#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count
SYNPO2L	79933	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	75406654	75406654	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-4942-01A-01D-1468-08	TCGA-CS-4942-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ee5832e7-577c-4507-a4fd-a70646fabc24	f2b83686-8044-4e74-9554-8b4d3c40b2b2	g.chr10:75406654A>G	ENST00000394810.2	-	4	2905	c.2756T>C	c.(2755-2757)aTc>aCc	p.I919T	SYNPO2L_ENST00000372873.4_Missense_Mutation_p.I695T	NM_001114133.1	NP_001107605.1	Q9H987	SYP2L_HUMAN	synaptopodin 2-like	919	Pro-rich.					cytoskeleton (GO:0005856)|nucleus (GO:0005634)|Z disc (GO:0030018)				breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Prostate(51;0.0112)					TGTTCTCCAGATGGGCTCATC	0.652																																																0													46.0	45.0	46.0					10																	75406654		2203	4300	6503	SO:0001583	missense	79933			AK022983	CCDS7331.1, CCDS44438.1	10q22.3	2007-12-19			ENSG00000166317	ENSG00000166317			23532	protein-coding gene	gene with protein product							Standard	XM_005270158		Approved	FLJ12921	uc001jut.4	Q9H987	OTTHUMG00000018471	ENST00000394810.2:c.2756T>C	10.37:g.75406654A>G	ENSP00000378289:p.Ile919Thr		A5PKV9|Q68A20	Missense_Mutation	SNP	ENST00000394810.2	37	CCDS44438.1	.	.	.	.	.	.	.	.	.	.	A	13.68	2.310783	0.40895	.	.	ENSG00000166317	ENST00000372873;ENST00000394810	T;T	0.22539	1.95;2.27	4.93	4.93	0.64822	.	0.332641	0.28983	N	0.013502	T	0.13670	0.0331	N	0.24115	0.695	0.29093	N	0.88199	B;B	0.33637	0.296;0.42	B;B	0.32928	0.074;0.155	T	0.09100	-1.0690	10	0.09338	T	0.73	-12.9654	14.7518	0.69530	1.0:0.0:0.0:0.0	.	919;695	Q9H987;Q9H987-2	SYP2L_HUMAN;.	T	695;919	ENSP00000361964:I695T;ENSP00000378289:I919T	ENSP00000361964:I695T	I	-	2	0	SYNPO2L	75076660	0.999000	0.42202	1.000000	0.80357	0.994000	0.84299	4.103000	0.57783	2.059000	0.61396	0.459000	0.35465	ATC		0.652	SYNPO2L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316562.2	NM_024875		36	47	36	47
F2	2147	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	11	46760818	46760818	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-4942-01A-01D-1468-08	TCGA-CS-4942-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ee5832e7-577c-4507-a4fd-a70646fabc24	f2b83686-8044-4e74-9554-8b4d3c40b2b2	g.chr11:46760818C>T	ENST00000311907.5	+	14	1785	c.1729C>T	c.(1729-1731)Ccc>Tcc	p.P577S	F2_ENST00000530231.1_Missense_Mutation_p.P538S	NM_000506.3	NP_000497.1	P00734	THRB_HUMAN	coagulation factor II (thrombin)	577	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell surface receptor signaling pathway (GO:0007166)|cellular protein metabolic process (GO:0044267)|cytosolic calcium ion homeostasis (GO:0051480)|fibrinolysis (GO:0042730)|leukocyte migration (GO:0050900)|multicellular organismal development (GO:0007275)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of platelet activation (GO:0010544)|negative regulation of proteolysis (GO:0045861)|peptidyl-glutamic acid carboxylation (GO:0017187)|platelet activation (GO:0030168)|positive regulation of blood coagulation (GO:0030194)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900738)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|regulation of blood coagulation (GO:0030193)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)	blood microparticle (GO:0072562)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|receptor binding (GO:0005102)|serine-type endopeptidase activity (GO:0004252)|thrombospondin receptor activity (GO:0070053)			endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	27		all_lung(304;0.000414)|Lung NSC(402;0.0011)		BRCA - Breast invasive adenocarcinoma(625;0.146)	Antihemophilic Factor(DB00025)|Argatroban(DB00278)|ART-123(DB05777)|Bivalirudin(DB00006)|Coagulation Factor IX(DB00100)|Dabigatran etexilate(DB06695)|Drotrecogin alfa(DB00055)|Lepirudin(DB00001)|Menadione(DB00170)|Proflavine(DB01123)|Suramin(DB04786)|Ximelagatran(DB04898)	TCTTCAGAGCCCCTTTAACAA	0.478																																					Esophageal Squamous(147;1147 1808 2148 38609 51144)											0													115.0	112.0	113.0					11																	46760818		2201	4299	6500	SO:0001583	missense	2147			M33031	CCDS31476.1	11p11.2	2013-02-28			ENSG00000180210	ENSG00000180210	3.4.21.5	"""Endogenous ligands"""	3535	protein-coding gene	gene with protein product	"""prepro-coagulation factor II"""	176930					Standard	NM_000506		Approved		uc001ndf.4	P00734	OTTHUMG00000150344	ENST00000311907.5:c.1729C>T	11.37:g.46760818C>T	ENSP00000308541:p.Pro577Ser		B2R7F7|B4E1A7|Q4QZ40|Q53H04|Q53H06|Q69EZ7|Q7Z7P3|Q9UCA1	Missense_Mutation	SNP	ENST00000311907.5	37	CCDS31476.1	.	.	.	.	.	.	.	.	.	.	C	13.99	2.400391	0.42613	.	.	ENSG00000180210	ENST00000311907;ENST00000530231	D;D	0.88277	-2.36;-2.36	5.1	4.18	0.49190	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.109676	0.64402	D	0.000005	D	0.83482	0.5264	L	0.31157	0.91	0.58432	D	0.999999	P	0.41232	0.743	B	0.41332	0.354	D	0.84188	0.0443	10	0.87932	D	0	.	11.7098	0.51618	0.0:0.918:0.0:0.082	.	577	P00734	THRB_HUMAN	S	577;538	ENSP00000308541:P577S;ENSP00000433907:P538S	ENSP00000308541:P577S	P	+	1	0	F2	46717394	1.000000	0.71417	0.919000	0.36401	0.006000	0.05464	3.291000	0.51764	1.162000	0.42619	0.558000	0.71614	CCC		0.478	F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317706.1			51	95	51	95
DGKH	160851	hgsc.bcm.edu;broad.mit.edu	37	13	42763202	42763202	+	Silent	SNP	C	C	T			TCGA-CS-4942-01A-01D-1468-08	TCGA-CS-4942-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ee5832e7-577c-4507-a4fd-a70646fabc24	f2b83686-8044-4e74-9554-8b4d3c40b2b2	g.chr13:42763202C>T	ENST00000337343.4	+	15	1690	c.1669C>T	c.(1669-1671)Ctg>Ttg	p.L557L	DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000536612.1_Silent_p.L421L|DGKH_ENST00000261491.5_Silent_p.L557L|DGKH_ENST00000538674.1_Silent_p.L312L|DGKH_ENST00000379274.2_Silent_p.L421L|DGKH_ENST00000540693.1_Silent_p.L557L	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	557					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		GCTCGAACAACTGCTGCAGGC	0.463																																																0													59.0	61.0	61.0					13																	42763202		2203	4300	6503	SO:0001819	synonymous_variant	160851			AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2854	protein-coding gene	gene with protein product		604071				8702685	Standard	XM_005266271		Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	ENST00000337343.4:c.1669C>T	13.37:g.42763202C>T			A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Silent	SNP	ENST00000337343.4	37	CCDS9381.1																																																																																				0.463	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009		7	125	7	125
TP53	7157	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	17	7577114	7577114	+	Missense_Mutation	SNP	C	C	A			TCGA-CS-4942-01A-01D-1468-08	TCGA-CS-4942-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ee5832e7-577c-4507-a4fd-a70646fabc24	f2b83686-8044-4e74-9554-8b4d3c40b2b2	g.chr17:7577114C>A	ENST00000269305.4	-	8	1013	c.824G>T	c.(823-825)tGt>tTt	p.C275F	TP53_ENST00000455263.2_Missense_Mutation_p.C275F|TP53_ENST00000359597.4_Missense_Mutation_p.C275F|TP53_ENST00000445888.2_Missense_Mutation_p.C275F|TP53_ENST00000413465.2_Intron|TP53_ENST00000420246.2_Missense_Mutation_p.C275F|TP53_ENST00000574684.1_5'Flank	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	275	Interaction with AXIN1. {ECO:0000250}.|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		C -> F (in sporadic cancers; somatic mutation).|C -> G (in sporadic cancers; somatic mutation).|C -> R (in sporadic cancers; somatic mutation).|C -> S (in sporadic cancers; somatic mutation).|C -> W (in sporadic cancers; somatic mutation).|C -> Y (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:7887414}.		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.C275Y(53)|p.C275F(37)|p.0?(8)|p.C275fs*70(3)|p.?(2)|p.C275S(2)|p.C275fs*20(1)|p.L265_K305del41(1)|p.R273_C275delRVC(1)|p.F270_D281del12(1)|p.V274_P278del(1)|p.A276fs*29(1)|p.S269fs*21(1)|p.C275fs*67(1)|p.V272_K292del21(1)|p.C275_R283delCACPGRDRR(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)	AGGACAGGCACAAACACGCAC	0.552		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)																											Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	115	Substitution - Missense(92)|Whole gene deletion(8)|Deletion - Frameshift(7)|Deletion - In frame(6)|Unknown(2)	lung(14)|large_intestine(13)|breast(13)|upper_aerodigestive_tract(12)|central_nervous_system(10)|haematopoietic_and_lymphoid_tissue(10)|ovary(7)|urinary_tract(6)|stomach(5)|oesophagus(5)|bone(5)|liver(5)|skin(3)|pancreas(2)|NS(2)|prostate(2)|biliary_tract(1)	GRCh37	CM076568|CM951234	TP53	M							71.0	61.0	64.0					17																	7577114		2203	4300	6503	SO:0001583	missense	7157	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;	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.824G>T	17.37:g.7577114C>A	ENSP00000269305:p.Cys275Phe		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	24.5	4.536533	0.85812	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99874	-7.39;-7.39;-7.39;-7.39;-7.39;-7.39	4.92	4.92	0.64577	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	0.99883	0.9944	M	0.92738	3.34	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.998	D;D;D;D	0.97110	0.993;1.0;0.993;0.993	D	0.96317	0.9233	10	0.87932	D	0	-17.2181	15.662	0.77193	0.0:1.0:0.0:0.0	.	275;275;275;275	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	F	275;275;275;275;275;264;143	ENSP00000352610:C275F;ENSP00000269305:C275F;ENSP00000398846:C275F;ENSP00000391127:C275F;ENSP00000391478:C275F;ENSP00000425104:C143F	ENSP00000269305:C275F	C	-	2	0	TP53	7517839	1.000000	0.71417	0.999000	0.59377	0.904000	0.53231	7.587000	0.82613	2.556000	0.86216	0.462000	0.41574	TGT		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		52	11	52	11
YES1	7525	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	18	756710	756710	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-4942-01A-01D-1468-08	TCGA-CS-4942-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ee5832e7-577c-4507-a4fd-a70646fabc24	f2b83686-8044-4e74-9554-8b4d3c40b2b2	g.chr18:756710A>G	ENST00000584307.1	-	2	288	c.118T>C	c.(118-120)Tca>Cca	p.S40P	YES1_ENST00000577611.1_5'UTR|YES1_ENST00000577961.1_Missense_Mutation_p.S45P|YES1_ENST00000314574.4_Missense_Mutation_p.S40P			P07947	YES_HUMAN	YES proto-oncogene 1, Src family tyrosine kinase	40					blood coagulation (GO:0007596)|cellular protein modification process (GO:0006464)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|glucose transport (GO:0015758)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|regulation of vascular permeability (GO:0043114)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(1)	17					Dasatinib(DB01254)	GGACATGGTGACACTGTAGTG	0.453																																																0													231.0	195.0	207.0					18																	756710		2203	4300	6503	SO:0001583	missense	7525			M15990	CCDS11824.1	18p11.31-p11.21	2014-06-26	2014-06-26		ENSG00000176105	ENSG00000176105		"""SH2 domain containing"""	12841	protein-coding gene	gene with protein product		164880	"""v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1"""			2983418	Standard	NM_005433		Approved	Yes, c-yes, HsT441	uc002kky.3	P07947	OTTHUMG00000131472	ENST00000584307.1:c.118T>C	18.37:g.756710A>G	ENSP00000462468:p.Ser40Pro		A6NLB3|D3DUH1	Missense_Mutation	SNP	ENST00000584307.1	37	CCDS11824.1	.	.	.	.	.	.	.	.	.	.	A	4.888	0.165111	0.09339	.	.	ENSG00000176105	ENST00000359834;ENST00000314574	T	0.75050	-0.9	4.66	-1.53	0.08611	.	1.103580	0.06679	N	0.767566	T	0.49525	0.1562	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25882	-1.0119	10	0.27785	T	0.31	.	4.3571	0.11183	0.2588:0.2688:0.0:0.4724	.	40	P07947	YES_HUMAN	P	40	ENSP00000324740:S40P	ENSP00000324740:S40P	S	-	1	0	YES1	746710	0.001000	0.12720	0.019000	0.16419	0.870000	0.49936	-0.540000	0.06106	-0.181000	0.10619	0.260000	0.18958	TCA		0.453	YES1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440827.2	NM_005433		115	183	115	183
ASPM	259266	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	1	197072215	197072215	+	Missense_Mutation	SNP	C	C	G			TCGA-CS-4942-01A-01D-1468-08	TCGA-CS-4942-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ee5832e7-577c-4507-a4fd-a70646fabc24	f2b83686-8044-4e74-9554-8b4d3c40b2b2	g.chr1:197072215C>G	ENST00000367409.4	-	18	6422	c.6166G>C	c.(6166-6168)Gct>Cct	p.A2056P	ASPM_ENST00000367408.1_Intron|ASPM_ENST00000294732.7_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2056	IQ 15. {ECO:0000255|PROSITE- ProRule:PRU00116}.				developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						GTTTTGTAAGCTCTGTATTTA	0.343																																																0													100.0	106.0	104.0					1																	197072215		2202	4296	6498	SO:0001583	missense	259266			AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"""microcephaly, primary autosomal recessive 5"", ""asp (abnormal spindle)-like, microcephaly associated (Drosophila)"""	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.6166G>C	1.37:g.197072215C>G	ENSP00000356379:p.Ala2056Pro		Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	37	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	c	13.77	2.337602	0.41398	.	.	ENSG00000066279	ENST00000367409	T	0.28666	1.6	5.46	3.42	0.39159	.	0.162904	0.43416	D	0.000568	T	0.55924	0.1951	M	0.90595	3.13	0.21386	N	0.999702	D	0.76494	0.999	D	0.72075	0.976	T	0.49390	-0.8945	10	0.56958	D	0.05	.	6.5108	0.22220	0.3905:0.5134:0.0:0.0961	.	2056	Q8IZT6	ASPM_HUMAN	P	2056	ENSP00000356379:A2056P	ENSP00000356379:A2056P	A	-	1	0	ASPM	195338838	0.970000	0.33590	0.154000	0.22540	0.548000	0.35241	1.549000	0.36212	1.293000	0.44690	0.632000	0.83419	GCT		0.343	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		95	202	95	202
POLR1A	25885	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	86316951	86316951	+	Silent	SNP	G	G	A	rs199538363	byFrequency	TCGA-CS-4942-01A-01D-1468-08	TCGA-CS-4942-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ee5832e7-577c-4507-a4fd-a70646fabc24	f2b83686-8044-4e74-9554-8b4d3c40b2b2	g.chr2:86316951G>A	ENST00000263857.6	-	4	912	c.534C>T	c.(532-534)ggC>ggT	p.G178G	POLR1A_ENST00000409681.1_Silent_p.G178G			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	178					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						TCACATGTGCGCCCTGGGACC	0.458													G|||	2	0.000399361	0.0	0.0	5008	,	,		20977	0.002		0.0	False		,,,				2504	0.0															0								G		0,3838		0,0,1919	153.0	152.0	152.0		534	-10.4	0.0	2		152	1,8261		0,1,4130	no	coding-synonymous	POLR1A	NM_015425.3		0,1,6049	AA,AG,GG		0.0121,0.0,0.0083		178/1721	86316951	1,12099	1919	4131	6050	SO:0001819	synonymous_variant	25885			AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"""RNA polymerase subunits"""	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.534C>T	2.37:g.86316951G>A			B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Silent	SNP	ENST00000263857.6	37	CCDS42706.1																																																																																				0.458	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425		44	98	44	98
SLC9A4	389015	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	103149082	103149082	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-4942-01A-01D-1468-08	TCGA-CS-4942-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ee5832e7-577c-4507-a4fd-a70646fabc24	f2b83686-8044-4e74-9554-8b4d3c40b2b2	g.chr2:103149082A>G	ENST00000295269.4	+	12	2789	c.2332A>G	c.(2332-2334)Aca>Gca	p.T778A		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	778					epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						GTCGAGGTGGACAGCTGACCA	0.502																																																0													79.0	50.0	60.0					2																	103149082		2203	4300	6503	SO:0001583	missense	389015				CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"""Solute carriers"""	11077	protein-coding gene	gene with protein product		600531	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 4"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 4"""			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.2332A>G	2.37:g.103149082A>G	ENSP00000295269:p.Thr778Ala		Q69YK0	Missense_Mutation	SNP	ENST00000295269.4	37	CCDS33264.1	.	.	.	.	.	.	.	.	.	.	A	10.96	1.497360	0.26861	.	.	ENSG00000180251	ENST00000295269	T	0.43688	0.94	5.31	1.5	0.22942	.	0.351810	0.29369	N	0.012348	T	0.21103	0.0508	L	0.27053	0.805	0.27206	N	0.960035	B	0.16603	0.018	B	0.14023	0.01	T	0.27434	-1.0074	10	0.06494	T	0.89	.	5.4417	0.16513	0.4952:0.1276:0.0:0.3773	.	778	Q6AI14	SL9A4_HUMAN	A	778	ENSP00000295269:T778A	ENSP00000295269:T778A	T	+	1	0	SLC9A4	102515514	0.678000	0.27586	0.137000	0.22149	0.131000	0.20780	0.565000	0.23578	0.067000	0.16545	0.533000	0.62120	ACA		0.502	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3		13	23	13	23
RGPD4	285190	hgsc.bcm.edu;broad.mit.edu	37	2	108496508	108496508	+	Missense_Mutation	SNP	A	A	T			TCGA-CS-4942-01A-01D-1468-08	TCGA-CS-4942-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ee5832e7-577c-4507-a4fd-a70646fabc24	f2b83686-8044-4e74-9554-8b4d3c40b2b2	g.chr2:108496508A>T	ENST00000408999.3	+	21	5086	c.5009A>T	c.(5008-5010)aAc>aTc	p.N1670I	RGPD4_ENST00000354986.4_Missense_Mutation_p.N1670I	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	1670					protein targeting to Golgi (GO:0000042)					breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						GATCACTTAAACGGCCTGCTT	0.453																																																0													163.0	136.0	144.0					2																	108496508		692	1591	2283	SO:0001583	missense	285190			BX537861	CCDS46381.1	2q12.3	2013-01-10			ENSG00000196862	ENSG00000196862		"""Tetratricopeptide (TTC) repeat domain containing"""	32417	protein-coding gene	gene with protein product		612707				15710750, 15815621	Standard	NM_182588		Approved	RGP4, DKFZp686P0288	uc010ywk.2	Q7Z3J3	OTTHUMG00000153208	ENST00000408999.3:c.5009A>T	2.37:g.108496508A>T	ENSP00000386810:p.Asn1670Ile		B9A029	Missense_Mutation	SNP	ENST00000408999.3	37	CCDS46381.1	.	.	.	.	.	.	.	.	.	.	a	8.364	0.833727	0.16820	.	.	ENSG00000196862	ENST00000354986;ENST00000408999;ENST00000439322	T;T	0.40476	1.03;1.03	0.854	-0.379	0.12493	.	.	.	.	.	T	0.28499	0.0705	L	0.40543	1.245	0.24770	N	0.992875	B	0.27498	0.18	B	0.23275	0.045	T	0.20107	-1.0285	9	0.51188	T	0.08	-5.0008	4.6074	0.12385	0.5863:0.0:0.4137:0.0	.	1670	Q7Z3J3	RGPD4_HUMAN	I	1670;1670;1037	ENSP00000347081:N1670I;ENSP00000386810:N1670I	ENSP00000347081:N1670I	N	+	2	0	RGPD4	107862940	1.000000	0.71417	0.969000	0.41365	0.821000	0.46438	3.742000	0.55097	-0.138000	0.11434	0.327000	0.21459	AAC		0.453	RGPD4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330096.2	XM_496581		18	326	18	326
ACTR3	10096	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	114699855	114699855	+	Silent	SNP	C	C	T			TCGA-CS-4942-01A-01D-1468-08	TCGA-CS-4942-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ee5832e7-577c-4507-a4fd-a70646fabc24	f2b83686-8044-4e74-9554-8b4d3c40b2b2	g.chr2:114699855C>T	ENST00000263238.2	+	8	1097	c.777C>T	c.(775-777)atC>atT	p.I259I	ACTR3_ENST00000535589.2_Silent_p.I208I|ACTR3_ENST00000536059.1_Silent_p.I197I	NM_001277140.1|NM_005721.3	NP_001264069.1|NP_005712.1	P61158	ARP3_HUMAN	ARP3 actin-related protein 3 homolog (yeast)	259					Arp2/3 complex-mediated actin nucleation (GO:0034314)|asymmetric cell division (GO:0008356)|cellular component movement (GO:0006928)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|meiotic chromosome movement towards spindle pole (GO:0016344)|meiotic cytokinesis (GO:0033206)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of neuron differentiation (GO:0045666)|regulation of myosin II filament organization (GO:0043519)|response to antibiotic (GO:0046677)|response to carbohydrate (GO:0009743)|spindle localization (GO:0051653)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|excitatory synapse (GO:0060076)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|hemidesmosome (GO:0030056)|lamellipodium (GO:0030027)|membrane (GO:0016020)|podosome (GO:0002102)	ATP binding (GO:0005524)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(2)	15						ATACTGGAATCAATGCTATCT	0.328																																																0													105.0	106.0	106.0					2																	114699855		2203	4298	6501	SO:0001819	synonymous_variant	10096			AF006083	CCDS33277.1, CCDS63000.1	2q14.1	2010-07-20	2001-11-28		ENSG00000115091	ENSG00000115091			170	protein-coding gene	gene with protein product		604222	"""ARP3 (actin-related protein 3, yeast) homolog"""			9230079	Standard	NM_005721		Approved	ARP3	uc002tkx.2	P61158	OTTHUMG00000153497	ENST00000263238.2:c.777C>T	2.37:g.114699855C>T			P32391|Q53QM2	Silent	SNP	ENST00000263238.2	37	CCDS33277.1																																																																																				0.328	ACTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331366.2	NM_005721		55	78	55	78
IDH1	3417	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	C	T	rs121913500		TCGA-CS-4942-01A-01D-1468-08	TCGA-CS-4942-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ee5832e7-577c-4507-a4fd-a70646fabc24	f2b83686-8044-4e74-9554-8b4d3c40b2b2	g.chr2:209113112C>T	ENST00000415913.1	-	4	776	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_ENST00000345146.2_Missense_Mutation_p.R132H|IDH1_ENST00000446179.1_Missense_Mutation_p.R132H	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:19117336}.|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation). {ECO:0000269|PubMed:19117336}.|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:19117336}.|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate). {ECO:0000269|PubMed:18772396}.		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R132H(2774)|p.R132L(59)|p.R132V(1)|p.G131_R132>VL(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393			Mis		gliobastoma																																Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	2835	Substitution - Missense(2834)|Complex - compound substitution(1)	central_nervous_system(2579)|haematopoietic_and_lymphoid_tissue(205)|bone(43)|prostate(4)|biliary_tract(2)|urinary_tract(1)|skin(1)											79.0	73.0	75.0					2																	209113112		2203	4300	6503	SO:0001583	missense	3417				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.395G>A	2.37:g.209113112C>T	ENSP00000390265:p.Arg132His		Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657324	0.88154	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913;ENST00000415282	D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.19	5.57	4.69	0.59074	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	H	0.99379	4.54	0.80722	D	1	B	0.25486	0.127	B	0.25405	0.06	D	0.92324	0.5868	10	0.87932	D	0	-20.0399	14.3783	0.66895	0.0:0.9288:0.0:0.0712	.	132	O75874	IDHC_HUMAN	H	132	ENSP00000260985:R132H;ENSP00000410513:R132H;ENSP00000390265:R132H;ENSP00000391075:R132H	ENSP00000260985:R132H	R	-	2	0	IDH1	208821357	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	6.088000	0.71371	1.356000	0.45884	0.555000	0.69702	CGT		0.393	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			34	71	34	71
LAMB2	3913	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	3	49159715	49159715	+	Silent	SNP	G	G	A			TCGA-CS-4942-01A-01D-1468-08	TCGA-CS-4942-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ee5832e7-577c-4507-a4fd-a70646fabc24	f2b83686-8044-4e74-9554-8b4d3c40b2b2	g.chr3:49159715G>A	ENST00000418109.1	-	29	4826	c.4662C>T	c.(4660-4662)caC>caT	p.H1554H	USP19_ENST00000398888.2_5'Flank|USP19_ENST00000488993.1_5'Flank|USP19_ENST00000417901.1_5'Flank|USP19_ENST00000398892.3_5'Flank|LAMB2_ENST00000305544.4_Silent_p.H1554H|LAMB2_ENST00000464891.1_5'Flank|USP19_ENST00000434032.2_5'Flank|USP19_ENST00000453664.1_5'Flank|USP19_ENST00000398898.2_5'Flank	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	1554	Domain I.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CACCCGCCAGGTGCTGGATCT	0.597																																																0													60.0	58.0	59.0					3																	49159715		2203	4300	6503	SO:0001819	synonymous_variant	3913				CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"""Laminins"""	6487	protein-coding gene	gene with protein product	"""laminin S"""	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.4662C>T	3.37:g.49159715G>A			Q16321	Silent	SNP	ENST00000418109.1	37	CCDS2789.1																																																																																				0.597	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		34	71	34	71
TBC1D9	23158	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	141578954	141578954	+	Missense_Mutation	SNP	T	T	C			TCGA-CS-4942-01A-01D-1468-08	TCGA-CS-4942-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ee5832e7-577c-4507-a4fd-a70646fabc24	f2b83686-8044-4e74-9554-8b4d3c40b2b2	g.chr4:141578954T>C	ENST00000442267.2	-	12	2008	c.1934A>G	c.(1933-1935)gAc>gGc	p.D645G		NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	645	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	31	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				GACACCTTGGTCCACCAGTGC	0.502																																																0													179.0	175.0	177.0					4																	141578954		2120	4242	6362	SO:0001583	missense	23158			AB020689	CCDS47136.1	4q31.1	2013-01-10	2006-07-12		ENSG00000109436	ENSG00000109436		"""EF-hand domain containing"""	21710	protein-coding gene	gene with protein product			"""TBC1 domain family, member 9"""			12970790	Standard	NM_015130		Approved	KIAA0882, MDR1	uc010ioj.3	Q6ZT07	OTTHUMG00000161405	ENST00000442267.2:c.1934A>G	4.37:g.141578954T>C	ENSP00000411197:p.Asp645Gly		A6H8U8|D3DNZ1|O94958	Missense_Mutation	SNP	ENST00000442267.2	37	CCDS47136.1	.	.	.	.	.	.	.	.	.	.	T	26.5	4.744557	0.89663	.	.	ENSG00000109436	ENST00000442267	T	0.24538	1.85	5.63	5.63	0.86233	Rab-GAP/TBC domain (5);	0.000000	0.85682	D	0.000000	T	0.66137	0.2759	H	0.97103	3.94	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79055	-0.1960	10	0.87932	D	0	-12.2754	15.8552	0.78972	0.0:0.0:0.0:1.0	.	645	Q6ZT07	TBCD9_HUMAN	G	645	ENSP00000411197:D645G	ENSP00000411197:D645G	D	-	2	0	TBC1D9	141798404	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.991000	0.88244	2.141000	0.66446	0.528000	0.53228	GAC		0.502	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364806.1	NM_015130		96	162	96	162
GLRB	2743	hgsc.bcm.edu;broad.mit.edu	37	4	158065079	158065079	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-4942-01A-01D-1468-08	TCGA-CS-4942-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ee5832e7-577c-4507-a4fd-a70646fabc24	f2b83686-8044-4e74-9554-8b4d3c40b2b2	g.chr4:158065079A>G	ENST00000264428.4	+	8	1142	c.872A>G	c.(871-873)aAc>aGc	p.N291S	GLRB_ENST00000512619.1_Intron|GLRB_ENST00000541722.1_Missense_Mutation_p.N291S|GLRB_ENST00000509282.1_Missense_Mutation_p.N291S	NM_000824.4	NP_000815.1	P48167	GLRB_HUMAN	glycine receptor, beta	291					acrosome reaction (GO:0007340)|adult walking behavior (GO:0007628)|chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|righting reflex (GO:0060013)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|extracellular-glycine-gated ion channel activity (GO:0016933)|glycine binding (GO:0016594)			central_nervous_system(1)|endometrium(3)|large_intestine(11)|lung(6)|skin(5)|upper_aerodigestive_tract(1)	27	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.0564)|COAD - Colon adenocarcinoma(41;0.0642)|Kidney(143;0.0707)	Enflurane(DB00228)|Glycine(DB00145)|Lindane(DB00431)	TTCTGGATCAACCCGGACGCG	0.488																																																0													171.0	141.0	151.0					4																	158065079		2203	4300	6503	SO:0001583	missense	2743			U33267	CCDS3796.1, CCDS54813.1	4q31.3	2008-02-05			ENSG00000109738	ENSG00000109738			4329	protein-coding gene	gene with protein product		138492				9676428, 8717357	Standard	NM_000824		Approved		uc003ipj.2	P48167	OTTHUMG00000161954	ENST00000264428.4:c.872A>G	4.37:g.158065079A>G	ENSP00000264428:p.Asn291Ser		A8K3K2|D3DP23|F5GWE1	Missense_Mutation	SNP	ENST00000264428.4	37	CCDS3796.1	.	.	.	.	.	.	.	.	.	.	A	18.48	3.633673	0.67130	.	.	ENSG00000109738	ENST00000264428;ENST00000541722;ENST00000509282	D;D;D	0.87729	-2.29;-2.29;-2.29	5.93	5.93	0.95920	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.91050	0.7184	L	0.43152	1.355	0.58432	D	0.999999	D	0.57257	0.979	D	0.74023	0.982	D	0.91929	0.5553	10	0.87932	D	0	.	16.3797	0.83452	1.0:0.0:0.0:0.0	.	291	P48167	GLRB_HUMAN	S	291	ENSP00000264428:N291S;ENSP00000441873:N291S;ENSP00000427186:N291S	ENSP00000264428:N291S	N	+	2	0	GLRB	158284529	1.000000	0.71417	1.000000	0.80357	0.646000	0.38490	9.270000	0.95690	2.271000	0.75665	0.533000	0.62120	AAC		0.488	GLRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366507.1	NM_000824		12	189	12	189
CDC20B	166979	hgsc.bcm.edu;broad.mit.edu	37	5	54436230	54436230	+	Silent	SNP	G	G	A			TCGA-CS-4942-01A-01D-1468-08	TCGA-CS-4942-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ee5832e7-577c-4507-a4fd-a70646fabc24	f2b83686-8044-4e74-9554-8b4d3c40b2b2	g.chr5:54436230G>A	ENST00000381375.2	-	5	637	c.492C>T	c.(490-492)tgC>tgT	p.C164C	CDC20B_ENST00000296733.1_Silent_p.C164C|CDC20B_ENST00000331730.3_Silent_p.C143C|CDC20B_ENST00000322374.6_Silent_p.C164C|CDC20B_ENST00000334206.5_Silent_p.C164C			Q86Y33	CD20B_HUMAN	cell division cycle 20B	164										kidney(1)|large_intestine(5)|lung(7)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	19		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)			GTTGTTTTAGGCATTTCTGAA	0.333																																																0													94.0	84.0	88.0					5																	54436230		2203	4300	6503	SO:0001819	synonymous_variant	166979			AB086378	CCDS3966.1, CCDS47207.1, CCDS54852.1	5q11.2	2013-01-17	2013-01-17		ENSG00000164287	ENSG00000164287		"""WD repeat domain containing"""	24222	protein-coding gene	gene with protein product			"""CDC20 cell division cycle 20 homolog B (S. cerevisiae)"", ""cell division cycle 20 homolog B (S. cerevisiae)"""				Standard	NM_152623		Approved	FLJ37927	uc003jpo.2	Q86Y33	OTTHUMG00000131185	ENST00000381375.2:c.492C>T	5.37:g.54436230G>A			B7WNV8|B9EGL8|C9J6X8|C9JHE9|C9JKL5|Q86Y31|Q86Y32|Q8IUZ8|Q8N1S1|Q8NG56	Silent	SNP	ENST00000381375.2	37	CCDS54852.1																																																																																				0.333	CDC20B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369715.1	NM_152623		27	65	27	65
PIK3R1	5295	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	67575480	67575480	+	Missense_Mutation	SNP	G	G	A			TCGA-CS-4942-01A-01D-1468-08	TCGA-CS-4942-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ee5832e7-577c-4507-a4fd-a70646fabc24	f2b83686-8044-4e74-9554-8b4d3c40b2b2	g.chr5:67575480G>A	ENST00000521381.1	+	5	1169	c.553G>A	c.(553-555)Gct>Act	p.A185T	PIK3R1_ENST00000396611.1_Missense_Mutation_p.A185T|PIK3R1_ENST00000521657.1_Missense_Mutation_p.A185T|PIK3R1_ENST00000274335.5_Missense_Mutation_p.A185T	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	185	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.0?(1)|p.?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	TTTGGCTGACGCTTTCAAACG	0.383			"""Mis, F, O"""		"""gliobastoma, ovarian, colorectal"""					TCGA GBM(4;<1E-08)																													Rec	yes		5	5q13.1	5295	"""phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"""		"""E, O"""	2	Whole gene deletion(1)|Unknown(1)	large_intestine(1)|lung(1)											153.0	142.0	146.0					5																	67575480		2203	4300	6503	SO:0001583	missense	5295			M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"""SH2 domain containing"""	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.553G>A	5.37:g.67575480G>A	ENSP00000428056:p.Ala185Thr		B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Missense_Mutation	SNP	ENST00000521381.1	37	CCDS3993.1	.	.	.	.	.	.	.	.	.	.	G	16.41	3.114336	0.56505	.	.	ENSG00000145675	ENST00000521381;ENST00000521657;ENST00000396611;ENST00000274335;ENST00000520675	T;T;T;T;T	0.20598	2.06;2.06;2.06;2.06;2.06	5.51	2.75	0.32379	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.053188	0.85682	D	0.000000	T	0.15003	0.0362	L	0.41573	1.285	0.46954	D	0.999263	B	0.31949	0.348	B	0.20384	0.029	T	0.06917	-1.0800	10	0.40728	T	0.16	-7.3182	11.232	0.48918	0.2012:0.0:0.7988:0.0	.	185	P27986	P85A_HUMAN	T	185;185;185;185;87	ENSP00000428056:A185T;ENSP00000429277:A185T;ENSP00000379855:A185T;ENSP00000274335:A185T;ENSP00000428566:A87T	ENSP00000274335:A185T	A	+	1	0	PIK3R1	67611236	1.000000	0.71417	0.990000	0.47175	0.647000	0.38526	3.942000	0.56614	0.906000	0.36621	-0.259000	0.10710	GCT		0.383	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504		24	174	24	174
HLA-DRA	3122	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	32410420	32410420	+	Missense_Mutation	SNP	C	C	A			TCGA-CS-4942-01A-01D-1468-08	TCGA-CS-4942-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ee5832e7-577c-4507-a4fd-a70646fabc24	f2b83686-8044-4e74-9554-8b4d3c40b2b2	g.chr6:32410420C>A	ENST00000374982.5	+	2	351	c.278C>A	c.(277-279)gCc>gAc	p.A93D	HLA-DRA_ENST00000395388.2_Missense_Mutation_p.A93D			P01903	DRA_HUMAN	major histocompatibility complex, class II, DR alpha	93	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002504)|cognition (GO:0050890)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|peptide antigen assembly with MHC class II protein complex (GO:0002503)|polysaccharide assembly with MHC class II protein complex (GO:0002506)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II protein complex binding (GO:0023026)|MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|breast(1)|large_intestine(6)|lung(5)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	19						GTGGACAAAGCCAACCTGGAA	0.493									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Kaposi Sarcoma, Familial Clustering of																																							0													213.0	200.0	205.0					6																	32410420		1511	2709	4220	SO:0001583	missense	3122	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;		CCDS4750.1	6p21.3	2013-01-11			ENSG00000204287	ENSG00000204287		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4947	protein-coding gene	gene with protein product		142860		HLA-DRA1			Standard	NM_019111		Approved		uc003obh.3	P01903	OTTHUMG00000031269	ENST00000374982.5:c.278C>A	6.37:g.32410420C>A	ENSP00000364121:p.Ala93Asp		A2BET4|Q30160|Q6IAZ1|Q861I2|Q9TP70	Missense_Mutation	SNP	ENST00000374982.5	37		.	.	.	.	.	.	.	.	.	.	.	17.88	3.496990	0.64186	.	.	ENSG00000204287	ENST00000395388;ENST00000374982	T;T	0.00760	5.73;5.73	5.38	4.52	0.55395	MHC class II, alpha/beta chain, N-terminal (1);MHC classes I/II-like antigen recognition protein (1);MHC class II, alpha chain, N-terminal (2);	0.908722	0.09649	N	0.773952	T	0.01489	0.0048	M	0.69463	2.115	0.31368	N	0.680485	D;D	0.64830	0.994;0.988	D;D	0.69654	0.965;0.918	T	0.50849	-0.8779	10	0.49607	T	0.09	.	9.7988	0.40751	0.0:0.9082:0.0:0.0918	.	93;93	Q30118;P01903	.;DRA_HUMAN	D	93	ENSP00000378786:A93D;ENSP00000364121:A93D	ENSP00000364121:A93D	A	+	2	0	HLA-DRA	32518398	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.508000	0.35769	1.523000	0.49018	0.638000	0.83543	GCC		0.493	HLA-DRA-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000076587.3	NM_019111		80	147	80	147
PDE1C	5137	hgsc.bcm.edu;broad.mit.edu	37	7	31877484	31877484	+	Splice_Site	SNP	G	G	A			TCGA-CS-4942-01A-01D-1468-08	TCGA-CS-4942-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ee5832e7-577c-4507-a4fd-a70646fabc24	f2b83686-8044-4e74-9554-8b4d3c40b2b2	g.chr7:31877484G>A	ENST00000396191.1	-	10	1537	c.1082C>T	c.(1081-1083)gCc>gTc	p.A361V	PDE1C_ENST00000396182.2_Splice_Site_p.A361V|PDE1C_ENST00000396193.1_Splice_Site_p.A421V|PDE1C_ENST00000396184.3_Splice_Site_p.A361V|PDE1C_ENST00000321453.7_Splice_Site_p.A361V	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	361	Catalytic. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	GCACACTTACGCTTCTGGCTG	0.428																																																0													164.0	157.0	159.0					7																	31877484		2203	4300	6503	SO:0001630	splice_region_variant	5137			U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"""Phosphodiesterases"""	8776	protein-coding gene	gene with protein product		602987	"""phosphodiesterase 1C, calmodulin-dependent (70kD)"""			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396191.1:c.1082+1C>T	7.37:g.31877484G>A			B3KPC6|E9PE92|Q14124|Q8NB10	Splice_Site	SNP	ENST00000396191.1	37	CCDS55099.1	.	.	.	.	.	.	.	.	.	.	G	17.82	3.484068	0.63962	.	.	ENSG00000154678	ENST00000396193;ENST00000396191;ENST00000321453;ENST00000396184;ENST00000396182	T;T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06;-1.06	5.53	3.62	0.41486	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.249731	0.46145	N	0.000313	T	0.62295	0.2416	L	0.28504	0.86	0.42711	D	0.993648	P;P;P	0.52061	0.651;0.657;0.95	B;B;B	0.42798	0.378;0.342;0.398	T	0.59862	-0.7374	9	.	.	.	.	4.5311	0.12006	0.0839:0.267:0.522:0.127	.	361;421;361	Q14123-2;E9PE92;Q14123	.;.;PDE1C_HUMAN	V	421;361;361;361;361	ENSP00000379496:A421V;ENSP00000379494:A361V;ENSP00000318105:A361V;ENSP00000379487:A361V;ENSP00000379485:A361V	.	A	-	2	0	PDE1C	31844009	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.816000	0.55658	1.339000	0.45563	0.655000	0.94253	GCC		0.428	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1		Missense_Mutation	91	265	91	265
KAL1	3730	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	8555923	8555923	+	Missense_Mutation	SNP	T	T	C			TCGA-CS-4942-01A-01D-1468-08	TCGA-CS-4942-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ee5832e7-577c-4507-a4fd-a70646fabc24	f2b83686-8044-4e74-9554-8b4d3c40b2b2	g.chrX:8555923T>C	ENST00000262648.3	-	5	787	c.638A>G	c.(637-639)gAg>gGg	p.E213G		NM_000216.2	NP_000207.2	P23352	KALM_HUMAN	Kallmann syndrome 1 sequence	213	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(1)	32						GATCACAGGCTCAATAGAAAT	0.468																																																0													89.0	71.0	77.0					X																	8555923		2203	4300	6503	SO:0001583	missense	3730				CCDS14130.1	Xp22.32	2013-02-11			ENSG00000011201	ENSG00000011201		"""WAP four-disulfide core domain containing"", ""Fibronectin type III domain containing"""	6211	protein-coding gene	gene with protein product	"""anosmin-1"", ""WAP four-disulfide core domain 19"""	300836		KAL, ADMLX		11463336	Standard	NM_000216		Approved	KALIG-1, WFDC19	uc004csf.3	P23352	OTTHUMG00000021107	ENST00000262648.3:c.638A>G	X.37:g.8555923T>C	ENSP00000262648:p.Glu213Gly		B2RPF8	Missense_Mutation	SNP	ENST00000262648.3	37	CCDS14130.1	.	.	.	.	.	.	.	.	.	.	T	16.70	3.195957	0.58126	.	.	ENSG00000011201	ENST00000262648	T	0.59364	0.27	4.04	4.04	0.47022	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.74068	0.3668	M	0.78916	2.43	0.58432	D	0.999994	D	0.89917	1.0	D	0.97110	1.0	T	0.76299	-0.3010	10	0.56958	D	0.05	.	11.6198	0.51111	0.0:0.0:0.0:1.0	.	213	P23352	KALM_HUMAN	G	213	ENSP00000262648:E213G	ENSP00000262648:E213G	E	-	2	0	KAL1	8515923	1.000000	0.71417	0.916000	0.36221	0.759000	0.43091	6.810000	0.75216	1.316000	0.45131	0.481000	0.45027	GAG		0.468	KAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055692.1	NM_000216		19	25	19	25
USP51	158880	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	55514658	55514658	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-4942-01A-01D-1468-08	TCGA-CS-4942-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ee5832e7-577c-4507-a4fd-a70646fabc24	f2b83686-8044-4e74-9554-8b4d3c40b2b2	g.chrX:55514658A>G	ENST00000500968.3	-	2	797	c.715T>C	c.(715-717)Tgt>Cgt	p.C239R	USP51_ENST00000586165.1_Intron	NM_201286.3	NP_958443.1	Q70EK9	UBP51_HUMAN	ubiquitin specific peptidase 51	239					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	30						TGGGTACTACATACGTGACAG	0.453																																																0													150.0	129.0	136.0					X																	55514658		2203	4300	6503	SO:0001583	missense	158880			BF741256	CCDS14370.1	Xp11	2009-03-19	2005-08-08		ENSG00000247746	ENSG00000247746		"""Ubiquitin-specific peptidases"""	23086	protein-coding gene	gene with protein product			"""ubiquitin specific protease 51"""			12838346	Standard	NM_201286		Approved		uc004dun.2	Q70EK9	OTTHUMG00000021656	ENST00000500968.3:c.715T>C	X.37:g.55514658A>G	ENSP00000423333:p.Cys239Arg		Q8IWJ8	Missense_Mutation	SNP	ENST00000500968.3	37	CCDS14370.1	.	.	.	.	.	.	.	.	.	.	.	15.70	2.912403	0.52439	.	.	ENSG00000247746	ENST00000500968	T	0.74737	-0.87	3.08	3.08	0.35506	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, UBP-type (2);	0.413995	0.26700	U	0.022957	D	0.86802	0.6020	M	0.91196	3.185	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87726	0.2576	10	0.87932	D	0	.	8.9283	0.35655	1.0:0.0:0.0:0.0	.	239	Q70EK9	UBP51_HUMAN	R	239	ENSP00000423333:C239R	ENSP00000423333:C239R	C	-	1	0	USP51	55531383	1.000000	0.71417	0.997000	0.53966	0.982000	0.71751	7.495000	0.81514	1.456000	0.47831	0.408000	0.27601	TGT		0.453	USP51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056871.2	NM_201286		42	70	42	70
FRMD7	90167	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	131216497	131216497	+	Missense_Mutation	SNP	A	A	G			TCGA-CS-4942-01A-01D-1468-08	TCGA-CS-4942-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ee5832e7-577c-4507-a4fd-a70646fabc24	f2b83686-8044-4e74-9554-8b4d3c40b2b2	g.chrX:131216497A>G	ENST00000298542.4	-	9	974	c.799T>C	c.(799-801)Ttc>Ctc	p.F267L	FRMD7_ENST00000464296.1_Missense_Mutation_p.F252L|FRMD7_ENST00000370879.1_Missense_Mutation_p.F147L	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	267	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				regulation of neuron projection development (GO:0010975)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Acute lymphoblastic leukemia(192;0.000127)					GTCTTCCAGAAAGCCTTGCAG	0.463																																																0													182.0	171.0	175.0					X																	131216497		2203	4300	6503	SO:0001583	missense	90167			AL161984	CCDS35397.1	Xq26.2	2014-09-17	2006-09-01	2006-09-01	ENSG00000165694	ENSG00000165694			8079	protein-coding gene	gene with protein product		300628	"""nystagmus 1, congenital"""	NYS, NYS1		2063919, 17013395	Standard	NM_194277		Approved	FLJ43346	uc004ewn.3	Q6ZUT3	OTTHUMG00000022421	ENST00000298542.4:c.799T>C	X.37:g.131216497A>G	ENSP00000298542:p.Phe267Leu		C0LLJ3|Q5JX99	Missense_Mutation	SNP	ENST00000298542.4	37	CCDS35397.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.547576	0.86022	.	.	ENSG00000165694	ENST00000370879;ENST00000298542;ENST00000464296	T;T;T	0.73681	-0.77;-0.77;-0.77	5.2	5.2	0.72013	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	T	0.75258	0.3825	L	0.31476	0.935	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.91635	0.987;0.999	T	0.70212	-0.4934	10	0.06365	T	0.9	.	13.467	0.61260	1.0:0.0:0.0:0.0	.	252;267	Q6ZUT3-2;Q6ZUT3	.;FRMD7_HUMAN	L	147;267;252	ENSP00000359916:F147L;ENSP00000298542:F267L;ENSP00000417996:F252L	ENSP00000298542:F267L	F	-	1	0	FRMD7	131044178	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.287000	0.95975	1.844000	0.53588	0.441000	0.28932	TTC		0.463	FRMD7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355031.1	NM_194277		140	259	140	259
POC1A	25886	broad.mit.edu;ucsc.edu	37	3	52159164	52159164	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-4942-01A-01D-1468-08	TCGA-CS-4942-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ee5832e7-577c-4507-a4fd-a70646fabc24	f2b83686-8044-4e74-9554-8b4d3c40b2b2	g.chr3:52159164C>T	ENST00000296484.2	-	8	886	c.847G>A	c.(847-849)Ggg>Agg	p.G283R	POC1A_ENST00000394970.2_Missense_Mutation_p.G283R|POC1A_ENST00000474012.1_Missense_Mutation_p.G245R	NM_015426.4	NP_056241.3	Q8NBT0	POC1A_HUMAN	POC1 centriolar protein A	283					cell projection organization (GO:0030030)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|spindle pole (GO:0000922)				endometrium(1)|large_intestine(4)|liver(1)|lung(4)|prostate(3)|skin(1)	14						AAATACTCCCCCGTTCTTGAA	0.433																																																0													128.0	119.0	122.0					3																	52159164		2203	4300	6503	SO:0001583	missense	25886			AL117629	CCDS2846.1, CCDS54591.1, CCDS54592.1	3p21.2	2014-05-02	2013-08-21	2010-03-26	ENSG00000164087	ENSG00000164087		"""WD repeat domain containing"""	24488	protein-coding gene	gene with protein product		614783	"""WD repeat domain 51A"", ""POC1 centriolar protein homolog A (Chlamydomonas)"""	WDR51A		19109428, 22840364	Standard	NM_015426		Approved	DKFZP434C245	uc003dcu.3	Q8NBT0	OTTHUMG00000157817	ENST00000296484.2:c.847G>A	3.37:g.52159164C>T	ENSP00000296484:p.Gly283Arg		A4FUW4|E9PFC6|Q0VDF8|Q2TAK6|Q96IK6|Q9UFJ8	Missense_Mutation	SNP	ENST00000296484.2	37	CCDS2846.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.005309	0.74932	.	.	ENSG00000164087	ENST00000296484;ENST00000394970;ENST00000474012	T;T;T	0.65549	-0.16;-0.16;-0.16	4.74	4.74	0.60224	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.163742	0.56097	D	0.000039	T	0.80330	0.4603	M	0.86953	2.85	0.45272	D	0.998278	D;D	0.76494	0.998;0.999	D;D	0.72075	0.969;0.976	D	0.83724	0.0194	10	0.87932	D	0	.	13.1014	0.59222	0.0:1.0:0.0:0.0	.	283;283	Q8NBT0-2;Q8NBT0	.;POC1A_HUMAN	R	283;283;245	ENSP00000296484:G283R;ENSP00000378421:G283R;ENSP00000418968:G245R	ENSP00000296484:G283R	G	-	1	0	POC1A	52134204	0.996000	0.38824	0.958000	0.39756	0.927000	0.56198	4.596000	0.61055	2.463000	0.83235	0.561000	0.74099	GGG		0.433	POC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349685.1	NM_015426		29	74	29	74
BCOR	54880	broad.mit.edu;ucsc.edu	37	X	39923699	39923699	+	Missense_Mutation	SNP	C	C	T			TCGA-CS-4942-01A-01D-1468-08	TCGA-CS-4942-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ee5832e7-577c-4507-a4fd-a70646fabc24	f2b83686-8044-4e74-9554-8b4d3c40b2b2	g.chrX:39923699C>T	ENST00000378444.4	-	7	3620	c.3392G>A	c.(3391-3393)cGg>cAg	p.R1131Q	BCOR_ENST00000342274.4_Missense_Mutation_p.R1131Q|BCOR_ENST00000378455.4_Missense_Mutation_p.R1113Q|BCOR_ENST00000397354.3_Missense_Mutation_p.R1131Q|BCOR_ENST00000378463.1_Missense_Mutation_p.R8Q	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	1131					heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.R1131L(1)		breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						CCTGTCCACCCGGAGGGTGGG	0.607			"""F, N, S, T"""	RARA	"""retinoblastoma, AML, APL(translocation)"""		oculo-facio-cardio-dental genetic																																Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		1	Substitution - Missense(1)	lung(1)											56.0	49.0	51.0					X																	39923699		2202	4300	6502	SO:0001583	missense	54880			AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"""Ankyrin repeat domain containing"""	20893	protein-coding gene	gene with protein product		300485	"""BCL6 co-repressor"""			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.3392G>A	X.37:g.39923699C>T	ENSP00000367705:p.Arg1131Gln		D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Missense_Mutation	SNP	ENST00000378444.4	37	CCDS48093.1	.	.	.	.	.	.	.	.	.	.	C	16.59	3.166809	0.57476	.	.	ENSG00000183337	ENST00000413905;ENST00000378463;ENST00000378455;ENST00000397354;ENST00000378444;ENST00000342274;ENST00000406200	T;T;T;T;T;T;T	0.10668	2.85;2.85;2.85;2.85;2.85;2.85;2.85	5.63	1.9	0.25705	.	.	.	.	.	T	0.06645	0.0170	N	0.17082	0.46	0.40297	D	0.978561	B;B;B	0.14805	0.005;0.011;0.008	B;B;B	0.12156	0.007;0.004;0.007	T	0.28396	-1.0045	9	0.44086	T	0.13	-8.93	8.3989	0.32574	0.0:0.6662:0.0:0.3338	.	1113;1131;1131	Q6W2J9-4;Q6W2J9;Q6W2J9-2	.;BCOR_HUMAN;.	Q	35;8;1113;1131;1131;1131;1131	ENSP00000408006:R35Q;ENSP00000367724:R8Q;ENSP00000367716:R1113Q;ENSP00000380512:R1131Q;ENSP00000367705:R1131Q;ENSP00000345923:R1131Q;ENSP00000384485:R1131Q	ENSP00000345923:R1131Q	R	-	2	0	BCOR	39808643	1.000000	0.71417	0.988000	0.46212	0.959000	0.62525	1.519000	0.35888	0.201000	0.20466	0.529000	0.55759	CGG		0.607	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745		29	64	29	64
ATRX	546	broad.mit.edu;hgsc.bcm.edu	37	X	76854942	76854942	+	Frame_Shift_Del	DEL	C	C	-			TCGA-CS-4942-01A-01D-1468-08	TCGA-CS-4942-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ee5832e7-577c-4507-a4fd-a70646fabc24	f2b83686-8044-4e74-9554-8b4d3c40b2b2	g.chrX:76854942delC	ENST00000373344.5	-	25	6108	c.5894delG	c.(5893-5895)ggtfs	p.G1966fs	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Frame_Shift_Del_p.G1928fs	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	1966					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						TCCTTCACCACCTCCCCGAGA	0.388			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																																Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	1	Unknown(1)	bone(1)											348.0	325.0	332.0					X																	76854942		2203	4296	6499	SO:0001589	frameshift_variant	546			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.5894delG	X.37:g.76854942delC	ENSP00000362441:p.Gly1966fs		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Frame_Shift_Del	DEL	ENST00000373344.5	37	CCDS14434.1																																																																																				0.388	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		308	491	308	491
ATRX	546	hgsc.bcm.edu	37	X	76854944	76854944	+	Silent	SNP	T	T	G			TCGA-CS-4942-01A-01D-1468-08	TCGA-CS-4942-10A-01D-1468-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ee5832e7-577c-4507-a4fd-a70646fabc24	f2b83686-8044-4e74-9554-8b4d3c40b2b2	g.chrX:76854944T>G	ENST00000373344.5	-	25	6106	c.5892A>C	c.(5890-5892)ggA>ggC	p.G1964G	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Silent_p.G1926G	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	1964					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						CTTCACCACCTCCCCGAGATC	0.393			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																																Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	1	Unknown(1)	bone(1)											349.0	327.0	335.0					X																	76854944		2203	4296	6499	SO:0001819	synonymous_variant	546			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.5892A>C	X.37:g.76854944T>G			D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Silent	SNP	ENST00000373344.5	37	CCDS14434.1																																																																																				0.393	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		323	505	323	505
