p.Q189L	ADAMTS9_ENST00000295903.4_Missense_Mutation_p.Q189L|ADAMTS9_ENST00000459780.1_Missense_Mutation_p.Q189L	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	189					glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		ATCCATAGACTGTAGTGGTTC	0.468																																					p.Q189L		.											.	ADAMTS9	230	0			c.A566T						.						181.0	168.0	172.0					3																	64666990		2203	4300	6503	SO:0001583	missense	56999	exon3			ATAGACTGTAGTG	AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	13202	protein-coding gene	gene with protein product		605421	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"""			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.566A>T	3.37:g.64666990T>A	ENSP00000418735:p.Gln189Leu	176.0	0.0		156.0	74.0	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Missense_Mutation	SNP	ENST00000498707.1	37	CCDS2903.1	.	.	.	.	.	.	.	.	.	.	T	3.539	-0.094104	0.07053	.	.	ENSG00000163638	ENST00000295903;ENST00000498707;ENST00000459780	T;T;T	0.61392	0.3;0.31;0.11	6.04	2.18	0.27775	Peptidase M12B, propeptide (1);	0.382752	0.24769	N	0.035749	T	0.27933	0.0688	N	0.01800	-0.715	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.17198	-1.0377	10	0.23891	T	0.37	.	11.2942	0.49269	0.6405:0.0:0.0:0.3595	.	189;189;189;189	B7ZVX9;Q9P2N4-2;Q9P2N4-1;Q9P2N4	.;.;.;ATS9_HUMAN	L	189	ENSP00000295903:Q189L;ENSP00000418735:Q189L;ENSP00000419217:Q189L	ENSP00000295903:Q189L	Q	-	2	0	ADAMTS9	64642030	0.911000	0.30947	0.007000	0.13788	0.335000	0.28730	2.693000	0.47027	0.122000	0.18314	-0.527000	0.04329	CAG	.		0.468	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1		
ALG5	29880	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;mdanderson.org	37	13	37524129	37524129	+	Nonsense_Mutation	SNP	G	G	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr13:37524129G>A	ENST00000239891.3	-	10	991	c.925C>T	c.(925-927)Cga>Tga	p.R309*	ALG5_ENST00000443765.1_Nonsense_Mutation_p.R279*	NM_013338.4	NP_037470.1	Q9Y673	ALG5_HUMAN	ALG5, dolichyl-phosphate beta-glucosyltransferase	309					cellular protein metabolic process (GO:0044267)|determination of left/right symmetry (GO:0007368)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	dolichyl-phosphate beta-glucosyltransferase activity (GO:0004581)|oligosaccharyl transferase activity (GO:0004576)	p.R309*(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	11		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)		all cancers(112;5.79e-07)|Epithelial(112;1.81e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00785)|BRCA - Breast invasive adenocarcinoma(63;0.0127)|GBM - Glioblastoma multiforme(144;0.0472)		GTCAAATATCGAAGTCGTATA	0.358																																					p.R309X		.											.	ALG5	90	1	Substitution - Nonsense(1)	large_intestine(1)	c.C925T						.						85.0	83.0	84.0					13																	37524129		2203	4300	6503	SO:0001587	stop_gained	29880	exon10			AATATCGAAGTCG	AF088028	CCDS9361.1, CCDS45033.1	13q13.1	2013-02-22	2013-02-21		ENSG00000120697	ENSG00000120697	2.4.1.117	"""Glycosyltransferase family 2 domain containing"""	20266	protein-coding gene	gene with protein product		604565	"""asparagine-linked glycosylation 5 homolog (yeast, dolichyl-phosphate beta-glucosyltransferase)"", ""asparagine-linked glycosylation 5, dolichyl-phosphate beta-glucosyltransferase homolog (S. cerevisiae)"""			10359825	Standard	NM_013338		Approved	bA421P11.2	uc001uvy.3	Q9Y673	OTTHUMG00000016741	ENST00000239891.3:c.925C>T	13.37:g.37524129G>A	ENSP00000239891:p.Arg309*	52.0	0.0		31.0	16.0	NM_013338	B4DR37|Q5TBA6	Nonsense_Mutation	SNP	ENST00000239891.3	37	CCDS9361.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.245912	0.80024	.	.	ENSG00000120697	ENST00000443765;ENST00000239891	.	.	.	5.86	5.01	0.66863	.	0.054432	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.6453	0.62277	0.0:0.0:0.6013:0.3987	.	.	.	.	X	279;309	.	ENSP00000239891:R309X	R	-	1	2	ALG5	36422129	1.000000	0.71417	0.984000	0.44739	0.927000	0.56198	3.338000	0.52128	1.462000	0.47948	-0.182000	0.12963	CGA	.		0.358	ALG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044528.2	NM_013338	
AMY2A	279	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	104160634	104160634	+	Missense_Mutation	SNP	G	G	T	rs371720173		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr1:104160634G>T	ENST00000414303.2	+	2	291	c.227G>T	c.(226-228)aGa>aTa	p.R76I		NM_000699.2	NP_000690.1	P04746	AMYP_HUMAN	amylase, alpha 2A (pancreatic)	76					carbohydrate catabolic process (GO:0016052)|carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|calcium ion binding (GO:0005509)|chloride ion binding (GO:0031404)			endometrium(3)|kidney(1)|large_intestine(5)|liver(3)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0654)|all cancers(265;0.0808)|Epithelial(280;0.0921)|Lung(183;0.111)	Acarbose(DB00284)|Icodextrin(DB00702)|Miglitol(DB00491)	TGGTGGGAAAGATACCAACCA	0.353																																					p.R76I		.											.	AMY2A	92	0			c.G227T						.						170.0	155.0	160.0					1																	104160634		2201	4279	6480	SO:0001583	missense	279	exon2			GGGAAAGATACCA	BC007060	CCDS783.1	1p21.1	2012-10-02	2007-05-03		ENSG00000243480	ENSG00000243480	3.2.1.1		477	protein-coding gene	gene with protein product		104650	"""amylase, alpha 2A; pancreatic"""	AMY2		3260028	Standard	NM_000699		Approved		uc001dut.3	P04746	OTTHUMG00000011023	ENST00000414303.2:c.227G>T	1.37:g.104160634G>T	ENSP00000397582:p.Arg76Ile	414.0	0.0		307.0	107.0	NM_000699	B9EJG1|Q9UBH3	Missense_Mutation	SNP	ENST00000414303.2	37	CCDS783.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	22.0|22.0	4.230811|4.230811	0.79688|0.79688	.|.	.|.	ENSG00000243480|ENSG00000243480	ENST00000423678|ENST00000414303;ENST00000393932	.|D	.|0.98437	.|-4.93	3.47|3.47	3.47|3.47	0.39725|0.39725	.|Glycoside hydrolase, subgroup, catalytic domain (1);Glycosyl hydrolase, family 13, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycosyl hydrolase, family 13, subfamily, catalytic domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.99080|0.99080	0.9684|0.9684	M|M	0.92738|0.92738	3.34|3.34	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|0.999;1.0	D|D	0.99285|0.99285	1.0897|1.0897	5|10	.|0.87932	.|D	.|0	.|.	15.0729|15.0729	0.72053|0.72053	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|76;76	.|B9EJG1;P04746	.|.;AMYP_HUMAN	N|I	74|76	.|ENSP00000397582:R76I	.|ENSP00000377509:R76I	K|R	+|+	3|2	2|0	AMY2A|AMY2A	103962157|103962157	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.951000|0.951000	0.60555|0.60555	9.276000|9.276000	0.95745|0.95745	1.927000|1.927000	0.55829|0.55829	0.455000|0.455000	0.32223|0.32223	AAG|AGA	.		0.353	AMY2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030315.1	NM_000699	
ANGEL1	23357	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	14	77275409	77275409	+	Silent	SNP	T	T	C			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr14:77275409T>C	ENST00000251089.2	-	2	754	c.642A>G	c.(640-642)ccA>ccG	p.P214P	ANGEL1_ENST00000554941.1_5'Flank	NM_015305.3	NP_056120.2	Q9UNK9	ANGE1_HUMAN	angel homolog 1 (Drosophila)	214										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	22			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0285)		CACCATGATATGGTATTTCCA	0.562																																					p.P214P		.											.	ANGEL1	93	0			c.A642G						.						55.0	49.0	51.0					14																	77275409		2203	4300	6503	SO:0001819	synonymous_variant	23357	exon2			ATGATATGGTATT	AF111169	CCDS9852.1	14q24.3	2014-06-17		2005-08-04	ENSG00000013523	ENSG00000013523			19961	protein-coding gene	gene with protein product				KIAA0759		11943475	Standard	NM_015305		Approved	Ccr4e	uc001xsv.3	Q9UNK9	OTTHUMG00000171494	ENST00000251089.2:c.642A>G	14.37:g.77275409T>C		39.0	0.0		37.0	9.0	NM_015305	B4DWL7|O94859|Q8NCS9	Silent	SNP	ENST00000251089.2	37	CCDS9852.1																																																																																			.		0.562	ANGEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413712.2	NM_015305	
ARID1B	57492	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	157150470	157150470	+	Missense_Mutation	SNP	G	G	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr6:157150470G>A	ENST00000350026.5	+	2	1653	c.1652G>A	c.(1651-1653)gGc>gAc	p.G551D	ARID1B_ENST00000275248.4_Missense_Mutation_p.G493D|ARID1B_ENST00000367148.1_Missense_Mutation_p.G551D|ARID1B_ENST00000346085.5_Missense_Mutation_p.G551D	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	551					chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		GGTTCCTATGGCCCTCCAGGC	0.587																																					p.G551D		.											.	ARID1B	154	0			c.G1652A						.						93.0	85.0	87.0					6																	157150470		2203	4300	6503	SO:0001583	missense	57492	exon2			CCTATGGCCCTCC	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"""-"""	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.1652G>A	6.37:g.157150470G>A	ENSP00000055163:p.Gly551Asp	91.0	0.0		85.0	35.0	NM_017519	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	37	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	G	15.88	2.964519	0.53507	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248;ENST00000414678	T;T;T;T;T	0.03553	4.05;3.89;3.96;3.99;4.07	5.09	5.09	0.68999	.	0.186876	0.33327	N	0.005028	T	0.07863	0.0197	L	0.43923	1.385	0.38507	D	0.948366	D;D;D	0.76494	0.997;0.999;0.999	P;D;D	0.65323	0.861;0.934;0.934	T	0.22906	-1.0203	10	0.56958	D	0.05	.	18.8734	0.92325	0.0:0.0:1.0:0.0	.	551;551;493	Q8NFD5;Q8NFD5-2;G3XAA0	ARI1B_HUMAN;.;.	D	551;551;551;493;50	ENSP00000344546:G551D;ENSP00000055163:G551D;ENSP00000356116:G551D;ENSP00000275248:G493D;ENSP00000412835:G50D	ENSP00000275248:G493D	G	+	2	0	ARID1B	157192162	1.000000	0.71417	0.960000	0.40013	0.982000	0.71751	6.257000	0.72480	2.515000	0.84797	0.650000	0.86243	GGC	.		0.587	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732	
BBX	56987	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	3	107491784	107491817	+	Frame_Shift_Del	DEL	TTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	TTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	-	rs113054196|rs566303124|rs557240456		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	TTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	TTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr3:107491784_107491817delTTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	ENST00000325805.8	+	11	1503_1536	c.1216_1249delTTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	c.(1216-1251)tttcctgatttttcttattctgccagtagcaagatafs	p.FPDFSYSASSKI406fs	BBX_ENST00000402543.1_Frame_Shift_Del_p.FPDFSYSASSKI406fs|BBX_ENST00000406780.1_Frame_Shift_Del_p.FPDFSYSASSKI406fs|BBX_ENST00000416476.2_Intron|BBX_ENST00000415149.2_Frame_Shift_Del_p.FPDFSYSASSKI406fs			Q8WY36	BBX_HUMAN	bobby sox homolog (Drosophila)	406					bone development (GO:0060348)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(18)|ovary(4)|pancreas(1)|skin(2)	49			OV - Ovarian serous cystadenocarcinoma(3;0.112)			ATGTAGTCATTTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGATAATAATTAG	0.355																																					p.406_417del		.											.	BBX	94	0			c.1216_1249del						.																																			SO:0001589	frameshift_variant	56987	exon11			AGTCATTTTCCTG	AF168718	CCDS2950.1, CCDS46881.1, CCDS63712.1	3q13.1	2008-07-18			ENSG00000114439	ENSG00000114439			14422	protein-coding gene	gene with protein product	"""x 001 protein"""					11680820	Standard	NM_001142568		Approved	MDS001, HSPC339, HBP2	uc010hpr.4	Q8WY36	OTTHUMG00000150360	ENST00000325805.8:c.1216_1249delTTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	3.37:g.107491784_107491817delTTTCCTGATTTTTCTTATTCTGCCAGTAGCAAGA	ENSP00000319974:p.Phe406fs	122.0	0.0		69.0	7.0	NM_001142568	A2RRM7|Q2TAJ1|Q7L3J8|Q7LBY8|Q8NDB0|Q8WY35|Q9H0J6	Frame_Shift_Del	DEL	ENST00000325805.8	37	CCDS46881.1																																																																																			.		0.355	BBX-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317820.1	NM_020235	
CAPN3	825	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	15	42698136	42698151	+	Splice_Site	DEL	ACCAAGGTAGGTGTGT	ACCAAGGTAGGTGTGT	-	rs373194123		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	ACCAAGGTAGGTGTGT	ACCAAGGTAGGTGTGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr15:42698136_42698151delACCAAGGTAGGTGTGT	ENST00000397163.3	+	15	2014_2019	c.1795_1800delACCAAGGTAGGTGTGT	c.(1795-1800)accaagdel	p.TK599fs	CAPN3_ENST00000569136.1_5'UTR|CAPN3_ENST00000397204.4_5'UTR|CAPN3_ENST00000561817.1_Intron|CAPN3_ENST00000357568.3_Intron|RP11-164J13.1_ENST00000495723.1_RNA|CAPN3_ENST00000337571.4_Intron|CAPN3_ENST00000356316.3_Intron|CAPN3_ENST00000397200.4_Splice_Site_p.TK87fs|CAPN3_ENST00000318023.7_Intron|CAPN3_ENST00000349748.3_Intron	NM_000070.2	NP_000061.1	P20807	CAN3_HUMAN	calpain 3, (p94)	599	Linker.				apoptotic process (GO:0006915)|autolysis (GO:0001896)|cellular response to calcium ion (GO:0071277)|cellular response to salt stress (GO:0071472)|G1 to G0 transition involved in cell differentiation (GO:0070315)|muscle cell cellular homeostasis (GO:0046716)|muscle organ development (GO:0007517)|muscle structure development (GO:0061061)|myofibril assembly (GO:0030239)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein localization to membrane (GO:0072657)|proteolysis (GO:0006508)|regulation of catalytic activity (GO:0050790)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of myoblast differentiation (GO:0045661)|response to calcium ion (GO:0051592)|response to muscle activity (GO:0014850)|sarcomere organization (GO:0045214)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|myofibril (GO:0030016)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)|ligase regulator activity (GO:0055103)|peptidase activity (GO:0008233)|protein complex scaffold (GO:0032947)|signal transducer activity (GO:0004871)|sodium ion binding (GO:0031402)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	47		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		AAAGAAAAAAACCAAGGTAGGTGTGTGGGTAGAGAG	0.431																																					p.599_600del		.											.	CAPN3	514	0			c.1795_1800del	GRCh37	CI983047|CS052038	CAPN3	I|S	rs80338803	.																																			SO:0001630	splice_region_variant	825	exon15			AAAAAAACCAAGG	X85030	CCDS10085.1, CCDS10086.1, CCDS32207.1, CCDS45245.1, CCDS45246.1	15q15.1	2014-09-17			ENSG00000092529	ENSG00000092529	3.4.22.52	"""EF-hand domain containing"""	1480	protein-coding gene	gene with protein product		114240		LGMD2, LGMD2A		2555341, 7720071	Standard	NM_024344		Approved	CANP3, p94, nCL-1	uc001zpn.1	P20807	OTTHUMG00000130619	ENST00000397163.3:c.1800+1ACCAAGGTAGGTGTGT>-	15.37:g.42698136_42698151delACCAAGGTAGGTGTGT		148.0	0.0		60.0	17.0	NM_000070	A6H8K6|Q7L4R0|Q9BQC8|Q9BTU4|Q9Y5S6|Q9Y5S7	In_Frame_Del	DEL	ENST00000397163.3	37	CCDS45245.1																																																																																			.		0.431	CAPN3-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421075.1		Frame_Shift_Del
CCDC73	493860	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	11	32657339	32657339	+	Frame_Shift_Del	DEL	T	T	-			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr11:32657339delT	ENST00000335185.5	-	14	1131	c.1088delA	c.(1087-1089)aatfs	p.N363fs	CCDC73_ENST00000534415.1_5'UTR	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73	363										NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	51	Breast(20;0.112)					TGATAATTCATTTTTAATCTT	0.244																																					p.X363X		.											.	CCDC73	91	0			c.1088delA						.						38.0	35.0	36.0					11																	32657339		1763	4012	5775	SO:0001589	frameshift_variant	493860	exon14			AATTCATTTTTAA	AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714			23261	protein-coding gene	gene with protein product		612328					Standard	NM_001008391		Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279	ENST00000335185.5:c.1088delA	11.37:g.32657339delT	ENSP00000335325:p.Asn363fs	119.0	0.0		69.0	38.0	NM_001008391	Q6P5Q7|Q6ZMW0|Q86WE7	In_Frame_Del	DEL	ENST00000335185.5	37	CCDS41630.1																																																																																			.		0.244	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391	
CDH7	1005	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	18	63526260	63526260	+	Missense_Mutation	SNP	G	G	T			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr18:63526260G>T	ENST00000397968.2	+	9	1898	c.1472G>T	c.(1471-1473)tGt>tTt	p.C491F	CDH7_ENST00000323011.3_Missense_Mutation_p.C491F|CDH7_ENST00000536984.2_Missense_Mutation_p.C491F	NM_004361.2	NP_004352.2	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2	491	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(43)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	80		Esophageal squamous(42;0.129)				ACCACCGTCTGTGAAAATGCC	0.438																																					p.C491F		.											.	CDH7	94	0			c.G1472T						.						76.0	74.0	75.0					18																	63526260		2203	4300	6503	SO:0001583	missense	1005	exon9			CCGTCTGTGAAAA	AB035301	CCDS11993.1	18q22.1	2010-01-26			ENSG00000081138	ENSG00000081138		"""Cadherins / Major cadherins"""	1766	protein-coding gene	gene with protein product		605806				9615235	Standard	NM_033646		Approved		uc002ljz.3	Q9ULB5	OTTHUMG00000132800	ENST00000397968.2:c.1472G>T	18.37:g.63526260G>T	ENSP00000381058:p.Cys491Phe	164.0	0.0		127.0	49.0	NM_004361	Q9H157	Missense_Mutation	SNP	ENST00000397968.2	37	CCDS11993.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.575129	0.86542	.	.	ENSG00000081138	ENST00000323011;ENST00000536984;ENST00000397966;ENST00000397968	T;T;T	0.53423	0.62;0.62;0.62	5.32	5.32	0.75619	Cadherin (3);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.72293	0.3442	M	0.82056	2.57	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.75880	-0.3161	10	0.87932	D	0	.	19.347	0.94367	0.0:0.0:1.0:0.0	.	491;491	F5H5X9;Q9ULB5	.;CADH7_HUMAN	F	491	ENSP00000319166:C491F;ENSP00000443030:C491F;ENSP00000381058:C491F	ENSP00000319166:C491F	C	+	2	0	CDH7	61677240	1.000000	0.71417	0.961000	0.40146	0.978000	0.69477	9.666000	0.98612	2.648000	0.89879	0.467000	0.42956	TGT	.		0.438	CDH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256217.2	NM_033646	
CEACAM8	1088	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	19	43098033	43098033	+	Missense_Mutation	SNP	C	C	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr19:43098033C>A	ENST00000244336.5	-	2	185	c.84G>T	c.(82-84)tgG>tgT	p.W28C	LIPE-AS1_ENST00000594688.1_RNA|CEACAM8_ENST00000599005.1_Intron|LIPE-AS1_ENST00000594624.2_RNA	NM_001816.3	NP_001807.2	P31997	CEAM8_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 8	28					immune response (GO:0006955)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	16		Prostate(69;0.00899)				TGGGCGGGTTCCAGAAGGTGA	0.502																																					p.W28C		.											.	CEACAM8	91	0			c.G84T						.						105.0	98.0	100.0					19																	43098033		2203	4300	6503	SO:0001583	missense	1088	exon2			CGGGTTCCAGAAG	D90064	CCDS12610.1	19q13.2	2013-01-29			ENSG00000124469	ENSG00000124469		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1820	protein-coding gene	gene with protein product		615747		CGM6		2208113, 2306228	Standard	NM_001816		Approved	CD66b	uc002oud.2	P31997	OTTHUMG00000151124	ENST00000244336.5:c.84G>T	19.37:g.43098033C>A	ENSP00000244336:p.Trp28Cys	42.0	0.0		44.0	19.0	NM_001816	O60399|Q16574	Missense_Mutation	SNP	ENST00000244336.5	37	CCDS12610.1	.	.	.	.	.	.	.	.	.	.	c	13.17	2.157915	0.38119	.	.	ENSG00000124469	ENST00000244336	T	0.22336	1.96	1.63	1.63	0.23807	.	.	.	.	.	T	0.35740	0.0942	M	0.66939	2.045	0.20638	N	0.999872	D	0.56035	0.974	P	0.60117	0.869	T	0.07462	-1.0771	9	0.87932	D	0	.	6.707	0.23257	0.0:1.0:0.0:0.0	.	28	P31997	CEAM8_HUMAN	C	28	ENSP00000244336:W28C	ENSP00000244336:W28C	W	-	3	0	CEACAM8	47789873	0.516000	0.26218	0.146000	0.22360	0.618000	0.37518	1.947000	0.40293	1.205000	0.43262	0.313000	0.20887	TGG	.		0.502	CEACAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321430.1		
CISD3	284106	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	17	36887631	36887631	+	Missense_Mutation	SNP	A	A	C			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr17:36887631A>C	ENST00000439660.2	+	3	267	c.143A>C	c.(142-144)aAg>aCg	p.K48T	CISD3_ENST00000578573.1_3'UTR|RNA5SP440_ENST00000363245.1_RNA	NM_001136498.1	NP_001129970.1	P0C7P0	CISD3_HUMAN	CDGSH iron sulfur domain 3	48						mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|metal ion binding (GO:0046872)			endometrium(2)	2						ACCCCCATCAAGGTGGAGCTG	0.612																																					p.K48T		.											.	.	.	0			c.A143C						.						88.0	98.0	95.0					17																	36887631		692	1591	2283	SO:0001583	missense	284106	exon3			CCATCAAGGTGGA	AK097047	CCDS45662.1	17q12	2007-08-10				ENSG00000277972		"""CDGSH iron sulfur domain containing"""	27578	protein-coding gene	gene with protein product	"""mitoNEET related 2"""	611933				17376863, 17584744	Standard	NM_001136498		Approved	Miner2	uc010wds.1	P0C7P0		ENST00000439660.2:c.143A>C	17.37:g.36887631A>C	ENSP00000391402:p.Lys48Thr	38.0	0.0		22.0	11.0	NM_001136498		Missense_Mutation	SNP	ENST00000439660.2	37	CCDS45662.1	.	.	.	.	.	.	.	.	.	.	A	17.50	3.405223	0.62288	.	.	ENSG00000230055	ENST00000439660	.	.	.	4.86	2.62	0.31277	Iron sulphur-containing domain, CDGSH-type, subfamily (1);Iron sulphur-containing domain, CDGSH-type (1);	.	.	.	.	T	0.50854	0.1640	L	0.61387	1.9	0.32514	N	0.537194	P	0.43231	0.801	P	0.49012	0.598	T	0.59904	-0.7366	8	0.87932	D	0	-3.5241	6.1161	0.20127	0.7857:0.0:0.2143:0.0	.	48	P0C7P0	CISD3_HUMAN	T	48	.	ENSP00000391402:K48T	K	+	2	0	CISD3	34141157	0.997000	0.39634	0.995000	0.50966	0.816000	0.46133	1.512000	0.35812	0.242000	0.21303	0.454000	0.30748	AAG	.		0.612	CISD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441921.1		
DDX42	11325	broad.mit.edu;bcgsc.ca;mdanderson.org	37	17	61882440	61882440	+	Missense_Mutation	SNP	C	C	G			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr17:61882440C>G	ENST00000578681.1	+	8	1232	c.631C>G	c.(631-633)Cca>Gca	p.P211A	DDX42_ENST00000457800.2_Missense_Mutation_p.P211A|DDX42_ENST00000389924.2_Missense_Mutation_p.P211A|DDX42_ENST00000583590.1_Missense_Mutation_p.P211A|DDX42_ENST00000359353.5_Missense_Mutation_p.P92A	NM_007372.2	NP_031398.2	Q86XP3	DDX42_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 42	211					protein localization (GO:0008104)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)	46						GATTGACTATCCACCATTTGA	0.338																																					p.P211A		.											.	DDX42	230	0			c.C631G						.						114.0	86.0	95.0					17																	61882440		2203	4300	6503	SO:0001583	missense	11325	exon7			GACTATCCACCAT	BC015505	CCDS32704.1	17q23	2014-02-14	2013-05-13			ENSG00000198231		"""DEAD-boxes"""	18676	protein-coding gene	gene with protein product	"""splicing factor 3b, subunit 8"""	613369	"""DEAD (Asp-Glu-Ala-Asp) box polypeptide 42"""			10727850, 16397294	Standard	NM_007372		Approved	RNAHP, RHELP, SF3b125, SF3B8	uc002jbv.3	Q86XP3		ENST00000578681.1:c.631C>G	17.37:g.61882440C>G	ENSP00000464050:p.Pro211Ala	144.0	2.0		180.0	15.0	NM_203499	A6NML1|A8KA43|O75619|Q68G51|Q96BK1|Q96HR7|Q9Y3V8	Missense_Mutation	SNP	ENST00000578681.1	37	CCDS32704.1	.	.	.	.	.	.	.	.	.	.	C	10.19	1.281692	0.23392	.	.	ENSG00000198231	ENST00000389924;ENST00000457800	T;T	0.20069	2.1;2.1	6.17	6.17	0.99709	.	0.314175	0.40385	N	0.001104	T	0.15609	0.0376	N	0.25426	0.745	0.47476	D	0.999439	B	0.17268	0.021	B	0.15052	0.012	T	0.10753	-1.0616	10	0.15952	T	0.53	-8.6707	14.6754	0.68975	0.1449:0.8551:0.0:0.0	.	211	Q86XP3	DDX42_HUMAN	A	211	ENSP00000374574:P211A;ENSP00000390121:P211A	ENSP00000374574:P211A	P	+	1	0	DDX42	59236172	0.997000	0.39634	1.000000	0.80357	0.997000	0.91878	2.927000	0.48900	2.941000	0.99782	0.655000	0.94253	CCA	.		0.338	DDX42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444368.1	NM_007372	
DNAH5	1767	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	13700904	13700904	+	Missense_Mutation	SNP	T	T	C			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr5:13700904T>C	ENST00000265104.4	-	78	13672	c.13568A>G	c.(13567-13569)gAc>gGc	p.D4523G		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4523					cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					AGAAATGTCGTCCTTCATCCA	0.463									Kartagener syndrome																												p.D4523G		.											.	DNAH5	182	0			c.A13568G						.						184.0	170.0	174.0					5																	13700904		2203	4300	6503	SO:0001583	missense	1767	exon78	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	ATGTCGTCCTTCA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.13568A>G	5.37:g.13700904T>C	ENSP00000265104:p.Asp4523Gly	118.0	0.0		88.0	31.0	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.250156	0.80024	.	.	ENSG00000039139	ENST00000265104	T	0.09255	3.0	5.95	5.95	0.96441	Dynein heavy chain (1);	0.049262	0.85682	D	0.000000	T	0.19604	0.0471	L	0.55743	1.74	0.80722	D	1	B	0.28552	0.215	B	0.39465	0.3	T	0.01608	-1.1313	10	0.87932	D	0	.	16.4323	0.83853	0.0:0.0:0.0:1.0	.	4523	Q8TE73	DYH5_HUMAN	G	4523	ENSP00000265104:D4523G	ENSP00000265104:D4523G	D	-	2	0	DNAH5	13753904	1.000000	0.71417	0.985000	0.45067	0.989000	0.77384	7.992000	0.88273	2.281000	0.76405	0.528000	0.53228	GAC	.		0.463	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
EGF	1950	broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	110862303	110862303	+	Splice_Site	SNP	T	T	C			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr4:110862303T>C	ENST00000265171.5	+	2	772		c.e2+2		EGF_ENST00000503392.1_Splice_Site|EGF_ENST00000502723.1_Splice_Site|EGF_ENST00000509793.1_Splice_Site	NM_001178130.1|NM_001963.4	NP_001171601.1|NP_001954.2	P01133	EGF_HUMAN	epidermal growth factor						activation of MAPKK activity (GO:0000186)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|DNA replication (GO:0006260)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mammary gland alveolus development (GO:0060749)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of secretion (GO:0051048)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)|positive regulation of DNA binding (GO:0043388)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of calcium ion import (GO:0090279)|regulation of protein localization to cell surface (GO:2000008)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sucralfate(DB00364)	AGGCAAGAGGTAAAATACCCT	0.308																																					.		.											.	EGF	524	0			c.327+2T>C						.						38.0	40.0	39.0					4																	110862303		2203	4300	6503	SO:0001630	splice_region_variant	1950	exon2			AAGAGGTAAAATA	X04571	CCDS3689.1, CCDS54794.1, CCDS54795.1	4q25	2012-10-02	2010-05-11		ENSG00000138798	ENSG00000138798			3229	protein-coding gene	gene with protein product		131530	"""epidermal growth factor (beta-urogastrone)"""				Standard	NM_001963		Approved		uc003hzy.4	P01133	OTTHUMG00000132044	ENST00000265171.5:c.327+2T>C	4.37:g.110862303T>C		62.0	1.0		26.0	14.0	NM_001178130	B4DRK7|E7EVD2|E9PBF0|Q52LZ6	Splice_Site	SNP	ENST00000265171.5	37	CCDS3689.1	.	.	.	.	.	.	.	.	.	.	T	16.14	3.039941	0.55003	.	.	ENSG00000138798	ENST00000509793;ENST00000265171;ENST00000503392	.	.	.	4.9	4.9	0.64082	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5246	0.67878	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	EGF	111081752	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	5.678000	0.68153	1.844000	0.53588	0.402000	0.26972	.	.		0.308	EGF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255065.1		Intron
FAM104A	84923	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	71208818	71208818	+	Intron	SNP	G	G	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr17:71208818G>A	ENST00000403627.3	-	3	382				FAM104A_ENST00000583178.1_Intron|FAM104A_ENST00000580032.1_Splice_Site_p.A17V|FAM104A_ENST00000581110.1_Intron|FAM104A_ENST00000405159.3_Splice_Site_p.A128V|FAM104A_ENST00000583024.1_Intron	NM_032837.2	NP_116226.2	Q969W3	F104A_HUMAN	family with sequence similarity 104, member A											endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6			LUSC - Lung squamous cell carcinoma(166;0.197)			GAAACCCACCGCGCAGAACGC	0.393																																					p.A128V		.											.	.	.	0			c.C383T						.						145.0	141.0	142.0					17																	71208818		1872	4095	5967	SO:0001627	intron_variant	84923	exon3			CCCACCGCGCAGA	AK027681	CCDS11693.2, CCDS45766.1, CCDS74143.1, CCDS74144.1	17q25.1	2005-12-16			ENSG00000133193	ENSG00000133193			25918	protein-coding gene	gene with protein product							Standard	NM_032837		Approved	FLJ14775	uc002jjj.4	Q969W3	OTTHUMG00000150564	ENST00000403627.3:c.322-2911C>T	17.37:g.71208818G>A		105.0	0.0		88.0	29.0	NM_001098832	B4E339	Missense_Mutation	SNP	ENST00000403627.3	37	CCDS11693.2	.	.	.	.	.	.	.	.	.	.	G	8.869	0.948798	0.18356	.	.	ENSG00000133193	ENST00000405159	T	0.46819	0.86	5.17	-2.07	0.07276	.	.	.	.	.	T	0.33118	0.0852	.	.	.	0.39723	D	0.971497	B	0.15719	0.014	B	0.09377	0.004	T	0.03175	-1.1064	8	0.48119	T	0.1	.	7.2665	0.26232	0.3617:0.1142:0.5241:0.0	.	128	Q969W3-2	.	V	128	ENSP00000384832:A128V	ENSP00000384832:A128V	A	-	2	0	FAM104A	68720413	0.302000	0.24454	0.016000	0.15963	0.653000	0.38743	0.098000	0.15189	-0.849000	0.04158	-1.731000	0.00696	GCG	.		0.393	FAM104A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318935.1	NM_032837	
EXOC7	23265	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	74085293	74085293	+	Missense_Mutation	SNP	T	T	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr17:74085293T>A	ENST00000335146.7	-	9	1216	c.1163A>T	c.(1162-1164)gAg>gTg	p.E388V	EXOC7_ENST00000607838.1_Missense_Mutation_p.E360V|EXOC7_ENST00000589210.1_Missense_Mutation_p.E337V|EXOC7_ENST00000411744.2_Missense_Mutation_p.E329V|EXOC7_ENST00000467929.2_Missense_Mutation_p.E296V|EXOC7_ENST00000405575.4_Missense_Mutation_p.E360V|EXOC7_ENST00000332065.5_Missense_Mutation_p.E306V			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7	388					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)				NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	14			LUSC - Lung squamous cell carcinoma(166;0.187)			CTGGTGGTGCTCGGGGATGAT	0.627																																					p.E388V		.											.	EXOC7	90	0			c.A1163T						.						105.0	105.0	105.0					17																	74085293		2203	4300	6503	SO:0001583	missense	23265	exon9			TGGTGCTCGGGGA	BC029432	CCDS11741.1, CCDS32738.1, CCDS45781.1, CCDS45782.1, CCDS45784.1, CCDS74164.1	17q25.3	2013-01-22			ENSG00000182473	ENSG00000182473			23214	protein-coding gene	gene with protein product		608163				12477932	Standard	NM_001013839		Approved	EXO70, KIAA1067, YJL085W, Exo70p	uc010wsw.2	Q9UPT5	OTTHUMG00000150720	ENST00000335146.7:c.1163A>T	17.37:g.74085293T>A	ENSP00000334100:p.Glu388Val	40.0	0.0		35.0	16.0	NM_001145297	B5MC69|B8XXP2|Q8ND93|Q8WV91|Q96FF0|Q9H8C3|Q9H9X3|Q9HA32	Missense_Mutation	SNP	ENST00000335146.7	37	CCDS45782.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.758980	0.89843	.	.	ENSG00000182473	ENST00000332065;ENST00000351709;ENST00000405575;ENST00000335146;ENST00000357231;ENST00000425372;ENST00000411744	.	.	.	4.98	4.98	0.66077	Cullin repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.72574	0.3477	M	0.70595	2.14	0.80722	D	1	P;B;D;P;B;P;B	0.57571	0.572;0.24;0.98;0.727;0.03;0.835;0.24	B;B;P;B;B;P;B	0.56088	0.349;0.092;0.791;0.266;0.045;0.65;0.062	T	0.73681	-0.3906	9	0.39692	T	0.17	-34.598	14.6773	0.68989	0.0:0.0:0.0:1.0	.	329;360;296;296;388;306;337	Q9UPT5-5;Q9UPT5-6;B4DJ07;F5H1P1;Q9UPT5;Q9UPT5-2;Q9UPT5-1	.;.;.;.;EXOC7_HUMAN;.;.	V	306;226;360;388;337;296;329	.	ENSP00000333806:E306V	E	-	2	0	EXOC7	71596888	1.000000	0.71417	0.992000	0.48379	0.935000	0.57460	7.571000	0.82399	1.864000	0.54056	0.455000	0.32223	GAG	.		0.627	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	NM_015219	
FNDC1	84624	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	159655130	159655130	+	Silent	SNP	C	C	T			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr6:159655130C>T	ENST00000297267.9	+	11	3786	c.3586C>T	c.(3586-3588)Ctg>Ttg	p.L1196L	FNDC1_ENST00000340366.6_Silent_p.L1133L	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1196					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		AGAAGACCTTCTGTCTTCCTC	0.617																																					p.L1196L		.											.	FNDC1	138	0			c.C3586T						.						22.0	25.0	24.0					6																	159655130		1886	4090	5976	SO:0001819	synonymous_variant	84624	exon11			GACCTTCTGTCTT	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"""Fibronectin type III domain containing"""	21184	protein-coding gene	gene with protein product		609991	"""fibronectin type III domain containing 2"""	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.3586C>T	6.37:g.159655130C>T		64.0	0.0		38.0	19.0	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Silent	SNP	ENST00000297267.9	37	CCDS47512.1	.	.	.	.	.	.	.	.	.	.	C	5.706	0.314817	0.10789	.	.	ENSG00000164694	ENST00000329629	.	.	.	4.85	0.59	0.17458	.	.	.	.	.	T	0.08846	0.0219	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.32613	-0.9900	4	.	.	.	-7.7516	3.3856	0.07270	0.2295:0.4522:0.229:0.0893	.	.	.	.	F	1091	.	.	S	+	2	0	FNDC1	159575120	0.001000	0.12720	0.000000	0.03702	0.125000	0.20455	0.559000	0.23485	0.415000	0.25817	-0.244000	0.11960	TCT	.		0.617	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
GPD1L	23171	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	32181733	32181733	+	Missense_Mutation	SNP	G	G	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr3:32181733G>A	ENST00000282541.5	+	4	581	c.380G>A	c.(379-381)gGc>gAc	p.G127D		NM_015141.3	NP_055956.1	Q8N335	GPD1L_HUMAN	glycerol-3-phosphate dehydrogenase 1-like	127					carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|glycerol-3-phosphate catabolic process (GO:0046168)|glycerophospholipid biosynthetic process (GO:0046474)|NAD metabolic process (GO:0019674)|NADH metabolic process (GO:0006734)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase C signaling (GO:0090038)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate (GO:0002027)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|ventricular cardiac muscle cell action potential (GO:0086005)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycerol-3-phosphate dehydrogenase complex (GO:0009331)|plasma membrane (GO:0005886)	glycerol-3-phosphate dehydrogenase [NAD+] activity (GO:0004367)|ion channel binding (GO:0044325)|NAD binding (GO:0051287)|sodium channel regulator activity (GO:0017080)			large_intestine(4)|lung(7)|ovary(1)	12						ATAGACGAGGGCCCCGAGGGG	0.507																																					p.G127D		.											.	GPD1L	90	0			c.G380A						.						175.0	185.0	182.0					3																	32181733		2203	4300	6503	SO:0001583	missense	23171	exon4			ACGAGGGCCCCGA	D42047	CCDS33729.1	3p22.3	2014-09-17			ENSG00000152642	ENSG00000152642			28956	protein-coding gene	gene with protein product		611778				7788527	Standard	NM_015141		Approved	KIAA0089	uc003cew.3	Q8N335	OTTHUMG00000155846	ENST00000282541.5:c.380G>A	3.37:g.32181733G>A	ENSP00000282541:p.Gly127Asp	76.0	0.0		57.0	16.0	NM_015141	A8K9U3|Q14702|Q9BRM5	Missense_Mutation	SNP	ENST00000282541.5	37	CCDS33729.1	.	.	.	.	.	.	.	.	.	.	G	18.52	3.641917	0.67244	.	.	ENSG00000152642	ENST00000429432;ENST00000282541;ENST00000425459;ENST00000431009	T;T;T;T	0.56611	0.45;0.45;0.65;0.45	5.46	5.46	0.80206	Glycerol-3-phosphate dehydrogenase, NAD-dependent, N-terminal (1);NAD(P)-binding domain (1);	0.094278	0.64402	D	0.000001	T	0.53254	0.1785	L	0.60067	1.865	0.80722	D	1	P	0.44309	0.832	B	0.40940	0.344	T	0.51803	-0.8659	10	0.30854	T	0.27	-17.0625	19.6998	0.96048	0.0:0.0:1.0:0.0	.	127	Q8N335	GPD1L_HUMAN	D	88;127;80;88	ENSP00000393861:G88D;ENSP00000282541:G127D;ENSP00000408770:G80D;ENSP00000416518:G88D	ENSP00000282541:G127D	G	+	2	0	GPD1L	32156737	1.000000	0.71417	0.997000	0.53966	0.977000	0.68977	9.736000	0.98828	2.728000	0.93425	0.655000	0.94253	GGC	.		0.507	GPD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341975.2	NM_015141	
GRM8	2918	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	126086303	126086303	+	Missense_Mutation	SNP	G	G	A	rs139289550		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr7:126086303G>A	ENST00000339582.2	-	10	3362	c.2554C>T	c.(2554-2556)Cgc>Tgc	p.R852C	GRM8_ENST00000444921.2_Missense_Mutation_p.R852C|GRM8_ENST00000358373.3_Missense_Mutation_p.R852C			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	852					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of cAMP biosynthetic process (GO:0030818)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(16)|lung(62)|ovary(5)|pancreas(1)|prostate(1)|skin(14)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(4)	125		Prostate(267;0.186)				CTCCTCTTGCGTTTTTGAACA	0.418										HNSCC(24;0.065)																											p.R852C		.											.	GRM8	581	0			c.C2554T						.	G	CYS/ARG,CYS/ARG	0,4406		0,0,2203	137.0	126.0	130.0		2554,2554	5.9	1.0	7	dbSNP_134	130	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	GRM8	NM_000845.2,NM_001127323.1	180,180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	852/909,852/909	126086303	1,13005	2203	4300	6503	SO:0001583	missense	2918	exon9			TCTTGCGTTTTTG		CCDS5794.1, CCDS47696.1	7q31.3-q32.1	2012-08-29			ENSG00000179603	ENSG00000179603		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4600	protein-coding gene	gene with protein product		601116				8824806	Standard	NM_000845		Approved	GLUR8, GPRC1H, mGlu8, MGLUR8	uc003vlr.2	O00222	OTTHUMG00000022888	ENST00000339582.2:c.2554C>T	7.37:g.126086303G>A	ENSP00000344173:p.Arg852Cys	155.0	0.0		112.0	48.0	NM_000845	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	Missense_Mutation	SNP	ENST00000339582.2	37	CCDS5794.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.774220	0.90108	0.0	1.16E-4	ENSG00000179603	ENST00000339582;ENST00000444921;ENST00000358373	D;D;D	0.89552	-2.45;-2.45;-2.53	5.93	5.93	0.95920	GPCR, family 3, C-terminal (1);	0.022582	0.85682	D	0.000000	D	0.93187	0.7830	M	0.66297	2.02	0.80722	D	1	D;D	0.76494	0.999;0.998	P;P	0.59703	0.862;0.836	D	0.93269	0.6650	10	0.87932	D	0	.	19.3421	0.94347	0.0:0.0:1.0:0.0	.	852;852	O00222-2;O00222	.;GRM8_HUMAN	C	852	ENSP00000344173:R852C;ENSP00000409790:R852C;ENSP00000351142:R852C	ENSP00000344173:R852C	R	-	1	0	GRM8	125873539	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.638000	0.67861	2.826000	0.97356	0.655000	0.94253	CGC	G|1.000;A|0.000		0.418	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4		
HAPLN1	1404	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	82940454	82940454	+	Missense_Mutation	SNP	C	C	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr5:82940454C>A	ENST00000274341.4	-	4	1353	c.503G>T	c.(502-504)gGg>gTg	p.G168V		NM_001884.3	NP_001875.1	P10915	HPLN1_HUMAN	hyaluronan and proteoglycan link protein 1	168	Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|liver(1)|lung(15)|ovary(1)|prostate(1)|skin(1)	34		Lung NSC(167;0.0484)|all_lung(232;0.0522)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;7.82e-42)|Epithelial(54;5.88e-35)|all cancers(79;1.14e-29)	Hyaluronan(DB08818)	ATTGTAGCGCCCCAGTCGTGG	0.552																																					p.G168V		.											.	HAPLN1	580	0			c.G503T						.						34.0	32.0	33.0					5																	82940454		2203	4300	6503	SO:0001583	missense	1404	exon4			TAGCGCCCCAGTC		CCDS4061.1	5q14.3	2013-01-11	2004-03-16	2004-03-17	ENSG00000145681	ENSG00000145681		"""Immunoglobulin superfamily / V-set domain containing"""	2380	protein-coding gene	gene with protein product	"""Cartilage link protein"", ""hyaluronan and proteoglycan link protein 1"""	115435	"""cartilage linking protein 1"""	CRTL1		2286376, 2320422	Standard	NM_001884		Approved		uc003kin.3	P10915	OTTHUMG00000119045	ENST00000274341.4:c.503G>T	5.37:g.82940454C>A	ENSP00000274341:p.Gly168Val	68.0	0.0		44.0	20.0	NM_001884	B2R9A9	Missense_Mutation	SNP	ENST00000274341.4	37	CCDS4061.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.020264	0.93462	.	.	ENSG00000145681	ENST00000274341;ENST00000510978;ENST00000508307;ENST00000503117	T;T;T;T	0.13420	2.59;2.59;2.59;2.59	5.8	5.8	0.92144	C-type lectin fold (1);Link (3);C-type lectin-like (1);	0.000000	0.85682	D	0.000000	T	0.53706	0.1813	H	0.95294	3.65	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.67304	-0.5704	10	0.87932	D	0	.	20.0608	0.97674	0.0:1.0:0.0:0.0	.	168	P10915	HPLN1_HUMAN	V	168;168;168;167	ENSP00000274341:G168V;ENSP00000422592:G168V;ENSP00000421341:G168V;ENSP00000426610:G167V	ENSP00000274341:G168V	G	-	2	0	HAPLN1	82976210	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.466000	0.80914	2.733000	0.93635	0.650000	0.86243	GGG	.		0.552	HAPLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239256.2	NM_001884	
HDGFRP2	84717	broad.mit.edu;ucsc.edu;mdanderson.org	37	19	4498350	4498350	+	Missense_Mutation	SNP	T	T	C			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr19:4498350T>C	ENST00000301284.4	+	12	1514	c.1450T>C	c.(1450-1452)Ttt>Ctt	p.F484L	HDGFRP2_ENST00000586684.1_Missense_Mutation_p.F484L	NM_001001520.1|NM_032631.2	NP_001001520|NP_116020.1	Q7Z4V5	HDGR2_HUMAN		484					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										TGAGATCAAGTTTGCCCTAAA	0.642																																					p.F484L		.											.	.	.	0			c.T1450C						.						45.0	47.0	47.0					19																	4498350		2039	4195	6234	SO:0001583	missense	0	exon12			ATCAAGTTTGCCC																												ENST00000301284.4:c.1450T>C	19.37:g.4498350T>C	ENSP00000301284:p.Phe484Leu	26.0	0.0		10.0	4.0	NM_032631	I3L080|K7EQZ6|Q96GI5|Q9BW08	Missense_Mutation	SNP	ENST00000301284.4	37	CCDS42472.1	.	.	.	.	.	.	.	.	.	.	T	15.79	2.937733	0.52972	.	.	ENSG00000167674	ENST00000301284	T	0.43294	0.95	4.95	3.91	0.45181	Transcription factor IIS, N-terminal (1);	0.172702	0.52532	D	0.000079	T	0.39253	0.1071	L	0.50333	1.59	0.39496	D	0.968122	B;B	0.22346	0.068;0.068	B;B	0.28849	0.095;0.095	T	0.29882	-0.9997	10	0.56958	D	0.05	.	10.7825	0.46386	0.0:0.0:0.1598:0.8402	.	484;484	C9JEE1;Q7Z4V5	.;HDGR2_HUMAN	L	484	ENSP00000301284:F484L	ENSP00000301284:F484L	F	+	1	0	AC011498.1	4449350	1.000000	0.71417	0.998000	0.56505	0.748000	0.42578	1.340000	0.33896	0.716000	0.32124	0.444000	0.29173	TTT	.		0.642	HDGFRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458642.1		
HK2	3099	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	75081454	75081454	+	Missense_Mutation	SNP	A	A	G			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr2:75081454A>G	ENST00000290573.2	+	2	698	c.98A>G	c.(97-99)gAt>gGt	p.D33G	HK2_ENST00000409174.1_Missense_Mutation_p.D5G	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	33	Hexokinase type-1 1.|Regulatory.				apoptotic mitochondrial changes (GO:0008637)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|lactation (GO:0007595)|regulation of glucose import (GO:0046324)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	43						CGCCTCTCTGATGAGACCCTC	0.502																																					p.D33G		.											.	HK2	252	0			c.A98G						.						228.0	238.0	234.0					2																	75081454		2203	4300	6503	SO:0001583	missense	3099	exon2			TCTCTGATGAGAC		CCDS1956.1	2p13	2010-03-19			ENSG00000159399	ENSG00000159399	2.7.1.1		4923	protein-coding gene	gene with protein product		601125					Standard	NM_000189		Approved		uc002snd.3	P52789	OTTHUMG00000129972	ENST00000290573.2:c.98A>G	2.37:g.75081454A>G	ENSP00000290573:p.Asp33Gly	101.0	0.0		73.0	7.0	NM_000189	D6W5J2|Q8WU87|Q9UN82	Missense_Mutation	SNP	ENST00000290573.2	37	CCDS1956.1	.	.	.	.	.	.	.	.	.	.	A	17.81	3.480340	0.63849	.	.	ENSG00000159399	ENST00000290573;ENST00000535740;ENST00000409174	D;D	0.98249	-4.82;-4.82	5.13	5.13	0.70059	Hexokinase, N-terminal (1);	0.169639	0.49916	D	0.000128	D	0.98166	0.9394	M	0.64630	1.985	0.80722	D	1	D	0.53619	0.961	P	0.59288	0.855	D	0.98296	1.0516	10	0.52906	T	0.07	-22.2667	12.941	0.58345	1.0:0.0:0.0:0.0	.	33	P52789	HXK2_HUMAN	G	33;33;5	ENSP00000290573:D33G;ENSP00000387140:D5G	ENSP00000290573:D33G	D	+	2	0	HK2	74934962	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	8.761000	0.91691	2.153000	0.67306	0.459000	0.35465	GAT	.		0.502	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2	NM_000189	
HIBCH	26275	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;mdanderson.org	37	2	191110920	191110920	+	Nonsense_Mutation	SNP	T	T	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr2:191110920T>A	ENST00000359678.5	-	10	1063	c.769A>T	c.(769-771)Aag>Tag	p.K257*	HIBCH_ENST00000392332.3_Nonsense_Mutation_p.K257*|HIBCH_ENST00000410045.1_Nonsense_Mutation_p.K34*	NM_014362.3|NM_198047.2	NP_055177.2|NP_932164.1	Q6NVY1	HIBCH_HUMAN	3-hydroxyisobutyryl-CoA hydrolase	257					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|valine catabolic process (GO:0006574)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	3-hydroxyisobutyryl-CoA hydrolase activity (GO:0003860)			NS(1)|breast(2)|endometrium(1)|large_intestine(1)|lung(5)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	13			OV - Ovarian serous cystadenocarcinoma(117;0.000586)|Epithelial(96;0.0286)|all cancers(119;0.0814)			ATAAAAGACTTGTCTCGATCA	0.249																																					p.K257X		.											.	HIBCH	90	0			c.A769T						.						80.0	78.0	79.0					2																	191110920		2198	4294	6492	SO:0001587	stop_gained	26275	exon10			AAGACTTGTCTCG	U66669	CCDS2304.1, CCDS46475.1	2q32.3	2010-04-29	2010-04-29		ENSG00000198130	ENSG00000198130	3.1.2.4		4908	protein-coding gene	gene with protein product		610690	"""3-hydroxyisobutyryl-Coenzyme A hydrolase"""			8824301	Standard	NM_014362		Approved		uc002uru.3	Q6NVY1	OTTHUMG00000132673	ENST00000359678.5:c.769A>T	2.37:g.191110920T>A	ENSP00000352706:p.Lys257*	97.0	0.0		95.0	40.0	NM_014362	D3DPI4|Q53GA8|Q53GF2|Q53RF7|Q53TC6|Q92931|Q9BS94	Nonsense_Mutation	SNP	ENST00000359678.5	37	CCDS2304.1	.	.	.	.	.	.	.	.	.	.	T	39	7.798293	0.98495	.	.	ENSG00000198130	ENST00000392332;ENST00000359678;ENST00000410045;ENST00000416732;ENST00000409820	.	.	.	4.73	4.73	0.59995	.	0.418322	0.27715	N	0.018156	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-21.0883	12.3549	0.55169	0.0:0.0:0.0:1.0	.	.	.	.	X	257;257;34;8;37	.	ENSP00000352706:K257X	K	-	1	0	HIBCH	190819165	1.000000	0.71417	0.987000	0.45799	0.800000	0.45204	5.426000	0.66476	2.108000	0.64289	0.533000	0.62120	AAG	.		0.249	HIBCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255933.1		
HS3ST1	9957	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	4	11401189	11401189	+	Silent	SNP	T	T	C			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr4:11401189T>C	ENST00000002596.5	-	2	1615	c.441A>G	c.(439-441)cgA>cgG	p.R147R		NM_005114.2	NP_005105.1	O14792	HS3S1_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	147					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)|sulfotransferase activity (GO:0008146)	p.L146_D148delLRD(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|skin(3)	15						CCGACGGGTCTCGCAGGATGA	0.592																																					p.R147R		.											.	HS3ST1	91	1	Deletion - In frame(1)	liver(1)	c.A441G						.						63.0	59.0	61.0					4																	11401189		2203	4300	6503	SO:0001819	synonymous_variant	9957	exon2			CGGGTCTCGCAGG	AF019386	CCDS3408.1	4p16	2008-02-05			ENSG00000002587	ENSG00000002587	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5194	protein-coding gene	gene with protein product		603244				9988767	Standard	NM_005114		Approved	3OST1	uc003gmq.3	O14792	OTTHUMG00000090547	ENST00000002596.5:c.441A>G	4.37:g.11401189T>C		59.0	0.0		46.0	20.0	NM_005114	B3KUA6|Q6PEY8	Silent	SNP	ENST00000002596.5	37	CCDS3408.1																																																																																			.		0.592	HS3ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207073.3	NM_005114	
IGFBP4	3487	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	38610218	38610218	+	Silent	SNP	G	G	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr17:38610218G>A	ENST00000269593.4	+	3	821	c.546G>A	c.(544-546)ctG>ctA	p.L182L	IGFBP4_ENST00000542955.1_Silent_p.L82L	NM_001552.2	NP_001543.2	P22692	IBP4_HUMAN	insulin-like growth factor binding protein 4	182	Thyroglobulin type-1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|DNA metabolic process (GO:0006259)|inflammatory response (GO:0006954)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of MAPK cascade (GO:0043410)|regulation of cell growth (GO:0001558)|regulation of glucose metabolic process (GO:0010906)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|type B pancreatic cell proliferation (GO:0044342)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|endometrium(1)|kidney(1)|large_intestine(2)	5		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)			ACCGGGCGCTGGAGCGGCTGG	0.657																																					p.L182L	GBM(160;940 3581 26177)	.											.	IGFBP4	522	0			c.G546A						.						57.0	60.0	59.0					17																	38610218		2203	4298	6501	SO:0001819	synonymous_variant	3487	exon3			GGCGCTGGAGCGG	M38177	CCDS11367.1	17q21.2	2014-09-16	2001-11-28		ENSG00000141753	ENSG00000141753			5473	protein-coding gene	gene with protein product	"""IGF-binding protein 4"""	146733	"""insulin-like growth factor-binding protein 4"""			1707125, 1704481	Standard	NM_001552		Approved	IBP4, BP-4, HT29-IGFBP, IGFBP-4	uc002hus.3	P22692	OTTHUMG00000133326	ENST00000269593.4:c.546G>A	17.37:g.38610218G>A		29.0	0.0		17.0	6.0	NM_001552	A0N9W2|B4E351|Q5U012|Q9UCL6	Silent	SNP	ENST00000269593.4	37	CCDS11367.1																																																																																			.		0.657	IGFBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257134.1	NM_001552	
KAAG1	353219	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	24358008	24358008	+	Silent	SNP	T	T	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr6:24358008T>A	ENST00000274766.1	+	1	878	c.141T>A	c.(139-141)gcT>gcA	p.A47A	DCDC2_ENST00000378454.3_5'UTR	NM_181337.3	NP_851854.1	Q9UBP8	KAAG1_HUMAN	kidney associated antigen 1	47					immune response (GO:0006955)					central_nervous_system(1)|lung(1)|prostate(1)	3						CTCAGCTCGCTGCTTCGCGTC	0.672																																					p.A47A		.											.	KAAG1	90	0			c.T141A						.						25.0	27.0	26.0					6																	24358008		2199	4294	6493	SO:0001819	synonymous_variant	353219	exon1			GCTCGCTGCTTCG	AF181722	CCDS4551.1	6p22.1	2010-11-23			ENSG00000146049	ENSG00000146049			21031	protein-coding gene	gene with protein product		608211				10601354	Standard	NM_181337		Approved	RU2, RU2AS	uc003ndz.1	Q9UBP8	OTTHUMG00000014354	ENST00000274766.1:c.141T>A	6.37:g.24358008T>A		32.0	0.0		23.0	5.0	NM_181337		Silent	SNP	ENST00000274766.1	37	CCDS4551.1																																																																																			.		0.672	KAAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040001.1		
LPO	4025	broad.mit.edu;ucsc.edu	37	17	56332171	56332171	+	Splice_Site	SNP	G	G	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr17:56332171G>A	ENST00000262290.4	+	9	1421		c.e9-1		LPO_ENST00000421678.2_Splice_Site|LPO_ENST00000582328.1_Splice_Site|LPO_ENST00000543544.1_Splice_Site	NM_006151.2	NP_006142.1	P22079	PERL_HUMAN	lactoperoxidase						defense response to bacterium (GO:0042742)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|hydrogen peroxide catabolic process (GO:0042744)|response to oxidative stress (GO:0006979)|thiocyanate metabolic process (GO:0018969)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|thiocyanate peroxidase activity (GO:0036393)			breast(5)|cervix(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30						TGGGCTTTCAGGAGATTCTCG	0.572																																					.		.											.	LPO	91	0			c.857-1G>A						.						65.0	63.0	63.0					17																	56332171		2203	4300	6503	SO:0001630	splice_region_variant	4025	exon7			CTTTCAGGAGATT	M58151	CCDS32689.1, CCDS54149.1	17q23.1	2008-02-05				ENSG00000167419	1.11.1.7		6678	protein-coding gene	gene with protein product		150205				2222811, 8964511	Standard	NM_006151		Approved	SPO	uc002ivt.3	P22079		ENST00000262290.4:c.1106-1G>A	17.37:g.56332171G>A		49.0	0.0		33.0	4.0	NM_001160102	A5JUY4|E7EMJ3|Q13408|Q3KNQ2	Splice_Site	SNP	ENST00000262290.4	37	CCDS32689.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.611701	0.87258	.	.	ENSG00000167419	ENST00000262290;ENST00000421678;ENST00000543544;ENST00000389576	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.4336	0.90636	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	LPO	53687170	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	9.373000	0.97168	2.832000	0.97577	0.655000	0.94253	.	.		0.572	LPO-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443961.1		Intron
LRP1B	53353	ucsc.edu;bcgsc.ca	37	2	141299516	141299516	+	Missense_Mutation	SNP	T	T	C			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr2:141299516T>C	ENST00000389484.3	-	44	8190	c.7219A>G	c.(7219-7221)Act>Gct	p.T2407A		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2407					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)		CTGAGGAAAGTCCCTGGCCCA	0.363										TSP Lung(27;0.18)																											p.T2407A	Colon(99;50 2074 2507 20106)	.											.	LRP1B	311	0			c.A7219G						.						66.0	63.0	64.0					2																	141299516		2203	4298	6501	SO:0001583	missense	53353	exon44			GGAAAGTCCCTGG	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.7219A>G	2.37:g.141299516T>C	ENSP00000374135:p.Thr2407Ala	117.0	2.0		83.0	33.0	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	T	9.999	1.233081	0.22626	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.90732	-2.72	5.46	4.3	0.51218	Six-bladed beta-propeller, TolB-like (1);	0.067460	0.56097	U	0.000026	D	0.84853	0.5564	L	0.36672	1.1	0.33510	D	0.591073	B	0.06786	0.001	B	0.04013	0.001	T	0.82333	-0.0509	10	0.32370	T	0.25	.	11.4448	0.50116	0.0:0.0712:0.0:0.9288	.	2407	Q9NZR2	LRP1B_HUMAN	A	2407;2345	ENSP00000374135:T2407A	ENSP00000374135:T2407A	T	-	1	0	LRP1B	141015986	1.000000	0.71417	0.861000	0.33841	0.115000	0.19883	3.379000	0.52440	0.893000	0.36288	0.402000	0.26972	ACT	.		0.363	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
MAGEC3	139081	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	140953292	140953292	+	Silent	SNP	C	C	T			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chrX:140953292C>T	ENST00000298296.1	+	2	159	c.159C>T	c.(157-159)gcC>gcT	p.A53A		NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	53								p.A53A(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					ACTATTCTGCCTTTCATCTTG	0.512																																					p.A53A		.											.	MAGEC3	555	1	Substitution - coding silent(1)	kidney(1)	c.C159T						.						190.0	150.0	164.0					X																	140953292		2203	4300	6503	SO:0001819	synonymous_variant	139081	exon2			TTCTGCCTTTCAT	AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 2"""	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.159C>T	X.37:g.140953292C>T		59.0	0.0		30.0	23.0	NM_138702	Q3SYA7|Q5JZ43|Q9BZ80	Silent	SNP	ENST00000298296.1	37	CCDS14676.1																																																																																			.		0.512	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702	
MAGEL2	54551	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	15	23889381	23889381	+	Missense_Mutation	SNP	C	C	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr15:23889381C>A	ENST00000532292.1	-	1	1794	c.1700G>T	c.(1699-1701)aGg>aTg	p.R567M		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2	450					Arp2/3 complex-mediated actin nucleation (GO:0034314)|protein K63-linked ubiquitination (GO:0070534)|retrograde transport, endosome to Golgi (GO:0042147)	endosome (GO:0005768)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)		AGGGATTCGCCTGTACTCTAG	0.502																																					p.R1170M		.											.	.	.	0			c.G3509T						.						49.0	49.0	49.0					15																	23889381		1910	4132	6042	SO:0001583	missense	54551	exon1			ATTCGCCTGTACT	AJ243531	CCDS73700.1	15q11-q12	2008-07-18				ENSG00000254585			6814	protein-coding gene	gene with protein product		605283		NDNL1		10556298	Standard	NM_019066		Approved	nM15	uc001ywj.4	Q9UJ55		ENST00000532292.1:c.1700G>T	15.37:g.23889381C>A	ENSP00000433433:p.Arg567Met	50.0	0.0		27.0	12.0	NM_019066		Missense_Mutation	SNP	ENST00000532292.1	37		.	.	.	.	.	.	.	.	.	.	C	15.88	2.963694	0.53507	.	.	ENSG00000254585	ENST00000532292	.	.	.	4.57	3.64	0.41730	.	.	.	.	.	T	0.66307	0.2776	M	0.91406	3.205	0.22737	N	0.998791	.	.	.	.	.	.	T	0.60480	-0.7255	5	.	.	.	.	7.8955	0.29704	0.0:0.8906:0.0:0.1094	.	.	.	.	C	599	.	.	G	-	1	0	MAGEL2	21440474	0.657000	0.27393	0.914000	0.36105	0.909000	0.53808	0.950000	0.29122	2.545000	0.85829	0.462000	0.41574	GGC	.		0.502	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395182.2	NM_019066	
MIB1	57534	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	18	19359600	19359600	+	Missense_Mutation	SNP	A	A	T			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr18:19359600A>T	ENST00000261537.6	+	6	1126	c.862A>T	c.(862-864)Att>Ttt	p.I288F	MIB1_ENST00000578646.1_3'UTR|AC091038.1_ENST00000582102.1_RNA	NM_020774.2	NP_065825.1	Q86YT6	MIB1_HUMAN	mindbomb E3 ubiquitin protein ligase 1	288					blood vessel development (GO:0001568)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|negative regulation of neuron differentiation (GO:0045665)|neural tube formation (GO:0001841)|Notch signaling pathway (GO:0007219)|positive regulation of endocytosis (GO:0045807)|somitogenesis (GO:0001756)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|ovary(5)	27			STAD - Stomach adenocarcinoma(5;0.212)			TGTTTGTGGCATTGATGAAGA	0.378																																					p.I288F		.											.	MIB1	526	0			c.A862T						.						303.0	266.0	279.0					18																	19359600		2203	4300	6503	SO:0001583	missense	57534	exon6			TGTGGCATTGATG	AB037744	CCDS11871.1	18q11.2	2014-09-17	2012-02-23		ENSG00000101752	ENSG00000101752		"""Zinc fingers, ZZ-type"", ""Ankyrin repeat domain containing"""	21086	protein-coding gene	gene with protein product		608677	"""mindbomb homolog 1 (Drosophila)"""				Standard	NM_020774		Approved	DIP-1, MIB, KIAA1323, ZZANK2, ZZZ6	uc002ktq.3	Q86YT6	OTTHUMG00000131753	ENST00000261537.6:c.862A>T	18.37:g.19359600A>T	ENSP00000261537:p.Ile288Phe	180.0	0.0		149.0	54.0	NM_020774	B0YJ38|Q2TB37|Q68D01|Q6YI51|Q8NBY0|Q8TCB5|Q8TCL7|Q9P2M3	Missense_Mutation	SNP	ENST00000261537.6	37	CCDS11871.1	.	.	.	.	.	.	.	.	.	.	A	19.31	3.802349	0.70682	.	.	ENSG00000101752	ENST00000261537	T	0.44482	0.92	4.65	4.65	0.58169	.	0.000000	0.85682	D	0.000000	T	0.58395	0.2119	M	0.84326	2.69	0.80722	D	1	P	0.40431	0.717	P	0.49047	0.599	T	0.65335	-0.6193	10	0.62326	D	0.03	-13.8232	14.365	0.66801	1.0:0.0:0.0:0.0	.	288	Q86YT6	MIB1_HUMAN	F	288	ENSP00000261537:I288F	ENSP00000261537:I288F	I	+	1	0	MIB1	17613598	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.279000	0.95777	1.869000	0.54173	0.240000	0.17902	ATT	.		0.378	MIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254675.1	NM_020774	
KMT2D	8085	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	12	49425062	49425062	+	Frame_Shift_Del	DEL	T	T	-			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr12:49425062delT	ENST00000301067.7	-	39	13425	c.13426delA	c.(13426-13428)actfs	p.T4476fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	4476					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										CCCCGCCCAGTGCTGAGTTGC	0.607																																					p.T4476fs		.											.	MLL2	612	0			c.13426delA						.						71.0	77.0	75.0					12																	49425062		2049	4201	6250	SO:0001589	frameshift_variant	8085	exon39			GCCCAGTGCTGAG	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.13426delA	12.37:g.49425062delT	ENSP00000301067:p.Thr4476fs	54.0	0.0		42.0	20.0	NM_003482	O14687	Frame_Shift_Del	DEL	ENST00000301067.7	37	CCDS44873.1																																																																																			.		0.607	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
MRPL45	84311	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	17	36478418	36478418	+	Silent	SNP	G	G	C			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr17:36478418G>C	ENST00000312513.5	+	8	1022	c.861G>C	c.(859-861)ctG>ctC	p.L287L	GPR179_ENST00000584976.1_5'Flank	NM_032351.4	NP_115727.4	Q9BRJ2	RM45_HUMAN	mitochondrial ribosomal protein L45	287						mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	13	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				GCCCTCAGCTGAAACCAGAAG	0.542											OREG0024353	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L287L		.											.	MRPL45	90	0			c.G861C						.						67.0	67.0	67.0					17																	36478418		2203	4300	6503	SO:0001819	synonymous_variant	84311	exon8			TCAGCTGAAACCA	BC006235	CCDS11326.1, CCDS74047.1	17q21.2	2014-05-06			ENSG00000174100	ENSG00000278845		"""Mitochondrial ribosomal proteins / large subunits"""	16651	protein-coding gene	gene with protein product		611850				11551941, 12706105	Standard	XM_006725366		Approved	MGC11321	uc002hpy.3	Q9BRJ2	OTTHUMG00000188489	ENST00000312513.5:c.861G>C	17.37:g.36478418G>C		51.0	0.0	863	41.0	20.0	NM_032351	A1L436|Q6ZMJ5	Silent	SNP	ENST00000312513.5	37	CCDS11326.1																																																																																			.		0.542	MRPL45-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256792.3	NM_032351	
MTSS1	9788	hgsc.bcm.edu;broad.mit.edu	37	8	125565827	125565828	+	In_Frame_Ins	INS	-	-	TAT			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr8:125565827_125565828insTAT	ENST00000518547.1	-	14	2146_2147	c.1673_1674insATA	c.(1672-1674)tac>taATAc	p.557_558ins*	MTSS1_ENST00000524090.1_In_Frame_Ins_p.447_448ins*|MTSS1_ENST00000325064.5_In_Frame_Ins_p.561_562ins*|NDUFB9_ENST00000522532.1_Intron|MTSS1_ENST00000354184.4_In_Frame_Ins_p.275_276ins*|MTSS1_ENST00000431961.2_In_Frame_Ins_p.275_276ins*|MTSS1_ENST00000523587.1_5'UTR|MTSS1_ENST00000395508.2_In_Frame_Ins_p.331_332ins*|MTSS1_ENST00000378017.3_In_Frame_Ins_p.532_533ins*	NM_001282971.1|NM_014751.4	NP_001269900.1|NP_055566.3	O43312	MTSS1_HUMAN	metastasis suppressor 1	557					actin cytoskeleton organization (GO:0030036)|actin filament polymerization (GO:0030041)|adherens junction maintenance (GO:0034334)|bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|cellular response to fluid shear stress (GO:0071498)|epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)|filopodium assembly (GO:0046847)|glomerulus morphogenesis (GO:0072102)|in utero embryonic development (GO:0001701)|magnesium ion homeostasis (GO:0010960)|microspike assembly (GO:0030035)|negative regulation of epithelial cell proliferation (GO:0050680)|nephron tubule epithelial cell differentiation (GO:0072160)|positive regulation of actin filament bundle assembly (GO:0032233)|renal tubule morphogenesis (GO:0061333)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			ACATCCGTCGGTAGGACTGGCT	0.55																																					p.Y558delinsX	Esophageal Squamous(160;622 1893 3862 8546 12509)	.											.	MTSS1	91	0			c.1674_1675insATA						.																																			SO:0001652	inframe_insertion	9788	exon14			CCGTCGGTAGGAC	AF086645	CCDS6353.1, CCDS64968.1, CCDS64969.1	8p22	2008-02-05			ENSG00000170873	ENSG00000170873			20443	protein-coding gene	gene with protein product		608486				12482861, 12082544	Standard	XM_005251111		Approved	KIAA0429, MIMA, MIMB, MIM	uc003yrk.2	O43312	OTTHUMG00000048189	ENST00000518547.1:c.1673_1674insATA	8.37:g.125565827_125565828insTAT	ENSP00000429064:p.Tyr558*	121.0	0.0		91.0	34.0	NM_014751	J3KNK6|Q8TCA2|Q96RX2	Nonsense_Mutation	INS	ENST00000518547.1	37	CCDS6353.1																																																																																			.		0.550	MTSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109625.3	NM_014751	
MYF6	4618	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	81101780	81101780	+	Silent	SNP	G	G	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr12:81101780G>A	ENST00000228641.3	+	1	504	c.282G>A	c.(280-282)cgG>cgA	p.R94R		NM_002469.2	NP_002460.1	P23409	MYF6_HUMAN	myogenic factor 6 (herculin)	94	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				muscle cell differentiation (GO:0042692)|muscle cell fate commitment (GO:0042693)|muscle tissue morphogenesis (GO:0060415)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle cell differentiation (GO:0035914)|skeletal muscle tissue development (GO:0007519)|skeletal muscle tissue regeneration (GO:0043403)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|skin(1)	26						CCACTGACCGGCGAAAAGCCG	0.627																																					p.R94R		.											.	MYF6	90	0			c.G282A						.						34.0	40.0	38.0					12																	81101780		2202	4300	6502	SO:0001819	synonymous_variant	4618	exon1			TGACCGGCGAAAA		CCDS9019.1	12q21	2013-05-21				ENSG00000111046		"""Basic helix-loop-helix proteins"""	7566	protein-coding gene	gene with protein product	"""muscle-specific regulatory factor 4"""	159991				8978788	Standard	NM_002469		Approved	MRF4, bHLHc4	uc001szf.2	P23409		ENST00000228641.3:c.282G>A	12.37:g.81101780G>A		26.0	0.0		25.0	8.0	NM_002469	B2R898|Q53X80|Q6FHI9	Silent	SNP	ENST00000228641.3	37	CCDS9019.1																																																																																			.		0.627	MYF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407756.1	NM_002469	
NABP1	64859	ucsc.edu;bcgsc.ca	37	2	192543347	192543347	+	Missense_Mutation	SNP	A	A	G			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr2:192543347A>G	ENST00000425611.2	+	1	90	c.7A>G	c.(7-9)Agg>Ggg	p.R3G	NABP1_ENST00000410026.2_Intron|NABP1_ENST00000409510.1_Intron	NM_001031716.2	NP_001026886.1	Q96AH0	SOSB2_HUMAN	nucleic acid binding protein 1	3					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SOSS complex (GO:0070876)	RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)										CAATATGAATAGGGTCAACGA	0.537																																					p.R3G		.											.	.	.	0			c.A7G						.						28.0	35.0	33.0					2																	192543347		2203	4300	6503	SO:0001583	missense	64859	exon1			ATGAATAGGGTCA	BC017114	CCDS33352.1, CCDS58745.1	2q32.3	2012-06-19	2012-06-19	2012-06-19	ENSG00000173559	ENSG00000173559			26232	protein-coding gene	gene with protein product	"""single-stranded DNA-binding protein 2"", ""sensor of single-strand DNA complex subunit B2"""	612103	"""oligonucleotide/oligosaccharide-binding fold containing 2A"""	OBFC2A			Standard	NM_001031716		Approved	FLJ22833, DKFZp667M1322, FLJ13624, MGC111163, SSB2, hSSB2, SOSS-B2	uc002usx.3	Q96AH0	OTTHUMG00000132720	ENST00000425611.2:c.7A>G	2.37:g.192543347A>G	ENSP00000403683:p.Arg3Gly	31.0	0.0		26.0	4.0	NM_001031716	Q658Y8|Q9H5X6	Missense_Mutation	SNP	ENST00000425611.2	37	CCDS33352.1	.	.	.	.	.	.	.	.	.	.	A	3.293	-0.144436	0.06627	.	.	ENSG00000173559	ENST00000425611	T	0.39787	1.06	5.51	4.62	0.57501	.	0.519985	0.19723	N	0.107552	T	0.16471	0.0396	N	0.02011	-0.69	0.22737	N	0.998791	B	0.02656	0.0	B	0.01281	0.0	T	0.17018	-1.0383	10	0.21540	T	0.41	.	8.2915	0.31960	0.0861:0.1564:0.7575:0.0	.	3	Q96AH0	SOSB2_HUMAN	G	3	ENSP00000403683:R3G	ENSP00000307968:R3G	R	+	1	2	OBFC2A	192251592	0.999000	0.42202	0.993000	0.49108	0.432000	0.31715	2.239000	0.43079	1.287000	0.44583	-0.242000	0.12053	AGG	.		0.537	NABP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256060.1	NM_022837	
NDNL2	56160	broad.mit.edu;mdanderson.org	37	15	29561699	29561699	+	Missense_Mutation	SNP	C	C	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr15:29561699C>A	ENST00000332303.4	-	1	334	c.211G>T	c.(211-213)Gcc>Tcc	p.A71S	FAM189A1_ENST00000261275.4_Intron	NM_138704.3	NP_619649.1	Q96MG7	MAGG1_HUMAN	necdin-like 2	71					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)|regulation of growth (GO:0040008)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Smc5-Smc6 complex (GO:0030915)				breast(3)|large_intestine(2)|lung(3)	8		all_lung(180;4.69e-11)|Breast(32;0.0013)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00736)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		gcggcctgggcccggcgggcg	0.701											OREG0032044	type=REGULATORY REGION|TFbs=RELA|Dataset=RELA (p65) ChIP-PET Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with paired-end diTag sequencing (ChIP-PET)																									p.A71S		.											.	NDNL2	90	0			c.G211T						.						17.0	19.0	18.0					15																	29561699		2193	4287	6480	SO:0001583	missense	56160	exon1			CCTGGGCCCGGCG	AF490510	CCDS10023.1	15q13.1	2008-02-01			ENSG00000185115	ENSG00000185115			7677	protein-coding gene	gene with protein product		608243				18086888	Standard	NM_138704		Approved	HCA4, MAGEG1, MAGEL3, NSE3, NSMCE3	uc001zco.3	Q96MG7	OTTHUMG00000129261	ENST00000332303.4:c.211G>T	15.37:g.29561699C>A	ENSP00000330694:p.Ala71Ser	20.0	0.0	810	14.0	7.0	NM_138704	Q8IW16|Q8TEI6|Q9H214	Missense_Mutation	SNP	ENST00000332303.4	37	CCDS10023.1	.	.	.	.	.	.	.	.	.	.	C	2.263	-0.368859	0.05069	.	.	ENSG00000185115	ENST00000332303	T	0.02763	4.17	3.06	-1.9	0.07665	.	.	.	.	.	T	0.01124	0.0037	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46843	-0.9162	9	0.02654	T	1	.	5.3054	0.15801	0.4141:0.454:0.0:0.1319	.	71	Q96MG7	MAGG1_HUMAN	S	71	ENSP00000330694:A71S	ENSP00000330694:A71S	A	-	1	0	NDNL2	27348991	0.001000	0.12720	0.000000	0.03702	0.010000	0.07245	-0.586000	0.05787	-0.395000	0.07715	-0.520000	0.04383	GCC	.		0.701	NDNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251370.1	NM_138704	
NEB	4703	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	152499357	152499357	+	Silent	SNP	T	T	C			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr2:152499357T>C	ENST00000172853.10	-	59	8334	c.8187A>G	c.(8185-8187)aaA>aaG	p.K2729K	NEB_ENST00000397345.3_Silent_p.K2729K|NEB_ENST00000604864.1_Silent_p.K2729K|NEB_ENST00000409198.1_Silent_p.K2729K|NEB_ENST00000603639.1_Silent_p.K2729K|NEB_ENST00000427231.2_Silent_p.K2729K			P20929	NEBU_HUMAN	nebulin	2729					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TGGTTTTATCTTTATCCCAAG	0.348																																					p.K2729K		.											.	NEB	145	0			c.A8187G						.						48.0	47.0	47.0					2																	152499357		1829	4080	5909	SO:0001819	synonymous_variant	4703	exon59			TTTATCTTTATCC	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.8187A>G	2.37:g.152499357T>C		88.0	0.0		73.0	22.0	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				.		0.348	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
NEB	4703	broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	152525647	152525647	+	Splice_Site	SNP	T	T	G			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr2:152525647T>G	ENST00000172853.10	-	39	4654		c.e39-2		NEB_ENST00000397345.3_Splice_Site|NEB_ENST00000604864.1_Splice_Site|NEB_ENST00000409198.1_Splice_Site|NEB_ENST00000603639.1_Splice_Site|NEB_ENST00000427231.2_Splice_Site			P20929	NEBU_HUMAN	nebulin						muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		GTAGTTCAACTAAAAACAAAG	0.383																																					.		.											.	NEB	145	0			c.4507-2A>C						.						91.0	87.0	88.0					2																	152525647		1901	4137	6038	SO:0001630	splice_region_variant	4703	exon40			TTCAACTAAAAAC	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.4507-2A>C	2.37:g.152525647T>G		97.0	1.0		79.0	27.0	NM_001164507	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Splice_Site	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	T	17.09	3.300397	0.60195	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	.	.	.	5.85	5.85	0.93711	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2421	0.82418	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	NEB	152233893	1.000000	0.71417	0.961000	0.40146	0.661000	0.39034	6.446000	0.73460	2.234000	0.73211	0.533000	0.62120	.	.		0.383	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	Intron
NLGN3	54413	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	70389592	70389592	+	Missense_Mutation	SNP	A	A	G			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chrX:70389592A>G	ENST00000358741.3	+	8	2495	c.2192A>G	c.(2191-2193)tAc>tGc	p.Y731C	NLGN3_ENST00000536169.1_Missense_Mutation_p.Y691C|NLGN3_ENST00000374051.3_Missense_Mutation_p.Y711C|NLGN3_ENST00000476589.1_3'UTR	NM_181303.1	NP_851820.1	Q9NZ94	NLGN3_HUMAN	neuroligin 3	731					adult behavior (GO:0030534)|axon extension (GO:0048675)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|oligodendrocyte differentiation (GO:0048709)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor-mediated endocytosis (GO:0006898)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term synaptic potentiation (GO:1900271)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of synaptic transmission (GO:0050804)|regulation of terminal button organization (GO:2000331)|rhythmic synaptic transmission (GO:0060024)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse organization (GO:0050808)|visual learning (GO:0008542)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|endocytic vesicle (GO:0030139)|excitatory synapse (GO:0060076)|integral component of plasma membrane (GO:0005887)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			biliary_tract(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	37	Renal(35;0.156)					GCCCTCTACTACCGTAAGGAC	0.642																																					p.Y731C	Esophageal Squamous(103;760 1488 16849 22250 40351)	.											.	NLGN3	131	0			c.A2192G						.						28.0	25.0	26.0					X																	70389592		2203	4300	6503	SO:0001583	missense	54413	exon8			TCTACTACCGTAA	AB040913	CCDS14407.1, CCDS55441.1, CCDS55442.1	Xq13.1	2008-08-01			ENSG00000196338	ENSG00000196338			14289	protein-coding gene	gene with protein product		300336				10767552, 10819331	Standard	NM_181303		Approved	HNL3, KIAA1480, ASPGX1, AUTSX1	uc004dzd.2	Q9NZ94	OTTHUMG00000021790	ENST00000358741.3:c.2192A>G	X.37:g.70389592A>G	ENSP00000351591:p.Tyr731Cys	36.0	0.0		23.0	20.0	NM_181303	B2RBK1|D2X2H6|D3DVV0|D3DVV1|Q86V51|Q8NCD0|Q9NZ95|Q9NZ96|Q9NZ97|Q9P248	Missense_Mutation	SNP	ENST00000358741.3	37	CCDS55441.1	.	.	.	.	.	.	.	.	.	.	A	17.38	3.373920	0.61735	.	.	ENSG00000196338	ENST00000536169;ENST00000374051;ENST00000358741	T;T;T	0.78481	-1.18;-1.18;-1.18	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	D	0.88698	0.6507	M	0.86268	2.805	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.997;0.999	D	0.90571	0.4522	10	0.87932	D	0	.	14.0645	0.64819	1.0:0.0:0.0:0.0	.	691;731;711	D3DVV1;Q9NZ94;Q9NZ94-2	.;NLGN3_HUMAN;.	C	691;711;731	ENSP00000445298:Y691C;ENSP00000363163:Y711C;ENSP00000351591:Y731C	ENSP00000351591:Y731C	Y	+	2	0	NLGN3	70306317	1.000000	0.71417	0.992000	0.48379	0.995000	0.86356	9.139000	0.94554	1.897000	0.54924	0.352000	0.21897	TAC	.		0.642	NLGN3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057121.1	NM_018977	
NLRP12	91662	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	54307234	54307234	+	Missense_Mutation	SNP	G	G	T			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr19:54307234G>T	ENST00000324134.6	-	6	2725	c.2557C>A	c.(2557-2559)Cac>Aac	p.H853N	NLRP12_ENST00000354278.3_Missense_Mutation_p.H853N|NLRP12_ENST00000345770.5_Missense_Mutation_p.H854N|NLRP12_ENST00000391772.1_Missense_Mutation_p.H854N|NLRP12_ENST00000535162.1_Missense_Mutation_p.H853N|NLRP12_ENST00000391775.3_Missense_Mutation_p.H853N|NLRP12_ENST00000391773.1_Missense_Mutation_p.H854N|NLRP12_ENST00000351894.4_Missense_Mutation_p.H853N	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	853					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		CAGACTGGGTGCCTCAGTCCC	0.478																																					p.C853S		.											.	NLRP12	211	0			c.T2557A						.						85.0	70.0	75.0					19																	54307234		2203	4300	6503	SO:0001583	missense	91662	exon6			CTGGGTGCCTCAG	AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"""Nucleotide-binding domain and leucine rich repeat containing"""	22938	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"""	609648	"""NACHT, leucine rich repeat and PYD containing 12"""	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.2557C>A	19.37:g.54307234G>T	ENSP00000319377:p.His853Asn	50.0	0.0		30.0	10.0	NM_144687	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Missense_Mutation	SNP	ENST00000324134.6	37	CCDS12864.1	.	.	.	.	.	.	.	.	.	.	G	11.08	1.533586	0.27387	.	.	ENSG00000142405	ENST00000324134;ENST00000535162;ENST00000351894;ENST00000354278;ENST00000358661;ENST00000391775;ENST00000391773;ENST00000345770;ENST00000391772	T;T;T;T;T;T;T	0.49432	1.05;1.05;0.78;0.78;1.05;1.05;0.78	4.52	2.3	0.28687	.	0.458810	0.15793	N	0.244365	T	0.40909	0.1136	L	0.45698	1.435	0.09310	N	1	B;B;B;B;B	0.20368	0.009;0.044;0.005;0.009;0.006	B;B;B;B;B	0.24155	0.012;0.051;0.011;0.012;0.023	T	0.39057	-0.9632	10	0.56958	D	0.05	.	10.1919	0.43032	0.0:0.0:0.6431:0.3569	.	854;136;853;853;853	F2Z321;P59046-5;A8K407;A8MTQ2;P59046	.;.;.;.;NAL12_HUMAN	N	853;853;853;853;136;853;854;854;854	ENSP00000319377:H853N;ENSP00000438030:H853N;ENSP00000340473:H853N;ENSP00000346231:H853N;ENSP00000375655:H853N;ENSP00000375653:H854N;ENSP00000375652:H854N	ENSP00000319377:H853N	H	-	1	0	NLRP12	58999046	0.167000	0.22975	0.014000	0.15608	0.640000	0.38277	1.890000	0.39728	0.576000	0.29452	0.442000	0.29010	CAC	.		0.478	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687	
NLRP5	126206	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	56539102	56539102	+	Silent	SNP	G	G	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr19:56539102G>A	ENST00000390649.3	+	7	1503	c.1503G>A	c.(1501-1503)ctG>ctA	p.L501L		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	501	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		TCACAGGCCTGCACGCCGCTT	0.637																																					p.L501L		.											.	NLRP5	162	0			c.G1503A						.						33.0	35.0	34.0					19																	56539102		2126	4223	6349	SO:0001819	synonymous_variant	126206	exon7			AGGCCTGCACGCC	AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"""Nucleotide-binding domain and leucine rich repeat containing"""	21269	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"""	609658	"""NACHT, leucine rich repeat and PYD containing 5"""	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.1503G>A	19.37:g.56539102G>A		58.0	1.0		41.0	17.0	NM_153447	A8MTY4|Q86W29	Silent	SNP	ENST00000390649.3	37	CCDS12938.1																																																																																			.		0.637	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
OPRM1	4988	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	154411035	154411035	+	Missense_Mutation	SNP	C	C	G			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr6:154411035C>G	ENST00000330432.7	+	2	602	c.365C>G	c.(364-366)aCc>aGc	p.T122S	OPRM1_ENST00000337049.4_Missense_Mutation_p.T122S|OPRM1_ENST00000435918.2_Missense_Mutation_p.T122S|OPRM1_ENST00000434900.2_Missense_Mutation_p.T215S|OPRM1_ENST00000414028.2_Missense_Mutation_p.T122S|OPRM1_ENST00000522236.1_Missense_Mutation_p.T22S|OPRM1_ENST00000419506.2_Missense_Mutation_p.T122S|OPRM1_ENST00000520708.1_Missense_Mutation_p.T22S|OPRM1_ENST00000452687.2_Missense_Mutation_p.T122S|OPRM1_ENST00000229768.5_Missense_Mutation_p.T122S|OPRM1_ENST00000428397.2_Missense_Mutation_p.T122S|OPRM1_ENST00000524163.1_Missense_Mutation_p.T122S|OPRM1_ENST00000518759.1_Missense_Mutation_p.T41S|OPRM1_ENST00000522555.1_Missense_Mutation_p.T22S|OPRM1_ENST00000360422.4_Missense_Mutation_p.T122S	NM_000914.3	NP_000905.3	P35372	OPRM_HUMAN	opioid receptor, mu 1	122					adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral response to ethanol (GO:0048149)|calcium ion transmembrane transport (GO:0070588)|cellular response to stress (GO:0033554)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|locomotory behavior (GO:0007626)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of Wnt protein secretion (GO:0061358)|neuropeptide signaling pathway (GO:0007218)|opioid receptor signaling pathway (GO:0038003)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neurogenesis (GO:0050769)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-endorphin receptor activity (GO:0004979)|G-protein alpha-subunit binding (GO:0001965)|G-protein coupled receptor activity (GO:0004930)|morphine receptor activity (GO:0038047)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	33		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;9.26e-11)|BRCA - Breast invasive adenocarcinoma(81;0.0154)	Alfentanil(DB00802)|Alvimopan(DB06274)|Amitriptyline(DB00321)|Anileridine(DB00913)|Buprenorphine(DB00921)|Butorphanol(DB00611)|Codeine(DB00318)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dezocine(DB01209)|Diphenoxylate(DB01081)|Ethylmorphine(DB01466)|Fentanyl(DB00813)|Heroin(DB01452)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Ketamine(DB01221)|Ketobemidone(DB06738)|Levallorphan(DB00504)|Levomethadyl Acetate(DB01227)|Levorphanol(DB00854)|Loperamide(DB00836)|Methadone(DB00333)|Methadyl Acetate(DB01433)|Methylnaltrexone(DB06800)|Morphine(DB00295)|Nalbuphine(DB00844)|Naloxone(DB01183)|Naltrexone(DB00704)|Ondansetron(DB00904)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Pentazocine(DB00652)|Pethidine(DB00454)|Remifentanil(DB00899)|Sufentanil(DB00708)|Tapentadol(DB06204)|Tramadol(DB00193)	GCCACCAGTACCCTGCCCTTC	0.443																																					p.T215S		.											.	OPRM1	69	0			c.C644G						.						141.0	135.0	137.0					6																	154411035		2065	4238	6303	SO:0001583	missense	4988	exon4			CCAGTACCCTGCC	L29301	CCDS43517.1, CCDS43518.1, CCDS47503.1, CCDS47504.1, CCDS47505.1, CCDS47506.1, CCDS47507.1, CCDS47508.1, CCDS55071.1, CCDS55068.1, CCDS55069.1, CCDS55070.1	6q24-q25	2012-08-08			ENSG00000112038	ENSG00000112038		"""GPCR / Class A : Opioid receptors"""	8156	protein-coding gene	gene with protein product		600018					Standard	NM_001145285		Approved	MOR1	uc003qpo.1	P35372	OTTHUMG00000015870	ENST00000330432.7:c.365C>G	6.37:g.154411035C>G	ENSP00000328264:p.Thr122Ser	64.0	0.0		63.0	30.0	NM_001145279	B0FXJ1|B2R9S7|B8Q1L7|B8Q1L8|B8Q1L9|E7EWZ3|G8XRH6|G8XRH8|Q12930|Q4VWM1|Q4VWM2|Q4VWM3|Q4VWM4|Q4VWM6|Q4VWX6|Q5TDA1|Q6UPP1|Q6UQ80|Q7Z2D8|Q86V80|Q8IWW3|Q8IWW4|Q9UCZ4|Q9UN57	Missense_Mutation	SNP	ENST00000330432.7	37	CCDS55070.1	.	.	.	.	.	.	.	.	.	.	C	17.57	3.422052	0.62622	.	.	ENSG00000112038	ENST00000434900;ENST00000520708;ENST00000518759;ENST00000330432;ENST00000360422;ENST00000428397;ENST00000452687;ENST00000229768;ENST00000419506;ENST00000524163;ENST00000414028;ENST00000435918;ENST00000337049;ENST00000522555;ENST00000522236	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.72942	-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7	5.7	5.7	0.88788	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.72542	0.3473	L	0.37850	1.14	0.58432	D	0.999999	D;D;D;D;D;D;D;D;D;D;P;D;D	0.89917	0.999;1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0;1.0;0.851;1.0;0.994	D;D;D;D;D;D;D;D;D;D;P;D;D	0.97110	0.997;1.0;1.0;0.997;1.0;1.0;1.0;1.0;1.0;1.0;0.673;1.0;0.966	T	0.65874	-0.6062	10	0.20046	T	0.44	.	19.8351	0.96655	0.0:1.0:0.0:0.0	.	122;122;122;122;215;41;122;22;122;122;122;122;122	P35372-4;P35372-8;P35372-11;P35372-9;P35372-10;B8Q1L9;P35372-6;Q6UPP1;P35372-5;P35372;P35372-7;P35372-3;P35372-2	.;.;.;.;.;.;.;.;.;OPRM_HUMAN;.;.;.	S	215;22;41;122;122;122;122;122;122;122;122;122;122;22;22	ENSP00000394624:T215S;ENSP00000430876:T22S;ENSP00000430260:T41S;ENSP00000328264:T122S;ENSP00000353598:T122S;ENSP00000411903:T122S;ENSP00000410497:T122S;ENSP00000229768:T122S;ENSP00000403549:T122S;ENSP00000430097:T122S;ENSP00000399359:T122S;ENSP00000413752:T122S;ENSP00000338381:T122S;ENSP00000429719:T22S;ENSP00000429373:T22S	ENSP00000229768:T122S	T	+	2	0	OPRM1	154452728	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.818000	0.86416	2.687000	0.91594	0.655000	0.94253	ACC	.		0.443	OPRM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042786.2	NM_000914	
PAH	5053	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	103237549	103237549	+	Silent	SNP	T	T	C	rs376480977		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr12:103237549T>C	ENST00000553106.1	-	11	1546	c.1074A>G	c.(1072-1074)ttA>ttG	p.L358L	PAH_ENST00000307000.2_Silent_p.L353L	NM_000277.1	NP_000268.1	P00439	PH4H_HUMAN	phenylalanine hydroxylase	358					catecholamine biosynthetic process (GO:0042423)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|phenylalanine 4-monooxygenase activity (GO:0004505)			endometrium(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(5)|skin(2)|urinary_tract(1)	27					Droxidopa(DB06262)|Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	GCTTCTCTGATAAGCAGTACT	0.483																																					p.L358L		.											.	PAH	72	0			c.A1074G						.						85.0	84.0	84.0					12																	103237549		2203	4300	6503	SO:0001819	synonymous_variant	5053	exon11			CTCTGATAAGCAG	U49897	CCDS9092.1	12q22-q24.2	2010-04-27				ENSG00000171759	1.14.16.1		8582	protein-coding gene	gene with protein product	"""phenylalanine 4-monooxygenase"""	612349				2063869	Standard	NM_000277		Approved	PH	uc001tjq.1	P00439		ENST00000553106.1:c.1074A>G	12.37:g.103237549T>C		51.0	0.0		51.0	17.0	NM_000277	Q16717|Q8TC14	Silent	SNP	ENST00000553106.1	37	CCDS9092.1																																																																																			.		0.483	PAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406692.1		
PCDH17	27253	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	13	58299074	58299074	+	Silent	SNP	G	G	C	rs534412507		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr13:58299074G>C	ENST00000377918.3	+	4	3152	c.3126G>C	c.(3124-3126)gcG>gcC	p.A1042A		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	1042					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		CAACCAAGGCGTGCATCGAGC	0.532																																					p.A1042A	Melanoma(72;952 1291 1619 12849 33676)	.											.	PCDH17	97	0			c.G3126C						.						85.0	84.0	84.0					13																	58299074		2203	4300	6503	SO:0001819	synonymous_variant	27253	exon4			CAAGGCGTGCATC	AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"""Cadherins / Protocadherins : Non-clustered"""	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.3126G>C	13.37:g.58299074G>C		68.0	0.0		37.0	17.0	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Silent	SNP	ENST00000377918.3	37	CCDS31986.1																																																																																			.		0.532	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429	
PCDHA7	56141	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	140216124	140216124	+	Missense_Mutation	SNP	C	C	G			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr5:140216124C>G	ENST00000525929.1	+	1	2156	c.2156C>G	c.(2155-2157)aCg>aGg	p.T719R	PCDHA1_ENST00000504120.2_Intron|PCDHA7_ENST00000378125.3_Missense_Mutation_p.T719R|PCDHA5_ENST00000529859.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7	719					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|biliary_tract(1)|breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGCTGTACACGGCGTTGCGG	0.607																																					p.T719R	NSCLC(160;258 2013 5070 22440 28951)	.											.	PCDHA7	94	0			c.C2156G						.						106.0	88.0	94.0					5																	140216124		2203	4300	6503	SO:0001583	missense	56141	exon1			TGTACACGGCGTT	AF152485	CCDS54918.1	5q31	2010-11-26				ENSG00000204963		"""Cadherins / Protocadherins : Clustered"""	8673	other	complex locus constituent	"""KIAA0345-like 7"", ""ortholog to mouse CNR4"""	606313		CNRS4		10380929, 10662547	Standard	NM_018910		Approved	CNR4, CRNR4		Q9UN72		ENST00000525929.1:c.2156C>G	5.37:g.140216124C>G	ENSP00000436426:p.Thr719Arg	50.0	0.0		38.0	14.0	NM_031852	O75282	Missense_Mutation	SNP	ENST00000525929.1	37	CCDS54918.1	.	.	.	.	.	.	.	.	.	.	C	13.51	2.257257	0.39896	.	.	ENSG00000204963	ENST00000525929;ENST00000378125	T;T	0.15603	2.41;2.41	3.57	0.749	0.18381	.	0.739382	0.10174	U	0.706779	T	0.44540	0.1298	M	0.93720	3.45	0.09310	N	1	D;P	0.53462	0.96;0.934	P;P	0.58970	0.849;0.71	T	0.24261	-1.0165	10	0.62326	D	0.03	.	8.4633	0.32940	0.0:0.6311:0.0:0.3689	.	719;719	Q9UN72-2;Q9UN72	.;PCDA7_HUMAN	R	719	ENSP00000436426:T719R;ENSP00000367365:T719R	ENSP00000367365:T719R	T	+	2	0	PCDHA7	140196308	0.000000	0.05858	0.469000	0.27204	0.694000	0.40290	-1.159000	0.03150	0.304000	0.22809	0.462000	0.41574	ACG	.		0.607	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	NM_018910	
PCDHGC3	5098	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	140856286	140856286	+	Silent	SNP	C	C	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr5:140856286C>A	ENST00000308177.3	+	1	707	c.603C>A	c.(601-603)gcC>gcA	p.A201A	PCDHGA11_ENST00000518882.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB7_ENST00000398594.2_Intron|RN7SL68P_ENST00000488078.2_RNA|PCDHGA12_ENST00000252085.3_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	201	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(2)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGAGCGCGCCCTGGACCGAG	0.597																																					p.A201A		.											.	PCDHGC3	24	0			c.C603A						.						39.0	33.0	35.0					5																	140856286		2203	4300	6503	SO:0001819	synonymous_variant	5098	exon1			GCGCGCCCTGGAC	AF152337	CCDS4261.1, CCDS75347.1, CCDS75348.1	5q31	2010-01-26			ENSG00000240184	ENSG00000240184		"""Cadherins / Protocadherins : Clustered"""	8716	other	protocadherin	"""cadherin-like 2"", ""protocadherin 2"", ""protocadherin 43"""	603627		PCDH2		9360932, 8508762	Standard	NM_032402		Approved	PC-43, PC43, PCDH-GAMMA-C3		Q9UN70	OTTHUMG00000129613	ENST00000308177.3:c.603C>A	5.37:g.140856286C>A		34.0	0.0		26.0	11.0	NM_032402	O60622|Q08192|Q9Y5C4	Silent	SNP	ENST00000308177.3	37	CCDS4261.1																																																																																			.		0.597	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588	
PLCB2	5330	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	15	40584571	40584571	+	Silent	SNP	C	C	T			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr15:40584571C>T	ENST00000260402.3	-	22	2649	c.2400G>A	c.(2398-2400)gaG>gaA	p.E800E	PLCB2_ENST00000456256.2_Silent_p.E800E|PLCB2_ENST00000557821.1_Silent_p.E796E	NM_001284297.1|NM_004573.2	NP_001271226.1|NP_004564.2	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	800					activation of phospholipase C activity (GO:0007202)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|sensory perception of bitter taste (GO:0050913)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(3)	39		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)		AGTCCTTCATCTCCAGGAAGA	0.592																																					p.E800E		.											.	PLCB2	275	0			c.G2400A						.						68.0	76.0	73.0					15																	40584571		2065	4204	6269	SO:0001819	synonymous_variant	5330	exon22			CTTCATCTCCAGG		CCDS42020.1, CCDS61591.1, CCDS61592.1, CCDS73704.1	15q15.1	2012-01-23			ENSG00000137841	ENSG00000137841	3.1.4.11		9055	protein-coding gene	gene with protein product		604114				1644792, 9925923	Standard	XM_005254448		Approved	FLJ38135	uc001zld.3	Q00722	OTTHUMG00000172412	ENST00000260402.3:c.2400G>A	15.37:g.40584571C>T		43.0	0.0		32.0	12.0	NM_004573	A8K6J2|B9EGH5	Silent	SNP	ENST00000260402.3	37	CCDS42020.1																																																																																			.		0.592	PLCB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418430.1		
PLD3	23646	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	40872766	40872766	+	Silent	SNP	C	C	T	rs375652785		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr19:40872766C>T	ENST00000409587.1	+	5	586	c.189C>T	c.(187-189)ggC>ggT	p.G63G	PLD3_ENST00000409735.4_Silent_p.G63G|PLD3_ENST00000409419.1_Silent_p.G63G|PLD3_ENST00000356508.5_Silent_p.G63G|PLD3_ENST00000409281.1_Silent_p.G63G			Q8IV08	PLD3_HUMAN	phospholipase D family, member 3	63					cell death (GO:0008219)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phospholipase D activity (GO:0004630)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	20			Lung(22;0.000636)|LUSC - Lung squamous cell carcinoma(20;0.00248)			GGGAATACGGCGACTTGCATC	0.627																																					p.G63G		.											.	PLD3	228	0			c.C189T						.	C	,	1,4405	2.1+/-5.4	0,1,2202	73.0	69.0	71.0		189,189	-5.5	0.9	19		71	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PLD3	NM_001031696.2,NM_012268.2	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	63/491,63/491	40872766	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23646	exon5			ATACGGCGACTTG	BC000553	CCDS33027.1	19q13.2	2014-03-14	2005-05-20		ENSG00000105223	ENSG00000105223			17158	protein-coding gene	gene with protein product		615698	"""phospholipase D3"""			9140189, 15794758	Standard	XM_005258704		Approved	HU-K4	uc002onj.4	Q8IV08	OTTHUMG00000152736	ENST00000409587.1:c.189C>T	19.37:g.40872766C>T		49.0	0.0		33.0	16.0	NM_012268	Q92853|Q9BW87	Silent	SNP	ENST00000409587.1	37	CCDS33027.1																																																																																			.		0.627	PLD3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327721.1	NM_012268	
PNPLA4	8228	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	7889813	7889813	+	Missense_Mutation	SNP	C	C	A	rs186093844		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chrX:7889813C>A	ENST00000381042.4	-	4	522	c.352G>T	c.(352-354)Gcc>Tcc	p.A118S	PNPLA4_ENST00000537427.1_Missense_Mutation_p.A31S|PNPLA4_ENST00000444736.1_Missense_Mutation_p.A118S	NM_004650.2	NP_004641.1	P41247	PLPL4_HUMAN	patatin-like phospholipase domain containing 4	118	Patatin.				lipid catabolic process (GO:0016042)		triglyceride lipase activity (GO:0004806)			kidney(1)|large_intestine(3)|lung(2)|prostate(1)	7		Colorectal(8;0.0329)|Medulloblastoma(8;0.232)				CTGGTTTTGGCGTTGGTGATG	0.463																																					p.A118S		.											.	PNPLA4	130	0			c.G352T						.						144.0	122.0	130.0					X																	7889813		2203	4299	6502	SO:0001583	missense	8228	exon4			TTTTGGCGTTGGT	U03886	CCDS14129.1, CCDS55368.1	Xp22.3	2014-03-14			ENSG00000006757	ENSG00000006757	3.1.1.3	"""Patatin-like phospholipase domain containing"""	24887	protein-coding gene	gene with protein product		300102				7806223, 16799181, 19029121	Standard	NM_004650		Approved	DXS1283E, GS2, iPLA2eta	uc011mhr.1	P41247	OTTHUMG00000021103	ENST00000381042.4:c.352G>T	X.37:g.7889813C>A	ENSP00000370430:p.Ala118Ser	106.0	1.0		65.0	44.0	NM_004650	A8K1H3|B4E362|Q8WW83	Missense_Mutation	SNP	ENST00000381042.4	37	CCDS14129.1	.	.	.	.	.	.	.	.	.	.	C	8.026	0.760686	0.15914	.	.	ENSG00000006757	ENST00000381042;ENST00000444736;ENST00000537427;ENST00000442940	T;T;T;T	0.77750	-1.12;-1.12;-1.12;-1.12	4.69	2.22	0.28083	Acyl transferase/acyl hydrolase/lysophospholipase (1);Patatin/Phospholipase A2-related (1);	0.672537	0.14795	N	0.298011	T	0.62282	0.2415	N	0.21097	0.63	0.09310	N	1	B	0.12630	0.006	B	0.12156	0.007	T	0.53592	-0.8417	10	0.52906	T	0.07	-17.7914	7.1838	0.25789	0.0:0.3747:0.0:0.6253	.	118	P41247	PLPL4_HUMAN	S	118;118;31;118	ENSP00000370430:A118S;ENSP00000415245:A118S;ENSP00000443157:A31S;ENSP00000406698:A118S	ENSP00000370430:A118S	A	-	1	0	PNPLA4	7849813	0.970000	0.33590	0.649000	0.29536	0.252000	0.25951	0.637000	0.24659	0.496000	0.27904	-0.366000	0.07423	GCC	C|0.999;T|0.001		0.463	PNPLA4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055687.1	NM_004650	
PSG9	5678	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	43762554	43762554	+	Missense_Mutation	SNP	T	T	C			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr19:43762554T>C	ENST00000270077.3	-	5	1139	c.1043A>G	c.(1042-1044)gAa>gGa	p.E348G	PSG9_ENST00000596730.1_Missense_Mutation_p.E162G|PSG9_ENST00000593948.1_Missense_Mutation_p.E255G|PSG9_ENST00000443718.3_Missense_Mutation_p.E255G|PSG9_ENST00000418820.2_Missense_Mutation_p.E255G|PSG9_ENST00000291752.5_Missense_Mutation_p.E162G|PSG9_ENST00000244293.7_Missense_Mutation_p.E255G	NM_002784.3	NP_002775.3	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9	348	Ig-like C2-type 3.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Prostate(69;0.00682)				GTCGAGGTTTTCTCCTGAACG	0.453																																					p.E348G		.											.	PSG9	92	0			c.A1043G						.						134.0	163.0	153.0					19																	43762554		2137	4278	6415	SO:0001583	missense	5678	exon5			AGGTTTTCTCCTG	M34481	CCDS12618.1	19q13.2	2013-01-29			ENSG00000183668	ENSG00000183668		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9526	protein-coding gene	gene with protein product		176398		PSG11		7806221	Standard	XM_005259076		Approved	PSGII	uc002owd.4	Q00887	OTTHUMG00000182826	ENST00000270077.3:c.1043A>G	19.37:g.43762554T>C	ENSP00000270077:p.Glu348Gly	32.0	0.0		20.0	13.0	NM_002784	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000270077.3	37	CCDS12618.1	.	.	.	.	.	.	.	.	.	.	N	10.10	1.257419	0.22965	.	.	ENSG00000183668	ENST00000270077;ENST00000291752;ENST00000443718;ENST00000435220;ENST00000244293	T;T;T;T	0.12879	2.64;2.64;2.64;2.64	1.58	-2.54	0.06307	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.19446	0.0467	L	0.43757	1.38	0.09310	N	1	P;D;P;P;B;P	0.53745	0.729;0.962;0.87;0.951;0.001;0.602	P;D;P;P;B;P	0.64410	0.791;0.925;0.654;0.823;0.053;0.73	T	0.13872	-1.0493	9	0.59425	D	0.04	.	2.2184	0.03966	0.2161:0.0:0.4831:0.3008	.	255;204;255;162;348;348	E7EW65;Q15225;Q15227;G3XAA7;Q6LEU7;Q00887	.;.;.;.;.;PSG9_HUMAN	G	348;162;255;309;255	ENSP00000270077:E348G;ENSP00000291752:E162G;ENSP00000396753:E255G;ENSP00000244293:E255G	ENSP00000244293:E255G	E	-	2	0	PSG9	48454394	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.759000	0.04761	-0.634000	0.05538	0.163000	0.16589	GAA	.		0.453	PSG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323065.1	NM_002784	
PTPN12	5782	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	77240326	77240326	+	Missense_Mutation	SNP	A	A	T			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr7:77240326A>T	ENST00000248594.6	+	11	1174	c.902A>T	c.(901-903)tAt>tTt	p.Y301F	PTPN12_ENST00000435495.2_Missense_Mutation_p.Y171F|PTPN12_ENST00000415482.2_Missense_Mutation_p.Y182F	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12	301					protein dephosphorylation (GO:0006470)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|podosome (GO:0002102)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|SH3 domain binding (GO:0017124)			breast(2)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(12)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	39						CTACAACTATATGAAATTCAT	0.313																																					p.Y301F		.											.	PTPN12	228	0			c.A902T						.						129.0	145.0	139.0					7																	77240326		2203	4298	6501	SO:0001583	missense	5782	exon11			AACTATATGAAAT		CCDS5592.1, CCDS47619.1, CCDS47620.1	7q11.23	2011-06-09			ENSG00000127947	ENSG00000127947		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9645	protein-coding gene	gene with protein product		600079				7509295	Standard	NM_002835		Approved	PTPG1, PTP-PEST	uc003ugh.2	Q05209	OTTHUMG00000023501	ENST00000248594.6:c.902A>T	7.37:g.77240326A>T	ENSP00000248594:p.Tyr301Phe	283.0	0.0		203.0	94.0	NM_002835	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	Missense_Mutation	SNP	ENST00000248594.6	37	CCDS5592.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.361736	0.82353	.	.	ENSG00000127947	ENST00000248594;ENST00000415482;ENST00000543073;ENST00000435495	T;T;T	0.07021	3.83;3.23;3.23	5.47	5.47	0.80525	.	0.208920	0.43579	D	0.000557	T	0.17280	0.0415	M	0.65975	2.015	0.48830	D	0.999714	P	0.50156	0.932	P	0.48304	0.573	T	0.00749	-1.1582	10	0.41790	T	0.15	.	15.8381	0.78814	1.0:0.0:0.0:0.0	.	301	Q05209	PTN12_HUMAN	F	301;182;182;171	ENSP00000248594:Y301F;ENSP00000392429:Y182F;ENSP00000397991:Y171F	ENSP00000248594:Y301F	Y	+	2	0	PTPN12	77078262	1.000000	0.71417	0.994000	0.49952	0.979000	0.70002	5.071000	0.64382	2.191000	0.70037	0.533000	0.62120	TAT	.		0.313	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253183.3		
R3HCC1L	27291	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	10	99968219	99968219	+	Silent	SNP	A	A	G			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr10:99968219A>G	ENST00000298999.3	+	5	651	c.348A>G	c.(346-348)gtA>gtG	p.V116V	R3HCC1L_ENST00000370584.3_Silent_p.V116V|R3HCC1L_ENST00000370586.2_Intron|R3HCC1L_ENST00000314594.5_5'UTR	NM_014472.4	NP_055287	Q7Z5L2	R3HCL_HUMAN	R3H domain and coiled-coil containing 1-like	116							nucleotide binding (GO:0000166)										CCAAAGAAGTATTATCCCAAG	0.388																																					p.V116V		.											.	.	.	0			c.A348G						.						99.0	104.0	102.0					10																	99968219		2203	4300	6503	SO:0001819	synonymous_variant	27291	exon4			AGAAGTATTATCC	AF525304	CCDS31267.1, CCDS58093.1, CCDS73178.1	10q24.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166024	ENSG00000166024			23512	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 28"""	C10orf28			Standard	NM_014472		Approved	GIDRP86, PSORT	uc001kox.4	Q7Z5L2	OTTHUMG00000018873	ENST00000298999.3:c.348A>G	10.37:g.99968219A>G		106.0	1.0		43.0	29.0	NM_001256620	O60598|Q5W0B4|Q5W0B5|Q86VT9|Q8N9H0	Silent	SNP	ENST00000298999.3	37	CCDS31267.1																																																																																			.		0.388	R3HCC1L-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049764.1	NM_014472	
R3HDM2	22864	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	12	57663679	57663679	+	Silent	SNP	A	A	G			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr12:57663679A>G	ENST00000347140.3	-	15	1791	c.1401T>C	c.(1399-1401)ctT>ctC	p.L467L	R3HDM2_ENST00000546843.1_5'Flank|R3HDM2_ENST00000403821.2_Silent_p.L501L|RP11-123K3.4_ENST00000548184.1_3'UTR|R3HDM2_ENST00000402412.1_Silent_p.L481L|R3HDM2_ENST00000441731.2_Silent_p.L162L|R3HDM2_ENST00000358907.2_Silent_p.L467L|R3HDM2_ENST00000413953.2_Silent_p.L194L			Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	467	Gln-rich.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	22						GCTGGGAGATAAGTGGGGTCT	0.547																																					p.L467L		.											.	R3HDM2	92	0			c.T1401C						.						126.0	113.0	117.0					12																	57663679		2203	4300	6503	SO:0001819	synonymous_variant	22864	exon13			GGAGATAAGTGGG	AB023219	CCDS8937.2	12q13.3	2012-11-19			ENSG00000179912	ENSG00000179912			29167	protein-coding gene	gene with protein product							Standard	NM_014925		Approved	KIAA1002	uc009zpm.1	Q9Y2K5	OTTHUMG00000171568	ENST00000347140.3:c.1401T>C	12.37:g.57663679A>G		69.0	0.0		63.0	18.0	NM_014925	Q2M1T9|Q3ZCT5	Silent	SNP	ENST00000347140.3	37	CCDS8937.2	.	.	.	.	.	.	.	.	.	.	A	14.69	2.611037	0.46631	.	.	ENSG00000179912	ENST00000466401	.	.	.	5.15	2.73	0.32206	.	0.173114	0.42548	N	0.000681	T	0.57007	0.2024	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54886	-0.8226	6	0.56958	D	0.05	-10.9705	3.8692	0.09029	0.5704:0.1795:0.2501:0.0	.	.	.	.	S	65	.	ENSP00000449326:L65S	L	-	2	0	R3HDM2	55949946	0.942000	0.31987	1.000000	0.80357	0.917000	0.54804	0.452000	0.21795	0.500000	0.27991	0.528000	0.53228	TTA	.		0.547	R3HDM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326570.2	NM_014925	
RAI14	26064	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	34823713	34823713	+	Missense_Mutation	SNP	A	A	G			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr5:34823713A>G	ENST00000265109.3	+	15	2053	c.1766A>G	c.(1765-1767)aAt>aGt	p.N589S	RAI14_ENST00000512629.1_Missense_Mutation_p.N560S|RAI14_ENST00000515799.1_Missense_Mutation_p.N592S|RAI14_ENST00000506376.1_Missense_Mutation_p.N581S|RAI14_ENST00000397449.1_Missense_Mutation_p.N582S|RAI14_ENST00000428746.2_Missense_Mutation_p.N589S|RAI14_ENST00000503673.1_Missense_Mutation_p.N589S	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	589						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					GTTATTGAGAATATGAATAAG	0.358																																					p.N592S		.											.	RAI14	91	0			c.A1775G						.						58.0	61.0	60.0					5																	34823713		2203	4300	6503	SO:0001583	missense	26064	exon17			TTGAGAATATGAA	AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"""Ankyrin repeat domain containing"""	14873	protein-coding gene	gene with protein product	"""novel retinal pigment epithelial"""	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.1766A>G	5.37:g.34823713A>G	ENSP00000265109:p.Asn589Ser	96.0	0.0		73.0	26.0	NM_001145525	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Missense_Mutation	SNP	ENST00000265109.3	37	CCDS34142.1	.	.	.	.	.	.	.	.	.	.	A	17.05	3.289782	0.59976	.	.	ENSG00000039560	ENST00000265109;ENST00000512629;ENST00000428746;ENST00000503673;ENST00000515799;ENST00000506376;ENST00000397449	T;T;T;T;T;T;T	0.36878	1.26;1.23;1.26;1.26;1.26;1.3;1.3	5.42	5.42	0.78866	.	.	.	.	.	T	0.48537	0.1505	L	0.29908	0.895	0.45035	D	0.998058	D;D;D;D	0.71674	0.998;0.982;0.978;0.982	D;P;P;P	0.80764	0.994;0.473;0.741;0.473	T	0.48854	-0.8998	9	0.52906	T	0.07	-27.1897	15.4697	0.75432	1.0:0.0:0.0:0.0	.	581;560;592;589	Q9P0K7-3;E9PED3;Q9P0K7-2;Q9P0K7	.;.;.;RAI14_HUMAN	S	589;560;589;589;592;581;582	ENSP00000265109:N589S;ENSP00000422377:N560S;ENSP00000388725:N589S;ENSP00000422942:N589S;ENSP00000427123:N592S;ENSP00000423854:N581S;ENSP00000380591:N582S	ENSP00000265109:N589S	N	+	2	0	RAI14	34859470	1.000000	0.71417	0.989000	0.46669	0.917000	0.54804	6.348000	0.73009	2.067000	0.61834	0.454000	0.30748	AAT	.		0.358	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577	
RBM12B	389677	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	8	94748274	94748274	+	Missense_Mutation	SNP	T	T	C			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr8:94748274T>C	ENST00000399300.2	-	3	578	c.365A>G	c.(364-366)tAt>tGt	p.Y122C	RBM12B_ENST00000520961.1_Intron|RBM12B_ENST00000517700.1_Missense_Mutation_p.Y122C|RP11-10N23.4_ENST00000517998.1_RNA	NM_203390.2	NP_976324.2	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	122							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	30	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			TGAAGAGCCATATCCAGAATT	0.438																																					p.Y122C		.											.	RBM12B	90	0			c.A365G						.						143.0	137.0	139.0					8																	94748274		1856	4091	5947	SO:0001583	missense	389677	exon3			GAGCCATATCCAG		CCDS43755.1	8q22	2014-05-20			ENSG00000183808	ENSG00000183808		"""RNA binding motif (RRM) containing"""	32310	protein-coding gene	gene with protein product							Standard	NM_203390		Approved		uc003yfz.3	Q8IXT5	OTTHUMG00000164317	ENST00000399300.2:c.365A>G	8.37:g.94748274T>C	ENSP00000382239:p.Tyr122Cys	111.0	0.0		97.0	31.0	NM_203390	A8MYB5	Missense_Mutation	SNP	ENST00000399300.2	37	CCDS43755.1	.	.	.	.	.	.	.	.	.	.	T	13.48	2.250781	0.39797	.	.	ENSG00000183808	ENST00000399300;ENST00000517700;ENST00000519109;ENST00000518597;ENST00000520560	T;T;T;T;T	0.19394	2.72;2.76;2.29;2.32;2.15	5.08	5.08	0.68730	.	0.272209	0.26560	N	0.023700	T	0.31136	0.0787	N	0.24115	0.695	0.30625	N	0.758055	D	0.76494	0.999	D	0.66847	0.947	T	0.15178	-1.0446	10	0.54805	T	0.06	-28.0135	14.6864	0.69052	0.0:0.0:0.0:1.0	.	122	Q8IXT5	RB12B_HUMAN	C	122	ENSP00000382239:Y122C;ENSP00000427729:Y122C;ENSP00000430474:Y122C;ENSP00000428269:Y122C;ENSP00000429807:Y122C	ENSP00000382239:Y122C	Y	-	2	0	RBM12B	94817450	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	2.239000	0.43079	2.132000	0.65825	0.533000	0.62120	TAT	.		0.438	RBM12B-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383603.1	NM_203390	
RPLP0	6175	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	12	120636498	120636498	+	Silent	SNP	G	G	A	rs138718343		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr12:120636498G>A	ENST00000551150.1	-	5	825	c.510C>T	c.(508-510)agC>agT	p.S170S	PXN-AS1_ENST00000538804.1_RNA|PXN-AS1_ENST00000539446.1_RNA|RPLP0_ENST00000392514.4_Silent_p.S170S|RPLP0_ENST00000550296.1_5'Flank|RPLP0_ENST00000546989.1_Intron|RPLP0_ENST00000552292.1_5'Flank|RPLP0_ENST00000228306.4_Silent_p.S170S|PXN-AS1_ENST00000535200.1_RNA|PXN-AS1_ENST00000542265.1_RNA|RPLP0_ENST00000313104.5_Intron|PXN-AS1_ENST00000542314.1_RNA			P05388	RLA0_HUMAN	ribosomal protein, large, P0	170					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)|ribosome biogenesis (GO:0042254)|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)	cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GCGTGGCTTCGCTGGCTCCCA	0.527																																					p.S170S		.											.	RPLP0	91	0			c.C510T						.	G	,	0,4406		0,0,2203	72.0	69.0	70.0		510,510	-0.5	1.0	12	dbSNP_134	70	3,8593	3.0+/-9.4	0,3,4295	no	coding-synonymous,coding-synonymous	RPLP0	NM_001002.3,NM_053275.3	,	0,3,6498	AA,AG,GG		0.0349,0.0,0.0231	,	170/318,170/318	120636498	3,12999	2203	4298	6501	SO:0001819	synonymous_variant	6175	exon6			GGCTTCGCTGGCT	AB007187	CCDS9193.1	12q24.2	2011-07-29			ENSG00000089157	ENSG00000089157		"""L ribosomal proteins"""	10371	protein-coding gene	gene with protein product	"""acidic ribosomal phosphoprotein P0"""	180510				9582194	Standard	NM_053275		Approved	PRLP0, P0, L10E, RPP0, LP0	uc001txq.3	P05388	OTTHUMG00000169317	ENST00000551150.1:c.510C>T	12.37:g.120636498G>A		68.0	0.0		52.0	16.0	NM_053275	Q3B7A4|Q9BVK4	Silent	SNP	ENST00000551150.1	37	CCDS9193.1																																																																																			G|1.000;A|0.000		0.527	RPLP0-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403448.3	NM_053275	
SETD5	55209	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	9517712	9517712	+	Silent	SNP	G	G	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr3:9517712G>A	ENST00000406341.1	+	22	4456	c.4266G>A	c.(4264-4266)gtG>gtA	p.V1422V	SETD5_ENST00000402198.1_Silent_p.V1422V|SETD5_ENST00000402466.1_Silent_p.V1324V|SETD5_ENST00000302463.6_Silent_p.V1324V|SETD5_ENST00000407969.1_Silent_p.V1441V			Q9C0A6	SETD5_HUMAN	SET domain containing 5	1422										NS(2)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(3)|prostate(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		GTGGGGGTGTGCACCAGTACC	0.577																																					p.V1422V		.											.	SETD5	70	0			c.G4266A						.						27.0	29.0	28.0					3																	9517712		1964	4153	6117	SO:0001819	synonymous_variant	55209	exon23			GGGTGTGCACCAG	BC020956	CCDS46741.1, CCDS74892.1	3p25.3	2011-12-13			ENSG00000168137	ENSG00000168137			25566	protein-coding gene	gene with protein product		615743				11214970	Standard	XM_005265299		Approved	FLJ10707	uc003brt.3	Q9C0A6	OTTHUMG00000150491	ENST00000406341.1:c.4266G>A	3.37:g.9517712G>A		49.0	0.0		46.0	19.0	NM_001080517	Q6AI17|Q8WUB6|Q9H3X4|Q9H6V7|Q9H7S3|Q9NVI9	Silent	SNP	ENST00000406341.1	37	CCDS46741.1																																																																																			.		0.577	SETD5-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318425.1	XM_371614	
SIRT2	22933	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	39374291	39374291	+	Missense_Mutation	SNP	C	C	T	rs200953200		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr19:39374291C>T	ENST00000249396.7	-	9	908	c.607G>A	c.(607-609)Gaa>Aaa	p.E203K	SIRT2_ENST00000392081.2_Missense_Mutation_p.E166K|SIRT2_ENST00000358931.5_Missense_Mutation_p.E203K	NM_012237.3	NP_036369.2	Q8IXJ6	SIR2_HUMAN	sirtuin 2	203	Deacetylase sirtuin-type. {ECO:0000255|PROSITE-ProRule:PRU00236}.				autophagy (GO:0006914)|cellular lipid catabolic process (GO:0044242)|cellular response to caloric restriction (GO:0061433)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to hypoxia (GO:0071456)|cellular response to molecule of bacterial origin (GO:0071219)|cellular response to oxidative stress (GO:0034599)|chromatin silencing (GO:0006342)|chromatin silencing at rDNA (GO:0000183)|chromatin silencing at telomere (GO:0006348)|gene silencing (GO:0016458)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|innate immune response (GO:0045087)|meiotic nuclear division (GO:0007126)|mitotic nuclear division (GO:0007067)|myelination in peripheral nervous system (GO:0022011)|negative regulation of autophagy (GO:0010507)|negative regulation of cell proliferation (GO:0008285)|negative regulation of defense response to bacterium (GO:1900425)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of oligodendrocyte progenitor proliferation (GO:0070446)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of attachment of spindle microtubules to kinetochore (GO:0051987)|positive regulation of cell division (GO:0051781)|positive regulation of DNA binding (GO:0043388)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of meiosis (GO:0045836)|positive regulation of oocyte maturation (GO:1900195)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process involved in cellular response to hypoxia (GO:2000777)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ADP-ribosylation (GO:0006471)|protein deacetylation (GO:0006476)|protein kinase B signaling (GO:0043491)|regulation of cell cycle (GO:0051726)|regulation of exit from mitosis (GO:0007096)|regulation of myelination (GO:0031641)|regulation of phosphorylation (GO:0042325)|response to redox state (GO:0051775)|ripoptosome assembly involved in necroptotic process (GO:1901026)|substantia nigra development (GO:0021762)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)	centriole (GO:0005814)|centrosome (GO:0005813)|chromatin silencing complex (GO:0005677)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|glial cell projection (GO:0097386)|juxtaparanode region of axon (GO:0044224)|lateral loop (GO:0043219)|meiotic spindle (GO:0072687)|microtubule (GO:0005874)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|myelin sheath (GO:0043209)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|spindle (GO:0005819)	chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (GO:0017136)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|NAD-dependent protein deacetylase activity (GO:0034979)|protein deacetylase activity (GO:0033558)|transcription factor binding (GO:0008134)|tubulin deacetylase activity (GO:0042903)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(5)|skin(1)	9	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00125)|LUSC - Lung squamous cell carcinoma(53;0.00191)			AGCGGGTATTCGTGCCGGCAG	0.617																																					p.E203K		.											.	SIRT2	226	0			c.G607A						.						88.0	72.0	78.0					19																	39374291		2203	4300	6503	SO:0001583	missense	22933	exon9			GGTATTCGTGCCG	AF083107	CCDS12523.1, CCDS46069.1, CCDS74361.1	19q13	2010-06-25	2010-06-25		ENSG00000068903	ENSG00000068903			10886	protein-coding gene	gene with protein product		604480	"""sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 2"", ""sirtuin (silent mating type information regulation 2 homolog) 2 (S. cerevisiae)"""	SIR2L		10393250, 10381378	Standard	NM_012237		Approved		uc002ojt.2	Q8IXJ6	OTTHUMG00000150480	ENST00000249396.7:c.607G>A	19.37:g.39374291C>T	ENSP00000249396:p.Glu203Lys	64.0	0.0		36.0	15.0	NM_012237	A8K3V1|B2RB45|O95889|Q924Y7|Q9P0G8|Q9UNT0|Q9Y6E9|U5TP13	Missense_Mutation	SNP	ENST00000249396.7	37	CCDS12523.1	.	.	.	.	.	.	.	.	.	.	C	13.20	2.165115	0.38217	.	.	ENSG00000068903	ENST00000249396;ENST00000392081;ENST00000358931;ENST00000456703;ENST00000414941;ENST00000407552	T;T;T;T;T	0.39406	1.08;1.08;1.08;1.08;2.29	4.31	4.31	0.51392	.	0.197758	0.40554	N	0.001067	T	0.23370	0.0565	N	0.16266	0.395	0.53005	D	0.999969	B;B;B;B	0.32409	0.196;0.125;0.37;0.24	B;B;B;B	0.27262	0.015;0.008;0.078;0.01	T	0.06625	-1.0816	10	0.25106	T	0.35	-9.9569	10.3892	0.44158	0.0:0.9032:0.0:0.0968	.	203;166;203;183	Q8IXJ6-4;Q8IXJ6-2;Q8IXJ6;Q8IXJ6-3	.;.;SIRT2_HUMAN;.	K	203;166;203;188;166;166	ENSP00000249396:E203K;ENSP00000375931:E166K;ENSP00000351809:E203K;ENSP00000404309:E166K;ENSP00000385146:E166K	ENSP00000249396:E203K	E	-	1	0	SIRT2	44066131	0.960000	0.32886	0.736000	0.30914	0.274000	0.26718	2.146000	0.42216	2.405000	0.81733	0.491000	0.48974	GAA	.		0.617	SIRT2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318278.1		
SLC4A11	83959	hgsc.bcm.edu;broad.mit.edu;mdanderson.org	37	20	3209657	3209657	+	Splice_Site	SNP	C	C	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr20:3209657C>A	ENST00000380056.3	-	16	2114	c.2067G>T	c.(2065-2067)agG>agT	p.R689S	SLC4A11_ENST00000380059.3_Splice_Site_p.R716S|SLC4A11_ENST00000539553.2_Splice_Site_p.R673S|SLC4A11_ENST00000488544.1_5'UTR	NM_032034.3	NP_114423.1	Q8NBS3	S4A11_HUMAN	solute carrier family 4, sodium borate transporter, member 11	689	Membrane (bicarbonate transporter).				bicarbonate transport (GO:0015701)|borate transmembrane transport (GO:0035445)|borate transport (GO:0046713)|cellular cation homeostasis (GO:0030003)|fluid transport (GO:0042044)|proton transport (GO:0015992)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	bicarbonate transmembrane transporter activity (GO:0015106)|borate transmembrane transporter activity (GO:0046715)|hydrogen ion channel activity (GO:0015252)|inorganic anion exchanger activity (GO:0005452)|protein dimerization activity (GO:0046983)|sodium channel activity (GO:0005272)|symporter activity (GO:0015293)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(4)|soft_tissue(1)|urinary_tract(1)	40						CCTTCACCAGCCTGCAGCAGA	0.657																																					p.R716S	NSCLC(190;922 2139 10266 10292 38692)	.											.	SLC4A11	91	0			c.G2148T						.						85.0	71.0	76.0					20																	3209657		2202	4300	6502	SO:0001630	splice_region_variant	83959	exon17			CACCAGCCTGCAG	AF336127	CCDS13052.1, CCDS54445.1, CCDS54446.1	20p13	2014-02-14	2007-08-03		ENSG00000088836	ENSG00000088836		"""Solute carriers"""	16438	protein-coding gene	gene with protein product		610206	"""corneal endothelial dystrophy 2 (autosomal recessive)"", ""solute carrier family 4, sodium bicarbonate transporter-like, member 11"", ""corneal dystrophy and perceptive deafness 1"""	CHED2, CDPD1		10843999, 11302728, 16767101	Standard	NM_001174089		Approved	dJ794I6.2, BTR1, NaBC1, FECD4	uc010zqe.2	Q8NBS3	OTTHUMG00000031740	ENST00000380056.3:c.2067-1G>T	20.37:g.3209657C>A		18.0	0.0		21.0	10.0	NM_001174090	B4DKC8|B4DKX9|G3V1M3|Q2TB62|Q2TB63|Q9BXF4|Q9NTW9	Missense_Mutation	SNP	ENST00000380056.3	37	CCDS13052.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.085299	0.76642	.	.	ENSG00000088836	ENST00000380059;ENST00000380056;ENST00000539553	T;T;T	0.78924	-1.22;-1.22;-1.22	4.93	2.99	0.34606	Bicarbonate transporter, C-terminal (1);	0.096978	0.64402	D	0.000001	D	0.82600	0.5072	M	0.69185	2.1	0.80722	D	1	P;P;P	0.49635	0.909;0.926;0.844	P;P;P	0.56612	0.701;0.802;0.73	T	0.82961	-0.0197	10	0.87932	D	0	.	11.3086	0.49351	0.0:0.8502:0.0:0.1498	.	673;716;689	G3V1M3;B4DKC8;Q8NBS3	.;.;S4A11_HUMAN	S	716;689;673	ENSP00000369399:R716S;ENSP00000369396:R689S;ENSP00000441370:R673S	ENSP00000369396:R689S	R	-	3	2	SLC4A11	3157657	1.000000	0.71417	0.999000	0.59377	0.947000	0.59692	4.877000	0.63086	0.606000	0.29965	0.462000	0.41574	AGG	.		0.657	SLC4A11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077728.1		Missense_Mutation
STK40	83931	broad.mit.edu;bcgsc.ca	37	1	36809753	36809754	+	Frame_Shift_Del	DEL	GC	GC	-	rs188394458		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	GC	GC	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr1:36809753_36809754delGC	ENST00000373129.3	-	9	1257_1258	c.851_852delGC	c.(850-852)cgcfs	p.R284fs	STK40_ENST00000373132.3_Frame_Shift_Del_p.R284fs|STK40_ENST00000373130.3_Frame_Shift_Del_p.R289fs|STK40_ENST00000359297.2_Frame_Shift_Del_p.R284fs	NM_032017.1	NP_114406.1	Q8N2I9	STK40_HUMAN	serine/threonine kinase 40	284	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				glycogen metabolic process (GO:0005977)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|regulation of gene expression (GO:0010468)|regulation of MAPK cascade (GO:0043408)|respiratory system process (GO:0003016)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)|stomach(1)	13		Myeloproliferative disorder(586;0.0393)				CCTTGATCTTGCGGAAGAGCTC	0.629																																					p.284_284del		.											.	STK40	83	0			c.851_852del						.																																			SO:0001589	frameshift_variant	83931	exon9			GATCTTGCGGAAG	BC008344	CCDS407.1, CCDS60089.1	1p34.3	2008-02-05			ENSG00000196182	ENSG00000196182			21373	protein-coding gene	gene with protein product		609437					Standard	NM_032017		Approved	MGC4796, SgK495	uc001cak.1	Q8N2I9	OTTHUMG00000008238	ENST00000373129.3:c.851_852delGC	1.37:g.36809753_36809754delGC	ENSP00000362221:p.Arg284fs	37.0	0.0		18.0	7.0	NM_032017	D3DPS8|Q5VTK8|Q5VTK9|Q6ZMN1|Q8N2J8|Q8N3I6|Q96HN6|Q96I44|Q9BSA3|Q9H7H6	Frame_Shift_Del	DEL	ENST00000373129.3	37	CCDS407.1																																																																																			.		0.629	STK40-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022592.1	NM_032017	
TAPBPL	55080	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	6570035	6570035	+	Missense_Mutation	SNP	T	T	G			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr12:6570035T>G	ENST00000266556.7	+	6	1387	c.1222T>G	c.(1222-1224)Ttg>Gtg	p.L408V	VAMP1_ENST00000544432.1_5'Flank|TAPBPL_ENST00000545700.1_3'UTR	NM_018009.4	NP_060479.3	Q9BX59	TPSNR_HUMAN	TAP binding protein-like	408					negative regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002590)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)			endometrium(2)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	6						GAGAACAGCCTTGGGAGTCAT	0.602																																					p.L408V		.											.	TAPBPL	90	0			c.T1222G						.						219.0	165.0	183.0					12																	6570035		2203	4300	6503	SO:0001583	missense	55080	exon6			ACAGCCTTGGGAG	AK001005	CCDS8546.1	12p13.31	2013-01-11						"""Immunoglobulin superfamily / C1-set domain containing"""	30683	protein-coding gene	gene with protein product		607081				11920573	Standard	NM_018009		Approved	TAPBP-R, FLJ10143, TAPBPR	uc001qog.4	Q9BX59		ENST00000266556.7:c.1222T>G	12.37:g.6570035T>G	ENSP00000266556:p.Leu408Val	49.0	0.0		38.0	16.0	NM_018009	Q9NWB8	Missense_Mutation	SNP	ENST00000266556.7	37	CCDS8546.1	.	.	.	.	.	.	.	.	.	.	T	8.380	0.837234	0.16891	.	.	ENSG00000139192	ENST00000266556	T	0.08102	3.13	5.24	1.35	0.21983	Immunoglobulin-like fold (1);	0.776617	0.12688	N	0.447397	T	0.04998	0.0134	L	0.38175	1.15	0.09310	N	1	B	0.26318	0.146	B	0.21360	0.034	T	0.44528	-0.9322	10	0.07030	T	0.85	-0.11	4.3505	0.11153	0.2938:0.0866:0.0:0.6196	.	408	Q9BX59	TPSNR_HUMAN	V	408	ENSP00000266556:L408V	ENSP00000266556:L408V	L	+	1	2	TAPBPL	6440296	0.001000	0.12720	0.001000	0.08648	0.488000	0.33401	0.454000	0.21827	0.117000	0.18138	0.533000	0.62120	TTG	.		0.602	TAPBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399263.1	NM_018009	
TBC1D4	9882	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	13	75884197	75884197	+	Missense_Mutation	SNP	T	T	A	rs531614085	byFrequency	TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr13:75884197T>A	ENST00000377636.3	-	14	2820	c.2474A>T	c.(2473-2475)gAt>gTt	p.D825V	TBC1D4_ENST00000431480.2_Missense_Mutation_p.D817V|TBC1D4_ENST00000425511.1_Missense_Mutation_p.D42V|TBC1D4_ENST00000377625.2_Missense_Mutation_p.D762V	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	825					cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		TTCTGGGTCATCCTCCCCAGA	0.463													T|||	2	0.000399361	0.0	0.0	5008	,	,		17576	0.0		0.0	False		,,,				2504	0.002				p.D825V		.											.	TBC1D4	95	0			c.A2474T						.						107.0	95.0	99.0					13																	75884197		1858	4094	5952	SO:0001583	missense	9882	exon14			GGGTCATCCTCCC	AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"""Akt substrate of 160 kDa"""	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.2474A>T	13.37:g.75884197T>A	ENSP00000366863:p.Asp825Val	94.0	0.0		60.0	30.0	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Missense_Mutation	SNP	ENST00000377636.3	37	CCDS41901.1	.	.	.	.	.	.	.	.	.	.	T	17.45	3.392953	0.62066	.	.	ENSG00000136111	ENST00000377636;ENST00000431480;ENST00000377625;ENST00000425511;ENST00000413735	T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;1.73	5.93	5.93	0.95920	.	0.244954	0.35436	N	0.003213	T	0.50854	0.1640	L	0.54323	1.7	0.52501	D	0.999954	B;B;B;P	0.40619	0.116;0.404;0.21;0.724	B;B;B;P	0.48063	0.046;0.281;0.124;0.565	T	0.48854	-0.8998	10	0.49607	T	0.09	-9.4382	16.3798	0.83452	0.0:0.0:0.0:1.0	.	42;762;817;825	O60343-4;O60343-2;O60343-3;O60343	.;.;.;TBCD4_HUMAN	V	825;817;762;42;274	ENSP00000366863:D825V;ENSP00000395986:D817V;ENSP00000366852:D762V;ENSP00000390654:D42V;ENSP00000396932:D274V	ENSP00000366852:D762V	D	-	2	0	TBC1D4	74782198	1.000000	0.71417	0.883000	0.34634	0.956000	0.61745	3.447000	0.52936	2.271000	0.75665	0.533000	0.62120	GAT	.		0.463	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832	
TBR1	10716	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	162273413	162273413	+	Silent	SNP	C	C	T			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr2:162273413C>T	ENST00000389554.3	+	1	809	c.492C>T	c.(490-492)tcC>tcT	p.S164S	TBR1_ENST00000410035.1_5'Flank	NM_006593.2	NP_006584.1	Q16650	TBR1_HUMAN	T-box, brain, 1	164					axon guidance (GO:0007411)|brain development (GO:0007420)|hindbrain development (GO:0030902)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of neuron projection development (GO:0010975)|specification of organ identity (GO:0010092)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(1)|skin(3)	30						TGTCCAACTCCTCGCCGCAGG	0.662																																					p.S164S		.											.	TBR1	91	0			c.C492T						.						71.0	74.0	73.0					2																	162273413		2203	4300	6503	SO:0001819	synonymous_variant	10716	exon1			CAACTCCTCGCCG	U49250	CCDS33310.1	2q24.2	2011-06-13			ENSG00000136535	ENSG00000136535		"""T-boxes"""	11590	protein-coding gene	gene with protein product		604616				7619531	Standard	NM_006593		Approved		uc002ubw.1	Q16650	OTTHUMG00000153888	ENST00000389554.3:c.492C>T	2.37:g.162273413C>T		80.0	0.0		50.0	19.0	NM_006593	B0AZS4|B2R6G5|Q14DC5|Q53TH0|Q56A81	Silent	SNP	ENST00000389554.3	37	CCDS33310.1																																																																																			.		0.662	TBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332845.1	NM_006593	
TCF15	6939	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	20	585251	585251	+	Missense_Mutation	SNP	C	C	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr20:585251C>A	ENST00000246080.3	-	2	744	c.584G>T	c.(583-585)cGa>cTa	p.R195L		NM_004609.3	NP_004600.2	Q12870	TCF15_HUMAN	transcription factor 15 (basic helix-loop-helix)	195					death (GO:0016265)|ear development (GO:0043583)|eating behavior (GO:0042755)|establishment of epithelial cell apical/basal polarity (GO:0045198)|mesenchymal to epithelial transition (GO:0060231)|mesoderm development (GO:0007498)|muscle organ morphogenesis (GO:0048644)|neuromuscular process controlling posture (GO:0050884)|paraxial mesoderm development (GO:0048339)|post-anal tail morphogenesis (GO:0036342)|regulation of gene expression involved in extracellular matrix organization (GO:1901311)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|respiratory system process (GO:0003016)|skeletal system morphogenesis (GO:0048705)|skin development (GO:0043588)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|lung(2)|prostate(1)	4		Breast(17;0.231)				CCGTGGCCCTCGAAGGGGGGC	0.642																																					p.R195L		.											.	TCF15	90	0			c.G584T						.						11.0	12.0	12.0					20																	585251		2121	4169	6290	SO:0001583	missense	6939	exon2			GGCCCTCGAAGGG		CCDS33432.1	20p13	2013-05-21			ENSG00000125878	ENSG00000125878		"""Basic helix-loop-helix proteins"""	11627	protein-coding gene	gene with protein product		601010				8825648, 8041747	Standard	NM_004609		Approved	EC2, PARAXIS, bHLHa40	uc002wdz.3	Q12870	OTTHUMG00000031640	ENST00000246080.3:c.584G>T	20.37:g.585251C>A	ENSP00000246080:p.Arg195Leu	82.0	0.0		80.0	36.0	NM_004609	Q9NQQ1	Missense_Mutation	SNP	ENST00000246080.3	37	CCDS33432.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.190772	0.78789	.	.	ENSG00000125878	ENST00000246080	D	0.96265	-3.96	5.08	4.13	0.48395	.	0.000000	0.64402	D	0.000003	D	0.96975	0.9012	L	0.55481	1.735	0.30769	N	0.743195	D	0.63880	0.993	D	0.67725	0.953	D	0.95442	0.8526	10	0.72032	D	0.01	-1.0614	13.52	0.61561	0.0:0.8441:0.1559:0.0	.	195	Q12870	TCF15_HUMAN	L	195	ENSP00000246080:R195L	ENSP00000246080:R195L	R	-	2	0	TCF15	533251	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	4.235000	0.58666	1.489000	0.48450	0.655000	0.94253	CGA	.		0.642	TCF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077475.2	NM_004609	
THUMPD1	55623	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	16	20749100	20749100	+	Silent	SNP	T	T	C			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	T	T	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr16:20749100T>C	ENST00000381337.2	-	3	929	c.585A>G	c.(583-585)acA>acG	p.T195T	THUMPD1_ENST00000396083.2_Silent_p.T195T|THUMPD1_ENST00000431224.2_Silent_p.T281T	NM_017736.3	NP_060206.2	Q9NXG2	THUM1_HUMAN	THUMP domain containing 1	195	THUMP. {ECO:0000255|PROSITE- ProRule:PRU00529}.						poly(A) RNA binding (GO:0044822)			NS(2)|large_intestine(2)|lung(6)|pancreas(1)|urinary_tract(1)	12						CAATCTGAAATGTCCCTTTGT	0.363																																					p.T195T		.											.	THUMPD1	90	0			c.A585G						.						126.0	122.0	124.0					16																	20749100		2201	4300	6501	SO:0001819	synonymous_variant	55623	exon3			CTGAAATGTCCCT	BC000448	CCDS10588.1	16p13.11	2010-06-17			ENSG00000066654	ENSG00000066654			23807	protein-coding gene	gene with protein product							Standard	XM_005255422		Approved	FLJ20274	uc002dho.3	Q9NXG2	OTTHUMG00000131558	ENST00000381337.2:c.585A>G	16.37:g.20749100T>C		268.0	1.0		187.0	60.0	NM_017736	Q9BWC3	Silent	SNP	ENST00000381337.2	37	CCDS10588.1																																																																																			.		0.363	THUMPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254420.1	NM_017736	
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	7577509	7577509	+	Missense_Mutation	SNP	C	C	T	rs121912652		TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr17:7577509C>T	ENST00000269305.4	-	7	961	c.772G>A	c.(772-774)Gaa>Aaa	p.E258K	TP53_ENST00000574684.1_5'Flank|TP53_ENST00000420246.2_Missense_Mutation_p.E258K|TP53_ENST00000359597.4_Missense_Mutation_p.E258K|TP53_ENST00000413465.2_Missense_Mutation_p.E258K|TP53_ENST00000455263.2_Missense_Mutation_p.E258K|TP53_ENST00000445888.2_Missense_Mutation_p.E258K	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	258	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		E -> A (in sporadic cancers; somatic mutation).|E -> D (in sporadic cancers; somatic mutation).|E -> G (in sporadic cancers; somatic mutation).|E -> K (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1978757}.|E -> L (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|E -> Q (in sporadic cancers; somatic mutation).|E -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|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 transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.E258K(40)|p.E258*(15)|p.E258Q(9)|p.0?(8)|p.?(1)|p.E258fs*85(1)|p.E258>XX(1)|p.E258fs*71(1)|p.E258fs*2(1)|p.E258_S260delEDS(1)|p.E258del(1)|p.T256fs*87(1)|p.E258L(1)|p.E258fs*87(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CTGGAGTCTTCCAGTGTGATG	0.587		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.E258K	Pancreas(47;798 1329 9957 10801)	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	TP53,NS,carcinoma,0	TP53	70225	82	Substitution - Missense(50)|Substitution - Nonsense(15)|Whole gene deletion(8)|Deletion - Frameshift(5)|Deletion - In frame(2)|Unknown(1)|Complex - insertion inframe(1)	large_intestine(14)|urinary_tract(10)|upper_aerodigestive_tract(7)|haematopoietic_and_lymphoid_tissue(7)|skin(7)|lung(6)|oesophagus(5)|central_nervous_system(4)|breast(4)|ovary(4)|bone(4)|stomach(2)|liver(2)|thyroid(1)|soft_tissue(1)|peritoneum(1)|biliary_tract(1)|endometrium(1)|pancreas(1)	c.G772A	GRCh37	CM900213	TP53	M	rs121912652	.						137.0	97.0	111.0					17																	7577509		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AGTCTTCCAGTGT	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.772G>A	17.37:g.7577509C>T	ENSP00000269305:p.Glu258Lys	67.0	1.0		24.0	18.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	19.81	3.896324	0.72639	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D;D	0.99856	-7.21;-7.21;-7.21;-7.21;-7.21;-7.21;-7.21	4.62	3.62	0.41486	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99871	0.9939	M	0.92367	3.3	0.80722	A	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	0.998;0.999;0.999;0.999;1.0	D	0.96542	0.9401	9	0.87932	D	0	-21.9865	12.6215	0.56605	0.0:0.8318:0.1682:0.0	.	258;258;258;258;258	P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;P53_HUMAN;.;.	K	258;258;258;258;258;258;247;126	ENSP00000410739:E258K;ENSP00000352610:E258K;ENSP00000269305:E258K;ENSP00000398846:E258K;ENSP00000391127:E258K;ENSP00000391478:E258K;ENSP00000425104:E126K	ENSP00000269305:E258K	E	-	1	0	TP53	7518234	1.000000	0.71417	1.000000	0.80357	0.402000	0.30811	7.609000	0.82925	1.266000	0.44231	0.462000	0.41574	GAA	.		0.587	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
USP25	29761	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	21	17238655	17238655	+	Missense_Mutation	SNP	G	G	C			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr21:17238655G>C	ENST00000285679.6	+	20	2956	c.2587G>C	c.(2587-2589)Gaa>Caa	p.E863Q	USP25_ENST00000285681.2_Missense_Mutation_p.E895Q|USP25_ENST00000351097.5_Intron|USP25_ENST00000400183.2_Missense_Mutation_p.E933Q	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	863					cellular protein modification process (GO:0006464)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|proteolysis (GO:0006508)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|SUMO binding (GO:0032183)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)		AAACTTGGAGGAATATGAGGT	0.348																																					p.E863Q		.											.	USP25	663	0			c.G2587C						.						120.0	126.0	124.0					21																	17238655		2203	4299	6502	SO:0001583	missense	29761	exon20			TTGGAGGAATATG	AF170562	CCDS33515.1, CCDS63336.1, CCDS63337.1	21q11.2	2011-02-24	2005-08-08		ENSG00000155313	ENSG00000155313		"""Ubiquitin-specific peptidases"""	12624	protein-coding gene	gene with protein product		604736	"""ubiquitin specific protease 25"""			12838346, 10612803	Standard	NM_013396		Approved	USP21	uc002yjy.1	Q9UHP3	OTTHUMG00000074343	ENST00000285679.6:c.2587G>C	21.37:g.17238655G>C	ENSP00000285679:p.Glu863Gln	54.0	0.0		39.0	11.0	NM_013396	C0LSZ0|Q6DHZ9|Q9H9W1	Missense_Mutation	SNP	ENST00000285679.6	37	CCDS33515.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.56|15.56	2.871012|2.871012	0.51695|0.51695	.|.	.|.	ENSG00000155313|ENSG00000155313	ENST00000285681;ENST00000285679;ENST00000400183|ENST00000449491	T;T;T|.	0.30448|.	1.59;1.71;1.53|.	5.93|5.93	5.93|5.93	0.95920|0.95920	.|.	0.091372|.	0.85682|.	D|.	0.000000|.	T|T	0.77061|0.77061	0.4075|0.4075	M|M	0.70275|0.70275	2.135|2.135	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	0.959;1.0;0.993|.	P;D;P|.	0.75484|.	0.835;0.986;0.777|.	T|T	0.74087|0.74087	-0.3778|-0.3778	10|5	0.87932|.	D|.	0|.	.|.	20.3465|20.3465	0.98790|0.98790	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	933;895;863|.	Q9UHP3-3;Q9UHP3-1;Q9UHP3|.	.;.;UBP25_HUMAN|.	Q|S	895;863;933|161	ENSP00000285681:E895Q;ENSP00000285679:E863Q;ENSP00000383044:E933Q|.	ENSP00000285679:E863Q|.	E|R	+|+	1|3	0|2	USP25|USP25	16160526|16160526	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.094000|0.094000	0.18550|0.18550	7.275000|7.275000	0.78548|0.78548	2.798000|2.798000	0.96311|0.96311	0.655000|0.655000	0.94253|0.94253	GAA|AGG	.		0.348	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1		
ZBTB38	253461	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	141163098	141163098	+	Missense_Mutation	SNP	A	A	G			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr3:141163098A>G	ENST00000514251.1	+	4	2147	c.1868A>G	c.(1867-1869)aAc>aGc	p.N623S	ZBTB38_ENST00000321464.5_Missense_Mutation_p.N624S|ZBTB38_ENST00000441582.2_Missense_Mutation_p.N623S					zinc finger and BTB domain containing 38											breast(3)|cervix(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	41						GATACTGTAAACACCCTGACC	0.453																																					p.N623S		.											.	ZBTB38	25	0			c.A1868G						.						88.0	85.0	86.0					3																	141163098		1980	4180	6160	SO:0001583	missense	253461	exon8			CTGTAAACACCCT	BC015444	CCDS43157.1	3q23	2014-06-13			ENSG00000177311	ENSG00000177311		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	26636	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 171"""	612218				12477932	Standard	NM_001080412		Approved	FLJ35036, CIBZ, ZNF921, PPP1R171	uc003etw.3	Q8NAP3	OTTHUMG00000160128	ENST00000514251.1:c.1868A>G	3.37:g.141163098A>G	ENSP00000426387:p.Asn623Ser	72.0	0.0		52.0	16.0	NM_001080412		Missense_Mutation	SNP	ENST00000514251.1	37	CCDS43157.1	.	.	.	.	.	.	.	.	.	.	A	5.842	0.339587	0.11069	.	.	ENSG00000177311	ENST00000509883;ENST00000514251;ENST00000441582;ENST00000321464	T;T;T;T	0.08370	3.58;3.1;3.1;3.1	5.55	-0.817	0.10836	.	0.630837	0.16193	N	0.225297	T	0.04318	0.0119	N	0.12182	0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.43621	-0.9380	9	.	.	.	-4.4441	11.5098	0.50486	0.4476:0.0:0.5524:0.0	.	624;623	B4DYR8;Q8NAP3	.;ZBT38_HUMAN	S	623;623;623;624	ENSP00000424254:N623S;ENSP00000426387:N623S;ENSP00000406955:N623S;ENSP00000372635:N624S	.	N	+	2	0	ZBTB38	142645788	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.076000	0.11412	-0.138000	0.11434	0.528000	0.53228	AAC	.		0.453	ZBTB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359329.2		
ZNF208	7757	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	22170097	22170097	+	Missense_Mutation	SNP	C	C	A			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	C	C	.	.	.	.	.	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr19:22170097C>A	ENST00000397126.4	-	3	295	c.147G>T	c.(145-147)aaG>aaT	p.K49N	ZNF208_ENST00000599916.1_Missense_Mutation_p.K49N|ZNF208_ENST00000601773.1_Missense_Mutation_p.K49N|ZNF208_ENST00000597040.1_Missense_Mutation_p.K17N	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	49	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				TCAGGTCTGGCTTAAAGGCAG	0.398																																					p.K49N		.											.	ZNF208	7	0			c.G147T						.						66.0	69.0	68.0					19																	22170097		2191	4296	6487	SO:0001583	missense	7757	exon3			GTCTGGCTTAAAG	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"""Zinc fingers, C2H2-type"", ""-"""	12999	protein-coding gene	gene with protein product	"""zinc finger protein 95"""	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.147G>T	19.37:g.22170097C>A	ENSP00000380315:p.Lys49Asn	143.0	1.0		98.0	42.0	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	C	3.792	-0.043550	0.07452	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.00932	5.53	0.207	0.207	0.15214	Krueppel-associated box (3);	.	.	.	.	T	0.00815	0.0027	.	.	.	0.09310	N	1	B;B	0.32918	0.259;0.39	B;B	0.31686	0.039;0.134	T	0.49418	-0.8942	7	0.44086	T	0.13	.	.	.	.	.	49;49	O43345;F8WEA0	ZN208_HUMAN;.	N	49	ENSP00000380315:K49N	ENSP00000380315:K49N	K	-	3	2	ZNF208	21961937	0.000000	0.05858	0.032000	0.17829	0.032000	0.12392	-0.170000	0.09897	0.284000	0.22305	0.289000	0.19496	AAG	.		0.398	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153	
ZNF677	342926	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	53740390	53740390	+	Silent	SNP	G	G	C			TCGA-RC-A7SB-01A-21D-A34Z-10	TCGA-RC-A7SB-10A-01D-A34Z-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	906caed8-06ec-4a56-b592-ea4c8715c043	071958a4-a5e0-4313-ada8-998353863ae3	g.chr19:53740390G>C	ENST00000598513.1	-	5	1740	c.1590C>G	c.(1588-1590)ctC>ctG	p.L530L	ZNF677_ENST00000333952.4_Silent_p.L530L	NM_182609.2	NP_872415.1	Q86XU0	ZN677_HUMAN	zinc finger protein 677	530					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(13)|lung(6)|ovary(1)|pancreas(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(134;0.00352)		GGTGTCTAGTGAGGTTTGCAA	0.333																																					p.L530L		.											.	ZNF677	91	0			c.C1590G						.						134.0	127.0	130.0					19																	53740390		2203	4299	6502	SO:0001819	synonymous_variant	342926	exon5			TCTAGTGAGGTTT	BC050038	CCDS12861.1	19q13.42	2013-01-08				ENSG00000197928		"""Zinc fingers, C2H2-type"", ""-"""	28730	protein-coding gene	gene with protein product	"""hypothetical protein MGC48625"""					12477932	Standard	NM_182609		Approved	MGC48625	uc002qbg.1	Q86XU0		ENST00000598513.1:c.1590C>G	19.37:g.53740390G>C		229.0	0.0		157.0	68.0	NM_182609		Silent	SNP	ENST00000598513.1	37	CCDS12861.1																																																																																			.		0.333	ZNF677-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464189.1	NM_182609	
